Filamentous bacteriophage non-lytic virion assembly and trans-envelope extrusion

A reusable module representing the chronic, non-lytic virion assembly and trans-envelope extrusion pathway of filamentous single-stranded DNA bacteriophages (Inoviridae, exemplified by Ff coliphages M13, fd, and f1). Unlike lytic phages that assemble capsids in the cytoplasm and lyse the host, filamentous phages package progeny circular (+)ssDNA into a left-handed helical nucleoprotein complex with the dimeric ssDNA-binding protein pV in the cytoplasm, store all five structural coat proteins (pVIII, pIII, pVI, pVII, pIX) as integral inner-membrane proteins, and continuously extrude mature filaments across both bacterial membranes without killing the host cell (GO:0099045 viral extrusion). Extrusion is driven by a trans-envelope assembly nanomachine comprising the inner-membrane ATPase motor complex pI/pXI (encoded by gene I via full-length translation and internal initiation) coupled across the periplasm to the gated outer-membrane secretin channel pIV. Assembly initiates when the packaging hairpin of the pV-ssDNA complex is recognized at the pI/pXI motor and capped by the distal tip proteins pVII and pIX, proceeds via ATP- and proton-motive-force-driven replacement of cytoplasmic pV dimers by ~2,700 membrane-embedded major coat subunits pVIII, and terminates when the proximal tip complex pVI-pIII caps the trailing end and releases the virion through the pIV secretin pore.

MODULE:phage_filamentous_extrusionCOMPLETECONCRETEBiological Processmodules/phage_filamentous_extrusion.yaml
viral extrusionGO:0099045 virion assemblyGO:0019068
GO:0099045
viral extrusion
Ontology grounding for non-lytic filamentous phage release by continuous extrusion across the host cell envelope.
file:genes/BPM13/I/I-uniprot.txt
UniProtKB/Swiss-Prot entry P03656 (G1P_BPM13)
Establishes that M13 gene I encodes the inner-membrane isoforms G1P (pI) and G11P (pXI), which form a pore-like oligomeric ATP-hydrolyzing complex with outer-membrane G4P (pIV) through which the phage is assembled and extruded.
Part of a viral G1P-G11P-G4P transmembrane assembly machine, through which the phage is assembled and extruded (PubMed:35746635). Together with G11P, generates an oligomeric structure with a pore-like inner cavity and an ATP hydrolyzing domain (PubMed:35746635).
file:genes/BPM13/IV/IV-uniprot.txt
UniProtKB/Swiss-Prot entry P03665 (G4P_BPM13)
Establishes that M13 pIV (G4P) is a secretin-family outer-membrane channel that interacts via its periplasmic N-terminus with inner-membrane G1P/G11P to span both host membranes.
Interacts (via N-terminus) with G1P/G11P; this interaction allows the formation of the transmembrane assembly machine that spans the host inner and outer membranes (By similarity).
6Nodes
5Parts
0Variant Sets
0Variants
8Annotons
5Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:phage_filamentous_extrusion 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

7 gene-function check(s) reflected in core functions · 0 conflict(s) · 7 evidence or coverage gap(s) (14 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
m13_pV_ssdna_binding V (Enterobacteria phage M13 protein G5P)
UniProtKB:P69544
Family Representative 		single-stranded DNA binding
GO:0003697 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
m13_pVII_initiator VII (Enterobacteria phage M13 capsid protein G7P)
UniProtKB:P69535
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).
m13_pIX_initiator IX (Enterobacteria phage M13 capsid protein G9P)
UniProtKB:P69538
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).
m13_pI_pXI_motor I (Enterobacteria phage M13 assembly protein G1P/G11P)
UniProtKB:P03656
Family Representative 		ATP binding
GO:0005524 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
m13_pVIII_major_coat VIII (Enterobacteria phage M13 capsid protein G8P)
UniProtKB:P69541
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).
m13_pVI_terminator VI (Enterobacteria phage M13 capsid protein G6P)
UniProtKB:P69532
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).
m13_pIII_adhesin_terminator III (Enterobacteria phage M13 attachment protein G3P)
UniProtKB:P69168
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).
m13_pV_ssdna_binding Inovirus ssDNA-binding protein G5P (pV) family
Family 		single-stranded DNA binding
GO:0003697 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pVII_initiator Inovirus distal tip coat protein G7P (pVII) family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pIX_initiator Inovirus distal tip coat protein G9P (pIX) family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pI_pXI_motor Inovirus assembly ATPase G1P/G11P (pI/pXI) family
Family 		ATP binding
GO:0005524 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pVIII_major_coat Inovirus major coat protein G8P (pVIII) family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pVI_terminator Inovirus proximal tip protein G6P (pVI) family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.
m13_pIII_adhesin_terminator Inovirus attachment and terminal release protein G3P (pIII) family
Family 		structural constituent of virion
GO:0039660 		Family Id Missing
The family has no identifier linking it to a curated family review.

