recA

Gene Description

RecA is the central bacterial recombinase and the master regulator of the SOS DNA damage response. It binds single-stranded DNA and assembles into a right-handed helical nucleoprotein filament that, in an ATP-dependent manner, searches homologous duplex DNA and catalyzes DNA pairing and strand exchange (synapsis). This activity underpins homologous recombination, recombinational repair of double-strand breaks, and the rescue of stalled or collapsed replication forks. The activated filament (RecA*) also acts as a co-protease platform that stimulates autocatalytic self-cleavage of the LexA repressor, thereby derepressing the SOS regulon and inducing DNA repair and damage-tolerance genes. RecA hydrolyzes ATP in the presence of single-stranded DNA, which drives filament dynamics and strand exchange. In Pseudomonas putida KT2440 the protein acts in the cytoplasm on DNA; the activated RecA filament is competent to cleave the principal SOS repressor LexA1, and the gene contributes to survival of DNA-damaging and other stresses.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003677 DNA binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: RecA binds DNA as an intrinsic part of its recombinase function. Reason: Correct but general. RecA's biologically meaningful binding activities are single-stranded DNA binding (GO:0003697) and damaged DNA binding (GO:0003684), which are separately annotated and capture the core function more precisely. Retained as a true but non-core parent term.
GO:0003684 damaged DNA binding	IEA GO_REF:0000104	ACCEPT	Summary: RecA recognizes and binds ssDNA generated at damaged/stalled DNA sites, a key step in recombinational repair and SOS activation. Reason: Consistent with RecA's role in sensing DNA damage substrates and forming the activated nucleoprotein filament. Well supported by family-level conservation and UniRule transfer.
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: Core molecular function of RecA, strongly conserved across the RecA family and consistent with the UniProt FUNCTION annotation.
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: Directly supported by the conserved P-loop NTPase / AAA+ domain and the annotated ATP binding site in the UniProt record.
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: RecA acts in the cytoplasm on chromosomal DNA. Reason: Consistent with the UniProt subcellular location (Cytoplasm) and the nature of RecA as a soluble DNA-acting protein. Cytosol (GO:0005829) is the more specific term.
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: RecA is a soluble cytosolic protein that assembles on DNA. Reason: Appropriate, more specific localization consistent with the cytoplasmic location and PANTHER tree-based transfer.
GO:0006259 DNA metabolic process	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: RecA participates in DNA metabolism through recombination and repair. Reason: Correct but very general; the specific processes (DNA recombination, DNA repair, SOS response) are separately annotated and better represent the gene's function. Retained as a true parent term.
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: Core biological role, supported by conservation and consistent with P. putida phenotypes (recA mutants hypersensitive to formaldehyde-induced DNA damage).
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: Defining core function of RecA, conserved across bacteria and consistent with the UniProt FUNCTION (ATP-dependent uptake/hybridization of homologous ssDNA).
GO:0006974 DNA damage response	IEA GO_REF:0000104	ACCEPT	Summary: RecA senses DNA damage (via ssDNA) and triggers the SOS response, the core cellular DNA damage response in bacteria. Reason: Correct and central to RecA function; the more specific SOS response (GO:0009432) is also annotated.
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: Accurately captures the ATP-driven, DNA-acting motor-like activity of RecA, consistent with the UniProt FUNCTION (ATP hydrolysis in the presence of ssDNA).
GO:0009432 SOS response	IEA GO_REF:0000104	ACCEPT	Summary: Activated RecA (RecA) promotes LexA autocleavage, derepressing the SOS regulon. In P. putida KT2440 RecA fully cleaves the main repressor LexA1. Reason: Core function strongly supported by both conservation and direct organism-specific evidence that P. putida RecA* cleaves LexA1 (Akkaya et al. 2021).
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: Appropriate molecular-function term for RecA's role as the SOS damage sensor that triggers LexA co-protease activity; consistent with InterPro mapping and RecA biology.

Core Functions

ATP-dependent DNA recombinase that nucleates on single-stranded DNA, forms a helical nucleoprotein filament, performs homology search, and catalyzes DNA pairing and strand exchange (homologous recombination and recombinational DNA repair).

Molecular Function:

ATP-dependent activity, acting on DNA

Directly Involved In:

DNA recombination

Substrates:

single-stranded DNA

Supporting Evidence:

file:PSEPK/recA/recA-deep-research-falcon.md

Single-stranded DNA binding and filament assembly that constitutes the structural basis of homology search and strand exchange.

Molecular Function:

single-stranded DNA binding

Directly Involved In:

DNA repair

Supporting Evidence:

file:PSEPK/recA/recA-deep-research-falcon.md

SOS co-protease activity - the activated RecA filament (RecA) acts as an ATP-dependent DNA-damage sensor that stimulates autocatalytic cleavage of the LexA repressor, inducing the SOS response. In P. putida KT2440 RecA fully cleaves the principal repressor LexA1.

Molecular Function:

ATP-dependent DNA damage sensor activity

Directly Involved In:

SOS response

Supporting Evidence:

file:PSEPK/recA/recA-deep-research-falcon.md

Gene Description

Existing Annotations Review

Core Functions

ATP-dependent DNA recombinase that nucleates on single-stranded DNA, forms a helical nucleoprotein filament, performs homology search, and catalyzes DNA pairing and strand exchange (homologous recombination and recombinational DNA repair).

Single-stranded DNA binding and filament assembly that constitutes the structural basis of homology search and strand exchange.

SOS co-protease activity - the activated RecA filament (RecA) acts as an ATP-dependent DNA-damage sensor that stimulates autocatalytic cleavage of the LexA repressor, inducing the SOS response. In P. putida KT2440 RecA fully cleaves the principal repressor LexA1.

References

Deep Research

Falcon

📄 View Raw YAML

recA

Gene Description

Existing Annotations Review

Core Functions

ATP-dependent DNA recombinase that nucleates on single-stranded DNA, forms a helical nucleoprotein filament, performs homology search, and catalyzes DNA pairing and strand exchange (homologous recombination and recombinational DNA repair).

Single-stranded DNA binding and filament assembly that constitutes the structural basis of homology search and strand exchange.

SOS co-protease activity - the activated RecA filament (RecA*) acts as an ATP-dependent DNA-damage sensor that stimulates autocatalytic cleavage of the LexA repressor, inducing the SOS response. In P. putida KT2440 RecA* fully cleaves the principal repressor LexA1.

References

Deep Research

Falcon

📄 View Raw YAML

SOS co-protease activity - the activated RecA filament (RecA) acts as an ATP-dependent DNA-damage sensor that stimulates autocatalytic cleavage of the LexA repressor, inducing the SOS response. In P. putida KT2440 RecA fully cleaves the principal repressor LexA1.