Temperate Bacteriophage Lysis-Lysogeny Decision, Prophage Integration, and Induction

A reusable module capturing the regulatory decision (`GO:0098689`), establishment (`GO:0019043`), maintenance (`GO:0019044`), and induction/release (`GO:0019046`, `GO:0032359`) of viral latency (lysogeny) in temperate bacteriophages. Two orthogonal variant axes are modeled: (1) the bistable lysis-lysogeny decision circuit (`CI`/`Cro`/`CII`/`CIII` host-protease sensing in lambdoid phages, `C` repressor/Cox switch in P2-like phages, and the arbitrium `AimP`/`AimR`/`AimX` peptide quorum-sensing circuit in Bacillus SPbeta/phi3T phages), and (2) the prophage maintenance state (`GO:0075713` site-specific integrated chromosomal prophage via tyrosine/serine integrase vs. `GO:0075720` extrachromosomal circular or `GO:0075530` linear telomeric plasmid prophage in P1 and N15 vs. replicative transposition prophage integration via DDE transposase `GO:0004803` / `GO:0015074` in Mu-like phages).

MODULE:phage_temperate_latency_switchCOMPLETECONCRETEBiological Processmodules/phage_temperate_latency_switch.yaml
latency-replication decisionGO:0098689 viral latencyGO:0019042 release from viral latencyGO:0019046
PMID:28099413
Communication between viruses guides lysis-lysogeny decisions.
Bacillus phages phi3T and SPbeta use the arbitrium peptide signaling system (AimP peptide, AimR receptor transcription factor, and AimX non-coding RNA regulator) to guide the lysis-lysogeny decision across infection cycles.
Here we show that viruses (phages) of the SPbeta group use a small-molecule communication system to coordinate lysis-lysogeny decisions.
file:projects/PHAGES.md
Bacteriophage Genome & Module Curation Plan
Defines the temperate phage latency-replication decision and prophage maintenance variant sets and notes that GO uses general viral latency terms (`GO:0019042`) in place of "lysogeny".
In phages, the **temperate latency module** (`GO:0098689` latency-replication decision, `GO:0075713` proviral integration, `GO:0032359` provirus excision) is **biologically absent** in obligately lytic genomes (T4, T7, φX174, MS2, φ29).

Curated for the Bacteriophage Genome & Module Curation project. Gene Ontology does not contain terms labeled "lysogeny" or "prophage induction"; temperate phage curators must use the viral latency hierarchy (`GO:0098689` latency-replication decision, `GO:0019042` viral latency, `GO:0019043` establishment of viral latency, `GO:0075713` establishment of integrated proviral latency, `GO:0075720` establishment of episomal latency, `GO:0075530` establishment of latency as a linear episome, `GO:0019044` maintenance of viral latency, `GO:0019046` release from viral latency, and `GO:0032359` provirus excision).

8Nodes
2Parts
2Variant Sets
5Variants
6Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

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

Leaf nodes lacking representative members

1 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

0 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (6 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
cii_activator_activity ANY_WITH_FUNCTION
Gene 		DNA-binding transcription factor activity
GO:0003700 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
ci_repressor_maintenance ANY_WITH_FUNCTION
Gene 		DNA-binding transcription factor activity
GO:0003700 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
aimp_aimr_arbitrium_signaling ANY_WITH_FUNCTION
Gene 		DNA-binding transcription factor activity
GO:0003700 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
prophage_integrase_and_excisionase ANY_WITH_FUNCTION
Gene 		prophage integrase activity
GO:0008979 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
episomal_prophage_maintenance ANY_PARTICIPANT
Gene 		DNA binding
GO:0003677 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
mu_transposase_integration ANY_WITH_FUNCTION
Gene 		transposase activity
GO:0004803 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.

