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.

MODULE:bacterial_recbcd_end_resectionDRAFTCONCRETEBiological Processmodules/bacterial_recbcd_end_resection.yaml
double-strand break repair via homologous recombinationGO:0000724
GO:0000724
double-strand break repair via homologous recombination
Defines the double-strand-break repair process initiated by RecBCD end resection.
GO:0009338
exodeoxyribonuclease V complex
Defines the RecB-RecC-RecD complex that performs the pathway's coupled motor and nuclease activities.
RHEA:13065
ATP hydrolysis reaction
Defines the ATPase chemistry that powers the RecB and RecD motors.
PANTHER:PTN000116141
PAINT RecB/UvrD-family directional-helicase node
The local PTHR11070 PAINT table assigns 3-prime-to-5-prime DNA helicase activity to this ancestral node using RecB and UvrD-family experimental seeds.
PMID:20195537
All three subunits of RecBCD enzyme are essential for DNA repair and low-temperature growth in the Antarctic Pseudomonas syringae Lz4W
Pseudomonad genetics supports a functional three-subunit RecBCD complex and shows that RecD loss causes a DNA-repair defect that differs from E. coli.
sensitive to DNA-damaging agents and fail to grow at 4 degrees C.
PMID:2559208
Activation of Chi recombinational hotspots by RecBCD-like enzymes from enteric bacteria
Primary clone experiments show that P. aeruginosa and P. putida RecBCD-like enzymes confer recombination and ATP-dependent nuclease activity but do not activate the E. coli Chi hotspot.
proficiency and ATP-dependent nuclease activity, but neither Chi hotspot
file:projects/P_PUTIDA/deep-research/PSEPK__recbcd-end-resection__ppu03440-deep-research-openscientist.md
OpenScientist PSEPK RecBCD end-resection synthesis
Species-aware retrieval resolves the contiguous KT2440 recD-recB-recC operon, confirms the expected subunit domains, and identifies the Pseudomonas-specific Chi-recognition boundary.

The module is species-neutral and represents RecBCD rather than the analogous AddAB system. Pseudomonas putida KT2440 supplies a concrete representative for each protein role. A sequence-dependent switch is retained as a mechanistic part because it is central in characterized RecBCD systems, but the module does not require the E. coli Chi octamer. KT2440's controlling signal is unresolved. RecC and RecD contribute to Exonuclease V activity; only RecB carries the nuclease active site. The broad PTHR43788:SF6 family also contains standalone RecD2/HelB helicases, so it is not used as the canonical RecBCD RecD selector; the RecBCD-specific NCBIfam model and cognate RecB-RecC context are required.

6Nodes
5Parts
0Variant Sets
0Variants
7Annotons
4Connections

Derived QC

Recommended-field compliance

53.8% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_recbcd_end_resection deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • recc_end_engagement → recbd_unwinding [NOT_CHECKED]
    RecC organizes end engagement before the RecB and RecD motors unwind the duplex.
  • recbd_unwinding → recc_resection_switch [NOT_CHECKED]
    Processive unwinding exposes the lineage-specific signal that can alter resection behavior.
  • recc_resection_switch → recb_resection [NOT_CHECKED]
    The switch biases RecB nuclease processing toward production of a recombinogenic 3-prime tail.

Gene-review completeness (4/8 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 4 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
E. coli RecD P04993 ✗ — —
E. coli RecC P07648 ✗ — —
E. coli RecB P08394 ✗ — —
E. coli RecA P0A7G6 ✗ — —
recA Q88ME4 ✓ ✓ ✓
recB Q88DZ5 ✓ ✓ ✓
recC Q88DZ4 ✓ ✓ ✗
recD Q88DZ6 ✓ ✓ ✗

Details

Bacterial RecBCD double-strand-end resectionBiological Processbacterial_recbcd_end_resection
double-strand break repair via homologous recombinationGO:0000724

Connections

recb_resection -> recbcd_reca_loading Provides Input For
Part 1: double-strand-end engagement and holoenzyme organization
RecC-dependent end engagement and RecBCD organizationProtein Complexrecc_end_engagement

Annotons

RecC DNA-binding scaffold
recc_scaffold_activity
Participant: Family: RecC family
Family:
RecC familyPANTHER:PTHR30591:SF1
Representative Members: PSEPK RecCUniProtKB:Q88DZ4 E. coli RecCUniProtKB:P07648
Required Function:
DNA bindingGO:0003677

Function

DNA bindingGO:0003677

Processes

double-strand break repair via homologous recombinationGO:0000724

Channels a DNA end into the RecB and RecD motors and organizes the functional RecBCD holoenzyme.

