Bacteriophage Host Attachment and Genome Ejection Systems

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).

MODULE:phage_attachment_and_genome_ejectionCOMPLETECONCRETEBiological Processmodules/phage_attachment_and_genome_ejection.yaml
virion attachment to host cellGO:0019062 symbiont genome ejection through host cell envelopeGO:0039678 symbiont entry into host cellGO:0046718
PMID:27193680
Structure of the T4 baseplate and its function in triggering sheath contraction.
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.
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.
PMID:19229296
The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria.
Contraction of the T4 gp18 tail sheath drives the inner gp19 tail tube and gp5-gp27 cell-puncturing complex across the bacterial outer membrane.
The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery.
PMID:11823865
Structure of the cell-puncturing device of bacteriophage T4.
The T4 baseplate central hub complex (gp5-gp27) forms a membrane-puncturing needle carrying a lysozyme domain that digests periplasmic peptidoglycan during entry.
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.
PMID:15701513
Control of bacteriophage T4 tail lysozyme activity during the infection process.
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.
The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space.
file:projects/PHAGES.md
Bacteriophage Genome & Module Curation Plan
Synthesizes the receptor-binding and genome ejection variants across myoviruses, siphoviruses, podoviruses, filamentous phages, microviruses, and enveloped cystoviruses.
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.

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.

10Nodes
3Parts
1Variant Sets
6Variants
9Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:phage_attachment_and_genome_ejection 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

0 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (9 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
ltf_adhesion_receptor_binding ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
stf_entry_receptor_binding ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
tail_sheath_contraction ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
baseplate_hub_tail_lysozyme_puncturing ANY_WITH_FUNCTION
Gene 		lysozyme activity
GO:0003796 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
siphovirus_tail_tip_and_tube_ejection ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
podovirus_short_tail_ejection ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
pilus_attachment_and_entry ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
microvirus_spike_and_pilot_protein ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
cystovirus_envelope_fusion_entry ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.

Gene-review completeness (9/9 grounded genes reviewed)

9 complete review(s) · 4 with deep research · 0 missing review · 5 reviewed but lacking deep research

Gene Review Complete Deep research
12 P10930 ✓ ✓ ✓
16 P03726 ✓ ✓ ✗
18 P13332 ✓ ✓ ✓
37 P03744 ✓ ✓ ✓
5 P16009 ✓ ✓ ✓
H P03646 ✓ ✓ ✗
III P69168 ✓ ✓ ✗
J P03749 ✓ ✓ ✗
P6 P11128 ✓ ✓ ✗

Details

Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Bacteriophage Host Attachment and Genome EjectionBiological Processphage_attachment_and_genome_ejection
virion attachment to host cellGO:0019062 symbiont genome ejection through host cell envelopeGO:0039678 symbiont entry into host cellGO:0046718
Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Variant set: Bacteriophage attachment and genome ejection architecture by virion tail/capsid morphology and entry mechanism (Exactly One)

Bacteriophages use distinct structural machines to couple receptor recognition to genome translocation across the bacterial cell envelope.

Myovirus contractile tail genome ejection (T4/P2-type)Biological Processcontractile_tail_ejection

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`).

Connections

positively regulatesRO:0002213
Reversible binding of long tail fibers to primary receptors transmits a mechanical signal via gp9/gp10/gp11 to deploy the short tail fibers.
positively regulatesRO:0002213
Hexagonal-to-star expansion of the baseplate wedge and hub initiates wave-like contraction of the gp18 tail sheath.
Part 1: reversible primary adsorption by long tail fibers
Long tail fiber reversible host recognitionBiological Processmyovirus_reversible_adsorption

Annotons

Long tail fiber distal tip adhesion receptor recognition
ltf_adhesion_receptor_binding
Participant: Any With Function: 37 (Bacteriophage T4)
Gene Product:
37 (Bacteriophage T4)UniProtKB:P03744
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

adhesion receptor-mediated virion attachment to host cellGO:0098671 lipopolysaccharide-mediated virion attachment to host cellGO:0039638

Mediates initial reversible scanning and attachment to host outer membrane receptors.

Part 2: irreversible commitment and baseplate triggering
Short tail fiber irreversible attachment and baseplate expansionBiological Processmyovirus_irreversible_baseplate_commitment

Annotons

Short tail fiber irreversible receptor binding
stf_entry_receptor_binding
Participant: Any With Function: 12 (Bacteriophage T4)
Gene Product:
12 (Bacteriophage T4)UniProtKB:P10930
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

entry receptor-mediated virion attachment to host cellGO:0098670 symbiont genome ejection through host cell envelope, contractile tail mechanismGO:0099000

Irreversibly anchors the baseplate to the bacterial outer membrane and triggers sheath contraction.

PMID:27193680
Baseplate conformational transition couples short tail fiber attachment to tail sheath contraction.
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.
Part 3: contractile sheath drive and peptidoglycan puncturing
Contractile sheath drive and gp5 tail lysozyme cell wall penetrationBiological Processmyovirus_sheath_contraction_and_puncturing

Annotons

Tail sheath contraction driving tail tube penetration
tail_sheath_contraction
Participant: Any With Function: 18 (Bacteriophage T4)
Gene Product:
18 (Bacteriophage T4)UniProtKB:P13332
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

symbiont genome ejection through host cell envelope, contractile tail mechanismGO:0099000

Provides the mechanical force to puncture the host outer membrane and advance the tail tube to the inner membrane.

