Bacterial nucleotide-excision repair system

A reusable bacterial nucleotide-excision repair module in which UvrA and UvrB recognize bulky, helix-distorting DNA lesions, UvrC incises the damaged strand on both sides of the lesion, UvrD releases the damage-containing oligonucleotide, DNA polymerase I fills the resulting gap, and an NAD-dependent DNA ligase seals the nick. Mfd supplies an optional transcription-coupled entry route by removing lesion-stalled RNA polymerase and recruiting the Uvr machinery. Base-excision repair, mismatch repair, homologous-recombination repair, translesion synthesis, and eukaryotic XPD/TFIIH excision repair are outside this module.

The module is species-neutral and represents both global-genome NER and the Mfd-dependent transcription-coupled entry route. The UvrABC-UvrD-PolA-LigA relay is conserved across bacteria, so each role carries two exemplars: Escherichia coli K-12, where the experimental characterization was done, and Pseudomonas putida KT2440, the original concrete instance. Both exemplars of every role have complete gene reviews whose core functions include the annoton's molecular function. Family groundings use the subfamily that the family reviews scope the function to: UvrA PTHR43152:SF3, UvrB PTHR24029:SF0, UvrC PTHR30562:SF1, UvrD PTHR11070:SF2 (the UvrD/PcrA/Srs2 subfamily; the 3'-5' helicase activity is not family-wide in PTHR11070), and LigA PTHR23389:SF9 (the family id alone also takes in eukaryotic RFC1, CTF18 and ATAD5/Elg1 clamp-loader subunits). PolA stays at family level because PTHR10133 supports DNA-directed DNA polymerase activity family-wide. Mfd is grounded to PTHR47964, whose family review (RecG/Mfd) is curated separately; PANTHER 19.0 classification files place E. coli Mfd in PTHR14025:SF29 while UniProt places it in PTHR47964:SF1, and the membership check accepts either. The UvrC annoton stays at GO:0004520 DNA endonuclease activity, the subunit-level catalytic activity carried by the PTHR30562 PAINT node PTN000778007, while both UvrC exemplars record the more specific GO:0009381 excinuclease ABC activity as their core function (an is_a child of GO:0004520). GO:0009381 names the dual-incision activity of the assembled UvrBC incision complex, to which UvrA and UvrB contribute, so it is kept as module-level evidence rather than assigned to one subunit's annoton. The UvrA ancestral node PTN000655914 is the PTHR43152 root and asserts only generic DNA binding; the damaged-DNA-binding claim rests on the SF3 subfamily scope. A phage-associated DNA polymerase I proposed as a PolA representative in a bulk grounding pass was not adopted, because phage replication polymerases are not members of this repair relay. Mfd is optional for the global-genome route. Cho-family alternative incision proteins and lineage-specific UvrA2 accessory paralogs are not universal requirements. PolA and LigA are shared with replication and other DNA-repair pathways. GO:0009381 describes the assembled UvrABC activity and is retained only as module-level evidence; each subunit leaf is represented by its distinguishable activity.