PaperBLAST

PaperBLAST Hits for CA265_RS20885 (81 a.a., MNLTEQVEQA...)

Show query sequence

>CA265_RS20885
MNLTEQVEQALETIRPYLKADGGDVSVEEITSEGTVKLKLLGNCGSCPMSFMTMKSGIEQ
AIMKAVPQITSVVAVNMAEQE

Running BLASTp...

Found 98 similar proteins in the literature:

Npun_R0364 Rieske (2Fe-2S) domain-containing protein from Nostoc punctiforme
50% identity, 26% coverage

• Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133
  Holmqvist, BMC research notes 2011
  • “...strain PCC 7120 asr0689 asr0690 alr0691 alr0692 alr069 Nostoc punctiforme ATCC 29133 Npun_R0366 Npun_R0365 Npun_R0367 Npun_R0364 Npun_R0363 N. punctiforme and Nostoc PCC 7120 are two filamentous, heterocyst forming cyanobacterial strains used in the present study. Both possess an uptake hydrogenase while Nostoc PCC 7120 in addition...”
  • “...reverse CAGCAGGACTAACTAATAAC RT primers N. punctiforme gsp hypF TCGGATTTTCTTGACGAAGG - gsp Npun_R0363 TTCGATTATTTCCAGAATCAGC - gsp Npun_R0364 ATCAGGCACGGTTAAGCATT - Primers to amplify cDNA, generated with random primers, from cultures and isolated heterocysts of Nostoc punctiforme ATCC 29133 and cultures of Nostoc sp. strain PCC 7120 are shown...”

HWX41_RS22890 NifU family protein from Bacillus paramycoides
51% identity, 88% coverage

• Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits
  Adeleke, Plants (Basel, Switzerland) 2021
  • “...3 -like nitrogen fixation protein Nif 3-like HWX41_RS02785/HWX41_RS08235/HWX41_RS00530 nif U nitrogen fixation protein Nif U HWX41_RS22890 nif Flavodoxin HWX41_RS17075 Nitrogen metabolism glt P glutamate/aspartate: proton symporter Glt P HWX41_RS16800 glt X GlutamatetRNA ligase HWX41_RS26220 glnR transcriptional repressor Gln R HWX41_RS05880 gln A gln H type I...”

2z51A / Q93W20 Crystal structure of arabidopsis cnfu involved in iron-sulfur cluster biosynthesis (see paper)
52% identity, 46% coverage

• Ligand: magnesium ion (2z51A)

NIFU2_ARATH / Q93W20 NifU-like protein 2, chloroplastic; AtCNfu2; AtCnfU-V from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
NP_568715 NIFU-like protein 2 from Arabidopsis thaliana
AT5G49940 NFU2 (NIFU-LIKE PROTEIN 2); structural molecule from Arabidopsis thaliana
52% identity, 30% coverage

• function: Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins. Required for biogenesis of ferredoxin, a major photosynthetic electron carrier containing [2Fe-2S] cluster. Required for the assembly of photosystem I complex.
  cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
  subunit: Homodimer; disulfide-linked.
  disruption phenotype: Plants are dwarf with faint pale-green leaves, decreased amount of ferredoxin and impaired photosystem I accumulation.
• Identification of client iron-sulfur proteins of the chloroplastic NFU2 transfer protein in Arabidopsis thaliana.
  Berger, Journal of experimental botany 2020 (PubMed)
  • GeneRIF: Identification of client iron-sulfur proteins of the chloroplastic NFU2 transfer protein in Arabidopsis thaliana.
• Iron-sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots.
  Touraine, Journal of experimental botany 2019 (PubMed)
  • GeneRIF: According to the strong photosynthetic defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2, and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream of HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits.
• Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins.
  Gao, Biochemistry 2013
  • GeneRIF: [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S](2 ) cluster donor for glutaredoxin S16 but not glutaredoxin S14
• Nfu2: a scaffold protein required for [4Fe-4S] and ferredoxin iron-sulphur cluster assembly in Arabidopsis chloroplasts.
  Touraine, The Plant journal : for cell and molecular biology 2004 (PubMed)
  • GeneRIF: requirement of Nfu2 protein for iron-sulfate proteins and ferredoxin cluster assembly [Nfu2]
• Exploration of the molecular mechanism behind a novel natural genic male-sterile mutation of 1205A in Brassica napus
  Xiao, BMC plant biology 2025
  • “...identified a QTL region measuring 181.47kb that exhibited collinearity with the genomic fragment located between At5g49940 and At5g50320 on chromosome 5 in Arabidopsis. This discovery facilitated the identification of 13 candidate genes, ultimately leading to the identification of the candidate gene BnaC03g27700D . Apoptosis-like PCD is...”
• Structure, function, and assembly of PSI in thylakoid membranes of vascular plants
  Rolo, The Plant cell 2024
  • “...AT5G08720 LHCA5 Gramene: AT1G45474 LHCA5 Araport: AT1G45474 LHCA6 Gramene: AT1G19150 LHCA6 Araport: AT1G19150 NFU2 Gramene: AT5G49940 NFU2 Araport: AT5G49940 OTP51 Gramene: AT2G15820 OTP51 Araport: AT2G15820 PBF2 Gramene: AT3G42630 PBF2 Araport: AT3G42630 CEPA1/PBF8 Gramene: AT3G56010 CEPA1/PBF8 Araport: AT3G56010 PSA2 Gramene: AT2G34860 PSA2 Araport: AT2G34860 PsaB Gramene: ATCG00340...”
• Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses
  Han, BMC plant biology 2024
  • “...and proteasomal protein catabolic process (Fig. 3 A). In Cluster 1, transcription levels of the AT5G49940 homologue, the iron-sulfur cluster assembler NFU2 ( CaDEM01G12270 ), and AT3G14250 homologues, RBR E3 ubiquitin ligase genes ( CaDEM03G39660 and CaDEM03G41470 ), were significantly increased, with log 2 |FC| values...”
• Functional relationships of three NFU proteins in the biogenesis of chloroplastic iron-sulfur clusters
  Satyanarayan, Plant direct 2021
  • “...in the GenBank/EMBL databases under the following accession numbers: N FU1 , At4g01940; NFU2 , At5g49940; NFU3 , At4g25910; and ACT2 , At3g18780. CONFLICTS OF INTERESTS The authors declare no conflict of interest. AUTHOR CONTRIBUTIONS M.B.S. and Jun Zhao performed most of the experiments and analyzed...”
• Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae
  Przybyla-Toscano, International journal of molecular sciences 2021
  • “...NFU1 Cre17.g710800 Transfer protein, involved in Fe-S cluster trafficking At4g01940 ( NFU1 ) NFU2 Cre18.g748447 At5g49940 ( NFU2 ) At4g25910 ( NFU3 ) HCF101 Cre01.g045902 Transfer protein, involved in Fe-S cluster trafficking At3g24430 ( HCF101 ) ijms-22-03175-t002_Table 2 Table 2 SUF components in representative microalgae. Sequences...”
• A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3
  Berger, International journal of molecular sciences 2020
  • “...Iron homeostasis NEET At4g01940 NFU1 n.v. n.q. 4Fe4S Fe-S cluster transfer NFU domain protein 1 At5g49940 NFU2 n.q. n.q. 2Fe2S or 4Fe4S Fe-S cluster transfer NFU domain protein 2 At4g25910 NFU3 n.d. n.q. 2Fe2S or 4Fe4S Fe-S cluster transfer NFU domain protein 3 At2g15620 NIR 0.45...”
• Regulation of Iron Homeostasis and Use in Chloroplasts
  Kroh, International journal of molecular sciences 2020
  • “...Cre07.g349600.t1.2 [ 128 ] slr1417 [ 128 ] Nitrogen Fixation U-Like (NFU) (1) AT4G01940 (2) AT5G49940 (3) AT4G25910 (1) Cre18.g748447.t1.1 (2) Cre12.g504150.t2.1 (3) Cre17.g710800.t2.1 [ 128 ] ssl2667 [ 128 ] High Chlorophyll Fluorescence 101 (HCF101) At3g24430 Cre01.g045902.t1.1 [ 128 ] slr0067 [ 128 ] Monothiol...”
• Assembly and Transfer of Iron-Sulfur Clusters in the Plastid
  Lu, Frontiers in plant science 2018
  • “...yeast isu1 nfu1 double mutant Not yet described Lon et al., 2003 Carrier protein NFU2 At5g49940 Carrier of classic 2Fe-2S and 4Fe-4S; complements yeast isu1 nfu1 double mutant Pale green; growth retardation; reduced levels of 2Fe-2S and 4Fe-4S proteins Lon et al., 2003 ; Touraine et...”
• More

Q816B6 NifU protein from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
B7HUU3 NifU domain protein from Bacillus cereus (strain AH187)
BC4952 NifU protein from Bacillus cereus ATCC 14579
49% identity, 88% coverage

• Redox proteomic study of Bacillus cereus thiol proteome during fermentative anaerobic growth
  Hamitouche, BMC genomics 2021
  • “...C NS NS Lipid and Fatty acid metabolism Q814Y7 91 FabZ 3-hydroxyacyl-[acyl-carrier-protein] dehydratase NS NS Q816B6 46/49 NfuA (YutI) NifU protein 1.9 1,68 Q816D2 117 HESB protein NS NS Secondary metabolites biosynthesis, transport and catabolism Q81DQ3 14 DhbC Isochorismate synthase 2.71 3.06 Q81DQ1 67 DhbB Isochorismatase...”
  • “...these classes of proteins, we identified RedCys residues in iron-sulfur cluster proteins such as NifU (Q816B6), which is involved in the biogenesis of bacterial Fe/S proteins, and is thus responsible for several functions, including redox catalysis [ 34 ]. The abundance of NifU increased significantly during...”
• Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature
  Duport, Toxins 2020
  • “...CspD and AcpP and increased for Hpr and B7HXP4, and to a lesser extent for B7HUU3 and B7HS68 ( Figure 4 ). Interestingly, AcpP is a predicted acyl carrier protein linked to fatty acid synthesis regulation in response to cold stress [ 38 ], and CspD...”
  • “...shares extensive sequence similarity with the S-layer Sap protein from B. anthracis [ 40 ]; B7HUU3 is a NifU-containing protein that may contribute to Fe-S cluster assembly in proteins, mainly at low temperatures; and B7HS68 is a predicted component of pathways controlling lipid transport and metabolism....”
• SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
  Yeak, BMC microbiology 2023
  • “...YrdC Isochorismatase -0.7 Q 84 BC0851 YraB Mercuric resistance operon regulatory protein -0.7 K 85 BC4952 YutI NifU protein -0.7 O 86 BC1901 BC1901 Phage protein -0.7 -1.9 S 87 BC3093 BC3093 hypothetical protein -0.7 S 88 BC0873 YckJ Cystine transport system permease protein -0.7 E...”

Tery_3360 nitrogen-fixing NifU-like from Trichodesmium erythraeum IMS101
45% identity, 42% coverage

• Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120
  Agervald, BMC microbiology 2008
  • “...with the exception of additional ORFs within the cluster Trichodesmium erythraeum IMS101 tery_3363 tery_3362 tery_3364 tery_3360 tery_0790 a identical genomic arrangement as the subgroup above, with the exception of additional ORFs within the cluster a Positioned directly upstream hypF with a distance of 3.8 Mb to...”

SYNPCC7002_A1413 NifU like protein from Synechococcus sp. PCC 7002
52% identity, 85% coverage

• Biogenesis of iron-sulfur clusters in photosystem I: holo-NfuA from the cyanobacterium Synechococcus sp. PCC 7002 rapidly and efficiently transfers [4Fe-4S] clusters to apo-PsaC in vitro
  Jin, The Journal of biological chemistry 2008
  • “...Construction of the nfuA Expression Plasmid--The nfuA gene (SYNPCC7002_A1413) was amplified by PCR from chromosomal DNA of Synechococcus sp. PCC 7002 using the...”

BSU32220 putative iron-sulfur scaffold protein from Bacillus subtilis subsp. subtilis str. 168
51% identity, 55% coverage

• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU03950 No BSU32670 BSU32680 BSU32700 BSU32690 BSU32710 BSU05750 BSU32220 Yes Yes Yes Yes Yes No No BSU28390 Yes Metals and iron-sulfur clusters Sodium export...”

alr0692 similar to NifU protein from Nostoc sp. PCC 7120
43% identity, 47% coverage

• Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133
  Holmqvist, BMC research notes 2011
  • “...their homologues in Nostoc punctiforme ATCC 29133 Nostoc sp. strain PCC 7120 asr0689 asr0690 alr0691 alr0692 alr069 Nostoc punctiforme ATCC 29133 Npun_R0366 Npun_R0365 Npun_R0367 Npun_R0364 Npun_R0363 N. punctiforme and Nostoc PCC 7120 are two filamentous, heterocyst forming cyanobacterial strains used in the present study. Both possess...”
  • “...alr0693 homologue Npun_0363 harbor TPR and NHL repeats, respectively. The deduced amino acid sequence of alr0692 was described as being similar to the C-terminal of NifU. When analyzing the homologue of alr0692 in N. punctiforme we found that Npun_R0364 as well was annotated as being similar...”
• The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications
  Stucken, PloS one 2010
  • “...NHL repeat-containing protein alr0693 no no SynJA3, SynJA2, Cya7425, Mcht 186680893 Rieske (2Fe-2S) domain-containing protein alr0692 no no 186680895 hypothetical protein asr0689 no CRC_01692 SynJA3, SynJA2, Cya7425, Mcht 186680897 hupS Ni Fe-hydrogenase small subunit, HupS all0688 no CRC_02736 SynJA3, SynJA2, Cya7425, Mcht 186680898 hupL Ni Fe-hydrogenase...”
• Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120
  Agervald, BMC microbiology 2008
  • “...in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL , and the hyp genes are found in...”
  • “...The four upstream ORFs asr0689, asr0690, alr0691, and alr0693, encode unknown or hypothetical proteins, and alr0692 is annotated as a gene encoding a protein similar to NifU. All proteins have conserved domains; asr0689 and asr0690 encodes possible ABC-transporters with membrane spanning regions, alr0691 encodes a protein...”
• Group 3 sigma factor gene, sigJ, a key regulator of desiccation tolerance, regulates the synthesis of extracellular polysaccharide in cyanobacterium Anabaena sp. strain PCC 7120
  Yoshimura, DNA research : an international journal for rapid publication of reports on genes and genomes 2007
  • “...Probable short-chain dehydrogenase 2.94 0.70 alr0564 Hypothetical protein 2.35 1.02 alr0655 Hypothetical protein 2.08 1.57 alr0692 Similar to NifU protein 2.77 0.81 alr1016 Hypothetical protein 2.41 2.01 alr1183 Unknown protein 2.76 1.30 alr1372 Hypothetical protein 2.27 1.56 alr1534 Hypothetical protein 2.09 0.80 alr2071 Unknown protein 2.13...”

SACOL0939 NifU domain protein from Staphylococcus aureus subsp. aureus COL
44% identity, 86% coverage

• Virulence and Metabolism
  Richardson, Microbiology spectrum 2019 (secret)
• Transcriptomic data for analyzing global gene expression patterns in Methicillin-resistance Staphylococcus aureus in response to spermine and oxacillin stress
  Pawar, Data in brief 2018
  • “...a at 0 0 1.99 2 GLTD sa c7412s6438 a at 0 0 0 2.08 SACOL0939 sa c8086s7067 a at 0 1.6 1.56 0 SACOL0770 sa c8202s7182 a at 0 1.84 0 0 SACOL0706 sa c7993s6980 at 0 0 1.56 0 SACOL0705 sa c7989s6976 at 0...”
• Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
  Tsuchiya, The Biochemical journal 2018
  • “...biosynthesis MoeB protein 37.894 YATLC*GR 87.806 cshB DEAD-box ATP-dependent RNA helicase CshB 51.064 C*NAQPQLIIGTPTR 86.016 SACOL0939 NifU domain protein 7.9651 DGGDC*SLIDVEDGIVK 163.45 SAKOR_00091 Ornithine cyclodeaminase family protein 37.776 VVVDDWSQC*NR 91.592 SA2277 Uncharacterized protein 50.847 TILC*ALDVR 107.34 glnA Glutamine synthetase 50.854 GFTAVC*NPLVNSYK 229.96 glnA Glutamine synthetase 50.854...”
• Importance of bacillithiol in the oxidative stress response of Staphylococcus aureus
  Posada, Infection and immunity 2014
  • “...SACOL0615 SACOL0625 SACOL0632 SACOL0671 SACOL0820 SACOL0939 SACOL1175 SACOL1226 SACOL1294 SACOL1331 SACOL1358 SACOL1359 SACOL1376 SACOL1544 SACOL1548 Homoserine...”