Gene-review completeness (4/5 grounded genes reviewed)

4 complete review(s) · 0 with deep research · 1 missing review · 4 reviewed but lacking deep research

Gene Review Complete Deep research
cI P03034 ✓ ✓ ✗
cII P03042 ✓ ✓ ✗
int P03700 ✓ ✓ ✗
A (Escherichia phage Mu) P07636 ✗ — —
parA P07620 ✓ ✓ ✗

Details

Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Temperate Bacteriophage Lysis-Lysogeny Switch and Prophage MaintenanceBiological Processphage_temperate_latency_switch
latency-replication decisionGO:0098689 viral latencyGO:0019042 release from viral latencyGO:0019046
Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Variant set: Temperate phage lysis-lysogeny decision circuit by regulatory signal integration and transcriptional switch (Exactly One)

Temperate phages evaluate host physiological state, multiplicity of infection, or extracellular phage-encoded peptide concentration to choose between lytic replication and lysogenic latency.

Lambdoid CII/CIII host-protease sensing and CI-Cro bistable switch (lambda/P22-type)Biological Processlambdoid_cII_cI_cro_bistable_switch

Phage-encoded CIII inhibits host FtsH (HflB) protease to stabilize the CII transcriptional activator at high multiplicity of infection; CII activates the pRE, pI, and paQ promoters to express the CI master repressor and Int integrase while Cro competes at oR/oL to drive lytic gene expression.

Connections

positively regulatesRO:0002213
CII activates initial CI synthesis from the pRE promoter, enabling CI to occupy oR1/oR2 and establish self-sustaining maintenance from pRM.
Part 1: CII/CIII commitment to latency establishment
CII transcriptional activation and CIII protease inhibitionBiological Processcii_ciii_latency_commitment

Annotons

CII activation of lysogenic promoters pRE, pI, and paQ
cii_activator_activity
Participant: Any With Function: cII (Escherichia phage lambda)
Gene Product:
cII (Escherichia phage lambda)UniProtKB:P03042
Required Function:
DNA-binding transcription factor activityGO:0003700
Lambdoid CII transcription activator (stabilized by CIII inhibition of host FtsH protease) that activates CI repressor and Int integrase transcription.

Function

DNA-binding transcription factor activityGO:0003700

Processes

latency-replication decisionGO:0098689 establishment of viral latencyGO:0019043

Locations

host cell cytoplasmGO:0030430

Integrates MOI and host protease status to activate transcription of the lysogenic repressor and integrase.

Part 2: CI-Cro bistable operator maintenance and SOS induction
CI repressor maintenance of latency and RecA-stimulated inductionBiological Processci_cro_bistable_maintenance

Annotons

CI master repressor operator binding and SOS autocleavage
ci_repressor_maintenance
Participant: Any With Function: cI (Escherichia phage lambda)
Gene Product:
cI (Escherichia phage lambda)UniProtKB:P03034
Required Function:
DNA-binding transcription factor activityGO:0003700
Master lysogenic repressor CI (and competing lytic repressor Cro) binding oR/oL operators to maintain viral latency until host SOS-activated RecA* stimulates CI autoproteolysis (`GO:0019046`).

Function

DNA-binding transcription factor activityGO:0003700

Processes

latency-replication decisionGO:0098689 maintenance of viral latencyGO:0019044 release from viral latencyGO:0019046

Locations

host cell cytoplasmGO:0030430

Silences lytic promoters during prophage maintenance and undergoes RecA*-stimulated cleavage upon host DNA damage to trigger prophage induction.

Arbitrium peptide quorum-sensing lysis-lysogeny switch (SPbeta/phi3T-type)Biological Processarbitrium_peptide_quorum_switch

Bacillus phages encode a secreted hexapeptide signal (AimP) that is imported into neighboring bacteria via Opp oligopeptide permease and bound by the intracellular receptor transcription factor AimR, inhibiting AimX expression to promote lysogeny at high phage population density.

Annotons

Arbitrium AimP-AimR peptide-regulated latency decision
aimp_aimr_arbitrium_signaling
Participant: Any With Function: DNA-binding transcription factor activity
Required Function:
DNA-binding transcription factor activityGO:0003700
Arbitrium peptide receptor transcription factor AimR and signaling peptide AimP in SPbeta-group Bacillus phages.

Function

DNA-binding transcription factor activityGO:0003700

Processes

latency-replication decisionGO:0098689

Locations

host cell cytoplasmGO:0030430

Senses extracellular arbitrium peptide accumulation to switch infected cells from lytic replication to lysogeny.

