PaperBLAST
PaperBLAST Hits for tr|Q9I5E2|Q9I5E2_PSEAE 2-methylisocitrate lyase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=prpB PE=1 SV=1 (298 a.a., MSQTSLTPGQ...)
Show query sequence
>tr|Q9I5E2|Q9I5E2_PSEAE 2-methylisocitrate lyase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=prpB PE=1 SV=1
MSQTSLTPGQRFREAVATEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGLPD
LGISGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAMHIEDQV
GAKRCGHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLQAAIDRACACV
EAGADMIFPEAMTELAMYKEFAAAVKVPVLANITEFGATPLFTTDELASADVSLVLYPLS
AFRAMNKAAENVYTAIRRDGTQKNVIDTMQTRMELYDRIDYHSFEQKLDALFAQKKNA
Running BLASTp...
Found 250 similar proteins in the literature:
PA0796 carboxyphosphonoenolpyruvate phosphonomutase from Pseudomonas aeruginosa PAO1
Q9I5E2 2-methylisocitrate lyase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_53940 carboxyphosphonoenolpyruvate phosphonomutase from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage
- PmiR senses 2-methylisocitrate levels to regulate bacterial virulence in Pseudomonas aeruginosa
Cui, Science advances 2022 - “...gene clusters involved in 2-MCC Notably, RNA-seq analysis identified the expression of the PA0792 to PA0796 cluster as among the most highly (20- to 60-fold) up-regulated genes (table S1). The database of P. aeruginosa genome showed that PA0793 and PA0794 share the same operon; it is...”
- “...role of these genes in 2-methylcitrate metabolism, we generated three mutant strains, including prpB ( PA0796 ), prpC ( PA0795 ), and prpD ( PA0792 ) and measured their growth in M9 medium supplemented with the corresponding substrate as a sole carbon source. Our data showed...”
- Genes required for and effects of alginate overproduction induced by growth of Pseudomonas aeruginosa on Pseudomonas isolation agar supplemented with ammonium metavanadate
Damron, Journal of bacteriology 2013 - “...phzB1 phzE1 PA0394 PA0558 PA0593 PA0597 PA0793 PA0794 PA0796 PA1838 PA2068 PA2531 PA2796 PA2804 PA3113 PA3772 PA4007 PA4402 PA4465 PA4640 PA4758 PA5236 PA5331...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...20 * PA0766 mucD Serine protease O P 50.3 50 7.04 6.11 0.646 0.057 21 PA0796 prpB Carboxyphophonoenolpyruvate phosphonomutase G C 32.1 34 5.33 5.27 0.765 0.032 22 PA0871 phhB Pterin alpha carbinolamine dehydratase H C 13.3 12 5.94 5.96 0.607 0.336 23 * PA0888 aotJ...”
- Pseudomonas aeruginosa twitching motility-mediated chemotaxis towards phospholipids and fatty acids: specificity and metabolic requirements
Miller, Journal of bacteriology 2008 - “...att::aceA PAO1 aceB (PA0482) malate synthase, glyoxylate shunt PAO1 prpB (PA0796) methyl isocitrate lyase 3 Reuben Ramphal (2) 3 P NM P P NM N This study (aa...”
- “...PA0507 PA0508 PA0743 PA0744 PA0745 PA0746 PA0792 PA0795 PA0796 PA0797 PA0887 PA1137 PA1288 PA1736 PA1737 PA2011 PA2012 PA2013 PA2014 PA2015 PA2142 PA2552 PA2553...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - Increased Virulence of Bloodstream Over Peripheral Isolates of P. aeruginosa Identified Through Post-transcriptional Regulation of Virulence Factors
Hickey, Frontiers in cellular and infection microbiology 2018 - “...oxidoreductase pauB3 Carbon compound catabolism 2.616 P57109 6 Maleylacetoacetate isomerase maiA Carbon compound catabolism 4.037 Q9I5E2 4 Carboxyphosphonoenolpyruvate phosphonomutase prpB Fatty acid and phospholipid metabolism 3.577 Q05097 2 * LecA lecA Motility & Attachment 6.844 Q9HUV8 13 Phosphoribosylamineglycine ligase purD Nucleotide biosynthesis and metabolism 2.024 Q9I4I2...”
- Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease
Flynn, PLoS pathogens 2016 - “...on LB agar. Generation of clean-deletion mutants Unmarked deletions were generated for the genes prpB (PA14_53940) and acsA (PA14_52800) in the PA14 wild-type background. Flanking regions (~1kb in length) containing the first and last codons of for acsA and prpB were generated using primers listed in...”
6t4vC / Q9I5E2 Crystal structure of 2-methylisocitrate lyase (prpb) from pseudomonas aeruginosa in apo form.
96% identity, 97% coverage
- Ligand: pyruvic acid (6t4vC)
Pf6N2E2_6061 Methylisocitrate lyase (EC 4.1.3.30) from Pseudomonas fluorescens FW300-N2E2
91% identity, 97% coverage
- mutant phenotype: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (4.1.3.30) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
PP2334, PP_2334 carboxyvinyl-carboxyphosphonate phosphorylmutase, putative from Pseudomonas putida KT2440
91% identity, 97% coverage
VT47_09985 methylisocitrate lyase from Pseudomonas syringae pv. syringae
87% identity, 99% coverage
- Identification of the Genes of the Plant Pathogen Pseudomonas syringae MB03 Required for the Nematicidal Activity Against Caenorhabditis elegans Through an Integrated Approach
Ali, Frontiers in microbiology 2022 - “...putative acyl-CoA carboxylase alpha chain (VT47_11875), acyl-CoA carboxyltransferase beta chain (VT47_11885), prpC (VT47_09990), and PrpB (VT47_09985). On the other hand, crfX (VT47_10030), (VT47_19750) and hypothetical protein (VT47_10035) were down regulated ( Table 2 ). Regarding nematicidal genes of PAO1, homologs of 30 genes were found in...”
- “...subunit VT47_11885 Yes Unchanged Up Propionyl-CoA carboxylase prpC VT47_09990 Yes Unchanged Up 2-Methylcitrate synthase prpB VT47_09985 Yes Unchanged Up 2-Methylisocitrate lyase cmpX VT47_10035 Yes Unchanged Down Hypothetical protein ibaG VT47_19750 Yes Unchanged Down BolA-like protein VT47_10030 Yes Unchanged Down CrfX protein kdpB VT47_09695 Yes Unchanged Up...”
prpB / Q0KAG5 2-methylcitrate lyase (EC 4.1.3.30) from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) (see paper)
84% identity, 98% coverage
RR42_RS11260 Methylisocitrate lyase (EC 4.1.3.30) from Cupriavidus basilensis FW507-4G11
83% identity, 98% coverage
- mutant phenotype: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (4.1.3.30) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
PRPB_CUPNE / Q937P0 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Cupriavidus necator (Alcaligenes eutrophus) (Ralstonia eutropha) (see paper)
83% identity, 98% coverage
- function: Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2- methylisocitrate to yield pyruvate and succinate via an alpha-carboxy- carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers.
disruption phenotype: Cells lacking this gene show an accumulation of 2-methylisocitric acid.
FQU82_00159 methylisocitrate lyase from Acinetobacter baumannii
83% identity, 97% coverage
- Transcriptomic analysis reveals the regulatory role of quorum sensing in the Acinetobacter baumannii ATCC 19606 via RNA-seq
Xiong, BMC microbiology 2022 - “...propanoate metabolism: FQU82_00191, FQU82_00562, FQU82_03635, FQU82_01642 ( paaF ), FQU82_00192, FQU82_00189 ( mmsA ), FQU82_00193, FQU82_00159 ( prpB ), FQU82_00160 ( prpC ), and FQU82_00161 ( acnD ). In purine metabolism, 8 DEGs were downregulated, including FQU82_00576 ( ndk ), FQU82_02944 ( purL ), FQU82_02508 (...”
A1S_0073 2-methylisocitrate lyase from Acinetobacter baumannii ATCC 17978
84% identity, 92% coverage
- Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
Colquhoun, Frontiers in cellular and infection microbiology 2020 - “...ATCC 17978, MAR002, MAR002 Rumbo-Feal et al., 2013 ; Alvarez-Fraga et al., 2016 Metabolism prpB A1S_0073 2-methylisocitrate lyase 3.29, 6.6 AB5075_UW, ATCC 17978 Rumbo-Feal et al., 2013 ; Penesyan et al., 2019 atpA A1S_0153 ATP synthase F1, alpha subunit 3.39, 1.13 AB5075_UW, ATCC 17978 Rumbo-Feal et...”
- Mucin acts as a nutrient source and a signal for the differential expression of genes coding for cellular processes and virulence factors in Acinetobacter baumannii
Ohneck, PloS one 2018 - “...transport protein A1S_2763 2.206786121 0.000130274 Aromatic amino acid APC transporter Lipid catabolism and transport prpB (A1S_0073) 2.256823408 0.001232441 2-methylisocitrate lyasePrpB A1S_0103 2.291988117 0.016345817 3-hydroxyisobutyrate dehydrogenase A1S_0104 2.214320009 0.031303506 Acetyl-CoA synthetase/AMP-(fatty) acid ligaseAcsA A1S_0105 2.217156233 0.01599743 Acyl-CoA dehydrogenase A1S_0106 2.557525827 0.00316474 Anoyl-CoA hydratase/isomerase A1S_0107 2.960278778 0.001415848 Anoyl-CoA...”
- “...production of lipid degradation products is particularly supported by the significantly increased expression of the A1S_0073 and A1S_0104 genes when bacteria were cultured in SB+M ( Table 1 ). A1S_0073 codes for a predicted PrpB 2-methylisocitrate lyase ortholog, a component of the methylcitrate cycle involved in...”
- Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
Rumbo-Feal, PloS one 2013 - “...gyrase 0.44 0.19 A1S_0009 RND type efflux pump 2.57 4.84 A1S_0032 signal peptide 32.18 4.82 A1S_0073 2-methylisocitrate lyase 6.60 1.61 A1S_0087 short-chain dehydrogenase 2.57 6.37 A1S_0103 3-hydroxyisobutyrate dehydrogenase 61.82 3.81 A1S_0107 enoyl-CoA hydratase 5.51 5.97 A1S_0109 homoserine lactone synthase 60.22 16.74 A1S_0112 acyl-CoA synthetase/AMP-acid ligases II...”
prpB / Q56062 2-methylisocitrate lyase subunit (EC 4.1.3.30) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
PRPB_SALTY / Q56062 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 4 papers)
STM0368 putative carboxyphosphonoenolpyruvate mutase from Salmonella typhimurium LT2
78% identity, 98% coverage
- function: Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2- methylisocitrate to yield pyruvate and succinate via an alpha-carboxy- carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers.
disruption phenotype: Cells lacking this gene are unable to accumulate 2-methylcitrate and 2-methyl-cis-aconitate. - Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2
Samuels, BMC genomics 2013 - “...ratio b Orientation c PSSM d Start End Sequence Sites located within intergenic regions : STM0368 prpB 11 + 20.7 417914 417931 TGGCATAGCCTTTGCTTT STM0448 clpP 4.6 + 14.6 503028 503045 TGTCACGTATTTTGCATG STM0462 glnK 3.2 + 20.0 520445 520462 TGGCACATCCTTTGCAAT STM0577 8.3 + 17.9 636883 636866 TGGCACGCCGTTTGCCAT...”
- Identification and characterization of Helicobacter pylori genes essential for gastric colonization
Kavermann, The Journal of experimental medicine 2003 - “...dppF 2 Dipeptide ABC transporter, ATP-binding protein <0.0100 STM0312 1091 a kgtP 2 Alpha-ketoglutarate permease STM0368 1082 a msbA 2 Multidrug resistance protein STM0341 1206 a hetA 2 Multidrug resistance protein <0.0016 STM0308 1506 a gltS 2 Glutamate permease Stress response and acid survival STM0190 0073...”
YahQ / b0331 2-methylisocitrate lyase (EC 4.1.3.30) from Escherichia coli K-12 substr. MG1655 (see 7 papers)
prpB / P77541 2-methylisocitrate lyase (EC 4.1.3.30) from Escherichia coli (strain K12) (see 6 papers)
PRPB_ECOLI / P77541 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Escherichia coli (strain K12) (see 3 papers)
W8T6L6 2-methylisocitrate lyase from Escherichia coli
b0331 2-methylisocitrate lyase from Escherichia coli str. K-12 substr. MG1655
78% identity, 97% coverage
- function: Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2- methylisocitrate to yield pyruvate and succinate via an alpha-carboxy- carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers. - Proteomics-Based Mechanistic Investigation of Escherichia coli Inactivation by Pulsed Electric Field
Liu, Frontiers in microbiology 2019 - “...Putative glucarate dehydratase, GN=ECs3648 5 1 28.3712 0.0232 V0UHA6 Octanoyltransferase, GN=lipB 35.1 3 18.3945 0.0002 W8T6L6 2-methylisocitrate lyase, GN=prpB 24 1 15.7546 0.0040 A0A2B7LUZ2 Aconitate hydratase B, GN=BMR23_08950 73.8 0 12.0020 0.0275 M9FZM4 2-methylcitrate dehydratase, GN=prpD 48.4 16 7.4411 0.02615 A0A0G3K113 Bifunctional protein PutA, GN=putA 49.8...”
- “...transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. W8T6L6 prpB Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate. W8ZVZ2 cysND Sulfur metabolism V6FYL6 arnA The modified arabinose is attached to lipid A and...”
- Identification of regions of the chromosome of Neisseria meningitidis and Neisseria gonorrhoeae which are specific to the pathogenic Neisseria species
Perrin, Infection and immunity 1999 - “...AF169456 49 CppM (putative CPEP phosphomutase), E. coli (P77541) CisZ (citrate synthase), E. coli (P31660) CisZ 8e-91 Coding AF169436 12 8e-28 Coding Coding...”
- Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...metabolism acnB b , f b0118 aconitate hydrase B -3.0 ** prpB b , f b0331 putative carboxyphosphoenolpyruvate mutase 17.0 15.8 prpC f b0333 citrate synthase, propionate metabolism 30.8 * 17.6 prpD f b0334 2-methyl citrate dehydratase 5.6 7.6 prpE f b0335 putative propionyl-CoA synthetase 5.9...”
- Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...j Ecocyc k Intergenic Sense OS01 347850 17 G TGGC ACACCCC TTGC T 347851 + b0331 prpB 36 9.469 P OS02 455741 5 T TG T C ATGAATT TTGC A 455728 + b0437 clpP 154 10.247 OS03 471768 18 C TGGC ACACCGC TTGC A 471761 +...”
- More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
Göhler, BMC systems biology 2011 - “...yfgH 0.820 0.425 b0822 ybiV 0.284 3.653 b0333 prpC 0.729 0.021 b2683 ygaH -0.077 3.628 b0331 prpB 0.713 0.024 b0436 tig -0.260 3.620 b3939 metB 0.677 2.667 b4290 fecB * 0.315 3.561 b3547 yhjX 0.668 2.931 b0083 ftsL $ 0.119 3.536 b3426 glpD 0.659 0.904 Top-ranking...”
- Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis
Zhao, Nucleic acids research 2010 - “...296 aaaaTGGCAGGGTTTTCTCTTTgtgc b4002 zraP periplasmic Zn-binding protein, zinc resistance-associated Unknown 4.1 3.1 51 34 tcgtTGGCACGGAAGATGCAATaccc b0331 prpB putative carboxyphosphonoenolpyruvate mutase Not classified 2.2 2.8 62 45 attgTGGCACACCCCTTGCTTTgtct b4003 zraS sensory histidine kinase in two-component regulatory system with ZraR, regulates zraP expression, senses Zn Energy metabolism, carbon:...”
- YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
Zhang, Journal of bacteriology 2007 - “...pykF yjgA deoA deoC deoD pyrG yfhN yfhO b2135 b0331 b0334 b0453 b2392 b1678 b1676 b4234 b4382 b4381 b4384 b2780 b2529 b2530 Predicted GTP-binding transport...”
- Definition of the Escherichia coli MC4100 genome by use of a DNA array
Peters, Journal of bacteriology 2003 - “...yeiQ, b0271, b0349 cynS, cynT, yagC, yagE, yagT, ykfD,a b0331, b0333 eaeH b0323, b0324, b0325, b0350a yagA, yagB, yagJ, yagK, yagP, yagQ, yagR, yagS, yagU,...”
1mumA / P77541 Structure of the 2-methylisocitrate lyase (prpb) from escherichia coli (see paper)
78% identity, 96% coverage
- Ligand: magnesium ion (1mumA)
Z_RS01960 methylisocitrate lyase from Escherichia coli O157:H7 str. EDL933
77% identity, 97% coverage
- Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Zhong, Microorganisms 2019 - “...Z_RS21350, Z_RS21150, Z_RS21140, Z_RS21025, Z_RS19885, Z_RS18625, Z_RS16005, Z_RS12610, Z_RS12490, Z_RS09475, Z_RS09120, Z_RS04060, Z_RS03890, Z_RS02910, Z_RS02490, Z_RS01960, sec F, pst S, pst A, nep I, lam B, gld A, gcv T, gcv H, fuc I, fgh A, fad E IT, SMCP, SSTTA IT = ion transport; SMCP...”
FLFIOBJN_01257 methylisocitrate lyase from Stenotrophomonas maltophilia
75% identity, 99% coverage
XAC1137 carboxyphosphonoenolpyruvate phosphonomutase from Xanthomonas axonopodis pv. citri str. 306
72% identity, 97% coverage
XOO0892 2-methylisocitrate lyase from Xanthomonas oryzae pv. oryzae KACC10331
PXO_RS20635 methylisocitrate lyase from Xanthomonas oryzae pv. oryzae PXO99A
73% identity, 97% coverage
- The ColRS system of Xanthomonas oryzae pv. oryzae is required for virulence and growth in iron-limiting conditions
Subramoni, Molecular plant pathology 2012 - “...(397) 15; Vir+, Lir- XOO0891 (591) 1; Vir-, Lir- XOO0892 (298) XOO1207 (450) 1; Vir-, Lir4; Vir-, Lir- XOO1806 (289) 2; Vir-, Lir- XOO2862 (863) 2; Vir-,...”
- “...which encodes a putative aconitase (Acn); prpB (XOO0892), which encodes a putative methyl isocitrate lyase involved in propionate catabolism; prpR (XOO0891),...”
- PXO_RS20535, Encoding a Novel Response Regulator, Is Required for Chemotactic Motility, Biofilm Formation, and Tolerance to Oxidative Stress in Xanthomonas oryzae pv. oryzae
Antar, Pathogens (Basel, Switzerland) 2020 - “...DUF2946 domain-containing protein PXO_RS25705 2.29 Hypothetical protein PXO_RS23540 2.29 Hypothetical protein PXO_RS23950 2.34 Hypothetical protein PXO_RS20635 2.48 Methylisocitrate lyase PXO_RS16940 2.50 DUF378 domain-containing protein PXO_RS06660 2.59 MerC domain-containing protein PXO_RS25610 2.62 Hypothetical protein PXO_RS05075 2.80 Hemin uptake protein HemP PXO_RS19360 4.08 C4-dicarboxylate transporter PXO_RS04930 4.63 Hypothetical...”
- Melatonin Treatment Inhibits the Growth of Xanthomonas oryzae pv. oryzae
Chen, Frontiers in microbiology 2018 - “...3-Methylcrotonyl-CoA carboxylase subunit alpha 25 PXO_RS11720 -2.07 3-Hydroxyacyl-CoA dehydrogenase 26 PXO_RS12650 -2.07 3-Hydroxyacyl-CoA dehydrogenase 27 PXO_RS20635 -1.90 2-Methylisocitrate lyase 28 PXO_RS20105 -2.20 Malate dehydrogenase 29 PXO_RS02070 -2.19 NADH-dependent FMN reductase 30 PXO_RS27075 +1.86 Fumarylacetoacetate hydrolase domain protein 31 PXO_RS08315 -2.97 Bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 32...”
XAUB_41570 methylisocitrate lyase from Xanthomonas citri pv. aurantifolii str. ICPB 11122
72% identity, 98% coverage
VC1336 carboxyphosphonoenolpyruvate phosphonomutase from Vibrio cholerae O1 biovar eltor str. N16961
67% identity, 94% coverage
- Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity
Toulouse, Journal of bacteriology 2018 - “...reactions A0A0H3AKS4 A0A0H3AMD5 A0A0H3AMM1 A0A0H3AHX2 VC1338 VC0736 VC0734 VC1336 acnA aceA aceB prpB 2.4 2.3 2 2.3 Aconitate hydratase Isocitrate lyase Malate...”
- The acetate switch of an intestinal pathogen disrupts host insulin signaling and lipid metabolism
Hang, Cell host & microbe 2014 - “...( acs1 ; VC0298), and the propionate metabolism enzyme 2-methyl isocitrate lyase ( prpB , VC1336) ( Van Dellen et al., 2008 ). Therefore, we named VC0303 CrbS for c ar b oxylic acid s ensor. Bacterial histidine kinases regulate protein expression at the level of...”
- “...we compared transcription of sssA, acs1, and VC1335, the first gene in the operon encoding VC1336, in wild-type V. cholerae as well as crbS and VC2702 mutants ( Figure 1D ). Transcription of each of these genes was greatly decreased in both the crbS and VC2702...”
- Identification of novel stage-specific genetic requirements through whole genome transcription profiling of Vibrio cholerae biofilm development
Moorthy, Molecular microbiology 2005 - “...Upregulated VC1075 VC1077 VC1330 VC1332 VC1333 VC1334 VC1335 VC1336 VC1338 VC1339 VC1514 VC1515 VC1516 VC1517 VC1518 VC1519 VC2705 VC2706 VC2708 VC2709 VC2711...”
A1KVK6 2-methylisocitrate lyase from Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18)
NMB0430 putative carboxyphosphonoenolpyruvate phosphonomutase from Neisseria meningitidis MC58
NMC1733 putative carboxyphosphonoenol pyruvate phosphonomutase from Neisseria meningitidis FAM18
70% identity, 98% coverage
- Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed
Neri, BMC microbiology 2010 - “...41 184 36168/4.94 up Genetic Information Processing: transcription 18 Carboxyphosphonoenol pyruvate phosphonomutase ( prp B) A1KVK6 NMC1733 73 234 31876/5.22 down Carbohydrate metabolism: propanoate metabolism 19 Putative malonyl Co-A acyl carrier protein transacylase ( fab D) A1KRY7 NMC0305 57 158 31958/5.44 down Lipid metabolism: fatty acid...”
- Neisseria meningitidis Sibling Small Regulatory RNAs Connect Metabolism with Colonization by Controlling Propionate Use
Man-Bovenkerk, Journal of bacteriology 2023 (secret) - The Hfq regulon of Neisseria meningitidis
Huis, FEBS open bio 2017 - “...reductase tRNA modification 4.5 4.5 NMB0325 rplU 50S ribosomal protein L21 Ribosomal proteins 22.9 5.2 NMB0430 prpB 2methylisocitrate lyase Propionate metabolism 9.1 20.4 28.2 NMB0431 prpC Methylcitrate synthase Propionate metabolism 3.8 1.6 23.9 56.7 NMB0432 tuaE f Anion (sulfite) transporter Membrane components & Propionate metabolism 5.9...”
- A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx
Catenazzi, Molecular microbiology 2014 - “...to pyruvate (Fig. 2 A), which supports growth and/or limits the toxicity of propionic acid. NMB0430 and NMB0431 are homologues of methylisocitrate lyase ( prpB ) (Grimek et al ., 2003 ) and methylcitrate synthase ( prpC ) (Horswill and Escalante-Semerena, 1999a ) respectively. NMB0433 and...”
- “...explain the different propionic acid utilization patterns in different media. Genes in the prp cluster NMB0430, NMB0433 and NMB0434 are highly similar to genes required for methylcitrate cycle action in other bacteria, but NMB0432 and NMB0435 are not similar to methylcitrate cycle genes from other organisms....”
- Analysis of the regulated transcriptome of Neisseria meningitidis in human blood using a tiling array
Del, Journal of bacteriology 2012 - “...(Fig. 7A). As an example, the three genes NMB0429, NMB0430, and NMB0431 were part of the same transcriptional unit containing both probes inside the genes and...”
- “...protein of 34 amino acids (aa), while NMB0430 and NMB0431 code for PrpB (2-methylisocitrate lyase) and PrpC (methylcitrate synthase), respectively, and...”
- In the NadR regulon, adhesins and diverse meningococcal functions are regulated in response to signals in human saliva
Fagnocchi, Journal of bacteriology 2012 - “...2 Proline dehydrogenase, putA 1.9b 1.2E04 2.4 3.1 NMB0429 NMB0430 P P 1.9b 1.9b 3.1E06 9.6E04 ND ND ND ND NMB0431 2 Hypothetical protein, putative regulatory...”
- The Neisseria meningitidis ZnuD zinc receptor contributes to interactions with epithelial cells and supports heme utilization when expressed in Escherichia coli
Kumar, Infection and immunity 2012 - “...permissive intergenic chromosomal location (flanked by NMB0428 and NMB0430) was verified by colony PCR. The zur mutation was introduced into the reporter...”
- Role of Hfq in iron-dependent and -independent gene regulation in Neisseria meningitidis
Mellin, Microbiology (Reading, England) 2010 - “...WT vs JM23 Low WT vs JM30 Hi WT vs JM30 Low Upregulated genes Metabolism: NMB0430 prpB 2-Methylisocitrate lyase 20.35 15.32 1.18 1.85 NMB0431 pprC Methylcitrate synthase 23.87 19.69 1.19 1.82 NMB0435 ackA-1 Acetate kinase 13.65 10.26 1.75 2.43 NMB0546 adhP Alcohol dehydrogenase 1.71 3.09 1.15...”
- Requirement of NMB0065 for connecting assembly and export of sialic acid capsular polysaccharides in Neisseria meningitidis
Hobb, Microbes and infection 2010 - “...transcriptional fusion to the lacZ gene that is flanked by meningococcal sequences of NMB0428 and NMB0430. Correct orientation of the promoter relative to the lacZ gene was confirmed by colony PCR using a lacZ 5 outward primer, YT168, and a forward primer within the cloned promoter...”
- More
- Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed
Neri, BMC microbiology 2010 - “...184 36168/4.94 up Genetic Information Processing: transcription 18 Carboxyphosphonoenol pyruvate phosphonomutase ( prp B) A1KVK6 NMC1733 73 234 31876/5.22 down Carbohydrate metabolism: propanoate metabolism 19 Putative malonyl Co-A acyl carrier protein transacylase ( fab D) A1KRY7 NMC0305 57 158 31958/5.44 down Lipid metabolism: fatty acid biosynthesis...”
NMA2055 putative carboxyphosphonoenol pyruvate phosphonomutase from Neisseria meningitidis Z2491
70% identity, 98% coverage
VpaChn25_1639 methylisocitrate lyase from Vibrio parahaemolyticus
67% identity, 98% coverage
- Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival
Zhu, BMC genomics 2017 - “...dehydrogenase Propanoate metabolism VpaChn25_1376 6.0834 4-aminobutyrate aminotransferase VpaChn25_1635 6.3526 PrpE protein VpaChn25_1638 8.5787 Methylcitrate synthase VpaChn25_1639 6.7065 2-methylisocitrate lyase VpaChn25_2798 3.959 Acetyl-CoA synthetase ABC transporters VpaChn25A_0128 0.4376 ABC transporter substrate-binding protein VpaChn25A_0130 0.428 ABC transporter ATP-binding protein VpaChn25A_0533 3.1521 High-affinity branched-chain amino acid transport ATP-binding protein...”
- “...alpha VpaChn25_2076 0.4816 3-ketoacyl-CoA thiolase Propanoate metabolism VpaChn25_1635 2.316 PrpE protein VpaChn25_1638 4.6552 Methylcitrate synthase VpaChn25_1639 3.654 2-methylisocitrate lyase VpaChn25_2433 3.0153 Bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase VpaChn25_2798 2.1035 Acetyl-CoA synthetase Nitrogen metabolism VpaChn25A_0296 4.3124 Oxidoreductase protein VpaChn25A_0917 3.7442 Nitrite reductase large subunit VpaChn25A_1392 0.4447 Carbonic anhydrase...”
BCAM2703 probable methylisocitrate lyase from Burkholderia cenocepacia J2315
66% identity, 91% coverage
- Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Sass, BMC genomics 2015 - “...2703876..2704169 2703900 GTG ATG shorter 3026129 + BCAM2679 3026111..3026374 3026153 TTG ATG shorter 3058373 - BCAM2703 Complement (3057460..3058437) 3058353 GTG ATG shorter 3077665 - BCAM2719 Complement (3077106..3077669) 3077606 ATG ATG shorter 3133147 + BCAM2769 3133305..3134042 3133281 GTG ATG longer Replicon 3 69880 - BCAS0060 Complement (68555..69688)...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...putative membrane protein 1.8 BCAM2701 acnA, aconitate hydratase 1 2.7 BCAM2702 prpC, 2-methylcitrate synthase 5.9 BCAM2703 prpB, probable methylisocitrate lyase 2.8 METAL ION TRANSPORT OR METABOLISM BCAL0269 Oxidoreductase, molybdopterin-binding domain 1.6 BCAL0366 Nitroreductase family protein, metal ion oxidation 1.6 BCAL0580 Putative chromate transport protein 1.6 BCAL1789...”
- “...c BCAM2700 Putative membrane protein 1.81 BCAM2701 Aconitate hydratase 1 2.66 BCAM2702 2-Methylcitrate synthase 5.88 BCAM2703 Probable methylisocitrate lyase 2.78 BCAM2730 Putative tripeptide permease 1.54 BCAS0028 Succinylglutamate desuccinylase/aspartoacylase 2.80 BCAS0043 Putative l -lysine 6-monooxygenase 3.11 BCAS0050 Putative amidohydrolase 1.53 BCAS0053 FMN reductase 2.34 BCAS0097 Putative cobalamin...”
RS_RS17740 methylisocitrate lyase from Ralstonia pseudosolanacearum GMI1000
RSp0122 2-methylisocitrate lyase from Ralstonia solanacearum GMI1000
66% identity, 99% coverage
BGLU_RS28435 methylisocitrate lyase from Burkholderia glumae BGR1
65% identity, 99% coverage
Bcep1808_3680 2-methylisocitrate lyase from Burkholderia vietnamiensis G4
A4JK62 2-methylisocitrate lyase from Burkholderia vietnamiensis (strain G4 / LMG 22486)
67% identity, 100% coverage
- Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?
Cauduro, International journal of microbiology 2020 - “...NCBI old locus Tag Coordinates Gene length Gene name Product description Significant in BAP A4JK62 Bcep1808_3680 427848..428741(-) 894 prpB 2-Methylisocitrate lyase Yes A4JAP4 Bcep1808_0334 378768..379043(+) 276 rpsS 30S ribosomal protein S19 Yes A4JJM7 Bcep1808_3492 203642..205642() 2001 3-Methylcrotonoyl-CoA carboxylase subunit alpha Yes A4JDT5 Bcep1808_1430 1537771..1538475(+) 705 3-Oxoacid...”
- Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?
Cauduro, International journal of microbiology 2020 - “...accession NCBI old locus Tag Coordinates Gene length Gene name Product description Significant in BAP A4JK62 Bcep1808_3680 427848..428741(-) 894 prpB 2-Methylisocitrate lyase Yes A4JAP4 Bcep1808_0334 378768..379043(+) 276 rpsS 30S ribosomal protein S19 Yes A4JJM7 Bcep1808_3492 203642..205642() 2001 3-Methylcrotonoyl-CoA carboxylase subunit alpha Yes A4JDT5 Bcep1808_1430 1537771..1538475(+) 705...”
PRPB_SHEON / Q8EJW1 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1) (see paper)
SO0345 methylisocitrate lyase from Shewanella oneidensis MR-1
61% identity, 99% coverage
- function: Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2- methylisocitrate to yield pyruvate and succinate via an alpha-carboxy- carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers. - Snapshot of iron response in Shewanella oneidensis by gene network reconstruction
Yang, BMC genomics 2009 - “...methylcitrate synthase (PrpC) 0.81 0.61 0.52 1.77 4.17 8.74 0.90 0.63 0.30 0.11 0.19 0.22 SO0345 2-methylisocitrate lyase (PrpB) 0.73 0.70 0.71 2.54 4.35 8.07 1.05 0.45 0.24 0.15 0.33 0.33 SO1538 isocitrate dehydrogenase 0.69 0.95 1.01 5.25 4.04 4.08 0.73 0.44 0.62 0.55 0.66 0.59...”