Gene-review completeness (8/8 grounded genes reviewed)

8 complete review(s) · 0 with deep research · 0 missing review · 8 reviewed but lacking deep research

Gene Review Complete Deep research
I P03656 ✓ ✓ ✗
III P69168 ✓ ✓ ✗
IV P03665 ✓ ✓ ✗
IX P69538 ✓ ✓ ✗
V P69544 ✓ ✓ ✗
VI P69532 ✓ ✓ ✗
VII P69535 ✓ ✓ ✗
VIII P69541 ✓ ✓ ✗

Details

Context
InoviridaeNCBITaxon:10860
Filamentous phage non-lytic assembly and extrusionBiological Processphage_filamentous_extrusion
viral extrusionGO:0099045 virion assemblyGO:0019068
Context
InoviridaeNCBITaxon:10860

Exemplar phages: Enterobacteria phage M13 (NCBITaxon:1977402): Canonical F-pilus-specific filamentous coliphage (Inoviridae) whose 9 genes (encoding 11 proteins pI-pXI) execute chronic non-lytic extrusion via the pI/pXI-pIV trans-envelope assembly machine.

Connections

The pV-coated (+)ssDNA nucleoprotein filament presents the exposed packaging hairpin to initiate assembly with pVII and pIX at the inner membrane.
Initiation by pVII-pIX nucleates progressive replacement of pV by membrane-stored pVIII subunits driven by the pI/pXI motor.
Once the entire ssDNA circle is coated with pVIII, pVI and pIII cap the trailing proximal tip and sever the virion from the inner membrane.
The elongating filament is threaded directly from the inner-membrane pI/pXI motor into the coupled periplasmic/outer-membrane pIV secretin channel.
Proximal tip capping by pVI-pIII releases the completed virion to exit through the pIV secretin pore.
Part 1: Cytoplasmic pre-extrusion ssDNA sequestration
Formation of the intracellular pV-ssDNA pre-extrusion filamentProtein ComplexpV_ssdna_sequestration

Annotons

Single-stranded DNA-binding protein pV
m13_pV_ssdna_binding
Participant: Family: Inovirus ssDNA-binding protein G5P (pV) family
Family:
Inovirus ssDNA-binding protein G5P (pV) family
Representative Members: V (Enterobacteria phage M13 protein G5P)UniProtKB:P69544

Function

single-stranded DNA bindingGO:0003697

Processes

virion assemblyGO:0019068

Locations

host cell cytoplasmGO:0030430

Cooperatively coats progeny viral (+)ssDNA rings to prevent conversion to replicative-form dsDNA and presents the exposed packaging hairpin to the inner-membrane extrusion motor.

Part 2: Distal tip initiation at the inner membrane
Packaging signal recognition and distal virion tip initiation (pVII-pIX)Protein ComplexpVII_pIX_tip_initiation

Annotons

Distal tip minor coat protein pVII
m13_pVII_initiator
Participant: Family: Inovirus distal tip coat protein G7P (pVII) family
Family:
Inovirus distal tip coat protein G7P (pVII) family
Representative Members: VII (Enterobacteria phage M13 capsid protein G7P)UniProtKB:P69535

Function

structural constituent of virionGO:0039660

Processes

viral extrusionGO:0099045

Locations

host cell plasma membraneGO:0020002

Integral inner-membrane minor coat protein (~5 copies) that pairs with pIX at the leading distal tip of the emerging filament to nucleate capsid assembly on the packaging signal.