PMID:28099413
Phage-encoded arbitrium peptides and AimR receptors regulate the lysis-lysogeny decision.
Here we show that viruses (phages) of the SPbeta group use a small-molecule communication system to coordinate lysis-lysogeny decisions.
Variant set: Prophage genome persistence and excision mechanism by site-specific chromosomal integration vs. extrachromosomal episomal maintenance vs. replicative transposition integration (Exactly One)

Once committed to latency, temperate phages maintain their prophage genome either integrated at an att site via a tyrosine/serine integrase, as an extrachromosomal circular/linear plasmid replicon, or integrated across host chromosome sites via a DDE transposase.

Site-specific chromosomal integration and excisionase-directed excision (lambda/P22/P2-type)Biological Processsite_specific_integrated_prophage

A phage-encoded tyrosine or serine site-specific integrase (`Int`, `GO:0008979`) catalyzes recombination between phage `attP` and host `attB` (`GO:0075713`), assisted by host IHF; upon induction, excisionase (`Xis` or `Cox`) bends DNA to direct integrase-catalyzed excisive recombination (`attL` x `attR`, `GO:0032359`).

Annotons

Prophage site-specific integration and Xis-directed excision
prophage_integrase_and_excisionase
Participant: Any With Function: int (Escherichia phage lambda)
Gene Product:
int (Escherichia phage lambda)UniProtKB:P03700
Required Function:
prophage integrase activityGO:0008979
Temperate phage tyrosine/serine integrase (lambda Int, P2 Int, P4 Int) and directionality factor/excisionase (lambda Xis, P2 Cox).

Function

prophage integrase activityGO:0008979

Processes

establishment of integrated proviral latencyGO:0075713 provirus excisionGO:0032359

Locations

host cell cytoplasmGO:0030430

Catalyzes site-specific integration of the phage genome into the host chromosome and Xis-dependent excision upon induction.

Extrachromosomal circular or linear telomeric plasmid prophage (P1/N15-type)Biological Processepisomal_plasmid_prophage

Temperate phages such as P1 (circular plasmid prophage maintained by RepA and partitioned by ParA/ParB, `GO:0075720`) and N15 (linear plasmid prophage with hairpin telomeres generated by protelomerase TelN, `GO:0075530`) persist extrachromosomally during latency without integrating into the host chromosome.

Annotons

Episomal circular or linear plasmid prophage maintenance
episomal_prophage_maintenance
Participant: Any Participant: parA (Escherichia phage P1)
Gene Product:
parA (Escherichia phage P1)UniProtKB:P07620
Plasmid prophage replication/partition proteins (P1 RepA, ParA, ParB; N15 TelN protelomerase and RepA) that maintain extrachromosomal viral latency.

Function

DNA bindingGO:0003677

Processes

establishment of episomal latencyGO:0075720 establishment of latency as a linear episomeGO:0075530 maintenance of viral latencyGO:0019044

Locations

host cell cytoplasmGO:0030430

Establishes and partitions an extrachromosomal circular or linear prophage replicon during host cell division.

Replicative transposition prophage integration and maintenance (Mu-type)Biological Processtransposable_prophage_integration

Transposable temperate phages (such as Escherichia phage Mu and Pseudomonas phage D3112) use a DDE-family transposase (`MuA`, `GO:0004803`) and ATP-dependent target-site immunity protein (`MuB`) to integrate randomly into the host chromosome (`GO:0075713`, `GO:0015074`) and amplify via replicative transposition upon prophage induction without excising a circular genome.

Annotons

Transposase-mediated proviral chromosomal integration
mu_transposase_integration
Participant: Any With Function: A (Escherichia phage Mu)
Gene Product:
A (Escherichia phage Mu)UniProtKB:P07636
Required Function:
transposase activityGO:0004803
Phage-encoded DDE transposase (such as Mu gpA) and transposition regulator (Mu gpB) catalyzing non-site-specific chromosomal integration and replicative transposition.

Function

transposase activityGO:0004803

Processes

establishment of integrated proviral latencyGO:0075713 DNA integrationGO:0015074

Locations

host cell cytoplasmGO:0030430

Integrates the phage genome into random host chromosomal target sites and drives replicative transposition during lytic induction.