USA300HOU_0897 possible NifU family protein from Staphylococcus aureus subsp. aureus USA300_TCH1516
SA0797 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0936 nitrogen fixation protein NifU from Staphylococcus aureus subsp. aureus Mu50
SAUSA300_0839 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAR0898 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
44% identity, 88% coverage

• Involvement of Small Colony Variant-Related Heme Biosynthesis Genes in Staphylococcus aureus Persister Formation in vitro
  Wang, Frontiers in microbiology 2021
  • “...alsD ), arginine biosynthesis (a rcD3, arcB3 , and arcA3 ), transporters ( USA300HOU_0762 and USA300HOU_0897 ), and a multidrug efflux pump ( USA300HOU_2333 and USA300HOU_2334 ). The RNA-seq results were further confirmed by real-time PCR using the wild type as a control ( Supplementary Table...”
• Identification of N-terminal protein processing sites by chemical labeling mass spectrometry
  Misal, Rapid communications in mass spectrometry : RCM 2019
  • “...M SNNFKDDFEKNR Q Q7A5I6 Elastin-binding protein EbpS Membrane 2 2 4 M PTEDTTMFDQVAEVIER L A0A0H3JM38 SA0797 protein Predicted Cytoplasm/membrane 2 2 5 M AVNLYDYANQLEQALR E Q7A4V3 UPF0342 protein SA1663 Cytoplasm/membrane 12 12 6 M AVFKVFYQHNR D Q99V08 UPF0356 protein SA0941 Cytoplasm/membrane 2 2 7 M AVPNELKY...”
• The application of FAST-NMR for the identification of novel drug discovery targets
  Powers, Drug discovery today 2008
  • “...complex. Rosetta Stone [63] analysis suggests hypothetical protein SAV0936 may be a binding partner of SAV1430. SAV0936 Exhibits 47% sequence identity with the...”
  • “...analysis of SAV1430, based on the results with SAV0936, indicates the protein shares 30% sequence identity with the C-terminal region of the C-terminal domain...”
• FAST-NMR: functional annotation screening technology using NMR spectroscopy
  Mercier, Journal of the American Chemical Society 2006
  • “...indicated a gene fusion for proteins SAV1430 and SAV0936 based on hypothetical proteins Q92GV4 and the Q9ZCQ2 in Rickettsia conorii and Rickettsia proazeki,...”
  • “...for the predicted fusion of genes SAV1430 and SAV0936. BLAST, FASTA and ClustalW were used with the SAV1430 and SAV0936 sequences to identify bacterial...”
• Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
  Xiao, Antibiotics (Basel, Switzerland) 2022
  • “...decarboxylase 16.34 8.94 SAUSA300_1339 hypothetical hypothetical protein 16.25 5.49 SAUSA300_0585 hypothetical hypothetical protein 16.24 13.38 SAUSA300_0839 nfu hypothetical protein 16.23 12.30 SAUSA300_0071 hypothetical ISSep1-like transposase 16.19 3.17 SAUSA300_0651 hypothetical CHAP domain-contain protein 16.09 6.91 SAUSA300_1599 hypothetical hypothetical protein 16.02 7.75 SAUSA300_1607 hypothetical hypothetical protein 16.02 8.76...”
• The A-type domain in Escherichia coli NfuA is required for regenerating the auxiliary [4Fe-4S] cluster in Escherichia coli lipoyl synthase
  McCarthy, The Journal of biological chemistry 2019 (secret)
• Genetic requirements for Staphylococcus aureus nitric oxide resistance and virulence
  Grosser, PLoS pathogens 2018
  • “...determinants such as ldh 1 (SAUSA300_0235), hmp (SAUSA300_0234), pyk (SAUSA300_1644), ccpA (SAUSA300_1682), codY (SAUSA300_1148), nfu (SAUSA300_0839), srrAB (SAUSA300_1442/1) and qoxABD (SAUSA300_0963/2/0) [ 8 , 9 , 12 , 14 , 26 , 27 ]. However, additional genes not previously known to contribute to NO resistance in...”
• The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils
  Roberts, Infection and immunity 2017
  • “...sigB (SAUSA300_2022) acnA::tetM (SAUSA300_1246) nfu (SAUSA300_0839) kat::Tn (ermB) (SAUSA300_1232) nth::Tn (ermB) (SAUSA300_1343) mutY::Tn (ermB)...”
• Staphylococcus aureus SufT: an essential iron-sulphur cluster assembly factor in cells experiencing a high-demand for lipoic acid
  Mashruwala, Molecular microbiology 2016
  • “...study JMB7385 clpC :: tetM lipA :: TN ( ermR ) This work JMB1165 nfu (SAUSA300_0839) ( Mashruwala et al. , 2015 ) JMB2223 sufA::tetM (SAUSA300_0843) ( Rosario-Cruz et al. , 2015 ) JMB2224 sufA::tetM sufT ( Mashruwala et al. , 2016 ) JMB6834 sufA::tetM nfu::kanR...”
  • “...work pEPSA5_ acnA SAUSA300_1246 acnA overexpression ( Mashruwala et al. , 2015 ) pEPSA5_ nfu SAUSA300_0839 nfu overexpression ( Mashruwala et al. , 2015 ) pEPSA5_ sufA SAUSA300_0839 sufA overexpression ( Rosario-Cruz et al. , 2015 ) pCM28 None Genetic complementation ( Pang et al. ,...”
• Nfu facilitates the maturation of iron-sulfur proteins and participates in virulence in Staphylococcus aureus
  Mashruwala, Molecular microbiology 2015
  • “...( Vinella et al. , 2009 )). An additional gene was identified ( nfu ; SAUSA300_0839) that displayed homology to the nfuA and nifU genes from A. vinelandii , but the shared homology is confined to the C-terminal Nfu domains of these proteins ( Dos Santos...”
  • “...the construction of plasmids. Approximately 500 base pairs upstream and downstream of the nfu gene (SAUSA300_0839) was amplified using PCR and the following primer pairs; nfuup5EcoRI and nfuup3NheI; nfudwn3BamHI and nfudwn5MluI. Amplicons were joined by PCR using the nfuup5EcoRI and nfudwn3BamHI primer pair. The PCR product...”
• Bacillithiol has a role in Fe-S cluster biogenesis in Staphylococcus aureus
  Rosario-Cruz, Molecular microbiology 2015
  • “...Barras, 2010 ). Work by our group has shown that the S. aureus nfu gene (SAUSA300_0839) encodes for an Fe-S cluster carrier ( Mashruwala et al. , 2015 ). The S. aureus genome also encodes for a putative A-type Fe-S cluster carrier ( Vinella et al....”
  • “...involved in Fe-S cluster biogenesis. Work in our group has found that the Nfu protein (SAUSA300_0839) can bind and transfer Fe-S clusters in vitro and that a nfu mutant strain has decreased activity of Fe-S cluster requiring proteins in vivo leading to the hypothesis that Nfu...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...homolog 2.17 1.94E-02 SAR0890 conserved hypothetical protein 2.56 8.06E-04 SAR0893 putative membrane protein 2.13 4.74E-02 SAR0898 conserved hypothetical protein 2.70 1.59E-02 SAR0899 conserved hypothetical protein 2.33 4.94E-03 SAR0915 kinase-associated protein B 2.44 8.06E-04 SAR0970 protozoan/cyanobacterial globin family protein 2.38 1.11E-02 SAR0971 conserved hypothetical protein 2.78 1.87E-03...”

NIFU3_ARATH / Q84RQ7 NifU-like protein 3, chloroplastic; AtCNfu3; AtCnfU-IVa from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G25910 NFU3; structural molecule from Arabidopsis thaliana
NP_567735 NFU domain protein 3 from Arabidopsis thaliana
52% identity, 31% coverage

• function: Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins.
  subunit: Homodimer; disulfide-linked.
• Structure, function, and assembly of PSI in thylakoid membranes of vascular plants
  Rolo, The Plant cell 2024
  • “...AT1G24490 LHCA2 Gramene: AT3G61470 LHCA2 Araport: AT3G61470 LHCA3 Gramene: AT1G61520 LHCA3 Araport: AT1G61520 NFU3 Gramene: AT4G25910 NFU3 Araport: AT4G25910 ycf37 Gramene: slr0171 ycf37 Araport: slr0171 HCF101 Gramene: AT3G24430 HCF101 Araport: AT3G24430 PSAF Gramene: AT1G31330 PSAF Araport: AT1G31330 PSAG Gramene: AT1G55670 PSAG Araport: AT1G55670 PSAL Gramene: AT4G12800...”
• Functional relationships of three NFU proteins in the biogenesis of chloroplastic iron-sulfur clusters
  Satyanarayan, Plant direct 2021
  • “...databases under the following accession numbers: N FU1 , At4g01940; NFU2 , At5g49940; NFU3 , At4g25910; and ACT2 , At3g18780. CONFLICTS OF INTERESTS The authors declare no conflict of interest. AUTHOR CONTRIBUTIONS M.B.S. and Jun Zhao performed most of the experiments and analyzed most of the...”
• Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae
  Przybyla-Toscano, International journal of molecular sciences 2021
  • “...involved in Fe-S cluster trafficking At4g01940 ( NFU1 ) NFU2 Cre18.g748447 At5g49940 ( NFU2 ) At4g25910 ( NFU3 ) HCF101 Cre01.g045902 Transfer protein, involved in Fe-S cluster trafficking At3g24430 ( HCF101 ) ijms-22-03175-t002_Table 2 Table 2 SUF components in representative microalgae. Sequences were retrieved in 25...”
• A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3
  Berger, International journal of molecular sciences 2020
  • “...1 At5g49940 NFU2 n.q. n.q. 2Fe2S or 4Fe4S Fe-S cluster transfer NFU domain protein 2 At4g25910 NFU3 n.d. n.q. 2Fe2S or 4Fe4S Fe-S cluster transfer NFU domain protein 3 At2g15620 NIR 0.45 ** n.v. 4Fe4S Nitrate assimilation Nitrite reductase At3g44880 PAO +1.30 * 0.25 * rieske...”
• Regulation of Iron Homeostasis and Use in Chloroplasts
  Kroh, International journal of molecular sciences 2020
  • “...128 ] slr1417 [ 128 ] Nitrogen Fixation U-Like (NFU) (1) AT4G01940 (2) AT5G49940 (3) AT4G25910 (1) Cre18.g748447.t1.1 (2) Cre12.g504150.t2.1 (3) Cre17.g710800.t2.1 [ 128 ] ssl2667 [ 128 ] High Chlorophyll Fluorescence 101 (HCF101) At3g24430 Cre01.g045902.t1.1 [ 128 ] slr0067 [ 128 ] Monothiol Glutaredoxins (GRXS)...”
• Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis
  Leškovï, Plant & cell physiology 2020
  • “...ETHYLENE-INSENSITIVE3-LIKE 1 (EIL1) 0.21 0.0139 Fe cluster assembly AT5G51720 NEET GROUP PROTEIN (NEET) 0.43 0.3219 AT4G25910 NFU DOMAIN PROTEIN 3 (NFU3) 0.25 0.0050 AT2G16710 Iron-sulfur cluster biosynthesis family protein 0.04 0.6154 AT4G01940 NFU DOMAIN PROTEIN 1 (NFU1) 0.01 0.9386 AT3G12260 LYR family of Fe/S cluster biogenesis...”
• Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
  Hu, Frontiers in plant science 2019
  • “...Disease resistance protein Glyma09g06275 AT5G51630 Disease resistance protein Glyma09g06290 AT2G18969 bHLH family transcription factor Glyma09g06300 AT4G25910 NFU domain protein Glyma09g06310 AT5G57340 Ras guanine nucleotide exchange factor Q-like protein Glyma09g06320 AT3G62360 Carbohydrate-binding-like fold Glyma09g06330 AT5G41540 Disease resistance protein Glyma09g06350 AT2G18980 Peroxidase superfamily protein Glyma09g06365 AT1G62520 Sulfated surface-like...”
• Assembly and Transfer of Iron-Sulfur Clusters in the Plastid
  Lu, Frontiers in plant science 2018
  • “...al., 2004 ; Gao et al., 2013 ; Hu et al., 2017a Carrier protein NFU3 At4g25910 Carrier of 3Fe-4S and 4Fe-4S Pale green; growth retardation; reduced levels of 3Fe-4S and 4Fe-4S proteins Lon et al., 2003 ; Nath et al., 2016 , 2017 Carrier protein HCF101...”
• More
• Iron-sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots.
  Touraine, Journal of experimental botany 2019 (PubMed)
  • GeneRIF: According to the strong photosynthetic defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2, and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream of HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits.
• A Nitrogen-Fixing Subunit Essential for Accumulating 4Fe-4S-Containing Photosystem I Core Proteins.
  Nath, Plant physiology 2016
  • GeneRIF: the molecular function of a chloroplastic Nitrogen-fixation-subunit-U type iron-sulfur scaffold protein, NFU3, in Arabidopsis (Arabidopsis thaliana) using genetics approaches, is reported.

LMOf2365_2371 NifU family protein from Listeria monocytogenes str. 4b F2365
46% identity, 86% coverage

• Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
  Chakravarty, Frontiers in microbiology 2021
  • “...LMOf2365_0234 Cysteine synthase A 6.1 6.2 LMOf2365_1038 Putative PTS system, glucose-specific, IIA component 6.3 4.4 LMOf2365_2371 NifU family protein 6.9 27.1 Cah LMOf2365_0827 Carbonic anhydrase 7.1 7.2 LMOf2365_1419 Acetyltransferase, GNAT family 7.3 3.7 trxB LMOf2365_2451 Selenocompound metabolism 8.7 5.0 glnA LMOf2365_1317 Glutamine synthetase, type I 9.9...”
• Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation
  Shu, PloS one 2021
  • “...are important for defense mechanisms, including the Rrf2 family protein gene (LMOf2365_2331), NifU family protein (LMOf2365_2371), FUR family transcriptional regulator (LMOf2365_1986), and GlnR family transcriptional regulator (LMOf2365_1316) ( S1 Table ). In both E . coli and L . monocytogenes , the peculiar gene expression signatures...”

lmo2397 similar to NifU protein from Listeria monocytogenes EGD-e
46% identity, 86% coverage

• Transcriptomic and phenotypic responses of Listeria monocytogenes strains possessing different growth efficiencies under acidic conditions
  Bowman, Applied and environmental microbiology 2010
  • “...or known function pH 5.0 lmo2201, lmo2202 (fabFH) lmo2397 lmo2522 lmo2528-lmo2536 lmo2720 (acs) pH 5.0 SD Fatty acid biosynthesis 1.8, 1.4 1.4, 2.6 1.9,...”
  • “...relate to putative FeS cluster assembly genes (lmo0800, lmo2397, and lmo2411 to -2415), fatty acid biosynthesis (lmo2201 to -2202), regulation of iron uptake...”
• Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
  Oliver, Applied and environmental microbiology 2010
  • “...lmo2167 lmo2208 lmo2216 lmo2217 lmo2223 lmo2232 lmo2240 lmo2397 lmo2415 lmo2507 lmo2547 lmo2633 lmo2660 lmo2664 lmo2665 lmo2666 lmo2667 lmo2668 lmo2758 lmo2791...”
• Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...1.52 1.82 1.22 2.53 2.00 1.05 1.14 1.24 1.02 lmo2397 lmo2433 lmo2452 lmo2468 lmo2827 0.025 0.210 0.285 <0.001 0.201 1.57 1.53 1.25 4.76 1.39 0.633 0.001 0.034...”

WP_060381373 NifU family protein from Flavobacterium covae
45% identity, 91% coverage

• Transcriptome analysis of the fish pathogen Flavobacterium columnare in biofilm suggests calcium role in pathogenesis
  Cai, BMC microbiology 2019
  • “...Iron transfer WP_060383657.1 Iron transporter 2.45 3.7E-13 WP_060383656.1 Ferrous iron transport protein B 1.53 3.2E-09 WP_060381373.1 NifU family protein (iron-sulfur cluster binding) 1.19 4.7E-10 T9SS secretion WP_060382679.1 T9SS C-terminal target domain-containing protein 7.61 8.0E-43 WP_060383582.1 T9SS C-terminal target domain-containing protein 1.58 2.8E-05 WP_060383035.1 T9SS C-terminal target...”
  • “...iron transporter (WP_060383657), ferrous iron transport protein (WP_060383656), and NifU family protein containing iron-sulphur cluster (WP_060381373). There were up to 3 siderophore biosynthesis genes (log2Fc=5.68.2) and 5 TonB dependent receptor genes associated with siderophore transportation (log2Fc=1.16.1) were upregulated totally in the calcium-supplemented medium (Table 2 )....”

SERP0522 NifU domain protein from Staphylococcus epidermidis RP62A
SE0630 nitrogen fixation protein NifU from Staphylococcus epidermidis ATCC 12228
42% identity, 88% coverage

• Silver coordination polymers for prevention of implant infection: thiol interaction, impact on respiratory chain enzymes, and hydroxyl radical induction
  Gordon, Antimicrobial agents and chemotherapy 2010
  • “...SERP2126 SERP0292 SERP0291 SERP0290 SERP0293 SERP1431 SERP0522 SERP0499 Oxidative stress response SERP2194 SERP0500 SERP0151 SERP0728 SERP0432 SERP0059 SERP0060...”
• FAST-NMR: functional annotation screening technology using NMR spectroscopy
  Mercier, Journal of the American Chemical Society 2006
  • “...surface shape and electrostatic charge and potential distributions. SE0630 was preferentially docked to SAV1430 in the same binding site determined by the NMR...”
  • “...Solution Structure Of The Staphylococcus Epidermidis Protein SE0630. Northest Strucutral Genomics Consortium Target SeR8. 2004. PDB-ID: 1XHJ 33. Dos Santos PC,...”

ssl2667 NifU family protein from Synechocystis sp. PCC 6803
49% identity, 89% coverage

• Spectroscopic and functional characterization of the [2Fe-2S] scaffold protein Nfu from Synechocystis PCC6803
  Thompson, Biochimie 2022
  • “...the protein level in Synechocystis . The only nif gene reported for Synechocystis PCC6803 is ssl2667 and corresponds to the formerly named NifU (SyNfu). The SyNfu protein is composed of 76 amino acids and was initially studied based on its sequence homology with the C-terminal domain...”
  • “...of the NFU domain. 2. Material and Methods 2.1 Cloning of SyNfu Synechocystis PCC6803 gene ssl2667 18 , encoding the only NifU-like protein in this cyanobacterium, was synthesized by GenScript. The gene was amplified by PCR to introduce the restriction sites of NdeI and HindIII using...”
• Iron-Sulfur Cluster Biogenesis and Iron Homeostasis in Cyanobacteria
  Gao, Frontiers in microbiology 2020
  • “...chaperone Not studied Uncharacterized Fdx Slr0148 Electron transfer Not studied Uncharacterized NIF system NifU like ssl2667 Fe-S cluster assembly Lethal Nishio and Nakai, 2000 ; Seidler et al., 2001 ; Balasubramanian et al., 2006 FIGURE 1 A proposed principle for the FeS cluster biogenesis. Three FeS...”
• Regulation of Iron Homeostasis and Use in Chloroplasts
  Kroh, International journal of molecular sciences 2020
  • “...(1) AT4G01940 (2) AT5G49940 (3) AT4G25910 (1) Cre18.g748447.t1.1 (2) Cre12.g504150.t2.1 (3) Cre17.g710800.t2.1 [ 128 ] ssl2667 [ 128 ] High Chlorophyll Fluorescence 101 (HCF101) At3g24430 Cre01.g045902.t1.1 [ 128 ] slr0067 [ 128 ] Monothiol Glutaredoxins (GRXS) (14) AT3G54900 (16) AT2G38270 (14) Cre07.g325743.t1.1 (16) Cre01.g047800.t1.1 [ 128...”
• Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803
  Pei, Biotechnology for biofuels 2017
  • “...monomethyl ester cyclase 131 Nc1 0.881 1.274 nc121 3,316,7523,317,151 ><< 108.3 slr1464 Hypothetical protein 17 ssl2667 NifU protein 212 Nc121 (tmRNA) 1.315 0.646 nc81 2,250,4902,250,580 ><> 34.9 ssr3307 Preprotein translocase subunit SecG 16 slr1946 Hypothetical protein 131 Nc81 1.133 3.577 nc110 3,138,6483,138,738 <<< 18.2 sll0737 Hypothetical...”
• Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803
  Wang, Biotechnology for biofuels 2016
  • “...or down-regulation) for a quantitative RT-PCR analysis. Among them, 10 proteins were down-regulated (i.e., Sll0992, Ssl2667, Ssr2061, Slr0447, Sll0541, Slr1019, Sll0482, Slr1856, Sll1087 and Slr1200) and 10 proteins were up-regulated (i.e., Slr0420, Sll1773, Slr0431, Slr1227, Sll1869, Sll0385, Sll1699, Slr0844, Sll1598 and Sll1491) according to the iTRAQ...”
  • “...transporter, sll1491 1.320.49 4.350.03 Periplasmic WD repeat-containing protein Down-regulated sll0992 0.420.01 0.800.08 Conserved hypothetical protein ssl2667 0.510.03 0.680.05 Putative NifU protein ssr2061 0.440.03 0.650.09 Glutaredoxin 3 ( grx3 ) slr0447 0.490.02 0.680.23 Urea/short-chain amide ABC transporter sll0541 0.650.13 0.750.29 Delta -9 desaturase slr1019 0.560.08 1.750.35 PhzF...”
• Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions
  Kopf, The ISME journal 2015
  • “...08) None Slr1255 (2e 135) Ssr3451 (2e 45) Sml0008 (2e 04) Ssl2667 (e 43) Sll1694HL (e 32) Slr1900 (e 49) Slr8038 (3e 39) None None Sll0141 (e 83) Slr2049 (e 59)...”
• Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
  Liu, Biotechnology for biofuels 2012
  • “...2.08 NAD (P) H-quinone oxidoreductioase subunit 2 Sll1262 1.52 NAD (P) H-quinone oxidoreductioase subunit N Ssl2667 2.92 2.82 NifU protein Slr0513 1.58 1.81 1.58 Periplasmic iron-binding protein Slr1160 1.66 1.51 Periplasmic protein, function unknown Slr2144 3.66 Periplasmic protein, function unknown Slr1513 4.31 Periplasmic protein, function unknown...”
• Genome analysis of Chlamydomonas reinhardtii reveals the existence of multiple, compartmentalized iron-sulfur protein assembly machineries of different evolutionary origins
  Godman, Genetics 2008
  • “...SufB SufC SufD SufE Mrp CyaY Grx Mrp HscA HscB Fdx Ssl2667 Slr0077 Ssl2667 Cfd1 Nbp35 Nar1 Cia1 Atm1 Atm1 Atm1 Erv1 Ssq1 Jac1 Mge1 Yfh1 Grx5 Arh1 Yah1 Nfu1...”
• More

DN052_04095 NifU family protein from Acidithiobacillus ferrooxidans
42% identity, 24% coverage

• A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans
  Kucera, Frontiers in microbiology 2020
  • “...[FeS] center in the hup operon. The first candidate is the nifU gene, a locus DN052_04095, which encodes the Rieske protein with [2Fe-2S] iron-sulfur domain. Rieske proteins are components of cytochrome bc 1 (proteobacteria) and b 6 f (cyanobacteria) complexes that are responsible for electron transfer...”

