Enveloped segmented dsRNA bacteriophage (Cystoviridae) procapsid packaging, replication, and envelope morphogenesis

A reusable module representing the intracellular assembly, sequential plus-strand RNA packaging, intra-capsid double-stranded RNA synthesis, and intracellular lipid envelope acquisition of enveloped trisegmented dsRNA bacteriophages (family Cystoviridae, exemplified by Pseudomonas phage phi6). Unlike DNA phages, cystoviruses never expose naked genomic dsRNA to the host cytoplasm. Instead, a dodecahedral polymerase complex (procapsid) is pre-assembled from 120 copies of major inner shell protein P1, 12 copies of the RNA-directed RNA polymerase P2, 12 hexamers of the packaging NTPase turret P4 at the five-fold vertices, and the assembly/packaging cofactor P7. The empty procapsid sequentially packages single-stranded (+)-sense precursor transcripts s+, m+, and l+ in strict order via P4 NTPase translocation, synthesizes complementary (-)-strands inside the expanded core via P2 RdRP to yield the S, M, and L dsRNA segments, and transcribes late mRNAs by semi-conservative strand displacement. The dsRNA-filled core is subsequently enclosed by the T=13 icosahedral outer shell protein P8 (forming the nucleocapsid), enveloped inside the host cytoplasm by host-derived lipid vesicles containing viral membrane proteins P9, P6, P10, and P13 through the action of the nonstructural membrane morphogenetic factor P12, decorated with the pilus-attachment spike P3 anchored to P6, and released by P5 muralytic endopeptidase and P10 holin-like membrane lysis.

MODULE:phage_dsrna_cystovirus_lifecycleCOMPLETECONCRETEBiological Processmodules/phage_dsrna_cystovirus_lifecycle.yaml
viral genome packagingGO:0019072 viral RNA genome replicationGO:0039694 virion assemblyGO:0019068
GO:0019072
viral genome packaging
Ontology grounding for NTP-driven translocation of viral (+)-strand RNA precursors into the pre-assembled cystovirus procapsid.
GO:0039694
viral RNA genome replication
Ontology grounding for intra-capsid minus-strand synthesis and semi-conservative dsRNA replication by the cystovirus polymerase complex.
file:genes/BPPH6/P1/P1-uniprot.txt
UniProtKB/Swiss-Prot entry P11126 (P1_BPPH6)
Establishes that phi6 P1 forms the 120-copy inner capsid framework of the polymerase complex, binds RNA, and participates in genomic packaging.
Binds to RNA and may be involved in genomic packaging.
file:genes/BPPH6/P4/P4-uniprot.txt
UniProtKB/Swiss-Prot entry P11125 (P4_BPPH6)
Establishes that phi6 P4 is a hexameric ssRNA-stimulated NTPase packaging motor that packages the viral RNA segments into the procapsid for replication and transcription.
Packaging motor with helicase and translocase activities. Part of the packaging complex that packages the viral RNA segments, replicate them into a double-stranded form and transcribe them.
file:genes/BPPH6/P12/P12-uniprot.txt
UniProtKB/Swiss-Prot entry P07580 (P12_BPPH6)
Establishes that nonstructural protein P12 is the morphogenetic assembly factor required for intracellular viral membrane morphogenesis.
Assembly factor active in membrane morphogenesis.
7Nodes
6Parts
0Variant Sets
0Variants
11Annotons
5Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