BP1026B_II0229 methylisocitrate lyase from Burkholderia pseudomallei 1026b
BPSS0206 probable methylisocitrate lyase from Burkholderia pseudomallei K96243
65% identity, 98% coverage
CBU_0771 methylisocitrate lyase from Coxiella burnetii RSA 493
62% identity, 98% coverage
HBZC1_08230 methylisocitrate lyase from Helicobacter bizzozeronii CIII-1
59% identity, 97% coverage
Gmet_1122 Methylisocitrate lyase from Geobacter metallireducens GS-15
60% identity, 96% coverage
BA2350 carboxyvinyl-carboxyphosphonate phosphorylmutase from Bacillus anthracis str. Ames
47% identity, 91% coverage
4iqdA / A0A6L7HJ56 Crystal structure of carboxyvinyl-carboxyphosphonate phosphorylmutase from bacillus anthracis
47% identity, 93% coverage
- Ligand: pyruvic acid (4iqdA)
MMGF_BACSU / P54528 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- from Bacillus subtilis (strain 168) (see paper)
P54528 Methylisocitrate lyase (EC 4.1.3.30) from Bacillus subtilis (see paper)
45% identity, 91% coverage
- function: Involved in the methylcitric acid cycle. Catalyzes the cleavage of 2-methylisocitrate to yield pyruvate and succinate.
catalytic activity: 3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:57504)
cofactor: Mg(2+)
Rru_A2320 Ankyrin from Rhodospirillum rubrum ATCC 11170
46% identity, 93% coverage
MAB_4618 Probable carboxyvinyl-carboxyphosphonate phosphorylmutase; possible methylisocitrate lyase (PrpB) from Mycobacterium abscessus ATCC 19977
43% identity, 90% coverage
CGS9114_RS02685 methylisocitrate lyase from Corynebacterium glutamicum S9114
46% identity, 82% coverage
PRPB2_CORGL / Q8NSL2 Probable 2-methylisocitrate lyase 2; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) (see paper)
cg0760 methylisocitric acid lyase from Corynebacterium glutamicum ATCC 13032
NCgl0629 methylisocitrate lyase from Corynebacterium glutamicum ATCC 13032
45% identity, 82% coverage
- function: Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2- methylisocitrate to yield pyruvate and succinate via an alpha-carboxy- carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers. - Physiological Response of Corynebacterium glutamicum to Indole
Walter, Microorganisms 2020 - “...1.59 cg0569 cation transporting ATPase 2.05 cg0759 prpD2 methylcitrate dehydratase, involved in propionate catabolism 2.38 cg0760 prpB2 methylisocitrate lyase, involved in propionate metabolism 2.53 cg0762 prpC2 methylcitrate synthase, involved in propionate catabolism 2.57 cg0796 prpD1 putative (2-methyl) citrate dehydratase 1.65 cg0797 prpB1 putative (methyl)isocitrate lyase 1.82...”
- Comprehensive Analysis of C. glutamicum Anaplerotic Deletion Mutants Under Defined d-Glucose Conditions
Kappelmann, Frontiers in bioengineering and biotechnology 2020 - “...CAF20673 cg2559 aceB Malate synthase 9.45 6.63e-41 CAF19365 cg0762 prpC2 2-methylcitrate synthase 6.49 4.73e-18 CAF19364 cg0760 prpB2 2-methylcitrate lyase 5.05 1.07e-21 CAF21548 cg1737 acn Aconitase 3.86 8.53e-37 CAF20774 cg3047 ackA Acetate kinase 3.75 7.39e-28 CAF21597 cg1792 whiA Putative transcriptional regulator-WhiA homolog 3.75 9.38e-06 CAF20775 cg3048 pta...”
- “...(cg0762), 2-methylcitrate dehydratase (PrpD2) encoded by prpD2 (cg0759) and 2-methylcitrate lyase (PrpB2) encoded by prpB2 (cg0760) ( Table 3 ). Together with the activities of AK and PTA this cycle is known to be the predominant route for the degradation of propionate into pyruvate and succinate...”
- Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
Ruwe, Frontiers in microbiology 2019 - “...0 0.6 0.435792 cg3391 idhA1 5.90 7.57E91 4.84 1.22E24 cg0762 prpC2 5.76 0 1.58 A cg0760 prpB2 5.66 1.3E118 1.65 0.02341 A cg0012 ssuR 5.57 6.7E296 0.19 0.81453 R A cg3390 5.53 1.08E97 4.95 4.6E28 cg3280 5.49 0 4.67 0 cg0464 5.31 0 5.63 0 cg3392...”
- The copper-deprivation stimulon of Corynebacterium glutamicum comprises proteins for biogenesis of the actinobacterial cytochrome bc1-aa3 supercomplex
Morosov, The Journal of biological chemistry 2018 - “...copC ssb ctiP ftn ppmA tagA1 cg0133 cg0759 cg0760 cg0762 cg0899 cg0924 cg0952 cg0953 cg1293 cg1836 cg2403a cg2406a cg2546 cg2557 cg2836 cg2837 cg3022 cg3195...”
- Single-Domain Peptidyl-Prolyl cis/trans Isomerase FkpA from Corynebacterium glutamicum Improves the Biomass Yield at Increased Growth Temperatures
Kallscheuer, Applied and environmental microbiology 2015 - “...cg2870 cg3323 cg1345 cg1076 cg1697 cg3431 cg0149 cg3096 cg0444 cg0760 cg0759 cg0950 ldhA farR lexA mdh cysQ uspA3 divS znr fthC ugpA ipsH cysK pgi oppB glpD...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...cg3216 cg2504 cg2181 cg2182 cg2183 cg2184 cg3151 cg0759 cg0760 cg0762 cg2938 cg2940 cg2836 cg2837 cg3047 cg3048 cg0961 cg2426 cg1612 cg2610 cg3107 cg3195...”
- Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
Follmann, BMC genomics 2009 - “...like protein 1 -1.55 -0.47 0.6 2.7 1.6 3.4 2.3 1.8 4.4 4.7 3.4 34 cg0760 prpB2 Methylisocitrate lyase 2 0 -1.54 -0.80 - 3.2 0.9 -0.4 0.8 - - - - 35 cg0762 prpC2 2-methylcitrate synthase 2 0 -1.39 n.d. - 1.7 0.8 - -...”
- Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
Kocan, Journal of bacteriology 2006 - “...cg0470 cg0500 cg0569 cg0589 cg0590 cg0591 cg0759 cg0760 cg0762 cg0767 cg0768 cg0769 cg0771 Annotation c TWO-COMPONENT SIGNAL TRANSDUCTION IN C. GLUTAMICUM...”
- The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
Zhang, Heliyon 2024 - “...2.01 0.02 NCgl0597 Phytoene dehydrogenase 1.31 1.93E-03 NCgl0609 D-methionine transport system ATP-binding protein 1.7 6.35E-04 NCgl0629 Methylisocitrate lyase 1.48 1.20E-06 NCgl0630 Citrate synthase 1.28 9.92E-05 NCgl0653 Hypothetical protein 4.56 2.06E-04 NCgl0664 2-methylcitrate dehydratase 1.25 6.60E-05 NCgl0704 Helicase 1.18 1.71E-03 NCgl0760 Hypothetical protein 1.16 7.42E-03 NCgl0822 Hypothetical...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...NCgl2201 NCgl1915 NCgl1916 NCgl1917 NCgl1918 NCgl2131 NCgl0629 NCgl0630 NCgl2563 NCgl2565 NCgl2476 NCgl2477 NCgl2656 NCgl2657 NCgl0805 NCgl1368 NCgl2294...”
- Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
Kocan, Journal of bacteriology 2006 - “...NCgl0405 NCgl0465 NCgl0482 NCgl0483 NCgl0484 NCgl0628 NCgl0629 NCgl0630 NCgl0635 NCgl0636 NCgl0637 NCgl0639 cg0812 cg0921 cg0922 NCgl0678 NCgl0773 NCgl0774...”
- Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine
Lange, Applied and environmental microbiology 2003 - “...NCgl0628 Methylaconitase prpD2 (C. glutamicum) 1161e NCgl0629 Methylisocitrate lyase prpB2 (C. glutamicum) 1162e NCgl0630 Methyl citrate synthase prpC2...”
CGS9114_RS13300 methylisocitrate lyase from Corynebacterium glutamicum S9114
43% identity, 91% coverage
PRPB1_CORGL / Q8NSH8 Probable 2-methylisocitrate lyase 1; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) (see paper)
cg0797 methylisocitric acid lyase from Corynebacterium glutamicum ATCC 13032
NCgl0665 methylisocitrate lyase from Corynebacterium glutamicum ATCC 13032
43% identity, 91% coverage
- function: Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate via an alpha-carboxy-carbanion intermediate.
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer; dimer of dimers. - Physiological Response of Corynebacterium glutamicum to Indole
Walter, Microorganisms 2020 - “...prpC2 methylcitrate synthase, involved in propionate catabolism 2.57 cg0796 prpD1 putative (2-methyl) citrate dehydratase 1.65 cg0797 prpB1 putative (methyl)isocitrate lyase 1.82 cg0798 prpC1 putative (methyl)citrate synthase 1.76 cg1279 putative secreted protein 2.05 cg1327 putative transcriptional regulator, Crp-family 1.53 cg1328 putative heavy-metal ion transporting P-type ATPase 1.72...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...NCgl0337 wzz cell surface polysaccharide biosynthesis/chain length determinant protein 0.25 cg0424 NCgl0347 putative glycosyltransferase 0.09 cg0797 NCgl0665 prpB1 methylisocitric acid lyase 3.16 cg0998 NCgl0841 trypsin-like serine protease 3.53 cg1055 NCgl0888 menG ribonuclease activity regulator protein RraA 3.24 cg1290 NCgl1094 metE 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 0.29 cg1487 NCgl1262 leuC...”
- Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2
Frunzke, Molecular microbiology 2008 - “...1.11 1.15 1.55 cg2616 Vanillate O-demethylase oxygenase subunit 5.87 1.21 0.79 0.61 1.24 1.04 1.36 cg0797 Methylisocitrate lyase, prpB1 5.91 1.01 0.90 1.51 0.86 0.85 0.89 cg0796 2-methylcitrate dehydratase, prpD1 6.34 1.08 0.78 0.93 0.73 0.89 0.81 cg0798 2-methylcitrate synthase, prpC1 6.69 1.14 0.68 1.24 0.88...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...wzz cell surface polysaccharide biosynthesis/chain length determinant protein 0.25 cg0424 NCgl0347 putative glycosyltransferase 0.09 cg0797 NCgl0665 prpB1 methylisocitric acid lyase 3.16 cg0998 NCgl0841 trypsin-like serine protease 3.53 cg1055 NCgl0888 menG ribonuclease activity regulator protein RraA 3.24 cg1290 NCgl1094 metE 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 0.29 cg1487 NCgl1262 leuC isopropylmalate...”
- Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine
Lange, Applied and environmental microbiology 2003 - “...NCgl0664 Methylaconitase prpD1 (C. glutamicum) e 1205 NCgl0665 Methylisocitrate lyase prpB1 (C. glutamicum) e 1206 NCgl0666 Methyl citrate synthase prpC1 (C....”
PDEN_RS06650 methylisocitrate lyase from Paracoccus denitrificans
45% identity, 91% coverage
Pden_1346 methylisocitrate lyase from Paracoccus denitrificans PD1222
45% identity, 91% coverage
MAP0296c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
44% identity, 85% coverage
bcpA / P11435 carboxyphosphonoenolpyruvate phosphonomutase monomer (EC 2.7.8.23) from Streptomyces hygroscopicus (see 3 papers)
P11435 Carboxyvinyl-carboxyphosphonate phosphorylmutase from Streptomyces hygroscopicus
37% identity, 98% coverage
MIM_c31320 oxaloacetate decarboxylase from Advenella mimigardefordensis DPN7
38% identity, 93% coverage
- Proteomic analysis of organic sulfur compound utilisation in Advenella mimigardefordensis strain DPN7T
Meinert, PloS one 2017 - “...MIM_c31280, putative membrane protein, DoxX family; MIM_c31290, hypothetical protein; MIM_c31300, hypothetical protein; MIM_c31310, hypothetical protein; MIM_c31320, methylisocitrate lyase; MIM_c31330, putative AcnD-accessory protein PrpF; MIM_c31340, Fe/S-dependent 2-methylisocitrate dehydratase; MIM_c31350, 2-methylcitrate synthase; MIM_c31360, transcriptional regulator, XRE family ; MIM_c31370, transcriptional regulator, LysR family ; MIM_c31380, acyl-CoA transferase, family...”
NCLIV_000780 carboxyvinyl-carboxyphosphonate phosphorylmutase protein, related from Neospora caninum Liverpool
39% identity, 90% coverage
- The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii
Limenitakis, Molecular microbiology 2013 - “...Nc Et Pf Cp Tp PrpE NCLIV_032540 ETH_00007195 PrpC NCLIV_024780 ETH_00026655 PrpD NCLIV_013410 ETH_00015105 PrpB NCLIV_000780 Contig 1606+713 Acn NCLIV_046260 ETH_00020300 PF13_0229 TP01_1050 NCLIV_033680 ETH_00021115 PF08_0031 cgd1_600 TP02_0450 Abbreviations Bb Pm Pt Tt PrpE XP_001460124 XP_001025576 PrpC XP_002787782 XP_001447471 XP_001023516 PrpD EER04808 XP_001457033 EAS06482 PrpB XP_002772756...”
dml / Q0QLE4 2,3-dimethylmalate lyase subunit (EC 4.1.3.32) from Eubacterium barkeri (see 2 papers)
DML_EUBBA / Q0QLE4 2,3-dimethylmalate lyase; EC 4.1.3.32 from Eubacterium barkeri (Clostridium barkeri) (see 3 papers)
39% identity, 90% coverage
- function: Catalyzes the formation of proponate and pyruvate from (2R,3S)-2,3-dimethylmalate. Has no activity toward dimethylmaleate, malate, citramalate, isocitrate and citrate.
catalytic activity: (2R,3S)-2,3-dimethylmalate = propanoate + pyruvate (RHEA:10472)
cofactor: Mg(2+)
subunit: Homotetramer.
Q2L8W6 Methylisocitrate lyase (EC 4.1.3.30) from Toxoplasma gondii (see paper)
40% identity, 74% coverage
- The Effects and Mechanism of ATM Kinase Inhibitors in Toxoplasma gondii
Xue, International journal of molecular sciences 2024 - “...results. The Uniprot IDs of TGGT1_273920, TGGT1_293810, TGGT1_220140, TGGT1_297730, TGGT1_246730, TGGT1_318490, and TGGT1_236920 are S7V3L0, Q2L8W6, S7UGW6, A0A125YVV4, S7W9L9, A0A125YG85, and A0A125YZE1, respectively. 4.16. Anti-T. gondii Activity of KU in Mice A total of 100 freshly released RH Ku80 tachyzoites per mouse and either 1000, 3000...”
Tery_4268 putative methylisocitrate lyase from Trichodesmium erythraeum IMS101
36% identity, 95% coverage
phpI / A0A0M3WPI5 carboxyphosphonoenolpyruvate phosphonomutase (EC 2.7.8.23) from Kitasatospora phosalacinea (see 4 papers)
36% identity, 95% coverage
MSMEG_6646 methylisocitrate lyase from Mycobacterium smegmatis str. MC2 155
41% identity, 90% coverage
- Dynamic Characterization of Protein and Posttranslational Modification Levels in Mycobacterial Cholesterol Catabolism
Xu, mSystems 2020 - “...including aconitate hydratase (MSMEG_3143), isocitrate lyase (MSMEG_0911), methylmalonyl-CoA epimerase (MSMEG_4921), methylmalonyl-CoA mutase (MSMEG_3158), methylisocitrate lyase (MSMEG_6646), and 2-methylcitrate dehydratase (MSMEG_6645), showed higher protein expression levels in the presence of cholesterol ( Fig.2B ). This result strongly suggested that cholesterol-derived acetyl-CoA and propionyl-CoA were used as the...”
- The Nitrogen Regulator GlnR Directly Controls Transcription of the prpDBC Operon Involved in Methylcitrate Cycle in Mycobacterium smegmatis
Liu, Journal of bacteriology 2019 - “...three enzymes involved in the methylcitrate cycle (msmeg_6645, msmeg_6646, and msmeg_6647 products). The prpD(B)C operon plays a key role in assimilation of...”
- Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis
Chopra, Molecular & cellular proteomics : MCP 2014 - “...(PrpD, MSMEG_6645), and 2-methylisocitrate lyase (PrpB, MSMEG_6646) (supplemental Figs. S8B and S10). Proteins specific to the methylmalonate pathway...”
A9762_13050 oxaloacetate decarboxylase from Pandoraea sp. ISTKB
39% identity, 93% coverage
XP_001459690 uncharacterized protein from Paramecium tetraurelia
39% identity, 91% coverage
XP_002772756 2-methylisocitrate lyase, putative from Perkinsus marinus ATCC 50983
37% identity, 90% coverage
all1863 carboxyphosphonoenolpyruvate phosphonomutase from Nostoc sp. PCC 7120
35% identity, 96% coverage
MSMEG_2506 carboxyvinyl-carboxyphosphonatephosphorylmutase from Mycobacterium smegmatis str. MC2 155
40% identity, 78% coverage
- The Synergistic Effect of Exogenous Glutamine and Rifampicin Against Mycobacterium Persisters
Huang, Frontiers in microbiology 2018 - “...the phenylalanine degradation into fumarate, methylcitrate dehydratase ( MSMEG_6645 ) (4.50- fold), carboxyvinyl-carboxyphosphonate phosphorylmutase ( MSMEG_2506 ) (4.06- fold) and MSMEG_6855 (6.75- fold) underlying the succinate formation from the asparate degradation. FIGURE 3 Amino acid degradation pathways and TCA cycle in M. smegmatis . Metabolites identified...”
Q501F7 At1g21440 from Arabidopsis thaliana
AT1G21440 mutase family protein from Arabidopsis thaliana
35% identity, 86% coverage
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...S 1.600.08 26 Fructose-bisphosphatealdolase 3(FBA3) Q9ZU52 AT2G01140 S 1.480.13 27 Phosphoenolpyruvate carboxylase family protein (PEPCK) Q501F7 AT1G21440 S 1.370.05 28 Plastidial pyruvate kinase 1 (PKP1) Q9LIK0 AT3G22960 S 1.470.09 29 Dihydrolipoyl dehydrogenase 1 (LPD1) A8MS68 AT3G16950 S 1.340.06 30 Glutamine synthetase (GS) B9DGD1 AT1G63770 S 1.640.06...”
- A binary interaction map between turnip mosaic virus and Arabidopsis thaliana proteomes
Martínez, Communications biology 2023 - “...VPg; SCE1, SUMO 3 (SUMO3), HEAT SHOCK PROTEIN 70-3 (HSP70-3), the protein encoded in locus AT1G21440 (a phosphoenolpyruvate carboxylase), and 40S RIBOSOMAL PROTEIN SA (RP40), all targeted by NIb. Collectively, all the above results indicate that virus targets display higher expression levels than expected by chance,...”
- Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach
Harun, PeerJ 2021 - “...from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1 , and At3g14220 . A total of Four potential genes ( MTO1, SIR, SAL1 , and IMDH3 ) were identified from the pathway enrichment analysis on...”
- “...5.79E17 Cluster 131 34 MRSA2 (1) 2.27E13 Cluster 127 44 T19K24.17, SIR, MRSA2, ASP4, CGS1, At1g21440 (6) 2.75E11 Cluster 125 46 T19K24.17, SIR, MRSA2, ASP4, CGS1, At1g21440, HMT3 (7) 4.65E11 Cluster 129 41 At3g47420, PS1, SIR, T19K24.17, SAL1, CGS1 (6) 4.77E10 Cluster 128 42 At3g14220, T19K24.17,...”
- Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
Niu, PeerJ 2019 - “...AT4G16447 AT1G22500 NIR1 AT5G06610 CER4 AT1G12080 AT4G31910 LAX3 AT1G33340 LCR69 UCC1 ENODL8 GA3OX1 AT4G39070 CYP93D1 AT1G21440 AT4G01140 CKX4 AT3G12900 RVE2 AT3G20015 AT1G09750 AT2G40900 AT3G23880 PIP1;5 AGP4 AT3G32040 AT2G01900 AT1G51820 AIR1 AT5G04730 AT5G42860 BT2 CYP71B2 AT5G26280 AT1G24800 AT1G24881 AT1G25055 AT1G25150 AT1G25211 Down-regulated DIN2 WRKY75 AT4G15120 CYP81F2 AT1G73480...”
- Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots
Rodríguez-Celma, Scientific reports 2016 - “...Polyketide cyclase/dehydrase and lipid transport 34.68 1.36 AT1G62660 Glycosyl hydrolases family 32 protein 34.23 1.27 AT1G21440 Phosphoenolpyruvate carboxylase family protein 33.73 1.23 AT2G36380 ABCG34 Pleiotropic drug resistance 6 29.82 1.25 AT5G13750 ZIFL1 Zinc induced facilitator-like 1 29.66 AT1G78660 GGH1 Gamma-glutamyl hydrolase 1 26.72 1.13 AT4G24160 Alpha/beta-Hydrolases...”
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...1.600.08 26 Fructose-bisphosphatealdolase 3(FBA3) Q9ZU52 AT2G01140 S 1.480.13 27 Phosphoenolpyruvate carboxylase family protein (PEPCK) Q501F7 AT1G21440 S 1.370.05 28 Plastidial pyruvate kinase 1 (PKP1) Q9LIK0 AT3G22960 S 1.470.09 29 Dihydrolipoyl dehydrogenase 1 (LPD1) A8MS68 AT3G16950 S 1.340.06 30 Glutamine synthetase (GS) B9DGD1 AT1G63770 S 1.640.06 31...”
- Expression profiling and functional analysis reveals that TOR is a key player in regulating photosynthesis and phytohormone signaling pathways in Arabidopsis
Dong, Frontiers in plant science 2015 - “...0.91 AT4G15530 Pyruvate orthophosphate diskinase (PPDK) 2.69 0.93 AT4G21210 Pyruvate orthophosphate diskinase (PPDK) 1.25 0.86 AT1G21440 Phosphoenolpyruvate carboxylase family protein 2.18 0.90 AT5G17380 Thiamine pyrophosphate dependent pyruvate decarboxylase family protein 1.47 0.88 AT5G54960 Pyruvate decarboxylase-2 (PDC2) 1.62 0.89 AT3G60750 Transketolase 1 (TKL1) 1.13 0.86 AT1G67090 Rubisco...”
- Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting
Coker, Frontiers in plant science 2015 - “...DML1, ROS1 AT1G12244 AT3G04850 AT1G11720 ATSS3, SS3 AT3G05730 AT1G16350 AT3G23670 PAKRP1L, KINESIN-12B AT1G12845 AT3G15353 MT3 AT1G21440 AT3G28460 AT1G13380 AT3G19450 ATCAD4, AT1G48620 HON5 AT4G11990 AT1G14690 MAP65-7 AT3G45850 AT1G48650 AT4G21270 ATK1, KATAP AT1G27385 AT3G54190 AT1G54820 AT4G22930 PYR4, DHOASE AT1G35780 AT3G60840 MAP65-4 AT1G58060 AT4G30610 BRS1, SCPL24 AT1G48600 AtPMEAMT AT4G37080...”
- Role of callose synthases in transfer cell wall development in tocopherol deficient Arabidopsis mutants
Maeda, Frontiers in plant science 2014 - “...0.02 2.61 Photosystem II 5 kD protein At4g08290 1.22 0.02 2.56 Nodulin MtN21 family protein At1g21440 1.17 0.03 2.18 Mutase family protein At1g01620 0.83 0.03 2.02 Plasma membrane intrinsic protein 1C (PIP1C)/aquaporin PIP1.3 (PIP1.3)/transmembrane protein B (TMPB) At3g08940 0.82 0.03 1.95 Chlorophyll A-B binding protein (LHCB4.2)...”
- More
CPPM_ARATH / O49290 Carboxyvinyl-carboxyphosphonate phosphorylmutase, chloroplastic; Carboxyphosphonoenolpyruvate phosphonomutase; CPEP phosphonomutase; EC 2.7.8.23 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G77060 mutase family protein from Arabidopsis thaliana
33% identity, 85% coverage
- catalytic activity: 1-carboxyvinyl carboxyphosphonate + H(+) = 3- (hydrohydroxyphosphoryl)pyruvate + CO2 (RHEA:14045)
- A novel CLAVATA1 mutation causes multilocularity in Brassica rapa
Chow, Plant direct 2023 - “...EMSinduced variants (Table 1 , highlighted). A07p049690.1_BraROA is a putative carboxyphosphoenolpyruvate mutase (BrCPEPM; homologous to At1g77060 ; 86% nucleotide identity, evalue: 3e163), whereas A07p048430.1_BraROA is BrCLV1 (82% nucleotide identity, evalue: .0). Using domain similarity with AtCLV1 to annotate LRRs and the kinase domain, we determined that...”
- “...to A A07p048430.1 At1g75820; CLAVATA1 CLV1 (predicted) 15 1 A07, 26401682 G to A A07p049690.1 At1g77060; phosphoenolpyruvate carboxylase family protein B. rapa carboxyvinylcarboxyphosphonate phosphorylmutase, chloroplastic 34 1 A07, 26703213 C to T A07p050080.1 No hits Uncharacterized protein 28 .9286 a The hit with the smallest evalue...”
- Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators
Nikonorova, Journal of experimental botany 2018 - “...group were mainly down-regulated under mannitol stress, except for a PHOSPHOENOLPYRUVATE CARBOXYLASE family protein (PEPC, AT1G77060). To conclude, our results point towards a down-regulation of photosynthesis and up-regulation of CAT1 probably for reactive oxygen species (ROS) scavenging; both systems potentially reduce ROS production. In addition, our...”
- Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration
Qin, PloS one 2017 - “...96h/0h 24h/0h, 48h/0h, 72h/0h, 96h/0h CYP707A4 46 Ethanolamine-phosphate cytidylyltransferase/Phosphorylethanolamine transferase cassava4.1_008241m 6.68/53.93 67/3 2.0490.113(-) 72h/0h AT1G77060 71 * myosin cassava4.1_000217m 4.79/200.17 44/3 2.6240.096(-)/2.4610.108(-) 96h/0h 48h/0h, 72h/0h CIP1 94 Mitochondrial outer membrane translocase complex, subunit Tom7 cassava4.1_020644m 10.62/8.20 122/5 (-) 48h/0h AT5G41685 116 dynactin sununit P25 cassava4.1_013839m...”
- Full-length messenger RNA sequences greatly improve genome annotation
Haas, Genome biology 2002 - “...Ceres:32935. 6 of 7 24 AG<CATGCTTACTACCTTGACTTCCAG>GT At3g55920 Cyclophilin-like protein Ceres:94608. 5 of 8 24 AG<AGAACTTTCGGTCACTTTGCACGG>GT At1g77060 Carboxyphosphonoenol-pyruvate mutase, putative Ceres:12293. 4 of 6 25 AG<GACCAAGCATGGCCAAAGAAGTGTG>GT At4g15900 PRL1 protein Ceres:123113. 2 of 17 25 AG<CAAGCAGATTCGTCTCAGCCATAAG>GT At2g47640 Putative small nuclear ribonucleoprotein D2 Ceres:26123. 3 of 6 25 AG<CAAGCCAATGGAAGAGGATACCAAT>GT...”
Q2L886 oxaloacetase (EC 3.7.1.1) from Aspergillus niger (see paper)
An15g07720 uncharacterized protein from Aspergillus niger
36% identity, 84% coverage
- Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways
Hossain, Fungal biology and biotechnology 2019 - “...9.81 ANI_1_2054064 Oxaloacetate acetylhydrolase An07g08390 Cytosol 10.41 7.31 7.55 11.70 ANI_1_1800134 Oxaloacetate hydrolase class protein An15g07720 Cytosol 49.63 70.43 95.09 67.85 IA bioconversion ANI_1_1432064 Itaconyl-CoA transferase A ( ictA ) An07g00760 Mito 13.07 108.35 170.34 375.89 ANI_1_676164 CoA transferase superfamily enzyme An18g05120 Mito 11.10 9.36 11.79...”
XP_002447699 uncharacterized protein LOC8070958 from Sorghum bicolor
34% identity, 92% coverage
PDP_DIACA / Q05957 Petal death protein; (R)-2-methylmalate lyase; D-citramalate lyase; Oxalacetic hydrolase; PSR132; EC 3.7.1.1; EC 4.1.3.- from Dianthus caryophyllus (Carnation) (Clove pink) (see 3 papers)
Q05957 isocitrate lyase (EC 4.1.3.1) from Dianthus caryophyllus (see paper)
36% identity, 81% coverage
- function: Catalyzes cleavage of the C(2)-C(3) bond in oxaloacetate and in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl carboxylates and R-ketocarboxylates, respectively.
catalytic activity: oxaloacetate + H2O = oxalate + acetate + H(+) (RHEA:24432)
cofactor: Mg(2+) Mn(2+) Fe(2+) Co(2+) (Binds 1 Mg(2+) ion per subunit. Can bind other divalent cations such as Mn(2+), Fe(2+) and Co(2+).)
subunit: Homodimer and homotetramer formed by a dimer of homodimer. - Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply
Ceballos-Laita, Frontiers in plant science 2015 - “...P16016, U5GK55 C, S nCS, CS One-carbon metabolic process 1 Oxaloacetase ( Dianthus caryophyllus ) Q05957 Metabolic process STRESS AND DEFENSE (23) 3 Osmotin-like protein Q38745 S CS Defense response 4 Thaumatin-like protein Q6PP01, A9ZMG1, A9ZMG0, XP_004297839 , S, S, S nCS, CS, CS, CS Defense...”
- Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids
Lu, Biochemistry 2005 (PubMed)- “...flowering plant Dianthus caryophyllus. This protein (Swiss-Prot entry Q05957) is synthesized in the senescent flower petals and is named the "petal death...”
- “...death protein (PDP) (316 amino acids; Swiss-Prot entry Q05957), was discovered through the sequencing of a cDNA transcript prepared from mRNA synthesized in...”
1zlpB / Q05957 Petal death protein psr132 with cysteine-linked glutaraldehyde forming a thiohemiacetal adduct (see paper)
36% identity, 87% coverage
- Ligand: 5-hydroxypentanal (1zlpB)
I1KZI4 Uncharacterized protein from Glycine max
34% identity, 61% coverage
An15g02980 uncharacterized protein from Aspergillus niger
39% identity, 66% coverage
- Identification of novel citramalate biosynthesis pathways in Aspergillus niger
Hossain, Fungal biology and biotechnology 2019 - “...0.00 0.15 13 ANI_1_1256014 An01g09270 Isocitrate lyase acuD Per 86.38 61.77 65.20 42.26 13 ANI_1_1336134 An15g02980 Isocitrate lyase/malate synthase Per 33.76 34.75 25.03 22.66 13 ANI_1_1826104 An12g05180 Isocitrate lyase/malate synthase Cyto 0.00 0.09 0.00 0.48 14 ANI_1_320134 An15g01860 Malate synthase Per 112.41 98.34 72.33 34.38 15...”
AFUA_2G03820, Afu2g03820 carboxyphosphonoenolpyruvate phosphonomutase, putative from Aspergillus fumigatus Af293
36% identity, 77% coverage
- Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus
Wiemann, Frontiers in microbiology 2014 - “...HAS leads these strains to experience iron-deficiency. Among those genes were eight putative oxidoreductases (AFUA_1g17430; AFUA_2g03820; AFUA_2g09355; AFUA_3g00150; AFUA_3g01070; AFUA_4g13780; AFUA_5g09720; AFUA_6g03290) (Table 4 ). In line with this finding we observed an up-regulation of the cytochrome C-encoding gene ( cycA ) in northern blot analysis...”