Ava_4600 Nitrogen-fixing NifU-like from Anabaena variabilis ATCC 29413
42% identity, 47% coverage

• Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120
  Agervald, BMC microbiology 2008
  • “...prenyltransferase ava_4599 (97.5) UniProtKB/TrEMBL-Q9WWQ1, IPR001440/PF00515, IPR008940 alr0692 similar to NifU protein NifU (C-terminal), Thioredoxin-like domains ava_4600 (95.6) UniProtKB/TrEMBL-Q8YYZ9, PF01106, COG0694 alr0693 unknown protein NHL and TPR repeats ava_4601 (96.9) UniProtKB/TrEMBL-Q8YYZ8, Q9WWQ1, IPR001258/PF01436 hypF hydrogenase maturation protein Hydrogenase expression/formation protein (HUPF/HYPC) ava_4602 (91.5) hypC hydrogenase expression/formation protein...”
  • “...asr0689 asr0690 alr0691 alr0692 alr0693 identical genomic arrangement Anabaena variabilis ATCC 29413 ava_4597 ava_4598 ava_4599 ava_4600 ava_4601 identical genomic arrangement Nostoc punctiforme PCC 73102 NpR0366 NpR0365 NpR0367 NpR0364 NpR0363 identical genomic arrangement Nodularia spumigena CCY9414 ORF2 ORF3 ORF1 ORF4 ORF5 identical genomic arrangement Lyngbya majuscula CCAP...”

XP_001470367 conserved hypothetical protein from Leishmania infantum JPCM5
52% identity, 20% coverage

• The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis
  Jedelský, PloS one 2011
  • “...EAA38809; Trichomonas, Trichomonas vaginalis , TVAG_146780; Trypanosoma, Trypanosoma brucei , XP_845796; Leishmania, Leishmania infantum , XP_001470367; Toxoplasma, Toxoplasma gondii , XP_002371042; Plasmodium, Plasmodium falciparum , CAX64255; Saccharomyces, Saccharomyces cerevisiae , NP_012884; Homo, Homo sapiens , AAI13695; Rickettsia, Rickettsia prowazekii , NP_221029; Stigmatella, Stigmatella aurantiaca , ZP_01463912....”

I0YUZ0 HIRA-interacting protein 5 from Coccomyxa subellipsoidea (strain C-169)
43% identity, 35% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...(c) E1Z6T8 Chloropicon primus A0A5B8MHP9 QDZ20066.1 A0A5B8MCM2 A0A5B8MHC3 QDZ23877 QDZ21836.1 Coccomyxa subellipsoidea I0Z0B3 (c) XP_005649671.1 I0YUZ0 (c) I0Z768 I0YWN6 I0YSD5 XP_005644009.1 (c) Dunaniella salina KAF5838253 KAF5839176 (c) KAF5837283.1 KAF5830450.1 KAF5832491.1 KAF5832703.1 KAF5833575.1 Gonium pectorale KXZ49215.1 A0A150GMI8 KXZ55931 (c) A0A150GAM8 KXZ42691.1 (c) Haematococcus lacustris GFH16011.1 A0A699ZQI7 GFH07090...”

E1ZCG7 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Chlorella variabilis
44% identity, 32% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...PRW56423.1 A0A2P6TLS6 A0A2P6U0I2 A0A2P6TM18 A0A2P6TMK0 (c) A0A2P6TBX9 Chlorella variabilis XP_005843562.1 (c) XP_005848297.1 (c) XP_005850086.1 (c) E1ZCG7 (c) E1ZMD2 XP_005845092 (c) E1Z6T8 Chloropicon primus A0A5B8MHP9 QDZ20066.1 A0A5B8MCM2 A0A5B8MHC3 QDZ23877 QDZ21836.1 Coccomyxa subellipsoidea I0Z0B3 (c) XP_005649671.1 I0YUZ0 (c) I0Z768 I0YWN6 I0YSD5 XP_005644009.1 (c) Dunaniella salina KAF5838253 KAF5839176 (c)...”

MLD56_21125 NifU family protein from Paenibacillus peoriae
40% identity, 90% coverage

• Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms
  Yuan, Frontiers in microbiology 2022
  • “...protein NifD MLD56_05445 UMY55889.1 NA NA WP_007429043.1 97.93 NA 95.69 nifU Nitrogenase fixation protein NifU MLD56_21125 UMY54031.1 WP_013373004.1 100 WP_013373004.1 100 NA 100 nifE Nitrogenase molybdenum-cofator synthesis protein NifE MLD56_05455 UMY55891.1 NA NA WP_014280099.1 96.91 NA 99.56 nifK Nitrogenase molybdenum-iron protein subunit beta MLD56_RS05450 UMY55890.1 NA...”

CD630_08500 NifU family protein from Clostridioides difficile 630
41% identity, 90% coverage

• Myxopyronin B inhibits growth of a Fidaxomicin-resistant Clostridioides difficile isolate and interferes with toxin synthesis
  Brauer, Gut pathogens 2022
  • “...post Rifaximin administration compared to control cells (Fig. 3 A). Whereas two proteins (CD630_08490 and CD630_08500) were significantly higher abundant in Fidaxomicin-treated cells but only slightly higher abundant in the presence of MyxopyroninB, the other two proteins were exclusively identified in Fidaxomicin- (CD630_08470 and CD630_08480) and...”
  • “...required for DNA and RNA synthesis [ 65 ]. The last gene of the operon, CD630_08500 , encodes for a NifU-like protein. Nif system proteins are involved in the formation of FeS clusters [ 66 ]. The remaining two genes of the operon, CD630_08470 and CD630_08480...”

GPNADHDJ_02081 NfuA family Fe-S biogenesis protein from Stenotrophomonas maltophilia
39% identity, 36% coverage

• Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle
  Alio, Applied and environmental microbiology 2020
  • “...hydrolase GPNADHDJ_04044 Acetyl-CoA C -acyltransferase GPNADHDJ_01835 Sulfoxide reductase catalytic subunit YedY GPNADHDJ_03735 Cupin domain-containing protein GPNADHDJ_02081 Fe-S biogenesis protein NfuA GPNADHDJ_00856 Ax21 family protein GPNADHDJ_01207 ParA family protein GPNADHDJ_02348 DNA-binding response regulator GPNADHDJ_01752 Oar protein S. maltophilia isolate ICU331 EIELFIGP_03830 Fis family transcriptional regulator EIELFIGP_00484 Membrane...”

Sb01g037130 No description from Sorghum bicolor
48% identity, 26% coverage

• Molecular evolution of the Sorghum Maturity Gene Ma3
  Wang, PloS one 2015
  • “...0.00159 0.00000 0.00000 0.00000 f002 Sb01g037090 Sobic.001G391300 0.00561 0.00664 0.00617 0.00491 0.01289 0.00820 0.01092 f003 Sb01g037130 Sobic.001G391900 0.00194 0.00251 0.00239 0.00064 0.00619 0.00370 0.00371 f004 Sb01g037190 no hit 0.01367 0.00437 0.00394 0.00178 0.00265 0.00199 0.00398 f005 Sb01g037235 no hit 0.00378 0.00074 0.00054 0.00000 0.00000 0.00000 0.01325...”
  • “...0.00052 0.00045 0.00068 0.00000 0.00000 f002 Sb01g037090 Sobic.001G391300 0.00561 0.00525 0.00611 0.00504 0.00496 0.00273 f003 Sb01g037130 Sobic.001G391900 0.00194 0.00263 0.00132 0.00295 0.00125 0.00264 f004 Sb01g037190 no hit 0.01367 0.00546 0.00206 0.00650 0.00323 0.00284 f005 Sb01g037235 no hit 0.00378 0.00312 0.00165 0.00196 0.00685 0.00378 f006 Sb01g037280 Sobic.001G393500...”

MSMEG_2718 iron-sulfur cluster-binding protein, Rieske family protein, putative from Mycobacterium smegmatis str. MC2 155
37% identity, 25% coverage

• Putative Iron-Sulfur Proteins Are Required for Hydrogen Consumption and Enhance Survival of Mycobacteria
  Islam, Frontiers in microbiology 2019
  • “...Berney et al., 2014b ). Putative iron-sulfur proteins, tentatively annotated as HucE (MSMEG_2268) and HhyE (MSMEG_2718), were encoded downstream of the hydrogenase structural subunits and may potentially fulfill this role instead ( Berney et al., 2014b ; Greening et al., 2015b ). In this work, we...”
  • “...produce markerless deletions of the genes encoding two putative iron-sulfur proteins, hucE (MSMEG_2268) and hhyE (MSMEG_2718) ( Supplementary Figure S2 ). Briefly, a fragment containing fused left and right flanks of the MSMEG_2268 (1800 bp) and MSMEG_2718 (3098 bp) genes were synthesized by GenScript. These fragments...”
• Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
  Cordero, The Journal of biological chemistry 2019 (secret)
• Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives
  Kruse, BMC genomics 2019
  • “...in close proximity to hhySL in strains Kam1, SolV or V4. A blastP search, using MSMEG_2718 coding for HhyE in Mycobacterium smegmatis strain MC 2 155, against the genomes of strains Kam1, SolV and V4 gave no hits, indicating that they do not possess hhyE genes...”
• A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases
  Greening, Proceedings of the National Academy of Sciences of the United States of America 2014
  • “...other group 5 [NiFe] hydrogenases (17), including Hyd2 (MSMEG_2718) (23), but are absent from most cyanobacterial genomes. We propose that such proteins may...”
• Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia
  Berney, PloS one 2010
  • “...1.5 12.1 hydrogenase assembly chaperone HypC/HupF MSMEG_2713 14.5 1.4 8.9 peptidase M52, hydrogen uptake protein MSMEG_2718 15.4 0.9 3.5 iron-sulfur cluster-binding protein, Rieske family MSMEG_2719 18.2 1.1 6.6 hydrogen:quinone oxidoreductase MSMEG_2720 27.8 1.2 3.1 NADH ubiquinone oxidoreductase, 20 kda subunit MSMEG_2721 hypB 7.9 1.0 1.0 hydrogenase...”
  • “...wild-type parent strain ( Figure 5A ). Complementation of msmeg_2719 with the operon msmeg_2720 - msmeg_2718 , under control of its native promoter, restored growth behavior to wild type levels ( Figure 5B ). The difference in growth yield was significantly greater (40%) when grown in...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...conserved hypothetical protein 2.0 9.8 0.00 94% MSMEG_2716 conserved hypothetical protein 2.1 10.2 0.00 100% MSMEG_2718 iron-sulfur cluster-binding protein, Rieske family protein, putative 2.4 10.3 0.00 95% MSMEG_2719 hydrogen:quinone oxidoreductase 2.7 10.8 0.00 98% MSMEG_2720 NADH ubiquinone oxidoreductase, 20 kda subunit 2.7 11.3 0.00 99% Oxydative...”

AMET1_0462 NifU family protein from Methanonatronarchaeum thermophilum
44% identity, 79% coverage

• Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia"
  Ferrer, Genes 2018
  • “...DOWN (11.8) AMET1_0222 (2R,3R)-3-methylornithine synthase PylB DOWN (10/8) AMET1_0748 Methanogenic corrinoid protein MtaC DOWN (7.0) AMET1_0462 Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain UP (13.7) AMET1_1183 Energy-coupling factor transporter ATP-binding protein EcfA2 UP (5.5) AMET1_0093 ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component UP (5.4) AMET1_1336 HTH domain...”
  • “...KaiC family ATPase FlaH involved in archaellum biogenesis DOWN (8.5) AMET1_0181 Nucleoside 2-deoxyribosyltransferase UP (6.6) AMET1_0462 Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain UP (6.2) AMET1_0880 ABC-type metal ion transport system, periplasmic component/surface adhesin LraI UP (5.9) AMET1_0879 ABC-type Mn/Zn transport system, ATPase component ZhuC UP...”

DET1632 NifU-like protein from Dehalococcoides ethenogenes 195
47% identity, 89% coverage

• Iron Sulfide Enhanced the Dechlorination of Trichloroethene by Dehalococcoides mccartyi Strain 195
  Li, Frontiers in microbiology 2021
  • “...after the addition of FeS, including those responsible for the ironsulfur cluster assembly protein gene (DET1632) and transmembrane transport of iron (DET1503, DET0685), cobalamin (DET0685, DET1139), and molybdenum (DET1161) genes. Meanwhile, the reverse transcription of tceA was increased approximately five times on the 12th day. These...”
  • “...(DET1161), involved in molybdenum transport and periplasmic molybdate binding, was upregulated 2.16 times; the gene (DET1632) encoding ironsulfur cluster assembly protein was upregulated 2.11 times. Given the molybdenum and ironsulfur clusters as the CISM center and the electron transporter, respectively ( Mansfeldt et al., 2014 ;...”

NP_501917 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial from Caenorhabditis elegans
40% identity, 33% coverage

• Allele-specific mitochondrial stress induced by Multiple Mitochondrial Dysfunctions Syndrome 1 pathogenic mutations modeled in Caenorhabditis elegans.
  Kropp, PLoS genetics 2021
  • GeneRIF: Allele-specific mitochondrial stress induced by Multiple Mitochondrial Dysfunctions Syndrome 1 pathogenic mutations modeled in Caenorhabditis elegans.

XP_007510766 nitrogen-fixing NifU domain protein from Bathycoccus prasinos
48% identity, 20% coverage

• Physiological and Proteomic Insights Into Red and Blue Light-Mediated Enhancement of in vitro Growth in Scrophularia kakudensis-A Potential Medicinal Plant
  Manivannan, Frontiers in plant science 2020
  • “...KHN29290 30,653 7.55 ALBINO 3 -like protein 2, chloroplastic Glycine soja 30 68 2.5 2 XP_007510766 32,506 6.86 Nitrogen-fixing NifU domain protein Bathycoccus prasinos 56 44 3.8 3 XP_002532859 25,792 6.11 Proteasome subunit alpha type, putative Ricinus communis 48 50 2.7 4 AAP46638 108,300 8.16 PG1...”

A0A2K3D340 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Chlamydomonas reinhardtii
41% identity, 27% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...Chlamydomonas eustigma GAX73632.1 A0A250XNZ5 A0A250XIU3 GAX75929 A0A250WTW6 GAX72625.1 (c) Chlamydomonas reinhardtii PNW80545.1 PNW87417.1 XP_001693712.1 A0A2K3D318 A0A2K3D340 A8IZ28 A8IZU0 (c) A8IK66 Q6UKY4 A0A2K3D5B5 Chlorella sorokiniana A0A2P6U3X4 PRW56423.1 A0A2P6TLS6 A0A2P6U0I2 A0A2P6TM18 A0A2P6TMK0 (c) A0A2P6TBX9 Chlorella variabilis XP_005843562.1 (c) XP_005848297.1 (c) XP_005850086.1 (c) E1ZCG7 (c) E1ZMD2 XP_005845092 (c) E1Z6T8...”

A4RUX0 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Ostreococcus lucimarinus (strain CCE9901)
43% identity, 33% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...C1MP69 XP_003057174 C1N9A6 XP_003059868.1 (c) Monoraphidium neglectum A0A0D2M031 (c) XP_013897551.1 XP_013898922 A0A0D2MT62 Ostreococcus lucimarinus XP_001415848.1 A4RUX0 A4RYZ0 A4RWG3 XP_001419576 A4S9X3 XP_001416215.1 Ostreococcus tauri XP_003078141.1 XP_003081355.2 XP_022838219.1 0US42676.1 Q01C69 A0A090M6V6 Q01AH9 XP_022839639 Q00SL4 XP_022840717.1 OUS42049.1 (c) Pycnococcus provasolii GHP08054.1 GHP08944.1 (p) Raphidocelis subcapitata A0A2V0PAY6 GBF95838.1 A0A2V0PLS6 A0A2V0PIR9...”

SPBC1709.19c NifU-like protein from Schizosaccharomyces pombe
40% identity, 29% coverage

• Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast
  Mercier, Eukaryotic cell 2008
  • “...3.1 SPAC17G8.06c SPAC343.16 SPBC21H7.07c SPAC1782.11 SPBC27.08c SPBC1709.19c Fe related SPBC1683.10c SPAC23E2.01 pcl1 fep1 Ferrous iron transporter Iron-sensing...”
• Swi5 acts in meiotic DNA joint molecule formation in Schizosaccharomyces pombe
  Ellermeier, Genetics 2004
  • “...genes in common; the largest of these genes is SPBC1709.19c (Figure 1). Substitution of the 1.8-kb HindIII fragment containing ura4 (Grimm et al. 1988) for 2.8...”
  • “...a subclone, designated pHE12-S1.1 and containing all of SPBC1709.19c (Figure 1), failed to complement swi5-39 (data not shown). These results indicated that the...”

PXO_01524 protein GntY from Xanthomonas oryzae pv. oryzae PXO99A
38% identity, 36% coverage

• Deciphering the Role of Tyrosine Sulfation in Xanthomonas oryzae pv. oryzae Using Shotgun Proteomic Analysis
  Park, The plant pathology journal 2016
  • “...protein 1.97 188577175 PXO_01117 UDP-N-acetylglucosamine acyltransferase 1.86 O (post-translational modification, protein turnover, and chaperones) 188577468 PXO_01524 Protein GntY 1.55 Q (secondary metabolites biosynthesis, transport, and catabolism) 188579085 PXO_03211 ABC transporter ATP-binding protein * 188576165 PXO_00406 Acetoacetyl-CoA reductase 1.61 I, R R (general function prediction only) 188576411...”

Francci3_4477 HesB/YadR/YfhF from Frankia sp. CcI3
40% identity, 36% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...Francci3_4475 aminotransferase, class V 2.90 1.52 0.90 Francci3_4476 UBA/THIF-type NAD/FAD binding fold 1.20* 2.08 1.73 Francci3_4477 HesB/YadR/YfhF 2.09 2.00 0.04 Francci3_4478 nitrogenase cofactor biosynthesis protein NifB 1.35 2.17 1.61 Francci3_4479 NifZ 0.54 1.45 2.23 Francci3_4480 nitrogen fixation protein NifW 2.49 2.14 0.16* Francci3_4481 protein of unknown...”

ZP_01463912 NifU domain protein from Stigmatella aurantiaca DW4/3-1
40% identity, 33% coverage

• The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis
  Jedelský, PloS one 2011
  • “...NP_012884; Homo, Homo sapiens , AAI13695; Rickettsia, Rickettsia prowazekii , NP_221029; Stigmatella, Stigmatella aurantiaca , ZP_01463912. (PDF) Click here for additional data file. Figure S2 Sequence alignment of Giardia IscA against eukaryotic and bacterial orthologs. The conserved cysteine residues are highlited in yellow. Organism names and...”

