Single-gene bacteriophage lysis (peptidoglycan biosynthesis inhibition and envelope destabilization)

A reusable module representing single-gene lysis (SGL) systems of small single-stranded DNA (Microviridae) and single-stranded RNA (Fiersviridae / Leviviricetes) bacteriophages. Unlike double-stranded DNA phages that deploy multigene holin-endolysin-spanin cassettes to degrade existing peptidoglycan, small-genome phages encode a single lysis protein—frequently overlapping essential structural or replication genes or embedded within the virion maturation protein—that triggers host bacteriolysis during cell division. Two principal mechanistic branches are represented: (1) "protein antibiotic" SGL proteins that directly inhibit conserved cytoplasmic or inner-membrane enzymes of the host peptidoglycan precursor pathway, exemplified by phiX174 protein E (which forms a transmembrane ternary YES complex with host phospho-N-acetylmuramoyl-pentapeptide-transferase MraY and the peptidyl-prolyl isomerase chaperone SlyD to block lipid I synthesis) and Qbeta maturation/lysis protein A2 (which binds and inhibits host UDP-N-acetylglucosamine 1-carboxyvinyltransferase MurA in a closed conformation to block the first committed step of murein synthesis); and (2) small transmembrane membrane-destabilizing SGL proteins such as MS2 protein L, which insert into inner-outer membrane adhesion sites and induce autolysis without inhibiting murein precursor enzymes.

MODULE:phage_single_gene_lysisCOMPLETEABSTRACTBiological Processmodules/phage_single_gene_lysis.yaml
viral release via suppression of host peptidoglycan biosynthetic processGO:0039640 viral release from host cell by cytolysisGO:0044659
GO:0039640
viral release via suppression of host peptidoglycan biosynthetic process
Ontology grounding for the "protein antibiotic" single-gene lysis pathway in which a viral lysis protein inhibits host peptidoglycan precursor biosynthesis to induce bacteriolysis.
GO:0044659
viral release from host cell by cytolysis
Parent biological process encompassing both peptidoglycan-biosynthesis-inhibiting and membrane-destabilizing single-gene phage lysis mechanisms.
file:genes/BPPHS/E/E-uniprot.txt
UniProtKB/Swiss-Prot entry P03639 (LYS_BPPHS)
Establishes that phiX174 lysis protein E induces host cell lysis by inhibiting the host translocase MraY that catalyzes lipid I synthesis.
Inhibits the host translocase MraY activity that catalyzes the synthesis of lipid I, a necessary step for the host cell wall biosynthesis
file:genes/BPQBE/A2/A2-uniprot.txt
UniProtKB/Swiss-Prot entry Q8LTE2 (MATA2_BPQBE)
Establishes that Qbeta maturation protein A2 mediates host cell lysis by interacting with and inhibiting host MurA, blocking the first step in host cell wall synthesis.
Inhibits host MurA activity thereby blocking the synthesis of murein precursors necessary for the host cell wall biosynthesis
file:genes/BPMS2/L/L-uniprot.txt
UniProtKB/Swiss-Prot entry P03609 (LYS_BPMS2)
Establishes that MS2 lysis protein L localizes to membrane adhesion sites between the inner and outer membranes to induce host cell lysis.
Induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis.
5Nodes
1Parts
1Variant Sets
3Variants
3Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

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

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

2 gene-function check(s) reflected in core functions · 0 conflict(s) · 2 evidence or coverage gap(s) (4 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
phiX174_E_mraY_inhibitor E (Enterobacteria phage phiX174 lysis protein E)
UniProtKB:P03639
Family Representative 		enzyme inhibitor activity
GO:0004857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
qbeta_A2_murA_inhibitor A2 (Escherichia virus Qbeta maturation protein A2)
UniProtKB:Q8LTE2
Family Representative 		enzyme inhibitor activity
GO:0004857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phiX174_E_mraY_inhibitor Microviridae MraY-inhibiting lysis protein E family
Family 		enzyme inhibitor activity
GO:0004857 		Family Id Missing
The family has no identifier linking it to a curated family review.
qbeta_A2_murA_inhibitor Qubevirus MurA-inhibiting maturation/lysis protein A2 family
Family 		enzyme inhibitor activity
GO:0004857 		Family Id Missing
The family has no identifier linking it to a curated family review.

