Bacterial RecBCD double-strand-end resection

A reusable bacterial homologous-recombination initiation module in which the RecBCD complex engages a double-strand DNA end, the oppositely directed RecB and RecD motors unwind the duplex, RecC participates in a taxon-dependent recombinogenic switch, the RecB nuclease produces a 3-prime single-stranded tail, and RecB promotes RecA loading. The identity and even sequence dependence of the switch vary among bacteria. RecFOR single-strand-gap repair, RecA strand exchange, RuvABC branch migration and resolution, replication restart, and bacterial nonhomologous end joining are separate modules.

The module is species-neutral. It represents the RecBCD system of Proteobacteria, Actinobacteria and other RecBCD-encoding bacteria, not the analogous AddAB system of Firmicutes, which uses a different subunit set (AddA, AddB) and has a nuclease in each subunit. E. coli K-12 is the experimental exemplar for every RecBCD role. P. putida KT2440 is a second, inferred exemplar for the Pseudomonas lineage, whose RecBCD-like enzymes are recombination-proficient but do not respond to the E. coli Chi octamer. The sequence-dependent switch is kept as a mechanistic part because it is central in characterized RecBCD systems, but the module does not require the E. coli Chi octamer. Only RecB carries the nuclease active site. RecC and RecD contribute to Exonuclease V activity as subunits (their gene reviews record contributes_to), so the nuclease annoton is placed on RecB alone. Family selectors were chosen to exclude non-RecBCD paralogs. RecB is selected with PTHR11070:SF23, a RecB-only subfamily. RecC is selected with NCBIfam TIGR01450, because the only PANTHER subfamily of PTHR30591 (SF1) mixes RecC with AddB/RexB. RecD is selected with NCBIfam TIGR01447 plus cognate RecB-RecC context, because PTHR43788:SF6 also contains standalone RecD2 helicases and eukaryotic HELB. All four PANTHER families have family reviews, and PTHR11070, PTHR30591 and PTHR43788 were written for this module. Their PAINT placement, including a PTHR30591 slice artefact and RecD2/HELB over-propagation, is documented in analysis/module_audits/bacterial_recbcd_end_resection/RESULTS.md. The RecA-loading step (GO:0000730 DNA recombinase assembly) is carried at gene level by NEW rows on E. coli RecB, which loads RecA through its nuclease domain, and on E. coli RecA, the recombinase whose ATP-dependent polymerization builds the filament. GO annotates both mediators (BRCA2, Rad52) and recombinases (S. pombe rad51, dmc1) to this term. The P. putida exemplars carry no such row. For P. putida RecB the loading role is inferred only by homology from E. coli, and the P. putida RecA review is being edited by other open pull requests.