id: MODULE:phage_capsid_packaging_and_tail_assembly title: Bacteriophage Capsid Morphogenesis, Genome Packaging, and Tail Assembly description: A reusable module capturing bacteriophage virion morphogenesis (`GO:0019068`) across tailed dsDNA phages (Caudoviricetes), tailless icosahedral phages, internal-membrane phages (Tectiviridae), and segmented dsRNA cystoviruses. The core tailed-phage assembly pathway comprises procapsid assembly on a portal vertex (`GO:0019069`, `GO:0046798`), proteolytic or conformational procapsid maturation and expansion (`GO:0046797`, `GO:0019082`), ATP-driven genome packaging (`GO:0019073`) via a `VariantSetDescriptor` distinguishing 5'-cos (`GO:0098037`), headful pac/non-pac (`GO:0098006`), terminal-protein-primed phi29 packaging, PRD1 vertex ATPase P9 packaging, and phi6 hexameric P4 ssRNA packaging, followed by head completion/decoration (`GO:0098021`), independent tail and tail fiber assembly (`GO:0098003`, `GO:0098004`), and head-tail joining (`GO:0098005`). Also captures satellite phage capsid hijacking (such as P4 Sid redirecting helper P2 gpN procapsids into small T=4 heads). status: COMPLETE scope: CONCRETE evidence: - source_id: PMID:28893988 title: Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. statement: High-resolution cryo-EM structure of the T4 capsid defines the HK97-fold major capsid protein gp23*, vertex protein gp24*, and outer capsid decoration proteins Hoc and Soc. supporting_text: The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. - source_id: PMID:26144253 title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. statement: The dodecameric T4 gp20 portal complex nucleates prohead assembly, docks the gp17 terminase motor for DNA packaging, and connects to the neck and tail after packaging completion. supporting_text: The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. - source_id: PMID:4920094 title: Analysis of T4 phage proteins. I. Conversion of precursor proteins into lower molecular weight peptides during normal capsid formation. statement: Proteolytic cleavage of capsid and internal scaffold precursors by the T4 prohead protease gp21 drives procapsid maturation and expansion prior to DNA packaging. supporting_text: Pulse-chase experiments combined with differential extraction indicated that conversion of P23 into A-protein and alteration of the protein coded by gene 22 (P22) appeared to be vital steps in formation of normal capsids. - source_id: PMID:8892827 title: Characterization of the helper proteins for the assembly of tail fibers of coliphages T4 and lambda. statement: Dedicated phage-encoded tail fiber assembly chaperones (such as T4 gp38 and gp57A, and lambda Tfa) catalyze folding and trimerization of distal tail fibers without remaining in the mature virion or acting as minor fiber components. supporting_text: Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize. - source_id: file:projects/PHAGES.md title: Bacteriophage Genome & Module Curation Plan statement: Defines the capsid morphogenesis, genome packaging variant set, tail assembly, and satellite capsid redirection architecture. supporting_text: '`GO:0098006` headful packaging (T4, P22, P1) vs. `GO:0098037` 5''-extended `cos` packaging (λ, P2) vs. terminal-protein (`gp3`)/pRNA-primed packaging (φ29) vs. vertex ATPase packaging without a canonical terminase (PRD1, φ6).' notes: Curated for the Bacteriophage Genome & Module Curation project. Notice that in cellular location slots (`locations`), `GO:0110165` (cellular anatomical entity) descendants such as `GO:0030430` (host cell cytoplasm, where intracellular virion assembly and packaging take place) are used because `GO:0044423` (virion component) and its descendants (`GO:0019030` icosahedral viral capsid, `GO:0098021` viral capsid, decoration, `GO:0098015` virus tail) sit directly under `GO:0005575` (cellular_component) rather than `GO:0110165`, while protein-complex terms (`GO:0046798` viral portal complex, `GO:0043493` viral terminase complex) are placed in `protein_complex` when