id: MODULE:phage_attachment_and_genome_ejection title: Bacteriophage Host Attachment and Genome Ejection Systems description: 'A reusable module capturing the mechanisms by which bacteriophages recognize host surface receptors, penetrate the bacterial cell envelope, and deliver their viral genome into the host cytoplasm. Adsorption proceeds via reversible binding to primary adhesion receptors (`GO:0098671`, including LPS `GO:0039638`, outer membrane porins, pili `GO:0039666`, or flagella `GO:0098931`) followed by irreversible commitment to secondary entry receptors (`GO:0098670`). Genome delivery (`GO:0039678`) is modeled as a variant set across six morphologically distinct architectures: (1) contractile myovirus tail sheath contraction and cell-puncturing needle penetration (`GO:0099000`, e.g. T4), (2) long non-contractile siphovirus tail tip/tape-measure channel translocation (`GO:0099001`, e.g. lambda, T5), (3) short podovirus tail extendable internal core/ejectosome formation (`GO:0099002`, e.g. T7, P22), (4) pilus retraction and TolQRA-dependent translocation in ssDNA/ssRNA filamentous and leviphages (e.g. M13, MS2, Qbeta), (5) spike-guided DNA pilot tube translocation in icosahedral Microviridae (e.g. phiX174 gpG/gpH), and (6) envelope membrane fusion + nucleocapsid shell peptidoglycan digestion in enveloped dsRNA Cystoviridae (e.g. phi6 P3/P6/P5).' status: COMPLETE scope: CONCRETE evidence: - source_id: PMID:27193680 title: Structure of the T4 baseplate and its function in triggering sheath contraction. statement: Reversible and irreversible tail fiber binding induces a hexagonal-to-star conformational transition in the T4 baseplate that triggers tail sheath contraction and genome ejection. supporting_text: Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. - source_id: PMID:19229296 title: 'The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria.' statement: Contraction of the T4 gp18 tail sheath drives the inner gp19 tail tube and gp5-gp27 cell-puncturing complex across the bacterial outer membrane. supporting_text: The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. - source_id: PMID:11823865 title: Structure of the cell-puncturing device of bacteriophage T4. statement: The T4 baseplate central hub complex (gp5-gp27) forms a membrane-puncturing needle carrying a lysozyme domain that digests periplasmic peptidoglycan during entry. supporting_text: The carboxy-terminal domain of gp5 is a triple-stranded beta-helix that forms an equilateral triangular prism, which acts as a membrane-puncturing needle. The middle lysozyme domain of gp5, situated on the periphery of the prism, serves to digest the peptidoglycan layer. - source_id: PMID:15701513 title: Control of bacteriophage T4 tail lysozyme activity during the infection process. statement: Bacteriophage T4 gp5 tail lysozyme activity is sterically inhibited in the mature virion and activated upon tail contraction to locally degrade host peptidoglycan during entry. supporting_text: The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. - source_id: file:projects/PHAGES.md title: Bacteriophage Genome & Module Curation Plan statement: Synthesizes the receptor-binding and genome ejection variants across myoviruses, siphoviruses, podoviruses, filamentous phages, microviruses, and enveloped cystoviruses. supporting_text: Three mutually exclusive mechanism children exist in GO (`GO:0099000` contractile tail, `GO:0099001` long flexible tail, `GO:0099002` short tail), plus pilus-retraction (`M13`, `MS2`), DNA pilot tube (`φX174`), and membrane-fusion/spike (`φ6`, `PRD1`) routes. notes: Curated for the Bacteriophage Genome & Module Curation project. Distinguishes tail-associated peptidoglycan hydrolases acting during viral entry ("lysis from without", annotated to `GO:0098932` symbiont entry into host cell via disruption of host cell wall peptidoglycan, e.g. T4 gp5, T7 gp16, phi6 P5) from late-expressed cytoplasmic/periplasmic endolysins acting during progeny release (`GO:0044659`, e.g. T4 gpE, lambda R, T7 gp3.5). Because virion component terms (`GO:0044423`, `GO:0098015` virus tail, `GO:0098024` virus tail, fiber, `GO:0098025` virus tail, baseplate, `GO:0098027` virus tail, sheath, `GO:0098026` virus tail, tube, `GO:0098023` virus tail, tip) sit under `GO:0044423` rather than `GO:0110165` (`cellular anatomical