id: MODULE:phage_virion_release_and_lysis title: Bacteriophage Virion Release and Host Cell Lysis Systems description: 'A reusable module capturing the four principal bacteriophage progeny release architectures across bacterial hosts, structured as a variant set for host-envelope-aware pathway satisfiability and abduction: (1) the canonical three-step dsDNA phage lysis system for Gram-negative diderm hosts (holin / pinholin inner membrane pore formation, endolysin peptidoglycan degradation, and two-component Rz/Rz1 or unimolecular o-spanin outer membrane disruption), modulated in Tevenvirinae by antiholin-mediated lysis inhibition (LIN); (2) the two-step holin + endolysin system sufficient for Gram-positive monoderm hosts lacking an outer membrane (with an optional mycolate esterase LysB step in mycobacteriophages); (3) single-gene lysis (SGL) systems of small ssDNA and ssRNA phages that inhibit host peptidoglycan biosynthesis enzymes (such as MraY or MurA) or destabilize the cell envelope via an amrazin membrane protein; and (4) non-lytic chronic filamentous phage extrusion through a trans-envelope pIV/pI/pXI assembly complex.' status: COMPLETE scope: CONCRETE evidence: - source_id: PMID:17900620 title: Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. statement: In phages of Gram-negative hosts, the periplasm-spanning Rz-Rz1 two-component spanin complex (or a unimolecular u-spanin) connects the inner and outer membranes and is required for outer membrane disruption and host lysis in the presence of divalent cations. supporting_text: Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. - source_id: PMID:22389108 title: Protein determinants of phage T4 lysis inhibition. statement: In phage T4, the T holin is regulated by the periplasmic RI antiholin to establish lysis inhibition in response to superinfection. supporting_text: Genetic studies have established that lysis inhibition in bacteriophage T4 infections occurs when the RI antiholin inhibits the lethal hole-forming function of the T holin. - source_id: PMID:34456892 title: The Phage T4 Antiholin RI Has a Cleavable Signal Peptide, Not a SAR Domain. statement: Phage T4 RI functions as a secreted periplasmic antiholin that binds the periplasmic domain of the T holin to delay lysis triggering. supporting_text: While regulation by the cytoplasmic RIII plays a minor role, the periplasmic antiholin RI binds tightly to the holin T and is believed to directly sense periplasmic phage DNA from superinfections as a trigger for the inhibition of lysis. - source_id: PMID:1201752 title: Studies on the specificity of action of bacteriophage T4 lysozyme. statement: Bacteriophage T4 endolysin (gpE) is a muramidase with lysozyme activity that cleaves host cell wall peptidoglycan during progeny release. supporting_text: Analysis of the enzymatic degradation products shows that T4 acts as an endo-acetylmuramidase capable of cleaving glycosidic bonds only at muramic acid residues that are substituted with peptide side-chains. - source_id: PMID:4582731 title: Bacteriophage T7 lysozyme is an N-acetylmuramyl-L-alanine amidase. statement: Bacteriophage T7 gp3.5 endolysin cleaves the amide bond between N-acetylmuramic acid and L-alanine in host peptidoglycan. - source_id: file:projects/PHAGES.md title: Bacteriophage Genome & Module Curation Plan statement: Defines the four mutually exclusive phage progeny release variants and documents the missing spanin and single-gene lysis ontology terms. supporting_text: Four distinct routes—canonical 3-step `holin + endolysin + spanin` (λ, T7, T4), 2-step `holin + endolysin` without spanin (Gram-positive phages like φ29, SPO1; or mycolate-cleaving `Lysin A + Lysin B` in Mycobacteriophage L5), `single-gene lysis (Sgl)` inhibiting peptidoglycan biosynthesis (`GO:0039640` in φX174 `E` and Qβ `A2`, or membrane-lesion `L` in MS2), and non-lytic `chronic filamentous extrusion` (`GO:0099045` in M13). notes: Curated for the Bacteriophage Genome & Module Curation project. Because GO currently lacks dedicated molecular function terms for holin activity, endolysin catalytic grouping, spanin outer-membrane fusion activity, and amrazin-type single-gene lysis proteins, participants are anchored to the most specific available GO molecular functions (`GO:0140911` pore-forming activity for holins, `GO:0003796` lysozyme activity for endolysins, `GO:0140678` molecular function inhibitor activity for antiholins, and `GO:0004857` enzyme inhibitor activity for peptidoglycan-synthesis-inhibiting SGL proteins, while `function` is omitted on spanin, amrazin MS2 L, and filamentous extrusion annotons where GO lacks a dedicated molecular function term) paired with specific biological process terms (`GO:0044660`, `GO:0044659`, `GO:0039640`, `GO:0039639`, `GO:0099045`). module: id: phage_virion_release_and_lysis label: Bacteriophage Virion Release and Host Cell Lysis module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: viral release from host cell term: id: GO:0019076 label: viral release from host cell description: Release of newly assembled bacteriophage