- “...hasA vs. WT OE:: hasA vs. OE:: hasA / hasD AFUA_1G17430 Putative oxidoreductase 1.75 1.58 AFUA_2G03820 Putative oxidoreductase 1.68 1.43 AFUA_2G09355 Putative oxidoreductase 1.28 1.10 AFUA_3G00150 Putative oxidoreductase 1.39 1.04 AFUA_3G01070 Putative oxidoreductase 1.64 1.35 AFUA_4G13780 Putative oxidoreductase 1.60 1.58 AFUA_5G09720 Putative oxidoreductase 1.54 1.27 AFUA_6G03290...”
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...Afu6g11600, Afu6g07480 27 3 Afu3g01170, Afu7g01590, Afu5g13810 28 3 Afu7g00420, Afu8g06100, Afu8g06590 29 3 Afu2g00120, Afu2g03820, Afu2g00540 30 3 Afu6g00500, Afu8g00930, Afu4g01290 31 2 Afu3g07860, Afu4g14070 32 2 Afu1g04780, Afu1g12910 33 2 Afu2g07940, Afu6g10990 34 2 Afu6g07640, Afu1g04460 35 2 Afu1g11290, Afu5g14230 36 2 Afu7g04800, Afu2g12640...”
3fa3B / Q2L887 Crystal structure of 2,3-dimethylmalate lyase, a pep mutase/isocitrate lyase superfamily member, trigonal crystal form (see paper)
35% identity, 81% coverage
- Ligand: 2,2-difluoro-3,3-dihydroxybutanedioic acid (3fa3B)
A2QP68 oxaloacetase (EC 3.7.1.1) from Aspergillus niger (see paper)
Q2L887 2,3-Dimethylmalate lyase (EC 4.1.3.32) from Aspergillus niger (see paper)
An07g08390 uncharacterized protein from Aspergillus niger
35% identity, 81% coverage
- Identification of novel citramalate biosynthesis pathways in Aspergillus niger
Hossain, Fungal biology and biotechnology 2019 - “...21.43 19.54 20 ANI_1_92174 An10g00820 Oxaloacetate acetylhydrolase oahA Cyto 1803.48 1122.69 323.44 9.81 20 ANI_1_2054064 An07g08390 Oxaloacetate acetylhydrolase Mito 10.41 7.31 7.55 11.70 21 ANI_1_1678104 An12g03440 Glucose oxidase Secreted 0.66 0.84 0.21 0.23 21 ANI_1_748094 An11g05580 Glucose oxidase Secreted 1.01 1.80 1.15 0.19 21 ANI_1_1398064 An07g00450...”
- Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways
Hossain, Fungal biology and biotechnology 2019 - “...ANI_1_92174 Oxaloacetate acetylhydrolase ( oahA ) An10g00820 Cytosol 1803.48 1122.69 323.44 9.81 ANI_1_2054064 Oxaloacetate acetylhydrolase An07g08390 Cytosol 10.41 7.31 7.55 11.70 ANI_1_1800134 Oxaloacetate hydrolase class protein An15g07720 Cytosol 49.63 70.43 95.09 67.85 IA bioconversion ANI_1_1432064 Itaconyl-CoA transferase A ( ictA ) An07g00760 Mito 13.07 108.35 170.34...”
- Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member
Narayanan, Journal of molecular biology 2009 (PubMed)- “...highest amino acid sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the protein in Escherichia coli and purified...”
- “...used to determine the catalytic function of An07g08390 as (2R,3S)-dimethylmalate lyase (DMML): kcat=19.2s1 and Km=220M. DMML also possesses significant OAH...”
- Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member
Narayanan, Journal of molecular biology 2009 (PubMed)- “...sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the protein in Escherichia coli and purified it for structural...”
- “...sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887 , 57% identity), we produced the protein in Escherichia coli and purified it for structural...”
BC1G_03473, BCIN_12g01020 Bcoah from Botrytis cinerea B05.10
36% identity, 66% coverage
- Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection-related development and host penetration
Zhang, Molecular plant pathology 2020 - “...possible roles of pathogen genes in host infection, we characterized some upregulated fungal DEGs, including BCIN_12g01020 encoding oxaloacetate acetylhydrolase (OAH) and BCIN_03g01540 encoding choline dehydrogenase (Tables 2 and S5 ). The pathogen may orchestrate these DEGs to facilitate host infection. TABLE 2 Highly upregulated (fold change40)...”
- “...genes Gene ID Protein symbol Fold change Annotation Secreted BCIN_03g01540 BCIN_03g01540 527.7 Choline dehydrogenase Yes BCIN_12g01020 Bcoah 402.4 Oxaloacetate acetylhydrolase (Bcoah1) No BCIN_15g05630 BCIN_15g05630 349.4 Putative NADdependent epimerase dehydratase family protein No BCIN_15g01960 BCIN_15g01960 211.3 RNA methyltransferase, TrmH family, group 3 Yes BCIN_08g00280 BCIN_08g00280 206.8 Similar...”
- Identification of Development and Pathogenicity Related Gene in Botrytis cinerea via Digital Gene Expression Profile
Zhao, Jundishapur journal of microbiology 2015 - “...e.g. up-regulated genes (BC1G_11615, BC1G_13891, BC1G_06046, BC1G_16009 and BC1G_05103) and down-regulated genes (BC1G_13087, BC1G_06990, BC1G_09505, BC1G_03473 and BC1G_13094), were measured using semi-quantitative RT-PCR with gene-specific primers ( Table 1 ). All RT-PCR experiments were performed in three biological replicates and each biological sample was analyzed in...”
- “...54C TATTCTCAACCGTGCTCGC CCATCTCCTCAAATCCAGC BC1G_13087 52C AGACAAAGGCGAAGAGGAC ACAGGTTTCGTTCCCTCCA BC1G_06990 56C AGCCTCATCAATGCTCTCG TCTCTCTCAGTTCAGTTGCTTG BC1G_09505 55C GAGAAACAGAAGGCAGAAGC TAAGCGTGAGAGGAGTGGA BC1G_03473 54C ACAACAGGGTTTGAGAGCG CGAGTAATCCAACATCTGCG BC1G_13094 54C CTCATCATCTGTGGCATCA AGACCGATTGTGCGAAAG BC1G_00122 (Tubulin) 52C GTTGGATTTGCTCCTTTGAC TGTTGGACTCAGCCTCAGT 4. Results 4.1. Sequence Analysis of Raw Data To investigate transcriptome response to the development and pathogenicity of...”
MSMEG_6855 carboxyvinyl-carboxyphosphonatephosphorylmutase from Mycobacterium smegmatis str. MC2 155
39% identity, 77% coverage
OAHA / Q6PNM8 oxaloacetate acetylhydrolase monomer (EC 3.7.1.1) from Botryotinia fuckeliana (see 4 papers)
Q6PNM8 oxaloacetase (EC 3.7.1.1) from Botrytis cinerea (see 2 papers)
36% identity, 75% coverage
Afu2g00120 carboxyvinyl-carboxyphosphonate phosphorylmutase from Aspergillus fumigatus Af293
40% identity, 60% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...Afu2g09520, Afu6g11600, Afu6g07480 27 3 Afu3g01170, Afu7g01590, Afu5g13810 28 3 Afu7g00420, Afu8g06100, Afu8g06590 29 3 Afu2g00120, Afu2g03820, Afu2g00540 30 3 Afu6g00500, Afu8g00930, Afu4g01290 31 2 Afu3g07860, Afu4g14070 32 2 Afu1g04780, Afu1g12910 33 2 Afu2g07940, Afu6g10990 34 2 Afu6g07640, Afu1g04460 35 2 Afu1g11290, Afu5g14230 36 2 Afu7g04800,...”
An12g05180 uncharacterized protein from Aspergillus niger
37% identity, 68% coverage
- Identification of novel citramalate biosynthesis pathways in Aspergillus niger
Hossain, Fungal biology and biotechnology 2019 - “...65.20 42.26 13 ANI_1_1336134 An15g02980 Isocitrate lyase/malate synthase Per 33.76 34.75 25.03 22.66 13 ANI_1_1826104 An12g05180 Isocitrate lyase/malate synthase Cyto 0.00 0.09 0.00 0.48 14 ANI_1_320134 An15g01860 Malate synthase Per 112.41 98.34 72.33 34.38 15 ANI_1_2114184 An04g08220 l -Lactate dehydrogenase Mito/Cyto 0.09 0.58 0.51 0.63 16...”
Pc18g05100 uncharacterized protein from Penicillium rubens
36% identity, 77% coverage
A7ESB3 oxaloacetase (EC 3.7.1.1) from Sclerotinia sclerotiorum (see paper)
SS1G_08218 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
36% identity, 68% coverage
- Recent advances in virulence of a broad host range plant pathogen Sclerotinia sclerotiorum: a mini-review
Zhu, Frontiers in microbiology 2024 - “...secretory protein with a putative Ca 2+ binding EF-hand motif Xiao et al. (2014) Ssoah1 (SS1G_08218) Knockout Reduced A . thaliana , soybean, tomato oxaloacetate acetylhydrolase gene, key enzyme of oxalic acid Liang et al. (2015a) Ss-odc2 (SS1G_10796) Knockout Reduced Soybean Oxalate decarboxylase Liang et al....”
- Efficacy of <i>Trichoderma longibrachiatum</i> SC5 Fermentation Filtrate in Inhibiting the <i>Sclerotinia sclerotiorum</i> Growth and Development in Sunflower
Li, International journal of molecular sciences 2024 - “...AAM22186 encoding polygalacturonase 1 [ 64 ] Ss-CutA XM_001590986 encoding cutinase [ 64 ] Ss-oah1 SS1G_08218 oxalic acid biosynthesis [ 65 ] Ss-pth2 SS1G_13339 sclerotia development, oxalic acid biosynthesis [ 66 ] Ss-sod1 SS1G_00699 growth, sclerotia development, oxalic acid biosynthesis, virulence [ 67 ]...”
- Spray-induced gene silencing of SsOah1 and SsCyp51 confers protection to Nicotiana benthamiana and Brassica juncea against Sclerotinia sclerotiorum
Pant, Physiological and molecular plant pathology 2023 - Transcriptome analysis of the plant pathogen Sclerotinia sclerotiorum interaction with resistant and susceptible canola (Brassica napus) lines
Chittem, PloS one 2020 - “...2.54 0.198 oxalic acid sscle_14g099710 SS1G_08814 0.20 0.862 0.91 0.231 1.01 0.239 1.13 0.121 sscle_10g075560 SS1G_08218 2.18 0.010 1.87 0.020 2.04 0.013 2.12 0.010 sscle_08g062640 SS1G_04900 0.29 0.601 1.20 0.017 0.40 0.476 1.35 0.008 glyoxylate cycle sscle_08g063200 SS1G_04975 3.50 0.001 4.20 0.000 3.72 0.001 4.39 0.000...”
- The Notorious Soilborne Pathogenic Fungus Sclerotinia sclerotiorum: An Update on Genes Studied with Mutant Analysis
Xia, Pathogens (Basel, Switzerland) 2019 - “...(Bush Blue Lake 47), soybean (Harosoy), tomato (Bonnie Best) and celery [ 64 ] sscle_10g075560 SS1G_08218 WMA1, Washington, USA oah Oxaloacetate acetylhydrolase T-DNA - - + + NA NA No Faba bean (Broad Windsor), pea (Guido), green bean (Great North Tara) and soybean (Skylla) [ 65...”
- “...bean (Bush Blue Lake 47), soybean (Harosoy), canola, Arabidopsis and sunflower [ 66 ] sscle_10g075560 SS1G_08218 1980, Nebraska, U.S.A.; UF1, Florida; WMA, Washington, USA oah1 Oxaloacetate acetylhydrolase Deletion by CRISPR - + + + + NA No Soybean, canola, tomato (Better Boy), faba bean (Windsor), and...”
- Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea
McLoughlin, Scientific reports 2018 - “.... Source Gene FPKM in vitro FPKM Westar 24dpi FPKM ZY821 24hpi Process Literature 1 SS1G_08218 7913.2 5211.0 6743.8 Oxaloacetate acetylhydrolase Essential Genes 2 SS1G_05899 268.7 259.1 244.4 Thioredoxin reductase Essential genes 2 SS1G_06487 87.3 82.0 114.3 TIM44 Essential genes 2 SS1G_07873 47.1 41.5 47.8 pre-40S...”
- “...triacylglycerol lipase), and kinetochore functions (SS1G_09261). Even a previously characterized genetic deletion target 29 , SS1G_08218 ( Ssoah ; oxaloacetate acetylhydrolase), had no significant impact on disease symptoms under the conditions tested size (p=0.5). While these targets did not show significant modulations in lesion size, they...”
- Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus
Seifbarghi, BMC genomics 2017 - “...and SS1G_05839 genes encoding SSITL, SsCaf1 and SsBi1, respectively) and four well-characterized S. sclerotiorum genes (SS1G_08218, SS1G_10796, SS1G_10167 and SS1G_07355 encoding oxaloacetate acetyl hydrolase (OAH), oxalate decarboxylase, SsPG1 and the Pac1 transcription factor, respectively). The ddPCR analysis generated patterns of expression for the induced genes that...”
- “...and reduced virulence [ 116 ]. In the current study, the S. sclerotiorum OAH gene (SS1G_08218) was expressed from 1 hpi, but only up-regulated at 48 hpi with 5- fold greater levels than the inoculum. OAH expression was also detected in the S. sclerotiorum P. vulgaris...”
- Comparative Transcriptome Analysis between the Fungal Plant Pathogens Sclerotinia sclerotiorum and S. trifoliorum Using RNA Sequencing
Qiu, The Journal of heredity 2016 - “...JP568434 (23), JP561743 (27) 4 5 6 SS1G_08218 N/A SS1G_04975 SS1G_04900 SS1G_05583 SS1G_12839 SS1G_14097 SS1G_03827 SS1G_08814 SS1G_10796 SS1G_09038 SS1G_08975...”
Q0IPL3 Os12g0189300 protein from Oryza sativa subsp. japonica
34% identity, 76% coverage
- ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...10 56.00 1.80 Q2QZH3 Os11g0687100 protein 12 16.43 2.15 A0A0P0Y5F2 Os11g0687200 protein 8 12.37 1.82 Q0IPL3 Os12g0189300 protein 15 50.00 3.37 Q2QWN3 Os12g0189400 protein 13 53.02 0.72 Q2QNS7 Os12g0555500 protein 10 70.25 2.58 a Peptides (95%) indicate the identified peptides having at least 95% confidence. b...”
- “...13 36.65 0.54 Q2QZH3 Os11g0687100 protein 12 16.43 1.67 A0A0P0Y5F2 Os11g0687200 protein 8 12.37 1.72 Q0IPL3 Os12g0189300 protein 15 50.00 2.51 Q2QSR7 Os12g0420200 protein 32 55.05 1.33 a Peptides (95%) indicate the identified peptides having at least 95% confidence. b Cov (95%) indicate percentage of matching...”
Afu2g00540 carboxyphosphonoenolpyruvate phosphonomutase, putative from Aspergillus fumigatus Af293
35% identity, 71% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...Afu6g07480 27 3 Afu3g01170, Afu7g01590, Afu5g13810 28 3 Afu7g00420, Afu8g06100, Afu8g06590 29 3 Afu2g00120, Afu2g03820, Afu2g00540 30 3 Afu6g00500, Afu8g00930, Afu4g01290 31 2 Afu3g07860, Afu4g14070 32 2 Afu1g04780, Afu1g12910 33 2 Afu2g07940, Afu6g10990 34 2 Afu6g07640, Afu1g04460 35 2 Afu1g11290, Afu5g14230 36 2 Afu7g04800, Afu2g12640 37...”
Hlac_2153 isocitrate lyase and phosphorylmutase from Halorubrum lacusprofundi ATCC 49239
38% identity, 52% coverage
- Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi
Liao, Scientific reports 2016 - “...acetyl-CoA synthesis (Hlac_1306, Hlac_0890, Hlac_0891, Hlac_0967); the utilization of acetyl-CoA via the glyoxylate cycle (Hlac_3040; Hlac_2153); the carboxylation of phosphoenolpyruvate (PEP) to oxaloacetate (Hlac_2311); the conversion of glycerol into dihydroxyacetone phosphate (DHAP) (Hlac_2109, Hlac_1458, Hlac_1122, Hlac_1124); and purine synthesis (Hlac_1295, Hlac_1250). Proteins associated with responses to...”
- “...alpha subunit (PorA) 1.2 ns 1.9 ns Hlac_1306 acetate:CoA ligase (Acs) 3.3 ns 2.3 ns Hlac_2153 isocitrate lyase (AceA) 3.9 ns 2.5 ns Hlac_2311 phosphoenolpyruvate carboxylase (Ppc) 1.5 ns 2.0 ns Hlac_3040 aconitate hydratase 1.3 ns 1.7 ns One carbon metabolism Hlac_1238 formate dehydrogenase, alpha subunit...”
FVEG_01044 methylisocitrate lyase from Fusarium verticillioides 7600
35% identity, 85% coverage
HFX_2079 isocitrate lyase from Haloferax mediterranei ATCC 33500
38% identity, 52% coverage
Pc22g24830, XP_002566371 uncharacterized protein from Penicillium rubens
32% identity, 72% coverage
Q7Z986 oxaloacetase (EC 3.7.1.1) from Aspergillus niger (see 2 papers)
33% identity, 74% coverage
D5LIR7 oxaloacetase (EC 3.7.1.1) from Cryphonectria parasitica (see paper)
35% identity, 64% coverage
An10g00820 uncharacterized protein from Aspergillus niger
33% identity, 85% coverage
- Evaluation of Aspergillus niger Six Constitutive Strong Promoters by Fluorescent-Auxotrophic Selection Coupled with Flow Cytometry: A Case for Citric Acid Production
Lu, Journal of fungi (Basel, Switzerland) 2022 - “...lyase (AcsA, An11g00510 and AcsB, An11g00530), mitochondrial cis-aconitase AcoA (An08g10530), and cytoplasmic oxaloacetate acetylhydrolase OahA (An10g00820) were dramatically downregulated ( Table 2 ). 4. Discussion The filamentous fungus A. niger is an important workhorse in industrial biotechnology. Well-characterized promoters in regard to gene expression strength and...”
- “...0.79 An11g00510 acsA ATP-citrate lyase 0.45 0.46 1.02 An11g00530 acsB ATP-citrate lyase 0.51 0.50 0.98 An10g00820 oahA Oxaloacetate acetylhydrolase 0.19 0.62 3.23 An15g00070 mdhAc Cytoplasmic malate dehydrogenase 1.26 1.44 1.14 An11g04810 aox1 Alternative oxidase 1.37 2.14 1.56 An01g09270 iclA Isocitrate lyase 1.11 5.23 4.72...”
- Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger
Zheng, Microbial biotechnology 2022 - “...transporter gene oacA (An14g06860) was significantly upregulated, while the gene encoding cytoplasmic oxaloacetate acetylhydrolase oahA (An10g00820), which catalysed oxaloacetate into oxalic acid, was significantly downregulated. Genes involved in TCA cycle have no significant changes, except the citA gene (An09g6680) and the mdhA gene (An07g02160) with slight...”
- Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways
Hossain, Fungal biology and biotechnology 2019 - “...1.14 ANI_1_1416134 An15g04010 Hypothetical protein Nucleus 0.27 0.20 5.87 7.79 288.73 208.03 3.11 0.09 ANI_1_92174 An10g00820 Oxaloacetate acetylhydrolase Cytosol 0.13 0.81 2.61 7.51 1803.48 1122.69 323.44 9.81 ANI_1_220174 An10g00800 Purine nucleoside permease Secreted 0.13 0.33 2.72 6.47 375.32 326.25 61.40 3.64 ANI_1_1046034 An03g01450 Major Facilitator Superfamily...”
- “...An02g14730 Cytosol 5.97 7.29 5.81 10.08 OahA class family ANI_1_92174 Oxaloacetate acetylhydrolase ( oahA ) An10g00820 Cytosol 1803.48 1122.69 323.44 9.81 ANI_1_2054064 Oxaloacetate acetylhydrolase An07g08390 Cytosol 10.41 7.31 7.55 11.70 ANI_1_1800134 Oxaloacetate hydrolase class protein An15g07720 Cytosol 49.63 70.43 95.09 67.85 IA bioconversion ANI_1_1432064 Itaconyl-CoA transferase...”
- Identification of novel citramalate biosynthesis pathways in Aspergillus niger
Hossain, Fungal biology and biotechnology 2019 - “...146.61 232.65 19 ANI_1_1156014 An01g08610 Citramalate-CoA lyase cclA Mito 10.17 12.59 21.43 19.54 20 ANI_1_92174 An10g00820 Oxaloacetate acetylhydrolase oahA Cyto 1803.48 1122.69 323.44 9.81 20 ANI_1_2054064 An07g08390 Oxaloacetate acetylhydrolase Mito 10.41 7.31 7.55 11.70 21 ANI_1_1678104 An12g03440 Glucose oxidase Secreted 0.66 0.84 0.21 0.23 21 ANI_1_748094...”
- Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites
Niu, G3 (Bethesda, Md.) 2015 - “...sure that the oahA gene was not mutated in the D15 mutant, the oahA gene (An10g00820), including 1000 nucleotide-flanking regions, was PCR-amplified from D15 and sequenced. No mutation in the gene was found, indicating that the mutation in D15 is not located in the oahA locus....”
3m0jA Structure of oxaloacetate acetylhydrolase in complex with the inhibitor 3,3-difluorooxalacetate (see paper)
35% identity, 79% coverage
- Ligands: 2,2-difluoro-3,3-dihydroxybutanedioic acid; calcium ion (3m0jA)
CCM_05734 carboxyphosphonoenolpyruvate phosphonomutase, putative from Cordyceps militaris CM01
36% identity, 64% coverage
ACEA_HALVD / D4GTL3 Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii) (see 2 papers)
36% identity, 52% coverage
- function: Involved in the metabolic adaptation in response to environmental changes. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+)
subunit: Homotetramer or homotrimer.
AT2G43180 catalytic from Arabidopsis thaliana
32% identity, 59% coverage
- Chromoplast plastoglobules recruit the carotenoid biosynthetic pathway and contribute to carotenoid accumulation during tomato fruit maturation
Zita, 2022 - Chromoplast plastoglobules recruit the carotenoid biosynthetic pathway and contribute to carotenoid accumulation during tomato fruit maturation
Zita, PloS one 2022 - “...Solyc01g006540.2.1 LOXC 18 55 AT1G17420 - - - Solyc05g056270.2.1 Phosphoenolpyruvate carboxylase family protein 62 39 AT2G43180 - - - Solyc06g083770.2.1 Glutathione S-transferase family protein 22 12 AT5G44000 - - - Solyc05g009390.2.1 Alpha/beta-Hydrolases superfamily protein 7 11 AT1G77420 - - - Solyc08g083035.1.1 Uncharacterized protein 10 6 AT5G41960...”
- Identification and characterization of suppressor mutants of stop1
Jiang, BMC plant biology 2017 - “...BBE16, FAD-binding Berberine family protein Cytosol Oxidation-reduction process, response to jasmonic acid, response to wounding At2g43180 Phosphoenolpyruvate carboxylase family protein Chloroplast Catalytic activity At2g44440 EML4, ENT domaincontaining protein Nucleus Defense response to fungus Table 3 Candidate genes in the TPS2 region at chromosome 1 Candidate Genes...”
- Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration
Qin, PloS one 2017 - “...436/3 3.3040.149(-) 96h/0h RBCL 63 * Carboxyvinyl-carboxyphosphonate phosphorylmutase/CPEP phosphonomutase cassava4.1_011697m 8.25/50.32 120/5 2.0140.106(-)/2.0230.111(-) 96h/0h 48h/0h AT2G43180 Inorganic ion transport and metabolism (1) 69 * calcium-binding protein CML15-related (CaM) cassava4.1_034063m 4.22/17.53 78/3 2.7320.077(-)/(-) 96h/0h 48h/0h, 72h/0h, 96h/0h AT3G25600 Defense (7) 18 thiamine thiazole synthase cassava4.1_010620m 5.30/39.74 78/5...”
- Proteomic analysis of endoplasmic reticulum stress responses in rice seeds
Qian, Scientific reports 2015 - “...3.416 AT4G15530 pyruvate, phosphate dikinase LOC_Os05g33570 gi|115465825 13.676 AT4G10960 UDP-glucose 4-epimerase 1 LOC_Os05g51670 gi|32490267 2.354 AT2G43180 carboxyvinyl-carboxyphosphonate phosphorylmutase LOC_Os04g42580 gi|115456435 2.048 AT1G50940 electron transfer flavoprotein subunit alpha LOC_Os03g61920 gi|115480417 3.038 AT5G66120 3-dehydroquinate synthase LOC_Os09g36800 gi|115436430 2.815 AT3G06860 3-hydroxyacyl-CoA dehydrogenase LOC_Os01g24680 gi|218188780 2.461 AT4G11030 AMP-binding enzyme LOC_Os01g46750...”
- Bidirectional promoters in seed development and related hormone/stress responses
Kourmpetli, BMC plant biology 2013 - “...mitochondrion golgi AT2G39460 AT2G39450 331 y 60S ribosomal protein L23aA manganese transporter cytosol golgi AT2G43190 AT2G43180 187 AtPOP4 (RNA processing) Phosphoenolpyruvate carboxylase family nucleolus plastid AT2G45740 AT2G45730 556 y peroxin11 (PEX11) family eukaryotic initiation factor 3 subunit peroxisome cytosol AT3G03160 AT3G03150 264 y y unknown protein...”
E9E7Q4 Carboxyphosphonoenolpyruvate phosphonomutase, putative from Metarhizium acridum (strain CQMa 102)
33% identity, 71% coverage
rhiH / D4HRI5 phosphoenolpyruvate mutase (EC 5.4.2.9) from Bacillus subtilis subsp. spizizenii ATCC 6633 (see paper)
WP_003223692 phosphoenolpyruvate mutase from Bacillus spizizenii
30% identity, 91% coverage
- The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis
Rice, Nature communications 2019 - “...numbers: Tetrahymena pyriformis (P33182); FrbD from Streptomyces rubellomurinus (ABB90393); Bacillus subtilis subsp. spizizenii str. W23 (WP_003223692); Streptomyces viridochromogenes (AAU00071); Streptomyces luridus (ACZ13456); S. wedmorensis (BAA32495); Streptomyces fradiae (ACG70831); Pseudomonas syringae (AFM38986). Cytidylyltransferase (PntC) protein sequences were retrieved from NCBI with the following accession numbers: Tde-PntC from...”
WP_102244880 phosphoenolpyruvate mutase from Bacteriovorax stolpii
34% identity, 46% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...840, Bacillus megaterium strain S188 , NZ_CP049296, WP_164797121; 761, Bacteriovorax stolpii strain DSM 12778, NZ_CP025704, WP_102244880; 539, Paenibacillus polymyxa E681, NZ_014483, WP_013312267; 864, Salmonella enterica strain 850120, NZ_CP054715, WP_171775701; 857, Serratia plymuthica S13, NZ_021659, WP_004946681; 640, Erwinia persicina strain B64, NZ_CP022725, WP_118663913; 333, Rathayibacter toxicus strain...”
ZP_02329666 putative phosphoenolpyruvate phosphomutase from Paenibacillus larvae subsp. larvae BRL-230010
29% identity, 98% coverage
WP_118663913 phosphoenolpyruvate mutase from Erwinia persicina
32% identity, 82% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...850120, NZ_CP054715, WP_171775701; 857, Serratia plymuthica S13, NZ_021659, WP_004946681; 640, Erwinia persicina strain B64, NZ_CP022725, WP_118663913; 333, Rathayibacter toxicus strain WAC3373, NZ_CP013292, WP_052493485; 880, Paraburkholderia sp. Msb3 isolate PDMSB31, NZ_LR699554, WP_165187990; 865, Paraburkholderia carabensis strain 852011, NZ_CP015959, WP_062917090; 600, Burkholderia vietnamiensis strain AU1233, NZ_CP013433, WP_060044431; 731,...”
WP_042112012 phosphoenolpyruvate mutase from Pandoraea apista
31% identity, 46% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...neighbourhood are as follows: Cupriavidus metallidurans strain FDAARGOS_675, NZ_CP046331, WP_011516537; Pandoraea apista strain AU2161, NZ_CP011501, WP_042112012; Burkholderia glumae strain 257sh-1 chromosome 2, NZ_CP035901, WP_017423874; Burkholderia gladioli strain ATCC 10248 chromosome 2, NZ_CP009322, WP_036031650; Burkholderia pseudomallei isolate UKMPMC2000 chromosome 2, NZ_LR595895, WP_004525540; Burkholderia pseudomallei B03 chromosome 2,...”
WP_060044431 phosphoenolpyruvate mutase from Burkholderia vietnamiensis
32% identity, 47% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...Burkholderia cenocepacia strain FL-5-3-30-S1-D7 chromosome 2, NZ_CP013396, WP_023477253; Burkholderia vietnamiensis strain AU1233 chromosome 1, NZ_CP013433, WP_060044431; Burkholderia territorii strain RF8-non-BP5 chromosome 2, NZ_CP013365, WP_059507240. Fig. 5. Diversity of AEPT-encoding gene neighbourhoods. Representative neighbourhoods for each family are shown on the left aligned by clinker [ 41...”
- “...NZ_LR699554, WP_165187990; 865, Paraburkholderia carabensis strain 852011, NZ_CP015959, WP_062917090; 600, Burkholderia vietnamiensis strain AU1233, NZ_CP013433, WP_060044431; 731, Nitrosococcus wardiae strain D1FHS, NZ_CP038033, WP_134359243; 743, Bacteroides fragilis strain NCTC 9343, NC_003228, WP_011202610; 321, Bacteroides thetaiotaomicron strain 7330, NZ_CP012937, WP_008767814; 863, Treponema denticola ATCC 35405, NZ_002967, WP_002679012; 866,...”
WP_059507240 phosphoenolpyruvate mutase from Burkholderia territorii
33% identity, 44% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...Burkholderia vietnamiensis strain AU1233 chromosome 1, NZ_CP013433, WP_060044431; Burkholderia territorii strain RF8-non-BP5 chromosome 2, NZ_CP013365, WP_059507240. Fig. 5. Diversity of AEPT-encoding gene neighbourhoods. Representative neighbourhoods for each family are shown on the left aligned by clinker [ 41 ] to highlight the key three-gene subcluster encoding...”
WP_011516537 phosphoenolpyruvate mutase from Cupriavidus metallidurans
30% identity, 47% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...protein accession numbers for each gene neighbourhood are as follows: Cupriavidus metallidurans strain FDAARGOS_675, NZ_CP046331, WP_011516537; Pandoraea apista strain AU2161, NZ_CP011501, WP_042112012; Burkholderia glumae strain 257sh-1 chromosome 2, NZ_CP035901, WP_017423874; Burkholderia gladioli strain ATCC 10248 chromosome 2, NZ_CP009322, WP_036031650; Burkholderia pseudomallei isolate UKMPMC2000 chromosome 2, NZ_LR595895,...”
pphA / Q84G06 phosphonopyruvate hydrolase subunit (EC 3.11.1.3) from Variovorax sp. (strain Pal2) (see 6 papers)
PPHA_VARSP / Q84G06 Phosphonopyruvate hydrolase; PPH; EC 3.11.1.3 from Variovorax sp. (strain Pal2) (see 3 papers)
Q84G06 phosphonopyruvate hydrolase (EC 3.11.1.3) from Variovorax sp. (see 2 papers)
34% identity, 87% coverage
- function: Hydrolyzes phosphonopyruvate. Not active towards phosphoenolpyruvate, glycerophosphate, phospho-L-serine or phosphoglycolic acid.
catalytic activity: 3-phosphonopyruvate + H2O = pyruvate + phosphate + H(+) (RHEA:16673)
cofactor: Co(2+) Mg(2+) Mn(2+) (Divalent metal cations. Co(2+), Mg(2+) or Mn(2+) can be used.)
subunit: Homodimer (PubMed:12697754). Homotetramer (PubMed:16981709).
