Autographiviridae host defense evasion, RNA polymerase shutoff, single-subunit transcription, and minimal T7 replisome

An integrated host-takeover, transcription, and genome-replication module characteristic of T7-like lytic podoviruses (Autographiviridae). Immediately upon entry of the leading left end of the linear genome, host Escherichia coli RNA polymerase transcribes the Class I early operon from promoters A1, A2, and A3, producing: (1) the B-form DNA mimic Ocr (gp0.3), which blocks Type I restriction-modification and BREX complexes; (2) the serine/threonine protein kinase gp0.7, which phosphorylates the beta-prime subunit of host RNA polymerase, RNase E, and translation factors to attenuate host gene expression; (3) the single-subunit phage RNA polymerase (gp1); and (4) the ATP-dependent DNA ligase (gp1.3). T7 RNA polymerase then drives high-velocity transcription of Class II replication and host-shutoff genes and Class III structural genes from phage-specific 23-bp promoters. Class II gene 2 protein (gp2) binds the beta-prime jaw domain of host sigma-70-RNA polymerase holoenzyme to completely shut off residual host transcription, while endonuclease I (gp3) and the 5'-3' exonuclease/RNase H (gp6) degrade the host chromosome to supply deoxynucleoside monophosphates for phage DNA synthesis. Genome replication is executed by a minimal four-protein replisome comprising the gp5 DNA polymerase complexed 1:1 with host Escherichia coli thioredoxin as its processivity factor, the hexameric ring bifunctional primase-helicase (gp4), and the C-terminally acidic single-stranded DNA-binding protein (gp2.5), followed by concatemer maturation and Holliday junction resolution assisted by gp6, gp1.3, and gp3.

MODULE:phage_t7_replisome_transcriptionCOMPLETECONCRETEBiological Processmodules/phage_t7_replisome_transcription.yaml
symbiont-mediated evasion of host restriction-modification systemGO:0099018 symbiont-mediated suppression of host transcriptionGO:0039653 DNA-templated viral transcriptionGO:0039695 viral DNA genome replicationGO:0039693 degradation of host chromosome by virusGO:0099015
PMID:30679383
Structures and operating principles of the replisome.
Establishes the structural organization and coordinated leading/lagging-strand operating mechanism of the minimal bacteriophage T7 replisome (gp5-thioredoxin, gp4 primase-helicase, and gp2.5 ssDNA-binding protein).
PMID:32009150
Dynamic structural insights into the molecular mechanism of DNA unwinding by the bacteriophage T7 helicase.
Cryo-EM and mechanistic characterization of hand-over-hand spiral translocation and DNA unwinding by the hexameric T7 gp4 helicase-primase.
PMID:10369763
Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein.
Demonstrates that T7 gp2 binds the beta-prime subunit of host sigma-70-RNA polymerase to inhibit open promoter complex formation and shut off host transcription.
PMID:8133519
Bacteriophage T7 RNA polymerase and its active-site mutants. Kinetic, spectroscopic and calorimetric characterization.
Characterizes the catalytic mechanism and promoter-specific transcription activity of the single-subunit T7 DNA-directed RNA polymerase (gp1).
PMID:9236119
The junction-resolving enzyme T7 endonuclease I: quaternary structure and interaction with DNA.
Establishes the homodimeric structure and four-way Holliday junction cleavage activity of T7 endonuclease I (gp3).
GO:0039693
viral DNA genome replication
Defines the biological process of replicating the viral double-stranded DNA genome inside the infected host cell.

Exemplar phage: Escherichia phage T7 (NCBITaxon:10760). Generalizes across Autographiviridae (coliphage T3, Yersinia phage phiYeO3-12, Klebsiella phage KP34, Pseudomonas phage gh-1) and provides the evolutionary archetype for eukaryotic mitochondrial transcription and replication machinery (POLRMT, TWINKLE helicase, and DNA polymerase gamma).