virions from the infected bacterial host cell by cytolysis or non-lytic extrusion. - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis description: Lytic release of progeny virions through sequential disruption of the host cell envelope. context: taxa: - preferred_term: Viruses term: id: NCBITaxon:10239 label: Viruses - preferred_term: Bacteria term: id: NCBITaxon:2 label: Bacteria variant_sets: - id: virion_release_strategy label: Bacteriophage virion release strategy axis: host envelope architecture and viral genome class selection: EXACTLY_ONE notes: Bacteriophages employ one of four release strategies depending on whether they are tailed dsDNA phages infecting diderm vs. monoderm hosts, small ssDNA/ssRNA phages encoding single-gene lysis proteins, or filamentous phages exiting by chronic non-lytic extrusion. variants: - id: diderm_three_step_lysis label: Gram-negative diderm three-step lysis (holin + endolysin + spanin) module_type: BIOLOGICAL_PROCESS description: Sequential disruption of the inner membrane by a holin or pinholin (modulated in some phages by an antiholin), degradation of the periplasmic peptidoglycan meshwork by an endolysin, and disruption of the outer membrane by a two-component Rz/Rz1 i-spanin/o-spanin complex or unimolecular o-spanin. parts: - order: 1 role: inner membrane holin pore formation node: id: holin_pore_formation label: Holin inner membrane pore formation module_type: BIOLOGICAL_PROCESS annotons: - id: holin_activity label: Holin inner membrane pore-forming activity participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: pore-forming activity term: id: GO:0140911 label: pore-forming activity gene_product: preferred_term: t (Bacteriophage T4) term: id: UniProtKB:P06808 label: Holin description: Phage holins and pinholins (such as T4 gpT, lambda S105, and T7 gp17.5) accumulate in the host inner membrane and trigger at an allele-specific time to collapse membrane potential and allow endolysin access or activation. function: preferred_term: pore-forming activity term: id: GO:0140911 label: pore-forming activity processes: - preferred_term: viral release via pore formation in host cell membrane term: id: GO:0044660 label: viral release via pore formation in host cell membrane - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis locations: - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane evidence: - source_id: PMID:22389108 statement: Phage T4 holin T forms lesions in the host inner membrane at the time of lysis. supporting_text: Genetic studies have established that lysis inhibition in bacteriophage T4 infections occurs when the RI antiholin inhibits the lethal hole-forming function of the T holin. role_description: Permeabilizes the host cytoplasmic membrane to release cytoplasmic endolysin into the periplasm or depolarize the membrane to activate SAR-endolysins. - order: 2 role: periplasmic peptidoglycan degradation node: id: endolysin_peptidoglycan_hydrolysis label: Endolysin peptidoglycan degradation module_type: BIOLOGICAL_PROCESS annotons: - id: endolysin_muramidase_or_amidase label: Endolysin peptidoglycan hydrolase activity participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity gene_product: preferred_term: e (Bacteriophage T4) term: id: UniProtKB:P00720 label: Endolysin description: Phage endolysins degrade the host peptidoglycan sacculus via muramidase/lysozyme activity (GO:0003796, e.g., T4 gpE), transglycosylase activity (lambda R), N-acetylmuramoyl-L-alanine amidase activity (GO:0008745, e.g., T7 gp3.5), or endopeptidase activity. function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity processes: - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis - preferred_term: peptidoglycan catabolic process term: id: GO:0009253 label: peptidoglycan catabolic process locations: - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space evidence: - source_id: PMID:1201752 statement: T4 endolysin hydrolyzes host cell wall peptidoglycan during phage lysis. supporting_text: Analysis of the enzymatic degradation products shows that T4 acts as an endo-acetylmuramidase capable of cleaving glycosidic bonds only at muramic acid residues that are substituted with peptide side-chains. role_description: Cleaves the load-bearing peptidoglycan meshwork once holin pore formation grants access or triggers SAR release. - order: 3 role: outer membrane disruption by spanin node: id: spanin_outer_membrane_disruption label: Spanin-mediated outer membrane disruption module_type: BIOLOGICAL_PROCESS annotons: - id: spanin_activity label: Spanin trans-periplasmic outer membrane disruption participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: Rz (Escherichia phage lambda) term: id: UniProtKB:P00726 label: Spanin, inner membrane subunit description: Two-component spanin complexes (inner membrane i-spanin Rz/pseT.3 paired with outer membrane lipoprotein o-spanin Rz1/pseT.2, or T7 gp18.5/gp18.7) or unimolecular o-spanins (T1 gp11) span the periplasm and undergo conformational collapse after peptidoglycan removal to fuse or disrupt the outer