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

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 9 evidence or coverage gap(s) (18 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
phi6_P1_inner_shell P1 (Pseudomonas phage phi6 major inner protein P1)
UniProtKB:P11126
Family Representative 		RNA binding
GO:0003723 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P7_packaging_cofactor P7 (Pseudomonas phage phi6 protein P7)
UniProtKB:P11123
Family Representative 		structural constituent of virion
GO:0039660 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P4_packaging_ntpase P4 (Pseudomonas phage phi6 packaging enzyme P4)
UniProtKB:P11125
Family Representative 		ribonucleoside triphosphate phosphatase activity
GO:0017111 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P2_rdrp P2 (Pseudomonas phage phi6 RNA-directed RNA polymerase P2)
UniProtKB:P11124
Family Representative 		RNA-directed RNA polymerase activity
GO:0003968 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P8_outer_shell P8 (Pseudomonas phage phi6 outer capsid protein P8)
UniProtKB:P07579
Family Representative 		structural constituent of virion
GO:0039660 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P9_envelope_protein P9 (Pseudomonas phage phi6 major envelope protein P9)
UniProtKB:P07581
Family Representative 		structural constituent of virion
GO:0039660 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P6_fusion_anchor P6 (Pseudomonas phage phi6 fusion protein P6)
UniProtKB:P11128
Family Representative 		structural constituent of virion
GO:0039660 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P3_pilus_spike P3 (Pseudomonas phage phi6 spike protein P3)
UniProtKB:P11129
Family Representative 		structural constituent of virion
GO:0039660 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P5_endolysin P5 (Pseudomonas phage phi6 lytic enzyme P5)
UniProtKB:P07582
Family Representative 		peptidoglycan muralytic activity
GO:0061783 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
phi6_P1_inner_shell Cystovirus major inner capsid protein P1 family
Family 		RNA binding
GO:0003723 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P7_packaging_cofactor Cystovirus procapsid packaging cofactor P7 family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P4_packaging_ntpase Cystovirus hexameric packaging NTPase P4 family
Family 		ribonucleoside triphosphate phosphatase activity
GO:0017111 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P2_rdrp Cystovirus RNA-directed RNA polymerase P2 family
Family 		RNA-directed RNA polymerase activity
GO:0003968 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P8_outer_shell Cystovirus outer capsid shell protein P8 family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P9_envelope_protein Cystovirus major envelope protein P9 family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P6_fusion_anchor Cystovirus membrane fusion protein P6 family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P3_pilus_spike Cystovirus receptor-binding spike protein P3 family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
phi6_P5_endolysin Cystovirus muralytic enzyme P5 family
Family 		peptidoglycan muralytic activity
GO:0061783 		Family Id Missing
The family has no identifier linking it to a curated family review.

Gene-review completeness (11/11 grounded genes reviewed)

11 complete review(s) · 0 with deep research · 0 missing review · 11 reviewed but lacking deep research

Gene Review Complete Deep research
P1 P11126 ✓ ✓ ✗
P10 P11127 ✓ ✓ ✗
P12 P07580 ✓ ✓ ✗
P2 P11124 ✓ ✓ ✗
P3 P11129 ✓ ✓ ✗
P4 P11125 ✓ ✓ ✗
P5 P07582 ✓ ✓ ✗
P6 P11128 ✓ ✓ ✗
P7 P11123 ✓ ✓ ✗
P8 P07579 ✓ ✓ ✗
P9 P07581 ✓ ✓ ✗

Details

Context
CystoviridaeNCBITaxon:10877
Enveloped dsRNA cystovirus procapsid packaging, replication, and envelope assemblyBiological Processphage_dsrna_cystovirus_lifecycle
viral genome packagingGO:0019072 viral RNA genome replicationGO:0039694 virion assemblyGO:0019068
Context
CystoviridaeNCBITaxon:10877

Exemplar phages: Pseudomonas phage phi6 (NCBITaxon:2928686): Type species of Cystoviridae whose 13 proteins (P1-P10, P12-P14) encoded across segments L, M, and S execute sequential procapsid packaging, intra-capsid dsRNA synthesis, T=13 nucleocapsid assembly, P12-assisted intracellular envelopment, type IV pilus attachment, outer-membrane fusion, and P5/P10 lysis.

Connections

The pre-assembled P1-P2-P4-P7 dodecahedral procapsid exposes the s+ packaging site and mounts the P4 NTPase motors at its five-fold vertices.
Sequential packaging of s+, m+, and l+ expands the procapsid and activates P2 RdRP to synthesize the complementary minus strands inside the core.
Completion of dsRNA synthesis and late transcription produces the mature dsRNA-filled core that templates T=13 P8 shell assembly.
The P8-coated nucleocapsid is enveloped in the cytoplasm by P9/P6/P10/P13 lipid vesicles through the action of morphogenetic factor P12 and decorated with P3 spikes.
Mature enveloped virions are released into the medium by P10/P5-mediated host cell lysis.
Part 1: Dodecahedral polymerase complex (procapsid) assembly
Assembly of the unexpanded P1-P2-P4-P7 procapsid (polymerase complex)Protein Complexprocapsid_polymerase_complex_assembly