Q9ZCQ2 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Rickettsia prowazekii (strain Madrid E)
RP667 unknown from Rickettsia prowazekii str. Madrid E
42% identity, 38% coverage

• FAST-NMR: functional annotation screening technology using NMR spectroscopy
  Mercier, Journal of the American Chemical Society 2006
  • “...SAV0936 based on hypothetical proteins Q92GV4 and the Q9ZCQ2 in Rickettsia conorii and Rickettsia proazeki, respectively.18 The quality of the predicted fusion...”
• The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer
  van, BMC evolutionary biology 2004
  • “...above with homologous proteins from Azotobacter vinelandii (NifU), Campylobacter jejuni (NifU), Rickettsia prowazekii (NifU and RP667), Saccharomyces cerevisiae (Isu1 and Nfu1), and Homo sapiens (IscU2 and HIRIP5). Both E. histolytica IscU and IscS contain structural motifs typical of FeS assembly proteins. Pfam (PF01106, PF01592), PRODOM (PD002830),...”

A0A2K3D318 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Chlamydomonas reinhardtii
42% identity, 22% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...(p) Chlamydomonas eustigma GAX73632.1 A0A250XNZ5 A0A250XIU3 GAX75929 A0A250WTW6 GAX72625.1 (c) Chlamydomonas reinhardtii PNW80545.1 PNW87417.1 XP_001693712.1 A0A2K3D318 A0A2K3D340 A8IZ28 A8IZU0 (c) A8IK66 Q6UKY4 A0A2K3D5B5 Chlorella sorokiniana A0A2P6U3X4 PRW56423.1 A0A2P6TLS6 A0A2P6U0I2 A0A2P6TM18 A0A2P6TMK0 (c) A0A2P6TBX9 Chlorella variabilis XP_005843562.1 (c) XP_005848297.1 (c) XP_005850086.1 (c) E1ZCG7 (c) E1ZMD2 XP_005845092 (c)...”

Q8Z223 Fe/S biogenesis protein NfuA from Salmonella typhi
42% identity, 37% coverage

• Metabolic Proteins Expression Up-Regulated in Blood-Borne Extensively Drug-Resistant Salmonella Typhi Isolates from Pakistan
  Yasin, Medicina (Kaunas, Lithuania) 2024
  • “...inner-membrane and cytoplasm Antigen A multidrug efflux complex, AdeABC, an outer membrane factor, AdeC. 14 Q8Z223 nfuA Iron-sulfur biogenesis Cytoplasm Antigen vanF of Paenibacillus popilliae ATCC 14706, vanI of Desulfitobacterium hafniense , vanB of Enterococcus faecium and confer resistance to vancomycin. 15 Q8Z7A8 Tpx Antioxidative stress...”

STM3511 putative Thioredoxin-like proteins and domain from Salmonella typhimurium LT2
Q8ZLI7 Fe/S biogenesis protein NfuA from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
42% identity, 37% coverage

• Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium
  Gruzdev, Applied and environmental microbiology 2012
  • “...Stress response dnaK (STM0012) hflB (STM3296) yhgI (STM3511) ydaA (STM 1661) ibpA (STM3809.S) hslU (STM4091) groEL (STM4330) sufD (STM1372) Molecular chaperone...”
• Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses
  Nikaido, Gut pathogens 2012
  • “...bfd Regulatory or redox component complexing with Bfr, in iron storage and mobility 8.0 20 STM3511 yhgI Putative thioredoxin-like proteins and domain 5.7 8.0 STM3606 yhjB Putative transcriptional regulator (LuxR/UhpA familiy) 7.0 20 STM3668 yiaK Putative malate dehydrogenase 7.0 9.2 STM3941 Putative inner membrane protein 8.6...”
• Repression of Salmonella enterica phoP expression by small molecules from physiological bile
  Antunes, Journal of bacteriology 2012
  • “...Common name Gene STM3146 STM3506 STM3150 STM1907 STM3511 STM3465 STM3505 STM1324 STM0629 STM3360 STM1200 STM1121 STM2856 STM3147 STM3302 STM0974 STM2532 STM0441...”
• Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium
  Lamichhane-Khadka, Journal of bacteriology 2011
  • “...2.0 Purine/pyrimidine/nucleotides STM0756 STM4452 STM0012/13 STM0757 STM2277/78 STM3511 STM0523 STM2807 STM2641 nadA nrdD dnaK/J pnuC nrdA/B yhgI allB nrdE nadB...”
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...maturation ND ND -7.504 1.598 ND ND ND ND ND ND Fe/S biogenesis protein NfuA Q8ZLI7 nfuA Protein maturation 2.317 1.761 0.908 0.593 -0.996 1.048 -1.033 1.106 -0.700 0.767 Iron-sulfur cluster assembly scaffold protein IscU Q7CQ11 nifU Protein maturation 9.913 1.176 -1.624 1.512 -8.446 1.151 9.074...”

Q01C69 NIF system FeS cluster assembly, NifU-like scaffold, N-terminal from Ostreococcus tauri
43% identity, 27% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...Ostreococcus lucimarinus XP_001415848.1 A4RUX0 A4RYZ0 A4RWG3 XP_001419576 A4S9X3 XP_001416215.1 Ostreococcus tauri XP_003078141.1 XP_003081355.2 XP_022838219.1 0US42676.1 Q01C69 A0A090M6V6 Q01AH9 XP_022839639 Q00SL4 XP_022840717.1 OUS42049.1 (c) Pycnococcus provasolii GHP08054.1 GHP08944.1 (p) Raphidocelis subcapitata A0A2V0PAY6 GBF95838.1 A0A2V0PLS6 A0A2V0PIR9 GBF88744 A0A2V0NV36 GBF91763.1 Scenedesmus sp. NREL46B-D3 KAF6244147.1 KAF6263471 KAF6260390.1 (c) Scenedesmus sp....”

K8F1V7 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Bathycoccus prasinos
41% identity, 22% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...(c) RMZ55380.1 (c) A0A087SIP0 A0A087SND2 XP_011400182 A0A087SCC7 RMZ53064.1 (c) Bathycoccus prasinos K8FF08 (p) XP_007511837.1 K8F7J7 K8F1V7 XP_007510865 K8FET8 XP_007511602.1 (p) Chlamydomonas eustigma GAX73632.1 A0A250XNZ5 A0A250XIU3 GAX75929 A0A250WTW6 GAX72625.1 (c) Chlamydomonas reinhardtii PNW80545.1 PNW87417.1 XP_001693712.1 A0A2K3D318 A0A2K3D340 A8IZ28 A8IZU0 (c) A8IK66 Q6UKY4 A0A2K3D5B5 Chlorella sorokiniana A0A2P6U3X4 PRW56423.1...”

D3ZA85 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial from Rattus norvegicus
42% identity, 26% coverage

• Global analysis of myocardial peptides containing cysteines with irreversible sulfinic and sulfonic acid post-translational modifications
  Paulech, Molecular & cellular proteomics : MCP 2015 (secret)

MMAR_1868 hypothetical protein from Mycobacterium marinum M
33% identity, 23% coverage

• Revealing of Mycobacterium marinum transcriptome by RNA-seq
  Wang, PloS one 2013
  • “...303 9 3581.075 MMAR_2706 495 3 3222.692 MMAR_2905 261 10 3211.932 MMAR_4784 915 X 3154.366 MMAR_1868 975 X 3115.166 cyp278A1 1284 X 3046.001 * 0 Virulence, detoxification, adaptation; 1 Lipid metabolism; 2 Information pathways; 3 Cell wall and cell processes; 5 Insertion seqs and phage; 6...”

XP_063141883 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial isoform X1 from Rattus norvegicus
41% identity, 27% coverage

• Single Mutation in the NFU1 Gene Metabolically Reprograms Pulmonary Artery Smooth Muscle Cells.
  James, Arteriosclerosis, thrombosis, and vascular biology 2021
  • GeneRIF: Single Mutation in the NFU1 Gene Metabolically Reprograms Pulmonary Artery Smooth Muscle Cells.

NIFU1_ARATH / Q93W77 NifU-like protein 1, chloroplastic; AtCNfu1; AtCnfU-IVb from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G01940 NFU1; structural molecule from Arabidopsis thaliana
NP_567219 NFU domain protein 1 from Arabidopsis thaliana
48% identity, 27% coverage

• function: Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins.
  subunit: Homodimer; disulfide-linked.
• Functional relationships of three NFU proteins in the biogenesis of chloroplastic iron-sulfur clusters
  Satyanarayan, Plant direct 2021
  • “...mutants carry the TDNA insertion in the first exon and the 50bp 5untranslated region of At4g01940, respectively (Figure 5a ). Quantitative reverse transcription (RT)PCR showed that the NFU1 transcript level is substantially decreased in the nfu1 mutants (Figure 5b ). This confirms that nfu11 and nfu12...”
  • “...can be found in the GenBank/EMBL databases under the following accession numbers: N FU1 , At4g01940; NFU2 , At5g49940; NFU3 , At4g25910; and ACT2 , At3g18780. CONFLICTS OF INTERESTS The authors declare no conflict of interest. AUTHOR CONTRIBUTIONS M.B.S. and Jun Zhao performed most of the...”
• Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae
  Przybyla-Toscano, International journal of molecular sciences 2021
  • “...cluster trafficking At1g60990 ( IBA57.2 ) NFU1 Cre17.g710800 Transfer protein, involved in Fe-S cluster trafficking At4g01940 ( NFU1 ) NFU2 Cre18.g748447 At5g49940 ( NFU2 ) At4g25910 ( NFU3 ) HCF101 Cre01.g045902 Transfer protein, involved in Fe-S cluster trafficking At3g24430 ( HCF101 ) ijms-22-03175-t002_Table 2 Table 2...”
• A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3
  Berger, International journal of molecular sciences 2020
  • “...n.v. 2x [4Fe4S] Photosynthesis NADH dehydrogenase subunit At5g51720 NEET n.v. n.v. 2Fe2S Iron homeostasis NEET At4g01940 NFU1 n.v. n.q. 4Fe4S Fe-S cluster transfer NFU domain protein 1 At5g49940 NFU2 n.q. n.q. 2Fe2S or 4Fe4S Fe-S cluster transfer NFU domain protein 2 At4g25910 NFU3 n.d. n.q. 2Fe2S...”
• Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis
  Leškovï, Plant & cell physiology 2020
  • “...NFU DOMAIN PROTEIN 3 (NFU3) 0.25 0.0050 AT2G16710 Iron-sulfur cluster biosynthesis family protein 0.04 0.6154 AT4G01940 NFU DOMAIN PROTEIN 1 (NFU1) 0.01 0.9386 AT3G12260 LYR family of Fe/S cluster biogenesis protein 0.00 0.9823 AT2G26060 CYTOSOLIC IRON-SULFUR PROTEIN ASSEMBLY 1 (CIA1) 0.21 0.0329 AT4G04080 ISCU-LIKE 3 (ISU3)...”
• Regulation of Iron Homeostasis and Use in Chloroplasts
  Kroh, International journal of molecular sciences 2020
  • “...SUFA AT1G10500 Cre07.g349600.t1.2 [ 128 ] slr1417 [ 128 ] Nitrogen Fixation U-Like (NFU) (1) AT4G01940 (2) AT5G49940 (3) AT4G25910 (1) Cre18.g748447.t1.1 (2) Cre12.g504150.t2.1 (3) Cre17.g710800.t2.1 [ 128 ] ssl2667 [ 128 ] High Chlorophyll Fluorescence 101 (HCF101) At3g24430 Cre01.g045902.t1.1 [ 128 ] slr0067 [ 128...”
• Iron-sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots
  Touraine, Journal of experimental botany 2019 (PubMed)
  • “...SUFD (AT1G32500), SUFA1 (AT1G10500), NFU1 (AT4G01940), NFU2 (AT5G49940), NFU3 (AT4G25910), HCF101 (AT3G24430), IBA57.2 (AT1G60990), GRXS14 (AT3G54900),...”
• Assembly and Transfer of Iron-Sulfur Clusters in the Plastid
  Lu, Frontiers in plant science 2018
  • “...No visible phenotype Abdel-Ghany et al., 2005 ; Yabe and Nakai, 2006 Carrier protein NFU1 At4g01940 Complements yeast isu1 nfu1 double mutant Not yet described Lon et al., 2003 Carrier protein NFU2 At5g49940 Carrier of classic 2Fe-2S and 4Fe-4S; complements yeast isu1 nfu1 double mutant Pale...”
• Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins
  Gao, Biochemistry 2013
  • “...by Yeast Two-Hybrid Studies The coding sequences for APR1 (At4g04610) and Nfu1, Nfu2, and Nfu3 (At4g01940, At5g49940, At4g25910, respectively) were cloned into pGAD.T7 and pGBK.T7 (Clontech), respectively, in frame with corresponding Gal4 domains, by introducing APR1 and Nfu CDS at NcoI (5) and BamHI (3) restriction...”
• More
• The plastidial Arabidopsis thaliana NFU1 protein binds and delivers [4Fe-4S] clusters to specific client proteins.
  Roland, The Journal of biological chemistry 2020
  • GeneRIF: The plastidial Arabidopsis thaliana NFU1 protein binds and delivers [4Fe-4S] clusters to specific client proteins.
• Iron-sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots.
  Touraine, Journal of experimental botany 2019 (PubMed)
  • GeneRIF: According to the strong photosynthetic defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2, and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream of HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits.

Q9QZ23 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial from Mus musculus
41% identity, 27% coverage

• Sex-Specific Differences in Oxytocin Receptor Expression and Function for Parental Behavior.
  Mitre, Gender and the genome 2017
• Proteomics analysis of amyloid and nonamyloid prion disease phenotypes reveals both common and divergent mechanisms of neuropathogenesis.
  Moore, Journal of proteome research 2014
  • “...DSTN Destrin 2.5 41 1.6 94 Q5PR73 DIRAS2 GTP-binding protein Di-Ras2 2.7 92 2.3 88 Q9QZ23 NFU1 NFU ironsulfur cluster scaffold homologue, mitochondrial 3.1 74 3.5 67 a Protein identifiers and gene names are from www.uniprot.org . b Fold change in abundance relative to uninfected control....”
• Inhibition of mitochondrial aconitase by succination in fumarate hydratase deficiency.
  Ternette, Cell reports 2013
  • “...176 42.8% 12 Q3UYV9 Ncbp1 nuclear cap-binding protein subunit 1 C44 M(n) 64 31.5% 9 Q9QZ23 Nfu1 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial C213 M(m) 47 43.5% 3 Q9CRB2 Nhp2 H\ACA ribonucleoprotein complex subunit 2 C18 M(n) 22 66.0% 7 Q99LX0 Park7 protein DJ-1 C106 K...”

Q9C8J2 NifU-like protein 5, mitochondrial from Arabidopsis thaliana
AT1G51390 NFU5; ATP binding / structural molecule from Arabidopsis thaliana
43% identity, 24% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...(HSCA1) At5g09590 (HSCA2) At5g06410 At2g44620 (mtACP1) At1g65290 (mtACP2) At5g47630 (mtACP3) At4g03240 UniProt O49543-1 O49627-1 Q9LIG6-1 Q9C8J2 Q8L9E3-1 Q8GUM2 Q9LDZ0 Q8L7K4 P53665 O80800 Q9FGJ4 Q9ZR07 Identified Protein Sequences Organism Auxenochlorella protothecoides A0A087SBH3 (c) RMZ55380.1 (c) A0A087SIP0 A0A087SND2 XP_011400182 A0A087SCC7 RMZ53064.1 (c) Bathycoccus prasinos K8FF08 (p) XP_007511837.1 K8F7J7...”
• Protein lipoylation in mitochondria requires Fe-S cluster assembly factors NFU4 and NFU5
  Przybyla-Toscano, Plant physiology 2022
  • “...are indeed targeted to plastids ( Len et al., 2003 ). NFU4 (AT3G20970) and NFU5 (AT1G51390) are type-II NFU proteins. Mitochondrial localization of Arabidopsis NFU4 was supported by transient expression of a GFP fusion protein ( Len et al., 2003 ). Furthermore, it was shown that...”
  • “...tests are given in figure legends. Accession numbers Accession numbers are as follows: AT3G20970, NFU4; AT1G51390, NFU5; AT4G22220, ISU1; AT2G20860, LIP1. Supplemental data The following materials are available in the online version of this article. Supplemental Figure S1 . NFU4 and NFU5 are localized in the...”
• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...Regulatory protein Chaperone Co-chaperone Regulatory protein Iron donor Arabidopsis thaliana genes At5g65720.1 At4g22220 At3g20970 (NFU4) At1g51390 (NFU5) At5g61220 At4g37910 (HSCA1) At5g09590 (HSCA2) At5g06410 At2g44620 (mtACP1) At1g65290 (mtACP2) At5g47630 (mtACP3) At4g03240 UniProt O49543-1 O49627-1 Q9LIG6-1 Q9C8J2 Q8L9E3-1 Q8GUM2 Q9LDZ0 Q8L7K4 P53665 O80800 Q9FGJ4 Q9ZR07 Identified Protein Sequences...”
• [4Fe-4S] cluster trafficking mediated by Arabidopsis mitochondrial ISCA and NFU proteins
  Azam, The Journal of biological chemistry 2020
  • “...in E. coli, and purification of recombinant proteins The cloning of NFU4 (At3g20970) and NFU5 (At1g51390) in pET3d was described previously ( 65 ). For cloning in pCDF Duet, ISCA1a (At2g16710) was subcloned from pET28a using the NcoI-BamHI restriction sites of pCDF Duet in which ISCA2...”
• Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis
  Leškovï, Plant & cell physiology 2020
  • “...AT2G26060 CYTOSOLIC IRON-SULFUR PROTEIN ASSEMBLY 1 (CIA1) 0.21 0.0329 AT4G04080 ISCU-LIKE 3 (ISU3) 0.09 0.5026 AT1G51390 NFU DOMAIN PROTEIN 5 (NFU5) 0.08 0.3304 AT4G22220 IRON-SULFUR CLUSTER ASSEMBLY PROTEIN 1 (ISU1) 0.07 0.2100 AT1G60990 Chloroplast-localized COG0354 protein 0.03 0.6810 AT3G01020 ISCU-LIKE 2 (ISU2) 0.02 0.6982 AT3G20970 NFU...”
• Mitochondrial Arabidopsis thaliana TRXo Isoforms Bind an Iron⁻Sulfur Cluster and Reduce NFU Proteins In Vitro
  Zannini, Antioxidants (Basel, Switzerland) 2018
  • “...and C40S. The sequences coding for the presumed mature forms of AtNFU4 (At3g20970) and AtNFU5 (At1g51390) were cloned into the Nco I and Bam HI restriction sites of pET3d and the sequence coding for E. coli IscS was cloned into the Nde I and Bam HI...”
• Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA
  Duc, PLoS genetics 2013
  • “...C ) Description of the R1 and R2 read-through transcripts. ( DF ) Characterisation of At1g51390 read-through RNAs. ( D ) Normalised reads mapping to At1g51390At1g51402At1g51400. ( E ) Identification of R1 and R2 contiguous RNAs. Three biological replicates (1, 2 and 3) were used for...”
  • “...read-through RNAs in fpa mutants, using RT-PCR to reveal read-through at the 3 end of At1g51390, for example ( Figure 7D ). A DCL1-dependent nat-siRNA1g51400 has recently been mapped to this genomic region [24] . Using RT-PCR analysis of poly(A)+ RNA, we identified similar read-through RNAs...”
• The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions
  Couturier, Frontiers in plant science 2013
  • “...At2g36260 None yet described ISCA4 At5g03905 None yet described NFU4 At3g20970 None yet described NFU5 At1g51390 None yet described IND1-like/INDH At4g19540 None yet described IBA57.1 At4g12130 Embryo lethal Waller et al., 2012 GRXS15 At3g15660 Sensitivity to H 2 O 2 Cheng, 2008 A. thaliana SUFE1 is...”
• Genome analysis of Chlamydomonas reinhardtii reveals the existence of multiple, compartmentalized iron-sulfur protein assembly machineries of different evolutionary origins
  Godman, Genetics 2008
  • “...At5g65720 At5g61220 At4g22220, At3g01020 At4g04080 At2g16710 At4g12130 At3g20970, At1g51390 At4g05450 A. t. AGI gene model Mit Mitf Mitb Mitb Mit Mit Mitb Mit...”