PMID:19229296
The T4 gp18 tail sheath contracts to propel the tail tube into the host envelope.
The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery.
Baseplate central hub needle and tail lysozyme peptidoglycan digestion
baseplate_hub_tail_lysozyme_puncturing
Participant: Any With Function: 5 (Bacteriophage T4)
Gene Product:
5 (Bacteriophage T4)UniProtKB:P16009
Required Function:
lysozyme activityGO:0003796
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

lysozyme activityGO:0003796

Processes

symbiont entry into host cell via disruption of host cell wall peptidoglycanGO:0098932 symbiont genome ejection through host cell envelope, contractile tail mechanismGO:0099000

Locations

host cell periplasmic spaceGO:0044229

Punctures the outer membrane and locally hydrolyzes the periplasmic peptidoglycan barrier during viral entry.

PMID:11823865
The T4 gp5-gp27 complex forms a cell-puncturing needle with a lysozyme domain.
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.
PMID:15701513
T4 gp5 tail lysozyme is activated during infection to locally cleave host peptidoglycan.
The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space.
Siphovirus long flexible non-contractile tail ejection (lambda/T5-type)Biological Processlong_flexible_tail_ejection

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

Siphovirus tail tip receptor binding and flexible tail genome ejection
siphovirus_tail_tip_and_tube_ejection
Participant: Any With Function: J (Escherichia phage lambda)
Gene Product:
J (Escherichia phage lambda)UniProtKB:P03749
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

entry receptor-mediated virion attachment to host cellGO:0098670 symbiont genome ejection through host cell envelope, long flexible tail mechanismGO:0099001

Locations

host cell outer membraneGO:0039662 host cell periplasmic spaceGO:0044229

Recognizes the outer membrane protein receptor and mediates genome translocation through a non-contractile tail conduit.

Podovirus short tail and extendable internal core ejection (T7/P22/phi29-type)Biological Processshort_tail_ejectosome_ejection

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

Podovirus tail fiber adsorption and internal core ejectosome assembly
podovirus_short_tail_ejection
Participant: Any With Function: 16 (Enterobacteria phage T7)
Gene Product:
16 (Enterobacteria phage T7)UniProtKB:P03726
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

lipopolysaccharide-mediated virion attachment to host cellGO:0039638 symbiont genome ejection through host cell envelope, short tail mechanismGO:0099002 symbiont entry into host cell via disruption of host cell wall peptidoglycanGO:0098932

Locations

host cell outer membraneGO:0039662 host cell periplasmic spaceGO:0044229

Adsorbs to host LPS and extrudes internal virion proteins to form an extendable genome-delivery channel across the envelope.

Pilus-mediated adsorption and retraction entry (Inoviridae and Fiersviridae)Biological Processpilus_mediated_entry

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

Virion attachment to host pilus and genome entry
pilus_attachment_and_entry
Participant: Any With Function: III (Enterobacteria phage M13)
Gene Product:
III (Enterobacteria phage M13)UniProtKB:P69168
Required Function:
structural constituent of virionGO:0039660
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

structural constituent of virionGO:0039660

Processes

virion attachment to host cell pilusGO:0039666 symbiont entry into host cellGO:0046718

Locations

host cell plasma membraneGO:0020002

Binds the bacterial pilus and couples pilus retraction to viral genome translocation across the cell envelope.

Tailless icosahedral spike and DNA pilot tube entry (Microviridae)Biological Processmicrovirus_pilot_tube_entry

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

Spike LPS attachment and gpH DNA pilot tube formation
microvirus_spike_and_pilot_protein
Participant: Any With Function: H (Escherichia phage phiX174)
Gene Product:
H (Escherichia phage phiX174)UniProtKB:P03646
Required Function:
structural constituent of virionGO:0039660
phiX174 major spike protein G (LPS recognition) and DNA pilot protein H (oligomeric trans-envelope DNA delivery tube with peptidoglycan hydrolase activity).

Function

structural constituent of virionGO:0039660

Processes

lipopolysaccharide-mediated virion attachment to host cellGO:0039638 symbiont entry into host cell via permeabilization of inner membraneGO:0099008 symbiont genome ejection through host cell envelopeGO:0039678

Locations

host cell outer membraneGO:0039662 host cell periplasmic spaceGO:0044229

Forms an inducible alpha-helical trans-envelope tube after LPS attachment to pilot the ssDNA genome into the cytoplasm.

Enveloped phage pilus attachment, outer membrane fusion, and nucleocapsid entry (Cystoviridae)Biological Processenveloped_phage_membrane_fusion_entry

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

Enveloped phage attachment, membrane fusion, and peptidoglycan penetration
cystovirus_envelope_fusion_entry
Participant: Any With Function: P6 (Pseudomonas phage phi6)
Gene Product:
P6 (Pseudomonas phage phi6)UniProtKB:P11128
Required Function:
structural constituent of virionGO:0039660
Envelope spike protein P3, membrane fusion protein P6, and virion-associated muralytic enzyme P5 of cystovirus phi6.

Function

structural constituent of virionGO:0039660

Processes

virion attachment to host cell pilusGO:0039666 symbiont entry into host cell via disruption of host cell wall peptidoglycanGO:0098932 symbiont entry into host cellGO:0046718

Locations

host cell outer membraneGO:0039662 host cell periplasmic spaceGO:0044229

Mediates pilus attachment, fusion of the viral lipid envelope with the host outer membrane, and peptidoglycan penetration.