Distal tip minor coat protein pIX
m13_pIX_initiator
Participant: Family: Inovirus distal tip coat protein G9P (pIX) family
Family:
Inovirus distal tip coat protein G9P (pIX) family
Representative Members: IX (Enterobacteria phage M13 capsid protein G9P)UniProtKB:P69538

Function

structural constituent of virionGO:0039660

Processes

viral extrusionGO:0099045

Locations

host cell plasma membraneGO:0020002

Integral inner-membrane minor coat protein (~5 copies) forming the distal tip cap with pVII.

Part 3: ATP-driven inner-membrane coat replacement and elongation
Inner-membrane pI/pXI motor-driven replacement of pV by major coat pVIIITransport SteppI_pXI_pVIII_elongation

Annotons

Inner-membrane assembly ATPase complex pI/pXI
m13_pI_pXI_motor
Participant: Family: Inovirus assembly ATPase G1P/G11P (pI/pXI) family
Family:
Inovirus assembly ATPase G1P/G11P (pI/pXI) family
Representative Members: I (Enterobacteria phage M13 assembly protein G1P/G11P)UniProtKB:P03656

Function

ATP bindingGO:0005524

Processes

viral extrusionGO:0099045

Locations

host cell plasma membraneGO:0020002

Oligomeric inner-membrane assembly motor formed by full-length pI (cytoplasmic Zot-family NTPase domain) and internal-initiation isoform pXI that couples ATP hydrolysis to ssDNA translocation and coat replacement.

Major helical capsid coat protein pVIII
m13_pVIII_major_coat
Participant: Family: Inovirus major coat protein G8P (pVIII) family
Family:
Inovirus major coat protein G8P (pVIII) family
Representative Members: VIII (Enterobacteria phage M13 capsid protein G8P)UniProtKB:P69541

Function

structural constituent of virionGO:0039660

Processes

viral extrusionGO:0099045

Locations

host cell plasma membraneGO:0020002

50-aa alpha-helical coat subunit (~2,700 copies per virion) stored in the inner membrane via YidC and transferred onto the extruding ssDNA core as pV dimers are stripped.

Part 4: Proximal tip capping and membrane release
Proximal virion tip capping and membrane scission by pVI-pIIIProtein ComplexpVI_pIII_termination

Annotons

Proximal tip minor coat protein pVI
m13_pVI_terminator
Participant: Family: Inovirus proximal tip protein G6P (pVI) family
Family:
Inovirus proximal tip protein G6P (pVI) family
Representative Members: VI (Enterobacteria phage M13 capsid protein G6P)UniProtKB:P69532

Function

structural constituent of virionGO:0039660

Processes

viral extrusionGO:0099045

Locations

host cell plasma membraneGO:0020002

Hydrophobic adapter protein (~5 copies) that bridges the terminal ring of pVIII subunits to the receptor-binding adhesin pIII to release the nascent virion from the inner membrane.

Proximal tip attachment and release protein pIII
m13_pIII_adhesin_terminator
Participant: Family: Inovirus attachment and terminal release protein G3P (pIII) family
Family:
Inovirus attachment and terminal release protein G3P (pIII) family
Representative Members: III (Enterobacteria phage M13 attachment protein G3P)UniProtKB:P69168

Function

structural constituent of virionGO:0039660

Processes

viral extrusionGO:0099045 virion attachment to host cell pilusGO:0039666

Locations

host cell plasma membraneGO:0020002

Five-copy proximal tip protein that caps the trailing end of the extruding virion with pVI and subsequently mediates F-pilus and TolA binding on the next host cell.

Part 5: Outer-membrane secretin conduit transit
Trans-outer-membrane extrusion through the pIV secretin channelTransport SteppIV_secretin_transit

Annotons

Outer-membrane virion export secretin pIV
m13_pIV_secretin
Participant: Family: Inovirus outer-membrane secretin G4P (pIV) family
Family:
Inovirus outer-membrane secretin G4P (pIV) family
Representative Members: IV (Enterobacteria phage M13 virion export protein G4P)UniProtKB:P03665

Processes

viral extrusionGO:0099045

Locations

host cell outer membraneGO:0039662

Tetradecameric/pentadecameric outer-membrane secretin channel that docks via its periplasmic N0/N3 domains onto the inner-membrane pI/pXI motor and opens its central gate to allow non-lytic passage of the 6.5 nm filament across the outer membrane.