TGME49_212930 NifU family domain-containing protein from Toxoplasma gondii ME49
34% identity, 22% coverage

• Iron-mediated post-transcriptional regulation in Toxoplasma gondii
  Sloan, PLoS pathogens 2025
  • “...regulated including downregulation of the FeS scaffold ISU1 (TGME49_237560) and the proposed FeS carrier NFU4 (TGME49_212930). The FeS co-chaperone MGE1 (TGME49_265220) and ferredoxin MFdx1 (TGME49_236000) were also downregulated, though fold changes were modest. However, ISD11 and NFS1, which provide sulphur to clusters, were upregulated. Supporting this,...”
• Keeping FIT: Iron-mediated post-transcriptional regulation inToxoplasma gondii
  Sloan, 2023

NFU1_HUMAN / Q9UMS0 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial; HIRA-interacting protein 5 from Homo sapiens (Human) (see 12 papers)
NP_001002755 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial isoform 2 from Homo sapiens
40% identity, 26% coverage

• function: Iron-sulfur cluster scaffold protein which can assemble [4Fe- 4S] clusters and deliver them to target proteins.
  subunit: Monomer and homohexamer; the apo-NFU1 is a monomer, while the holo-NFU1 is a hexamer composed of a trimer of dimer that is probably linked by some 4Fe-4S cluster (PubMed:27818104). Interacts with HIRA and EPM2A/laforin (PubMed:12915448). Interacts with BOLA3 (PubMed:27532772). Interacts with HSPA9 (PubMed:26702583).
• In Vitro Demonstration of Human Lipoyl Synthase Catalytic Activity in the Presence of NFU1
  Warui, ACS bio & med chem Au 2022
  • “...Amino acid sequence alignment of E. coli NfuA ( P63020 ) and human NFU1 ( Q9UMS0 ) showing the two conserved cysteine residues that ligate the FeS cluster highlighted in red. To study the effect of NFU1 on LIAS activity, we first expressed and purified the...”
• A Highly Conserved Iron-Sulfur Cluster Assembly Machinery between Humans and Amoeba Dictyostelium discoideum: The Characterization of Frataxin.
  Olmos, International journal of molecular sciences 2020
  • “...tRNA modification) 13266/3.99 10 42 NFU1NIF system Fe-S cluster scaffold protein LATE STAGE TRANSFER DDB_G0285593/XP_638146 Q9UMS0 37.4/50.1 73/3.00 10 64 pfam08712 (Nfu/NifU N- terminal) 100187/6.63 10 40 pfam01106 (NifU carboxy-terminal) 216282/2.11 10 31 BolA3 DDB_G0274439/XP_639996.1 + Q53S33 26.6/38.7 44/4.00 10 13 COG0271 (BolA Stress-induced morphogen, activity...”
• NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis.
  Cai, Molecules (Basel, Switzerland) 2018
  • “...Mitochondrial encephalomyopathy [ 76 ] [4Fe-4S] Involved in Fe-S cluster transfer to Complex I NFU1 Q9UMS0 Nfu1 Multiple mitochondrial dysfunction syndrome 1 (MMDS1) [ 47 , 48 ] [4Fe-4S] Fe-S delivery to specific recipients ISCA1 Q9BUE6 Isa1 Multiple mitochondrial dysfunction syndrome 5 (MMDS5) [ 77 ,...”
• Structural/Functional Properties of Human NFU1, an Intermediate [4Fe-4S] Carrier in Human Mitochondrial Iron-Sulfur Cluster Biogenesis
  Cai, Structure (London, England : 1993) 2016
  • “...Domains of Human NFU1 High-quality solution NMR structures were determined for both NFU1 NTD (UniProt Q9UMS0 residues 59155) and NFU1 CTD (UniProt residues 162247) ( Figure 1 and Table 1 ). The NTD has a fold with an additional short turn 1 between strand 3 and...”
  • “...them in a coordinated fashion. EXPERIMENTAL PROCEDURES Proteins and Buffers Samples of NFU1 NTD (UniProt: Q9UMS0 residues 59155 with N-terminal tag MGHHHHHHSH), NFU1 CTD (UniProt residues 162247 with N-terminal tag MGHHHHHHSHM), and NFU1(59254) containing both domains (UniProt residues 59254 with N-terminal tag MGSSHHHHHHSSGLVPRGSH) used for studies...”
• Characterization of the human NEK7 interactome suggests catalytic and regulatory properties distinct from those of NEK6.
  de, Journal of proteome research 2014
  • “...mitochondrial ALAS1 P13196 94640/640 0 1 0 1/0 NFU1 iron-sulfur cluster scaffold homologue, mitochondrial NFU1 Q9UMS0 22208/254 1 1 4 1/0 Tubulin beta-2B chain TUBB2B Q9BVA1 247430/445 0 0 1 1/1 Hemoglobin subunit alpha HBA1 P69905 1142/142 0 2 0 1/0 Hemoglobin subunit beta HBB P68871...”
• Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance.
  Tian, Proteomics. Clinical applications 2009
  • “...synthase catalytic subunit A, ubiquitous isoform P38606 6.3 1.35 0.90 1.07 IPI00160021 HIRA-interacting protein 5 Q9UMS0 10.2 1.35 1.17 1.10 IPI00291005 cytosolic malate dehydrogenase P40925 9.9 1.34 0.46 0.95 IPI00007928 PRP8 protein O14547 6.2 1.34 1.02 0.96 IPI00220834 ATP-dependant DNA helicase II P13010 14.1 1.34 1.38...”
• Patient-specific variants of NFU1/NFU-1 disrupt cholinergic signaling in a model of multiple mitochondrial dysfunctions syndrome 1.
  Kropp, Disease models & mechanisms 2023
  • GeneRIF: Patient-specific variants of NFU1/NFU-1 disrupt cholinergic signaling in a model of multiple mitochondrial dysfunctions syndrome 1.
• Structural Plasticity of NFU1 Upon Interaction with Binding Partners: Insights into the Mitochondrial [4Fe-4S] Cluster Pathway.
  Da, Journal of molecular biology 2023
  • GeneRIF: Structural Plasticity of NFU1 Upon Interaction with Binding Partners: Insights into the Mitochondrial [4Fe-4S] Cluster Pathway.
• BOLA3 and NFU1 link mitoribosome iron-sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome.
  Zhong, Nucleic acids research 2023
  • GeneRIF: BOLA3 and NFU1 link mitoribosome iron-sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome.
• Phenotypic continuum of NFU1-related disorders.
  Kaiyrzhanov, Annals of clinical and translational neurology 2022
  • GeneRIF: Phenotypic continuum of NFU1-related disorders.
• ISCA1 Orchestrates ISCA2 and NFU1 in the Maturation of Human Mitochondrial [4Fe-4S] Proteins.
  Suraci, Journal of molecular biology 2021 (PubMed)
  • GeneRIF: ISCA1 Orchestrates ISCA2 and NFU1 in the Maturation of Human Mitochondrial [4Fe-4S] Proteins.
• A pathway for assembling [4Fe-4S]2+ clusters in mitochondrial iron-sulfur protein biogenesis.
  Nasta, The FEBS journal 2020 (PubMed)
  • GeneRIF: A pathway for assembling [4Fe-4S](2+) clusters in mitochondrial iron-sulfur protein biogenesis.
• Multiple mitochondrial dysfunctions syndrome 1: An unusual cause of developmental pulmonary hypertension.
  Birjiniuk, American journal of medical genetics. Part A 2020 (PubMed)
  • GeneRIF: Multiple mitochondrial dysfunctions syndrome 1: An unusual cause of developmental pulmonary hypertension.
• Assembly of the [4Fe-4S] cluster of NFU1 requires the coordinated donation of two [2Fe-2S] clusters from the scaffold proteins, ISCU2 and ISCA1.
  Jain, Human molecular genetics 2020
  • GeneRIF: Assembly of the [4Fe-4S] cluster of NFU1 requires the coordinated donation of two [2Fe-2S] clusters from the scaffold proteins, ISCU2 and ISCA1.
• More

NIFU4_ARATH / Q9LIG6 NifU-like protein 4, mitochondrial; AtNfu-III; AtNfu4 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G20970 NFU4; structural molecule from Arabidopsis thaliana
43% identity, 23% coverage

• function: Molecular scaffold for [Fe-S] cluster assembly of mitochondrial iron-sulfur proteins.
• Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions
  Nose, PloS one 2023
  • “...AT1G71870 0.0 - MATE efflux family protein temp-30d -0.89 2.47E-28 CUST_11442_PI429951308 reCj26118:-SWR:isotig25970 2.56E-18 9.46E-25 1.12E-17 AT3G20970 2.1E-108 ATNFU2 NFU domain protein 4 temp-7d -0.89 2.72E-27 CUST_8195_PI429951308 reCj22821:-SWR:isotig22673 4.54E-20 2.02E-21 3.35E-19 AT3G51840 0.0 ACX4 acyl-CoA oxidase 4 temp-0h -0.88 1.16E-26 CUST_12080_PI429951308 reCj26768:-SWR:isotig26620 2.58E-19 5.01E-22 5.60E-17 AT3G25040 3.0E-116...”
• Protein lipoylation in mitochondria requires Fe-S cluster assembly factors NFU4 and NFU5
  Przybyla-Toscano, Plant physiology 2022
  • “...the plastid-type and are indeed targeted to plastids ( Len et al., 2003 ). NFU4 (AT3G20970) and NFU5 (AT1G51390) are type-II NFU proteins. Mitochondrial localization of Arabidopsis NFU4 was supported by transient expression of a GFP fusion protein ( Len et al., 2003 ). Furthermore, it...”
  • “...the statistical tests are given in figure legends. Accession numbers Accession numbers are as follows: AT3G20970, NFU4; AT1G51390, NFU5; AT4G22220, ISU1; AT2G20860, LIP1. Supplemental data The following materials are available in the online version of this article. Supplemental Figure S1 . NFU4 and NFU5 are localized...”
• Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review
  Ojeda-Martinez, Frontiers in plant science 2021
  • “...AT2G34250), plantpathogen interaction (the calmodulin-like CML24, AT5G37770), or mitochondrial processes (the NFU domain-containing protein NFU4, At3g20970). At later time points, P. brassicae oviposition correlated genes were associated to glutathione metabolism (the glutathione transferase GSTL1, AT5G02780), hormonal signal transduction (the GRAS transcription factor GAI, AT1G14920), apoptosis regulation...”
• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...Scaffold protein Regulatory protein Chaperone Co-chaperone Regulatory protein Iron donor Arabidopsis thaliana genes At5g65720.1 At4g22220 At3g20970 (NFU4) At1g51390 (NFU5) At5g61220 At4g37910 (HSCA1) At5g09590 (HSCA2) At5g06410 At2g44620 (mtACP1) At1g65290 (mtACP2) At5g47630 (mtACP3) At4g03240 UniProt O49543-1 O49627-1 Q9LIG6-1 Q9C8J2 Q8L9E3-1 Q8GUM2 Q9LDZ0 Q8L7K4 P53665 O80800 Q9FGJ4 Q9ZR07 Identified...”
• [4Fe-4S] cluster trafficking mediated by Arabidopsis mitochondrial ISCA and NFU proteins
  Azam, The Journal of biological chemistry 2020
  • “...scans. Cloning, overexpression in E. coli, and purification of recombinant proteins The cloning of NFU4 (At3g20970) and NFU5 (At1g51390) in pET3d was described previously ( 65 ). For cloning in pCDF Duet, ISCA1a (At2g16710) was subcloned from pET28a using the NcoI-BamHI restriction sites of pCDF Duet...”
• Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis
  Leškovï, Plant & cell physiology 2020
  • “...(ISU1) 0.07 0.2100 AT1G60990 Chloroplast-localized COG0354 protein 0.03 0.6810 AT3G01020 ISCU-LIKE 2 (ISU2) 0.02 0.6982 AT3G20970 NFU DOMAIN PROTEIN 4 (NFU4) 0.02 0.8424 * Adjusted P -values >0.05 are in italic. To further assess the degree of interplay between Ni and Fe deficiency, we compared the...”
• Mitochondrial Arabidopsis thaliana TRXo Isoforms Bind an Iron⁻Sulfur Cluster and Reduce NFU Proteins In Vitro
  Zannini, Antioxidants (Basel, Switzerland) 2018
  • “...named TRXo2 C37S and C40S. The sequences coding for the presumed mature forms of AtNFU4 (At3g20970) and AtNFU5 (At1g51390) were cloned into the Nco I and Bam HI restriction sites of pET3d and the sequence coding for E. coli IscS was cloned into the Nde I...”
• The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions
  Couturier, Frontiers in plant science 2013
  • “...At2g16710 None yet described ISCA3 At2g36260 None yet described ISCA4 At5g03905 None yet described NFU4 At3g20970 None yet described NFU5 At1g51390 None yet described IND1-like/INDH At4g19540 None yet described IBA57.1 At4g12130 Embryo lethal Waller et al., 2012 GRXS15 At3g15660 Sensitivity to H 2 O 2 Cheng,...”
• More

FRAAL6802 Hypothetical protein in nifB-nifU intergenic region (ORF2) from Frankia alni ACN14a
38% identity, 38% coverage

• Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24
  Gasser, Scientific reports 2023
  • “...protein FRAAL0596 2.20 4.24E04 Putative regulator FRAAL1002 2.13 3.31E02 Putative cytochrome C biogenesis membrane protein FRAAL6802 erpA 2.13 2.19E02 Conserved hypothetical protein; Thioredoxin-like domain FRAAL6860 2.13 3.70E02 Putative 1L-myo-inositol-1-phosphate synthase FRAAL0060 2.11 1.21E02 Putative transcription regulator protein FRAAL6803 nifB 2.08 2.09E02 FeMo cofactor biosynthesis protein nifB...”
• Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles
  Pujic, International journal of molecular sciences 2023
  • “...nifS Cysteine desulfurase (Nitrogenase metalloclusters biosynthesis protein) FRAAL6801 7408818 hesA Molybdenum cofactor biosynthesis protein hesA FRAAL6802 7409711 erpA Iron-sulfur cluster insertion protein ErpA FRAAL6803 7410328 nifB FeMo cofactor biosynthesis protein nifB FRAAL6805 7412516 nifW Nitrogenase stabilizing/protective protein nifW FRAAL6807 7413131 - Putative NifX-associated protein FRAAL6808 7413571...”
• The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
  Pujic, Microorganisms 2022
  • “...0.003 WP_011607846.1 FRAAL6812 nifD Nitrogenase molybdenumiron protein subunit alpha NifD 86.17 C S 0.002 WP_041939983.1 FRAAL6802 nifU Ironsulfur cluster assembly accessory protein NifU 84.17 O S 0.004 WP_041939982.1 FRAAL6799 korA 2-Oxoglutarate ferredoxin oxidoreductase subunit alpha KorA 82.00 C S 0.001 WP_011602860.1 FRAAL1673 mopB Molybdenum-binding protein MopB...”

XP_845796 HIRA-interacting protein 5, putative from Trypanosoma brucei brucei TREU927
46% identity, 21% coverage

• The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis
  Jedelský, PloS one 2011
  • “...in green. Giardia, Giardia intestinalis EAA38809; Trichomonas, Trichomonas vaginalis , TVAG_146780; Trypanosoma, Trypanosoma brucei , XP_845796; Leishmania, Leishmania infantum , XP_001470367; Toxoplasma, Toxoplasma gondii , XP_002371042; Plasmodium, Plasmodium falciparum , CAX64255; Saccharomyces, Saccharomyces cerevisiae , NP_012884; Homo, Homo sapiens , AAI13695; Rickettsia, Rickettsia prowazekii , NP_221029;...”

CG32857 uncharacterized protein from Drosophila melanogaster
CG32500 uncharacterized protein from Drosophila melanogaster
CG33502 uncharacterized protein from Drosophila melanogaster
Q8SY96 NFU1 iron-sulfur cluster scaffold homolog, mitochondrial from Drosophila melanogaster
39% identity, 24% coverage

• Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins
  Funikov, Scientific reports 2020
  • “...the studied insulator proteins in their promoters. Part of them ( CG17450 , CG33502 , CG32857, CG32820 , CG32819, and CG32500 ) are located within a gene cluster which includes eight closely spaced genes and covers 30Kb of the genome (Fig. S8 ). Such gene cluster...”
• Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation
  Tchurikov, Cells 2020
  • “...not possess any repeated sequences. There are several protein-coding genes ( CG32500 , CG32819 , CG32857 , CG32820 , and CG33502 ) in this area, which are shown on the left flank in Figure 9 . In normal S2 cells, this region has three sites of...”
• Glycogen branching enzyme controls cellular iron homeostasis via Iron Regulatory Protein 1 and mitoNEET
  Huynh, Nature communications 2019
  • “...1.4 >0.05 1.6 1.1E-02 170 CG31548 Short-chain dehydrogenase/reductase 2.7 3.1E-02 1.8 >0.05 1.4 >0.05 173 CG32857 Nfu1 homolog/iron sulfur cluster assembly 2.7 3.7E-02 1.2 >0.05 1.2 >0.05 184 ance Ecdysone biosynthesis/zinc finger 2.7 3.7E-02 2.0 >0.05 1.2 >0.05 202 Alas Heme biosynthesis 2.6 1.5E-02 1.0 >0.05...”
• Recent origins of sperm genes in Drosophila
  Dorus, Molecular biology and evolution 2008
  • “...exists between the ;6-kb region containing genes CG32820/ CG32857 and CG32819/CG33500. RT-PCR assays of the tektin loci demonstrated specific expression in the...”
• Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
  Popovic, International journal of molecular sciences 2021
  • “...is predicted to have cysteine desulphurase activity. We further detected upregulation in the expression of CG32500 , the protein orthologue of the iron-sulphur cluster scaffold protein NFU1 iron-sulphur cluster scaffold, and nucleotide binding protein 1 ( Nubp1 ), a component of the cytosolic Fe-S cluster assembly...”
• Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins
  Funikov, Scientific reports 2020
  • “...their promoters. Part of them ( CG17450 , CG33502 , CG32857, CG32820 , CG32819, and CG32500 ) are located within a gene cluster which includes eight closely spaced genes and covers 30Kb of the genome (Fig. S8 ). Such gene cluster is not typical for the...”
• Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation
  Tchurikov, Cells 2020
  • “...the region that does not possess any repeated sequences. There are several protein-coding genes ( CG32500 , CG32819 , CG32857 , CG32820 , and CG33502 ) in this area, which are shown on the left flank in Figure 9 . In normal S2 cells, this region...”
• [Analysis of the structure and expression of the cluster of Drosophila melanogaster genes DIP1, CG32500, CG32819, and CG14476 in the flamenco gene region]
  Potapova, Genetika 2009 (PubMed)
  • “...which eight open reading frames organized in a cluster were discovered: DIP1, three repeats of CG32500 and CG32819, and CG14476. Analysis of the genes composing the cluster indicates that their transcription in Drosophila melanogaster is a stage-specific process. Comparison of the expression of these genes in...”
• Phenotypic and transcriptomic impact of expressing mammalian TET2 in the Drosophila melanogaster model
  Ismail, Epigenetics 2023
  • “...and 8.95, respectively) ( Figure 5a,b , Supplemental Table S3). Another gene of interest was CG33502 , which encodes a protein involved in iron ion binding activity and iron-sulphur cluster binding activity and is predicted to be involved in iron-sulphur cluster assembly (UniProt, Q8SY96). This gene...”
• The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Drosophila Transcriptome and Metabolome Revealed by Multi-Omics Analysis
  Zhou, Metabolites 2021
  • “...transcripts were Met75Ca , CG42866 , and the most significant downregulated genes were CG30025 , CG33502 , Cpr49Ah , and CG17298 . Gene ontology analysis showed that most differentially expressed genes regulated by sodium butyrate were enriched in key biological processes ( Figure 4 C). Overall,...”
  • “...upregulated genes are Met75Ca , CG42866 , and the most downregulated genes are CG30025 , CG33502 , Cpr49Ah , CG17298 . The microbiome analysis showed that the relative abundance of Gram-positive bacteria was increased and that of Gram-negative bacteria was decreased by sodium butyrate treatment (...”
• Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation
  Tchurikov, Cells 2020
  • “...There are several protein-coding genes ( CG32500 , CG32819 , CG32857 , CG32820 , and CG33502 ) in this area, which are shown on the left flank in Figure 9 . In normal S2 cells, this region has three sites of rDNA contacts, which disappear after...”
• Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins
  Funikov, Scientific reports 2020
  • “...that lack the studied insulator proteins in their promoters. Part of them ( CG17450 , CG33502 , CG32857, CG32820 , CG32819, and CG32500 ) are located within a gene cluster which includes eight closely spaced genes and covers 30Kb of the genome (Fig. S8 ). Such...”
• The Effects of High Fat Diet-Induced Stress on Olfactory Sensitivity, Behaviors, and Transcriptional Profiling in Drosophila melanogaster
  Jung, International journal of molecular sciences 2018
  • “...FBtr0078769 RpL35A FBtr0084410 RpS3 FBgn0034475 Obp56h FBtr0300322 Sfp84E FBgn0033789 CG13324 FBtr0085463 Obp99c FBgn0038203 Or88a FBgn0053502 CG33502 FBtr0088525 RpL31 FBtr0070983 RpL17 FBtr0082370 RpS25 FBtr0087747 CG4716 FBtr0086672 GstE4 FBgn0041625 Or65a FBgn0028416 Met75Ca FBgn0036078 Or67c FBtr0071935 RpS24 FBtr0071096 RpS14b FBtr0075217 CG7630 FBtr0075884 RpS4 FBgn0032008 CG14277 FBtr0300635 CG42502 FBtr0070290 sta...”
• Recent origins of sperm genes in Drosophila
  Dorus, Molecular biology and evolution 2008
  • “...the ancestral region (also including the ancestor of CG33502) created a second region containing either 2162 Dorus et al. FIG. 3.--Maximum likelihood analysis...”
• Phenotypic and transcriptomic impact of expressing mammalian TET2 in the Drosophila melanogaster model
  Ismail, Epigenetics 2023
  • “...iron-sulphur cluster binding activity and is predicted to be involved in iron-sulphur cluster assembly (UniProt, Q8SY96). This gene was significantly upregulated in mTET2-R43G and mTET2-R1261C mutants (LogFC=3.30 and 2.77, respectively). Another alarming finding is that the expression of two genes, huckebein ( hkb ) and ichor...”

C9J8Q1 NFU1 iron-sulfur cluster scaffold (Fragment) from Homo sapiens
41% identity, 66% coverage

• Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
  Gao, Cancer biology & medicine 2015
  • “...protein OS=Homo sapiens GN=SCN1A PE=4 SV=1 - [E9PG49_HUMAN] 0.71 3 1 1 1,981 226.0 5.92 C9J8Q1 Uncharacterized protein OS=Homo sapiens GN=NFU1 PE=4 SV=1 - [C9J8Q1_HUMAN] 6.25 4 1 1 96 10.4 4.12 Q5T045 Novel protein (Fragment) OS=Homo sapiens GN=RP11-480N24.2-002 PE=2 SV=1 - [Q5T045_HUMAN] 21.05 4 1...”

YPO0127 conserved hypothetical protein from Yersinia pestis CO92
YPTB3773 hypothetical protein from Yersinia pseudotuberculosis IP 32953
39% identity, 37% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO3607 conserved hypothetical protein 0.589 (0.014) YPTB3748 YPO0153 conserved hypothetical membrane protein 0.614 (0.033) YPTB3773 YPO0127 conserved hypothetical protein 2.928 (< 0.001) YPTB3897 YPO4045 putative membrane protein 0.609 (0.015) T: signal transduction mechanisms YPTB0022 (ntrC) YPO0022 nitrogen regulation protein 0.723 (0.037) YPTB0035 (spoT) YPO0038 guanosine-3'.5'-bisbis(diphosphate) 3'-pyrophosphydrolase...”
• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...assembly protein iscA 13.0 YPTB2858 Fe-S assembly scaffold iscU 21.7 YPTB2859 cysteine desulfurase iscS 18.7 YPTB3773 Fe-S biogenesis protein nfuA 7.0 Sulfur Metabolism (11) YPTB0759 sulfite reductase, beta (flavoprotein) subunit cysJ 3.7 YPTB0760 sulfite reductase, alpha subunit cysI 2.2 YPTB0761 3-phosphoadenosine 5-phosphosulfate (PAPS) reductase cysH 2.0...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB3622 YPO3607 conserved hypothetical protein 0.589 (0.014) YPTB3748 YPO0153 conserved hypothetical membrane protein 0.614 (0.033) YPTB3773 YPO0127 conserved hypothetical protein 2.928 (< 0.001) YPTB3897 YPO4045 putative membrane protein 0.609 (0.015) T: signal transduction mechanisms YPTB0022 (ntrC) YPO0022 nitrogen regulation protein 0.723 (0.037) YPTB0035 (spoT) YPO0038 guanosine-3'.5'-bisbis(diphosphate)...”

YhgI / b3414 iron-sulfur cluster carrier protein NfuA from Escherichia coli K-12 substr. MG1655 (see 15 papers)
nfuA / P63020 iron-sulfur cluster carrier protein NfuA from Escherichia coli (strain K12) (see 13 papers)
NFUA_ECOLI / P63020 Fe/S biogenesis protein NfuA from Escherichia coli (strain K12) (see 4 papers)
nfuA / GB|AAC76439.1 Fe/S-biogenesis protein NfuA from Escherichia coli K12 (see 7 papers)
b3414 predicted gluconate transport associated protein from Escherichia coli str. K-12 substr. MG1655
NP_417873 iron-sulfur cluster carrier protein NfuA from Escherichia coli str. K-12 substr. MG1655
Z4769 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs4256 hypothetical protein from Escherichia coli O157:H7 str. Sakai
B21_RS17040 Fe-S biogenesis protein NfuA from Escherichia coli BL21(DE3)
39% identity, 37% coverage

• function: Involved in iron-sulfur cluster biogenesis under severe conditions such as iron starvation or oxidative stress. Binds a 4Fe-4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe/S proteins. Could also act as a scaffold/chaperone for damaged Fe/S proteins. Required for E.coli to sustain oxidative stress and iron starvation. Also necessary for the use of extracellular DNA as the sole source of carbon and energy.
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit.) The cluster is presumably bound at the interface of two monomers
  subunit: Homodimer.
  disruption phenotype: Cells express the stationary phase-specific competition-defective (SPCD) phenotype and are unable to catabolize dsDNA.
• Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
  Yung, Scientific reports 2016
  • “...3.81 3.07 2.00 Isc operon repressor; suf operon activator Regulator chp cp nmp nms t b3414 nfuA 0.66 1.31 1.71 0.5 0.23 1.75 1.41 1.32 Fe/S biogenesis protein; putative scaffold/chaperone Fe/S carrier b chp cp dms nmp nms b4705 mntS 1.14 2.06 2.34 0.89 1.12 2.64...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...structure and biogenesis ECs2571 b1861 ECs3536 ECs4256 b2673 b3414 ECs1715 ECs3045 ECs0502 b1210 b2153 b0448 ECs4194 ECs3393 ECs3306 ECs4898 ECs1752 b2435 b3967...”
• Sxy induces a CRP-S regulon in Escherichia coli
  Sinha, Journal of bacteriology 2009
  • “...smf (b4473) yifB (b3765) yicR (b3638) ssb (b4059) gntY (b3414) comG ssb radC comM dprA comQ comP pulJ/comO pulG/comN comE1 rec-2 pilD Downstream of comABCDEF in...”
• Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient
  Palchevskiy, Journal of bacteriology 2006
  • “...University of California, Berkeley b3395 b3394 b3393 b3392 b3391 b3413 b3414 b3499 H. influenzae gene 3909 3910 29. 30. 31. 32. 34. 35. 36. 37. 38. 39. 40. 41....”
• Escherichia coli nfuA is essential for maintenance of Shiga toxin phage Min27 lysogeny under iron-depleted condition.
  Cao, FEMS microbiology letters 2015 (PubMed)
  • GeneRIF: E. coli K12 MG1655 and its lysogenic strain carrying Stx2-encoding PhiMin27 followed by gene deletion, we provided clear evidence here that NfuA plays an important role in Fe metabolism and maintenance of Stx prophagy lysogeny.
• Physical and functional interactions of a monothiol glutaredoxin and an iron sulfur cluster carrier protein with the sulfur-donating radical S-adenosyl-L-methionine enzyme MiaB.
  Boutigny, The Journal of biological chemistry 2013
  • GeneRIF: GrxD and NfuA could play complementary roles in maturation and repair of MiaB
• Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.
  Py, Molecular microbiology 2012 (PubMed)
  • GeneRIF: In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide.
• In Vitro Demonstration of Human Lipoyl Synthase Catalytic Activity in the Presence of NFU1
  Warui, ACS bio & med chem Au 2022
  • “...relevant. 64 , 80 Figure 4 Amino acid sequence alignment of E. coli NfuA ( P63020 ) and human NFU1 ( Q9UMS0 ) showing the two conserved cysteine residues that ligate the FeS cluster highlighted in red. To study the effect of NFU1 on LIAS activity,...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...regulator 6.41/36,422.02 GntY (YhgI) Gor P63020 Protein GntY 4.52/20,997.70 P06715 Glutathione reductase 5.64/48,772.51 4.72/19,718 (4-5) 4.96/19,460...”
• Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933
  Bender, Applied and environmental microbiology 2012
  • “...by University of California, Berkeley Z3242 Z3796 Z3797 Z3907 Z4769 Z5105 Z5107 Z5112 Z5122 Z5137 Z5138 Z5182 Z5183 Z5204 Z5232 Z5233 Z5478 Z5479 Gene titative...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ribosomal structure and biogenesis ECs2571 b1861 ECs3536 ECs4256 b2673 b3414 ECs1715 ECs3045 ECs0502 b1210 b2153 b0448 ECs4194 ECs3393 ECs3306 ECs4898 ECs1752...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs3887 ECs3906 ECs3953 ECs3983 ECs4034 ECs4158 ECs4204 ECs4256 ECs4294 ECs4335 ECs4357 ECs4361 ECs4384 ECs4453 ECs4554 ECs4571 ECs4584 ECs4585 ECs4599 pchB...”
• Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
  Chen, mSystems 2021
  • “...dehydrogenase flavoprotein subunit SDH1 CHLRE_17g696600v5 0.55 <0.001 Fumarate reductase B21_RS12840 0.72 <0.001 l -Aspartate oxidase B21_RS17040 0.32 0.003 Fe-S biogenesis protein NfuA YKL040C 0.77 <0.001 Iron ion binding CHLRE_18g748447v5 2.23 <0.001 Iron-sulfur cluster assembly B21_RS16650 1.56 <0.001 Elongation factor YJL102W 0.57 <0.001 Elongation factor CHLRE_13g564950v5 1.17...”

RSP_2214 Nitrogen-fixing NifU from Rhodobacter sphaeroides 2.4.1
33% identity, 40% coverage

• Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
  Dufour, PLoS genetics 2012
  • “...RSP_1238, RSP_1241, RSP_1360, RSP_1406, RSP_1549, RSP_1563, RSP_1573, RSP_1581, RSP_1615, RSP_1671, RSP_1684, RSP_1743, RSP_1852, RSP_2121, RSP_2125, RSP_2214, RSP_2219, RSP_2387, RSP_2638, RSP_2640, RSP_2641, RSP_2739, RSP_2763, RSP_2764, RSP_2816, RSP_2952, RSP_2953, RSP_3067, RSP_3068, RSP_3378, RSP_3426, RSP_3552, RSP_3597, RSP_3598, RSP_3634, RSP_3809, RSP_3810, RSP_4244, RSP_4245, RSP_4248, RSP_4305 RpoHII regulon (99 genes) Energy...”

CC0062, CC_0062 NifU-like domain protein from Caulobacter crescentus CB15
38% identity, 30% coverage

• Global transcriptional response of Caulobacter crescentus to iron availability
  da, BMC genomics 2013
  • “...2.49 CC_3686 CCNA_03800 Diaminopimelate epimerase 2.25 Iron-sulfur cluster assembly/repair CC_0061 CCNA_00059 Oxygen-insensitive NADH nitroreductase 3.31 CC_0062 CCNA_00060 Mitochondrial-type Fe-S cluster assembly protein NFU 4.60 CC_0132 b CCNA_00131 Rrf2 family protein 3.30 CC_1857 CCNA_01933 Hypothetical protein 5.66 CC_1858 CCNA_01934 HesB protein family 5.66 CC_1859 CCNA_01935 FeS assembly...”
• Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
  Hu, Journal of bacteriology 2005
  • “...I (tetrahydrofolate biosythesis pathway) CC3557 2.2 CC1316 CC2434 CC0062 CC0110 CC3539 CC2505 CC0994 3.2 2.2 2.4 2 2.3 2.3 2.5 CC1039 2.3 CC0141 CC0885...”
  • “...this study, we noted three thioredoxin-coding transcripts (CC0062, CC0110, and CC3539) that were up-regulated Downloaded from http://jb.asm.org/ on February 10,...”

CCNA_00060 mitochondrial-type Fe-S cluster assembly protein NFU from Caulobacter crescentus NA1000
38% identity, 35% coverage

• The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter
  de, Microbiology spectrum 2023
  • “...Genes upregulated in low iron independent of FUR a CCNA_00059 1.427 1.124E-18 Oxygen-insensitive NADH nitroreductase CCNA_00060 1.028 1.517E-12 Mitochondrial-type Fe-S cluster assembly protein NFU CCNA_00722 1.096 9.184E-24 Chaperonin GroES CCNA_01376 1.04 3.043E-08 Glutathione S-transferase CCNA_02213 1.154 1.008E-10 Old yellow enzyme-family NADH:flavin oxidoreductase CCNA_02341 1.324 1.596E-06 Small...”
• Global transcriptional response of Caulobacter crescentus to iron availability
  da, BMC genomics 2013
  • “...CC_3686 CCNA_03800 Diaminopimelate epimerase 2.25 Iron-sulfur cluster assembly/repair CC_0061 CCNA_00059 Oxygen-insensitive NADH nitroreductase 3.31 CC_0062 CCNA_00060 Mitochondrial-type Fe-S cluster assembly protein NFU 4.60 CC_0132 b CCNA_00131 Rrf2 family protein 3.30 CC_1857 CCNA_01933 Hypothetical protein 5.66 CC_1858 CCNA_01934 HesB protein family 5.66 CC_1859 CCNA_01935 FeS assembly SUF...”

RLV_2767 NifU family protein from Rhizobium leguminosarum bv. viciae
35% identity, 36% coverage

• A microaerobically induced small heat shock protein contributes to <i>Rhizobium leguminosarum</i>/<i>Pisum sativum</i> symbiosis and interacts with a wide range of bacteroid proteins
  Domingo-Serrano, Applied and environmental microbiology 2025
  • “...protein beta chain (NifK) 1,356 4 379 1 RLV_1892 Protein (FixC) 116 29 54 139 RLV_2767 Scaffold Nfu/NifU N terminal family protein (NifU) 100 32 76 77 RLV_1839 Nitrogenase FeMo cofactor biosynthesis protein (NifN) 72 49 60 84 Stress-related proteins RLV_1399 Hsp20/alpha crystallin family protein 2,018...”

C1DLW0 Fe/S biogenesis protein NfuA from Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
37% identity, 36% coverage

• Biosynthesis of Nitrogenase Cofactors
  Burén, Chemical reviews 2020
  • “...NifU-2 truncated variants and with the homologous proteins IscU (Uniprot C1DE67) and human NfU (Uniprot C1DLW0). Conserved domains are color coded. % Identity and similarity between NifU and NfU or IscU are shown to the right. (C). Structural model of the N-terminal domain of NifU generated...”

