Family Search for PF13225 (D27-like_C)
PaperBLAST, GapMind, SitesBLAST, and Sites on a Tree will be down for server maintenance on Friday March 29.
Running HMMer for PF13225
PF13225 hits 6 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
Q9SGU7 At1g64680 from Arabidopsis thaliana
NP_564838 beta-carotene isomerase D27 from Arabidopsis thaliana
AT1G64680 hypothetical protein from Arabidopsis thaliana
Aligns to 140:222 / 250 (33.2%), covers 100.0% of PF13225, 131.7 bits
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...AT2G48070 Chl 1.640.04 Unknown (2) 54 Uncharacterized protein F4IYD5 AT3G01060 Chl 1.480.15 55 Uncharacterized protein Q9SGU7 AT1G64680 Chl 2.250.21 a Numberical list of dark-responsive proteins. b Protein name and the abbreviation commonly used for the protein. The proteins were classified according to their functions. c Protein...”
- “...essential NDH complex to transfer reduced power [ 64 ]. A two-fold increased uncharacterized protein (Q9SGU7) in our results were predicted to be correlated with the subunit of NDH complex ( http://atted.jp/data/ ), implying the growing evidence of chlororespiration. Conversion of Chlorophyll a to Chlorophyll b...”
- Subfunctionalization of D27 Isomerase Genes in Saffron
López-Jiménez, International journal of molecular sciences 2022 - “...[ 40 ] and in Lotus japonicus [ 41 ]. Expression analysis showed that AtD27-like-1 (NP_564838), the homolog of CsD27-3 , was highly expressed in cotyledons, young intermediate leaves and sepals [ 11 ], and the expression levels were 10-fold higher compared to the other AtD27-like...”
- “...specific transcriptome of A. thaliana plants under high-intensity light without heat stress revealed that AtD27-like-1 (NP_564838) was present among the 560 upregulated genes regulated by light, and showed an increased expression under high light stress conditions [ 43 ]. Further, this protein has been identified in...”
- Subfunctionalization of D27 Isomerase Genes in Saffron
López-Jiménez, International journal of molecular sciences 2022 - “...rice leaves ( Figure S9 ). The involvement of the protein encoded by the Arabidopsis (At1g64680) homolog to the CsD27-3 gene in photosynthesis was recently reported in a study looking for NFU3 (Chloroplastic maturation factor) targets [ 46 ]. Among other affected proteins were found PsaA,...”
- Rapid Detection and Quantification of Plant Innate Immunity Response Using Raman Spectroscopy
Chung, Frontiers in plant science 2021 - “...dioxygenase1 (At3g63520); CCD4 , At4g19170; CCD7 , At2g44990; CCD8 , At4g32810; D27 , -carotene isomerase (At1g64680); CYP711A , (At2g26170). The expression of the Arabidopsis Act2 (At3g18780) was used as an internal control. Primer pairs for RT-qPCR were designed using Primer-BLAST ( https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi ) or manually by...”
- 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 - “...chain amino acid biosynthesis Dihydroxyacid dehydratase At1g03055 DWARF27.1 n.d. n.q. 4Fe4S (?) Strigolactone biosynthesis DWARF27.1 At1g64680 DWARF27.2 1.05 * n.q. 4Fe4S (?) Unknown DWARF27.2 At4g01995 DWARF27.3 n.d. n.d. 4Fe4S (?) Unknown DWARF27.3 At1g10960 FD1 (PETF2) n.v. n.q. 2Fe2S Electron transport chain Ferredoxin 1 At1g60950 FD2 (PETF)...”
- Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis
Kurihara, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...of 813 genes overlapped with the 220 genes showing BL-enhanced transcription from dTSSs. HY5 and AT1G64680 were among these 45 genes ( Fig. 5 A ). The transcript from the uTSS of the HPR1 gene is also likely to accumulate in upf1-1 ( SI Appendix ,...”
