WapR (PA5000) is a GT2-family glycosyltransferase that adds the alpha-1,3-linked L-rhamnose to the outer core oligosaccharide of Pseudomonas aeruginosa lipopolysaccharide. This rhamnose forms the attachment point of the O antigen, so WapR makes the capped core glycoform; the paralogue MigA adds alpha-1,6-L-Rha to the uncapped glycoform. A wapR mutant has a truncated capped core lacking alpha-1,3-L-Rha and as a result its LPS carries no O antigen; complementation restores O-antigen capping. wapR is negatively regulated by RhlR/RhlI quorum sensing, and its expression level correlates with the amount of O-antigen-capped core. Core truncation in the mutant secondarily alters motility, surface attachment and biofilm mechanics.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009243 O antigen biosynthetic process | IMP PMID:18178733 Functional characterization of MigA and WapR: putative rhamn... | REMOVE | Summary: The wapR mutant's LPS lacks O antigen because the capped core lacks the alpha-1,3-L-Rha to which O antigen is attached. WapR builds the acceptor; it does not synthesise O antigen. Reason: The abstract states both facts: the mutant LPS lacks O antigen, and its capped core is truncated and lacks alpha-1,3-L-Rha, which is the linkage through which O antigen caps the core. Loss of O antigen from LPS is therefore a downstream effect of the missing acceptor (O antigen is polymerised separately and ligated to the completed core by WaaL), not participation in O antigen biosynthesis. The correct process, LPS core biosynthesis, is already on the gene. Supporting Evidence: PMID:18178733 one form is capped with O antigen through an alpha-1,3-linked L-rhamnose (L-Rha), while the other is uncapped and contains an alpha-1,6-linked L-Rha PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. PMID:18178733 The wapR mutant produced LPS lacking O antigen, and addition of wapR in trans complemented this defect. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: True for WapR, which has its own structural mutant evidence. The node PTN000531351, seeded only by WapR and MigA, also covers O-antigen and colanic acid glycosyltransferases, so the node term does not suit the clade. Reason: WapR adds the alpha-1,3-L-Rha of the capped LPS core, so the term is correct for this leaf. The node-level problem is recorded here once as a GO_CENTRAL defect: PAINT placed a pathway-specific term on a GT2 clade whose other members make O antigen (Salmonella RfbV) and colanic acid (E. coli WcaA). MigA (genes/PSEAE/migA) cross-references this defect. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000531351 · PTN000531351 SUPPORTS SOURCE BUT NOT TARGET Sound for WapR and MigA, but the clade (18 leaves, 10 taxa) includes RfbV and WcaA, whose experimental annotations are O antigen and colanic acid biosynthesis; the IBD over-reaches for those leaves (GO_CENTRAL defect on this row). UniProtKB:Q9HUG5 · wapR (PA5000) SUPPORTS TRANSFER PseudoCAP IMP and IDA seeds; mutant LPS structure shows loss of the alpha-1,3-L-Rha. Sound. UniProtKB:Q9I5M1 · migA (PA0705) SUPPORTS TRANSFER PseudoCAP IMP seed; mutant lacks alpha-1,6-L-Rha. Sound. Supporting Evidence: PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IDA PMID:22685285 Rhamnosyltransferase genes migA and wapR are regulated in a ... | ACCEPT | Summary: wapR expression correlates with the amount of O-antigen-capped core glycoform; consistent with WapR making the capped core. Reason: The process is correct for WapR (structural evidence in PMID:18178733). This regulation paper adds that the wapR expression level tracks the capped glycoform, so the row is accepted; the IDA code reflects glycoform quantification. Supporting Evidence: PMID:22685285 preferential expression of migA and wapR correlated with the levels of uncapped and O polysaccharide-capped core, respectively PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IMP PMID:18178733 Functional characterization of MigA and WapR: putative rhamn... | ACCEPT | Summary: PseudoCAP seed row: the wapR mutant has a truncated capped core lacking alpha-1,3-L-Rha (NMR, MS). Sound. Reason: The abstract states the structural result outright, and the missing sugar is the one WapR adds, so this is participation. Core process of the gene. Supporting Evidence: PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. |
| GO:0015920 lipopolysaccharide transport | IDA PMID:19589832 Truncation in the core oligosaccharide of lipopolysaccharide... | REMOVE | Summary: The cited study compared motility and surface attachment of wapR, migA/wapR and rmlC mutants with truncated core; it does not address LPS transport, and the wapR product builds the core rather than moving LPS. Reason: Core rhamnosyltransferases act at the cytoplasmic face of the inner membrane before LPS is exported by MsbA and the Lpt machinery. The abstract reports altered motility and attachment as consequences of LPS truncation. Neither result is LPS transport, and an IDA code on a mutant phenotype study does not fit. Removed with a PseudoCAP defect. Supporting Evidence: PMID:19589832 P. aeruginosa wild-type strain PAO1 and three isogenic mutants with defects in the rmlC, migA and wapR genes and producing truncated core oligosaccharide were investigated in terms of motility, attachment to glass and flagella expression. PMID:19589832 LPS truncations probably alter flagella-mediated motility in P. aeruginosa by modulating cell-surface attachment but not flagella synthesis PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. |
| GO:0016740 transferase activity | IMP PMID:18178733 Functional characterization of MigA and WapR: putative rhamn... | TOO GENERAL | Summary: True but uninformative; entailed by hexosyltransferase activity. Reason: GO:0016758 hexosyltransferase activity, accepted here, is a descendant of GO:0016740 transferase activity. Supporting Evidence: PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. |
| GO:0016757 glycosyltransferase activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: Correct, and entailed by hexosyltransferase activity, which WapR carries. The IBD at PTN000531320 (seven seeds) is sound. Reason: GO:0016758 hexosyltransferase activity, accepted here (rhamnosyltransferases are hexosyltransferases in GO), is_a GO:0016757. The IBD at PTN000531320 rests on seven seeds including IDA rows for Salmonella RfbV, E. coli WcaA, M. tuberculosis Rv2957 and B. subtilis SunS, and stands without WapR. Supporting Evidence: PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. file:PSEAE/wapR/wapR-uniprot.txt PF00535; Glycos_transf_2; 1. |
| GO:0016757 glycosyltransferase activity | IDA PMID:18178733 Functional characterization of MigA and WapR: putative rhamn... | TOO GENERAL | Summary: PseudoCAP seed row for PTN000531320: WapR is the alpha-1,3-rhamnosyltransferase. Term sound but entailed by hexosyltransferase activity. Reason: Sound as a seed: the specific loss of alpha-1,3-L-Rha in the mutant supports WapR as the transferase (the abstract describes no in vitro assay, so IMP would describe the evidence better than IDA). GO:0016758, accepted here, is_a GO:0016757. Supporting Evidence: PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. |
| GO:0016758 hexosyltransferase activity | IEA GO_REF:0000117 | ACCEPT | Summary: Hexosyltransferase activity: WapR transfers L-rhamnose, a 6-deoxyhexose, and GO places rhamnosyltransferases under this term. Reason: The ARBA prediction is correct; it is supported independently by the mutant structure evidence that WapR is the alpha-1,3-rhamnosyltransferase. No more specific GO term covers LPS core rhamnosyl transfer. Supporting Evidence: PMID:18178733 These results provide evidence that WapR is the alpha-1,3-rhamnosyltransferase, while MigA is the alpha-1,6-rhamnosyltransferase. PMID:18178733 The capped core of the wapR mutant was found to be truncated and lacked alpha-1,3-L-Rha. file:PSEAE/wapR/wapR-uniprot.txt GT2; Glycosyltransferase Family 2. |
| GO:0044010 single-species biofilm formation | IDA PMID:19717596 Differential lipopolysaccharide core capping leads to quanti... | MARK AS OVER ANNOTATED | Summary: Mutants lacking wapR make biofilms with altered mechanics and structure, a downstream consequence of LPS core truncation. Reason: The paper uses defined LPS mutants to study how core capping affects adhesion, cohesion and biofilm architecture. That shows LPS structure influences biofilm properties; the wapR product, a core glycosyltransferase, does no step of biofilm formation itself. Not removed because the mutant phenotype is real and the full text was not read. Supporting Evidence: PMID:19717596 Using isogenic migA, wapR, and rmlC mutants with defined LPS characteristics, we observed significant changes in cell mechanical properties among these strains compared to wild-type strain PAO1. PMID:19717596 truncation of core oligosaccharides enhanced both adhesive and cohesive forces by up to 10-fold |
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Download this section (compressed HTML)Q: Should PAINT place the LPS core biosynthesis IBD on a node restricted to the Pseudomonas core rhamnosyltransferases, given that PTN000531351 also contains O-antigen and colanic acid glycosyltransferases?
Experiment: Assay purified WapR with dTDP-L-rhamnose and core oligosaccharide isolated from a wapR mutant to confirm alpha-1,3 rhamnosyl transfer in vitro.
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