entity`) in GO, annoton `locations` slots here are omitted or restricted to host cell anatomical compartments while virion structural subcompartments are captured in `concepts`, `description`, and the per-gene reviews. module: id: phage_attachment_and_genome_ejection label: Bacteriophage Host Attachment and Genome Ejection module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: virion attachment to host cell term: id: GO:0019062 label: virion attachment to host cell description: Adsorption of a bacteriophage virion to surface receptors on the bacterial host envelope or appendages. - preferred_term: symbiont genome ejection through host cell envelope term: id: GO:0039678 label: symbiont genome ejection through host cell envelope description: Translocation of the bacteriophage genome from the virion capsid across the bacterial cell envelope into the host cytoplasm. - preferred_term: symbiont entry into host cell term: id: GO:0046718 label: symbiont entry into host cell description: Penetration of the bacterial host cell envelope by the phage genome or nucleocapsid. context: taxa: - preferred_term: Viruses term: id: NCBITaxon:10239 label: Viruses - preferred_term: Bacteria term: id: NCBITaxon:2 label: Bacteria variant_sets: - id: attachment_and_ejection_architecture label: Bacteriophage attachment and genome ejection architecture axis: virion tail/capsid morphology and entry mechanism selection: EXACTLY_ONE notes: Bacteriophages use distinct structural machines to couple receptor recognition to genome translocation across the bacterial cell envelope. variants: - id: contractile_tail_ejection label: Myovirus contractile tail genome ejection (T4/P2-type) module_type: BIOLOGICAL_PROCESS description: Long tail fibers (gp34-gp35-gp36-gp37) mediate reversible primary adsorption (`GO:0098671`), triggering baseplate conformational deployment of short tail fibers (gp12) for irreversible commitment (`GO:0098670`). Baseplate expansion triggers contraction of the tail sheath (gp18), driving the internal tail tube (gp19) and central hub puncturing needle/lysozyme (gp5-gp27) across the outer membrane and peptidoglycan layer (`GO:0098932`, `GO:0099000`). parts: - order: 1 role: reversible primary adsorption by long tail fibers node: id: myovirus_reversible_adsorption label: Long tail fiber reversible host recognition module_type: BIOLOGICAL_PROCESS annotons: - id: ltf_adhesion_receptor_binding label: Long tail fiber distal tip adhesion receptor recognition participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: 37 (Bacteriophage T4) term: id: UniProtKB:P03744 label: Long-tail fiber protein gp37 description: Distal long tail fiber subunits (such as T4 gp37) bind primary host surface receptors (e.g. LPS or OmpC) reversibly to orient the virion on the cell surface. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: adhesion receptor-mediated virion attachment to host cell term: id: GO:0098671 label: adhesion receptor-mediated virion attachment to host cell - preferred_term: lipopolysaccharide-mediated virion attachment to host cell term: id: GO:0039638 label: lipopolysaccharide-mediated virion attachment to host cell role_description: Mediates initial reversible scanning and attachment to host outer membrane receptors. - order: 2 role: irreversible commitment and baseplate triggering node: id: myovirus_irreversible_baseplate_commitment label: Short tail fiber irreversible attachment and baseplate expansion module_type: BIOLOGICAL_PROCESS annotons: - id: stf_entry_receptor_binding label: Short tail fiber irreversible receptor binding participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: 12 (Bacteriophage T4) term: id: UniProtKB:P10930 label: Short tail fiber protein gp12 description: Short tail fibers (T4 gp12) anchored to baseplate wedge subunits (gp6, gp7, gp8, gp9, gp10, gp11, gp25, gp53) unfold and bind irreversibly to the LPS core, locking the baseplate in its star conformation. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: entry receptor-mediated virion attachment to host cell term: id: GO:0098670 label: entry receptor-mediated virion attachment to host cell - preferred_term: symbiont genome ejection through host cell envelope, contractile tail mechanism term: id: GO:0099000 label: symbiont genome ejection through host cell envelope, contractile tail mechanism evidence: - source_id: PMID:27193680 statement: Baseplate conformational transition couples short tail fiber attachment to tail sheath contraction. supporting_text: Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. role_description: Irreversibly anchors the baseplate to the bacterial outer membrane and triggers sheath contraction. - order: 3 role: contractile sheath drive and peptidoglycan puncturing node: id: myovirus_sheath_contraction_and_puncturing label: Contractile sheath drive and gp5 tail lysozyme cell wall penetration module_type: BIOLOGICAL_PROCESS annotons: - id: tail_sheath_contraction label: Tail sheath contraction driving tail tube penetration participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: 18 (Bacteriophage T4) term: id: UniProtKB:P13332 label: Tail sheath protein description: Contractile tail sheath protein (T4 gp18) surrounding the rigid tail tube (gp19) rearranges into a shorter, wider helix to drive the tube through the outer membrane. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: symbiont genome ejection through host cell envelope, contractile tail mechanism term: id: GO:0099000 label: symbiont genome ejection through host cell envelope, contractile tail mechanism evidence: - source_id: PMID:19229296 statement: The T4 gp18 tail sheath contracts to propel the tail tube into the host envelope. supporting_text: The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. role_description: Provides the mechanical force to puncture the host outer membrane and advance the tail tube to the inner membrane. - id: baseplate_hub_tail_lysozyme_puncturing label: Baseplate central hub needle and tail lysozyme peptidoglycan digestion participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity gene_product: preferred_term: 5 (Bacteriophage T4) term: id: UniProtKB:P16009 label: Pre-baseplate central spike protein Gp5 description: Central hub needle-lysozyme complex (T4 gp5-gp27 capped by gp5.4) pierces the outer membrane and locally digests the periplasmic peptidoglycan layer so the tail tube can reach the inner membrane. function: preferred_term: lysozyme activity term: id: GO:0003796 label: lysozyme activity processes: - preferred_term: symbiont entry into host cell via disruption of host cell wall peptidoglycan term: id: GO:0098932 label: symbiont entry into host cell via disruption of host cell wall peptidoglycan - preferred_term: symbiont genome ejection through host cell envelope, contractile tail mechanism term: id: GO:0099000 label: symbiont genome ejection through host cell envelope, contractile tail mechanism locations: - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space evidence: - source_id: PMID:11823865 statement: The T4 gp5-gp27 complex forms a cell-puncturing needle with a lysozyme domain. supporting_text: The carboxy-terminal domain of gp5 is a triple-stranded beta-helix that forms an equilateral triangular prism, which acts as a membrane-puncturing needle. The middle lysozyme domain of gp5, situated on the periphery of the prism, serves to digest the peptidoglycan layer. - source_id: PMID:15701513 statement: T4 gp5 tail lysozyme is activated during infection to locally cleave host peptidoglycan. supporting_text: The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. role_description: Punctures the outer membrane and locally hydrolyzes the periplasmic peptidoglycan barrier during viral entry. connections: - source: myovirus_reversible_adsorption target: myovirus_irreversible_baseplate_commitment connection_type: POSITIVELY_REGULATES predicate: preferred_term: positively regulates term: id: RO:0002213 label: positively regulates description: Reversible binding of long tail fibers to primary receptors transmits a mechanical signal via gp9/gp10/gp11 to deploy the short tail fibers. - source: myovirus_irreversible_baseplate_commitment target: myovirus_sheath_contraction_and_puncturing connection_type: POSITIVELY_REGULATES predicate: preferred_term: positively regulates term: id: RO:0002213 label: positively regulates description: Hexagonal-to-star expansion of the baseplate wedge and hub initiates wave-like contraction of the gp18 tail sheath. - id: long_flexible_tail_ejection label: Siphovirus long flexible non-contractile tail ejection (lambda/T5-type) module_type: BIOLOGICAL_PROCESS description: Siphoviruses