IRX10L (IRX10-LIKE, At5g61840; also called GUT1 and XYLAN SYNTHASE-1, XYS1) is a glycosyltransferase family 47 (GT47) xylan synthase. The purified catalytic domain uses UDP-xylose to add multiple beta-1,4-linked xylosyl residues to the non-reducing end of xylooligosaccharide acceptors, polymerising xylan chains in vitro in a distributive manner without other proteins; it uses no other UDP-sugar donor and needs no divalent cation. The protein has an N-terminal hydrophobic signal/signal-anchor segment and a lumenal catalytic domain, and Golgi proteomics places it in the Golgi, enriched in medial cisternae. IRX10L is the main xylan backbone synthase in primary-wall tissues, where with IRX9L and IRX14 it makes the regularly substituted, GUX3-decorated primary-wall xylan; irx10l single mutants lose this xylan and most microsomal xylosyltransferase activity in callus. In secondary walls it is the minor partner of IRX10: irx10l alone has no visible phenotype, but irx10 irx10l double mutants nearly lack secondary-wall xylan, with collapsed xylem and severe dwarfing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000139 Golgi membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Golgi membrane from the UniProt subcellular location (by similarity to IRX7). Reason: Xylan backbone synthesis takes place in the Golgi, and the IRX10 clade acts with the membrane-anchored GT43 proteins IRX9 and IRX14 in a Golgi xylan synthase complex. The N terminus is a single hydrophobic segment that UniProt models as a type II signal anchor, while the original characterisation called it a signal peptide; either way the catalytic domain faces the Golgi lumen and the protein is held at the Golgi membrane, directly or through IRX9/IRX14. The ISS row is transferred from IRX7/FRA8 (Q9ZUV3), a GT47 type II protein, which is a reasonable donor for location. Golgi membrane is as precise as the evidence allows. Same action as the IRX10 review. Supporting Evidence: file:ARATH/IRX10L/IRX10L-uniprot.txt Golgi apparatus membrane file:ARATH/IRX10L/IRX10L-uniprot.txt Signal-anchor for type II membrane protein PMID:26951434 AoIRX9, AoIRX10, and AoIRX14A are core components of a Golgi-localized XSC PMID:25141999 membrane topology studies indicate that the catalytic domain of IRX10-L is localized in the Golgi lumen (Sogaard et al., 2012) PMID:25141999 Notably, IRX10 and IRX10-L are both predicted to contain signal peptides rather than transmembrane domains |
| GO:0000139 Golgi membrane | ISS GO_REF:0000024 | ACCEPT | Summary: Golgi membrane transferred from the GT47 protein IRX7/FRA8 (Q9ZUV3). Reason: Xylan backbone synthesis takes place in the Golgi, and the IRX10 clade acts with the membrane-anchored GT43 proteins IRX9 and IRX14 in a Golgi xylan synthase complex. The N terminus is a single hydrophobic segment that UniProt models as a type II signal anchor, while the original characterisation called it a signal peptide; either way the catalytic domain faces the Golgi lumen and the protein is held at the Golgi membrane, directly or through IRX9/IRX14. The ISS row is transferred from IRX7/FRA8 (Q9ZUV3), a GT47 type II protein, which is a reasonable donor for location. Golgi membrane is as precise as the evidence allows. Same action as the IRX10 review. Supporting Evidence: file:ARATH/IRX10L/IRX10L-uniprot.txt Golgi apparatus membrane file:ARATH/IRX10L/IRX10L-uniprot.txt Signal-anchor for type II membrane protein PMID:26951434 AoIRX9, AoIRX10, and AoIRX14A are core components of a Golgi-localized XSC PMID:25141999 membrane topology studies indicate that the catalytic domain of IRX10-L is localized in the Golgi lumen (Sogaard et al., 2012) PMID:25141999 Notably, IRX10 and IRX10-L are both predicted to contain signal peptides rather than transmembrane domains |
| GO:0005768 endosome | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | KEEP AS NON CORE | Summary: Endosome from LOPIT proteomics (Nikolovski et al. 2012). Reason: In plants the trans-Golgi network acts as the early endosome, and LOPIT clusters that overlap the Golgi/TGN can give an endosome call. IRX10L is a Golgi-resident enzyme; this is at most a peripheral or transit location and not where xylan is made. Kept as non-core, deferring to the experimental call. Supporting Evidence: PMID:22923678 We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14 |
| GO:0005794 Golgi apparatus | HDA PMID:16618929 Mapping the Arabidopsis organelle proteome. | ACCEPT | Summary: Golgi apparatus from LOPIT density-gradient proteomics (Dunkley et al. 2006). Reason: Golgi apparatus is a root organelle term and an informative location. Organelle proteomics cannot resolve the cisterna or membrane; ACCEPT per the organelle policy. Supporting Evidence: PMID:16618929 enabling confident and simultaneous localization of 527 proteins to the endoplasmic reticulum, Golgi apparatus, vacuolar membrane, plasma membrane, or mitochondria and plastids |
| GO:0005794 Golgi apparatus | HDA PMID:22430844 Isolation and proteomic characterization of the Arabidopsis ... | ACCEPT | Summary: Golgi apparatus from proteomics of purified Arabidopsis Golgi (Parsons et al. 2012). Reason: Golgi apparatus is a root organelle term and an informative location. Organelle proteomics cannot resolve the cisterna or membrane; ACCEPT per the organelle policy. Supporting Evidence: PMID:22430844 A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome |
| GO:0005794 Golgi apparatus | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | ACCEPT | Summary: Golgi apparatus from LOPIT proteomics, which names IRX10-L (Nikolovski et al. 2012). Reason: Golgi apparatus is a root organelle term and an informative location. Organelle proteomics cannot resolve the cisterna or membrane; ACCEPT per the organelle policy. Supporting Evidence: PMID:22923678 We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14 PMID:22923678 These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method |
| GO:0005794 Golgi apparatus | IDA PMID:25141999 Two Arabidopsis proteins synthesize acetylated xylan inΒ vitr... | ACCEPT | Summary: Golgi apparatus attributed to Urbanowicz et al. 2014. Reason: The location is right and is shown independently by three Golgi proteomics studies (HDA rows). The cited paper does not localise the protein itself: it cites a topology study (Sogaard et al. 2012) for the lumenal catalytic domain. See source_defects. Supporting Evidence: PMID:25141999 membrane topology studies indicate that the catalytic domain of IRX10-L is localized in the Golgi lumen (Sogaard et al., 2012) PMID:22923678 We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14 |
| GO:0005794 Golgi apparatus | ISM GO_REF:0000122 | ACCEPT | Summary: Golgi apparatus predicted by AtSubP. Reason: Golgi apparatus is a root organelle term and an informative location. The prediction agrees with the proteomics and with the protein's role in Golgi xylan synthesis, so the organelle claim holds. Supporting Evidence: file:ARATH/IRX10L/IRX10L-uniprot.txt Golgi apparatus membrane PMID:22923678 We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14 |
| GO:0005797 Golgi medial cisterna | HDA PMID:31266899 Separating Golgi Proteins from Cis to Trans Reveals Underlyi... | ACCEPT | Summary: Golgi medial cisterna from cisternal separation proteomics (Parsons et al. 2019). Reason: The most precise location call available for IRX10L, from a method designed to separate early and late Golgi cisternae. It fits the medial/trans Golgi site of hemicellulose synthesis. Abstract-only in cache; deferring to the curator who read the cisternal assignments. Supporting Evidence: PMID:31266899 we exploit differences in surface charge of intact cisternae to perform separation of early to late Golgi subcompartments |
| GO:0005802 trans-Golgi network | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | KEEP AS NON CORE | Summary: Trans-Golgi network from LOPIT proteomics (Nikolovski et al. 2012). Reason: A proteomic co-fractionation call. The xylan synthase acts in the Golgi stack (the cisternal study places IRX10L in medial cisternae); TGN presence is plausible for transit but peripheral. Supporting Evidence: PMID:22923678 We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14 |
| GO:0009101 glycoprotein biosynthetic process | IEA GO_REF:0000002 | REMOVE | Summary: Glycoprotein biosynthesis mapped from the exostosin (GT47) InterPro signature. Reason: InterPro2GO maps the exostosin family signature (IPR004263) to glycoprotein biosynthetic process because the animal exostosins (EXT1/EXT2) polymerise heparan sulfate on proteoglycan core proteins. The plant GT47 IRX10 clade polymerises the free polysaccharide xylan from UDP-xylose onto xylooligosaccharide acceptors, and no protein acceptor is involved. The mapping does not transfer to this clade. The same row on the paralog is removed for the same reason. Supporting Evidence: PMID:25141999 These data unambiguously establish that IRX10-L is a polymerizing GT that forms Ξ²-(1β4) linkages by transferring multiple xylosyl residues from UDP-Xyl to the non-reducing end of xylooligosaccharide acceptors PMID:25141999 our data indicates that IRX10-L, unaided by other enzymes, uses a distributive mechanism to catalyze xylan synthesis in vitro |
