SigX (PA1776) is an extracytoplasmic function (ECF) sigma factor of Pseudomonas aeruginosa PAO1. It is encoded immediately upstream of oprF, which encodes the major outer membrane porin, and directs transcription of oprF from a SigX-dependent promoter that overlaps a sigma-70 promoter. SigX is a cell-envelope stress sigma factor; low osmolarity and sucrose induce it. ChIP-seq and transcriptomics define a regulon covering fatty acid biosynthesis and membrane fluidity, type III secretion, swarming and cyclic di-GMP signalling. sigX mutants grow slowly in rich medium (especially at low osmolarity), are more sensitive to imipenem, have altered membrane fatty acid composition and show reduced cytotoxicity and increased biofilm formation. SigX has the sigma-70 region 2 and region 4 modules of the ECF family and acts as the promoter-specificity subunit of RNA polymerase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to DNA-binding transcription factor activity. In current GO, GO:0016987 sigma factor activity is_a GO:0003700, so this term is entailed by the sigma factor activity accepted in this review. Reason: True but uninformative; GO:0016987, accepted here, entails it. Supporting Evidence: file:PSEAE/sigX/sigX-uniprot.txt PF04542; