Bacterial non-homologous end joining

A reusable bacterial DNA double-strand-break repair module in which a Ku homodimer recognizes, protects, and aligns broken duplex ends, a LigD-family enzyme conditionally remodels non-ligatable termini through polymerase and 3-prime-phosphoesterase activities, and an ATP-dependent LigD ligase domain seals the DNA backbone. The module excludes homologous recombination, single-strand annealing, eukaryotic NHEJ factors, and accessory bacterial backup routes that do not require the Ku-LigD core.

MODULE:bacterial_nonhomologous_end_joiningDRAFTCONCRETEBiological Processmodules/bacterial_nonhomologous_end_joining.yaml
double-strand break repair via nonhomologous end joiningGO:0006303
GO:0006303
double-strand break repair via nonhomologous end joining
Defines the template-independent double-strand-break repair process represented by this module.
PMID:12215643
Identification of a DNA nonhomologous end-joining complex in bacteria.
Experimental work established bacterial Ku-mediated ligase recruitment and stimulation.
bacterial Ku specifically recruits DNA ligase to DNA ends
PMID:16023671
Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis.
Biochemical dissection established separable LigD catalytic activities.
ligase domains of Mt-Lig were cloned individually
PMID:20018881
Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein.
Pseudomonas reconstitution supports Ku-dependent end protection, gap filling, and end joining.
Pseudomonas Ku stimulates POL-catalyzed ribonucleotide addition to a plasmid DSB end and promotes plasmid end joining by full-length Pseudomonas LigD.
PANTHER:PTN002222140
PAINT prokaryotic Ku double-stranded-DNA-binding node
The local PTHR41251 PAINT export assigns GO:0003690 to this ancestral node.
PANTHER:PTN001627042
PAINT LigD polymerase, ligase, and NHEJ node
The local PTHR42705 PAINT export assigns GO:0003887, GO:0003910, and GO:0006303 to this ancestral node.

The core boundary is Ku plus LigD. End processing is conditional because directly compatible termini can proceed from Ku-bound ends to ligation, whereas blocked, gapped, or incompatible termini require one or both LigD processing activities. Some bacterial lineages split LigD activities among proteins or use backup ligases; those architectures require explicit, separately grounded variants. No generic cytoplasm location is asserted at module or annoton level because the target records do not directly establish a more specific cellular-component claim.

4Nodes
3Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_nonhomologous_end_joining-deep-research-openscientist.md (openscientist)

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.

  • ligd_end_processing → ligd_end_ligation [NOT_CHECKED]
    PMID:20018881 describes remodeling of broken 3-prime ends before sealing by the ligase component.

Function consistency and core coverage

6 gene-function check(s) reflected in core functions · 0 conflict(s) · 9 evidence or coverage gap(s) (15 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
ku_double_stranded_dna_binding PSEPK Ku
UniProtKB:Q88HU8
Family Representative 		double-stranded DNA binding
GO:0003690 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
ku_double_stranded_dna_binding Pseudomonas aeruginosa Ku
UniProtKB:Q9I1W5
Family Representative 		double-stranded DNA binding
GO:0003690 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ku_double_stranded_dna_binding Mycobacterium tuberculosis Ku
UniProtKB:P9WKD9
Family Representative 		double-stranded DNA binding
GO:0003690 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ligd_polymerase_activity PSEPK LigD
UniProtKB:Q88HU3
Family Representative 		DNA-directed DNA polymerase activity
GO:0003887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_polymerase_activity Pseudomonas aeruginosa LigD
UniProtKB:Q9I1X7
Family Representative 		DNA-directed DNA polymerase activity
GO:0003887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_polymerase_activity Mycobacterium tuberculosis LigD
UniProtKB:P9WNV3
Family Representative 		DNA-directed DNA polymerase activity
GO:0003887 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ligd_three_prime_phosphatase_activity PSEPK LigD
UniProtKB:Q88HU3
Family Representative 		polynucleotide 3-prime-phosphatase activity
GO:0046403 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_three_prime_phosphatase_activity Pseudomonas aeruginosa LigD
UniProtKB:Q9I1X7
Family Representative 		polynucleotide 3-prime-phosphatase activity
GO:0046403 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_atp_dependent_ligase_activity PSEPK LigD
UniProtKB:Q88HU3
Family Representative 		DNA ligase (ATP) activity
GO:0003910 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_atp_dependent_ligase_activity Pseudomonas aeruginosa LigD
UniProtKB:Q9I1X7
Family Representative 		DNA ligase (ATP) activity
GO:0003910 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ligd_atp_dependent_ligase_activity Mycobacterium tuberculosis LigD
UniProtKB:P9WNV3
Family Representative 		DNA ligase (ATP) activity
GO:0003910 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ku_double_stranded_dna_binding prokaryotic Ku family
PANTHER:PTHR41251:SF1
Family 		double-stranded DNA binding
GO:0003690 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR41251:SF1.
ligd_polymerase_activity bacterial LigD family
PANTHER:PTHR42705:SF2
Family 		DNA-directed DNA polymerase activity
GO:0003887 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR42705:SF2.
ligd_three_prime_phosphatase_activity bacterial LigD family with a phosphoesterase domain
PANTHER:PTHR42705:SF2
Family 		polynucleotide 3-prime-phosphatase activity
GO:0046403 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR42705:SF2.
ligd_atp_dependent_ligase_activity bacterial LigD family
PANTHER:PTHR42705:SF2
Family 		DNA ligase (ATP) activity
GO:0003910 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR42705:SF2.

Gene-review completeness (3/6 grounded genes reviewed)

3 complete review(s) · 2 with deep research · 3 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
ku Q88HU8 ✓ ✓ ✓
ligD Q88HU3 ✓ ✓ ✓
ligD Q9I1X7 ✓ ✓ ✗
Mycobacterium tuberculosis Ku P9WKD9 ✗ — —
Mycobacterium tuberculosis LigD P9WNV3 ✗ — —
Pseudomonas aeruginosa Ku Q9I1W5 ✗ — —

Details

Context
bacteriaNCBITaxon:2
Bacterial non-homologous end joiningBiological Processbacterial_nonhomologous_end_joining
double-strand break repair via nonhomologous end joiningGO:0006303
Context
bacteriaNCBITaxon:2

Connections

Ku-bound incompatible or blocked ends are delivered to LigD for conditional remodeling.
ku_end_recognition -> ligd_end_ligation Provides Input For
Ku-bound compatible ends can be sealed without an obligatory processing reaction.
When remodeling is required, polymerase or phosphatase activity generates a ligatable substrate before sealing.
Part 1: DNA-end recognition, protection, and synapsis
Ku-dependent double-strand-break end recognitionBiological Processku_end_recognition

A Ku homodimer binds exposed duplex ends, protects them from resection, promotes end alignment, and recruits LigD.

PMID:12215643
Bacterial Ku recruits DNA ligase to DNA ends and stimulates ligation.
bacterial Ku specifically recruits DNA ligase to DNA ends
PMID:20018881
Pseudomonas Ku binds and protects both ends of linear duplex DNA.
Ku afforded virtually complete protection from both exonucleases

Annotons

Prokaryotic Ku double-stranded-DNA-end binding
ku_double_stranded_dna_binding
Participant: Family: prokaryotic Ku family
Family:
prokaryotic Ku familyPANTHER:PTHR41251:SF1
Representative Members: PSEPK KuUniProtKB:Q88HU8 Pseudomonas aeruginosa KuUniProtKB:Q9I1W5 Mycobacterium tuberculosis KuUniProtKB:P9WKD9

Function

double-stranded DNA bindingGO:0003690
Substrates: double-strand-break DNA end

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Recognizes and protects broken duplex ends and recruits LigD to establish a repair-competent synaptic complex.

Part 2: conditional DNA-end remodeling (optional)
LigD-dependent DNA-end remodelingBiological Processligd_end_processing

Non-ligatable DNA ends are remodeled by autonomous LigD polymerase and 3-prime-phosphoesterase activities before sealing.

PMID:16023671
LigD contains experimentally separable catalytic domains.
ligase domains of Mt-Lig were cloned individually
PMID:20018881
The LigD polymerase and phosphoesterase components remodel broken DNA termini before ligation.
the POL and phosphoesterase components suggests that they provide a means of remodeling the 3′ ends of broken DNA strands prior to sealing by the ligase component

Annotons

LigD gap-filling polymerase activity
ligd_polymerase_activity
Participant: Family: bacterial LigD family
Family:
bacterial LigD familyPANTHER:PTHR42705:SF2
Representative Members: PSEPK LigDUniProtKB:Q88HU3 Pseudomonas aeruginosa LigDUniProtKB:Q9I1X7 Mycobacterium tuberculosis LigDUniProtKB:P9WNV3

Function

DNA-directed DNA polymerase activityGO:0003887
Substrates: gapped or incompatible DNA end ribonucleoside or deoxyribonucleoside triphosphate
Products: extended DNA end

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Adds templated or non-templated nucleotides to create an end that can be sealed by the LigD ligase domain.

LigD 3-prime-end healing activity
ligd_three_prime_phosphatase_activity
Participant: Family: bacterial LigD family with a phosphoesterase domain
Family:
bacterial LigD family with a phosphoesterase domainPANTHER:PTHR42705:SF2
Representative Members: PSEPK LigDUniProtKB:Q88HU3 Pseudomonas aeruginosa LigDUniProtKB:Q9I1X7

Function

polynucleotide 3-prime-phosphatase activityGO:0046403
Substrates: polynucleotide 3-prime phosphate end
Products: polynucleotide 3-prime hydroxyl end phosphate

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Converts a blocked 3-prime-phosphate terminus into the 3-prime hydroxyl required for DNA synthesis or ligation.

Part 3: ATP-dependent phosphodiester sealing
LigD-mediated DNA-end sealingReactionligd_end_ligation

The LigD ligase domain seals juxtaposed 3-prime-hydroxyl and 5-prime-phosphate DNA ends using ATP.

Annotons

LigD ATP-dependent DNA ligase activity
ligd_atp_dependent_ligase_activity
Participant: Family: bacterial LigD family
Family:
bacterial LigD familyPANTHER:PTHR42705:SF2
Representative Members: PSEPK LigDUniProtKB:Q88HU3 Pseudomonas aeruginosa LigDUniProtKB:Q9I1X7 Mycobacterium tuberculosis LigDUniProtKB:P9WNV3

Function

DNA ligase (ATP) activityGO:0003910
Substrates: ATP juxtaposed 3-prime-hydroxyl and 5-prime-phosphate DNA ends
Products: phosphodiester-linked DNA AMP diphosphate

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Completes repair by forming the phosphodiester bond across the prepared break junction.