5Nodes
4Parts
0Variant Sets
0Variants
10Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:phage_t7_replisome_transcription 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

10 gene-function check(s) reflected in core functions · 0 conflict(s) · 10 evidence or coverage gap(s) (20 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
gp0_3_ocr_antirestriction_activity 0.3 (Escherichia phage T7)
UniProtKB:P03775
Family Representative 		enzyme inhibitor activity
GO:0004857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp0_7_kinase_shutoff_activity 0.7 (Escherichia phage T7)
UniProtKB:P00513
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp1_rna_polymerase_activity 1 (Escherichia phage T7)
UniProtKB:P00573
Family Representative 		DNA-directed RNA polymerase activity
GO:0003899 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp2_host_rnap_inhibitor_activity 2 (Escherichia phage T7)
UniProtKB:P03704
Family Representative 		enzyme inhibitor activity
GO:0004857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp3_endonuclease_activity 3 (Escherichia phage T7)
UniProtKB:P00641
Family Representative 		crossover junction DNA endonuclease activity
GO:0008821 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp6_exonuclease_activity 6 (Escherichia phage T7)
UniProtKB:P00638
Family Representative 		double-stranded DNA 5'-3' DNA exonuclease activity
GO:0051908 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp4_helicase_primase_activity 4 (Escherichia phage T7)
UniProtKB:P03692
Family Representative 		5'-3' DNA helicase activity
GO:0043139 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp5_dna_polymerase_activity 5 (Escherichia phage T7)
UniProtKB:P00581
Family Representative 		DNA-directed DNA polymerase activity
GO:0003887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp2_5_ssdna_binding_activity 2.5 (Escherichia phage T7)
UniProtKB:P03696
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).
gp1_3_dna_ligase_activity 1.3 (Escherichia phage T7)
UniProtKB:P00969
Family Representative 		DNA ligase (ATP) activity
GO:0003910 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gp0_3_ocr_antirestriction_activity Phage T7 Ocr DNA-mimic anti-restriction protein family
Family 		enzyme inhibitor activity
GO:0004857 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp0_7_kinase_shutoff_activity Phage T7-type serine/threonine protein kinase family
Family 		protein serine/threonine kinase activity
GO:0004674 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp1_rna_polymerase_activity Phage-type single-subunit DNA-directed RNA polymerase family
Family 		DNA-directed RNA polymerase activity
GO:0003899 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp2_host_rnap_inhibitor_activity Phage T7 bacterial RNA polymerase inhibitor gp2 family
Family 		enzyme inhibitor activity
GO:0004857 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp3_endonuclease_activity Phage T7 endonuclease I gp3 family
Family 		crossover junction DNA endonuclease activity
GO:0008821 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp6_exonuclease_activity Phage T7 5'-3' exonuclease gp6 family
Family 		double-stranded DNA 5'-3' DNA exonuclease activity
GO:0051908 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp4_helicase_primase_activity Phage T7 bifunctional DNA helicase-primase gp4 family
Family 		5'-3' DNA helicase activity
GO:0043139 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp5_dna_polymerase_activity Phage T7 Family A DNA polymerase gp5 family
Family 		DNA-directed DNA polymerase activity
GO:0003887 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp2_5_ssdna_binding_activity Phage T7 single-stranded DNA-binding protein gp2.5 family
Family 		single-stranded DNA binding
GO:0003697 		Family Id Missing
The family has no identifier linking it to a curated family review.
gp1_3_dna_ligase_activity Phage T7 ATP-dependent DNA ligase gp1.3 family
Family 		DNA ligase (ATP) activity
GO:0003910 		Family Id Missing
The family has no identifier linking it to a curated family review.

Gene-review completeness (10/10 grounded genes reviewed)

10 complete review(s) · 0 with deep research · 0 missing review · 10 reviewed but lacking deep research

Gene Review Complete Deep research
0.3 P03775 ✓ ✓ ✗
0.7 P00513 ✓ ✓ ✗
1 P00573 ✓ ✓ ✗
1.3 P00969 ✓ ✓ ✗
2 P03704 ✓ ✓ ✗
2.5 P03696 ✓ ✓ ✗
3 P00641 ✓ ✓ ✗
4 P03692 ✓ ✓ ✗
5 P00581 ✓ ✓ ✗
6 P00638 ✓ ✓ ✗

Details

Context
CaudoviricetesNCBITaxon:2731619 Escherichia phage T7NCBITaxon:10760
Autographiviridae host takeover, single-subunit RNA polymerase transcription, and minimal replisomeBiological Processphage_t7_replisome_transcription
symbiont-mediated evasion of host restriction-modification systemGO:0099018 symbiont-mediated suppression of host transcriptionGO:0039653 DNA-templated viral transcriptionGO:0039695 viral DNA genome replicationGO:0039693 degradation of host chromosome by virusGO:0099015
Context
CaudoviricetesNCBITaxon:2731619 Escherichia phage T7NCBITaxon:10760

Connections

Part 1: immediate-early anti-restriction defense and host kinase signaling
Ocr DNA-mimic anti-restriction (gp0.3) and gp0.7 kinase-mediated host remodelingRegulatory Stepclass_i_anti_defense_and_kinase_step

Annotons

Anti-restriction protein Ocr (gp0.3)
gp0_3_ocr_antirestriction_activity
Participant: Family: Phage T7 Ocr DNA-mimic anti-restriction protein family
Family:
Phage T7 Ocr DNA-mimic anti-restriction protein family
Representative Members: 0.3 (Escherichia phage T7)UniProtKB:P03775

Function

enzyme inhibitor activityGO:0004857

Processes

symbiont-mediated evasion of host restriction-modification systemGO:0099018 symbiont-mediated suppression of host innate immune responseGO:0052170

Locations

host cell cytoplasmGO:0030430

Forms a polyanionic homodimer that structurally mimics ~24 bp of bent B-form DNA, sequestering host Type I restriction-modification (EcoKI) and BREX complexes with picomolar affinity to protect the incoming unmodified phage genome.

Serine/threonine protein kinase gp0.7
gp0_7_kinase_shutoff_activity
Participant: Family: Phage T7-type serine/threonine protein kinase family
Family:
Phage T7-type serine/threonine protein kinase family
Representative Members: 0.7 (Escherichia phage T7)UniProtKB:P00513

Function

protein serine/threonine kinase activityGO:0004674

Processes

symbiont-mediated suppression of host gene expressionGO:0039657

Locations

host cell cytoplasmGO:0030430

Phosphorylates the host RNA polymerase beta-prime subunit to promote transcription termination at early intergenic sites and phosphorylates host RNase E to stabilize T7 mRNAs synthesized by T7 RNA polymerase.

Part 2: phage-autonomous transcription and host RNA polymerase shutoff
Single-subunit T7 RNA polymerase (gp1) transcription and gp2 inhibition of host RNAPRegulatory Stept7_rnap_transcription_and_gp2_shutoff_step

Annotons

T7 DNA-directed RNA polymerase (gp1)
gp1_rna_polymerase_activity
Participant: Family: Phage-type single-subunit DNA-directed RNA polymerase family
Family:
Phage-type single-subunit DNA-directed RNA polymerase family
Representative Members: 1 (Escherichia phage T7)UniProtKB:P00573

Function

DNA-directed RNA polymerase activityGO:0003899

Processes

DNA-templated viral transcriptionGO:0039695

Locations

host cell cytoplasmGO:0030430

Rifampicin-resistant 99-kDa single-subunit RNA polymerase that specifically recognizes 23-bp T7 Class II and Class III promoters and elongates RNA chains at ~200-250 nt/s, fivefold faster than host bacterial RNA polymerase, while also synthesizing RNA primers at the primary replication origin.

Bacterial RNA polymerase inhibitor gp2
gp2_host_rnap_inhibitor_activity
Participant: Family: Phage T7 bacterial RNA polymerase inhibitor gp2 family
Family:
Phage T7 bacterial RNA polymerase inhibitor gp2 family
Representative Members: 2 (Escherichia phage T7)UniProtKB:P03704

Function

enzyme inhibitor activityGO:0004857

Processes

symbiont-mediated suppression of host transcriptionGO:0039653

Locations

host cell cytoplasmGO:0030430

Binds the beta-prime jaw domain of Escherichia coli sigma-70-RNA polymerase holoenzyme, allosterically preventing downstream DNA loading and transcription initiation at host and Class I promoters to complete the switch to T7 RNA polymerase-driven transcription and prevent host RNAP from colliding with packaging complexes.

Part 3: host chromosome degradation and nucleotide recycling
Host chromosome cleavage by endonuclease I (gp3) and exonuclease (gp6)Reactionhost_chromosome_degradation_step

Annotons

Endonuclease I (gp3)
gp3_endonuclease_activity
Participant: Family: Phage T7 endonuclease I gp3 family
Family:
Phage T7 endonuclease I gp3 family
Representative Members: 3 (Escherichia phage T7)UniProtKB:P00641

Function

crossover junction DNA endonuclease activityGO:0008821

Processes

degradation of host chromosome by virusGO:0099015 DNA recombinationGO:0006310

Locations

host cell cytoplasmGO:0030430

Structure-selective homodimeric PD-(D/E)XK endonuclease that cleaves four-way Holliday junctions during phage recombination and collaborates with gp6 exonuclease to fragment the host Escherichia coli chromosome into acid-soluble nucleotides.