NFU1_YEAST / P32860 NifU-like protein, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
NP_012884 Nfu1p from Saccharomyces cerevisiae S288C
NP_012884, YKL040C Nfu1p from Saccharomyces cerevisiae
37% identity, 31% coverage

• function: Involved in iron homeostasis within the mitochondrion where it is involved in the assembly of iron-sulfur proteins (PubMed:10468587, PubMed:27532773). Together with BOL3, required during the last step of iron-sulfur protein assembly when the iron-sulfur cluster is inserted into the target protein (PubMed:27532773). Required for protecting iron sulfur clusters from oxidative damage (PubMed:27532773).
  subunit: Homodimer; in absence of BOL3, probably bridged by an iron- sulfure cluster (PubMed:27532773). Interacts with BOL3 (PubMed:27532773). Interacts with apo-target proteins, such as ACO1, LYS4, ACO2 and SDH2 (PubMed:27532773).
  disruption phenotype: Cells are impaired in growth on synthetic complete medium with acetate as a carbon source due to defects in mitochondrial [4Fe-4S] cluster formation.
• Role of Nfu1 and Bol3 in iron-sulfur cluster transfer to mitochondrial clients.
  Melber, eLife 2016
  • GeneRIF: Additional studies focused on the mitochondrial BolA proteins, Bol1 and Bol3 (yeast homolog to human BOLA3), revealing that Bol1 functions earlier in iron-sulfur biogenesis with the monothiol glutaredoxin, Grx5, and Bol3 functions late with Nfu1.
• Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
  Chen, mSystems 2021
  • “...Fumarate reductase B21_RS12840 0.72 <0.001 l -Aspartate oxidase B21_RS17040 0.32 0.003 Fe-S biogenesis protein NfuA YKL040C 0.77 <0.001 Iron ion binding CHLRE_18g748447v5 2.23 <0.001 Iron-sulfur cluster assembly B21_RS16650 1.56 <0.001 Elongation factor YJL102W 0.57 <0.001 Elongation factor CHLRE_13g564950v5 1.17 <0.001 Elongation factor B21_RS12810 0.39 <0.001 Elongation...”
• Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
  Stenger, Microbial cell (Graz, Austria) 2020
  • “...FUM1 YPL262W MET7 YOR241W AIM22 YJL046W FZO1 YBR179C MGM1 YOR211C CAT5 YOR125C GCV3 YAL044C NFU1 YKL040C CEM1 YER061C GGC1 YDL198C OAR1 YKL055C COQ1 YBR003W GRX5 YPL059W OCT1 YKL134C COQ10 YOL008W HEM14 YER014W OXA1 YER154W COQ2 YNR041C HTD2 YHR067W PPA2 YMR267W COQ3 YOL096C IBA57 YJR122W PPT2 YPL148C...”
• The Recent De Novo Origin of Protein C-Termini
  Andreatta, Genome biology and evolution 2015
  • “...397 24 63 Frameshift 2 Strong Strong Alpha-1,6-mannosyltransferase activity; involved in cell wall mannan biosynthesis YKL040C NFU1 S. par 257 34 48 Frameshift 2 Strong Strong Involved in iron metabolism in mitochondria YKL212W SAC1 S. cer 624 5 7 Frameshift 2 Strong Strong Phosphatidylinositol phosphate phosphatase...”
• Functional genomics indicates yeast requires Golgi/ER transport, chromatin remodeling, and DNA repair for low dose DMSO tolerance
  Gaytán, Frontiers in genetics 2013
  • “...YGR089W NNF2 1.08 Interacts physically and genetically with Rpb8p (a subunit of RNA pols. I/II/III) YKL040C NFU1 1.06 Involved in iron metabolism in mitochondria YAL015C NTG1 1.05 DNA N-glycosylase and AP lyase involved in base excision repair S YGR108W CLB1 1.03 B-type cyclin involved in cell...”
• Inaccurately assembled cytochrome c oxidase can lead to oxidative stress-induced growth arrest
  Bode, Antioxidants & redox signaling 2013
  • “...YIL153W RRD1 Reduced Reduced Strong Minor Strong None YKL040C NFU1 Poor Reduced Minor Strong None None YBL082C ALG3 Reduced Reduced Strong None Minor None...”
• Expression profiling reveals an unexpected growth-stimulating effect of surplus iron on the yeast Saccharomyces cerevisiae
  Du, Molecules and cells 2012
  • “...stator stalk of mitochondrial F1Fo ATP synthase NFU1 YKL040C 2.33 1 Protein involved in iron metabolism in mitochondria PBI2 YNL015W 2.26 1 Cytosolic inhibitor...”
• The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis
  Jedelský, PloS one 2011
  • “...XP_001470367; Toxoplasma, Toxoplasma gondii , XP_002371042; Plasmodium, Plasmodium falciparum , CAX64255; Saccharomyces, Saccharomyces cerevisiae , NP_012884; Homo, Homo sapiens , AAI13695; Rickettsia, Rickettsia prowazekii , NP_221029; Stigmatella, Stigmatella aurantiaca , ZP_01463912. (PDF) Click here for additional data file. Figure S2 Sequence alignment of Giardia IscA against...”
• Genome-wide functional profiling reveals genes required for tolerance to benzene metabolites in yeast
  North, PloS one 2011
  • “...3.4 YNL148C ALF1 1.9 2.5 3.9 YGR139W 1.7 1.5 1.5 YHR030C SLT2 1.6 2.7 3.3 YKL040C NFU1 1.4 1.9 2.1 YIL162W SUC2 3.8 4.4 4.1 YMR022W UBC7 2.4 2.4 2.2 YBR035C PDX3 2.4 2.4 2.3 YPR074C TKL1 2.3 3.1 3.8 YDL225W SHS1 1.8 3.2 2.9 YDR112W...”
• More

RL0400 putative nifU iron-sulphur cluster scaffold protein from Rhizobium leguminosarum bv. viciae 3841
35% identity, 36% coverage

• The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability
  Todd, Molecular genetics and genomics : MGG 2006 (PubMed)
  • “...synthesis; rirA, a global, Fe-responsive transcriptional repressor; RL0400, which likely encodes an unusual FeS cluster scaffold; and the possible...”
  • “...cgcagtttagaacaaGCGgGGGcttgcatggcgatcc ggatcgccatgcaagCCCcCGCttgttctaaactgcg Amplifies RL0400 promoter Amplifies RL0400 promoter Used for...”

C1EHF7 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Micromonas commoda (strain RCC299 / NOUM17 / CCMP2709)
38% identity, 23% coverage

• Fe-S Protein Synthesis in Green Algae Mitochondria
  Gomez-Casati, Plants (Basel, Switzerland) 2021
  • “...(c) A0A2P6V9W1 A0A2P6VEW0 A0A2P6VHZ4 PSC73872 A0A2P6VF08 Micromonas commoda XP_002506217.1 (c) XP_002501646.1 (c) XP_002502856.1 XP_002507274.1 (c) C1EHF7 C1E8J2 C1EGS6 XP_002505982.1 C1E2X1 XP_002504509.1 Micromonas pusilla XP_003055300.1 C1MZU9 C1MP69 XP_003057174 C1N9A6 XP_003059868.1 (c) Monoraphidium neglectum A0A0D2M031 (c) XP_013897551.1 XP_013898922 A0A0D2MT62 Ostreococcus lucimarinus XP_001415848.1 A4RUX0 A4RYZ0 A4RWG3 XP_001419576 A4S9X3 XP_001416215.1...”

AFUA_1G04680 NifU-related protein from Aspergillus fumigatus Af293
38% identity, 24% coverage

• Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus
  Amich, PLoS pathogens 2013
  • “...0,00081 AFUA_5G11260 siderophore transcription factor SreA 0.505 3,0E-06 AFUA_1G15970 aldo-keto reductase (AKR13), putative 0.510 0,00262 AFUA_1G04680 NifU-related protein 0.534 0,00080 AFUA_4G11240 -aminoadipate reductase large subunit, putative 0.545 0,00090 AFUA_4G12530 vacuolar iron importer CccA 0.552 2,0E-05 AFUA_3G09970 vacuolar iron importer, putative 0.558 0,00150 AFUA_2G10690 MFS phosphate transporter,...”

A0QUN2 Rieske domain-containing protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2268 hypothetical protein from Mycobacterium smegmatis str. MC2 155
38% identity, 24% coverage

• A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations.
  Giddey, Scientific reports 2017
  • “...MSMEG_2264 1.48 1.02E-04 57.7 P0CH00/P0CG99 Ribonucleoside-diphosphate reductase subunit alpha 1/alpha 2 nrdE2 1.51 3.06E-03 78.8 A0QUN2 Rieske (2Fe-2S) region MSMEG_2268 1.54 6.79E-05 50.2 A0QXA8 Cytochrome D ubiquinol oxidase subunit 1 cydA 1.56 1.08E-04 17.2 A0R3I6 Peptidase S1 and S6, chymotrypsin/Hap MSMEG_5486 1.64 3.41E-03 65.1 A0QTK6 S30AE...”
• Putative Iron-Sulfur Proteins Are Required for Hydrogen Consumption and Enhance Survival of Mycobacteria
  Islam, Frontiers in microbiology 2019
  • “...S1 ) ( Berney et al., 2014b ). Putative iron-sulfur proteins, tentatively annotated as HucE (MSMEG_2268) and HhyE (MSMEG_2718), were encoded downstream of the hydrogenase structural subunits and may potentially fulfill this role instead ( Berney et al., 2014b ; Greening et al., 2015b ). In...”
  • “...was used to produce markerless deletions of the genes encoding two putative iron-sulfur proteins, hucE (MSMEG_2268) and hhyE (MSMEG_2718) ( Supplementary Figure S2 ). Briefly, a fragment containing fused left and right flanks of the MSMEG_2268 (1800 bp) and MSMEG_2718 (3098 bp) genes were synthesized by...”
• Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
  Cordero, The Journal of biological chemistry 2019 (secret)
• A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations
  Giddey, Scientific reports 2017
  • “...P0CH00/P0CG99 Ribonucleoside-diphosphate reductase subunit alpha 1/alpha 2 nrdE2 1.51 3.06E-03 78.8 A0QUN2 Rieske (2Fe-2S) region MSMEG_2268 1.54 6.79E-05 50.2 A0QXA8 Cytochrome D ubiquinol oxidase subunit 1 cydA 1.56 1.08E-04 17.2 A0R3I6 Peptidase S1 and S6, chymotrypsin/Hap MSMEG_5486 1.64 3.41E-03 65.1 A0QTK6 S30AE family protein MSMEG_1878 1.76...”
• A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases
  Greening, Proceedings of the National Academy of Sciences of the United States of America 2014
  • “...enzyme is cotranscribed with a putative [2Fe-2S] protein (MSMEG_2268), which is likely to serve as the physiological electron acceptor (23). Genes encoding...”
• Targeting drug tolerance in mycobacteria: a perspective from mycobacterial biofilms
  Islam, Expert review of anti-infective therapy 2012
  • “...Lhr Rv3296 MSMEG_1953 Unnamed protein product Rv3260c MSMEG_2188 Putative integral membrane protein MSMEG_2238 AldA Rv0768 MSMEG_2268 Thioredoxin-like protein MSMEG_2269 Conserved hypothetical protein MSMEG_2293 Conserved hypothetical protein MSMEG_2311 Predicted protein, putative MSMEG_2350 Conserved hypothetical protein Rv3030 MSMEG_2380 Sugar transporter family protein Rv2994 MSMEG_2601 Protocatechuate 3,4-dioxygenase subunit MSMEG_2735...”

Atu0351 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
36% identity, 37% coverage

• Regulation of the Cobalt/Nickel Efflux Operon dmeRF in Agrobacterium tumefaciens and a Link between the Iron-Sensing Regulator RirA and Cobalt/Nickel Resistance
  Dokpikul, Applied and environmental microbiology 2016
  • “...the sufS2 (Atu1825, Fe-S cluster biosynthesis) and fssA (Atu0351, Fe-S scaffold protein) promoters contain both IRO and ICE motifs (22). Cobalt toxicity in E....”

PADG_03852 uncharacterized protein from Paracoccidioides brasiliensis Pb18
38% identity, 24% coverage

• Iron Deprivation Modulates the Exoproteome in Paracoccidioides brasiliensis
  de, Frontiers in cellular and infection microbiology 2022
  • “...(PADG_08466), plasma membrane ATPase (PADG_08391), UBX domain-containing protein (PADG_08270), mitochondrial nuclease (PADG_05321), LiPid-depleted family member (PADG_03852), previously predicted as Fe ligands ( Tristo etal., 2015 ), and surprisingly, Cyb5 (PADG_03559), positively regulated 20.4 times. Iron Deprivation Promotes Upregulation of Transcripts of Paracoccidioides Cyb5 and Ggt2 Genes...”

BAB1_0139 Nitrogen-fixing NifU, C-terminal from Brucella melitensis biovar Abortus 2308
35% identity, 37% coverage

• Transposon Sequencing of Brucella abortus Uncovers Essential Genes for Growth In Vitro and Inside Macrophages
  Sternon, Infection and immunity 2018
  • “...redox BAB2_0727 BAB2_0728 BAB2_0729 BAB2_0730 BAB1_1435 BAB1_0051 BAB1_0139 pcuC nfuA Cell envelope BAB1_0351 BAB1_1217 BAB1_1462 wadB murI ampD-like Envelope,...”
• Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
  Roset, Scientific reports 2017
  • “...BAB1_2130 dnaJ cytochrome c heme-binding domain-containing protein C NO 0.51 0.06 Iron-sulfur cluster assembly GI:82699057 BAB1_0139 nifU nitrogen-fixing NifU, C-terminal C NO 1.52 0.07 GI:82699799 BAB1_0948 sufB cysteine desulfurase activator complex subunit U NO 1.72 0.15 Peptidases GI:82699040 BAB1_0118 Zn peptidase superfamily C NO 1.39 0.16...”
• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...BAB1_0118 Unknown BAB1_0896 ArgS BAB1_1547 PepQ BAB2_0162 L-carnitine BAB1_0122 GyrB BAB1_0898 NagZ BAB1_1549 PrsA dehydratase BAB1_0139 NifU BAB1_0918 GatB/Yqey BAB1_1553 YchF BAB2_0177 YafB BAB1_0159 S30EA BAB1_0924 AccC BAB1_1613 Unknown BAB2_0186 Fumarate hydratase BAB1_0160 PtsN-like BAB1_0933 PCRF 2 BAB1_1645 DhaK-1 BAB2_0187 Unknown BAB1_0191 GABAtrnsam BAB1_0943 TyrS BAB1_1646...”

NE1445 Nitrogen-fixing protein NifU from Nitrosomonas europaea ATCC 19718
37% identity, 39% coverage

• Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK)
  Cho, Applied and environmental microbiology 2006
  • “...fecR Transmembrane receptor 0.515 0.070 8 Biosynthesis NE1445 NE2150 nifU trpE Iron-sulfur cluster biosynthesis Anthranilate synthase 2.117 2.407 0.445 0.333 6...”
  • “...by nirK mutant N. europaea and also why NifU (NE1445), an FeS cluster biosynthesis gene, was more highly expressed in nirK mutant versus wild-type cells. nirB...”

PST_1350 Fe-S cluster assembly protein NifU from Pseudomonas stutzeri A1501
37% identity, 22% coverage

• Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associated Pseudomonas stutzeri A1501
  Lv, mSphere 2024
  • “...7.52 1.64 E 04 PST_1349 hesB Iron-sulfur cluster assembly accessory protein 1.58 7.58 E 03 PST_1350 nifU Fe-S cluster assembly protein NifU 1.92 3.53 E 04 PST_1351 nifS Cysteine desulfurase 1.23 1.04 E 05 PST_1352 nifV Homocitrate synthase 1.58 3.95 E 03 PST_1355 nifW Nitrogenase-stabilizing/protective protein...”

PGUG_02696 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
39% identity, 31% coverage

• Molecular Response of Meyerozyma guilliermondii to Patulin: Transcriptomic-Based Analysis
  Yang, Journal of fungi (Basel, Switzerland) 2023
  • “...dismutase 1 copper chaperone PGUG_04752 MIA40 1.05 Mitochondrial intermembrane space import and assembly protein 40 PGUG_02696 NFU1 1.21 NifU-like protein, mitochondrial PGUG_04929 COX17 1.24 Cytochrome c oxidase copper chaperone PGUG_04481 MAS1 1.76 Mitochondrial-processing peptidase subunit beta Transcription and translation regulation PGUG_00994 NOP53 1.41 Ribosome biogenesis protein...”

A4YC18 Fe/S biogenesis protein NfuA from Shewanella putrefaciens (strain CN-32 / ATCC BAA-453)
36% identity, 34% coverage

• Comparative Proteomics Reveals the Spoilage-Related Factors of Shewanella putrefaciens Under Refrigerated Condition
  Yi, Frontiers in microbiology 2021
  • “...Up Polyribonucleotide nucleotidyltransferase A4Y9B5 Extracellular Up S-Adenosylmethionine synthase E6XL87 Extracellular Up Fe/S biogenesis protein NfuA A4YC18 Extracellular Up Discussion Fish and fish products are highly susceptible to spoilage due to microbial activity. Thus, it is essential to elucidate the mechanisms of spoilage microorganisms in order to...”

Q9I2P8 Fe/S biogenesis protein NfuA from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NP_250538 Fe/S biogenesis protein NfuA from Pseudomonas aeruginosa PAO1
PA1847 hypothetical protein from Pseudomonas aeruginosa PAO1
32% identity, 38% coverage

• Targeting Essential Hypothetical Proteins of Pseudomonas aeruginosa PAO1 for Mining of Novel Therapeutics: An In Silico Approach
  Rahman, BioMed research international 2023
  • “...4750.0 9 NP_253326.1 Q9HVF5 PA4636 18 6466.58 10 NP_249286.1 Q9I5U2 ostA 3 10848.52 11 NP_250538.1 Q9I2P8 PA1847 3 5698.26 Table 5 Aspects of the proteins like nonhomology to human proteins and proteins of human gut flora, virulence of the pathogen, druggability for the 9 EHPs. serial...”
• Pseudomonas aeruginosa nfuA: Gene regulation and its physiological roles in sustaining growth under stress and anaerobic conditions and maintaining bacterial virulence.
  Romsang, PloS one 2018
  • GeneRIF: NfuA functions in Fe-S cluster delivery to selected target proteins that link to many physiological processes such as anaerobic growth, bacterial virulence and stress responses in P. aeruginosa
• Targeting Essential Hypothetical Proteins of Pseudomonas aeruginosa PAO1 for Mining of Novel Therapeutics: An In Silico Approach
  Rahman, BioMed research international 2023
  • “...3 nodes each. The nodes with only 3 connections (degree) are considered islands (ostA and PA1847) ( Table 4 ) [ 68 ]. The node degree and betweenness centrality range from 3 to 45 and 4750 to 17881.76, respectively. The interaction among the hub proteins can...”
  • “...9 NP_253326.1 Q9HVF5 PA4636 18 6466.58 10 NP_249286.1 Q9I5U2 ostA 3 10848.52 11 NP_250538.1 Q9I2P8 PA1847 3 5698.26 Table 5 Aspects of the proteins like nonhomology to human proteins and proteins of human gut flora, virulence of the pathogen, druggability for the 9 EHPs. serial No....”
• ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
  Cai, Microbiology spectrum 2022
  • “...B Dnr binding site 2.61 1.04E-05 PA0525 norD Denitrification protein Dnr binding site 2.68 8.35E-06 PA1847 nfuA Fe/S biogenesis protein 2.12 1.74E-10 PA3392 nosZ Nitrous-oxide reductase Dnr box 4.32 2.49E-39 PA3393 nosD Copper-binding periplasmic protein Dnr box 2.74 1.7E-31 PA3394 nosF Copper ABC transporter ATP-binding protein...”
• Transcriptional regulation of fatty acid cis-trans isomerization in the solvent-tolerant soil bacterium, Pseudomonas putida F1
  Kondakova, Environmental microbiology 2019
  • “...), indicating that in tested experimental conditions, cti is co-transcribed with the downstream genes. Gene PA1847 in P. aeruginosa PAO1, as well as Pput_3317 in P. putida F1, is annotated as coding for NfuA, a protein involved in Fe/S biogenesis in E. coli ( Angelini et...”
  • “...using one-way ANOVA (Turkey multiple comparison). ns, not significant. Strain names: 3317, PPut3317; 3318, PPut3317; PA1847, PAO1847....”
• Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
  Yung, NPJ biofilms and microbiomes 2019
  • “...KatA PA4236 Catalase NR o NR MtnB PA1683 Methylthioribulose-1-phosphate dehydratase NR NR NR NR NfuA PA1847 Fe/S biogenesis protein NR NR NR NR NirS PA0519 Nitrite reductase NR NR NR NR NuoB PA2638 NADH-quinone oxidoreductase subunit B NR NR NR NR NR NuoC PA2639 NADH-quinone oxidoreductase...”
• Protein complex formation during denitrification by Pseudomonas aeruginosa
  Borrero-de, Microbial biotechnology 2017
  • “...(Williams etal ., 2007 ). Proteins involved in the biogenesis of ironsulfur clusters, like NfuA (PA1847) (Roche etal ., 2013 ), of the molybdenum cofactor, like MoaB1 (PA3915) (Andreae etal ., 2014 ; Kasaragod and Schindelin, 2016 ; FernandezBarat etal ., 2017 ), and of ubiquinone,...”
• Antimicrobial targets localize to the extracellular vesicle-associated proteome of Pseudomonas aeruginosa grown in a biofilm
  Park, Frontiers in microbiology 2014
  • “...significantly more abundant in biofilms include four of the PCAP-R proteins, namely OprQ (PA2760), NfuA (PA1847), AmgR (PA5200), and NagZ (PA3005; Figure 3A ). These proteins have diverse GO annotations ( Winsor et al., 2010 ), and were increased at various time points throughout biofilm development;...”
• The Pseudomonas aeruginosa proteome during anaerobic growth
  Wu, Journal of bacteriology 2005
  • “...PA0934 PA0936 PA1155 PA1156 PA1398 PA1566 PA1681 PA1766 PA1847 PA1919 PA1920 PA2119 PA2127 PA2323 PA2567 PA2945 PA2991 PA2994 PA2999* PA3002 PA3150 PA3185...”
• Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
  Filiatrault, Infection and immunity 2005
  • “...PA1665 PA1666 PA1667 PA1668 PA1669 PA1761 PA1762 PA1790 PA1847 PA1855 PA1856 PA1883 PA1888 PA1902 PA1903 PA1904 PA1971 PA1985 PA1986 PA1987 PA1988 PA1989 PA1990...”