Annotons

Major inner capsid shell protein P1
phi6_P1_inner_shell
Participant: Family: Cystovirus major inner capsid protein P1 family
Family:
Cystovirus major inner capsid protein P1 family
Representative Members: P1 (Pseudomonas phage phi6 major inner protein P1)UniProtKB:P11126

Function

RNA bindingGO:0003723

Processes

viral genome packagingGO:0019072

Locations

host cell cytoplasmGO:0030430

Assembles as 60 asymmetric dimers (120 subunits) into the T=1 dodecahedral procapsid skeleton that houses P2 and mounts P4 and P7 at the five-fold vertices, undergoing conformational expansion during sequential s+, m+, and l+ packaging.

Procapsid assembly and packaging cofactor P7
phi6_P7_packaging_cofactor
Participant: Family: Cystovirus procapsid packaging cofactor P7 family
Family:
Cystovirus procapsid packaging cofactor P7 family
Representative Members: P7 (Pseudomonas phage phi6 protein P7)UniProtKB:P11123

Function

structural constituent of virionGO:0039660

Processes

viral capsid assemblyGO:0019069 viral genome packagingGO:0019072

Locations

host cell cytoplasmGO:0030430

Accessory procapsid protein that stabilizes P1-P2-P4 procapsid assembly and accelerates plus-strand RNA packaging and minus-strand synthesis.

Part 2: Sequential NTP-driven (+)-strand ssRNA packaging
Hexameric P4 NTPase-driven translocation of s+, m+, and l+ ssRNA segmentsTransport StepP4_sequential_ssrna_packaging

Annotons

Hexameric RNA packaging NTPase motor P4
phi6_P4_packaging_ntpase
Participant: Family: Cystovirus hexameric packaging NTPase P4 family
Family:
Cystovirus hexameric packaging NTPase P4 family
Representative Members: P4 (Pseudomonas phage phi6 packaging enzyme P4)UniProtKB:P11125

Function

ribonucleoside triphosphate phosphatase activityGO:0017111

Processes

viral genome packagingGO:0019072

Locations

host cell cytoplasmGO:0030430

Homohexameric P-loop NTPase turret mounted at the 12 five-fold procapsid vertices that couples NTP hydrolysis to 5'-to-3' translocation of viral (+)-strand RNA precursors into the procapsid lumen.

Part 3: Intra-capsid dsRNA synthesis and transcription
Intra-capsid minus-strand RNA synthesis and semi-conservative transcription by P2 RdRPReactionP2_intracapsid_dsrna_synthesis

Annotons

Primer-independent RNA-directed RNA polymerase P2
phi6_P2_rdrp
Participant: Family: Cystovirus RNA-directed RNA polymerase P2 family
Family:
Cystovirus RNA-directed RNA polymerase P2 family
Representative Members: P2 (Pseudomonas phage phi6 RNA-directed RNA polymerase P2)UniProtKB:P11124

Function

RNA-directed RNA polymerase activityGO:0003968

Processes

viral RNA genome replicationGO:0039694 RNA-templated transcriptionGO:0001172

Locations

host cell cytoplasmGO:0030430

Primer-independent RdRP inside the procapsid that initiates de novo (-)-strand synthesis once all three (+)-strands (s+, m+, l+) are packaged, and subsequently catalyzes semi-conservative (+)-strand mRNA transcription.

Part 4: Outer T=13 nucleocapsid shell assembly
Encapsidation of the dsRNA-filled core by the Ca2+-dependent T=13 P8 shellProtein ComplexP8_nucleocapsid_shell_assembly

Annotons

Outer capsid T=13 shell protein P8
phi6_P8_outer_shell
Participant: Family: Cystovirus outer capsid shell protein P8 family
Family:
Cystovirus outer capsid shell protein P8 family
Representative Members: P8 (Pseudomonas phage phi6 outer capsid protein P8)UniProtKB:P07579

Function

structural constituent of virionGO:0039660

Processes

symbiont entry into host cellGO:0046718

Locations

host cell cytoplasmGO:0030430

200 trimers (600 copies) of P8 assemble in a Ca2+-dependent T=13 lattice around the expanded dsRNA-filled polymerase core to form the mature nucleocapsid, and also mediate cytoplasmic-membrane penetration during entry.