Exonuclease gp6
gp6_exonuclease_activity
Participant: Family: Phage T7 5'-3' exonuclease gp6 family
Family:
Phage T7 5'-3' exonuclease gp6 family
Representative Members: 6 (Escherichia phage T7)UniProtKB:P00638

Function

double-stranded DNA 5'-3' DNA exonuclease activityGO:0051908

Processes

degradation of host chromosome by virusGO:0099015 viral DNA genome replicationGO:0039693

Locations

host cell cytoplasmGO:0030430

Hydrolyzes duplex DNA from 5' termini created by gp3 endonuclease to release deoxynucleoside 5'-monophosphates that fuel phage dNTP synthesis, removes RNA primers from Okazaki fragments via intrinsic RNase H activity, and generates 3' single-stranded overhangs at the 160-bp terminal repeats to form genomic concatemers.

Part 4: coordinated leading- and lagging-strand replisome synthesis
Coordinated DNA unwinding, priming, and synthesis by gp4, gp5, gp2.5, and gp1.3Reactionminimal_t7_replisome_step

Annotons

Bifunctional DNA helicase/primase gp4
gp4_helicase_primase_activity
Participant: Family: Phage T7 bifunctional DNA helicase-primase gp4 family
Family:
Phage T7 bifunctional DNA helicase-primase gp4 family
Representative Members: 4 (Escherichia phage T7)UniProtKB:P03692

Function

5'-3' DNA helicase activityGO:0043139

Processes

viral DNA genome replicationGO:0039693 DNA replication, synthesis of primerGO:0006269

Locations

host cell cytoplasmGO:0030430

Assembles as a hexameric ring on the lagging-strand template that unwinds duplex DNA in the 5'-to-3' direction via its C-terminal RecA-like helicase domain while its N-terminal zinc-ribbon and TOPRIM primase domains synthesize tetraribonucleotide primers (5'-pppACCC/A-3') at 5'-GTC-3' recognition sites and hand them directly to gp5 DNA polymerase.

DNA-directed DNA polymerase gp5
gp5_dna_polymerase_activity
Participant: Family: Phage T7 Family A DNA polymerase gp5 family
Family:
Phage T7 Family A DNA polymerase gp5 family
Representative Members: 5 (Escherichia phage T7)UniProtKB:P00581

Function

DNA-directed DNA polymerase activityGO:0003887

Processes

viral DNA genome replicationGO:0039693

Locations

host cell cytoplasmGO:0030430

Family A DNA polymerase with potent 3'-5' proofreading exonuclease activity that binds host Escherichia coli thioredoxin via a unique 76-residue thumb insertion (TBD) to achieve high-processivity leading- and lagging-strand synthesis coupled to the gp4 helicase.

Single-stranded DNA-binding protein gp2.5
gp2_5_ssdna_binding_activity
Participant: Family: Phage T7 single-stranded DNA-binding protein gp2.5 family
Family:
Phage T7 single-stranded DNA-binding protein gp2.5 family
Representative Members: 2.5 (Escherichia phage T7)UniProtKB:P03696

Function

single-stranded DNA bindingGO:0003697

Processes

viral DNA genome replicationGO:0039693 DNA recombinationGO:0006310

Locations

host cell cytoplasmGO:0030430

OB-fold single-stranded DNA-binding protein that coats lagging-strand ssDNA loops, coordinates gp5 DNA polymerase and gp4 helicase-primase via its acidic C-terminal tail, and catalyzes single-strand annealing of terminal repeats during concatemer formation.

ATP-dependent DNA ligase gp1.3
gp1_3_dna_ligase_activity
Participant: Family: Phage T7 ATP-dependent DNA ligase gp1.3 family
Family:
Phage T7 ATP-dependent DNA ligase gp1.3 family
Representative Members: 1.3 (Escherichia phage T7)UniProtKB:P00969

Function

DNA ligase (ATP) activityGO:0003910

Processes

DNA replicationGO:0006260 DNA repairGO:0006281

Locations

host cell cytoplasmGO:0030430

Seals nicked phosphodiester backbones between processed Okazaki fragments and annealed concatemer junctions using ATP as cofactor.