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

3 complete review(s) · 0 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
A2 Q8LTE2 ✓ ✓ ✗
E P03639 ✓ ✓ ✗
L P03609 ✓ ✓ ✗

Details

Context
VirusesNCBITaxon:10239
Single-gene bacteriophage lysisBiological Processphage_single_gene_lysis
viral release via suppression of host peptidoglycan biosynthetic processGO:0039640 viral release from host cell by cytolysisGO:0044659
Context
VirusesNCBITaxon:10239

Exemplar phages: Enterobacteria phage phiX174 (NCBITaxon:1217068): Canonical ssDNA microvirus whose overlapping gene E encodes a 91-aa transmembrane protein that inhibits host MraY in a ternary YES complex with host SlyD.; Escherichia virus Qbeta (NCBITaxon:39803): Canonical allolevivirus whose single-copy virion maturation protein A2 doubles as a cytoplasmic MurA inhibitor once unassembled A2 accumulates.; Escherichia phage MS2 (NCBITaxon:12022): Canonical levivirus whose overlapping lysis protein L induces lysis at membrane adhesion sites without inhibiting peptidoglycan precursor enzymes.

Connections

Inhibition of host MraY blocks lipid I synthesis and triggers septal cell-wall failure during division.
Inhibition of host MurA blocks UDP-MurNAc precursor synthesis and leads to osmotic bacteriolysis.
Insertion of L protein at inner-outer membrane adhesion sites activates host envelope autolysis.
Part 1: Osmotic bacteriolysis and progeny virion release
Host cell wall failure and cytolytic virion releaseBiological Processcytolytic_virion_release
viral release from host cell by cytolysisGO:0044659 symbiont-mediated suppression of host peptidoglycan biosynthetic processGO:0039635

Downstream outcome shared by all three single-gene lysis branches: septal or lateral cell wall failure under turgor pressure releases intracellular progeny virions into the extracellular medium. This node carries concepts but no annotons, so it compiles to an empty conjunction and contributes nothing to satisfiability: the module's whole requirement is the single_gene_lysis_mechanism variant set. Do not read the variant set as optional because a required part sits beside it. Note also that EXACTLY_ONE records the biology without constraining the engine: compile_node emits an Or for every variant set and is_satisfied treats it as at-least-one, so a hypothetical genome encoding two single-gene lysis proteins would still be satisfied.

Variant set: Single-gene lysis mechanism by host target inhibited by the single lysis protein (Exactly One)

A single-gene-lysis phage encodes exactly one of these lysis proteins, so the three branches are alternative mechanisms rather than co-occurring steps. Modelling them as a variant set, rather than as three independently optional parts, is what makes the module unsatisfiable in a genome that encodes no single-gene lysis protein.

Single-gene lysis via MraY inhibition (YES complex formation)Regulatory StepmraY_inhibition_sgl

MraY lipid I translocase inhibition branch.

Annotons

MraY-inhibiting transmembrane lysis protein E
phiX174_E_mraY_inhibitor
Participant: Family: Microviridae MraY-inhibiting lysis protein E family
Family:
Microviridae MraY-inhibiting lysis protein E family
Representative Members: E (Enterobacteria phage phiX174 lysis protein E)UniProtKB:P03639

Function

enzyme inhibitor activityGO:0004857

Processes

viral release via suppression of host peptidoglycan biosynthetic processGO:0039640

Locations

host cell plasma membraneGO:0020002

Single-pass transmembrane lysis protein that wedges into the active site cleft of host phospho-N-acetylmuramoyl-pentapeptide-transferase MraY together with the host chaperone SlyD (the YES complex), arresting lipid I biosynthesis and causing septal catastrophe during division.

Single-gene lysis via MurA inhibition by virion maturation proteinRegulatory StepmurA_inhibition_sgl

MurA enolpyruvyl-transferase inhibition branch.

Annotons

Bifunctional maturation and MurA-inhibiting lysis protein A2
qbeta_A2_murA_inhibitor
Participant: Family: Qubevirus MurA-inhibiting maturation/lysis protein A2 family
Family:
Qubevirus MurA-inhibiting maturation/lysis protein A2 family
Representative Members: A2 (Escherichia virus Qbeta maturation protein A2)UniProtKB:Q8LTE2

Function

enzyme inhibitor activityGO:0004857

Processes

viral release via suppression of host peptidoglycan biosynthetic processGO:0039640

Locations

host cell cytoplasmGO:0030430

Single-copy virion maturation protein that, as unassembled cytoplasmic copies accumulate late in infection, binds liganded host MurA and blocks UDP-GlcNAc enolpyruvyl transfer.

Single-gene lysis via host envelope destabilizationBiological Processenvelope_adhesion_sgl

Envelope adhesion-site destabilization branch.

Annotons

Envelope-destabilizing single-gene lysis protein L
ms2_L_envelope_lysis
Participant: Family: Emesvirus membrane-destabilizing lysis protein L family
Family:
Emesvirus membrane-destabilizing lysis protein L family
Representative Members: L (Escherichia phage MS2 lysis protein L)UniProtKB:P03609

Processes

viral release from host cell by cytolysisGO:0044659

Locations

host cell plasma membraneGO:0020002

Overlapping-frame single-pass membrane protein whose translation is coupled to coat-gene termination and that localizes to inner-outer membrane adhesion zones to trigger host autolysis without inhibiting cytoplasmic or membrane murein precursor enzymes.