WP_165187990 phosphoenolpyruvate mutase from Paraburkholderia dioscoreae
29% identity, 50% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...WP_118663913; 333, Rathayibacter toxicus strain WAC3373, NZ_CP013292, WP_052493485; 880, Paraburkholderia sp. Msb3 isolate PDMSB31, NZ_LR699554, WP_165187990; 865, Paraburkholderia carabensis strain 852011, NZ_CP015959, WP_062917090; 600, Burkholderia vietnamiensis strain AU1233, NZ_CP013433, WP_060044431; 731, Nitrosococcus wardiae strain D1FHS, NZ_CP038033, WP_134359243; 743, Bacteroides fragilis strain NCTC 9343, NC_003228, WP_011202610; 321,...”
KAI37_05154 phosphoenolpyruvate mutase from Paenibacillus sp. S25
30% identity, 89% coverage
KAI36_05277 phosphoenolpyruvate mutase from Paenibacillus sp. S02
29% identity, 89% coverage
- Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome
Li, Scientific reports 2021 - “...134.46* KAI36_03372 113.90* C15 Nrps Polymyxin (100%) KAI36_04684 9.61* KAI36_04687 8.61* KAI36_04688 9.86* C16 Phosphonate KAI36_05277 15.10* Clusters in bold: Known antimicrobial compounds. *Genes that were differentially expressed ( q-value <0.05 and absolute fold-change1.5) when comparing the two strains. The presence of F. verticillioides had different...”
- “...1.02 KAI37_04566 2.61* KAI37_04567 2.33* KAI36_04687 1.10 KAI37_04570 1.45* KAI36_04688 1.12 KAI37_04571 1.92* C16 Phosphonate KAI36_05277 1.38 KAI37_05154 1.77* Clusters in bold: Known antimicrobial compounds. N/A: Genes that didnt pass the abundance filter described in Transcriptome analysis section. *: Genes that were differentially expressed ( q-value...”
Q2T3Z7 phosphoenolpyruvate mutase from Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)
BTH_II1908 phosphoenolpyruvate phosphomutase from Burkholderia thailandensis E264
33% identity, 44% coverage
2duaA / Q84G06 Crystal structure of phosphonopyruvate hydrolase complex with oxalate and mg++ (see paper)
34% identity, 87% coverage
- Ligands: alpha-d-xylopyranose; oxalate ion (2duaA)
WP_043296855 phosphoenolpyruvate mutase from Burkholderia thailandensis
33% identity, 44% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NZ_LR595895, WP_004525540; Burkholderia pseudomallei B03 chromosome 2, NZ_CP009150, WP_004525540; Burkholderia thailandensis E254 chromosome 2, NZ_CP004382, WP_043296855; Burkholderia cepacia ATCC 25416 chromosome 2, NZ_CP007748, WP_021162084; Burkholderia cenocepacia strain FL-5-3-30-S1-D7 chromosome 2, NZ_CP013396, WP_023477253; Burkholderia vietnamiensis strain AU1233 chromosome 1, NZ_CP013433, WP_060044431; Burkholderia territorii strain RF8-non-BP5 chromosome 2,...”
WP_025716510 phosphoenolpyruvate mutase from Paenibacillus sp. 1-18
30% identity, 83% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NZ_CP019655, WP_023485328; 837, Brevibacillus sp. 7WMA2, NZ_CP048799, WP_013336797; 805 Paenibacillus brasilensis strain KACC 13842, NZ_CP09363115, WP_025716510; 453, Paenibacillus sp. IHB B3084, NZ_CP013203, WP_134911858; 859, Bacillus megaterium strain FDU301, NZ_CP045272, WP_171777684; 840, Bacillus megaterium strain S188 , NZ_CP049296, WP_164797121; 761, Bacteriovorax stolpii strain DSM 12778, NZ_CP025704, WP_102244880;...”
B479_21440 oxaloacetate decarboxylase from Pseudomonas putida HB3267
30% identity, 85% coverage
- RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium
Yang, MicrobiologyOpen 2016 - “...downregulated in M2013683LB were randomly selected for qRTPCR verification. The genes B479_13310, B479_22535, B479_14405, and B479_21440 which upregulated 2.2157, 1.6008, 4.4875, and 3.7257 log 2 fold in RNAsequencing data, showed 2.2155, 1.3599, 3.5096, and 3.0219 log 2 fold changes in the qRTPCR analyses, respectively. Likewise, in...”
WP_052493485 phosphonopyruvate decarboxylase from Rathayibacter toxicus
28% identity, 42% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NZ_021659, WP_004946681; 640, Erwinia persicina strain B64, NZ_CP022725, WP_118663913; 333, Rathayibacter toxicus strain WAC3373, NZ_CP013292, WP_052493485; 880, Paraburkholderia sp. Msb3 isolate PDMSB31, NZ_LR699554, WP_165187990; 865, Paraburkholderia carabensis strain 852011, NZ_CP015959, WP_062917090; 600, Burkholderia vietnamiensis strain AU1233, NZ_CP013433, WP_060044431; 731, Nitrosococcus wardiae strain D1FHS, NZ_CP038033, WP_134359243; 743,...”
WP_134911858 phosphoenolpyruvate mutase from Paenibacillus sp. IHB B 3084
29% identity, 89% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...WP_013336797; 805 Paenibacillus brasilensis strain KACC 13842, NZ_CP09363115, WP_025716510; 453, Paenibacillus sp. IHB B3084, NZ_CP013203, WP_134911858; 859, Bacillus megaterium strain FDU301, NZ_CP045272, WP_171777684; 840, Bacillus megaterium strain S188 , NZ_CP049296, WP_164797121; 761, Bacteriovorax stolpii strain DSM 12778, NZ_CP025704, WP_102244880; 539, Paenibacillus polymyxa E681, NZ_014483, WP_013312267; 864,...”
PP1389, PP_1389 carboxyphosphonoenolpyruvate phosphonomutase, putative from Pseudomonas putida KT2440
30% identity, 85% coverage
- UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soil Pseudomonas species
Mendonca, Proceedings of the National Academy of Sciences of the United States of America 2020 - “...Fe-limited cells compared to the Fe-replete cells: phosphoenolpyruvate carboxylase (ppc, by 25%) and oxaloacetate decarboxylase (PP1389, by 19%) ( Fig. 5 A ). For pyruvate biosynthesis, pyruvate was made from both the ED pathway (41%) and the TCA cycle (59%) in Fe-replete cells but only 4%...”
- New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure
Follonier, Microbial cell factories 2013 - “...1.3 E-02 PP_3662 decarboxylase family protein (possible lysine decarboxylase) -1.85 4.9 E-03 -1.69 3.9 E-03 PP_1389 carboxyphosphonoenolpyruvate phosphonomutase, putative -1.54 3.7 E-03 PP_5346 pyruvate carboxylase subunit B oadA -1.58 1.7 E-02 -1.51 1.1 E-01 PP_5347 pyruvate carboxylase subunit A accC-2 -2.23 1.9 E-03 -2.41 5.6 E-03...”
- “...2 . Only a small number of genes encoding enzymes involved in carboxylation/decarboxylation reactions (PP_1631, PP_1389, PP_3662, PP_5346/ oadA , PP_5347/ accC-2 ) were differentially regulated in the Pressure and Pressure Oxygen conditions (Table 3 ). For some genes, the differential expression was in agreement with...”
- The AauR-AauS two-component system regulates uptake and metabolism of acidic amino acids in Pseudomonas putida
Sonawane, Applied and environmental microbiology 2006 - “...was identified as the protein product of PP1389 (annotated as carboxyphosphonoenolpyruvate phosphonomutase), while spot R2 corresponds to a conserved protein of...”
- “...periplasmic amino acid binding protein PGA D2 a PP1389 R1 R4 Glucose-NH4 Masscalc (kDa)b Identification R2 R3 pIcalca No. of matching peptides Spot 6574...”
WP_004525540 phosphoenolpyruvate mutase from Burkholderia pseudomallei MSHR5855
32% identity, 44% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...dotted line marking a count of ten. The two largest bars represent sequences WP_004523200 and WP_004525540. ( b ) Sunburst chart of early branch point phosphonate biosynthetic steps based on 434 gene neighbourhoods; BGCs possessing the same Ppm sequence (e.g. WP_004523200) are treated as a single...”
- “...single genome, several were found in multiple genomes. In particular, two Ppm sequences (WP_004523200 and WP_004525540) together accounted for over 200 gene neighbourhoods in different genome assemblies of Burkholderia pseudomallei ; however, the phylogenetic separation of these two sequences in distinct clades implies different phosphonate products...”
WP_017423874 phosphoenolpyruvate mutase from Burkholderia glumae AU6208
32% identity, 46% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NZ_CP046331, WP_011516537; Pandoraea apista strain AU2161, NZ_CP011501, WP_042112012; Burkholderia glumae strain 257sh-1 chromosome 2, NZ_CP035901, WP_017423874; Burkholderia gladioli strain ATCC 10248 chromosome 2, NZ_CP009322, WP_036031650; Burkholderia pseudomallei isolate UKMPMC2000 chromosome 2, NZ_LR595895, WP_004525540; Burkholderia pseudomallei B03 chromosome 2, NZ_CP009150, WP_004525540; Burkholderia thailandensis E254 chromosome 2, NZ_CP004382,...”
3b8iA / Q9HUU1 Crystal structure of oxaloacetate decarboxylase from pseudomonas aeruginosa (pa4872) in complex with oxalate and mg2+. (see paper)
29% identity, 83% coverage
- Ligand: oxalate ion (3b8iA)
OADC_PSEAE / Q9HUU1 Oxaloacetate decarboxylase; EC 4.1.1.112 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
NP_253559 hypothetical protein from Pseudomonas aeruginosa PAO1
PA4872 hypothetical protein from Pseudomonas aeruginosa PAO1
29% identity, 83% coverage
- function: Catalyzes the decarboxylation of oxaloacetate into pyruvate with high efficiency. Is also able to decarboxylate 3- methyloxaloacetate. Seems to play a role in maintaining cellular concentrations of bicarbonate and pyruvate.
catalytic activity: oxaloacetate + H(+) = pyruvate + CO2 (RHEA:15641)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homotetramer; dimer of dimers. - Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
Narayanan, Biochemistry 2008 - GeneRIF: Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM).
- Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa
Fraser-Pitt, Frontiers in cellular and infection microbiology 2021 - “...NP_253705.1 peptide methionine sulfoxide reductase PA5018 msrA/pmsR Cellular response to oxidative stress NP_253559.1 hypothetical protein PA4872 Uncharacterised NP_250270.1 hypothetical protein PA1579 Uncharacterised NP_251947.1 periplasmic tail-specific protease PA3257 algO/prc Signal transduction, proteolysis NP_253977.1 hypothetical protein PA5290 yifB Uncharacterised NP_253012.1 hypothetical protein PA4322 AAA domain-containing protein, ATPase activity,...”
- Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy
McGill, Scientific reports 2021 - “...enzymes except the membrane-associated succinate dehydrogenase were detected and quantified. Additionally, the enzymes oxaloacetate decarboxylase (PA4872) and PEP synthase which process metabolic intermediates from the TCA cycle for gluconeogenesis, were expressed constitutively. The abundance of ATP synthase subunits was also constitutive. Membrane-associated, electron transport chain(ETC) enzymes...”
- New Insights about Antibiotic Production by Pseudomonas aeruginosa: A Gene Expression Analysis
Gionco, Frontiers in chemistry 2017 - “...PA3920) and one gene (PA3574a) was associated with chaperones group linked with copper. The gene (PA4872) was classified as a transcript regulator and gene (phzA2) was related to the phenazine biosynthesis. Three hyperexpressed genes were related to the efflux system (PA3521, PA3523, and PA3920) and one...”
- The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase
Lietzan, Archives of biochemistry and biophysics 2014 - “...the reaction cycle. A similar biotin-independent mechanism has been proposed for the nonhomologous oxaloacetate decarboxylase PA4872 from Pseudomonas putida , where a water molecule is thought to serve as the acid that donates a proton to the pyruvate enolate [ 51 ]. The biotin-independent mechanism in...”
- Structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase, a protocatechuate degradation enzyme evolutionarily convergent with the HpaI and DmpG pyruvate aldolases
Wang, The Journal of biological chemistry 2010 - “...as the residues contributed by D, lase (PA4872) (41) and 5,10-methylenetetrahydrofolate:3- have direct correlates in YER010c and PSPTO_3204 (Fig. 2G...”
- “...a magnesium ion in have arginine residues (Arg-159 for PA4872 and Arg-228 for the PSPTO_3204 structure is ligated directly to Asp-102 and KPHMT from M....”
- Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily
Narayanan, Biochemistry 2008 - “...47(1): 167-182. doi:10.1021/bi701954p. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP...”
- “...Manuscript Abstract NIH-PA Author Manuscript Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member...”
dhpE / D7PC17 phosphoenolpyruvate phosphomutase (EC 5.4.2.9) from Streptomyces luridus (see paper)
29% identity, 88% coverage
Ac3H11_2831 Isocitrate lyase (EC 4.1.3.1) from Acidovorax sp. GW101-3H11
28% identity, 46% coverage
- mutant phenotype: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Rta_23660 isocitrate lyase from Ramlibacter tataouinensis TTB310
27% identity, 57% coverage
ppm / A0A0M3WNK3 phosphoenolpyruvate phosphomutase (EC 5.4.2.9) from Kitasatospora phosalacinea (see 2 papers)
29% identity, 89% coverage
H16_A2227 isocitrate lyase from Cupriavidus necator H16
H16_A2227 isocitrate lyase from Ralstonia eutropha H16
27% identity, 58% coverage
- The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16
Arenas-López, Biotechnology for biofuels 2019 - “...highly upregulated in the presence of 3-HP were two genes encoding isocitrate lyase isoenzymes (H16_A2211, H16_A2227), in accordance with the proposed breakdown via the oxidative route, allowing the generated acetyl-CoA to enter the tricarboxylic acid cycle (TCA) via the glyoxylate shunt. Interestingly, genes encoding enzymes of...”
- “...3-HP were two genes encoding isoenzymes of isocitrate lyase ( aceA1, H16_A2211 and aceA2 , H16_A2227). The same genes were previously shown to be upregulated during growth on trioleate [ 7 ], the fatty acid components of which are metabolised via -oxidation and, like acetate, enter...”
- Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates
Sharma, AMB Express 2016 - “...AceB protein expression in any substarates. However, in our proteomes two proteins IclA (H16_A2211), IclB (H16_A2227) designated as isocitate lyase were highly expressed in RG-GB and RG-FFA media. In addition to this, another protein, AcnB (aconitate hydratase) was also highly upregulated in GB-RG and RG-FFA. These...”
- Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
Shimizu, BMC microbiology 2013 - “...level of expressions were very weak during the cultivation on fructose. iclA (H16_A2211) and iclB (H16_A2227), both encodes isocitrate lyase in glyoxylate bypass, were observed to be highly induced in the PHA production phase. In particular, the transcription of iclB in F26 increased 33-fold as compared...”
RS_RS06810 isocitrate lyase from Ralstonia pseudosolanacearum GMI1000
28% identity, 56% coverage
frbD / Q0ZQ45 phosphoenolpyruvate mutase (EC 5.4.2.9) from Streptomyces rubellomurinus (strain ATCC 31215) (see 2 papers)
PEPM_STRR3 / Q0ZQ45 Phosphoenolpyruvate phosphomutase; PEP mutase; PEP phosphomutase; Phosphoenolpyruvate mutase; EC 5.4.2.9 from Streptomyces rubellomurinus (strain ATCC 31215) (see paper)
33% identity, 80% coverage
- function: Isomerase involved in the biosynthesis of the phosphonate antibiotic FR-900098, a potent antimalarial agent that acts as an inhibitor of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), the first enzyme in the nonmevalonate pathway for isoprenoid biosynthesis (PubMed:18721747). Catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate (PubMed:18721747).
catalytic activity: phosphoenolpyruvate + H(+) = 3-phosphonopyruvate (RHEA:17013)
A8J244 isocitrate lyase from Chlamydomonas reinhardtii
XP_001695331 uncharacterized protein from Chlamydomonas reinhardtii
28% identity, 53% coverage
RSUY_RS08780 isocitrate lyase from Ralstonia solanacearum
26% identity, 58% coverage
RALTA_A1766 isocitrate lyase from Cupriavidus taiwanensis
27% identity, 58% coverage
- Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history
Klonowska, BMC genomics 2018 - “...metabolism of beta-rhizobia. First with the up-regulation of the aceA gene (BURPHK1_1476, FC 1.64 and RALTA_A1766, FC 11) encoding an isocitrate lyase, an enzyme of the glyoxylate bypass of the tricarboxylic acid (TCA) cycle. The FC was much higher in CT, which is linked with the...”
- “...up-regulated several genes involved in the glyoxylate bypass pathway: an isocitrate lyase ( aceA1 , RALTA_A1766, FC 11) and its paralog ( aceA2 , RALTA_B0267, FC 1.89) and a malate synthase ( aceB , RALTA_A1760, FC 1.6). Induction of these genes was also observed for R....”
SAR11_1240 isocitrate lyase from Candidatus Pelagibacter ubique HTCC1062
28% identity, 53% coverage
Rmet_1385 isocitrate lyase from Ralstonia metallidurans CH34
Rmet_1385 isocitrate lyase from Cupriavidus metallidurans CH34
27% identity, 58% coverage
WP_023485328 phosphoenolpyruvate mutase from Paenibacillus larvae
27% identity, 83% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...for each gene neighbourhood are as follows: 841, Paenibacillus larvae subsp. larvae strain Eric_III, NZ_CP019655, WP_023485328; 837, Brevibacillus sp. 7WMA2, NZ_CP048799, WP_013336797; 805 Paenibacillus brasilensis strain KACC 13842, NZ_CP09363115, WP_025716510; 453, Paenibacillus sp. IHB B3084, NZ_CP013203, WP_134911858; 859, Bacillus megaterium strain FDU301, NZ_CP045272, WP_171777684; 840, Bacillus...”
Q39577 isocitrate lyase from Chlamydomonas reinhardtii
27% identity, 54% coverage
Alvin_1848 isocitrate lyase from Allochromatium vinosum DSM 180
30% identity, 46% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...7.3E-26 FeoA family protein (Fe2 +transport) 23 Alvin_0019 3.51 2.4E-26 Ferrous-iron efflux pump FieF 26 Alvin_1848 3.51 1.1E-35 Isocitrate lyase 27 Alvin_2446 3.44 7.5E-17 Nitrite and sulphite reductase 4Fe-4S region 29 Alvin_1878 3.36 2.6E-03 Nitrogen fixation protein FixT 30 Alvin_0017 3.36 5.6E-29 XRE family transcriptional regulator...”
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...LT988_06350) as well as in the genome of Alc. vinosum DSM 180 T (isocitrate lyase, Alvin_1848 and malate synthase G, Alvin_2606). The lack of beneficial effect after adding certain substrates to an inorganic medium can be explained by the lack of their intracellular transport. The revealed...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...relative transcript and protein levels for isocitrate lyase (Alvin_1848), the key enzyme of the glyoxylate cycle in A. vinosum (48), significantly increased in...”
- “...Alvin_1366 Alvin_1394 Alvin_1502 Alvin_1503 Alvin_1508 Alvin_1848 Alvin_1971 Alvin_2001 Alvin_2107 Alvin_2019 Alvin_2037 Alvin_2038 Alvin_2136 Alvin_2421...”
- Metabolomic profiling of the purple sulfur bacterium Allochromatium vinosum during growth on different reduced sulfur compounds and malate
Weissgerber, Metabolomics : Official journal of the Metabolomic Society 2014 - “...palustris (McKinlay and Harwood 2011 ). Notably, relative transcript and protein levels for isocitrate lyase (Alvin_1848), the key enzyme of the glyoxylate cycle in A. vinosum (Fuller et al. 1961 ), significantly increased in the presence of elemental sulfur, while levels decreased on sulfide (Fig. 5...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...of the glyoxylate cycle (Alvin_3052 [citrate synthase] and Alvin_1848 [isocitrate lyase]) (Table 2; see also Table S3 in the supplemental material) exhibited...”
- “...Alvin_1197 Alvin_1420 Alvin_1436 Alvin_1525 Alvin_1527 Alvin_1848 Alvin_2012 Alvin_2245 Alvin_2262 Alvin_2337 Alvin_2338 Alvin_2339 Alvin_2340 Alvin_2341...”
ppm / P33182 phosphoenolpyruvate mutase subunit (EC 5.4.2.9) from Tetrahymena pyriformis (see paper)
pepm / AAA30123.1 phosphoenolpyruvate mutase from Tetrahymena pyriformis (see paper)
P33182 Phosphoenolpyruvate phosphomutase from Tetrahymena pyriformis
30% identity, 79% coverage
A9IUW1 Isocitrate lyase from Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448)
28% identity, 54% coverage
BB3339 putative isocitrate lyase from Bordetella bronchiseptica RB50
BPP1769 putative isocitrate lyase from Bordetella parapertussis 12822
27% identity, 54% coverage
PMI2763 isocitrate lyase from Proteus mirabilis HI4320
30% identity, 46% coverage
YP_716511 putative Phosphoenolpyruvate phosphomutase (Phosphoenolpyruvate mutase) (PEP mutase) (PEP phosphomutase) from Frankia alni ACN14a
28% identity, 84% coverage
- Molecular cloning and heterologous expression of the dehydrophos biosynthetic gene cluster
Circello, Chemistry & biology 2010 - “...Candidatus Pelagibacter ubique aspartate transaminase (ZP_01264754) 112/403 (28%) dhpE 296 Frankia alni putative PEP phosphomutase (YP_716511) 147/275 (53%) dhpF 381 Amycolatopsis orientalis putative phosphonopyruvate decarboxylase (CAB45023) 182/371(49%) dhpG 396 Amycolatopsis orientalis putative alcohol dehydrogenase (CAB45024) 152/367(41%) dhpH N terminal domain (355 AA) Amycolatopsis orientalis putative aminotransferase...”
MAC_05902 uncharacterized protein from Metarhizium acridum
33% identity, 62% coverage
BP2085 putative isocitrate lyase from Bordetella pertussis Tohama I
27% identity, 54% coverage
WU75_19150 isocitrate lyase from Vibrio parahaemolyticus
29% identity, 47% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...repressed (0.129-fold to 0.277-fold) ( p < 0.05). For instance, the DEGs ( aceAB , WU75_19150 , WU75_19145 , and WU75_00290 ), encoding an isocitrate lyase and a malate synthase of the glyoxylate shunt (GS) carbon cycle, were significantly inhibited (0.315-fold to 0.370-fold) ( p <...”
- “...lpd 0.35 Dihydrolipoamide dehydrogenase Glyoxylate and dicarboxylate metabolism WU75_19760 gltA 0.129 Type II citrate synthase WU75_19150 aceA 0.37 Isocitrate lyase WU75_19145 aceB 0.352 Malate synthase WU75_00290 aceB 0.315 Malate synthase WU75_10840 phbB 0.277 3-ketoacyl-ACP reductase WU75_03265 katE 2.389 Catalase Fatty acid degradation WU75_22235 fadB 0.151 Multifunctional...”
Q5A_023425 isocitrate lyase from Serratia inhibens PRI-2C
29% identity, 46% coverage
YPTS_3842 isocitrate lyase from Yersinia pseudotuberculosis PB1/+
YPTB3656 isocitrate lyase from Yersinia pseudotuberculosis IP 32953
29% identity, 46% coverage
- Impact of MgtC on the Fitness of Yersinia pseudotuberculosis
Li, Pathogens (Basel, Switzerland) 2023 - “...synthase A 5.255804 1.16 10 10 YPTS_2011 Aspartate aminotransferase family protein 5.083721 1.85 10 7 YPTS_3842 Isocitrate lyase 5.081315 4.39 10 9 YPTS_2313 Acid shock protein 3.712933 8.92 10 24 YPTS_0225 Glycerol-3-phosphate dehydrogenase subunit GlpB 3.838456 7.86 10 35 YPTS_0224 Anaerobic glycerol-3-phosphate dehydrogenase subunit A 4.235415...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...(< 0.001) YPTB0716 YPO3415 acnB putative aconitate hydratase 2 0.510 (< 0.001) 0.319 (< 0.001) YPTB3656 YPO3725 aceA, icl isocitrate lyase 2.068 (0.003) 1.298 (0.319) YPTB3657 YPO3726 aceB, mas malate synthase A 1.875 (0.053) 1.089 (0.710) YPTB2222 YPO2300 fnr, nirR putative fumarate and nitrate reduction regulatory...”
- “...(0.024) YPTB3539 YPO3694 putative cytochrome 0.544 (< 0.001) YPTB3592 YPO3637 putative carbohydrate kinase 1.585 (0.031) YPTB3656 (aceA) YPO3725 isocitrate lyase 2.069 (0.002) 1.963 (0.004) YPTB3762 (pckA) YPO0138 phosphoenolpyruvate carboxykinase [ATP] 0.395 (0.001) YPTB3782 (glpD) YPO3937 aerobic glycerol-3-phosphate dehydrogenase 0.409 (0.02) YPTB3927 (fdoG) or2536 formate dehydrogenase-O. major...”
ACEA_CORGL / P42449 Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) (see 3 papers)
cg2560 isocitrate lyase from Corynebacterium glutamicum ATCC 13032
NCgl2248 isocitrate lyase from Corynebacterium glutamicum ATCC 13032
27% identity, 55% coverage
- function: Involved in the metabolic adaptation in response to environmental changes. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+) (Divalent metal cations. Mn(2+) or Co(2+) can be used.)
subunit: Homotetramer.
disruption phenotype: Cells lacking this gene are unable to grow on acetate as carbon source. - CRISPRi-Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum
Göttl, Microorganisms 2021 - “...from S. pyogenes ; Cm R This work pS_dCas9_ aceA pS_dCas9 plasmid carrying the aceA (cg2560) sgRNA This work pS_dCas9_ aceB pS_dCas9 plasmid carrying the aceB (cg2559) sgRNA This work pS_dCas9_ aceE pS_dCas9 plasmid carrying the aceE (cg2466) sgRNA This work pS_dCas9_ ackA pS_dCas9 plasmid carrying...”
- Adaptive laboratory evolution accelerated glutarate production by Corynebacterium glutamicum
Prell, Microbial cell factories 2021 - “...downregulated in GluA T5. Among them, sucCD (cg2835, cg2837), coding for succinyl-CoA synthetase, and aceA (cg2560), encoding isocitrate lyase, are key enzymes of the TCA cycle and the glyoxylate shunt. Of the 62 genes upregulated in GluA T5, seven code for transporters, e.g., mediating uptake of...”
- Physiological Response of Corynebacterium glutamicum to Indole
Walter, Microorganisms 2020 - “...aroG 3-deoxy-7-phosphoheptulonate synthase 1.54 cg2500 putative transcriptional regulator. ArsR-family 1.59 cg2559 aceB malate synthase 1.79 cg2560 aceA isocitrate lyase 2.34 cg2719 putative enterochelin esterase 1.6 cg2836 sucD succinate-CoA ligase (ADP-forming), alpha subunit 2.06 cg2837 sucC succinate-CoA ligase (ADP-forming), beta subunit 2.23 cg2962 putative enzyme synthesing extracellular...”
- Comprehensive Analysis of C. glutamicum Anaplerotic Deletion Mutants Under Defined d-Glucose Conditions
Kappelmann, Frontiers in bioengineering and biotechnology 2020 - “...3.11e-02 CAF21195 cg2791 rpmJ 50S ribosomal protein L36 0.46 1.40e-02 C. glutamicum ppc pyc CAF20674 cg2560 aceA Isocitrate lyase 23.94 3.79e-44 CAF20673 cg2559 aceB Malate synthase 9.45 6.63e-41 CAF19365 cg0762 prpC2 2-methylcitrate synthase 6.49 4.73e-18 CAF19364 cg0760 prpB2 2-methylcitrate lyase 5.05 1.07e-21 CAF21548 cg1737 acn Aconitase...”
- “...(see Supplementary Table 6 ) were detected in the coding region for ICD. Moreover, ICL (cg2560), MS (cg2559), and cis -aconitase (ACN, cg1737) are highly up-regulated in C. glutamicum ppc pyc ( Figure 3 and Table 3 ) and only in this mutant intracellular and extracellular...”
- Impact of CO2/HCO3- Availability on Anaplerotic Flux in Pyruvate Dehydrogenase Complex-Deficient Corynebacterium glutamicum Strains
Krüger, Journal of bacteriology 2019 (secret) - Regulation of the pstSCAB operon in Corynebacterium glutamicum by the regulator of acetate metabolism RamB
Sorger-Herrmann, BMC microbiology 2015 - “...-sufficient to P i -limiting conditions Gene identifier Annotation a Relative mRNA level b glucose/acetate cg2560 aceA , isocitrate lyase 0.01 cg2559 aceB , malate synthase 0.05 cg3169 pck , phosphoenolpyruvate carboxykinase 0.22 cg3048 pta , phosphoacetyltransferase 0.27 cg2887 phoR , phosphate response regulator 0.33 cg1737...”
- Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum
Klaffl, Journal of bacteriology 2013 - “...NCgl0164 NCgl0167 NCgl0178 NCgl0900 NCgl1353 NCgl1650 iolC cg2560 cg2732 cg3096 cg3107 cg3169 cg3195 cg3216 NCgl2248 NCgl2399 NCgl2698 NCgl2709 NCgl2765...”
- Characterization of the biotin uptake system encoded by the biotin-inducible bioYMN operon of Corynebacterium glutamicum
Schneider, BMC microbiology 2012 - “...transport protein BioN 2.0 0.4 1.6 cg2320 predicted transcriptional regulator MarR family 2.0 0.5 1.6 cg2560 isocitrate lyase AceA 3.1 0.4 1.0 cg2747 metalloendopeptidases-like protein n.d. 0.4 2.3 cg2883 SAM-dependent methyltransferase 2.2 0.2 n.d. cg2884 putative dipeptide/tripeptide permease 8.9 0.1 5.6 cg2885 adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA 3.8...”
- More
- Development of a novel platform for recombinant protein production in Corynebacterium glutamicum on ethanol
Yu, Synthetic and systems biotechnology 2022 - “...block the EUT pathway, the genes adh (NCgl2382), aldh (NCgl2698), ak (NCgl2657), pta (NCgl2656), aceA (NCgl2248), and aceB (NCgl2247), which are encoding enzymes involved in the EUT pathway, were selected as individual targets for repression by our CRISPRi system. The sgRNAs were designed according to the...”
- Construction and application of a CRISPR/Cas9-assisted genomic editing system for Corynebacterium glutamicum
Yao, AMB Express 2021 - “...NCgl1345 pCCG1- argR TCGCGGGCGATGCTATCTAC TGG 564/625 gabTD NCgl0462, NCgl0463 pCCG1- gabTD CCAGTAATCAACCCCAGCGA TGG 754/754 aceAB NCgl2248, NCgl2247 pCCG1- aceAB GGAAATCCTCGTACGCCTCT TGG 810/829 poxB NCgl2521 pCCG1- poxB GGTCACCGGATACTTCACCG TGG 644/654 C. glutamicum ATCC 14067 gabP CEY17_02745 pCCG1- gabP-2 GTGGAGGCATTGATCACCAC TGG 553/580 C. glutamicum ssp. lactofermentum gabP ND...”
- Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
Sun, PloS one 2017 - “...the macromolecule synthesis and ATP production [ 30 ]. Meanwhile, because of the up-regulation of NCgl2248 encoding isocitrate lyase by 2.95-fold and the ICDH was lower in C . glutamicum EGFP than in C . glutamicum BZH 001, the glyoxylate cycle maybe increased. Second, the accumulation...”
- Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction
Mizuno, MicrobiologyOpen 2016 - “...kinase ( ackA , NCgl2656), phosphotransacetylase ( pta , NCgl2657), isocitrate lyase ( aceA , NCgl2248), and malate synthase ( glcB , NCgl2247) were constructed by a twostep homologous recombination procedure. Upstream and downstream regions (approximately 1.5kb each for the NCgl0078 or NCgl0616 deletion, and approximately...”