needed, satisfying GO branch constraints. module: id: phage_capsid_packaging_and_tail_assembly label: Bacteriophage Capsid Morphogenesis, Genome Packaging, and Tail Assembly module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: virion assembly term: id: GO:0019068 label: virion assembly description: Morphogenesis of infectious bacteriophage particles from structural proteins and replicated viral nucleic acid. - preferred_term: viral capsid assembly term: id: GO:0019069 label: viral capsid assembly description: Assembly and maturation of the icosahedral or prolate viral capsid shell. - preferred_term: viral DNA genome packaging term: id: GO:0019073 label: viral DNA genome packaging description: Encapsidation of the viral DNA genome into the procapsid or capsid. - preferred_term: viral tail assembly term: id: GO:0098003 label: viral tail assembly description: Assembly of the phage tail apparatus (baseplate/tip, tube, sheath, and tail fibers). context: taxa: - preferred_term: Viruses term: id: NCBITaxon:10239 label: Viruses - preferred_term: Bacteria term: id: NCBITaxon:2 label: Bacteria parts: - order: 1 role: major capsid shell assembly, maturation, and outer capsid decoration node: id: major_capsid_shell_assembly label: Major capsid shell assembly, procapsid maturation, and decoration module_type: BIOLOGICAL_PROCESS description: Every bacteriophage assembles a proteinaceous capsid or coat shell (`GO:0019069`) from major capsid subunits (e.g. T4 gp23, lambda gpE, T7 gp10A/B, phiX174 gpF, MS2 coat, PRD1 P3, phi6 P1) assisted where applicable by internal or external scaffolding proteins (`GO:0046806`, e.g. T4 gp22, lambda Nu3, T7 gp9, phiX174 gpB/gpD), prohead maturation proteases (`GO:0046797`, T4 gp21, lambda gpC), and outer capsid decoration clamps (`GO:0098021`, T4 Soc/Hoc, lambda gpD). annotons: - id: major_capsid_and_decoration_shell label: Major capsid shell assembly and outer capsid decoration 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: gp23 (Bacteriophage T4) term: id: UniProtKB:P04535 label: Major capsid protein description: Major capsid coat proteins (T4 gp23, lambda gpE, T7 gp10, P22 gp5, phiX174 gpF, MS2 coat, PRD1 P3) and outer capsid decoration clamp proteins (T4 Soc/Hoc, lambda gpD) that form and reinforce the mature virion capsid. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: viral capsid assembly term: id: GO:0019069 label: viral capsid assembly locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm evidence: - source_id: PMID:28893988 statement: T4 gp23* forms the hexameric capsid lattice reinforced by Soc and Hoc decoration proteins. supporting_text: The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. role_description: Assembles the procapsid or coat lattice and matures into the infectious capsid shell. - order: 2 role: dodecameric portal vertex nucleation and procapsid maturation in tailed phages node: id: portal_vertex_procapsid_nucleation label: Dodecameric portal vertex procapsid nucleation and maturation module_type: BIOLOGICAL_PROCESS description: In tailed dsDNA phages (Caudoviricetes), a dodecameric portal ring (e.g. T4 gp20, lambda gpB, T7 gp8, P22 gp1, phi29 gp10) forms a unique 12-fold vertex (`GO:0046798`) that nucleates procapsid assembly, coordinates scaffold/protease-mediated procapsid maturation (`GO:0046797`), docks the packaging motor, and serves as the attachment site for neck and tail completion proteins. annotons: - id: portal_vertex_nucleation label: Dodecameric portal vertex nucleation of procapsid assembly and maturation 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: 20 (Bacteriophage T4) term: id: UniProtKB:P13334 label: Portal protein description: Dodecameric portal vertex protein (T4 gp20, lambda gpB, T7 gp8, P22 gp1, phi29 gp10) that forms the unique 12-fold vertex for procapsid initiation, procapsid maturation, DNA translocation, and tail attachment. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: viral capsid assembly term: id: GO:0019069 label: viral capsid assembly - preferred_term: viral procapsid maturation term: id: GO:0046797 label: viral procapsid maturation - preferred_term: viral DNA genome packaging term: id: GO:0019073 label: viral DNA genome packaging locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm evidence: - source_id: PMID:26144253 statement: Dodecameric T4 gp20 forms the portal vertex for prohead assembly and DNA packaging. supporting_text: The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. role_description: Forms the conduit vertex that nucleates prohead assembly and docks the packaging motor. optional: true - order: 3 role: independent tail and tail fiber assembly and head-tail joining node: id: tail_assembly_and_head_tail_joining label: Tail morphogenesis, chaperone-assisted fiber assembly, and head-tail joining module_type: BIOLOGICAL_PROCESS description: In myoviruses and siphoviruses, the tail (baseplate/tip, tube, and sheath) and tail fibers assemble along independent morphogenetic pathways assisted by dedicated assembly chaperones (e.g. T4 gp51 baseplate hub assembly catalyst, gp26/gp28/gp48/gp54 baseplate-tube initiators, gp38 and gp57A tail fiber chaperones, and wac fibritin whiskers) before joining to the DNA-filled head via neck/connector proteins (`GO:0098005`). annotons: - id: baseplate_and_tail_tube_sheath_morphogenesis label: Baseplate, tail tube, and tail sheath 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: 19 (Bacteriophage T4) term: id: UniProtKB:P13333 label: Tail tube protein gp19 description: Baseplate hub and wedge structural subunits (T4 gp5, gp6, gp7, gp8, gp9, gp10, gp11, gp25, gp26, gp27, gp28, gp29, gp48, gp53, gp54), catalytic hub assembly protein (gp51), tail tube (gp19), and tail sheath (gp18). function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: viral tail assembly term: id: GO:0098003 label: viral tail assembly - preferred_term: viral head-tail joining term: id: GO:0098005 label: viral head-tail joining locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Constructs the contractile or non-contractile tail complex and joins it to the packaged capsid portal/neck vertex. - id: tail_fiber_chaperone_and_whisker_assembly label: Chaperone-catalyzed tail fiber folding and attachment participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: 38 (Bacteriophage T4) term: id: UniProtKB:P03739 label: Tail fiber assembly protein description: Non-structural tail fiber molecular chaperones (T4 gp38, gp57A) and collar/whisker attachment helpers (T4 wac fibritin) that mediate trimerization and attachment of long and short tail fibers (gp34, gp35, gp36, gp37, gp12). function: preferred_term: protein folding chaperone term: id: GO:0044183 label: protein folding chaperone processes: - preferred_term: virus tail fiber assembly term: id: GO:0098004 label: virus tail fiber assembly locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm evidence: - source_id: PMID:8892827 statement: Helper proteins such as T4 gp38 catalyze the folding and assembly of phage tail fibers. supporting_text: Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize. role_description: Directs folding, trimerization, and virion attachment of phage tail fibers. optional: true variant_sets: - id: genome_packaging_mechanism label: Bacteriophage genome packaging mechanism axis: packaging substrate recognition and translocation motor selection: EXACTLY_ONE notes: Bacteriophages package their replicated genomes into preformed procapsids using distinct recognition and motor strategies. variants: - id: headful_dna_packaging label: Headful dsDNA concatemer packaging (T4/P22/P1/P2-type) module_type: BIOLOGICAL_PROCESS description: Large terminase ATPase/nuclease (e.g. T4 gp17, P22 gp2) and small terminase DNA-recognition subunit (T4 gp16, P22 gp3) translocate concatemeric dsDNA (`GO:0015616`) until the capsid head is >100% full, making a terminal cleavage that yields circularly permuted, terminally redundant chromosomes (`GO:0098006`), protected against host RecBCD exonuclease by DNA end-protection proteins (such as T4 gp2). annotons: - id: headful_terminase_and_end_protection label: Headful terminase DNA translocation and genome end protection 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: 2 (Bacteriophage T4) term: id: UniProtKB:P15076 label: Terminal DNA protecting protein description: Headful packaging machinery (T4 terminase gp16/gp17) and packaged DNA-end protection protein (T4 gp2) that caps newly cleaved concatemer ends to prevent host RecBCD degradation after ejection. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: viral DNA genome packaging, headful term: id: GO:0098006 label: viral DNA genome packaging, headful locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Packages concatemeric dsDNA by a headful gauge mechanism and protects the packaged linear DNA termini. - id: cos_site_dna_packaging label: Cohesive-end (cos) sequence-specific dsDNA packaging (lambda/P2/P4-type) module_type: BIOLOGICAL_PROCESS description: Terminase complex (e.g. lambda Nu1 small subunit + A large subunit) recognizes specific cos sites on concatemeric DNA and introduces staggered nicks generating 5'-extended (`GO:0098037`) or 3'-extended (`GO:0098036`) cohesive ends at unit-length boundaries (`GO:0098035`). annotons: - id: cos_terminase_packaging label: Sequence-specific cos terminase DNA packaging participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: DNA translocase activity term: id: GO:0015616 label: DNA translocase activity gene_product: preferred_term: A (Escherichia phage lambda) term: id: UniProtKB:P03708 label: Terminase, large subunit description: Cohesive-end terminase holoenzyme (lambda Nu1/A, P2 M/P) that cleaves cos sites and translocates unit-length dsDNA into the procapsid. function: preferred_term: DNA translocase activity term: id: GO:0015616 label: DNA translocase activity processes: - preferred_term: viral DNA genome packaging, 5' extended cos packaging term: id: GO:0098037 label: viral DNA genome packaging, 5' extended cos packaging locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Introduces site-specific staggered nicks at cos sequences and packages unit-length genomes. - id: terminal_protein_pRNA_packaging label: Terminal-protein (gp3) and pRNA-assisted dsDNA packaging (phi29-type) module_type: BIOLOGICAL_PROCESS description: Unit-length dsDNA covalently linked at its 5' ends to terminal protein gp3 is translocated into the prohead by the gp16 packaging ATPase anchored on a prohead RNA (pRNA) ring at the gp10 connector. annotons: - id: phi29_tp_packaging_motor label: Terminal-protein-guided dsDNA packaging ATPase participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: DNA translocase activity term: id: GO:0015616 label: DNA translocase activity gene_product: preferred_term: 16 (Bacillus phage phi29) term: id: UniProtKB:P11014 label: DNA packaging protein description: phi29 packaging ATPase gp16 acting with connector gp10, pRNA, and terminal protein gp3 to package unit-length TP-DNA. function: preferred_term: DNA translocase activity term: id: GO:0015616 label: DNA translocase activity processes: - preferred_term: viral DNA genome packaging term: id: GO:0019073 label: viral DNA genome packaging locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Translocates covalent terminal-protein-dsDNA complexes into the procapsid. - id: internal_membrane_vertex_atpase_packaging label: Internal-membrane vertex ATPase dsDNA packaging (PRD1 P9-type) module_type: BIOLOGICAL_PROCESS description: Tailless internal-membrane dsDNA tectiviruses (PRD1) package unit-length linear TP-dsDNA into preformed procapsids through a unique membrane-associated vertex (P20/P22/P6) powered by the virion-incorporated packaging ATPase P9 (`GO:0016887`, `GO:0019073`) without a canonical terminase nuclease or prohead RNA. annotons: - id: prd1_p9_vertex_packaging_atpase label: Vertex-mounted ATPase linear dsDNA packaging motor participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: ATP hydrolysis activity term: id: GO:0016887 