- “...derived from uTSSs accumulate in upf1-1 . ( A ) Two examples of genes ( AT1G64680 and HY5 ) that show enhanced accumulation of transcripts from uTSSs in upf1-1 . Position A indicates uTSSs located upstream of uATG codons, while position B indicates dTSSs located downstream...”
- Roles and maturation of iron-sulfur proteins in plastids
Przybyla-Toscano, Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2018 - “...4 ] Knock-down Increase in axillary rosette branches Waters et al. [ 168 ] DWARF27.2 At1g64680 [Fe 4 S 4 ] Not yet described DWARF27.3 At4g01995 [Fe 4 S 4 ] Not yet described ISPG At5g60600 [Fe 4 S 4 ] Knock-out Albino phenotype, proplastid growth...”
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...Chl 1.640.04 Unknown (2) 54 Uncharacterized protein F4IYD5 AT3G01060 Chl 1.480.15 55 Uncharacterized protein Q9SGU7 AT1G64680 Chl 2.250.21 a Numberical list of dark-responsive proteins. b Protein name and the abbreviation commonly used for the protein. The proteins were classified according to their functions. c Protein number...”
- A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana
Meier, BMC systems biology 2011 - “...(ZDS) CMP AT1G77090 0.856 Thylakoid lumenal 29.8 kDa protein i PS, Pd, PP, TP, CPl AT1G64680 0.856 ExPr AT1G80030 0.855 DNAJ heat shock protein, Pd, PP, TP, CPl AT4G17600 0.855 Light-harvesting-like protein (Lil3:1) Pd, PP, TP, CPl AT5G08050 0.854 ExPr An expression correlation analysis was performed...”
D27_MEDTR / R4HZ96 Beta-carotene isomerase D27, chloroplastic; Protein DWARF-27; EC 5.2.1.14 from Medicago truncatula (Barrel medic) (Medicago tribuloides) (see 2 papers)
R4HZ96 beta-carotene isomerase (EC 5.2.1.14) from Medicago truncatula (see paper)
Aligns to 146:228 / 252 (32.9%), covers 97.7% of PF13225, 120.2 bits
- function: Involved in strigolactones biosynthesis by catalyzing the isomerization of the C9-C10 double bond in all-trans-beta-carotene leading to 9-cis-beta-carotene and providing the substrate for CCD7 (PubMed:26503135). Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signals that stimulate hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds (PubMed:26503135).
catalytic activity: all-trans-beta-carotene = 9-cis-beta-carotene (RHEA:34455)
cofactor: Fe cation
D27_ARATH / Q7XA78 Beta-carotene isomerase D27, chloroplastic; Protein DWARF-27 homolog; AtD27; EC 5.2.1.14 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G03055 hypothetical protein from Arabidopsis thaliana
NP_563673 beta-carotene isomerase D27-like protein from Arabidopsis thaliana
Aligns to 160:242 / 264 (31.4%), covers 98.9% of PF13225, 120.0 bits
- function: Involved in strigolactones biosynthesis by catalyzing the isomerization of the C9-C10 double bond in all-trans-beta-carotene leading to 9-cis-beta-carotene and providing the substrate for CCD7. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.
catalytic activity: all-trans-beta-carotene = 9-cis-beta-carotene (RHEA:34455)
cofactor: Fe cation
disruption phenotype: Increased shoot branching. - Identification of new potential downstream transcriptional targets of the strigolactone pathway including glucosinolate biosynthesis
Hellens, Plant direct 2023 - “...AT4G32880, AT4G34760, AT4G36110, AT5G13360, AT5G19530, AT5G20820, AT5G39610, AT5G43700, AT5G47370, AT5G54490, AT5G54510, AT5G55250, AT5G62380, AT5G65670, AT5G67480, AT1G03055, AT2G42620, AT3G21420, AT3G03990. AUTHOR CONTRIBUTIONS Alicia M. Hellens, Franziska Fichtner, Philip B. Brewer, and Christine A. Beveridge designed the research; Alicia M. Hellens, Franziska Fichtner, and Philip B. Brewer performed...”
- Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant
Bolortuya, Frontiers in plant science 2021 - “...BRC1 AT3G18550 Os09g0410500 Chloris9240c000010 2.542 1.050 SMXL7 AT2G29970 Chloris14785c000010 2.662 1.608 Strigolactones biosynthesis genes D27 AT1G03055 Chloris8648c000010 1.047 1.254 MAX3 At2g44990 Os04g0550600 Chloris8839c000010 0.773 1.307 MAX4 At4g32810 Os01g0746400 Chloris11425c000010 0.970 1.975 Chloris20143c000010 1.839 2.299 MAX1 At2g26170 Os01g0700900 Chloris23859c000010 1.079 0.797 CYP711A2 CYP711A3 - Os01g0700900 Os0190701400 Chloris16015c000010...”
- 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 - “...Choline monooxygenase (putative) At3g23940 DHAD n.v. n.v. 2Fe2S Branched chain amino acid biosynthesis Dihydroxyacid dehydratase At1g03055 DWARF27.1 n.d. n.q. 4Fe4S (?) Strigolactone biosynthesis DWARF27.1 At1g64680 DWARF27.2 1.05 * n.q. 4Fe4S (?) Unknown DWARF27.2 At4g01995 DWARF27.3 n.d. n.d. 4Fe4S (?) Unknown DWARF27.3 At1g10960 FD1 (PETF2) n.v. n.q....”
- Synergistic Interaction of Phytohormones in Determining Leaf Angle in Crops
Li, International journal of molecular sciences 2020 - “...cleavage dioxygenase (CCD) 7 related to the SL biosynthesis in rice. [ 78 ] AtD27 (AT1G03055) OsD27 (Os11g0587000) Negatively regulating leaf angle and encode -carotene isomerase, related to the SL biosynthesis in rice. [ 78 ] 1 Role of the corresponding gene in regulating leaf angle...”
- Abscisic acid influences tillering by modulation of strigolactones in barley
Wang, Journal of experimental botany 2018 - “...from Medicago truncatula ( van Zeijl et al. , 2015 ) and Arabidopsis, encoded by AT1G03055 ( Waters et al. , 2012 ). Thus, BAJ90178.1 (encoded by MLOC_67450, HORVU7Hr1G096930) was designated as HvD27. In order to identify the orthologous sequences of CCD7 and CCD8 in barley,...”
- Roles and maturation of iron-sulfur proteins in plastids
Przybyla-Toscano, Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2018 - “...growth abnormalities Sureshkumar et al. [ 152 ], Knill et al. [ 151 ] DWARF27.1 At1g03055 [Fe 4 S 4 ] Knock-down Increase in axillary rosette branches Waters et al. [ 168 ] DWARF27.2 At1g64680 [Fe 4 S 4 ] Not yet described DWARF27.3 At4g01995 [Fe...”
- In silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of Strigolactones in plants
Marzec, International journal of molecular sciences 2015 - “...--carotene [ 29 ]. This carotenoid isomerase is encoded by the D27 (Os11g0587000) and AtD27 (At1g03055) genes that were identified in Oryza sativa (rice) [ 30 ] and Arabidopsis thaliana [ 31 ], respectively. The product of the activity of the D27 isomerase is immobile and...”
- “...4. Experimental Section 4.1. Promoter Analysis The 1000 bp long promoter sequences of Arabidopsis genes (At1g03055; At2g42620; At4g32810 and At2g26170) were obtained using the PlantPAN analytical resource [ 89 , 90 ], whereas the same length of promoter sequences of rice genes (Os11g0587000; Os04g0550600; Os01g0746400 and...”