Part 5: Intracellular viral lipid envelope morphogenesis and spike attachment
P12-mediated acquisition of the P9/P6/P10/P13 lipid envelope and P3 spike attachmentProtein ComplexP9_P12_P6_P3_envelopment

Annotons

Major viral envelope transmembrane protein P9
phi6_P9_envelope_protein
Participant: Family: Cystovirus major envelope protein P9 family
Family:
Cystovirus major envelope protein P9 family
Representative Members: P9 (Pseudomonas phage phi6 major envelope protein P9)UniProtKB:P07581

Function

structural constituent of virionGO:0039660

Processes

virion assemblyGO:0019068

Locations

host cell cytoplasmGO:0030430

Major integral viral membrane protein that drives intracellular lipid-protein vesicle formation in concert with the nonstructural morphogenetic factor P12 to envelope the P8-coated nucleocapsid.

Nonstructural membrane morphogenetic assembly factor P12
phi6_P12_morphogenetic_factor
Participant: Family: Cystovirus membrane morphogenetic factor P12 family
Family:
Cystovirus membrane morphogenetic factor P12 family
Representative Members: P12 (Pseudomonas phage phi6 morphogenetic protein P12)UniProtKB:P07580

Processes

virion assemblyGO:0019068

Locations

host cell cytoplasmGO:0030430

Nonstructural cytoplasmic assembly chaperone that protects P9 from proteolysis and mediates intracellular acquisition of the host plasma-membrane-derived lipid bilayer around the nucleocapsid.

Envelope membrane-fusion and P3-anchoring protein P6
phi6_P6_fusion_anchor
Participant: Family: Cystovirus membrane fusion protein P6 family
Family:
Cystovirus membrane fusion protein P6 family
Representative Members: P6 (Pseudomonas phage phi6 fusion protein P6)UniProtKB:P11128

Function

structural constituent of virionGO:0039660

Processes

fusion of virus membrane with host outer membraneGO:0098997

Locations

host cell outer membraneGO:0039662

Multipass viral envelope protein that anchors the receptor-binding spike P3 on the virion surface and catalyzes fusion of the viral envelope with the host outer membrane during entry.

Host type IV pilus attachment spike protein P3
phi6_P3_pilus_spike
Participant: Family: Cystovirus receptor-binding spike protein P3 family
Family:
Cystovirus receptor-binding spike protein P3 family
Representative Members: P3 (Pseudomonas phage phi6 spike protein P3)UniProtKB:P11129

Function

structural constituent of virionGO:0039660

Processes

virion attachment to host cell pilusGO:0039666

Locations

host cell outer membraneGO:0039662

Surface spike protein anchored to P6 that binds the host Pseudomonas type IV pilus so pilus retraction brings the enveloped virion to the outer membrane.

Part 6: Muralytic and membrane-lytic release of enveloped virions
Host cell lysis mediated by envelope protein P10 and muralytic endopeptidase P5Biological ProcessP5_P10_virion_release

Annotons

Virion-associated muralytic endopeptidase P5
phi6_P5_endolysin
Participant: Family: Cystovirus muralytic enzyme P5 family
Family:
Cystovirus muralytic enzyme P5 family
Representative Members: P5 (Pseudomonas phage phi6 lytic enzyme P5)UniProtKB:P07582

Function

peptidoglycan muralytic activityGO:0061783

Processes

symbiont entry into host cell via disruption of host cell wall peptidoglycanGO:0098932 viral release from host cell by cytolysisGO:0044659

Locations

host cell periplasmic spaceGO:0044229

Periplasmic virion-associated muralytic enzyme located between the P8 shell and the lipid envelope that digests host peptidoglycan both during nucleocapsid entry and during P10-assisted host cell lysis at the end of infection.

Envelope holin-like membrane lysis protein P10
phi6_P10_holin_lysis
Participant: Family: Cystovirus membrane lysis protein P10 family
Family:
Cystovirus membrane lysis protein P10 family
Representative Members: P10 (Pseudomonas phage phi6 membrane protein P10)UniProtKB:P11127

Processes

viral release from host cell by cytolysisGO:0044659

Locations

host cell plasma membraneGO:0020002

Integral membrane protein incorporated into the viral envelope and host membrane that promotes membrane permeabilization for P5-driven bacteriolysis.