Bacterial DNA-directed RNA polymerase core enzyme

Species-neutral bacterial module for the DNA-directed RNA polymerase core enzyme that carries out DNA-templated RNA synthesis. The conserved bacterial canonical core enzyme is built from an alpha dimer, beta and beta-prime catalytic cleft subunits, and the omega assembly/stability subunit. This module deliberately stops at the core enzyme and excludes sigma factors, transcription elongation factors, and promoter-specific regulatory proteins.

MODULE:bacterial_rna_polymerase_coreDRAFTCONCRETEProtein Complexmodules/bacterial_rna_polymerase_core.yaml
DNA-directed RNA polymerase complexGO:0000428 DNA-templated transcriptionGO:0006351
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_rna_polymerase_core__ppu03020-deep-research-openscientist.md
OpenScientist PSEPK RNA polymerase pathway satisfiability review
The taxon-constrained report finds ppu03020 completely satisfiable through Q88QL1/RpoA, Q88QP2/RpoB, Q88QP1/RpoC, and Q88C82/RpoZ, with no missing core role or lineage-specific replacement. It supports excluding sigma factors and avoiding a PSEPK omega stringent-response claim.
file:modules/bacterial_rna_polymerase_core-deep-research-openscientist.md
OpenScientist review of the bacterial RNA polymerase core
The completed species-neutral review supports the alpha2-beta-beta-prime- omega canonical composition, assembly ordering, beta/beta-prime active cleft, and the distinction between omega-mediated stability and catalytic necessity.
KEGG:ppu03020
Pseudomonas putida KT2440 RNA polymerase
The local PSEPK pathway partition assigns rpoA, rpoB, rpoC, and rpoZ as the four primary genes in the compact KEGG ppu03020 RNA polymerase bucket.
GO:0000428
DNA-directed RNA polymerase complex
UniProt records for the PSEPK rpoA, rpoB, rpoC, and rpoZ exemplars all carry GO:0000428, supporting this module as a protein-complex module rather than a linear metabolic pathway.
GO:0003899
DNA-directed RNA polymerase activity
GO:0003899 captures the complex-level nucleotidyltransferase activity performed by the assembled core enzyme during transcription.
file:PSEPK/rpoA/rpoA-uniprot.txt
UniProtKB entry for PSEPK rpoA
Q88QL1 is the P. putida KT2440 DNA-directed RNA polymerase alpha subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, dimerization, and DNA-templated transcription annotations.
file:PSEPK/rpoB/rpoB-uniprot.txt
UniProtKB entry for PSEPK rpoB
Q88QP2 is the P. putida KT2440 DNA-directed RNA polymerase beta subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, ribonucleoside binding, and DNA-templated transcription annotations.
file:PSEPK/rpoC/rpoC-uniprot.txt
UniProtKB entry for PSEPK rpoC
Q88QP1 is the P. putida KT2440 DNA-directed RNA polymerase beta-prime subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, magnesium and zinc ion binding, and DNA-templated transcription annotations.
file:PSEPK/rpoZ/rpoZ-uniprot.txt
UniProtKB entry for PSEPK rpoZ
Q88C82 is the P. putida KT2440 DNA-directed RNA polymerase omega subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, and DNA-templated transcription annotations.

The reusable boundary is the alpha2-beta-beta-prime-omega core enzyme. Sigma factors, elongation and termination factors, and promoter-specific regulators belong to adjacent transcription modules rather than required core parts. PSEPK and Escherichia coli K-12 proteins are included as concrete exemplars, not as a restriction of the module's bacterial scope.

4Nodes
3Parts
0Variant Sets
0Variants
4Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_rna_polymerase_core-deep-research-openscientist.md (openscientist)

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

1 gene-function check(s) reflected in core functions · 0 conflict(s) · 11 evidence or coverage gap(s) (12 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
rpoa_alpha_subunit PSEPK rpoA exemplar
UniProtKB:Q88QL1
Family Representative 		protein dimerization activity
GO:0046983 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rpoa_alpha_subunit E. coli K-12 rpoA exemplar
UniProtKB:P0A7Z4
Family Representative 		protein dimerization activity
GO:0046983 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpob_beta_subunit PSEPK rpoB exemplar
UniProtKB:Q88QP2
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
rpob_beta_subunit E. coli K-12 rpoB exemplar
UniProtKB:P0A8V2
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpoc_beta_prime_subunit PSEPK rpoC exemplar
UniProtKB:Q88QP1
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
rpoc_beta_prime_subunit E. coli K-12 rpoC exemplar
UniProtKB:P0A8T7
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpoz_omega_subunit PSEPK rpoZ exemplar
UniProtKB:Q88C82
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
rpoz_omega_subunit E. coli K-12 rpoZ exemplar
UniProtKB:P0A800
Family Representative 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpoa_alpha_subunit bacterial DNA-directed RNA polymerase alpha subunit family
InterPro:IPR011773
Family 		protein dimerization activity
GO:0046983 		Family Review Missing
No supported structured family review is available for InterPro:IPR011773.
rpob_beta_subunit DNA-directed RNA polymerase beta subunit family
InterPro:IPR010243
Family 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Family Review Missing
No supported structured family review is available for InterPro:IPR010243.
rpoc_beta_prime_subunit bacterial DNA-directed RNA polymerase beta-prime subunit family
InterPro:IPR012754
Family 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Family Review Missing
No supported structured family review is available for InterPro:IPR012754.
rpoz_omega_subunit DNA-directed RNA polymerase omega subunit family
PANTHER:PTHR34476
Family 		contributes to DNA-directed RNA polymerase activity
GO:0003899 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR34476.

