id: A4GYQ0
gene_symbol: rpoB
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3694
  label: Populus trichocarpa
description: 'Chloroplast plastid-encoded RNA polymerase beta subunit that contributes to DNA-directed transcription
  and transcription elongation in plastids.'
existing_annotations:
- term:
    id: GO:0006354
    label: DNA-templated transcription elongation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Transcription elongation is an appropriate process for the plastid RNA polymerase beta subunit.
    action: ACCEPT
    reason: rpoB is part of the PEP catalytic core that synthesizes RNA from DNA templates.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
- term:
    id: GO:0003899
    label: DNA-directed RNA polymerase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    summary: rpoB contributes to DNA-directed RNA polymerase activity as a subunit of plastid-encoded RNA
      polymerase.
    action: ACCEPT
    reason: The catalytic activity belongs to the polymerase complex, so contributes_to is the correct
      relationship for this subunit.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: DNA binding is plausible for an RNA polymerase subunit but is less informative than polymerase
      contribution.
    action: KEEP_AS_NON_CORE
    reason: Retain as a non-core feature while treating RNA polymerase contribution as the central role.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
- term:
    id: GO:0003899
    label: DNA-directed RNA polymerase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: rpoB contributes to DNA-directed RNA polymerase activity as a subunit of plastid-encoded RNA
      polymerase.
    action: ACCEPT
    reason: The catalytic activity belongs to the polymerase complex, so contributes_to is the correct
      relationship for this subunit.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
  qualifier: contributes_to
- term:
    id: GO:0006351
    label: DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: DNA-templated transcription is the direct biological process for plastid RNA polymerase rpoB.
    action: ACCEPT
    reason: The reviewed entry describes DNA-dependent RNA polymerase activity producing RNA from a DNA
      template.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
- term:
    id: GO:0009507
    label: chloroplast
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Chloroplast localization is correct for this plastid-encoded RNA polymerase subunit.
    action: ACCEPT
    reason: The reviewed entry places rpoB in the chloroplast.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast.'
- term:
    id: GO:0032549
    label: ribonucleoside binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Ribonucleoside binding is a broad substrate-binding inference for an RNA polymerase subunit.
    action: KEEP_AS_NON_CORE
    reason: Keep as non-core; the more informative molecular role is contribution to DNA-directed RNA
      polymerase activity.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
- term:
    id: GO:0034062
    label: 5'-3' RNA polymerase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  review:
    summary: 5'-3' RNA polymerase activity reflects the RNA polymerase reaction but overstates the isolated
      subunit as the whole enzyme.
    action: MARK_AS_OVER_ANNOTATED
    reason: The catalytic reaction belongs to the plastid RNA polymerase complex, with rpoB contributing as
      one core subunit.
    supported_by:
    - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
      supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
        ribonucleoside triphosphates as substrates.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings:
  - statement: GO_REF:0000002 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: GO_REF:0000033 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings:
  - statement: GO_REF:0000116 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: GO_REF:0000120 supplied one or more source GOA annotations reviewed in this file.
- id: file:POPTR/rpoB/rpoB-uniprot.txt
  title: UniProtKB reviewed entry for rpoB
  findings:
  - statement: UniProt identifies rpoB as the chloroplast plastid-encoded RNA polymerase beta subunit, part of
      the DNA-dependent RNA polymerase catalytic core.
- id: file:POPTR/rpoB/rpoB-goa.tsv
  title: QuickGO GOA annotations for rpoB
  findings:
  - statement: GOA rows supplied the existing_annotations reviewed in this file.
core_functions:
- description: Contributes the beta subunit to plastid DNA-directed RNA polymerase for chloroplast
    transcription and elongation.
  contributes_to_molecular_function:
    id: GO:0003899
    label: DNA-directed RNA polymerase activity
  directly_involved_in:
  - id: GO:0006351
    label: DNA-templated transcription
  - id: GO:0006354
    label: DNA-templated transcription elongation
  locations:
  - id: GO:0009507
    label: chloroplast
  supported_by:
  - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
    supporting_text: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four
      ribonucleoside triphosphates as substrates.
  - reference_id: file:POPTR/rpoB/rpoB-uniprot.txt
    supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast.'
suggested_questions:
- question: Which chloroplast transcript classes in Populus are most sensitive to rpoB dosage or plastid
    editing?
suggested_experiments:
- description: Perturb rpoB expression or editing and quantify chloroplast transcription elongation with
    RNA-seq or run-on assays.
  experiment_type: targeted functional assay
proposed_new_terms: []