| GO:0009834 plant-type secondary cell wall biogenesis | IBA GO_REF:0000033 | ACCEPT | Summary: Secondary cell wall biogenesis inherited from the IRX10 clade node. Reason: IRX10L is the minor secondary-wall paralog but is fully redundant with IRX10 there: irx10-L alone has no phenotype, while the double mutant loses most secondary wall xylan, and IRX10L expression rescues irx10. It therefore does part of the work of secondary wall biogenesis. Supporting Evidence: PMID:18980662 irx10 irx10-L double mutant plants showed a much more severe irx and whole-plant phenotype, suggesting considerable functional redundancy between these two genes PMID:18980662 Detailed biochemical analysis of the irx10 irx10-L double mutant showed a large reduction of xylan in the secondary cell walls PMID:20424005 The IRX9-L, IRX10-L, IRX14-L, and F8H genes are able to partially substitute for their respective homologs and normally perform a minor function |
| GO:0009834 plant-type secondary cell wall biogenesis | IMP PMID:18980662 Characterization of IRX10 and IRX10-like reveals an essentia... | ACCEPT | Summary: Secondary cell wall biogenesis from irx10 irx10-L double-mutant phenotypes. Reason: Same evidence and action as the IBA row. Supporting Evidence: PMID:18980662 irx10 irx10-L double mutant plants showed a much more severe irx and whole-plant phenotype, suggesting considerable functional redundancy between these two genes PMID:18980649 Stem sections of the irx10 homozygous irx10-L heterozygous or irx10 irx10-L double mutants show decreased secondary cell-wall formation |
| GO:0010417 glucuronoxylan biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Glucuronoxylan biosynthesis inherited from the IRX10 clade node. Reason: Core process. IRX10L elongates the xylan backbone of glucuronoxylan in both primary and secondary walls. Supporting Evidence: PMID:18980649 These findings demonstrate that IRX10 and IRX10-L perform a critical function in the synthesis of glucuronoxylan during secondary cell-wall formation, and that this activity is associated with the formation of the xylan backbone structure PMID:25141999 These data unambiguously establish that IRX10-L is a polymerizing GT that forms Ξ²-(1β4) linkages by transferring multiple xylosyl residues from UDP-Xyl to the non-reducing end of xylooligosaccharide acceptors PMID:26043357 IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues |
| GO:0010417 glucuronoxylan biosynthetic process | IMP PMID:18980662 Characterization of IRX10 and IRX10-like reveals an essentia... | ACCEPT | Summary: Glucuronoxylan biosynthesis from irx10 irx10-L double-mutant chemistry. Reason: Consistent with the IBA row and with the direct biochemistry of IRX10L. Supporting Evidence: PMID:18980662 Detailed biochemical analysis of the irx10 irx10-L double mutant showed a large reduction of xylan in the secondary cell walls PMID:18980662 shows a severe reduction in beta(1,4) xylosyltransferase activity |
| GO:0016757 glycosyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Glycosyltransferase activity from the GT47 InterPro signature. Reason: Correct but uninformative. The specific activity, UDP-xylose-dependent beta-1,4-xylan synthase, has been shown biochemically for IRX10 and for IRX10L, and the gene already carries GO:0047517. Proposed replacements: 1,4-beta-D-xylan synthase activity Supporting Evidence: file:ARATH/IRX10L/IRX10L-uniprot.txt Belongs to the glycosyltransferase 47 family PMID:25139408 We also find lower but reproducible xylan xylosyltransferase activity with A. thaliana IRX10 PMID:25141999 In summary, we have demonstrated that IRX10-L has UDP-Xyl: Ξ²-(1β4) xylosyl transferase activity |
| GO:0042546 cell wall biogenesis | IMP PMID:25141999 Two Arabidopsis proteins synthesize acetylated xylan inΒ vitr... | MODIFY | Summary: Cell wall biogenesis attributed to Urbanowicz et al. 2014. Reason: True but general. IRX10L makes the xylan of both wall types: the primary-wall xylan (irx10L single mutant, Mortimer et al. 2015) and secondary-wall glucuronoxylan redundantly with IRX10 (double mutants). Both plant-type children are supported, and the gene already carries GO:0009834. The cited paper is purely in vitro biochemistry and contains no mutant data; see source_defects. Proposed replacements: plant-type primary cell wall biogenesis plant-type secondary cell wall biogenesis Supporting Evidence: PMID:26043357 IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues PMID:18980662 Detailed biochemical analysis of the irx10 irx10-L double mutant showed a large reduction of xylan in the secondary cell walls PMID:25141999 we expressed a recombinant tagged form this enzyme in human embroyonic kidney (HEK) 293 cells and purified it from the culture medium |
| GO:0045492 xylan biosynthetic process | IDA PMID:25141999 Two Arabidopsis proteins synthesize acetylated xylan inΒ vitr... | ACCEPT | Summary: Xylan biosynthesis from in vitro polymerisation by purified IRX10L. Reason: Purified IRX10L makes beta-1,4-xylan chains in vitro. The in vitro product is unsubstituted xylan, so xylan biosynthetic process, not glucuronoxylan, is the precise term for this row. Supporting Evidence: PMID:25141999 These data unambiguously establish that IRX10-L is a polymerizing GT that forms Ξ²-(1β4) linkages by transferring multiple xylosyl residues from UDP-Xyl to the non-reducing end of xylooligosaccharide acceptors PMID:25141999 our data indicates that IRX10-L, unaided by other enzymes, uses a distributive mechanism to catalyze xylan synthesis in vitro |
| GO:0045492 xylan biosynthetic process | IMP PMID:26043357 An unusual xylan in Arabidopsis primary cell walls is synthe... | MODIFY | Summary: Xylan biosynthesis from loss of primary-wall xylan and of microsomal XylT activity in irx10L. Reason: Mortimer et al. showed that IRX10L, not IRX10, makes the backbone of the primary-wall xylan: irx10L callus membranes have almost no xylosyltransferase activity and lose this xylan. That in vivo product is GlcA-substituted (GUX3 adds its GlcA), so it is a glucuronoxylan, and GO:0010417, which the gene already carries (IBA, IMP), is the term the evidence supports. Proposed replacements: glucuronoxylan biosynthetic process Supporting Evidence: PMID:26043357 IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues PMID:26043357 Membranes from irx10L callus had a small amount of residual XylT activity, but it was extremely low compared to WT PMID:26043357 IRX9 and IRX10 are not involved in the primary cell wall xylan synthesis but are functionally exchangeable with IRX9L and IRX10L PMID:26043357 GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan |
| GO:0047517 1,4-beta-D-xylan synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Xylan synthase activity inherited from the IRX10 clade node. Reason: Core function, shown directly for purified IRX10L and for orthologs across land plants; consistent with the IDA row. Supporting Evidence: PMID:25141999 In summary, we have demonstrated that IRX10-L has UDP-Xyl: Ξ²-(1β4) xylosyl transferase activity PMID:25139408 showing that xylan xylosyltransferase activity is conserved over large evolutionary distance for these proteins |
| GO:0047517 1,4-beta-D-xylan synthase activity | IDA PMID:25141999 Two Arabidopsis proteins synthesize acetylated xylan inΒ vitr... | ACCEPT | Summary: Purified IRX10L (XYS1) polymerises beta-1,4-xylan from UDP-Xyl (Urbanowicz et al. 2014). Reason: Core function. The secreted catalytic domain, purified from HEK293 cells, transfers multiple xylosyl residues from UDP-Xyl to the non-reducing end of xylooligosaccharide acceptors, forming beta-1,4 linkages, and uses no other UDP-sugar. On this basis the authors named the protein XYLAN SYNTHASE-1. Supporting Evidence: PMID:25141999 we expressed a recombinant tagged form this enzyme in human embroyonic kidney (HEK) 293 cells and purified it from the culture medium PMID:25141999 These data unambiguously establish that IRX10-L is a polymerizing GT that forms Ξ²-(1β4) linkages by transferring multiple xylosyl residues from UDP-Xyl to the non-reducing end of xylooligosaccharide acceptors PMID:25141999 In summary, we have demonstrated that IRX10-L has UDP-Xyl: Ξ²-(1β4) xylosyl transferase activity PMID:25141999 We tested whether IRX10-L can utilize other UDP-sugars, including UDP-arabinopyranose, UDP-galactose, UDP-galacturonic acid, UDP-glucose and UDP-glucuronic acid, as sugar donors |
| GO:0080116 glucuronoxylan glucuronosyltransferase activity | IBA GO_REF:0000033 | MODIFY | Summary: Glucuronoxylan glucuronosyltransferase activity inherited from PANTHER node PTN001667002, seeded only by IRX10L's own IMP row. Reason: GO:0080116 means transfer of glucuronate onto the xylan backbone. That reaction belongs to the GT8 GUX enzymes, not to IRX10/IRX10L. The term reflects the early 'GUT' (glucuronyltransferase) naming that came from the tobacco homolog NpGUT1, and the irx10 loss of GlcA side chains, which is secondary to the shortened backbone. The cited mutant paper itself reports a loss of beta-1,4-xylosyltransferase activity in irx10 irx10-L and concludes a role in backbone elongation. Purified IRX10L transfers xylose from UDP-Xyl and does not use UDP-GlcA, and GUX3 is the sole glucuronyltransferase for primary wall xylan. The underlying claim (an MF in glucuronoxylan synthesis, from the double-mutant phenotype) is right, so the row is redirected to xylan synthase activity rather than removed. Propagation Review Root cause: SOURCE BAD Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN001667002 Β· PTN001667002 SOURCE BAD The only listed descendant evidence is AT5G61840 itself, i.e. the IMP row from PMID:18980662. That row reads a backbone xylosyltransferase defect (with secondary loss of GlcA side chains) as glucuronosyltransferase activity. The node placement is sound for xylan synthase activity, which the clade carries; the MF on this node should be replaced, not the node moved. Proposed replacements: 1,4-beta-D-xylan synthase activity Supporting Evidence: PMID:18980662 shows a severe reduction in beta(1,4) xylosyltransferase activity PMID:18980662 suggests that IRX10 and IRX10-L also play a role in elongation of the xylan backbone PMID:25141999 In summary, we have demonstrated that IRX10-L has UDP-Xyl: Ξ²-(1β4) xylosyl transferase activity PMID:25141999 We tested whether IRX10-L can utilize other UDP-sugars, including UDP-arabinopyranose, UDP-galactose, UDP-galacturonic acid, UDP-glucose and UDP-glucuronic acid, as sugar donors PMID:26043357 GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan |
| GO:0080116 glucuronoxylan glucuronosyltransferase activity | IMP PMID:18980662 Characterization of IRX10 and IRX10-like reveals an essentia... | MODIFY | Summary: Glucuronoxylan glucuronosyltransferase activity from irx10 irx10-L mutants. Reason: GO:0080116 means transfer of glucuronate onto the xylan backbone. That reaction belongs to the GT8 GUX enzymes, not to IRX10/IRX10L. The term reflects the early 'GUT' (glucuronyltransferase) naming that came from the tobacco homolog NpGUT1, and the irx10 loss of GlcA side chains, which is secondary to the shortened backbone. The cited mutant paper itself reports a loss of beta-1,4-xylosyltransferase activity in irx10 irx10-L and concludes a role in backbone elongation. Purified IRX10L transfers xylose from UDP-Xyl and does not use UDP-GlcA, and GUX3 is the sole glucuronyltransferase for primary wall xylan. The underlying claim (an MF in glucuronoxylan synthesis, from the double-mutant phenotype) is right, so the row is redirected to xylan synthase activity rather than removed. Proposed replacements: 1,4-beta-D-xylan synthase activity Supporting Evidence: PMID:18980662 shows a severe reduction in beta(1,4) xylosyltransferase activity PMID:18980662 suggests that IRX10 and IRX10-L also play a role in elongation of the xylan backbone PMID:25141999 In summary, we have demonstrated that IRX10-L has UDP-Xyl: Ξ²-(1β4) xylosyl transferase activity PMID:25141999 We tested whether IRX10-L can utilize other UDP-sugars, including UDP-arabinopyranose, UDP-galactose, UDP-galacturonic acid, UDP-glucose and UDP-glucuronic acid, as sugar donors PMID:26043357 GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: IRX10L alone polymerises xylan in vitro, yet irx9L and irx14 lose primary-wall xylan and microsomal XylT activity. What do the GT43 partners contribute in vivo: anchoring, processivity or acceptor priming?
Q: Should the PAINT node for the IRX10 clade drop glucuronoxylan glucuronosyltransferase activity (GO:0080116), which rests on mutant phenotypes that indicate backbone xylosyl transfer?
Experiment: Express IRX10L with and without its N-terminal hydrophobic segment in irx10 irx10l plants and in Nicotiana with and without IRX9L/IRX14, and track Golgi retention and secretion.
Hypothesis: IRX10L is retained in the Golgi through the GT43 partners rather than its own signal anchor.
Type: localization and complementation
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)