Gene-review completeness (4/8 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 4 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
E. coli K-12 rpoA exemplar P0A7Z4 ✗ — —
E. coli K-12 rpoZ exemplar P0A800 ✗ — —
E. coli K-12 rpoC exemplar P0A8T7 ✗ — —
E. coli K-12 rpoB exemplar P0A8V2 ✗ — —
rpoA Q88QL1 ✓ ✓ ✓
rpoB Q88QP2 ✓ ✓ ✗
rpoC Q88QP1 ✓ ✓ ✓
rpoZ Q88C82 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
cytosolGO:0005829
Bacterial DNA-directed RNA polymerase core enzymeProtein Complexbacterial_rna_polymerase_core
DNA-directed RNA polymerase complexGO:0000428 DNA-templated transcriptionGO:0006351
Context
bacteriaNCBITaxon:2
cytosolGO:0005829

Connections

The alpha dimer provides the assembly platform for recruitment of the beta and beta-prime subunits into the core enzyme.
The omega subunit supports proper assembly and stability of the beta/beta-prime-containing core enzyme.
Part 1: alpha dimer assembly platform
RpoA alpha dimer platformProtein Complexrpoa_alpha_dimer_platform

The alpha subunit forms the dimeric assembly platform that nucleates core enzyme assembly and contributes to DNA/promoter contacts.

Annotons

rpoA: RNA polymerase alpha subunit
rpoa_alpha_subunit
Participant: Family: bacterial DNA-directed RNA polymerase alpha subunit family
Family:
bacterial DNA-directed RNA polymerase alpha subunit familyInterPro:IPR011773
Representative Members: PSEPK rpoA exemplarUniProtKB:Q88QL1 E. coli K-12 rpoA exemplarUniProtKB:P0A7Z4

Function

protein dimerization activityGO:0046983

Processes

DNA-templated transcriptionGO:0006351 protein-containing complex assemblyGO:0065003

Alpha subunit that dimerizes and forms the scaffold for beta and beta-prime subunit recruitment in the bacterial core enzyme.

Part 2: beta and beta-prime catalytic cleft
RpoB/RpoC catalytic cleftProtein Complexrpob_rpoc_catalytic_cleft

The beta and beta-prime subunits form the active-center cleft that binds DNA/RNA substrates, divalent metal ions, and incoming ribonucleotides for RNA-chain elongation.

Annotons

rpoB: RNA polymerase beta subunit
rpob_beta_subunit
Participant: Family: DNA-directed RNA polymerase beta subunit family
Family:
DNA-directed RNA polymerase beta subunit familyInterPro:IPR010243
Representative Members: PSEPK rpoB exemplarUniProtKB:Q88QP2 E. coli K-12 rpoB exemplarUniProtKB:P0A8V2

Function

contributes to DNA-directed RNA polymerase activityGO:0003899
Substrates: DNA template ribonucleoside triphosphates
Products: RNA transcript

Processes

DNA-templated transcriptionGO:0006351

Beta subunit that helps form the catalytic cleft and contributes substrate-binding surfaces for RNA synthesis by the assembled core.

rpoC: RNA polymerase beta-prime subunit
rpoc_beta_prime_subunit
Participant: Family: bacterial DNA-directed RNA polymerase beta-prime subunit family
Family:
bacterial DNA-directed RNA polymerase beta-prime subunit familyInterPro:IPR012754
Representative Members: PSEPK rpoC exemplarUniProtKB:Q88QP1 E. coli K-12 rpoC exemplarUniProtKB:P0A8T7

Function

contributes to DNA-directed RNA polymerase activityGO:0003899
Substrates: DNA template ribonucleoside triphosphates
Products: RNA transcript
Cofactors: magnesium ionGO:0000287 zinc ionGO:0008270

Processes

DNA-templated transcriptionGO:0006351

Beta-prime subunit that supplies core active-center architecture, metal-binding determinants, and DNA/RNA binding surfaces.

Part 3: omega assembly and stability subunit
RpoZ omega assembly/stability subunitProtein Complexrpoz_omega_assembly_subunit

The omega subunit is a small conserved component of the canonical core that promotes proper assembly and stability. It is not itself catalytic, and basal polymerase can remain active without omega in some bacterial systems.

Annotons

rpoZ: RNA polymerase omega subunit
rpoz_omega_subunit
Participant: Family: DNA-directed RNA polymerase omega subunit family
Family:
DNA-directed RNA polymerase omega subunit familyPANTHER:PTHR34476
Representative Members: PSEPK rpoZ exemplarUniProtKB:Q88C82 E. coli K-12 rpoZ exemplarUniProtKB:P0A800

Function

contributes to DNA-directed RNA polymerase activityGO:0003899

Processes

DNA-templated transcriptionGO:0006351 protein-containing complex assemblyGO:0065003

Small omega subunit that stabilizes and supports assembly of the bacterial RNA polymerase core enzyme.