membrane. processes: - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis locations: - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane evidence: - source_id: PMID:17900620 statement: In phages of Gram-negative hosts, the periplasm-spanning Rz-Rz1 two-component spanin complex (or a unimolecular u-spanin) connects the inner and outer membranes and is required for outer membrane disruption and host lysis in the presence of divalent cations. supporting_text: Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. role_description: Completes lysis of diderm Gram-negative bacteria by disrupting the outer membrane once the peptidoglycan barrier is degraded. optional: true - order: 4 optional: true role: optional antiholin-mediated lysis inhibition (LIN) node: id: antiholin_lysis_inhibition_regulation label: Antiholin-mediated lysis inhibition (LIN) module_type: BIOLOGICAL_PROCESS description: Optional regulation of lysis timing (lysis inhibition, LIN) by periplasmic or cytoplasmic antiholins (such as T4 RI/RIII or lambda S107) that inhibit holin pore formation. annotons: - id: antiholin_lysis_inhibition label: Antiholin-mediated lysis inhibition (optional modulator) participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: rI (Bacteriophage T4) term: id: UniProtKB:P13304 label: Antiholin description: Periplasmic or membrane-associated antiholins (such as T4 RI, T4 RIII, and lambda S107) inhibit holin oligomerization in response to superinfection or before the scheduled lysis time. function: preferred_term: molecular function inhibitor activity term: id: GO:0140678 label: molecular function inhibitor activity processes: - preferred_term: suppression by virus of host cell lysis in response to superinfection term: id: GO:0039639 label: suppression by virus of host cell lysis in response to superinfection locations: - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space evidence: - source_id: PMID:34456892 statement: Phage T4 RI antiholin is secreted into the periplasm where it binds the T holin to delay lysis. supporting_text: While regulation by the cytoplasmic RIII plays a minor role, the periplasmic antiholin RI binds tightly to the holin T and is believed to directly sense periplasmic phage DNA from superinfections as a trigger for the inhibition of lysis. role_description: Inhibits holin triggering in response to secondary phage adsorption (lysis inhibition). connections: - source: holin_pore_formation target: endolysin_peptidoglycan_hydrolysis connection_type: POSITIVELY_REGULATES predicate: preferred_term: positively regulates term: id: RO:0002213 label: positively regulates description: Holin pore formation releases canonical endolysin into the periplasm or depolarizes the inner membrane to release tethered SAR-endolysins. - source: endolysin_peptidoglycan_hydrolysis target: spanin_outer_membrane_disruption connection_type: POSITIVELY_REGULATES predicate: preferred_term: positively regulates term: id: RO:0002213 label: positively regulates description: Removal of the cross-linked peptidoglycan meshwork liberates periplasm-spanning spanin complexes to oligomerize and disrupt the outer membrane. - id: monoderm_two_step_lysis label: Gram-positive monoderm two-step lysis (holin + endolysin) module_type: BIOLOGICAL_PROCESS description: Phages infecting Gram-positive monoderm bacteria lack a spanin step because the host has no outer membrane; holin pore formation and endolysin peptidoglycan degradation suffice for cytolysis (augmented in mycobacteriophages by a LysB mycolylarabinogalactan esterase). parts: - order: 1 role: monoderm holin pore formation node: id: monoderm_holin_step label: Monoderm phage holin pore formation module_type: BIOLOGICAL_PROCESS annotons: - id: monoderm_holin_activity label: Holin pore-forming activity in monoderm host participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: pore-forming activity term: id: GO:0140911 label: pore-forming activity description: Holin of a Gram-positive phage (such as Bacillus phage phi29 gp14) that permeabilizes the cytoplasmic membrane. function: preferred_term: pore-forming activity term: id: GO:0140911 label: pore-forming activity processes: - preferred_term: viral release via pore formation in host cell membrane term: id: GO:0044660 label: viral release via pore formation in host cell membrane locations: - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane role_description: Permeabilizes the monoderm cytoplasmic membrane. - order: 2 role: monoderm endolysin cell wall cleavage node: id: monoderm_endolysin_step label: Monoderm phage endolysin cell wall hydrolysis module_type: BIOLOGICAL_PROCESS annotons: - id: monoderm_endolysin_activity label: Endolysin peptidoglycan hydrolase activity in monoderm host participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity description: Modular endolysin of a Gram-positive phage (such as phi29 gp15) combining a catalytic domain with cell-wall binding domains. function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity processes: - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis role_description: Cleaves the thick Gram-positive peptidoglycan wall. - id: single_gene_lysis label: Single-gene lysis (SGL) in small ssDNA and ssRNA phages module_type: BIOLOGICAL_PROCESS description: Small single-stranded DNA (Microviridae) and RNA (Fiersviridae) phages encode a single lysis protein that either inhibits a specific host peptidoglycan biosynthesis enzyme ("protein antibiotics" such as phiX174 E inhibiting MraY or Qbeta A2 inhibiting MurA, annotated to GO:0039640) or disrupts envelope integrity without inhibiting murein synthesis (amrazins such as MS2 L, annotated to GO:0044659). annotons: - id: sgl_peptidoglycan_inhibitor label: Single-gene lysis by inhibition of host peptidoglycan biosynthesis participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: enzyme inhibitor activity term: id: GO:0004857 label: enzyme inhibitor activity gene_product: preferred_term: E (Escherichia phage phiX174) term: id: UniProtKB:P03639 label: Lysis protein E description: Single-gene lysis proteins that inhibit host murein biosynthesis enzymes, including phiX174 gpE (inhibits MraY phospho-N-acetylmuramoyl-pentapeptide-transferase) and Qbeta A2 (maturation/coat-readthrough protein that inhibits MurA UDP-N-acetylglucosamine 1-carboxyvinyltransferase). function: preferred_term: enzyme inhibitor activity term: id: GO:0004857 label: enzyme inhibitor activity processes: - preferred_term: viral release via suppression of host peptidoglycan biosynthetic process term: id: GO:0039640 label: viral release via suppression of host peptidoglycan biosynthetic process - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis locations: - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane role_description: Blocks host peptidoglycan precursor synthesis during cell division, causing septal lesions and osmotic cytolysis. - id: sgl_amrazin_envelope_disruption label: Single-gene lysis by amrazin envelope destabilization (MS2 L-type) participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: L (Emesvirus zinderi) term: id: UniProtKB:P03609 label: Lysis protein description: Amrazin-class single-gene lysis proteins (such as MS2 L) that trigger host cell cytolysis via DnaJ-chaperone-dependent envelope destabilization rather than inhibiting peptidoglycan biosynthesis. processes: - preferred_term: viral release from host cell by cytolysis term: id: GO:0044659 label: viral release from host cell by cytolysis locations: - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane role_description: Induces host cell cytolysis without inhibiting murein biosynthetic enzymes. - id: filamentous_chronic_extrusion label: Non-lytic chronic filamentous extrusion (Inoviridae) module_type: BIOLOGICAL_PROCESS description: Filamentous ssDNA phages (such as M13, fd, and f1) assemble and extrude progeny virions continuously across the host cell envelope via a trans-envelope secretin/ATPase assembly complex (pI/pXI inner membrane motor and pIV outer membrane secretin channel) without lysing the host cell. annotons: - id: filamentous_extrusion_machinery label: Filamentous phage trans-envelope extrusion machinery participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: IV (Enterobacteria phage M13) term: id: UniProtKB:P03665 label: Virion export protein description: Trans-envelope filamentous phage assembly and export proteins (pI, pXI, and outer membrane secretin pIV) that extrude progeny virions while maintaining host membrane integrity. processes: - preferred_term: viral extrusion term: id: GO:0099045 label: viral extrusion locations: - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane role_description: Mediates non-lytic extrusion of filamentous phage particles across the bacterial cell envelope. knowledge_gaps: - gap_statement: Gene Ontology currently lacks a molecular function or biological process term specific to phage spanin-mediated outer membrane disruption/fusion (such as lambda Rz/Rz1 or T4 pseT.3/pseT.2). Biologically, whether two-component Rz/Rz1 and unimolecular spanins disrupt the Gram-negative outer membrane via direct inner-to-outer membrane lipid fusion or local periplasmic coiled-coil collapse remains under active investigation. boundary: Annotate spanin subunits to GO:0044659 (viral release from host cell by cytolysis) and their respective host envelope locations (GO:0020002, GO:0044229, GO:0039662) until a spanin-specific GO term is created. gap_kind: - BIOLOGY - ONTOLOGY - gap_statement: Amrazin-type single-gene lysis proteins such as MS2 L do not inhibit peptidoglycan biosynthesis and therefore must not be annotated to GO:0039640, yet no positive child term of GO:0044659 exists for chaperone-dependent amrazin lysis. Biologically, the molecular mechanism by which non-enzymatic single-gene lysis membrane proteins (such as MS2 protein L) destabilize the bacterial envelope remains incompletely resolved. boundary: Use GO:0044659 (viral release from host cell by cytolysis) for MS2 L and reserve GO:0039640 strictly for validated murein-synthesis inhibitors such as phiX174 E and Qbeta A2. gap_kind: - BIOLOGY - ONTOLOGY