bind an outer membrane entry receptor via a central tail tip fiber (e.g. lambda gpJ binding LamB maltoporin, modulated by side tail fibers Stf/Tfa) and eject their genome through the flexible gpV tail tube and extruded gpH tape-measure trans-envelope conduit (`GO:0099001`). annotons: - id: siphovirus_tail_tip_and_tube_ejection label: Siphovirus tail tip receptor binding and flexible tail genome ejection participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: J (Escherichia phage lambda) term: id: UniProtKB:P03749 label: Tip attachment protein J description: Siphovirus tail tip receptor-binding protein (lambda gpJ), flexible tail tube (gpV), and ejected tape-measure channel protein (gpH) that form a continuous conduit across the host cell envelope. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: entry receptor-mediated virion attachment to host cell term: id: GO:0098670 label: entry receptor-mediated virion attachment to host cell - preferred_term: symbiont genome ejection through host cell envelope, long flexible tail mechanism term: id: GO:0099001 label: symbiont genome ejection through host cell envelope, long flexible tail mechanism locations: - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space role_description: Recognizes the outer membrane protein receptor and mediates genome translocation through a non-contractile tail conduit. - id: short_tail_ejectosome_ejection label: Podovirus short tail and extendable internal core ejection (T7/P22/phi29-type) module_type: BIOLOGICAL_PROCESS description: Podoviruses adsorb via tail fibers or enzymatic tailspikes (e.g. T7 gp17, P22 gp9 endorhamnosidase) and eject internal core proteins (e.g. T7 gp14, gp15, gp16, where gp16 carries a transglycosylase domain) to assemble a transient trans-envelope ejectosome channel (`GO:0099002`, `GO:0098932`). annotons: - id: podovirus_short_tail_ejection label: Podovirus tail fiber adsorption and internal core ejectosome assembly participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: 16 (Enterobacteria phage T7) term: id: UniProtKB:P03726 label: Peptidoglycan transglycosylase gp16 description: Podovirus tail fiber/nozzle proteins (T7 gp11, gp12, gp17) and ejected internal virion core proteins (T7 gp14, gp15, gp16) that breach the peptidoglycan layer and form a trans-envelope DNA channel. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: lipopolysaccharide-mediated virion attachment to host cell term: id: GO:0039638 label: lipopolysaccharide-mediated virion attachment to host cell - preferred_term: symbiont genome ejection through host cell envelope, short tail mechanism term: id: GO:0099002 label: symbiont genome ejection through host cell envelope, short tail mechanism - preferred_term: symbiont entry into host cell via disruption of host cell wall peptidoglycan term: id: GO:0098932 label: symbiont entry into host cell via disruption of host cell wall peptidoglycan locations: - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space role_description: Adsorbs to host LPS and extrudes internal virion proteins to form an extendable genome-delivery channel across the envelope. - id: pilus_mediated_entry label: Pilus-mediated adsorption and retraction entry (Inoviridae and Fiersviridae) module_type: BIOLOGICAL_PROCESS description: Filamentous ssDNA phages (M13 pIII) and icosahedral ssRNA phages (MS2 maturation protein A, Qbeta maturation protein A2) adsorb to conjugative bacterial pili (`GO:0039666`) and exploit pilus retraction or TolQRA co-receptors to deliver their genome into the host cell (`GO:0046718`). annotons: - id: pilus_attachment_and_entry label: Virion attachment to host pilus and genome entry participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: III (Enterobacteria phage M13) term: id: UniProtKB:P69168 label: Attachment protein G3P description: Minor coat/maturation adhesins (M13 pIII, MS2 A, Qbeta A2) that bind the tip or shaft of the host F-pilus and mediate genome entry upon pilus retraction. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: virion attachment to host cell pilus term: id: GO:0039666 label: virion attachment to host cell pilus - preferred_term: symbiont entry into host cell term: id: GO:0046718 label: symbiont entry into host cell locations: - preferred_term: host cell plasma membrane term: id: GO:0020002 label: host cell plasma membrane role_description: Binds the bacterial pilus and couples pilus retraction to viral genome translocation across the cell envelope. - id: microvirus_pilot_tube_entry label: Tailless icosahedral spike and DNA pilot tube entry (Microviridae) module_type: BIOLOGICAL_PROCESS description: Tailless icosahedral ssDNA microviruses (such as phiX174) recognize host LPS via pentameric major spike proteins (gpG) and extrude 10-12 copies of the internal DNA pilot protein (gpH), which oligomerize into an alpha-helical barrel spanning the periplasm to conduct the ssDNA genome across the cell envelope (`GO:0099008`). annotons: - id: microvirus_spike_and_pilot_protein label: Spike LPS attachment and gpH DNA pilot tube formation participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: H (Escherichia phage phiX174) term: id: UniProtKB:P03646 label: Minor spike protein H description: phiX174 major spike protein G (LPS recognition) and DNA pilot protein H (oligomeric trans-envelope DNA delivery tube with peptidoglycan hydrolase activity). function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: lipopolysaccharide-mediated virion attachment to host cell term: id: GO:0039638 label: lipopolysaccharide-mediated virion attachment to host cell - preferred_term: symbiont entry into host cell via permeabilization of inner membrane term: id: GO:0099008 label: symbiont entry into host cell via permeabilization of inner membrane - preferred_term: symbiont genome ejection through host cell envelope term: id: GO:0039678 label: symbiont genome ejection through host cell envelope locations: - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space role_description: Forms an inducible alpha-helical trans-envelope tube after LPS attachment to pilot the ssDNA genome into the cytoplasm. - id: enveloped_phage_membrane_fusion_entry label: Enveloped phage pilus attachment, outer membrane fusion, and nucleocapsid entry (Cystoviridae) module_type: BIOLOGICAL_PROCESS description: Enveloped dsRNA phages (such as Pseudomonas phage phi6) attach to host type IV pili via spike complex P3 (`GO:0039666`), fuse their viral lipid envelope (`GO:0019031`) with the bacterial outer membrane via fusogenic protein P6, digest periplasmic peptidoglycan via muralytic enzyme P5 (`GO:0098932`), and deliver the transcriptionally active P8-coated nucleocapsid core across the cytoplasmic membrane. annotons: - id: cystovirus_envelope_fusion_entry label: Enveloped phage attachment, membrane fusion, and peptidoglycan penetration participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion gene_product: preferred_term: P6 (Pseudomonas phage phi6) term: id: UniProtKB:P11128 label: Fusion protein P6 description: Envelope spike protein P3, membrane fusion protein P6, and virion-associated muralytic enzyme P5 of cystovirus phi6. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: virion attachment to host cell pilus term: id: GO:0039666 label: virion attachment to host cell pilus - preferred_term: symbiont entry into host cell via disruption of host cell wall peptidoglycan term: id: GO:0098932 label: symbiont entry into host cell via disruption of host cell wall peptidoglycan - preferred_term: symbiont entry into host cell term: id: GO:0046718 label: symbiont entry into host cell locations: - preferred_term: host cell outer membrane term: id: GO:0039662 label: host cell outer membrane - preferred_term: host cell periplasmic space term: id: GO:0044229 label: host cell periplasmic space role_description: Mediates pilus attachment, fusion of the viral lipid envelope with the host outer membrane, and peptidoglycan penetration. knowledge_gaps: - gap_statement: GO lacks a child term under GO:0039678 (symbiont genome ejection through host cell envelope) for the inducible alpha-helical DNA pilot tube mechanism of tailless icosahedral Microviridae (phiX174 gpH). Biologically, the exact stoichiometry, lipid-protein rearrangement, and inner-membrane proton-motive-force coupling of trans-envelope ejectosome and DNA pilot channels (such as T7 gp14/gp15/gp16 and phiX174 gpH) remain incompletely resolved in vivo. boundary: Combine GO:0039678 with GO:0099008 (symbiont entry into host cell via permeabilization of inner membrane) for phiX174 gpH until a dedicated pilot-tube ejection child term is added. gap_kind: - BIOLOGY - ONTOLOGY