- The strigolactone biosynthesis gene DWARF27 is co-opted in rhizobium symbiosis
van, BMC plant biology 2015 - “...are highlighted in bold. The D27 orthology group containing rice OsD27 (gi|2549466546) and Arabidopsis AtD27 (At1G03055) is highlighted in blue. Mid-point rooting was applied for better tree visualization Next, we determined whether MtD27 represents a functional enzyme in the strigolactone biosynthesis pathway. To this end, we...”
- More
- The Arabidopsis D27-LIKE1 is a cis/cis/trans-β-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level.
Yang, The Plant journal : for cell and molecular biology 2023 (PubMed)- GeneRIF: The Arabidopsis D27-LIKE1 is a cis/cis/trans-beta-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level.
- The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1 in the control of plant development by strigolactones.
Waters, Plant physiology 2012 - GeneRIF: AtD27 operates on a nonmobile precursor upstream of MAX1 in the strigolactone biosynthesis pathway. [AtD27]
AT4G01995, NP_680560 hypothetical protein from Arabidopsis thaliana
Aligns to 149:232 / 258 (32.6%), covers 96.6% of PF13225, 119.3 bits
- Subfunctionalization of D27 Isomerase Genes in Saffron
López-Jiménez, International journal of molecular sciences 2022 - “...[ 11 ], and the expression levels were 10-fold higher compared to the other AtD27-like (NP_680560), the CsD27-2 homolog, which showed high expression levels in cotyledons, young, intermediate and mature leaves, silique pedicel, and sepals [ 11 ]. In the case of rice, the CsD27-3 homolog...”
- 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.q. 4Fe4S (?) Strigolactone biosynthesis DWARF27.1 At1g64680 DWARF27.2 1.05 * n.q. 4Fe4S (?) Unknown DWARF27.2 At4g01995 DWARF27.3 n.d. n.d. 4Fe4S (?) Unknown DWARF27.3 At1g10960 FD1 (PETF2) n.v. n.q. 2Fe2S Electron transport chain Ferredoxin 1 At1g60950 FD2 (PETF) n.v. n.q. 2Fe2S Photosynthesis Ferredoxin 2 At2g27510 FD3 n.q....”
- Roles and maturation of iron-sulfur proteins in plastids
Przybyla-Toscano, Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2018 - “...al. [ 168 ] DWARF27.2 At1g64680 [Fe 4 S 4 ] Not yet described DWARF27.3 At4g01995 [Fe 4 S 4 ] Not yet described ISPG At5g60600 [Fe 4 S 4 ] Knock-out Albino phenotype, proplastid growth and thylakoid membrane formation affected Gutirrez-Nava et al. [ 163...”
DWARF27 / C7AU21 β-carotene isomerase (EC 5.2.1.14) from Oryza sativa subsp. japonica (see 2 papers)
D27_ORYSJ / C7AU21 Beta-carotene isomerase D27, chloroplastic; Protein DWARF-27; EC 5.2.1.14 from Oryza sativa subsp. japonica (Rice) (see 4 papers)
C7AU21 beta-carotene isomerase (EC 5.2.1.14) from Oryza sativa (see paper)
Aligns to 173:254 / 278 (29.5%), covers 96.6% of PF13225, 115.0 bits
- function: Involved in strigolactones biosynthesis by catalyzing the isomerization of the C9-C10 double bond in all-trans-beta-carotene leading to 9-cis-beta-carotene and providing the substrate for CCD7. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signals that stimulate hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.
catalytic activity: all-trans-beta-carotene = 9-cis-beta-carotene (RHEA:34455)
cofactor: Fe cation (Recombinant protein contains about 1.7 mole of iron per mole of protein.)
disruption phenotype: Increased tillers and reduced plant height, reduced levels of strigolactone.
GRMZM2G116461 uncharacterized protein LOC100277925 precursor from Zea mays
Aligns to 157:238 / 262 (31.3%), covers 96.6% of PF13225, 113.8 bits
Or search for genetic data about PF13225 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory