Bacterial undecaprenyl-phosphate carrier supply

A reusable bacterial module that supplies the C55 polyprenyl-phosphate lipid carrier used for cell-envelope glycan assembly. A soluble cis-prenyltransferase, UppS, elongates (2E,6E)-farnesyl diphosphate with eight isopentenyl diphosphates to form di-trans,octa-cis-undecaprenyl diphosphate (C55-PP). An integral inner-membrane undecaprenyl-diphosphatase of the BacA/UppP family then removes the terminal phosphate to make undecaprenyl phosphate (C55-P). The same phosphatase reaction also returns C55-PP, released after glycan transfer, to the usable C55-P pool. The carrier supports several pathways, including peptidoglycan, lipopolysaccharide O-antigen and enterobacterial common antigen synthesis. Transfer of pathway-specific sugars onto the carrier, glycan polymerization, carrier flipping, and the unrelated PAP2-family phosphatases that partly overlap the second step are outside this module.

The module represents carrier supply, not a peptidoglycan-specific pathway: C55-P is shared by several bacterial envelope-glycan systems. Scope: the two steps are conserved across Bacteria. UppS (TIGR00055/HAMAP MF_01139) and BacA/UppP (TIGR00753/HAMAP MF_01006) are near-universal in bacterial genomes. The module therefore uses family selectors with Bacteria as context, and grounds them with the biochemically characterized E. coli K-12 enzymes (IspU/UppS P60472, BacA/UppP P60932) and the P. putida KT2440 orthologs (Q88MH6, Q88IY7). Firmicutes (B. subtilis UppS, UppP) carry the same two families but are not added as exemplars, because they would add no independent experimental grounding beyond E. coli. Family choice: PTHR10291:SF0 is asserted with its official label "DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE 2" because PANTHER places both bacterial UppS exemplars there. The family review (interpro/panther/PTHR10291) records that the subfamily also holds the mycobacterial C50 decaprenyl diphosphate synthases and plant plastid paralogs, so GO:0008834 should not be propagated across all of SF0. PTN000033434, the proteobacterial UppS node, is the PAINT anchor for the C55-specific activity, but it covers only Pseudomonadota. The Firmicutes/Actinobacteria node PTN007432212, which carries the same term, is NEEDS_PRUNING because its only seed is the mycobacterial C50 enzyme. The Bacteria-wide claim therefore rests on the experimental grounding in E. coli and KT2440 and on the conserved UppS family assignment (TIGR00055/HAMAP MF_01139), not on a sound Bacteria-wide PAINT node. PTHR30622 is functionally coherent, but its root-node peptidoglycan term also reaches archaeal members, which the family review marks TOO_DEEP. Ontology note: GO has no undecaprenyl-phosphate or polyprenyl-phosphate biosynthetic process term, so both steps use GO:0016094 polyprenol biosynthetic process, the term GO already applies to UppS. A dedicated "undecaprenyl phosphate biosynthetic process" term would describe the module more precisely. Some bacteria lacking an obvious bacA rely on PAP2-family C55-PP phosphatases (e.g. B. subtilis BcrC), which are a separate family and not modelled here. Species-aware research also identifies three P. putida PAP2-family candidates, but broad family membership is not enough to assign undecaprenyl-diphosphatase activity to them.