label: ATP hydrolysis activity gene_product: preferred_term: IX (Enterobacteria phage PRD1) term: id: UniProtKB:P27381 label: DNA packaging ATPase P9 description: Tectivirus PRD1 packaging ATPase P9 and unique vertex complex proteins (P6, P20, P22) that translocate linear terminal-protein-linked dsDNA across the internal viral membrane into the procapsid. function: preferred_term: ATP hydrolysis activity term: id: GO:0016887 label: ATP hydrolysis activity processes: - preferred_term: viral DNA genome packaging term: id: GO:0019073 label: viral DNA genome packaging locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Hydrolyzes ATP at the unique membrane vertex to package linear TP-dsDNA into the procapsid. - id: cystovirus_segmented_ssrna_packaging label: Sequential segmented (+)ssRNA procapsid packaging (phi6 P4-type) module_type: BIOLOGICAL_PROCESS description: Enveloped dsRNA cystoviruses (phi6) package single-stranded (+)RNA precursors (s+, m+, l+) in strict sequential order through vertex-mounted hexameric P4 NTPase motors into the P1/P2/P4/P7 procapsid prior to intra-capsid minus-strand dsRNA synthesis. annotons: - id: cystovirus_p4_rna_packaging_motor label: Hexameric P4 NTPase sequential (+)ssRNA packaging participant: selector_type: ANY_PARTICIPANT gene_product: preferred_term: P4 (Pseudomonas phage phi6) term: id: UniProtKB:P11125 label: Packaging enzyme P4 description: Hexameric NTP-driven RNA translocation motor P4 mounted at procapsid vertices of Pseudomonas phage phi6. function: preferred_term: nucleoside-triphosphatase activity term: id: GO:0017111 label: nucleoside-triphosphatase activity processes: - preferred_term: viral capsid assembly term: id: GO:0019069 label: viral capsid assembly locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Translocates the three (+)ssRNA genome segments into the procapsid in sequential order. - id: co_replicative_ssdna_ssrna_encapsidation label: Co-replicative ssDNA or RNA-operator-nucleated encapsidation (MS2/Qbeta/phiX174-type) module_type: BIOLOGICAL_PROCESS description: Tailless ssRNA leviviruses (MS2, Qbeta) and ssDNA microviruses (phiX174) lack an ATP-driven portal/terminase motor; instead, genomic ssRNA stem-loop operators nucleate coat-protein dimer assembly directly, or rolling-circle ssDNA displacement synthesis is coupled directly to procapsid encapsidation via gpJ/gpF. annotons: - id: coat_operator_or_ssdna_coupled_encapsidation label: RNA-operator or ssDNA-coupled capsid encapsidation 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: cp (Emesvirus zinderi) term: id: UniProtKB:P03612 label: Capsid protein description: Coat protein subunits (such as MS2 cp or phiX174 F/J) bind viral genomic RNA operator hairpins or nascent displaced ssDNA to couple genome encapsidation with capsid assembly without an ATPase packaging motor. function: preferred_term: structural constituent of virion term: id: GO:0039660 label: structural constituent of virion processes: - preferred_term: viral capsid assembly term: id: GO:0019069 label: viral capsid assembly locations: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm role_description: Couples viral genome encapsidation directly to icosahedral shell assembly without a portal/terminase motor. knowledge_gaps: - gap_statement: GO has specific child terms under GO:0019073 for headful (GO:0098006) and cos (GO:0098037, GO:0098036) dsDNA packaging, but lacks a child term for terminal-protein/pRNA-guided packaging (phi29) or internal-membrane vertex ATPase packaging (PRD1 P9), as well as a specific child term for sequential segmented (+)ssRNA packaging in dsRNA phages (phi6 P4). Biologically, the allosteric headful-sensing signal transmitted from the expanded capsid shell through the dodecameric portal ring to trigger terminase nuclease cleavage remains an active structural biology question. boundary: Use parent GO:0019073 (viral DNA genome packaging) for phi29 and PRD1 packaging motors, and GO:0019069 / GO:0019068 for phi6 RNA packaging. gap_kind: - BIOLOGY - ONTOLOGY