XP_638146 NIF system FeS cluster assembly domain-containing protein from Dictyostelium discoideum AX4
37% identity, 22% coverage

• A Highly Conserved Iron-Sulfur Cluster Assembly Machinery between Humans and Amoeba Dictyostelium discoideum: The Characterization of Frataxin
  Olmos, International journal of molecular sciences 2020
  • “...assembly and its transferring to client proteins: the orthologs ISCA1 (XP_641284.1), ISCA2 (XP_638418.1) and NFU1 (XP_638146). These findings as a whole suggest evolutionary constrains for the proteins that form the supercomplex for [Fe-S] cluster assembly, and more importantly, the relevance of D. discoideum as a model...”

VF_2461 putative DNA uptake protein from Vibrio fischeri ES114
40% identity, 31% coverage

• Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis
  An, BMC genomics 2009
  • “...luminescens , plu0592) 35/36 110 3E-14 - Protein folding trxA -Thioredoxin ( Vibrio fischeri , VF_2461) 83/98 159 4E-18 - TCA cycle pckA -Phosphoenolpyruvate carboxykinase ( P. luminescens , plu0100) 93/97 300 9E-48 Nutrition - Amino acid acquisition artM -Putative ABC amino acid transport system (...”

SG2325 hypothetical protein from Sodalis glossinidius str. 'morsitans'
37% identity, 37% coverage

• Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut
  Runyen-Janecky, PLoS neglected tropical diseases 2022
  • “...highly expressed by Sgm grown in BHI and induced 1.5-fold with the addition of heme), SG2325 (Fe/S biogenesis), and SG2047 (putative organic hydroperoxide resistance regulator). Other Sgm genes identified by Pontes et. al. [ 33 ] as potentially mitigating oxidative stress survival were not heme-induced in...”
• Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
  Pontes, PloS one 2008
  • “...and manganese (SG1516, SG1517, SG1518 and SG1519) and protein folding (e.g., SG0409, SG0584, SG0692 and SG2325; Supplementary Table S2 ). The addition of OHHL also increased the expression of bacterioferritin (SG2280) and genes involved in iron siderophore biosynthesis (SGP1_004146) [32] . Based on the fact that...”

NHN26_05060 iron-sulfur cluster assembly scaffold protein from Rhodovulum tesquicola
37% identity, 29% coverage

• Nitrogen Fixation Activity and Genome Analysis of a Moderately Haloalkaliphilic Anoxygenic Phototrophic Bacterium Rhodovulum tesquicola
  Komova, Microorganisms 2022
  • “...into two parts. 16 genes from nifA (NHN26_05215) to fdxB (NHN26_05140) are separated from nifU (NHN26_05060), nifV (NHN26_05055) and nifW (NHN26_05050) by a cluster of 15 genes coding mainly for RnfABCDGE type electron transport complex. This break may lead to a decreased nitrogenase activity in comparison...”

rrnAC3083 unknown from Haloarcula marismortui ATCC 43049
33% identity, 57% coverage

• Genome information management and integrated data analysis with HaloLex
  Pfeiffer, Archives of microbiology 2008
  • “...OE3959R, HQ3234A, NP5036A rrnAC3074 699 963 Shortened NP0072A, HQ3236A, OE3964R rrnAC3079 573 624 Shortened NP3402A rrnAC3083 375 423 Shortened NP0948A, OE4292F, HQ3465A rrnAC3100 2,010 2,049 Shortened NP2262A, HQ1094A, OE3832F rrnAC3121 651 1,194 Shortened HQ1495A rrnAC3130 939 645 Extended HQ1618A, rrnB0227 rrnAC3132 1,392 1,419 Shortened HQ1619A, rrnAC2624...”

nifU / AAC33371.1 NifU from Rippkaea orientalis PCC 8801 (see paper)
41% identity, 22% coverage

CRC_02888 Fe-S cluster assembly protein NifU from Cylindrospermopsis raciborskii CS-505
42% identity, 24% coverage

• The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications
  Stucken, PloS one 2010
  • “...NifH all1455 no CRC_02887 186680943 nifU core set Fe-S cluster assembly protein NifU all1456 no CRC_02888 186680944 nifS core set Nitrogenase metalloclusters biosynthesis protein NifS all1457 no CRC_02889 186680946 nifB core set nitrogenase cofactor biosynthesis protein all1517 no CRC_02891 186680953 cysE serine acetyltransferase alr1404 no no...”

bll0800 bll0800 from Bradyrhizobium japonicum USDA 110
32% identity, 36% coverage

• Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis
  Gomes, BMC genomics 2014
  • “...classified in the posttranslational modification, protein turnover, chaperones functional category, shows 97% of similarity with Bll0800 of B. diazoefficiens USDA 110. After comparison of databases, this hypothetical protein was assigned as a thioredoxin-like protein involved in iron transport (Table 2 ); however, it may be related...”

NIFU_AZOVI / P05340 Nitrogen fixation protein NifU from Azotobacter vinelandii (see 2 papers)
C1DH18 Nitrogen fixation protein NifU from Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
Avin_01620 Nitrogen fixation Fe-S cluster scaffold protein from Azotobacter vinelandii AvOP
33% identity, 24% coverage

• function: Involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins
  cofactor: Fe cation (Binds 1 Fe cation per subunit in a rubredoxin-type site.)
  cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
  subunit: Homodimer.
  disruption phenotype: No longer grows diazotrophically (without an external source of N) (PubMed:10819462).
• Biosynthesis of Nitrogenase Cofactors
  Burén, Chemical reviews 2020
  • “...NifU structure and function. (A) A. vinelandii NifU domain architecture and conserved Cys residues (Uniprot C1DH18). Three distinct NifU domains are shown in green, pink, and blue, and their roles in coordinating permanent or transient [FeS] clusters are indicated. (B) Alignment of full-length NifU with the...”
• Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes
  Dos, BMC genomics 2012
  • “...nitrogen fixing protein sequences: NifH (Avin_01380), NifD (Avin_01390), NifK (Avin_01400), NifE (Avin_01450), NifN (Avin_01460), NifU (Avin_01620), NifS (Avin_01630), NifV (Avin_01640), NifB (Avin_51010), NifQ (Avin_51040), AnfG (Avin_48980), and VnfG (Avin_02600). Initially hits were selected based on a relatively weak threshold ( 20%amino acid identity over the query...”

BJ6T_08050 NifU family protein from Bradyrhizobium japonicum USDA 6
32% identity, 36% coverage

• Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis
  Gomes, BMC genomics 2014
  • “...(Table 2 ). This protein probably plays a role in chromosomal partitioning during cell division. BJ6T_08050, classified in the posttranslational modification, protein turnover, chaperones functional category, shows 97% of similarity with Bll0800 of B. diazoefficiens USDA 110. After comparison of databases, this hypothetical protein was assigned...”

AM1146 hypothetical protein from Anaplasma marginale str. St. Maries
31% identity, 38% coverage

• Transcriptional pathways associated with the slow growth phenotype of transformed Anaplasma marginale
  Pierlé, BMC genomics 2013
  • “...opag3 1073 193 opag2 317 531 opag1 385 346 msp2 239 1170 AM1145 177 1357 AM1146 157 413 AM1148 120 112 orfX 55 45 *AmTR: transformed; A. marginale WT: wild type A. marginale. Since the genes immediately adjacent to the insertion site were not significantly altered,...”

A5F4R9 Fe/S biogenesis protein NfuA from Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
37% identity, 32% coverage

• Impact of Na⁺-Translocating NADH:Quinone Oxidoreductase on Iron Uptake and nqrM Expression in Vibrio cholerae
  Agarwal, Journal of bacteriology 2020 (secret)

VC2720 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
37% identity, 32% coverage

• 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
  • “...isozyme I 1.076 VC2699 dcuA C4-dicarboxylate transporter anaerobic 1.040 VC2706 conserved hypothetical protein 1.577 1.529 VC2720 nfuA conserved hypothetical protein 1.197 1.084 VC2738 pckA phosphoenolpyruvate carboxykinase 1.086 VCA0011 malT malT regulatory protein 1.882 VCA0013 malP maltodextrin phosphorylase 1.713 VCA0014 malQ 4-alpha-glucanotransferase 1.698 VCA0015 hypothetical protein 1.630...”
• Mannitol and the mannitol-specific enzyme IIB subunit activate Vibrio cholerae biofilm formation
  Ymele-Leki, Applied and environmental microbiology 2013
  • “...protein P-II 4.95 0.08 9.86 0.30 Other functions VC1742 VC2720 Hypothetical Conserved hypothetical 0.45 0.42 0.23 0.24 a Genes that are PTS components or are in...”
• Transcriptional profiling of Vibrio cholerae recovered directly from patient specimens during early and late stages of human infection
  Larocque, Infection and immunity 2005
  • “...VC0480 VC0641 VC0762 VC1317 VC1723 VC2479 VC2706 VC2720 VCA0769 Conserved Conserved Conserved Conserved Conserved Conserved Conserved Conserved Conserved 1.91...”

Q92GV4 Scaffold protein Nfu/NifU N-terminal domain-containing protein from Rickettsia conorii (strain ATCC VR-613 / Malish 7)
41% identity, 30% coverage

• FAST-NMR: functional annotation screening technology using NMR spectroscopy
  Mercier, Journal of the American Chemical Society 2006
  • “...proteins SAV1430 and SAV0936 based on hypothetical proteins Q92GV4 and the Q9ZCQ2 in Rickettsia conorii and Rickettsia proazeki, respectively.18 The quality of...”

Achr_1480 Fe-S cluster assembly protein NifU from Azotobacter chroococcum NCIMB 8003
32% identity, 24% coverage

• Holistic view of biological nitrogen fixation and phosphorus mobilization in Azotobacter chroococcum NCIMB 8003
  Biełło, Frontiers in microbiology 2023
  • “...reductases NifH and VnfH (A0A0C4WKV1, Achr_1260 and A0A0C4WIZ0, Achr_2560, respectively), and the proteins NifU (A0A0C4WNP4, Achr_1480) and NifZ (A0A0C4WFU7, Achr_1540), that are required for the maturation of nitrogenase ( Johnson et al., 2005 ), showed a marked decrease in the FPb condition. In the rest of...”

pE3SP1_p070 NifU family protein from Polaromonas sp. E3S
42% identity, 34% coverage

• Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments
  Ciok, Frontiers in microbiology 2018
  • “...(glutathione S -transferase), (ii) pE10SP1_p064 (cyanuric acid hydrolase), (iii) pH6NP1_p054 (MntH transporter), and (ivxi) pE3SP1_p017, pE3SP1_p070, pE5SP1_p017, pE10SP1_p040, pE3SP1_p015, pE3SP1_p063, pE5SP1_p015, and pE10SP1_p042 ([Fe-S] cluster biogenesis scaffold protein Nfu/NifU). The fact that genes encoding these proteins were found exclusively within the analyzed plasmids suggests that carrying...”

RAYM_01100 NifU family protein from Riemerella anatipestifer RA-YM
39% identity, 22% coverage

• The Role of the Regulator Fur in Gene Regulation and Virulence of Riemerella anatipestifer Assessed Using an Unmarked Gene Deletion System
  Guo, Frontiers in cellular and infection microbiology 2017
  • “...RAYM_09774 Leucine-rich repeat-containing protein 3.05 2.83 PROTEIN SYNTHESIS RAYM_00750 RNA polymerase Rpb6 2.24 1.43 1.08 RAYM_01100 Nitrogen-fixing NifU domain protein 1.87 1.15 RAYM_01495 FeS assembly SUF system protein 1.27 1.71 RAYM_06457 Probable iron binding protein from the HesB_IscA_SufA family 1.53 2.58 1.04 RAYM_06467 Cysteine desulfurase activator...”
  • “...by iron. In bacteria, Fe-S machinery is comprised of a nitrogen-fixing NifU domain protein ( RAYM_01100 ), SUF system protein ( RAYM_01495, RAYM_06457, RAYM_06467, RAYM_06507 ). Similar changes of NIF and SUF systems have been confirmed in E. coli in previous studies (Outten et al., 2004...”

JHW33_RS22810 Fe-S cluster assembly protein NifU from Rahnella aceris
32% identity, 25% coverage

• Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
  Xu, Frontiers in microbiology 2022
  • “...WP_014683027.1 NA NA WP_014683027.1 100 NA NA WP_014333914.1 98 nifU Fe-S cluster assembly protein NifU JHW33_RS22810 WP_014683029.1 NA NA WP_014683029.1 100 NA NA WP_014333912.1 97 nifS Cysteine desulfurase JHW33_RS22805 WP_200227559.1 NA NA WP_014683030.1 99 NA NA WP_014333911.1 99 nifV Homocitrate synthase NifV JHW33_RS22800 WP_014683031.1 NA NA...”

TA19885 Nifu-like protein, putative from Theileria annulata
33% identity, 42% coverage

• Experimental Genetics of Plasmodium berghei NFU in the Apicoplast Iron-Sulfur Cluster Biogenesis Pathway
  Haussig, PloS one 2013
  • “...acid sequence identities of NFUapi orthologs in P. falciparum (PF3D7_0921400), P. vivax (PVX_099490), Theileria annulata (TA19885), and Toxoplasma gondii (TGME49_021920) compared with P. berghei NFUapi (PBANKA_082230). Signal peptide (red), apicoplast-targeting sequence (green), and the NifU-like domain (brown) are shown. (B) Sequence alignment of three Plasmodium NFUapi...”

all1456 nitrogen fixation protein from Nostoc sp. PCC 7120
42% identity, 18% coverage

• Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria
  Pérez, 2024
• The small Ca²⁺-binding protein CSE links Ca²⁺ signalling with nitrogen metabolism and filament integrity in Anabaena sp. PCC 7120
  Walter, BMC microbiology 2020
  • “...cluster biosynthesis protein hesA/B, nifW/X/N/E/K 5.4 < 0.038 all1455 nifH nitrogenase iron protein 6.5 4.06E-06 all1456 nifU nitrogen fixation protein 4.2 0.009 all1457 nifS nitrogenase cofactor synthesis protein 6.0 0.025 all1517 nifB nitrogen fixation protein 6.4 7.81E-06 alr2520 nitrogenase-associated protein 4.6 7.18E-05 Hydrogenases all0688 alr0700 hup...”
• Functional Overlap of hetP and hetZ in Regulation of Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
  Zhang, Journal of bacteriology 2018
  • “...all1436 all1437 all1438 all1439 all1440 all1454 all1455 all1456 all1457 all1516 all1517 all2512 all2868 all3793 all4460 all4617 all5341 all5342 all5347 all7607...”
• Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120
  Walter, Journal of experimental botany 2016
  • “...nifK all1440 Nitrogenase iron-molybdenum protein 0.008 5 nifH all1455 Nitrogenase iron protein 0.003 5 nifU all1456 Nitrogen fixation protein 0.018 5 nifS all1457 Nitrogenase cofactor synthesis protein 0.004 5 chlN all5076 Protochlorophyllide reductase subunit 0.012 5 chlL all5078 Protochlorophyllide reductase iron-sulfur ATP-binding protein 0.006 5 clhB...”
• The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications
  Stucken, PloS one 2010
  • “...iron protein NifH all1455 no CRC_02887 186680943 nifU core set Fe-S cluster assembly protein NifU all1456 no CRC_02888 186680944 nifS core set Nitrogenase metalloclusters biosynthesis protein NifS all1457 no CRC_02889 186680946 nifB core set nitrogenase cofactor biosynthesis protein all1517 no CRC_02891 186680953 cysE serine acetyltransferase alr1404...”

Ava_3915 Fe-S cluster assembly protein NifU from Anabaena variabilis ATCC 29413
42% identity, 18% coverage

• Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically
  Park, BMC genomics 2013
  • “...conditions the upregulation of the nif1 genes in heterocysts ranged between 5.3-fold ( nifU , Ava_3915) and 22-fold ( nifB , Ava_3912), all with p<0.0001. The nifH , nifD , and nifK signals in heterocysts reached 44%, 39%, and 15% of the strongest signal in these...”

ECH_0202 NifU domain protein from Ehrlichia chaffeensis str. Arkansas
34% identity, 33% coverage

• Multiple Ehrlichia chaffeensis genes critical for persistent infection in a vertebrate host are identified as nonessential for its growth in the tick vector; Amblyomma americanum
  Jaworski, Frontiers in cellular and infection microbiology 2023
  • “...and ECH_0480 caused the transcriptionally silent ECH_0480 gene to be transcriptionally active; intergenic mutations between ECH_0202 and ECH_0203 and between ECH_0284 and ECH_0285 caused RNA expression enhancement from ECH_0203 and ECH_0285, respectively. Similarly, mutations within ECH_0379 and ECH_0660 resulted in preventing transcription from these genes as...”
• Amblyomma americanum ticks infected with in vitro cultured wild-type and mutants of Ehrlichia chaffeensis are competent to produce infection in naïve deer and dogs
  Jaworski, Ticks and tick-borne diseases 2017
  • “...two mutants which persist in deer (Ech_0284 and Ech_0480) and three mutants which clear rapidly (Ech_0202, Ech_0379, and Ech_0660) in deer and dogs ( Cheng et al., 2013 ; Cheng et al., 2015 ). We performed a tick-transmission experiment to test if the needle-infected ticks cause...”
  • “...with ticks that had received an injection with a pool of five equal-molar mixed mutants (Ech_0202, Ech_0284, Ech_0379, Ech_0480, and Ech_0660) or with a single mutant injection (Ech_0480) as described in ( Cheng et al 2015 ). Deer were monitored for infection for 6 weeks after...”
• Mutations in Ehrlichia chaffeensis Causing Polar Effects in Gene Expression and Differential Host Specificities
  Cheng, PloS one 2015
  • “...the insertion sites. Primer name Gene target Amplicon size (bp) Primer sequence (genomic coordinates) RRG1382 Ech_0202 312 5'-ttg ctg ata gtg tgg cag ctg aag (192727192746) RRG1383 5'-tct cca cca tct tgg ata aca gca gg (193038193013) RRG1384 Ech_0203 175 5'-tgt gtc ctg ttg tta tgg...”
  • “...dog was infected with this mutant. One deer was infected with GFPuv mutant pool containing Ech_0202, Ech_0601, and Ech_0760 [ 14 , 17 ]. Inocula were prepared and inoculated with an estimated concentration of ~2x10 8 Ehrlichia organisms in one ml [ 14 ]. Infections with...”
• Targeted and random mutagenesis of Ehrlichia chaffeensis for the identification of genes required for in vivo infection
  Cheng, PLoS pathogens 2013
  • “...the elimination of one of the three mutants from the pool (mutant downstream to the Ech_0202) (Lane 6c in Figure 5 ) 10.1371/journal.ppat.1003171.g005 Figure 5 Clonal isolation of the E. chaffeensis mCherry and GFP mutants. Host cell-free organisms recovered from nearly 90% infected culture flask were...”

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How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.