RecA is the conserved recombinase of Pseudomonas putida KT2440. It binds single-stranded DNA and assembles ATP-dependent nucleoprotein filaments that promote homologous DNA pairing and strand exchange, supporting recombination and recombinational repair. ATP turnover contributes to filament dynamics. Activated DNA-bound RecA also promotes LexA autocleavage in SOS signaling; it is a cofactor for the repressor's self-cleavage rather than the protease that cuts LexA. These molecular properties are supported by curated RecA-family evidence. Experiments in the prophage-free KT2440 derivative EM173 show unusually high basal recA/lexA1 expression and modest induction by norfloxacin, so the strength of the response differs from the canonical E. coli system.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: Refine generic DNA binding to the established single-stranded-DNA-binding function. Reason: DNA binding is true, and the target's curated RecA function specifies uptake and pairing of single-stranded DNA. Refine to the supported is_a child GO:0003697 already present in this review; this does not reject additional DNA contacts during synapsis. Proposed replacements: single-stranded DNA binding Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt DR InterPro; IPR020584; DNA_recomb/repair_RecA_CS. file:PSEPK/recA/recA-deep-research-falcon.md RecA is not a secreted or membrane protein; functionally it operates in the **cytosol on DNA** by assembling on ssDNA to form nucleoprotein filaments. |
| GO:0003684 damaged DNA binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: RecA recognizes and binds ssDNA generated at damaged/stalled DNA sites, a key step in recombinational repair and SOS activation. Reason: Retain the inherited binding claim as a qualified damage-associated context: RecA acts on single-stranded regions and gaps in damaged DNA, whereas lesion-specific recognition by Q88ME4 has not been directly measured. The broad term does not specify a damaged base or exclude damage-generated DNA structures. Curated RecA-family support and the gap-repair mechanism support this bounded interpretation; no lesion-specific binding constant or universal damage selectivity is asserted. Supporting Evidence: file:PSEPK/recA/recA-deep-research-falcon.md In canonical bacterial SOS regulation, DNA damage yields ssDNA substrates that support formation of the activated RecA nucleoprotein filament (often denoted RecA*). file:PSEPK/recA/recA-uniprot.txt DR HAMAP; MF_00268; RecA; 1. |
| GO:0003697 single-stranded DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: RecA nucleates and binds single-stranded DNA to form the helical nucleoprotein filament that performs homology search and strand exchange. Reason: Single-stranded DNA binding is intrinsic to the curated RecA filament and strand-exchange mechanism. HAMAP independently assigns this target the ATP-dependent uptake of ssDNA by duplex DNA. This is conserved-role inference, not a claim that a purified KT2440 binding assay was read; the EM173 SOS study is regulatory context, not an ssDNA-binding measurement. Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex file:PSEPK/recA/recA-deep-research-falcon.md RecA filament formation proceeds through nucleation and extension phases, nucleates preferentially on ssDNA, and filament growth is directionally biased (noted as 5′→3′ extension in a recent MMBR review). |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: RecA contains a P-loop (Walker A motif, residues 65-72) and binds ATP, which is required for active filament formation and strand exchange. Reason: The reviewed entry annotates an ATP binding site at residues 65-72 under the curated HAMAP rule, and the RecA ATP-binding region signature IPR020588 is matched. ATP binding is required for the active filament, so this supports rather than merely accompanies the core activity. Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt FT BINDING 65..72 file:PSEPK/recA/recA-uniprot.txt DR InterPro; IPR020588; RecA_ATP-bd. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | MODIFY | Summary: Refine the broad cytoplasmic location to the supported cytosolic site of RecA activity. Reason: Cytoplasmic localization is true and central to the DNA-associated function. Curated HAMAP localization plus the soluble nucleoprotein-filament mechanism support the cytosolic interpretation already represented by GO:0005829, a part_of descendant. This is a qualified cellular inference, not native fractionation data. Broadness is addressed by refinement, not by calling the core location peripheral. Proposed replacements: cytosol Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00268}. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: RecA is a soluble cytosolic protein that assembles on DNA. Reason: A soluble DNA-associated RecA filament acts in the cytosolic cellular interior, consistent with the independently curated HAMAP cytoplasm statement and conserved nucleoprotein mechanism. The location describes where its core activity occurs, so it is not peripheral merely because it is a component term. Native KT2440 localization was not measured in the evidence inspected. Supporting Evidence: file:PSEPK/recA/recA-deep-research-falcon.md RecA is not a secreted or membrane protein; functionally it operates in the **cytosol on DNA** by assembling on ssDNA to form nucleoprotein filaments. file:PSEPK/recA/recA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00268}. |
| GO:0006259 DNA metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: Refine DNA metabolism to its supported repair and recombination roles. Reason: RecA performs both repair-associated and broader homologous recombination. Both supported descendant processes already occur in the review and jointly preserve the broad DNA-metabolism scope. Proposed replacements: DNA repair DNA recombination Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt DR InterPro; IPR013765; DNA_recomb/repair_RecA. |
| GO:0006281 DNA repair | IEA GO_REF:0000120 | ACCEPT | Summary: RecA-mediated homologous recombination repairs double-strand breaks and stalled replication forks; recA mutants are hypersensitive to DNA-damaging agents. Reason: A core biological role. In this organism a recA deletion is hypersensitive to DNA-damaging stress and recA is induced by it, and the curated family rule supplies the recombinational-repair mechanism. Supporting Evidence: PMID:21261833 Repair and recombination systems, including uvrB (PP1974), uvrC (PP3254) and recA(PP1629), were induced more than twofold in response to sublethal HCOH concentrations (Table 2). file:PSEPK/recA/recA-uniprot.txt DR InterPro; IPR013765; DNA_recomb/repair_RecA. |
| GO:0006310 DNA recombination | IEA GO_REF:0000104 | ACCEPT | Summary: RecA is the central recombinase catalyzing homology search and DNA strand exchange in homologous recombination. Reason: Curated RecA-family function directly identifies homologous DNA pairing and strand exchange, supporting DNA recombination. The 2021 study uses EM173, a prophage-free KT2440 derivative, and reports poor recombination efficiency at the organism level; that observation is context rather than a purified target catalytic assay or proof that RecA is the sole cause. Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC DNA, and the ATP-dependent hybridization of homologous single-stranded PMID:33393180 sensitive to DNA damage and displays poor homologous recombination efficiencies. |
| GO:0006974 DNA damage response | IEA GO_REF:0000104 | MODIFY | Summary: Refine the general damage response to RecA-mediated SOS signaling. Reason: The supported specific damage-response pathway is SOS signaling through activated RecA and LexA autocleavage. GO:0009432 is a descendant of the broader response term and already occurs here. This refinement retains the response claim without equating every DNA-repair function with SOS. Proposed replacements: SOS response Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC DNAs. It interacts with LexA causing its activation and leading to its |
| GO:0008094 ATP-dependent activity, acting on DNA | IEA GO_REF:0000120 | ACCEPT | Summary: RecA couples ATP binding and hydrolysis to its action on DNA during filament dynamics and strand exchange. Reason: Curated target function assigns ssDNA-stimulated ATP hydrolysis and ATP-dependent homologous DNA transactions. Retain this ATP-dependent activity alongside the distinct strand-exchange and damage-sensor functions; GO:0000150 specifies synapsis but is not an is_a descendant that captures all ATP-dependent activity. No claim is made that every strand-pairing event strictly requires ATP hydrolysis rather than ATP binding. Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex file:PSEPK/recA/recA-deep-research-falcon.md RecA-mediated strand exchange is **coupled to ATP hydrolysis** and described as motor-like |
| GO:0009432 SOS response | IEA GO_REF:0000104 | ACCEPT | Summary: Activated DNA-bound RecA promotes LexA self-cleavage in SOS induction. Reason: The curated RecA mechanism supports a direct signaling contribution: activated filaments stimulate LexA autocleavage. The EM173 study establishes the native regulatory context and weak induction, but its accessible abstract does not establish the provider's stronger complete-cleavage assertion. That unverified quantitative claim is not required for accepting the conserved SOS role. Supporting Evidence: file:PSEPK/recA/recA-uniprot.txt CC DNAs. It interacts with LexA causing its activation and leading to its file:PSEPK/recA/recA-deep-research-falcon.md RecA* then serves as a scaffold that promotes **LexA autocatalytic self-cleavage**, de-repressing the SOS regulon. |
| GO:0140664 ATP-dependent DNA damage sensor activity | IEA GO_REF:0000002 | ACCEPT | Summary: RecA acts as an ATP-dependent sensor of DNA damage by forming the activated ssDNA-bound filament that initiates the SOS response. Reason: The current term describes recognition of toxic DNA structures and initiation of ATP-driven signaling. Activated ssDNA-associated RecA supplies the LexA-autocleavage signal, consistent with the curated target mechanism. This activity is a whole-gene role even though RecA-dependent induction is optional context for the downstream ImuABC machinery. Supporting Evidence: file:PSEPK/recA/recA-deep-research-falcon.md In canonical bacterial SOS regulation, DNA damage yields ssDNA substrates that support formation of the activated RecA nucleoprotein filament (often denoted RecA*). file:PSEPK/recA/recA-uniprot.txt CC DNAs. It interacts with LexA causing its activation and leading to its |
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