Q9KZ33

UniProt ID: Q9KZ33
Organism: Streptomyces coelicolor A3(2)
Review Status: COMPLETE
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Gene Description

SCO7099 (Q9KZ33) is a 300-residue extracytoplasmic function (ECF, group 4) RNA polymerase sigma factor of Streptomyces coelicolor A3(2). Its N-terminal half carries the sigma2 and sigma4 regions that, in ECF sigma factors, bind the -10 and -35 promoter elements and recruit core RNA polymerase to start transcription; its C-terminal ~130 residues form an NTF2-like (SnoaL-type) extension. This architecture, and its PANTHER subfamily placement together with Mycobacterium tuberculosis SigI (an ECF41 sigma factor), mark it as a probable member of group ECF41, whose members have no separate anti-sigma factor and instead use the fused C-terminal extension to regulate sigma activity. The protein is expected to act in the cytoplasm as the promoter-specificity subunit of RNA polymerase holoenzyme. Its promoter motif, target genes, activating signal and physiological role are unknown; the only direct experimental observation is that a constitutive overexpression construct could not be introduced into S. coelicolor.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0016987 sigma factor activity
IBA
GO_REF:0000033 		ACCEPT
Summary: Sigma factor activity propagated by PAINT from node PTN001249270 of PANTHER family PTHR30173 (ECF sigma factors), seeded by M. tuberculosis SigJ (L0TCG5). The seed sits in subfamily SF36 while Q9KZ33 sits in SF43 (with M. tuberculosis SigI), so the IBD node lies above both subfamilies; sigma factor activity is the family-wide function of intact ECF sigma factors and is not a subfamily-specific trait, so the different subfamily does not weaken the transfer. Q9KZ33 retains the ECF sigma2/sigma4 architecture (IPR052704, IPR013324, SSF88659) and a full-length ECF41-type C-terminal extension shared with both SigI and SigJ.
Reason: The target is inside the clade that inherited the function at PTN001249270, and its domain architecture is intact over the regions required for promoter recognition and RNA polymerase binding. There is no evidence of loss or divergence of sigma activity. For ECF41 sigma factors the C-terminal extension is itself required for activity (Wecke et al. 2012), and Q9KZ33 has this extension. No experimental data exist for Q9KZ33 itself, but the phylogenetic and structural case is strong; this is the core molecular function.
Supporting Evidence:
file:STRCO/Q9KZ33/Q9KZ33-uniprot.txt
DR InterPro; IPR052704; ECF_Sigma-70_Domain.
file:STRCO/Q9KZ33/Q9KZ33-uniprot.txt
DR SUPFAM; SSF88659; Sigma3 and sigma4 domains of RNA polymerase sigma factors; 1.
PMID:22950025
In contrast to other ECF Οƒ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for Οƒ factor activity.
file:STRCO/Q9KZ33/Q9KZ33-bioinformatics/RESULTS.md
Q9KZ33 aligns over essentially its full length (~270 of 300 residues) to both Mtb ECF41 sigma
GO:2000142 regulation of DNA-templated transcription initiation
IEA
GO_REF:0000108 		ACCEPT
Summary: Inter-ontology inference (GO_REF:0000108) from sigma factor activity. A sigma factor determines which promoters core RNA polymerase initiates from, so it directly takes part in regulating DNA-templated transcription initiation; this is the process-level counterpart of the core molecular function, not a downstream effect.
Reason: Follows directly from the accepted sigma factor activity. The term is as specific as the evidence allows: no regulon, inducing signal or physiological process is known for SCO7099, so no more specific process term (e.g. a particular stress response) can be justified.
Supporting Evidence:
PMID:26249679
Οƒ factors play a prominent role in transcription initiation as they govern both promoter recognition and promoter melting.
file:STRCO/Q9KZ33/Q9KZ33-uniprot.txt
DR InterPro; IPR052704; ECF_Sigma-70_Domain.

Core Functions

ECF (probable group ECF41) sigma factor: the promoter-specificity subunit that binds core RNA polymerase and directs transcription initiation at a currently unidentified set of promoters, with activity presumably controlled by its fused C-terminal NTF2-like extension rather than by a separate anti-sigma factor.

Molecular Function:
sigma factor activity
Directly Involved In:
regulation of DNA-templated transcription initiation
Cellular Locations:
cytoplasm
Supporting Evidence:
  • file:STRCO/Q9KZ33/Q9KZ33-uniprot.txt
    DR InterPro; IPR052704; ECF_Sigma-70_Domain.
  • PMID:22950025
    In contrast to other ECF Οƒ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for Οƒ factor activity.
  • PMID:32180013
    Mtb-SigI belongs to the ECF41 family of sigma factor

References

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Suggested Questions for Experts

Q: Does SCO7099 belong to group ECF41 (or a subgroup of it) in the current ECF classification, and which ECF41-specific promoter motif would it recognise?

Q: Is the failure to recover SCO7099 overexpression transformants due to toxicity from unregulated sigma activity, or a technical artifact?

Suggested Experiments

Experiment: Express SCO7099 from a tightly inducible promoter (e.g. tipA) at titrated levels, with and without its C-terminal extension, and profile transcription by RNA-seq; map transcription start sites of induced genes.

Hypothesis: SCO7099 directs RNA polymerase to a small set of promoters sharing an ECF41-type motif, and truncating the C-terminal extension changes its activity as for other ECF41 sigma factors.

Experiment: ChIP-seq of epitope-tagged SCO7099 expressed from its native locus under a range of stress and developmental conditions.

Hypothesis: SCO7099 binds a defined set of promoters with a characteristic ECF -35/-10 motif.

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Β· Q9KZ33-protnlm-predictions-review.yaml Β· Review status: COMPLETE

SCO7099 (Q9KZ33) is an ECF (probable group ECF41) RNA polymerase sigma factor whose sigma factor activity is supported by a PAINT IBA and an intact sigma2/sigma4 plus C-terminal-extension architecture. The single ProtNLM2 GO prediction, DNA-templated transcription initiation, is a correct process inference from that function and is not already carried by the gene in GOA.

Source documents: genes/STRCO/Q9KZ33/Q9KZ33-uniprot.txt Β· genes/STRCO/Q9KZ33/Q9KZ33-goa.tsv

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0006352 DNA-templated transcription initiation GO_BP
COR β€” Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: Q9KZ33 carries the ECF sigma-70 domain signature (IPR052704) and the sigma3/sigma4 superfamily, and its gene review accepts the PAINT IBA for sigma factor activity (node PTN001249270 of PTHR30173, with the target in subfamily SF43 alongside M. tuberculosis ECF41 SigI). Sigma factors do part of the work of initiation itself: they recognise the promoter and melt it as the initiating subunit of RNA polymerase holoenzyme, so participation in DNA-templated transcription initiation follows from the supported activity by family-wide transfer; the PTHR30173 family review grants this term family-wide. The gene's GOA set has sigma factor activity and regulation of DNA-templated transcription initiation (GO:2000142); OLS4 shows GO:2000142 is not an is_a/part_of descendant of GO:0006352, so the prediction is neither present nor less specific than an existing annotation. No experiment on SCO7099 addresses its transcriptional role (a PubMed search for SCO7099 returns no dedicated study), so this rests on the phylogenetic and domain inference rather than direct observation.
Supporting Evidence:

Deep Research

Falcon

(Q9KZ33-deep-research-falcon.md)

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πŸ“š Additional Documentation

Notes

(Q9KZ33-notes.md)

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Bioinformatics Results

(RESULTS.md)

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πŸ“„ View Raw YAML

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