Part 2: bipolar ATP-dependent duplex unwinding
RecB-RecD bidirectional DNA unwindingReactionrecbd_unwinding

Annotons

RecB 3-prime-to-5-prime motor
recb_motor_activity
Participant: Family: RecB helicase-nuclease family
Family:
RecB helicase-nuclease familyPANTHER:PTHR11070:SF23
Representative Members: PSEPK RecBUniProtKB:Q88DZ5 E. coli RecBUniProtKB:P08394
Required Function:
3-prime-to-5-prime DNA helicase activityGO:0043138

Function

3-prime-to-5-prime DNA helicase activityGO:0043138
Substrates: ATP double-strand DNA end
Products: ADP phosphate unwound DNA strands

Processes

double-strand break repair via homologous recombinationGO:0000724

Drives translocation on the strand with a 3-prime terminus and couples unwinding to the RecB nuclease domain.

RecD 5-prime-to-3-prime motor
recd_motor_activity
Participant: Family: RecBCD enzyme subunit RecD family
Family:
RecBCD enzyme subunit RecD familyNCBIfam:TIGR01447
Representative Members: PSEPK RecDUniProtKB:Q88DZ6 E. coli RecDUniProtKB:P04993
Required Function:
5-prime-to-3-prime DNA helicase activityGO:0043139

Function

5-prime-to-3-prime DNA helicase activityGO:0043139
Substrates: ATP double-strand DNA end
Products: ADP phosphate unwound DNA strands

Processes

double-strand break repair via homologous recombinationGO:0000724

Provides the fast motor on the strand with a 5-prime terminus and increases holoenzyme processivity.

Part 3: taxon-dependent recombinogenic switching
RecC-associated resection-mode switchBiological Processrecc_resection_switch

Annotons

RecC switch-recognition subunit
recc_switch_activity
Participant: Family: RecC family
Family:
RecC familyPANTHER:PTHR30591:SF1
Representative Members: PSEPK RecCUniProtKB:Q88DZ4 E. coli RecCUniProtKB:P07648

Processes

double-strand break repair via homologous recombinationGO:0000724

Alters RecBCD processing toward recombinogenic 3-prime-tail production in response to a lineage-specific signal.

Part 4: nuclease resection and 3-prime-tail generation
RecB Exonuclease V resectionReactionrecb_resection

Annotons

RecB Exonuclease V nuclease
recb_nuclease_activity
Participant: Family: RecB helicase-nuclease family
Family:
RecB helicase-nuclease familyPANTHER:PTHR11070:SF23
Representative Members: PSEPK RecBUniProtKB:Q88DZ5 E. coli RecBUniProtKB:P08394
Required Function:
exodeoxyribonuclease V activityGO:0008854

Function

exodeoxyribonuclease V activityGO:0008854
Substrates: unwound double-strand-break end
Products: recombinogenic 3-prime single-stranded DNA tail phosphooligonucleotides

Processes

double-strand break repair via homologous recombinationGO:0000724

Degrades unwound strands and leaves the 3-prime-ended ssDNA substrate used for RecA loading.

Part 5: RecA loading onto the resected 3-prime tail
RecBCD-mediated RecA loadingBiological Processrecbcd_reca_loading

Annotons

RecB recombinase-loader role
recb_loader_activity
Participant: Family: RecB helicase-nuclease family
Family:
RecB helicase-nuclease familyPANTHER:PTHR11070:SF23
Representative Members: PSEPK RecBUniProtKB:Q88DZ5 E. coli RecBUniProtKB:P08394

Processes

DNA recombinase assemblyGO:0000730

Promotes RecA nucleation on the newly generated 3-prime single-stranded tail.

RecA binding to the resected tail
reca_tail_binding
Participant: Family: RecA family
Family:
RecA familyPANTHER:PTHR45900
Representative Members: PSEPK RecAUniProtKB:Q88ME4 E. coli RecAUniProtKB:P0A7G6
Required Function:
single-stranded DNA bindingGO:0003697

Function

single-stranded DNA bindingGO:0003697
Substrates: recombinogenic 3-prime single-stranded DNA tail
Products: RecA-coated presynaptic filament

Processes

DNA recombinase assemblyGO:0000730

Forms the presynaptic filament that enters homology search and strand exchange.