- “...FumC, fumarate hydratase (NCgl0967); Mdh, malate dehydrogenase (NCgl2297); Mqo, malate:quinone oxidoreductase (NCgl1926); AceA, isocitrate lyase (NCgl2248); GlcB, malate synthase G (NCgl2247); Pta, phosphotransacetylase (NCgl2657); AckA, acetate kinase (NCgl2656); PoxB, pyruvate dehydrogenase (NCgl2521), Pyc, pyruvate carboxylase (NCgl0659); Ppc, phosphoenolpyruvate carboxylase (NCgl1523); PckG, phosphoenolpyruvate carboxykinase (NCgl2765); Gdh, glutamate...”
- Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum
Klaffl, Journal of bacteriology 2013 - “...cg2732 cg3096 cg3107 cg3169 cg3195 cg3216 NCgl2248 NCgl2399 NCgl2698 NCgl2709 NCgl2765 NCgl2787 NCgl2808 myo-Inositol catabolism, carbohydrate kinase...”
- Characterization of a Corynebacterium glutamicum lactate utilization operon induced during temperature-triggered glutamate production
Stansen, Applied and environmental microbiology 2005 - “...NCgl1263 NCgl1470 NCgl1472 NCgl1502 NCgl1646 NCgl1647 NCgl2248 NCgl2319 NCgl2353 NCgl2450 NCgl2451 NCgl2657 NCgl2713 NCgl2719 NCgl2816 NCgl2817 NCgl2965...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...0.23 0.43 0.33 NCgl2112 NCgl2437 NCgl2673 NCgl2247 NCgl2248 NCgl2709 pepB glnD glnK cgtR3 cgtS10 argR Annotation Putative regulatory protein (WhiB-related...”
O86937 Phosphoenolpyruvate phosphomutase from Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494)
29% identity, 89% coverage
YPO3725 isocitrate lyase from Yersinia pestis CO92
y0016 isocitrate lyase from Yersinia pestis KIM
29% identity, 46% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...0.001) YPTB0716 YPO3415 acnB putative aconitate hydratase 2 0.510 (< 0.001) 0.319 (< 0.001) YPTB3656 YPO3725 aceA, icl isocitrate lyase 2.068 (0.003) 1.298 (0.319) YPTB3657 YPO3726 aceB, mas malate synthase A 1.875 (0.053) 1.089 (0.710) YPTB2222 YPO2300 fnr, nirR putative fumarate and nitrate reduction regulatory protein...”
- “...YPO3694 putative cytochrome 0.544 (< 0.001) YPTB3592 YPO3637 putative carbohydrate kinase 1.585 (0.031) YPTB3656 (aceA) YPO3725 isocitrate lyase 2.069 (0.002) 1.963 (0.004) YPTB3762 (pckA) YPO0138 phosphoenolpyruvate carboxykinase [ATP] 0.395 (0.001) YPTB3782 (glpD) YPO3937 aerobic glycerol-3-phosphate dehydrogenase 0.409 (0.02) YPTB3927 (fdoG) or2536 formate dehydrogenase-O. major subunit 0.208...”
- Deletion of Yersinia pestis ail Causes Temperature-Sensitive Pleiotropic Effects, Including Cell Lysis, That Are Suppressed by Carbon Source, Cations, or Loss of Phospholipase A Activity
Kolodziejek, Journal of bacteriology 2021 - “...Unknown; putative factor 1 12.4 y0024 pgi Glucose-6-phosphate isomerase Energy metabolism, carbon: glycolysis 1 2.9 y0016 aceA Isocitrate lyase Central intermediary metabolism: glyoxylate bypass 1 3.4 a Number of peptides identified for indicated protein. b Peptide coverage (%) of indicated protein. The lack of Caf1 in...”
- Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
Fukuto, Infection and immunity 2010 - “...y0655 y2882 y1189 y1041 y0310 y1607 YPO1423a y3555 y0509 y0016 y0463 y0655 y1821 y2881 y2125 y3804 y2236 y0015 YPO3681 y3836 y2591 50S ribosomal protein L31...”
- Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
Pieper, BMC microbiology 2010 - “...aceB malate synthase A CY Fur 688 63974 5.86 0.06 1.73 0.036 0.000 0.421 2 y0016 aceA isocitrate lyase CY 741 54571 5.47 0.38 4.19 0.090 0.000 0.408 3 y0047 glpK glycerol kinase CY 828 60235 6.01 0.07 0.33 0.198 0.000 0.570 4 y0320 oxyR DNA-binding...”
5uncA / A0A0A0V023 The crystal structure of phosphoenolpyruvate phosphomutase from streptomyces platensis subsp. Rosaceus
29% identity, 89% coverage
- Ligand: alpha-d-xylopyranose (5uncA)
VC0736 isocitrate lyase from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 47% coverage
- Vibrio cholerae Alkalizes Its Environment via Citrate Metabolism to Inhibit Enteric Growth <i>In Vitro</i>
Kostiuk, Microbiology spectrum 2023 - “...of biomass. This pathway is mediated by isocitrate lyase (ICL), which V. cholerae C6706 carries (VC0736). Consistent with this alternate citrate metabolic pathway, we simulated V. cholerae metabolism using a previously constructed genome-scale metabolic model based on the V52 strain ( 54 ) with the software...”
- Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing
Huang, PeerJ 2019 - “...the V. cholerae wild-type strain, the differentially expressed genes VCA0875, VC2036, VC2646, VC0485, VCA0008 and VC0736 were significantly upregulated, while VC2738, VC0534 and VCA0843 were significantly downregulated, in the degS mutant strain. These results were consistent with those of the RNA-Seq analysis, indicating the reliability and...”
- Gluconeogenic growth of Vibrio cholerae is important for competing with host gut microbiota
Wang, Journal of medical microbiology 2018 (secret) - Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity
Toulouse, Journal of bacteriology 2018 - “...and connected reactions A0A0H3AKS4 A0A0H3AMD5 A0A0H3AMM1 A0A0H3AHX2 VC1338 VC0736 VC0734 VC1336 acnA aceA aceB prpB 2.4 2.3 2 2.3 Aconitate hydratase Isocitrate...”
- “...for the glyoxylate shunt with downstream enzymes isocitrate lyase (VC0736, RF of 2.3) and malate synthase (VC0734, RF of 2). By downregulation of the latter...”
- Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
Sepúlveda-Cisternas, Scientific reports 2018 - “...VC0711 clpB clpB protein 2.092 1.022 VC0734 malate synthase A 3.115 VC0735 hypothetical protein 3.069 VC0736 isocitrate lyase 1.788 VC0748 aminotransferase NifS class V 1.034 VC0749 NifU-related protein 1.254 VC0750 hesB hesB family protein 1.166 VC0753 ferredoxin 1.008 1.100 VC0754 conserved hypothetical protein 1.079 VC0765 conserved...”
WP_013312267 phosphoenolpyruvate mutase from Paenibacillus polymyxa E681
27% identity, 47% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NZ_CP049296, WP_164797121; 761, Bacteriovorax stolpii strain DSM 12778, NZ_CP025704, WP_102244880; 539, Paenibacillus polymyxa E681, NZ_014483, WP_013312267; 864, Salmonella enterica strain 850120, NZ_CP054715, WP_171775701; 857, Serratia plymuthica S13, NZ_021659, WP_004946681; 640, Erwinia persicina strain B64, NZ_CP022725, WP_118663913; 333, Rathayibacter toxicus strain WAC3373, NZ_CP013292, WP_052493485; 880, Paraburkholderia sp....”
N646_2741 isocitrate lyase from Vibrio alginolyticus NBRC 15630 = ATCC 17749
29% identity, 47% coverage
ppm / Q5IW38 phosphoenolpyruvate phosphomutase (EC 5.4.2.9) from Streptomyces viridochromogenes (see paper)
29% identity, 89% coverage
VV1_0449 isocitrate lyase from Vibrio vulnificus CMCP6
29% identity, 47% coverage
- In vivo characterisation of the Vibrio vulnificus stressosome: A complex involved in reshaping glucose metabolism and motility regulation, in nutrient- and iron-limited growth conditions
Cutugno, Current research in microbial sciences 2023 - “...Reverse: CTTCCGCTTTCGCTTTGGCG pta (VV1_2220) Forward: CGCCACGAGACAGGTCGTTT Reverse: GGCAGCGTCTAAAGCGCCTA acsA (VV1_1237) Forward: CGCGCACCATCTCCGGTAAA Reverse: AGCCTGCACTGGTGGACAAC aceA (VV1_0449) Forward: ACGCATTCAGCACACCACCA Reverse: CAATTCGTTCCGTCGCGCAG aceB (VV1_0450) Forward: CATTCCCCGAGATCCACGCC Reverse: TCACTCGCCAAGACGATGCG glcB (VV2_1647) Forward: TGCTGGGTTGCCACAAAGGT Reverse: AAGGTCGTGCGCGTTTCCAA rpoS (VV1_1588) Forward: CCAGAGCGTGGTTTCCGCTT Reverse: GAGAAAGCTCACGCGCCGTA toxR (VV1_0190) Forward: ATGCTGGCACGTCAACAAAGATGG Reverse: TGGTGAGCAAGACAACGCAAAGTG fleQ (VV1_1931)...”
- “...reduced de novo synthesis. qRT-PCR studies demonstrated an intermediate effect of deleting RSTX on aceA (VV1_0449), aceB (VV1_0450) and glcB (VV2_1647) transcription compared to D1 and WT. Likewise there was minimal influence of RSTX on AceA or AceB protein levels, though GlcB levels did decrease. These...”
WP_077842376 phosphoenolpyruvate mutase from Clostridium beijerinckii
26% identity, 61% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...Treponema denticola ATCC 35405, NZ_002967, WP_002679012; 866, Clostridium beijerinckii isolate C. beijerinckii DSM 6423, NZ_LN908213, WP_077842376; 476, Clostridium saccharobutylicum strain NCP 195, NZ_CP016092, WP_022744173; 856, Clostridium butyricum strain 41, NZ_CP039705, WP_002579294; 400, Selenomonas sp. oral taxon 478 strain F0592, NZ_CP012071, WP_050342316. The large group of AEPT-encoding...”
FZF21_08615 isocitrate lyase from Enterobacter sp. LU1
29% identity, 47% coverage
WP_022744173 phosphoenolpyruvate mutase from Clostridium saccharobutylicum
25% identity, 58% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...beijerinckii isolate C. beijerinckii DSM 6423, NZ_LN908213, WP_077842376; 476, Clostridium saccharobutylicum strain NCP 195, NZ_CP016092, WP_022744173; 856, Clostridium butyricum strain 41, NZ_CP039705, WP_002579294; 400, Selenomonas sp. oral taxon 478 strain F0592, NZ_CP012071, WP_050342316. The large group of AEPT-encoding gene neighbourhoods is diverse Apart from the Group...”
MAB_4095c Isocitrate lyase (AceA) from Mycobacterium abscessus ATCC 19977
27% identity, 56% coverage
- Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
Vermeire, Proteomics 2024 (secret) - Transition metal homoeostasis is key to metabolism and drug tolerance of Mycobacterium abscessus
Liu, npj antimicrobials and resistance 2024 - “...TCA cycle but also the oxidative phosphorylation (OXPHOS) further downstream. Lastly, the isocitrate lyase aceA (MAB_4095c), which is responsible for converting isocitrate into succinate and malate through the intermediate glyoxylate, was found to be upregulated in both the Co 2+ and Ni 2+ groups (log 2...”
- Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile
Dokic, Cell surface (Amsterdam, Netherlands) 2021 - “...persister cells ( Giffin et al., 2016 , Miranda-CasoLuengo et al., 2016 ). Isocitrate lyase, MAB_4095c, which is upregulated as part of this pathway, is necessary for establishment of chronic infections with M. tuberculosis ( McKinney et al., 2000 ), and inhibition of this enzyme forces...”
- Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages
Cushman, BMC microbiology 2021 - “...GTPase HflX 1.5 8.4E-33 MAB_3042c Probable GTP-binding protein HflX BB28_RS20665 isocitrate lyase (AceA) 1.5 3.9E-12 MAB_4095c Isocitrate lyase (AceA) BB28_RS06230 hypothetical protein 1.5 2.7E-03 MAB_1296 hypothetical protein BB28_RS06840 hypothetical protein 1.5 1.1E-05 MAB_1413 hypothetical protein BB28_RS00915 cation transporter 1.5 4.6E-29 MAB_0183c Putative cation transporter BB28_RS19745 LysE...”
- Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
Rifat, mBio 2021 - “...WhiB family GA MAB_3891c Probable transcriptional regulator, LuxR family NE MAB_4083c Heparin-binding hemagglutinin (adhesin) GA MAB_4095c Isocitrate lyase AceA NE MAB_4149c Hypothetical MCE-family protein LprN NE MAB_4158 Probable acyl-CoA dehydrogenase FadE NE MAB_4159 Probable acyl-CoA dehydrogenase NE MAB_4184c Superoxide dismutase [Cu-Zn] precursor NE MAB_4251 Conserved hypothetical...”
CHLNCDRAFT_29144 hypothetical protein from Chlorella variabilis
E1Z1Z7 isocitrate lyase from Chlorella variabilis
31% identity, 40% coverage
- Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
Rai, Scientific reports 2017 - “...1.0150.16 1.6420.33 34 E1ZKS0 Enolase CHLNCDRAFT_136652 2 1.6880.12 2.2440.81 1.7231.50 35 E1Z1Z7 Putative uncharacterized protein CHLNCDRAFT_29144 1.0220.44 1.4330.03 3.0320.67 36 E1ZKB3 Triosephosphate isomerase (b),(c),(d) CHLNCDRAFT_36334 2 1.2230.69 2.1841.52 2.2320.96 37 E1ZRS1 Reversibly glycosylated protein (b),(d) CHLNCDRAFT_56392 3 1.7360.11 3.0770.15 3.3290.20 Fatty acid metabolism 38 E1Z5W8 Acyl...”
- Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
Rai, Scientific reports 2017 - “...3-epimerase CHLNCDRAFT_56033 1 0.8000.02 1.0150.16 1.6420.33 34 E1ZKS0 Enolase CHLNCDRAFT_136652 2 1.6880.12 2.2440.81 1.7231.50 35 E1Z1Z7 Putative uncharacterized protein CHLNCDRAFT_29144 1.0220.44 1.4330.03 3.0320.67 36 E1ZKB3 Triosephosphate isomerase (b),(c),(d) CHLNCDRAFT_36334 2 1.2230.69 2.1841.52 2.2320.96 37 E1ZRS1 Reversibly glycosylated protein (b),(d) CHLNCDRAFT_56392 3 1.7360.11 3.0770.15 3.3290.20 Fatty acid...”
- “...E1ZT20, A0A087SEW0, A0A087SHU5, A0A087SU66, E1Z2U6, E1Z5A0, E1Z6L2, E1Z7C4, E1Z7S4, E1ZF27, E1ZKS0, E1ZN90, E1ZQQ5, E1ZRS4, F2YGL1, E1Z1Z7, E1ZKB3, E1ZRS1 Several of the enzymes associated with glycolysis, reductive PPP and TCA cycle are up-regulated to fulfil the energy needs of the N-starved FC2 cells. The glycolytic enzymes viz....”
SMLT_RS01090 isocitrate lyase from Stenotrophomonas maltophilia K279a
27% identity, 53% coverage
PFLU3817 isocitrate lyase from Pseudomonas fluorescens SBW25
29% identity, 46% coverage
Pf1N1B4_4042 Isocitrate lyase (EC 4.1.3.1) from Pseudomonas fluorescens FW300-N1B4
29% identity, 46% coverage
- mutant phenotype: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PPUBIRD1_1734 isocitrate lyase from Pseudomonas putida BIRD-1
29% identity, 46% coverage
BWI76_RS01665 Isocitrate lyase (EC 4.1.3.1) from Klebsiella michiganensis M5al
28% identity, 49% coverage
- mutant phenotype: Specifically important for utilizing Potassium acetate. Automated validation from mutant phenotype: the predicted function (4.1.3.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
PP_4116 isocitrate lyase from Pseudomonas putida KT2440
PP4116 isocitrate lyase from Pseudomonas putida KT2440
29% identity, 46% coverage
- Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida
Nayyara, PloS one 2024 - “...PP_2112, PP_2082, PP_1023, PP_0612, PP_3124, PP_0654, PP_2589, PP_0545, PP_2694, PP_1620, PP_0327, PP_1367, PP_1943, PP_1664, PP_5347, PP_4116, PP_1031, PP_4947 5 1 5 ALDD2y, FTHFD, ALDD2x, MDH, MICITDr, GLYOX, ACACT11, MALS, PGL, ACONTa, NACODA PP_2492, PP_0327, PP_1367, PP_1943, PP_2589, PP_0545, PP_2694, PP_0654, PP_2336, PP_4144, PP_0356, PP_1023, PP_2112, PP_2339,...”
- Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Dvořák, Nature communications 2024 - “...Zwf and Gap could explain the apparent upregulation of glyoxylate shunt enzymes isocitrate lyase AceA (PP_4116) and malate synthase GlcB (PP_0356), as discussed in the first part of the Results and discussion section. The modestly increased abundance of Tal transaldolase (PP_2168) (Fig. 6a , Supplementary Data...”
- Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach
Kratzl, Communications biology 2024 - “...Idh (PP_4012 log 2 -FC 1.9) combined with the down-regulation of the transcript encoding AceA (PP_4116 log 2 -FC -2.64). Fig. 6 Changes in the central carbon metabolism of P. putida cscRABY grown in co-culture. a Proteome level: Differentially abundant proteins (DAPs) are highlighted in orange...”
- Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production
Czajka, Metabolic engineering communications 2022 - “...a KT2440 PP_5402::arap-Sc.bpsA,Bc.sfp {p/pTE442 neo BBR1 lacuv5p-dcpf1 14 gene CRISPRi array dcpf1-RBS optimized sequence} KT2440 PP_4116 PP_5402::arap-Sc.bpsA,Bc.sfp {p/pTE442 neo BBR1 lacuv5p-dcpf1 14 gene CRISPRi array dcpf1-RBS optimized sequence} This study JBEI-230,534 This study JBEI-230,533 4185 4186 a KT2440 PP_4185 PP_4186 PP_5402::arap-Sc.bpsA,Bc.sfp {p/pTE442 neo BBR1 lacuv5p-dcpf1 14...”
- “...CRISPRi ( mdh, mqo-II, mqo-II , Fig. 4 ). Thus, two genes, isocitrate lyase, aceA (PP_4116) and the final malate dehydrogenase, mqo-III (PP_0751) were selected as deletion targets. The intracellular and extracellular metabolomic data sets demonstrated a build-up and secretion of succinate from the PSP strain...”
- Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element
Duque, Environmental microbiology reports 2022 - “...fatty acids and the oxidation cycle The second highest fold change (40fold) was isocitrate lyase (PP_4116) (Table S3 ), a protein that is involved in central metabolism through its role in the glyoxylate shunt, where glyoxylate is subsequently converted to malate and, as expected, malate synthase...”
- Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
Thompson, Applied and environmental microbiology 2020 (secret) - Comparative Transcriptome Analysis of Pseudomonas putida KT2440 Revealed Its Response Mechanisms to Elevated Levels of Zinc Stress
Peng, Frontiers in microbiology 2018 - “...0.06 4.09 0.90 3-Oxoacid CoA-transferase subunit A PP_3332 6.83 1.53 6.00 1.36 Cytochrome c-type protein PP_4116 aceA 3.25 0.16 11.00 0.28 Isocitrate lyase PP_4251 ccoO 1 5.47 1.05 cbb3-type cytochrome c oxidase subunit PP_4252 ccoQ1 5.40 1.12 cbb3-type cytochrome c oxidase subunit PP_4253 ccoP 1 1.11...”
- Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions
Crabbé, BMC microbiology 2012 - “...(PP_4034, 0.38-fold) and formation/downstream catabolism of urea (PP_0999, 0.23-fold; PP_1000, 0.28-fold; PP_1001, 0.24-fold) and glyoxylate (PP_4116, 0.27-fold; PP_2112, 0.42-fold and PP_4011, 0.25-fold), (iii) down-regulation of proteins involved in the production of ATP (PP_1478, 0.23-fold; PP_0126, 0.37-fold and PP_1478, 0.23-fold), (iv) differential expression of proteins involved in...”
- “...PP_4034 gi|26990737 0.38* Allantoate amidohydrolase PP_4037 gi|26990739 0.32* Putative oxidoreductase PP_4038 gi|26990740 0.26* Dihydropyrimidine dehydrogenase PP_4116 AceA gi|26990810 0.27* Isocitrate lyase PP_4486 gi|26991172 0.51 Cationic amino acid ABC transporter, periplasmic binding protein PP_4490 PhhA gi|26991176 0.47* Phenylalanine 4-monooxygenase PP_4593 gi|26991277 0.20* Hypothetical protein PP_4593 PP_4666 MmsB...”
- More
- Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...2.46 0.63 1.92 0.08 mdh PP0654 Malate dehydrogenase 0.79 0.52 0.42 0.15 Glyoxylate shunt aceA PP4116 Isocitrate lyase 0.78 0.03 3.10 3.91 glcB PP0356 Malate synthase 0.19 0.32 0.69 0.82 Carbon-limitation at high (CH) and low (CL) dilution rate, nitrogen-limitation at high (NH) and low (NL)...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...fumC PP0944 Fumarate hydratase 0.5 -1.1 mdh PP0654 Malate dehydrogenase -0.4 -1.3 Glyoxylate shunt aceA PP4116 Isocitrate lyase 2.9 1.3 glcB PP0356 Malate synthase 0.8 0.8 Bold numbers represent a differentiated gene expression pattern. Next, the pgl overexpressing strains without increased PHA production were analyzed for...”
- “...fumC PP0944 Fumarate hydratase 1.1 -0.4 mdh PP0654 Malate dehydrogenase 0.8 -0.8 Glyoxylate shunt aceA PP4116 Isocitrate lyase 1.2 -1.1 glcB PP0356 Malate synthase -0.4 -0.1 p -value<0.05. Bold numbers represent a differentiated gene expression pattern. The role of NADPH and NADH in P. putida PHA...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...GlcB -5.9 19 -1.9 n.s. thioredoxin reductase PP0786 TrxB -5.6 11 1.3 n.s. Isocitrate lyase PP4116 AceA -4.2 19 1.3 n.s. Isocitrate dehydrogenase PP4011 ICD -2.1 14 1.1 n.s. Fatty acid metabolism 3-hydroxyacyl-CoA dehydrogenase PP2047 only in N 18 20.9 0 Acetyl-CoA acetyltransferase PP2051 AtoB only...”
- Analysis of Pseudomonas putida KT2440 gene expression in the maize rhizosphere: in vivo [corrected] expression technology capture and identification of root-activated promoters
Ramos-González, Journal of bacteriology 2005 - “...(rap2-2) aceA (rap2-14) gnd (rap2-15) pgm (rap2-77) PP0339 PP4116 PP4043 PP5056 rap1-4 rap1-12 rap2-44 colS (rap2-63) rap1-9 PP4966 PP4424 PP2070 PP0902 PP0721...”
VDA_002723 isocitrate lyase from Photobacterium damselae subsp. damselae CIP 102761
29% identity, 47% coverage
bcpB / BAA00905.1 phosphoenolpyruvate phosphomutase from Streptomyces hygroscopicus (see paper)
P29247 Phosphoenolpyruvate phosphomutase from Streptomyces hygroscopicus
30% identity, 90% coverage
BV82_1237 isocitrate lyase from Pseudomonas donghuensis
29% identity, 46% coverage
BCAL2118 isocitrate lyase from Burkholderia cenocepacia J2315
25% identity, 57% coverage
- The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
Kiekens, mSphere 2018 - “...oxidase subunit I BCAM0166 20.6 58.3 NADH dehydrogenase BCAL3094 4.4 10.4 Oxygen-independent coproporphyrinogen III oxidase BCAL2118 2.3 47.3 Isocitrate lyase BCAM1588 11.5 Isocitrate lyase Motility BCAL3506 5.1 Flagellar motor switch protein FliM BCAL0140 4.6 Flagellar biosynthetic protein FlhB BCAL0524 3.3 Flagellar motor switch protein FliG BCAL0561...”
- “...low-oxygen-responsive regulator ( BCAM0049 ), an alternative NADH dehydrogenase ( BCAM0166 ), isocitrate lyase ( BCAL2118 ), low-iron-responsive regulators FecI and FecR ( BCAL1369 and BCAL1370 ), and certain chaperones and heat shock proteins. Computationally predicted targets of ncS35. To predict putative direct targets of ncS35,...”
- Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms
Slachmuylders, PloS one 2018 - “...vs. ctrl TOB+BH vs. TOB Glyoxylate shunt BCAL2122 ( aceB ) Malate synthase - -1.4 BCAL2118 ( aceA) Isocitrate lyase AceA - -1.5 BCAM1588 Isocitrate lyase - -1.9 TCA cycle BCAM0972 ( gltA ) Type II citrate synthase - 1.8 BCAM0961 ( acnA ) Aconitate hydratase...”
- The IclR-family regulator BapR controls biofilm formation in B. cenocepacia H111
Aguilar, PloS one 2014 - “...Interestingly, the expression of a gene coding for an isocitrate lyase ( aceA , CCE52795, BCAL2118) was down-regulated in the bapR mutant background. We validated this result by quantitative PCR, and we could measure a fold-change of 3.10.3 in the bapR mutant background compared to WT...”
- Response of Burkholderia cenocepacia H111 to micro-oxia
Pessi, PloS one 2013 - “...cepacian (BCAM1004-1005 and BCAM1010), several proteases ( Table 2 ) and an isocitrate lyase (ICL, BCAL2118). Several genes/proteins involved in reactive oxygen species (ROS) scavenging such as catalases, the alkyl hydroperoxide reductase AhpC and several thioredoxins showed increased expression in low-oxygen conditions. Among the highly up-regulated...”
- “...d ubiquinol oxidase subunit I TM 3.1 6.7 CCE50746 BCAL1831 Aldehyde dehydrogenase 3.1 1.3 CCE52795 BCAL2118 Isocitrate lyase 7.5 24.9 CCE49032 BCAL2685 Sulfite reductase [NADPH] hemoprotein -component 16.9 1.5 CCE51244 BCAL3285 Flavohemoprotein nd 51.7 CCE46730 BCAM0175 Malate:quinone oxidoreductase S 8.4 3.6 CCE47517 BCAM1250 Acetyl-CoA hydrolase 9.0...”
- Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species
Van, PloS one 2013 - “...Primer sequences. Gene Annotation FW primer RV primer Glyoxylate shunt BCAL2122 Malate synthase GGCCGACCGCTCGAAGATCA CGCCTTGTCGTTCGCTTCCG BCAL2118 Isocitrate lyase GCACCGTACGCCGACCTGAT GCTTGCCCGGGAACTGCTTG BCAM1588 Isocitrate lyase TCCTTGCCCGCTGCCTTCAT ATCCCGAACGCGAAGCTGGT Tricarboxylic acid cycle BCAM0961 Aconitate hydratase CTCGGCCAGCCGGTGTACTT CAGCGACTTCGTGCCTTCGC BCAM2701 Aconitate hydratase CGGTGATCCAGGCGCAGGAT CAGGCGCATCCACGATGCAC BCAM1833 Aconitate hydratase/methylisocitrate dehydratase GCATGCTGACGGTCGCCAAG GGTCGGGCAGGCCTTCGATT BCAL2735 Isocitrate...”
- “...Construction of ICL Mutant The genome of B. cenocepacia J2315 contains two ICL encoding genes, BCAL2118 and BCAM1588. To confirm their importance, we constructed a double ICL mutant. All B. cenocepacia mutant strains were constructed following the protocol described by Hamad et al., which allows for...”
- The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia
Sass, The ISME journal 2013 - “...genes involved in fatty acid metabolism (for example, BCAL00460047), the glyoxylate pathway (isocitrate lyases (ICLs); BCAL2118 and BCAM1588) and genes for storage polymer turnover (BCAL08310833). The quorum sensing-regulated extracellular protease ZmpA (BCAS0409) and nematocidal protein AidA (BCAS0293) were highly upregulated under growth arrest. Genes involved in...”
- A LuxR-type repressor of Burkholderia cenocepacia inhibits transcription via antiactivation and is inactivated by its cognate acylhomoserine lactone
Ryan, Molecular microbiology 2013 - “...bcal0831 1.66 (0.20) 2.88 (0.81) 2.27 n.d. bcal0833 0.87 (0.15) 1.29 (0.28) 1.08 n.d. phbB bcal2118 1.55 (0.24) 3.56 (0.93) 2.55 n.d. bcal3178 1.49 (0.41) 3.09 (0.54) 2.29 n.d. bcam0030 2.63 (1.41) 5.36 (2.27) 3.99 n.d. bcam0031 2.57 (1.21) 4.48 (3.18) 3.52 n.d. bcam0184 1.34 (0.28)...”
JHW33_RS14900 isocitrate lyase from Rahnella aceris
28% identity, 46% coverage
MMAR_0792 isocitrate lyase Icl from Mycobacterium marinum M
27% identity, 53% coverage
- Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals the genetic requirement for virulence and survival in amoebae and microglial cells
Lefrançois, mSystems 2024 - “...set of 42 essential genes specific to 2 48 hpi was identified. Among these, icl1 (MMAR_0792), encoding the enzyme isocitrate lyase involved in the TCA cycle, was notable. Indeed, disruption of this gene has been linked to impaired chronic-phase persistence of M. tuberculosis in mice (...”
- Temporal genome-wide fitness analysis ofMycobacterium marinumduring infection reveals genetic requirement for virulence and survival in amoebae and microglial cells
Lefrançois, 2023 - A uniform cloning platform for mycobacterial genetics and protein production
Arnold, Scientific reports 2018 - “...vector series for other mycobacterial species, the three genes sapM ( mmar_1216 ), icL ( mmar_0792 ) and phoP ( mmar_4942 ) were deleted in M. marinum . To our knowledge, so far only two publications describe the successful generation of defined gene deletions mutants in...”
- Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress
Abshire, NPJ microgravity 2016 - “...an enzyme that connects the TCA and glyoxylate cycle and transcript levels from icl ( MMAR_0792 ) decreased by ~10-fold in LSMMG bacteria after the long exposure time ( Supplementary Table 5 ). Transcription of genes involved in lipid degradation and catabolism of fatty acids were...”
STM14_5030 isocitrate lyase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM4184 isocitrate lyase from Salmonella typhimurium LT2
28% identity, 49% coverage
LT988_08090 isocitrate lyase from Thiocapsa bogorovii
29% identity, 47% coverage
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...(EC: 4.1.3.1) and malatesynthase (EC: 2.3.3.9)) are present in the genome of T. bogorovii BBS (LT988_08090 and LT988_06350) as well as in the genome of Alc. vinosum DSM 180 T (isocitrate lyase, Alvin_1848 and malate synthase G, Alvin_2606). The lack of beneficial effect after adding certain...”
- “...** - 16 K15234 citryl-CoA lyase (EC: 4.1.3.34) - - 17 K01637 isocitrate lyase [EC:4.1.3.1] LT988_08090 aceA ; isocitrate lyase 18 K01638 malate synthase [EC:2.3.3.9] LT988_06350 malate synthase G 19 K01895 acetyl-CoA synthetase [EC:6.2.1.1] LT988_16650 acs ; acetate--CoA ligase ** indicates that the sequence of a...”
SEN3966 isocitrate lyase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SG4044 isocitrate lyase from Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
28% identity, 49% coverage
- Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits
D'Alessandro, Scientific reports 2020 - “...E2 share the same variant for aas (2-acylglycerophosphoethanolamine acyltransferase/acyl-ACP synthetase, SEN2853) and aceA (isocitrate lyase, SEN3966) genes. In E1, most of the strains have an aas gene identical to the reference, and a few strains present either a non synonymous substitution (5 strains) or a synonymous...”
- Molecular characterization, occurrence, and immunogenicity in infected sheep and cattle of two minor outer membrane proteins of Brucella abortus
Tibor, Infection and immunity 1996 - “...purification of both rOMPs in E. coli. E. coli SG4044 (20) containing plasmid pAc1 was transformed with either plasmid pBru10 or plasmid pBru19.2. A 15-liter...”
- ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification
Grodberg, Journal of bacteriology 1988 - “...SK596 W3110 HMS174 ED8739 LE392 DH1 K803 SG4038 SG4044 KK2186 UT2300 UT4400 UT5600 Source or reference 6 ompB+ operon MC4100 envZII MC4100 envZ473 MC4100...”
- “...HMS174; (3) ED8739; (4) LE392; (5) DH1; (6) SG4038; (7) SG4044; (8) B707; (9) B834; (10) BL21; (11) HB101; (12) C1757; (13) KK2186. Equal Alo'm m units were...”
- lon transcriptional regulation of genes necessary for capsular polysaccharide synthesis in Escherichia coli K-12
Trisler, Journal of bacteriology 1984 - “...SG20001 + P1 (SA1775) SG20001 + P1 (SG1041) SG1038 + P1 (SG4044) SG20014 + P1 (SG1041) SG1038 + P1 (SA1775) SG20019 + P1 (SA1775) SG1041 + X561 SG1041 + X561...”
ABD05_RS00140 isocitrate lyase from Burkholderia pyrrocinia
25% identity, 56% coverage
MUL_4536 isocitrate lyase Icl from Mycobacterium ulcerans Agy99
27% identity, 53% coverage
BPSL2188 isocitrate lyase from Burkholderia pseudomallei K96243
25% identity, 56% coverage
- Transcriptomics Analysis Uncovers Transient Ceftazidime Tolerance in Burkholderia Biofilms
Chattagul, ACS infectious diseases 2021 - “...peptidoglycan synthesis [BPSL2408, BPSL3312, BPSS0424, BPSS0451, BPSS1684, BPSS1826, BPSS1828, and BPSS1840]), TCA cycle depression (e.g., BPSL2188, and BPSL2192), ATP synthase reduction (e.g., ATP consuming pathway [BPSL2885, BPSL3122, BPSS1144, and BPSS1571], and sulfur metabolism [BPSL1836, BPSL1837, and BPSS1241]. A group of genes up-regulated and down-regulated in planktonic-shedding...”
- GvmR - A Novel LysR-Type Transcriptional Regulator Involved in Virulence and Primary and Secondary Metabolism of Burkholderia pseudomallei
Duong, Frontiers in microbiology 2018 - “...( prpB ; BPSS0206) and simultaneous downregulation of the isocitrate lyase gene ( aceA ; BPSL2188) was observed in gvmR , which suggests a disturbance of the anaplerotic function of the TCA cycle ( Munoz-Elias and McKinney, 2005 , 2006 ). qRT-PCR confirmed the differential regulation...”
- Host-Adaptation of Burkholderia pseudomallei Alters Metabolism and Virulence: a Global Proteome Analysis
Mariappan, Scientific reports 2017 - “...dehydrogenase (alededh) 11* 6.15E-04 BPSL1550 3.2 30 50453/50353 5.67/5.67 cytoplamic Isocitrate lyase (aceA) 12 0.042 BPSL2188 2.0 12 52238/47644 7.68/5.73 cytoplamic Pyrophosphatase (ppa) 52* 0.026 BPSL1021 2.5 23 19149/19030 5.37/5.37 cytoplamic Isocitrate dehydrogenase (idhI) 77 0.043 BPSL0896 2.0 24 46116/46015 5.76/5.63 unknown F0F1 ATP synthase subunit...”
- Contribution of gene loss to the pathogenic evolution of Burkholderia pseudomallei and Burkholderia mallei
Moore, Infection and immunity 2004 - “...1.82906867 1.709388586 1.704217668 1.604675546 1.492801878 BPSL2188 BPSS1799 BPSL0638 BPSS1802 BPSL0688 BPSS0772 BPSL0687 BPSS1801 BPSS1800 BPSS1575 BPSS1485b...”
BTH_I1998 isocitrate lyase from Burkholderia thailandensis E264
Q2SX27 Isocitrate lyase from Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)
25% identity, 56% coverage
VSAL_I2438 isocitrate lyase from Aliivibrio salmonicida LFI1238
VSAL_I2438 isocitrate lyase from Vibrio salmonicida LFI1238
28% identity, 46% coverage
YP_001141352 isocitrate lyase from Aeromonas salmonicida subsp. salmonicida A449
29% identity, 46% coverage
- Directed culturing of microorganisms using metatranscriptomics
Bomar, mBio 2011 - “...1.38 10 89 Translation 2,275 A.veronii Malate synthase YP_001141353 0 Glyoxylate cycle 150 Isocitrate lyase YP_001141352 0 Glyoxylate cycle 876 Phosphofructokinase YP_856906 1.37 10 180 Glycolysis 138 Fructose-1,6 bisphosphatase YP_001141703 0 Gluconeogenesis 350 2-Oxoglutarate dehydrogenase E2 YP_856459 0 TCA cycle 282 CcoN YP_856818 0 Aerobic respiration...”
MAV_4682 isocitrate lyase from Mycobacterium avium 104
29% identity, 53% coverage
- Mycobacterium avium Subsp. hominissuis Interactions with Macrophage Killing Mechanisms
Abukhalid, Pathogens (Basel, Switzerland) 2021 - “...in the treatment of tuberculosis [ 57 ]. Another surface protein is the isocitrate lyase, MAV_4682, which under nutrient limited conditions utilizes fatty acid and acetate as a basic carbon source ( Table 1 ) [ 57 ]. In addition to the OxyR regulon, M. avium...”
- “...Catalyzes peroxide reduction Resistance to oxidative stress, such as reactive oxygen intermediates. [ 57 ] MAV_4682 isocitrate lyase Metabolism, glyoxylate shut Resistance to oxidative stress. [ 57 ] MAV_2043 Cu-Zn-SOD Catalysis, superoxide dismutase Resistance to oxidative stress phagosome acidification. [ 58 ] MAV_4264 Hypothetical protein Unknown...”
- Genetic Involvement of Mycobacterium avium Complex in the Regulation and Manipulation of Innate Immune Functions of Host Cells
Shin, International journal of molecular sciences 2021 - “...(ahpC) - Alkyl hydroperoxide reductase catalysis Protection from oxidative stress MAH 109 [ 84 ] MAV_4682 (aceA) - isocitrate lyase metabolism A key enzyme in glyoxylate shunt Use of fatty acids and acetates as basic carbon resources under carbon restricted conditions MAH 109 [ 84 ]...”
- “...McNamara et al. (2012) reported that alkyl hydroperoxide reductase (ahpC, MAV_2839) and isocitrate lyase (aceA, MAV_4682) were uniquely expressed after MAH were exposed to macrophages [ 84 ]. In particular, ahpC encodes a protein that catalyzes peroxide reduction, and exhibited resistance to oxidative stress, suggesting that...”
- Surface proteome of "Mycobacterium avium subsp. hominissuis" during the early stages of macrophage infection
McNamara, Infection and immunity 2012 - “...(ahpC, MAV_2839), isocitrate lyase (aceA, MAV_4682), a universal stress family protein (MAV_2506), and 5-methyl-tetrahydropteroyltriglutamate-homocysteine...”
- “...stress protein family protein 5-Methyl-tetrahydropteroyltriglutamate- homocysteine methyltransferase MAV_2839 MAV_4682 MAV_2506 MAV_1262 0 0 0 0 0 0 0 0 0 0 0 0...”
WP_050342316 phosphoenolpyruvate mutase from Selenomonas sp. oral taxon 478
29% identity, 52% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...Clostridium butyricum strain 41, NZ_CP039705, WP_002579294; 400, Selenomonas sp. oral taxon 478 strain F0592, NZ_CP012071, WP_050342316. The large group of AEPT-encoding gene neighbourhoods is diverse Apart from the Group 1 Burkholderiales_CDP-OH phosphonolipids, the AEPT-containing gene neighbourhoods are diverse ( Fig. 5 ). These neighbourhoods include those...”
CKS_4658 isocitrate lyase from Pantoea stewartii subsp. stewartii DC283
28% identity, 46% coverage
Q8T8D9 phosphoenolpyruvate mutase (EC 5.4.2.9) from Trypanosoma cruzi (see paper)
29% identity, 72% coverage
MMAR_0514 PEP phosphonomutase from Mycobacterium marinum M
29% identity, 64% coverage
MSMEG_0911 isocitrate lyase from Mycobacterium smegmatis str. MC2 155
MSMEG_0911 isocitrate lyase from Mycolicibacterium smegmatis MC2 155
28% identity, 53% coverage
- The Benefits of Toxicity: M. smegmatis VapBC TA Module Is Induced by Tetracycline Exposure and Promotes Survival
Zamakhaev, Microorganisms 2023 - “...of citrate synthase MSMEG_5672, which is involved in glyoxylate shunt, was increased, whereas isocitrate lyase MSMEG_0911 was replaced by isoenzyme MSMEG_3706. A similar phenomenon was observed for gamma-aminobutyric acid shunt, i.e., succinate-semialdehyde dehydrogenase MSMEG_6452 was substituted by isoenzyme MSMEG_0889. The data on the abundance of proteins...”
- Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis
Dow, Frontiers in microbiology 2022 - “...altRP/c (MSMEG_0117) ( Supplementary Table S15 ). The altRP mutant increased expression of isocitrate lyase (MSMEG_0911), also DE at the protein level, and glucose-6-phosphate 1-dehydrogenase (MSMEG_0314) ( Supplementary Table S15 ). Downregulated expression of coenzyme B12-dependent glycerol dehydrogenase was observed at the transcript (MSMEG_1546 and MSMEG_1547)...”
- “...5 ). Remarkably, the altRP mutant utilized the glyoxylate shunt via induction of isocitrate lyase (MSMEG_0911) while concurrently upregulating succinate dehydrogenase, an enzyme required in both the TCA cycle and the electron transport chain. During iron limitation, due to decreased activity of NADH dehydrogenase (containing seven...”
- Mycobacterium smegmatis GlnR Regulates the Glyoxylate Cycle and the Methylcitrate Cycle on Fatty Acid Metabolism by Repressing icl Transcription
Qi, Frontiers in microbiology 2021 - “...in the glyoxylate cycle and the methylcitrate cycle, isocitrate lyase (ICL, encoded by icl or MSMEG_0911 ) is indispensable for the growth of Msm and Mtb on short-chain fatty acids. However, regulation of icl in mycobacteria in response to nutrient availability remains largely unknown. Here, we...”
- “...icl . Here, we report the GlnR-mediated regulation of icl (also designed as aceA or MSMEG_0911 ) during Msm growth on fatty acids. We demonstrate that GlnR represses the transcription of icl and decreases the abundance of ICL products in the glyoxylate cycle and the methylcitrate...”
- Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis
Ko, Journal of bacteriology 2021 - “...Mycobacterium smegmatis has two isocitrate lyase (ICL) isozymes (MSMEG_0911 and MSMEG_3706). We demonstrated that ICL1 (MSMEG_0911) is the predominantly expressed ICL in M. smegmatis and plays a major role in growth on acetate or fatty acid as the sole...”
- Dynamic Characterization of Protein and Posttranslational Modification Levels in Mycobacterial Cholesterol Catabolism
Xu, mSystems 2020 - “...TCA cycle, glyoxylate shunt, methylcitrate cycle, and methylmalonyl pathway, including aconitate hydratase (MSMEG_3143), isocitrate lyase (MSMEG_0911), methylmalonyl-CoA epimerase (MSMEG_4921), methylmalonyl-CoA mutase (MSMEG_3158), methylisocitrate lyase (MSMEG_6646), and 2-methylcitrate dehydratase (MSMEG_6645), showed higher protein expression levels in the presence of cholesterol ( Fig.2B ). This result strongly suggested...”
- Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Hillion, Scientific reports 2017 - “...294 (+484)YR(L) 10,73 (R)ATLESIC 389 (+484)YQSR(D) 5,67 MSMEG_3086 TpiA Triosephosphate isomerase (R)VAGAADAQEVC 192 (+484)K(A) 2,04 MSMEG_0911 AceA Isocitrate lyase (K)NGLEPC 268 (+484)IAR(A) 11,36 MSMEG_5676 CitA Citrate synthase (R)TIDEC 143 (+484)PTVTAR(F) 14,23 MSMEG_5049 Kgd 2-oxoglutarate metabolism enzyme (R)SSEYC 695 (+484)TDVAK(M) 4,60 Metabolism of fatty acids and phospholipids...”
- “...13,7 23,9 MSMEG_6759 glpK3 Glycerol kinase 294 (MSH) B 10,7 8,9 16,8 9,9 19,9 29,8 MSMEG_0911 aceA Isocitrate lyase 191 B 11,3 8,5 20,8 11,0 22,3 33,7 268 (MSH) B 11,4 12,7 20,3 12,8 24,8 37,6 MSMEG_1670 sdhA2 Succinate DH 385 B 15,5 31,0 35,1 MSMEG_3640...”
- Dynamic exometabolome analysis reveals active metabolic pathways in non-replicating mycobacteria
Zimmermann, Environmental microbiology 2015 - “...isocitrate through the glyoxylate shunt enzyme isocitrate lyase, encoded by two isoenzymes ( icl1 , MSMEG_0911 and icl2 , MSMEG_3706). This finding is consistent with increased isocitrate lyase expression and enzymatic activity during the transition to hypoxia ( Wayne and Lin, 1982 ; Shi et al.,...”
- Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis
Chopra, Molecular & cellular proteomics : MCP 2014 - “...I (AcnA, MSMEG_3143) and isocitrate lyase 1 (Icl1, MSMEG_0911). Analysis of two more spots from the propionate gel also revealed higher abundance of...”
- “...S3). Among these proteins, isocitrate lyase 1 (Icl1, MSMEG_0911) was identified as the most highly induced protein in acetate-grown cells. Isocitrate lyase is a...”
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Bphy_1368 isocitrate lyase from Paraburkholderia phymatum STM815
Bphy_1368 isocitrate lyase from Burkholderia phymatum STM815
26% identity, 53% coverage
- Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris
Lardi, International journal of molecular sciences 2018 - “...more active in nodules induced by this Fix mutant. Indeed, the isocitrate lyase encoding gene (Bphy_1368), which catalyzes the cleavage of isocitrate to succinate and glyoxylate, showed increased expression in nodules infected by the Fix mutant. The down-regulation of the d -alanine: d -alanine ligase encoding...”
- Transcriptome Analysis of Paraburkholderia phymatum under Nitrogen Starvation and during Symbiosis with Phaseolus Vulgaris
Lardi, Genes 2017 - “...hydrogenase ( Figure 3 A,B). We also found a gene coding for an isocitrate lyase (Bphy_1368) and a potential cytochrome o ubiquinol oxidase cluster (Bphy_3646-49), which may play a role for respiration inside the nodule ( Figure 3 C). In the over-represented functional category P (inorganic...”
- “...situation in -rhizobia [ 84 , 85 ], a gene coding for an isocitrate lyase (Bphy_1368) was found inside the top 500 regulated genes in P. phymatum bacteroids, suggesting that the glyoxylate shunt pathway is active during -rhizobial symbiosis. In previous studies on Bradyrhizobium sp. ORS278,...”
icl / CAA82555.1 isocitrate lyase from Rhodococcus fascians (see paper)
27% identity, 57% coverage
MAP_3961 isocitrate lyase from Mycobacterium avium subsp. paratuberculosis K-10
MAP3961 AceA from Mycobacterium avium subsp. paratuberculosis str. k10
28% identity, 52% coverage
FQ188_12695 isocitrate lyase from Rhodococcus sp. ANT_H53B
27% identity, 57% coverage
7cmyC / Q81GQ9 Isocitrate lyase from bacillus cereus atcc 14579 in complex with magnessium ion, glyoxylate, and succinate
26% identity, 57% coverage
- Ligand: magnesium ion (7cmyC)
A0A3S5YB92 isocitrate lyase (EC 4.1.3.1) from Rhodococcus hoagii (see paper)
27% identity, 57% coverage
6c4aA / P9WKK7 Crystal structure of 3-nitropropionate modified isocitrate lyase from mycobacterium tuberculosis with pyruvate (see paper)
28% identity, 53% coverage
- Ligands: pyruvic acid; magnesium ion; 3-nitropropanoic acid (6c4aA)
icl / P9WKK7 isocitrate lyase subunit (EC 4.1.3.1) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
ACEA1_MYCTE / H8EVV4 Isocitrate lyase 1; ICL1; Isocitrase; Isocitratase; Methylisocitrate lyase; MICA; EC 4.1.3.1; EC 4.1.3.30 from Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) (see paper)
ACEA1_MYCBO / P0A5H4 Isocitrate lyase 1; ICL1; Isocitrase; Isocitratase; EC 4.1.3.1 from Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (see paper)
ACEA1_MYCTO / P9WKK6 Isocitrate lyase 1; ICL1; Isocitrase; Isocitratase; Methylisocitrate lyase; MICA; EC 4.1.3.1; EC 4.1.3.30 from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (see 3 papers)
ACEA_MYCTU / P9WKK7 Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 7 papers)
P9WKK7 isocitrate lyase (EC 4.1.3.1) from Mycobacterium tuberculosis (see 4 papers)
YP_177728 isocitrate lyase from Mycobacterium tuberculosis H37Rv
MT0483 isocitrate lyase from Mycobacterium tuberculosis CDC1551
Rv0467 isocitrate lyase from Mycobacterium tuberculosis H37Rv
MRA_0473 isocitrate lyase Icl from Mycobacterium tuberculosis H37Ra
Mb0476 ISOCITRATE LYASE ICL (ISOCITRASE) (ISOCITRATASE) from Mycobacterium bovis AF2122/97
RVBD_0467 isocitrate lyase from Mycobacterium tuberculosis H37Rv
28% identity, 53% coverage
- function: Involved in the persistence and virulence of M.tuberculosis. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates. It also catalyzes the formation of pyruvate and succinate from 2-methylisocitrate, a key step in the methylcitrate cycle (propionate degradation route).
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer.
disruption phenotype: Deletion of icl1 in cells growing on 0.1% propionate shows 10 and 8-fold decrease of isocitrate and methylisocitrate lyase activity, respectively. - function: Involved in the persistence and virulence of Mycobacterium. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+)
subunit: Homotetramer.
disruption phenotype: cells lacking this gene show a slight residual isocitrate lyase activity. - function: Involved in the persistence and virulence of M.tuberculosis. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates. It also catalyzes the formation of pyruvate and succinate from 2-methylisocitrate, a key step in the methylcitrate cycle (propionate degradation route).
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+) (Can also use Mn(2+) ion.)
subunit: Homotetramer.
disruption phenotype: Deletion of icl1 has little effect on replication in media containing glycerol, glucose, short-chain fatty acids or long- chain fatty acids. Deletion of icl1 results in a modest reduction of the bacterial load in the lungs during the chronic phase but not the acute phase of infection, and reduces tissue pathology. Deletion of both icl1 and icl2 eliminates growth on fatty acids but has little effect on use of carbohydrates. Cells lacking both genes are incapable of growth in mice and are rapidly eliminated from the lungs and spleen. - function: Involved in the persistence and virulence of M.tuberculosis. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates (PubMed:10932251, PubMed:10963599, PubMed:18275086, PubMed:24354272). It could also catalyze the formation of pyruvate and succinate from 2-methylisocitrate, a key step in the methylcitrate cycle (propionate degradation route) (By similarity).
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+) (Can also use Mn(2+) ion.)
subunit: Homotetramer.
disruption phenotype: Cells lacking this gene show an attenuated bacterial persistence and virulence in immune-competent mice without affecting bacterial growth during the acute phase of infection. - Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil
Soares, Microbiology spectrum 2023 - “...cereus ATCC 14579 52.76 NP_832067 dhbE 2,3-dihydroxybenzoate adenylase DhbE 256 Bacillus cereus ATCC 14579 63.99 YP_177728 icl Isocitrate lyase Icl 425 Mycobacterium tuberculosis H37Rv 54.08 YP_169203.1 tufA Elongation factor Tu 396 Francisella tularensis subsp. tularensis SCHU S4 78.28 NP_539767 kdsA 2-dehydro-3-deoxyphosphooctonate aldolase 300 Brucella melitensis bv....”
- Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil
Damas, Frontiers in medicine 2022 - “...Haemophilus influenzae 50.30 NP_933683 ilp A MetQ/NlpA family lipoprotein adhesin IlpA 268 Vibrio vulnificus 55.56 YP_177728 icl 1 Isocitrate lyase 426 Mycobacterium tuberculosis 61.15 NP_458740 tvi B Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB 431 Salmonella enterica 53.72 NP_462662 mgt B Magnesium-translocating P-type ATPase 890 Salmonella...”
- Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase.
Ibeji, Scientific reports 2020 - GeneRIF: Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase.
- Activity loss by H46A mutation in Mycobacterium tuberculosis isocitrate lyase is due to decrease in structural plasticity and collective motions of the active site.
Shukla, Tuberculosis (Edinburgh, Scotland) 2018 (PubMed)- GeneRIF: H46A mutation in Mycobacterium tuberculosis isocitrate lyase results in activity loss due to decrease in structural plasticity and collective motions of the active site.
- Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis.
Pham, Proceedings of the National Academy of Sciences of the United States of America 2017 - GeneRIF: 2-vinyl-d-isocitrate (2-VIC) is a mechanism-based inactivator of Mycobacterium tuberculosis ICL1 and ICL2
- Identification of a novel inhibitor of isocitrate lyase as a potent antitubercular agent against both active and non-replicating Mycobacterium tuberculosis.
Liu, Tuberculosis (Edinburgh, Scotland) 2016 (PubMed)- GeneRIF: Isocitrate lyase inhibitors were active in both log-phase M. tuberculosis in vitro and dormant M. tuberculosis in macrophages.
- Isocitrate lyase mediates broad antibiotic tolerance in Mycobacterium tuberculosis.
Nandakumar, Nature communications 2014 (PubMed)- GeneRIF: Icl1 and icl2 mediates broad antibiotic tolerance in Mycobacterium tuberculosis.
- ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.
Beste, PLoS pathogens 2011 - GeneRIF: (1)(3)C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.
- More
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis
Ko, Journal of bacteriology 2021 (secret) - Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence
Muñoz-Elías, Nature medicine 2005 - “...translated nucleotide sequences of icl1 (Entrez Gene locus tag MT0483) and icl2 (Entrez Gene locus tag MT1966) VOLUME 11 | NUMBER 6 | JUNE 2005 NATURE MEDICINE...”
- Tuberculosis vaccines and therapeutic drug: challenges and future directions
An, Molecular biomedicine 2025 - “...(PPE55) 3157 NA NA High Very High NA Unknown No PPE8, PPE56, cpnT, csm5, Rv2082 Rv0467 (icl) 428 C, M NA Moderate High + Key enzyme in glyoxylate bypass, contributes to MTB persistence and virulence No glcB, ackA, fadB2, aceAb, aceAa Rv1130 (prpD) 526 C, CW...”
- Gene Regulatory Mechanism of Mycobacterium Tuberculosis during Dormancy
Liu, Current issues in molecular biology 2024 - “...telacebec, OPC-167832, SQ 109 [ 186 ], tafenoquine [ 187 ], and so on. Notably, Rv0467 , encoding isocitrate lyase (ICL), is a drug target for the treatment of latent TB, but there is no ICL inhibitor that has reached clinical trials [ 188 ]. Moreover,...”
- “...[ 21 ], reduces growth and sensitivity to antituberculosis drugs [ 38 , 39 ]. Rv0467 (icl) Encodes isocitrate lyase and facilitates the persistence of Mtb [ 22 ], involved in antibiotic tolerance [ 40 ], mycobacterial glyoxylate and methylisocitrate cycles [ 41 ]. Rv1837c (GlcB)...”
- Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis
Khan, Scientific reports 2024 - “...map00410 beta-Alanine metabolism map00770Pantothenate and CoA biosynthesis map01100Metabolic pathways map01110Biosynthesis of secondary metabolites Isocitrate lyase Rv0467 K01637 map00630Glyoxylate and dicarboxylate metabolism map01100Metabolic pathways map01110 Biosynthesis of secondary metabolites map01120Microbial metabolism in diverse environments map01200 Carbon metabolism In the final stage of our analysis, the top 2...”
- “...quality scores. Proteins Rv number ZINC ID Binding affinity (kcal/mol) Fit quality score Isocitrate lyase Rv0467 ZINC3978005 (Dihydroergotamine) 10.3 1.082 ZINC164528615 (Glecaprevir) 10 1.334 ZINC52955754 (Ergotamine) 9.9 1.04 ZINC11679756 (Eltrombopag) 9.9 0.98 ZINC6716957 (Nilotinib) 9.9 1.005 ZINC150588351 (Elbasvir) 9.8 1.553 Pantothenate synthetase Rv3602c ZINC3797541 (Zytiga) 10.4...”
- Mycobacterium tuberculosis Adaptation in Response to Isoniazid Treatment in a Multi-Stress System That Mimics the Host Environment
Yimcharoen, Antibiotics (Basel, Switzerland) 2023 - “...Mtb after exposure to INH [ 24 ]. Isocitrate lyase 1 (Icl1) encoded by icl1 (Rv0467) is an enzyme in the glyoxylate shunt, and is associated with fatty acid metabolism, the critical pathway for Mtb during its infection in the host [ 25 , 26 ]....”
- “...[ 21 ] tgs1 (Rv3130c) F: TAGCTGGGCTCTCCGATGAA R: ATTGACACGGAATCCACCCC 107 bp [ 21 ] icl1 (Rv0467) F: GTTGGCCTCTGAGAAGAAGTG R: CAGCGTGATGAACTGGAACT 493 bp This work * sigE (Rv1221) F: GCAGTGCAAATTCGGAGGAT R: ATTGGTCAGACGGCTCCA 114 bp [ 21 ] pimB (Rv2188c) F: GCGGTAGGTATTCCAACGAAG R: TATGCACCGCAGTGGAAAG 394 bp [ 21...”
- Identification of New Mycobacterium bovis antigens and development of a multiplexed serological bead-immunoassay for the diagnosis of bovine tuberculosis in cattle
Moens, PloS one 2023 - “...were predicted to be extracellular by the Gpos-mPLoc tool alone. Proteins Rv2626c, Rv3841, Rv3509c, and Rv0467, although not identified as secreted by the bioinformatics tools used, were recorded as potentially extracellular or secreted in the UniProt database. Thus, a total of 82 potential secreted proteins was...”
- Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis
Singh, 2023 - From immunology to artificial intelligence: revolutionizing latent tuberculosis infection diagnosis with machine learning
Li, Military Medical Research 2023 - “...phospholipase C 1 (plcA, Rv2351c), plcB (Rv2350c), plcC (Rv2349c), plcD (Rv1755c), isocitrate lyases (ICLs) like Rv0467, Rv1915, and Rv1916, and malate synthases (MS) like Rv1837c, to overcome this toxicity and obtain the necessary energy during the latency and granuloma formation periods [ 168 170 ]. This...”
- A Novel Tool to Identify Bactericidal Compounds against Vulnerable Targets in Drug-Tolerant M. tuberculosis found in Caseum
Sarathy, mBio 2023 - “...Rv2245 kasA 1.16 1.04 Lipid metabolism Rv1169c lipX 1.00 1.03 Rv3130c tgs1 0.98 1.02 Respiration Rv0467 icl1 1.33 1.14 Rv2194 qcrC 1.12 1.09 Rv1854c ndh 1.01 1.03 Rv3145 nuoA 1.09 1.04 Rv2583c relA 1.09 1.10 Rv1131 gltA1 / prpC 1.12 1.05 Rv3341 metA 1.10 1.02 Rv1130...”
- More
- Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis
Bi, Scientific reports 2017 - “...activity of isocitrate lyase and methylcitrate lyase is carried out by a single protein (ICL1, MRA_0473, Rv0467) 33 . Some strains of M. tb , such as the Erdman strain, contain two copies of icl genes ( icl1 and icl2 ), but icl2 in H37Rv or...”
- Dissecting the Mycobacterium bovis BCG Response to Macrophage Infection to Help Prioritize Targets for Anti-Tuberculosis Drug and Vaccine Discovery
Medley, Vaccines 2022 - “...acid metabolism genes intracellularly [ 9 , 12 ]. The key indicator gene icl1 ( Mb0476 ; Rv0467 ), involved in the glyoxylate cycle to convert acetyl-CoA molecules derived from the -oxidation of fatty acids into oxaloacetate, was induced (L2FC 2.67) intracellularly by M. bovis BCG....”
- “...respiration Involved in glycolysis Mb2055c Rv2030c * - 3.64 Conserved hypothetical Unknown, induced under stress Mb0476 Rv0467 * icl 2.67 Intermediary metabolism and respiration Involved in glyoxylate shunt Mb1161 Rv1130 * prpD 10.42 Intermediary metabolism and respiration Involved in methylcitrate cycle...”
- The open pan-genome architecture and virulence landscape of Mycobacterium bovis
Reis, Microbial genomics 2021 - “...genomes NCBI Mb3601 Eu3 France 2014 Cattle na na [ 16 ] assemble/draft genomes NCBI Mb0476 Eu2 Canada 2002 Cattle na na na assemble/draft genomes NCBI MbSP38 Eu2 Brazil 2010 Cattle na na [ 69 ] assemble/draft genomes NCBI Mb1595 w/o CC Korea 2012 Cattle na...”
- Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis
Reis, Scientific reports 2021 - “...1985 Bison NA assemble/draft genomes NCBI Mb3601 Eu3 France 2014 Cattle 29 assemble/draft genomes NCBI Mb0476 Eu2 Canada 2002 Cattle NA assemble/draft genomes NCBI MbSP38 Eu2 Brazil 2010 Cattle 44 assemble/draft genomes NCBI Mb1595 w/o CC Korea 2012 Cattle 45 assemble/draft genomes NCBI Mb0030 w/o CC...”
- Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation
Golby, Microbiology (Reading, England) 2008 - “...genes M. bovis CDS M. tuberculosis CDS Gene Fold change * Mb0217 Rv0211 pckA 25.510 Mb0476 Rv0467 icl 1819.2 Mb0529c Rv0516c nc Mb1058 Rv1029 kdpA nc Mb1086 Rv1057 8.44.7 Mb1162 Rv1131 gltA1 nc Mb1214 Rv1182 papA3 nc Mb1216c Rv1184c 7.32.8 Mb1217c Rv1185c fadD21 4.82.4 Mb1438c Rv1403c...”
- “...274 13 Mb1439 Rv1404 160 45 Mb1440c Rv1405c 274 68 Mb0217 Rv0211 pckA 606 915 Mb0476 Rv0467 icl 428 1620 Mb1788 Rv1758 cut1 218 2123 Mb1217c Rv1185c fadD21 578 2430 Mb3163 Rv3139 fadE24 468 3136 Mb2454 Rv2428 ahpC 195 3738 Mb1086 Rv1057 393 3943 Mb1495 Rv1460...”
- Selective enrichment of mycobacterial proteins from infected host macrophages
Chande, Scientific reports 2015 - “...13 RVBD_2031c Heat shock protein HspX Yes 14 RVBD_3583c CarD family transcriptional regulator Yes 15 RVBD_0467 Isocitrate lyase Icl Yes 16 grpE Protein GrpE No 17 RVBD_1464 Cysteine desulfurase Yes 18 Rv2159c Alkylhydroperoxidase AhpD family core domain-containing protein Yes 19 RVBD_3131 Uncharacterized protein Yes 20 RVBD_2710...”
SACE_1449 isocitrate lyase from Saccharopolyspora erythraea NRRL 2338
27% identity, 46% coverage
- Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea
Karničar, Microbial cell factories 2016 - “...our genomic and transcriptomic data show that in the HP strain the isocitrate lyase gene (SACE_1449) carries a mutation in the 5-UTR and is significantly downregulated at the gene expression level, suggesting a possible role of conversion of methylmalonyl-CoA to succinyl-CoA as an anaplerotic step in...”
- “...uniquely mutated genes in ABE1441 include a significantly reduced expression levels of the isocitrate lyase (SACE_1449) gene, which further confirms a reduced role of the TCA cycle intermediates (e.g. succinyl-CoA) as sources for the supply of methylmalonyl-CoA extender unit in our HP strain. The high number...”
- Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome
Licona-Cassani, Molecular & cellular proteomics : MCP 2014 - “...clusters I, IV & VII Profile C SACE_1449 SACE_1473 SACE_2177-2 SACE_6385-2 SACE_0195-1 SACE_3899 SACE_3448 SACE_4140-2 SACE_6118 SACE_5364 SACE_6385-1 SACE_4660...”
- “...0.1 0 -0.1 20 -0.2 -0.3 16 log PA o o SACE_1449 3.5 3 2.5 2 1.5 1 0.5 0 -0.5 20 -1 -1.5 SACE_6385-oxoglutarate dehydrogenase E1 sucA2 SACE_1449-isocitrate lyase...”
Dgeo_1287 isocitrate lyase from Deinococcus geothermalis DSM 11300
32% identity, 37% coverage
Q8RPZ0 isocitrate lyase (EC 4.1.3.1) from Streptomyces clavuligerus (see paper)
27% identity, 52% coverage
KPHS_02300 isocitrate lyase from Klebsiella pneumoniae subsp. pneumoniae HS11286
28% identity, 45% coverage
- Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae
Lee, mSystems 2024 - “...genes participated in 4-hydroxypenylacetate catabolism, including phenylacetate breakdown. ( E ) Carbon metabolism. Expression of KPHS_02300 (isocitrate lyase), KPHS_02290 (malate synthase), and KPHS_23760 (3-hydroxy butyryl-CoA dehydrogenase) distinctly decreased in the K56_Co_Che combination treatment condition, whereas KPHS_31180 (pyruvate kinase), KPHS_51710 (triosephosphate isomerase), and KPHS_51160 (phosphoglyceromutase) showed enhanced...”
- “...closely associated with glycolysis and gluconeogenesis. In the anaerobic glyoxylate bypass pathway, downregulated genes, including KPHS_02300 (isocitrate lyase), KPHS_02290 (malate synthase), and KPHS_23760 (3-hydroxybutyryl-CoA dehydrogenase), contribute to the production of glucose from fatty acids. Conversely, three upregulated genes, KPHS_31180 (pyruvate kinase), KPHS_51710 (triosephosphate isomerase), and KPHS_51160...”
HD73_1290 isocitrate lyase from Bacillus thuringiensis serovar kurstaki str. HD73
30% identity, 39% coverage
GBAA_1132 isocitrate lyase from Bacillus anthracis str. 'Ames Ancestor'
30% identity, 39% coverage
DR0828, DR_0828 isocitrate lyase from Deinococcus radiodurans R1
27% identity, 48% coverage
- Development and Regulation of the Extreme Biofilm Formation of Deinococcus radiodurans R1 under Extreme Environmental Conditions
Guo, International journal of molecular sciences 2023 - “...oxidase subunit II 4.59 3.60 2.22 2.18 DR_1440 ATPase 3.06 3.55 4.24 3.63 Carbohydrate metabolism DR_0828 isocitrate lyase 4.74 4.57 6.13 4.72 DR_1778 3-isopropylmalate dehydratase large subunit 2 1.92 1.94 2.13 2.00 Environmental information processing DR_B0073 PTS fructose transporter subunit IIBC 1.41 3.92 5.02 2.06 DR_B0074...”
- A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans
Xue, Biomolecules 2019 - “...< 1. Gene Name Log 2 (FC) * p Value Description Down-regulated in Dsr11 strain dr_0828 1.9173 1.1710 5 Isocitrate lyase dr_2464 1.38547 4.0610 5 Peptidyl-prolyl cis-trans isomerase, FKBP-type dr_1325 1.2897 4.0210 5 Endopeptidase-related protein dr_0815 1.1394 4.2310 6 Transcriptional regulator, GntR family dr_A0367 1.12989 1.310...”
- A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans
Ul, PloS one 2014 - “...dr2523 , dr2283 , dr1709 , dr1236 , dr1998 , dr1506 , dr0348 , and dr0828 ) were quantified under normal growth conditions and after treatment with Mn 2+ . Four of these genes are Mn 2+ transport genes ( dr2523 , dr2283 , dr1709 and...”
- “...shown that dr1506 and dr0348 are associated with the production of ROS [1] . The dr0828 gene encodes an isocitrate lyase, which is an enzyme in the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate. Previous research has shown that when irradiated,...”
- Oxidative stress resistance in Deinococcus radiodurans
Slade, Microbiology and molecular biology reviews : MMBR 2011 - “...E ES ES OHSAC OHSAC S OHSC OHS DdrO? DR1155 DRA0277 DR0828 IrrE IrrE OxyR Induced after IR stressd RM IrrE IrrE Type(s) of stressc DM IrrE IrrE DR0952 DR0951...”
- Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage
Karlin, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...329 421 304 489 303 1.66 1.47 1.36 1.29 1.05 DR1720 DR0828 DR1540 DR0325 DR1247 DR0287 DR2627 DR1248 DR1674 DR0757 DR0083 905 463 430 329 385 955 812 300 332...”
BLi04207 putative protein from Bacillus licheniformis DSM 13
31% identity, 39% coverage
- The peroxide stress response of Bacillus licheniformis
Schroeter, Proteomics 2011 (PubMed)- “...induced during peroxide stress. Furthermore, the genes BLi04207 and BLi04208, which encode proteins homologous to glyoxylate cycle enzymes, were also induced...”
- “...[55-57]. Interestingly, we observed a strong induction of BLi04207 and BLi04208 encoding for the isocitrate lyase and the malate synthase of the glyoxylate...”
S3649 isocitrate lyase from Shigella flexneri 2a str. 2457T
SF4081 isocitrate lyase from Shigella flexneri 2a str. 301
27% identity, 46% coverage
Icl / b4015 isocitrate lyase (EC 4.1.3.1) from Escherichia coli K-12 substr. MG1655 (see paper)
aceA / P0A9G6 isocitrate lyase (EC 4.1.3.1) from Escherichia coli (strain K12) (see 25 papers)
ACEA_ECOLI / P0A9G6 Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 from Escherichia coli (strain K12) (see 7 papers)
b4015 isocitrate lyase from Escherichia coli str. K-12 substr. MG1655
NP_418439 isocitrate lyase from Escherichia coli str. K-12 substr. MG1655
C5Y66_09370 isocitrate lyase from Escherichia coli str. K-12 substr. MG1655
27% identity, 46% coverage
- function: Involved in the metabolic adaptation in response to environmental changes. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+) (Divalent metal cations. Can also use Mn(2+) ion.)
subunit: Homotetramer. - Chaperonin Abundance Enhances Bacterial Fitness
Kumar, Frontiers in molecular biosciences 2021 - “...(P0A9G6) Isocitrate lyase (EC:4.1.3.1) 47.4 5.16 11 40.32 Homo-tetramer C c.1.12.7 36.53 (Stable) Cytoplasm aceA (b4015) 0 11.5 DPO3B_ECOLI (P0A988) DNA polymerase III beta subunit protein (EC:2.7.7.7) 40.5 5.45 12 40.71 Hetero-Oligomer L d.131.1.1 42.49 (Unstable) Cytoplasm dnaN (b3701) 1 2.4 TALB_ECOLI (P0A870) Transaldolase B (EC:2.2.1.2)...”
- Engineering the transmission efficiency of the noncyclic glyoxylate pathway for fumarate production in Escherichia coli
Chen, Biotechnology for biofuels 2020 - “...( Ec CS, b0720), aconitase ( Ec ACN, b0118) and isocitrate lyase ( Ec ICL, b4015) genes from E. coli were amplified from plasmids pET28a- Ec CS, pET28a- Ec ACN, and pET28a- Ec ICL, respectively [ 7 ]. Succinate dehydrogenase (SDH, b0723) [ 22 ], the...”
- Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
Youngquist, Journal of industrial microbiology & biotechnology 2017 - “...fumC 3.2 1.2 10 2 fumarate hydratase b2210 mqo 17.4 3.1 10 4 malate dehydrogenase b4015 aceA 3.2 1.2 10 4 isocitrate lyase b4014 aceB 3.3 2.0 10 5 malate synthase A a . Fold change is calculated based on linear difference in average intensities between...”
- “...dehydrogenase, decarboxylase component E1, thiamin-binding b0115 aceF 1.2 5.510 4 pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 b4015 aceA 2.0 5.510 4 isocitrate lyase b4014 aceB 2.4 5.910 5 malate synthase A Respiration b0430 cyoC 1.8 7.810 4 cytochrome o ubiquinol oxidase subunit III b2277 nuoM 2.2 7.010...”
- Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...aceB c , f b4014 malate synthase A 4.1 aceA c , f , i b4015 isocitrate lyase 5.1 acs f , g , i b4069 acetyl-CoA synthetase 19.5 frdD b4151 fumarate reductase, anaerobic, membrane anchor polypeptide 4.1 frdB b b4153 fumarate reductase, anaerobic, iron-sulfur protein...”
- Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
Metris, Applied and environmental microbiology 2014 - “...b3941 b2286 b3417 b3417 b3783 b2041 b3306 b2890 b1274 b4015 b2296 b1276 b1000 b2266 b0757 b0759 b3431 b2053 b0220 b4014 b4014 b2684 b0678 b1482 b4376 b1896...”
- Accurate estimation of nucleic acids by amplification efficiency dependent PCR
Chatterjee, PloS one 2012 - “...dehydrogenase 1.80 1.87 0.60 0.93 1.32 b4016 isocitrate dehydrogenase kinase 1.91 1.82 37.32 8.20 2.41 b4015 isocitrate lyase 1.84 1.92 10.55 15.67 3.39 b2976 malate synthase G 1.94 1.95 4.78 4.75 2.83 b4014 malate synthase A 1.94 1.83 18.07 4.75 - b3236 malate dehydrogenase 1.87 1.94...”
- A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
Tzamali, BMC systems biology 2011 - “...the importance of studying group-wise metabolic variability. An example is observed in the triplet b0721, b4015 and b0728 when growing on limited pyruvate (Additional file 3 : Supplement FA). The mutants b0721 and b4015 do not interact. Furthermore, each of the constituent pairs of the triplet...”
- “...One such example was discussed previously and concerns the community consisting of the strain b0721, b4015 and b0728 when growing on limited pyruvate . Among these strains, b0721 and b4015 do not interact, while the strain b0728 both exploits the metabolites produced by these strains and...”
- Using genomic sequencing for classical genetics in E. coli K12
Lyons, PloS one 2011 - “...( Table S5 ), apparently accounts for reduced expression of the aceBA operon (b4014 and b4015) in NCM3722 [4] . The products of this operon malate synthase and isocitrate lyase constitute the glyoxylate bypass. Due to the absence of an IS5 insertion in the nmpC gene...”
- More
- Isolation, hyperexpression, and sequencing of the aceA gene encoding isocitrate lyase in Escherichia coli.
Matsuoka, Journal of bacteriology 1988 - GeneRIF: N-terminus verified by Edman degradation on complete protein
- The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
Muñoz-Villagrán, International journal of molecular sciences 2024 - “...subunit gamma atpG 5.33 0.003 P0ABA4 ATP synthase F1 complex subunit delta atpH 4.71 0.027 P0A9G6 isocitrate lyase aceA 7.77 0.038 P00363 fumarate reductase flavoprotein subunit frdA 5.29 0.045 E. Amino acid transport and metabolism P00968 carbamoyl-phosphate synthetase large subunit carB 2.63 0.003 P30750 L-methionine/D-methionine ABC...”
- Chaperonin Abundance Enhances Bacterial Fitness
Kumar, Frontiers in molecular biosciences 2021 - “...45.7 5.15 19 65.28 Homodimer C c.77.1.1 34.73 (Stable) Cytoplasm icd (b1136) 0 5.8 ACEA_ECOLI (P0A9G6) Isocitrate lyase (EC:4.1.3.1) 47.4 5.16 11 40.32 Homo-tetramer C c.1.12.7 36.53 (Stable) Cytoplasm aceA (b4015) 0 11.5 DPO3B_ECOLI (P0A988) DNA polymerase III beta subunit protein (EC:2.7.7.7) 40.5 5.45 12 40.71...”
- Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt
Durall, Microbial cell factories 2021 - “...t -test, p<0.05. Construction of plasmids Genes encoding ICL (encoded by aceA , accession number P0A9G6) and MS (encoded by aceB , accession number P08997) were cloned using Escherichia coli BL21 genomic DNA as a template. The aceA was amplified with oligos oligoF-AXS and oligoR-ABP and...”
- Comparative Analysis of Outer Membrane Vesicle Isolation Methods With an Escherichia coli tolA Mutant Reveals a Hypervesiculating Phenotype With Outer-Inner Membrane Vesicle Content
Reimer, Frontiers in microbiology 2021 - “...test ( p -value): ( p < 0.05) Fold change by sample Quantitative profile CYTOPLASM P0A9G6 aceA Isocitrate lyase BOTH <0.00010 1.1 Increased in tolA P06959 aceF Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex tolA 0.015 INF Increased in tolA P0A9Q7 adhE Aldehyde-alcohol dehydrogenase tolA <0.00010...”
- Low Bioavailability and High Immunogenicity of a New Brand of E. colil-Asparaginase with Active Host Contaminating Proteins
Zenatti, EBioMedicine 2018 - “...861 509 c P0ABZ6 Chaperone SurA 3 47.3 Peri P05793 Ketol-acid reductoisomerase 3 54.1 Cyto P0A9G6 Isocitrate lyase 2 47.5 Cyto Total peptide counts 743 867 601 Total HCP peptide counts 0 6 (0.7%) 2 (0.3%) Subcellular locations: Peri, periplasm; Cyto, cytoplasm; Memb, membrane, Inner memb,...”
- Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering
Trauchessec, Molecular & cellular proteomics : MCP 2014 - “...Proteomics 13.4 Uniprot accession number P0A9B2 P22259 P0A9G6 P0AC53 P0ABH7 P76558 P0A6V8 P00864 P33570 P0A6T1 P0AC41 P0A9P0 P61889 P0A836 P0A955 P62707...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...AccD P24182 P0A9Q5 6.65/49,320.74 7.58/33,321.89 AceA P0A9G6 Biotin carboxylase Acetyl-CoA carboxylase carboxyl transferase subunit beta Isocitrate lyase AceE...”
- Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans
Kremer, mBio 2019 - “...epimerase epi RSP_0812 Pden_2178 ( 2R )-MethylmalonylCoA mutase mcm RSP_2912 Pden_3681 GC Isocitrate lyase aceA C5Y66_09370 Pden_1363 Malate synthase aceB C5Y66_09365 Pden_1364 a Key enzymes of the two pathways are in bold. Missing enzyme homologues are indicated by dashes. To test whether both the EMCP and...”
ECs4933 isocitrate lyase from Escherichia coli O157:H7 str. Sakai
27% identity, 47% coverage
- Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
King, Molecular & cellular proteomics : MCP 2016 - “...TCA cycle ( sdhC / ECs0746 , sdhD / ECs0747 , sucC / ECs0753 , ECs4933 ), mixed acid fermentation ( aldA / ECs2021 ), glycolysis ( ECs2022 ), trehalose biosynthesis, and glycogen degradation ( glgX / ECs4276 ). However, as stated previously, the T-profiler analysis...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...thiC -2.35 1 ECs5179 rplI -3.90 1 ECs4928 purD -4.58 1 ECs5185 fklB -2.32 1 ECs4933 aceA 4.98 2 ECs5194 ytfJ 4.59 2 ECs4934 aceK 2.90 2 ECs5205 ytfQ 6.29 2 ECs4990 O157 2.13 2 ECs5206 - 2.57 3 ECs4991 O157 2.12 2 ECs5207 ytfT 3.32...”
SO1484 Isocitrate lyase (EC 4.1.3.1) from Shewanella oneidensis MR-1
SO1484, SO_1484 isocitrate lyase from Shewanella oneidensis MR-1
29% identity, 45% coverage
BGLU_RS06215 isocitrate lyase from Burkholderia glumae BGR1
30% identity, 38% coverage
1igwC / P0A9G6 Crystal structure of the isocitrate lyase from the a219c mutant of escherichia coli (see paper)
26% identity, 49% coverage
- Ligand: pyruvic acid (1igwC)
RC1_2686 isocitrate lyase from Rhodospirillum centenum SW
30% identity, 38% coverage
Mvan_0801 isocitrate lyase from Mycobacterium vanbaalenii PYR-1
27% identity, 53% coverage
- Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil
Kim, Applied and environmental microbiology 2015 - “...enzymes, succinyl-CoA synthetase (Mvan_4870) and isocitrate lyase (Mvan_0801) were upregulated. As shown in the functional network, all the upregulated enzymes...”
- “...route via -ketoglutarate and succinylCoA. Isocitrate lyase (Mvan_0801) is a hallmark enzyme for the glyoxylate bypass, catalyzing the cleavage of isocitrate...”
SMDB11_3752 isocitrate lyase from Serratia marcescens subsp. marcescens Db11
28% identity, 46% coverage
WP_002579294 phosphoenolpyruvate mutase from Clostridium sp.
25% identity, 61% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...WP_077842376; 476, Clostridium saccharobutylicum strain NCP 195, NZ_CP016092, WP_022744173; 856, Clostridium butyricum strain 41, NZ_CP039705, WP_002579294; 400, Selenomonas sp. oral taxon 478 strain F0592, NZ_CP012071, WP_050342316. The large group of AEPT-encoding gene neighbourhoods is diverse Apart from the Group 1 Burkholderiales_CDP-OH phosphonolipids, the AEPT-containing gene neighbourhoods...”
BMMGA3_RS01755 isocitrate lyase from Bacillus methanolicus MGA3
28% identity, 50% coverage
Sama_2380 Isocitrate lyase (EC 4.1.3.1) from Shewanella amazonensis SB2B
29% identity, 45% coverage
- mutant phenotype: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
lmo0075 similar to carboxyphosphonoenolpyruvate phosphonomutase from Listeria monocytogenes EGD-e
28% identity, 75% coverage
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...0.00 LMRG_02276 lmo0853 LMRG_02275-LMRG_02277 QacE family quaternary ammonium compound efflux SMR transporter 3.22 0.02 LMRG_02326 lmo0075 LMRG_02326-LMRG_02327 Phosphonomutase, probable carboxyvinyl-carboxyphosphonate phosphorylmutase 2.03 0.04 LMRG_02358 lmo0109 LMRG_02358-LMRG_02359 AraC family transcriptional regulator 2.18 0.00 LMRG_02386 lmo0137 LMRG_02385-LMRG_02386 Oligopeptide ABC transporter, permease protein 2.29 0.03 LMRG_02496 lmo1775 purE LMRG_02496-LMRG_02507...”
- Comparative genomics of human and non-human Listeria monocytogenes sequence type 121 strains
Rychli, PloS one 2017 - “...almost identical in all ST121 genomes (>99.7% similarity) is the region between the lmo0061 and lmo0075 homologues. This hypervariable hotspot 1 [ 23 ] harbors the putative type VII (T7SS, also called ESX-1, ESAT-6, WSS, or WXG100) secretion system. The region downstream of esaD ( lmo0066...”
- Genome sequencing of Listeria monocytogenes "Quargel" listeriosis outbreak strains reveals two different strains with distinct in vitro virulence potential
Rychli, PloS one 2014 - “...region with distinct differences between the two strains is the region between the lmo0061 and lmo0075 homologues, termed hypervariable hotspot 1 according to Kuenne et al. [26] . Interestingly, this region harbours the putative Listeria WSS (type VII/WXG100) secretion system. This secretion system has been shown...”
- Amplified intergenic locus polymorphism as a basis for bacterial typing of Listeria spp. and Escherichia coli
Somer, Applied and environmental microbiology 2005 - “...clpE BetL ATTM ltrC cheR lisR Lmo0672 Lmo0196 Lmo0075 Lin0694 Lmo0023 gid fhuB Lmo0042 Lmo0176 abc gbuA Allelea at following locus: LM6-4b LM8-4b LM26H-4b...”
MSMEG_0422 transferase from Mycobacterium smegmatis str. MC2 155
31% identity, 61% coverage
- A complex regulatory network controlling intrinsic multidrug resistance in Mycobacterium smegmatis
Bowman, Molecular microbiology 2014 - “...ABC transporter ATP-binding protein MSMEG_3203 4.3 transporter, LysE family MSMEG_5047 3.7 drug resistance transporter (Bcr/CfIA) MSMEG_0422 3.5 Transferase. Toxin production & resistance MSMEG_5659 3.1 ABC transporter, ATP-binding protein MSMEG_5660 3 ABC transporter ATP-binding protein MSMEG_6245 2.9 chloramphenicol resistance protein MSMEG_6595 2.6 ABC transporter complex Transcription Regulators...”
- Targeting drug tolerance in mycobacteria: a perspective from mycobacterial biofilms
Islam, Expert review of anti-infective therapy 2012 - “...MmpL family Rv2339 MSMEG_0313 6-phosphogluconate dehydratase Rv0189c MSMEG_0316 Transcription regulator ROK family VC2007 (imported), putative MSMEG_0422 Carboxyphosphonoenolpyruvatephosphonomutase-like protein Rv1998c MSMEG_0457 DNA gyrase subunit B, putative Rv0005 MSMEG_0504 Ribokinase Rv2436 MSMEG_0534 Multidrug-resistance protein, putative MSMEG_0550 ABC transporter, periplasmic substrate-binding protein MSMEG_0782 Aminotransferase, class III Rv2598 MSMEG_0790 MUTT3...”
TTHA1836 isocitrate lyase from Thermus thermophilus HB8
31% identity, 42% coverage
6lrtA / A9WDE7 Crystal structure of isocitrate lyase (caur_3889) from chloroflexus aurantiacus in complex with isocitrate and manganese ion
31% identity, 39% coverage
- Ligand: manganese (ii) ion (6lrtA)
Shew_1276 Isocitrate lyase (EC 4.1.3.1) from Shewanella loihica PV-4
29% identity, 44% coverage
- mutant phenotype: Specifically important for utilizing Potassium acetate. Automated validation from mutant phenotype: the predicted function (4.1.3.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
Caur_3889 isocitrate lyase from Chloroflexus aurantiacus J-10-fl
31% identity, 39% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...(Caur_0180) Glycolate assimilation and glyoxylate cycle glcDEF (Caur_1144 - 1145, Caur_2133, Caur_2135), glyr (Caur_0825), icl (Caur_3889) and mas (Caur_2969) Cobalamin biosynthesis cobS (Caur_1198), cobQ / cbiP (Caur_2560), N -transferase (Caur_2561), cobP / cobU (Caur_2562), cobB/cbiA (Caur_2563), cobA (Caur_2564, Caur_0687), cobJ (Caur_2565), cobM / cbiF (Caur_2566), cobI/cbiL...”
- “...(Figure 5 ), and is also produced by isocitrate lyase (EC 4.1.3.1) ( icl , Caur_3889) and consumed by malate synthase (EC 2.3.3.9) ( mas , Caur_2969) in the glyoxylate cycle. With acetate as the sole organic carbon source to support the photoheterotrophic growth of Cfl....”
BFX80_03560 isocitrate lyase from Cobetia marina
28% identity, 46% coverage
IZU87_14450 isocitrate lyase from Cobetia sp. MC34
28% identity, 46% coverage
- High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741T and in silico analyses of the genus specific PhaC2 polymerase variant
Christensen, Microbial cell factories 2021 - “...(EC 4.2.1.3) acnA/acnB +/+ IZU87_02425/IZU87_05790 +/+ BFX80_01545/BFX80_04820 +/+ C8233_12860/C8233_16190 Isocitrate lyase (EC 4.1.3.1) AceA + IZU87_14450 + BFX80_03560 + C8233_14950 Malate synthase (EC 2.3.3.9) AceB (glcB) + IZU87_07285 + BFX80_16805 + C8233_10755 Cation acetate symporter + IZU87_06430 + BFX80_02575 + C8233_13875 Phasin phaP 1 /P 2...”
- “...by aconitate hydratases AcnA/B ( acnA/B, IZU87_02425/IZU87_05790) to glyoxylate by isocitrate lyase AceA ( aceA, IZU87_14450), before malate is formed by addition of an acetyl-CoA molecule by AceB ( aceB, IZU87_07285) [ 88 ]. In contrast to the TCA cycle, the glyoxylate shunt does not lead...”
WP_004523200 phosphoenolpyruvate mutase from Burkholderia pseudomallei MSHR5855
BPSS0610 putative phosphoenolpyruvate phosphomutase from Burkholderia pseudomallei K96243
31% identity, 59% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...with the dotted line marking a count of ten. The two largest bars represent sequences WP_004523200 and WP_004525540. ( b ) Sunburst chart of early branch point phosphonate biosynthetic steps based on 434 gene neighbourhoods; BGCs possessing the same Ppm sequence (e.g. WP_004523200) are treated as...”
- “...in a single genome, several were found in multiple genomes. In particular, two Ppm sequences (WP_004523200 and WP_004525540) together accounted for over 200 gene neighbourhoods in different genome assemblies of Burkholderia pseudomallei ; however, the phylogenetic separation of these two sequences in distinct clades implies different...”
- GvmR - A Novel LysR-Type Transcriptional Regulator Involved in Virulence and Primary and Secondary Metabolism of Burkholderia pseudomallei
Duong, Frontiers in microbiology 2018 - “...the 6-phosphofructokinase (BPSS1957), the acetate kinase (BPSS1956), the phosphate acetyltransferase (BPSS1955), and the phosphoenolpyruvate phosphomutase (BPSS0610) involved in glycolysis, gluconeogenesis, phosphonate, or acetate metabolism showed increased transcript levels in the mutant. Upregulation of the 2-methylisocitrate lyase gene ( prpB ; BPSS0206) and simultaneous downregulation of the...”
WP_002679012 phosphoenolpyruvate mutase from Treponema denticola ATCC 35405
29% identity, 47% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...NC_003228, WP_011202610; 321, Bacteroides thetaiotaomicron strain 7330, NZ_CP012937, WP_008767814; 863, Treponema denticola ATCC 35405, NZ_002967, WP_002679012; 866, Clostridium beijerinckii isolate C. beijerinckii DSM 6423, NZ_LN908213, WP_077842376; 476, Clostridium saccharobutylicum strain NCP 195, NZ_CP016092, WP_022744173; 856, Clostridium butyricum strain 41, NZ_CP039705, WP_002579294; 400, Selenomonas sp. oral taxon...”
Atu0607 isocitrate lyase from Agrobacterium tumefaciens str. C58 (Cereon)
30% identity, 38% coverage
LMRG_RS00365 isocitrate lyase/phosphoenolpyruvate mutase family protein from Listeria monocytogenes 10403S
LMRG_02326 hypothetical protein from Listeria monocytogenes 10403S
27% identity, 75% coverage
- Genome-Wide Association Study of Listeria monocytogenes Isolates Causing Three Different Clinical Outcomes
Cardenas-Alvarez, Microorganisms 2022 - “...Locus Tag Gene Product Protein ID Region Start Region End Clinical Outcome 77,529 T C LMRG_RS00365 Phosphoenolpyruvate mutase WP_014600361.1 76,760 77,533 CNS 271,402 A G LMRG_RS01320 DNA-directed RNA polymerase subunit beta WP_003723046.1 268,638 272,243 CNS 38,820 C A LMRG_RS00170 PTS sugar transporter subunit IIC WP_003721657.1 38,033...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...2.14 0.00 LMRG_02276 lmo0853 LMRG_02275-LMRG_02277 QacE family quaternary ammonium compound efflux SMR transporter 3.22 0.02 LMRG_02326 lmo0075 LMRG_02326-LMRG_02327 Phosphonomutase, probable carboxyvinyl-carboxyphosphonate phosphorylmutase 2.03 0.04 LMRG_02358 lmo0109 LMRG_02358-LMRG_02359 AraC family transcriptional regulator 2.18 0.00 LMRG_02386 lmo0137 LMRG_02385-LMRG_02386 Oligopeptide ABC transporter, permease protein 2.29 0.03 LMRG_02496 lmo1775 purE...”
fom1 / P96074 phosphoenolpyruvate phosphomutase/2-hydroxyethylphosphonate cytidylyltransferase monomer (EC 2.7.7.104; EC 5.4.2.9) from Streptomyces wedmorensis (see 6 papers)
FOM1_STRWE / P96074 Fosfomycin biosynthesis bifunctional protein Fom1; EC 2.7.7.104; EC 5.4.2.9 from Streptomyces wedmorensis (see paper)
29% identity, 47% coverage
- function: Bifunctional enzyme that catalyzes two steps during fosfomycin biosynthesis (PubMed:28727444). It catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy), the first step of the pathway. It also catalyzes the cytidylylation of the 2- hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-2- hydroxyethylphosphonate (HEP-CMP), the fourth step of the pathway (PubMed:28727444).
catalytic activity: 2-hydroxyethylphosphonate + CTP = cytidine 5'-{[hydroxy(2- hydroxyethyl)phosphonoyl]phosphate} + diphosphate (RHEA:63420)
catalytic activity: phosphoenolpyruvate + H(+) = 3-phosphonopyruvate (RHEA:17013)
cofactor: a divalent metal cation (The CyTase reaction requires a divalent metal ion. Highest activity is observed with Co(2+), but it can also use Mg2(+), Ni2(+), Fe2(+) or Mn2(+).)
disruption phenotype: Deletion mutant does not produce fosfomycin. - Stereospecific Radical-Mediated B<sub>12</sub>-Dependent Methyl Transfer by the Fosfomycin Biosynthesis Enzyme Fom3
McLaughlin, Biochemistry 2018 - “...examine the mechanism of the Fom3 reaction, we used the cytidylyltransferase domain of Fom1 (UniProtKB P96074) to enzymatically synthesize 2-HEP-CMP ( Figure S1 ) and standards of (2 R )- and (2 S )-2-HPP-CMP. 11 Coexpression of N-terminally His 6 -tagged Fom3 from Streptomyces wedmorensis (UniProtKB...”
WP_008767814 phosphoenolpyruvate mutase from Bacteroides thetaiotaomicron
BT1720 phosphoenolpyruvate phosphomutase precursor from Bacteroides thetaiotaomicron VPI-5482
29% identity, 53% coverage
- An inventory of early branch points in microbial phosphonate biosynthesis
Li, Microbial genomics 2022 - “...WP_134359243; 743, Bacteroides fragilis strain NCTC 9343, NC_003228, WP_011202610; 321, Bacteroides thetaiotaomicron strain 7330, NZ_CP012937, WP_008767814; 863, Treponema denticola ATCC 35405, NZ_002967, WP_002679012; 866, Clostridium beijerinckii isolate C. beijerinckii DSM 6423, NZ_LN908213, WP_077842376; 476, Clostridium saccharobutylicum strain NCP 195, NZ_CP016092, WP_022744173; 856, Clostridium butyricum strain 41,...”
- Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D- galacto-nononic acid (KDN)
Wang, Chemistry & biology 2008 - “...transcriptional regulator, BT1723 O-antigen export protein, BT1722 O-antigen chain length determinant protein, BT1721 nucleotidyl transferase, BT1720 phosphoenolpyruvate phosphomutase, BT1719 phosphonopyruvate decarboxylase, BT1718 2-aminoethylphosphonate transaminase, BT1717 capsular polysaccharide repeat unit transporter (flippase), BT1716 CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase, BT1715 CMP-sialic acid synthase, BT1714 sialic acid synthase, BT1713 HADSF phosphatase, BT1712...”
ECA0487 phosphoenolpyruvate mutase from Pectobacterium atrosepticum SCRI1043
25% identity, 90% coverage
- Phosphonates of <i>Pectobacterium atrosepticum</i>: Discovery and Role in Plant-Pathogen Interactions
Parfirova, International journal of molecular sciences 2024 - “...compounds. Some Pectobacterium species, including Pba , have a marker gene encoding phosphoenolpyruvate mutase Fom1 (ECA0487) that catalyzes the formation of the C-P bond, yielding phosphonopyruvate, as well as a gene encoding phosphoenolpyruvate decarboxylase Fom2 (ECA0488), which provides the further common step of biosynthesis of most...”
- “...by the method described by Kaniga et al. [ 57 ]. The target gene fom1 (ECA0487 locus) together with adjacent regions (approximately 1000 bp up- and downstream of the fom1 ORF) was amplified by PCR with the primers up fom1 F and dn fom1 R (...”
- Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens
Pritchard, PLoS computational biology 2009 - “...of potential functional importance. Island Locus tags Genomic location Putative phenotype, and representative genes PbaI5 ECA0487 - ECA0491 563151-567396 phosphonate metabolism ( fom1 , fom2 , phnG ) PbaI7 ECA0600 - ECA0610 659712-682903 coronafacic acid synthesis ( cfa1-8B , cfl ) PbaI13 ECA1420 - ECA1441 1611940-1636204...”
BR1614 isocitrate lyase from Brucella suis 1330
30% identity, 38% coverage
Plav_0592 isocitrate lyase from Parvibaculum lavamentivorans DS-1
30% identity, 38% coverage
- Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T))
Schleheck, Standards in genomic sciences 2011 - “...during growth with acetate, the genome of P. lavamentivorans encodes the glyoxylate cycle (isocitrate lyase, Plav_0592; malate synthase, Plav_0593) to generate succinate for the synthesis of carbohydrates. The genome also encodes the complete ethyl-malonyl-CoA pathway to assimilate acetate [ 56 ]. This observation, i.e. glyoxylate cycle...”
SMc00768 PROBABLE ISOCITRATE LYASE PROTEIN from Sinorhizobium meliloti 1021
30% identity, 38% coverage
NP_001021367 Malate synthase from Caenorhabditis elegans
31% identity, 19% coverage
Q97YI8 isocitrate lyase (EC 4.1.3.1) from Saccharolobus solfataricus (see paper)
SSO1333 isocitrate lyase from Saccharolobus solfataricus P2
SSO1333 Isocitrate lyase (aceA/icl) from Sulfolobus solfataricus P2
24% identity, 50% coverage
- Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response
Wolf, Frontiers in microbiology 2020 - “...ferredoxin-NAD (+) reductase component (todA) 9.7 6.5 1.96E-01 Sso2178 1.2.1.11 Malonyl-CoA reductase 9.1 2.0 5.37E-06 Sso1333 4.1.3.1 Isocitrate lyase 7.2 0.3 3.94E-18 Sso0120 Assembly ATPase involved in the assembly of the UV induced pili 7.0 0.8 6.10E-17 Sso2942 1.2.99.8 Glyceraldehyde dehydrogenase (FAD-containing), large chain 6.7 0.6...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...genomic organization. Both genes, encoding isocitrate lyase (SSO1333) and malate synthase (SSO1334), are consecutively colocalized in the genome but are...”
- Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius
Nunn, The Journal of biological chemistry 2010 - “...pH 8.5. Isocitrate Lyase--The putative isocitrate lyase gene (SSO1333) annotated in the genome of S. solfataricus was cloned into pET19b using the NcoI and...”
- Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress
Maaty, PloS one 2009 - “...Y Arabinose ABC transporter, arabinose binding protein SSO3066 3.57E-05 2.37 COG1653 N Isocitrate lyase (aceA/icl) SSO1333 9.01E-04 2.37 COG2224 Y The mRNAs coding for DPSL (SSO2079), and the two flanking genes (SSO2078 and 2080) showed the largest changes in abundance, 31 to 41 fold increase (...”
GCP_CAEEL / Q10663 Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 from Caenorhabditis elegans (see 2 papers)
NP_503306 Malate synthase from Caenorhabditis elegans
31% identity, 17% coverage
- catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
catalytic activity: glyoxylate + acetyl-CoA + H2O = (S)-malate + CoA + H(+) (RHEA:18181) - Short-Term Mild Temperature-Stress-Induced Alterations in the C. elegans Phosphoproteome
Huang, International journal of molecular sciences 2020 - “...protein kinase A3QM97 cnnm-1 SMSpIVGTSELSAR 0.34 Metal transporter O18696 pde-1 SpYDNAPALESLEK 0.403 Probable 3,5-cyclic phosphodiesterase Q10663 icl-1 AGSpVVNRIPEAADLLEK 0.414 Bifunctional glyoxylate cycle protein Q17446 pmk-1 QTDSEMTpGYpVATR 0.537 Stress-activated protein kinase...”
- Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation
Kondrashov, Biology direct 2006 - “...This approach identified isotrate lyase genes that were annotated in A. gambiae (XP_561347), C. elegans (NP_503306), C. briggsae (CAE62276), Strongyloides ratti (BAD89436) and S. stercoralis (AAF00535), and malate synthase genes in A. gambiae (XP_315354), C. elegans (NP_503306), C. briggsae (CAE62276), S. purpuratus (XP_782946), D. rerio (XP_685378)...”
BAB1_1631 Isocitrate lyase and phosphorylmutase:Isocitrate lyase from Brucella melitensis biovar Abortus 2308
30% identity, 38% coverage
7rbxC / Q2YQA0 Crystal structure of isocitrate lyase and phosphorylmutase:isocitrate lyase from brucella melitensis biovar abortus 2308 bound to itaconic acid (see paper)
30% identity, 39% coverage
- Ligand: 2-methylidenebutanedioic acid (7rbxC)
BMEI0409 isocitrate lyase from Brucella melitensis bv. 1 str. 16M
30% identity, 38% coverage
- Vaccine-Elicited Antibodies Restrict Glucose Availability to Control Brucella Infection
Ponzilacqua-Silva, The Journal of infectious diseases 2024 - “...melitensis 16M with a chloramphenicol resistance cassette and complemented [ 10 ]. The aceA gene (BMEI0409) in B melitensis 16M was replaced in frame with a chloramphenicol resistance gene in the same manner as described for gluP [ 10 ] with primers described in Supplementary Table...”
- Genome-wide analysis of Brucella melitensis growth in spleen of infected mice allows rational selection of new vaccine candidates
Barbieux, PLoS pathogens 2024 - “...requiring gluconeogenesis [ 50 ] However, the two enzymes of this cycle, isocitrate lyase aceA (BMEI0409) and malate synthase glcB (BMEI0380), are not predicted to be essential in vivo , data in agreement with previous results in B . abortus [ 49 ] and B ....”
- Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis
Khan, Bioengineering (Basel, Switzerland) 2022 - “...with other proteins in the B. suis biovar 1330. The isocitrate lyase was represented by BMEI0409 and it mediates interactions with other proteins nearby like: malate synthase G, involved in the glycolate utilization (glcB); aconitate hydratase (BMEI1855), (BMEII0009), (BMEI1952), (BMEII1061), (BMEI1939), (BMEII1060), (BMEII1062), (BMEII1064); and ureidoglycolate...”
B7G518 Isocitrate lyase from Phaeodactylum tricornutum (strain CCAP 1055/1)
PHATRDRAFT_51088 predicted protein from Phaeodactylum tricornutum CCAP 1055/1
44% identity, 16% coverage
PCC7424_4054 isocitrate lyase from Cyanothece sp. PCC 7424
30% identity, 33% coverage
RL0761 putative isocitrate lyase from Rhizobium leguminosarum bv. viciae 3841
30% identity, 38% coverage
- Role of O2 in the Growth of Rhizobium leguminosarum bv. viciae 3841 on Glucose and Succinate
Wheatley, Journal of bacteriology 2017 - “...pRL120710 RL0037 RL0054 RL0182 RL0183 RL0751 RL0752 RL0753 RL0761 RL1010 RL1351 RL2234 RL2239 RL2241 RL2243 Role of O2 in the Growth of Rhizobium leguminosarum...”
- The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
Perry, Frontiers in microbiology 2016 - “...mdh Malate dehydrogenase GI 0.25 1.33 GD 0.17 1 GD 3.5.8 Putative malate dehydrogenase 3.10 RL0761 - Isocitrate lyase GN 0.91 17.29 NE 0.83 25.79 NE 3.3.5 Putative isocitrate lyase 3.11 RL0054 glcB Malate synthase G GN 0.88 20 NE 1 24.06 NE 3.3.5 Putative malate...”
- Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Ramachandran, Genome biology 2011 - “...it is particularly important in that of pea. Curiously, although the gene for isocitrate lyase (RL0761, aceA ) was up-regulated in both alfalfa and sugar beet rhizospheres, indicating elevated C2 metabolism, expression of RL0054, encoding malate synthase, was only elevated in that of pea (Figure 2...”
- Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca
Karunakaran, Journal of bacteriology 2009 - “...led to upregulation of genes encoding isocitrate lyase (RL0761) (20-fold) and malate synthase (glcB; Downloaded from http://jb.asm.org/ on February 10, 2017 by...”
- “...induction of the gene encoding isocitrate lyase (RL0761). This contrasts with inositol-grown free-living cultures, where both genes were strongly upregulated,...”
- The genome of Rhizobium leguminosarum has recognizable core and accessory components
Young, Genome biology 2006 - “...and Fe uptake [ 42 ]. The genome of Rlv3841 contains genes for isocitrate lyase (RL0761) and malate synthase (RL0054), which would allow a gloxylate cycle to operate, although strain 3841 does not grow on acetate. There are six genes whose products closely resemble succinate semialdehyde...”
RLV_3156 isocitrate lyase from Rhizobium leguminosarum bv. viciae
30% identity, 38% coverage
MMAR_2821 isocitrate lyase AceAb from Mycobacterium marinum M
31% identity, 20% coverage
BF638R_1867 phosphoenolpyruvate mutase from Bacteroides fragilis 638R
29% identity, 51% coverage
- New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile
Gough, MicrobiologyOpen 2024 - “...OadA1, pyruvate/oxaloacetate carboxyltransferase (BF638R_2828); OM, outer membrane; PckA, phosphoenolpyruvate carboxykinase (BF638R_4326); PEP mutase, phosphoenolpyruvate mutase (BF638R_1867); PFLA, phospholipid fatty acids; PflA, pyruvate formatelyase 1, activating enzyme (BF638R_1338); PflB, pyruvate formatelyase 1 [formate acetyltransferase 1] (BF638R_1339); PflC, pyruvate formatelyase 2, activating enzyme (BF638R_4262); PflD, pyruvate formatelyase 2...”
ACEA_BRANA / P25248 Isocitrate lyase; ICL; Isocitrase; Isocitratsysase; EC 4.1.3.1 from Brassica napus (Rape) (see paper)
40% identity, 16% coverage
- function: Involved in storage lipid mobilization during the growth of higher plant seedling.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+)
subunit: Homotetramer.
icl / P28297 isocitrate lyase (EC 4.1.3.1) from Arabidopsis thaliana (see paper)
ACEA_ARATH / P28297 Isocitrate lyase; ICL; Isocitrase; Isocitratsysase; EC 4.1.3.1 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT3G21720 ICL (ISOCITRATE LYASE); catalytic/ isocitrate lyase from Arabidopsis thaliana
40% identity, 16% coverage
- function: Involved in storage lipid mobilization during the growth of higher plant seedling.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+)
subunit: Homotetramer.
disruption phenotype: No visible phenotype under normal growth conditions, but mutant seedlings fail to establish into plantlets with true leaves under low light or short day conditions. - Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing <i>Brassica fruticulosa</i>
Busoms, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...that binds to RNA and is involved in drought, salt, and cold stress responses; jg21540 (AT3G21720) encodes a glyoxylate cycle enzyme IsoCitrate Lyase ( ICL ) involved in salt tolerance. We then focused on particular soil elements that significantly vary between coastal and inland sites (soil...”
- Local cryptic diversity in salinity adaptation mechanisms in a wild outcrossingBrassica
Busoms, 2024 - Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions
Pasandideh, Physiology and molecular biology of plants : an international journal of functional plant biology 2023 - “...Heat shock 70 kDa protein 4 AT5G03860 AT3G21720 AT2G05710 AT5G43330 AT3G04120 AT1G79550 AT1G70730 AT2G29560 AT5G56350 AT1G53310 AT1G13700 AT5G24420 AT5G13110...”
- Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming
Obermeyer, Frontiers in plant science 2022 - “...coverage of DRN1 (At2g45180), a gene repressed by elevated salt concentrations. (C) coverage of ICL (At3g21720), a gene, whose expression enhances salt tolerance. Further evaluation of genes specifically up- or down-regulated upon NaCl treatment in Col-0 or cdc73-2 revealed that in Col-0 the average length of...”
- Leaf-size control beyond transcription factors: Compensatory mechanisms
Tabeta, Frontiers in plant science 2022 - “...Tabeta etal. (2021) Class II ECH2 ( Katano etal., 2016 ; Tabeta etal., 2021 ) AT3G21720 ICL Loss-of-function Takahashi etal. (2017) Class II ECH2 ( Katano etal., 2016 ; Takahashi etal., 2017 ) AT2G23430 KRP1/ICK1 Over-expression Wang etal. (2000) AT3G50630 KRP2 Over-expression De Veylder etal. (2001)...”
- Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
Le, Frontiers in plant science 2022 - “...Glyoxylate/succinic semialdehyde reductase 2, chloroplastic Prupe_2G151800 AT1G12550 52 No -2.2 6.20E-05 HPR3; Glyoxylate/hydroxypyruvate reductase Prupe_3G219100 AT3G21720 84 Yes 4.3 2.50E-34 ICL; Isocitrate lyase Prupe_4G216900 AT4G26910 70 Yes -2.0 1.10E-03 ODH; Oxoglutarate dehydrogenase Prupe_1G155800 AT5G27600 76 Yes 1.3 2.30E-02 LACS7; Long chain acyl-CoA synthetase 7, peroxisomal Prupe_5G065100...”
- Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins
Ginsawaeng, International journal of molecular sciences 2021 - “...the de novo synthesis of key enzymes of the glyoxylate cycle, such as isocitrate lyase (AT3G21720), aconitase 3 (AT2G05710) and malate synthase (AT5G03860), was reported [ 22 ], pointing to lipid remobilization. All of them were also included in the heat-stable proteome of Col-0. Malate dehydrogenase...”
- Aconitase: To Be or not to Be Inside Plant Glyoxysomes, That Is the Question
De, Biology 2020 - “...ACO1: aconitase 1 (At4g35830); ACO2: aconitase 2 (At4g26970); ACO3: aconitase 3 (At2g05710); ICL: isocitrate lyase (AT3G21720); MLS: malate synthase (At5g03860). ( B ) Data expressed as log2 scale; ACO1: aconitase 1 (At4g35830); ACO2: aconitase 2 (At4g26970); ACO3: aconitase 3 (At2g05710); ICL: isocitrate lyase (AT3G21720); MLS: malate...”
- More
- Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions
Pasandideh, Physiology and molecular biology of plants : an international journal of functional plant biology 2023 - “...T3P18.20 KASI Hsp81.4 HSP90.1 HSFA1E AT-HSFB2B HSP70 Q9LZC3 P28297 Q9SIB9 P57106 P25858 Q9SAJ4 F4I6W4 Q9ZW34 Q9FM97 Q9MAH0 Q9LMX8 Q8LEV7 Q9FY99 Q9SH69 Q9LD43...”
GLRG_04226 isocitrate lyase family protein from Colletotrichum graminicola M1.001
42% identity, 17% coverage
A0A165Z711 Isocitrate lyase from Daucus carota subsp. sativus
40% identity, 16% coverage
LOC108215541 isocitrate lyase from Daucus carota subsp. sativus
40% identity, 16% coverage
- Hydro-Electro Hybrid Priming Promotes Carrot (Daucus carota L.) Seed Germination by Activating Lipid Utilization and Respiratory Metabolism
Zhao, International journal of molecular sciences 2021 - “...(none of these DEGs were in the CK vs. EF group). One of two DEGs (LOC108215541) encoding ICL was up-regulated in the HYD treatment compared with the CK. We also found that one DEG (LOC108204633) encoding succinate dehydrogenase (SDH) iron-sulfur subunit was upregulated in the HEHP...”
- “...< 0.01). The corresponding relationship between gene ID and its encoded enzyme are as follows: LOC108215541, ICL; LOC108224240, SDH iron-sulfur subunit; LOC108204633, FH; LOC108210669, LOC108223687, LOC108199904 and LOC108193312, MDH; LOC108206052 and LOC108205258, PEPCK; LOC108219027 and LOC108208954, PK; LOC108223320 and LOC108209732, PDC; LOC108199900 and LOC108214136, ADH. The...”
ACEA2_MYCTE / H8F3R6 Isocitrate lyase 2; ICL2; Isocitrase; Isocitratase; Methylisocitrate lyase; MICA; EC 4.1.3.1; EC 4.1.3.30 from Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) (see paper)
ACEA2_MYCTO / Q8VJU4 Isocitrate lyase 2; ICL2; Isocitrase; Isocitratase; EC 4.1.3.1 from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (see 3 papers)
Mb1950 PROBABLE ISOCITRATE LYASE aceA (ISOCITRASE) (ISOCITRATASE) (ICL) from Mycobacterium bovis AF2122/97
MT1966 isocitrate lyase from Mycobacterium tuberculosis CDC1551
MT18B_2492 isocitrate lyase ICL2 from Mycobacterium tuberculosis 18b
29% identity, 20% coverage
- function: Involved in the persistence and virulence of M.tuberculosis. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates. It also catalyzes the formation of pyruvate and succinate from 2-methylisocitrate, a key step in the methylcitrate cycle (propionate degradation route).
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
disruption phenotype: Deletion of icl2 in cells growing on 0.2% propionate shows a slightly decrease of both isocitrate and methylisocitrate lyase activity. - function: Involved in the persistence and virulence of M.tuberculosis. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
cofactor: Mg(2+)
disruption phenotype: Deletion of icl2 has a little effect on replication in media containing glycerol, glucose, short-chain fatty acids or long-chain fatty acids. Cells lacking icl2 have no discernible impact on the kinetics of M.tuberculosis growth and persistence. However deletion of both icl1 and icl2 eliminates growth on fatty acids but has little effect on use of carbohydrates. Cells lacking both genes are incapable of growth in mice and are rapidly eliminated from the lungs and spleen. - Proteomic analysis of protein purified derivative of Mycobacterium bovis
Roperto, Journal of translational medicine 2017 - “...29 ]. Fifty-two T cell antigens including Mb1301c (gene name: lprA), Mb1868c (gene name: glcB), Mb1950 (gene name: aceA), Mb3646c (gene name: espA), Mb3911c (gene name: espB) recently identified from M. tuberculosis, strain H37RV, via throughput proteome screening [ 30 ], have not been reported previously...”
- Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
Sreenu, BMC genomics 2006 - “...Fission with non-overlaping orf (16) T5 4 aceAa, aceAb *Rv1915 (367 *Rv1916 (398) MT1966 (766) Mb1950 (766) G5 6 Conserved hypothetical protein *Rv2561 (97) *Rv2562 (129) MT2638 (212) Mb2591 (245) T2 3 Conserved transmembrane protein Rv3453 (110), *Rv3454 (422) MT3561 (562) Mb3483 (561) C5 4 mmpL1...”
- Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Chekesa, PloS one 2024 - “...Rv3098A PemK-like protein V5QRX7 106 0 29 2.81E-16 5.05E-13 7.22E-14 LP icl2/aceA Isocitrate lyase 2 Q8VJU4 766 0 24 5.18E-09 9.31E-06 3.58E-07 LP Rv1928c Short-chain type dehydrogenase/reductase P95286 255 26 8 5.18E-09 9.31E-06 3.58E-07 HP PE_PGRS20 PE-PGRS family protein P9WIF9 463 26 11 2.51E-07 0.0005 1.46E-05...”
- Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis
Ko, Journal of bacteriology 2021 (secret) - Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH
Mehra, Journal of bacteriology 2009 - “...0.008 0.002 0.007 0.005 0.002 0.008 Virulence/detoxification MT1966 Rv1123c Rv2641 Rv3648c Rv3874 Rv3890c Rv3891c Rv3017c MT3105 Rv0169 Rv0170 Rv0171 Rv0172...”
- Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
Sreenu, BMC genomics 2006 - “...MB to be a secretory protein that may act as a surface antigen. The ORF MT1966 in MTC encoding a functional isocitrate lyase [ 18 ], is observed to have split into two ORFs (Rv1915 and Rv1916) in MTH due to a single nucleotide deletion in...”
- “...(121) d) Fission with non-overlaping orf (16) T5 4 aceAa, aceAb *Rv1915 (367 *Rv1916 (398) MT1966 (766) Mb1950 (766) G5 6 Conserved hypothetical protein *Rv2561 (97) *Rv2562 (129) MT2638 (212) Mb2591 (245) T2 3 Conserved transmembrane protein Rv3453 (110), *Rv3454 (422) MT3561 (562) Mb3483 (561) C5...”
- Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence
Muñoz-Elías, Nature medicine 2005 - “...locus tag MT0483) and icl2 (Entrez Gene locus tag MT1966) VOLUME 11 | NUMBER 6 | JUNE 2005 NATURE MEDICINE ARTICLES (c) 2005 Nature Publishing Group...”
- Characterization of activity and expression of isocitrate lyase in Mycobacterium avium and Mycobacterium tuberculosis
Höner, Journal of bacteriology 1999 - “...it is read as one continuous ORF in CSU93 (MT1966; The Institute for Genomic Research database). For ease of reference and in light of the current findings,...”
- “...is in contrast to the highly similar ORF in CSU93 (MT1966; TIGR database), as well as a closely related ORF from M. leprae (7), which both show a single,...”
- Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b
Benjak, BMC genomics 2016 - “...tuberculosis sequences, the long version of kdpE was found to be exclusive to 18b. The MT18B_2492 gene, coding for isocitrate lyase (Icl), is intact in 18b, while it is frameshifted in H37Rv. Therefore, 18b possesses two functional isocitrate lyase genes ( icl1 and icl2 ), like...”
6edwB / Q8VJU4 Crystal structure of mycobacterium tuberculosis icl2 in the apo form (see paper)
29% identity, 21% coverage
- Ligand: magnesium ion (6edwB)
6edwC / Q8VJU4 Crystal structure of mycobacterium tuberculosis icl2 in the apo form (see paper)
29% identity, 22% coverage
- Ligand: magnesium ion (6edwC)
ACEA_YARLI / P41555 Isocitrate lyase; ICL; Isocitrase; Isocitratase; Methylisocitrate lyase; MICA; Threo-D(S)-isocitrate glyoxylate-lyase; EC 4.1.3.1; EC 4.1.3.30 from Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica) (see paper)
40% identity, 19% coverage
- function: Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2- methylisocitrate.
catalytic activity: D-threo-isocitrate = glyoxylate + succinate (RHEA:13245)
catalytic activity: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate (RHEA:16809)
cofactor: Mg(2+)
subunit: Homotetramer.
disruption phenotype: Inhibits the utilization of acetate, ethanol, and fatty acids, but also reduces the growth rate on glucose. - Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer
Lajus, Frontiers in bioengineering and biotechnology 2020 - “...to the last 14 amino acids of the Y. lipolytica isocitrate dehydrogenase (Uniprot accession number: P41555 ) was introduced at the C-terminal part of the protein of interest ( Smith et al., 2000 ). For mitochondria targeting, MTS tag corresponds to the first 26 amino acids...”
AFUA_6G02860, Afu6g02860, XP_747790 isocitrate lyase from Aspergillus fumigatus Af293
32% identity, 31% coverage
- Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach
Kaltdorf, Frontiers in molecular biosciences 2016 - “...synthase AFUA_5G07210 0.000 0.588 1.909 AA Homoserine O-acetyltransferase AFUA_4G07360 0.622 0.052 0.000 AA Methionine synthase AFUA_6G02860 0.000 1.827 1.566 GLU 12 2-methylisocitrate lyase AFUA_6G03730 0.668 2.433 1.286 AA 2-methylcitrate hydrolyase AFUA_1G09050 0.000 1.883 0.000 PCS 13 Methylene-fatty-acyl-phospholipid synthase AFUA_4G12990 0.000 1.271 0.000 1416 Thioredoxin reductase AFUA_2G11290...”
- Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Do, BMC genomics 2009 - “...dehydrogenases acyltransferase, putative 2(+) AFU6G03730 2-methyl citrate dehydratase, putative AFU6G03060 MFS monosaccharide transporter, putative 2(+) AFU6G02860 Isocitratelyase AFU6G03730 2-methylcitrate dehydratase, putative 2(+) AFU4G11310 Fructose-1,6-bisphosphatase Fbp1, putative AFU6G02860 Isocitrate lyase 2(+) AFU7G01000 Aldehyde dehydrogenase, putative AFU3G01450 3-methyl-2-oxobutanoate dehydrogenase, putative 2(+) AFU6G14200 Acetyl-CoA-acetyltransferase, putative AFU6G06470 Heatshock protein Hsp30...”
- Genes differentially expressed in conidia and hyphae of Aspergillus fumigatus upon exposure to human neutrophils
Sugui, PloS one 2008 - “...facC Afu2g12530 carnitine acetyl transferase AN6279.2/ acuJ Glyoxylate cycle: Afu4g13510 isocitrate lyase AcuD AN5634.2/ acuD Afu6g02860 isocitrate lyase AN8755.2 Citric acid cycle: Afu6g12930 aconitate hydratase, mitochondrial AN5525.2 Afu3g07810 succinate dehydrogenase subunit Sdh1 AN2916.2 Afu4g12010 2-oxo acid dehydrogenases acyltransferase AN3639.2 Afu5g10370 iron-sulfur protein subunit of succinate Sdh2...”
- Protein kinase A regulates growth, sporulation, and pigment formation in Aspergillus fumigatus
Grosse, Applied and environmental microbiology 2008 - “...synthase Isocitrate lyase (AcuD) AFUA_6G03540 AFUA_6G03540 AFUA_6G03540 AFUA_6G02860 32.4 25.4 37.9 17.4 2.4 2.7 2.7 2.4 Gluconeogenesis 619 2203...”
- Aspergillus fumigatus does not require fatty acid metabolism via isocitrate lyase for development of invasive aspergillosis.
Schöbel, Infection and immunity 2007 - GeneRIF: The glyoxylate cycle from A. fumigatus is not required for the anaplerotic synthesis of oxaloacetate under infectious conditions.
1igwA / P0A9G6 Crystal structure of the isocitrate lyase from the a219c mutant of escherichia coli (see paper)
28% identity, 46% coverage
- Ligand: pyruvic acid (1igwA)
LIC12331 conserved hypothetical protein from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
28% identity, 84% coverage
NP_001233878 isocitrate lyase from Solanum lycopersicum
39% identity, 16% coverage
MAP1643 AceAb from Mycobacterium avium subsp. paratuberculosis str. k10
MAP_1643 isocitrate lyase ICL2 from Mycobacterium avium subsp. paratuberculosis K-10
30% identity, 22% coverage
- Evaluation of Mycobacterium avium subsp. paratuberculosis isocitrate lyase (IcL) and ABC transporter (BacA) knockout mutants as vaccine candidates
Eshraghisamani, Frontiers in cellular and infection microbiology 2023 - “...create two MAP live attenuated strains by knocking out one essential gene ( IcL , MAP1643) and one growth-defect gene ( BacA , MAP1531c) ( Figure1A ). The essential genes are identified to be necessary for MAP growth in vivo and the absence of growth-defect genes...”
- “...us to select a gene to knockout that is essential for MAP survival in vivo (MAP1643, IcL ) or one which is required for intracellular growth (MAP1531c, BacA ) ( EshraghiSamani etal., 2022 ). The results of the current study confirmed the attenuation of these mutants...”
- Profiling bovine antibody responses to Mycobacterium avium subsp. paratuberculosis infection by using protein arrays
Bannantine, Infection and immunity 2008 - “...MAP1345 MAP1388 MAP1416c MAP1417c MAP1609c MAP1636c MAP1643 MAP1655c MAP1730c MAP1931c MAP2077c MAP2116c MAP2121c MAP2121c-His MAP2151 MAP2155 MAP2156 MAP2157...”
- “...is shown in Fig. 1. The largest fusion protein purified was MAP1643 at 127 kDa (Fig. 1), and the smallest protein was MAP4228 at 50.4 kDa (data not shown). The...”
- Early antibody response against Mycobacterium avium subspecies paratuberculosis antigens in subclinical cattle
Bannantine, Proteome science 2008 - “...hits MAP1609c 0.05 987 328/330 antigen 85B, mycolyltransferase MAP1636c 1.12 425 141/157 no BLAST hits MAP1643 0.45 2277 759/762 isocitrate lyase, [beta] module MAP1655c 0.93 381 126 hypothetical protein MAP1730c 0.26 1023 340 putative ATP/GTP-binding protein MAP1931c 0.32 1104 367 anthranilate phosphoribosyltransferase MAP2077c 1.66 330 109...”
- “...1.003 5.292 0 0 G2 MAP1636c 3.286 6.944 13.249 17.272 1.701 0 17.226 12.06 B4 MAP1643 0 4.155 0 1.534 1.827 0 0 0 H8 MAP1655c 2.788 0 0 0 0 2.049 0 0 G6 MAP1730c 1.147 29.831 43.872 52.35 0 12.272 57.799 57.47 B10 MAP1931c...”
- Development and characterization of monoclonal antibodies and aptamers against major antigens of Mycobacterium avium subsp. paratuberculosis
Bannantine, Clinical and vaccine immunology : CVI 2007 - “...library. This approach revealed that MAb 9G10 detects MAP1643 (isocitrate lyase) and that MAb 11G4 detects MAP3840 (a 70-kDa heat shock protein), two proteins...”
- “...MAb 9G10 bound to the C-terminal half of MAP1643. Aptamers, nucleic acids that bind to specific protein sequences, against the hypothetical protein encoded by...”
- Proteome and differential expression analysis of membrane and cytosolic proteins from Mycobacterium avium subsp. paratuberculosis strains K-10 and 187
Radosevich, Journal of bacteriology 2007 - “...paratuberculosis monoclonal antibodies were used in this study. MAP1643 codes for the AceAb protein, MAP3840 codes for the DnaK protein, and MAP2121c codes for...”
- “...available anti-M. avium subsp. paratuberculosis monoclonal antibodies. MAP1643 and MAP3840 are found predominantly in the cytosolic fractions, while MAP2121c is...”
- Defining the stressome of Mycobacterium avium subsp. paratuberculosis in vitro and in naturally infected cows
Wu, Journal of bacteriology 2007 - “...California, Berkeley MAP0834c, prrA MAP1228, lipL MAP3006c, lipN MAP1643, aceAB MAP1872c, mbtH2 MAP4288, lpqP Fold change 7884 WU ET AL. J. BACTERIOL. among...”
- Characterization of Ethanol Extracted Cell Wall Components of Mycobacterium avium Subsp. paratuberculosis
Bannantine, Veterinary sciences 2019 - “...NlpC/P60; peptidoglycan hydrolase 8G6 Murine mAb IgG1 MAP_1272c NlpC/P60; peptidoglycan hydrolase 9G10 Murine mAb IgG2a MAP_1643 Isocitrate lyase, AceAb 8G2 Murine mAb IgG1 MAP_2121c Major membrane protein (MMP) 14G3 Murine mAb IgG2a unknown 14D4 Murine mAb IgG3 MAP_2698c Fatty acid desaturase 6C9 Murine mAb IgG1 MAP_3060c...”
- “...17A12 - - MAP_1272c NlpC/P60 protein 14C5 - - MAP_1272c NlpC/P60 protein 8G6 - - MAP_1643 Isocitrate lyase, AceAb 11F6 - - MAP_2121c Membrane protein 8G2 - - MAP_2121c Membrane protein 13E1 - - MAP_2698c Fatty acid desaturase 14D4 + - MAP_3060c Electron transfer protein 6C9...”
- Membrane and Cytoplasmic Proteins of Mycobacterium avium subspecies paratuberculosis that Bind to Novel Monoclonal Antibodies
Bannantine, Microorganisms 2018 - “...identified as the corresponding antigen for mAbs 11G4 and 13A4, along with isocitrate lyase enzyme (MAP_1643) for mAbs 9G10 and 11F6 [ 4 ]. A proline-rich antigen (MAP_1025) was later identified using a similar screening approach with mAb 17A12 [ 5 ]. However, the remaining five...”
- “...from either library. Three antibodies (1C8, 8C6, and 10D2) bound to the isocitrate lyase protein (MAP_1643), adding to two mAbs (9G10 and 11F6) that had been obtained in a previous study [ 4 ]. Five antibodies bound to acetyl-CoA carboxylase (MAP_3404), three mAbs bound to the...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory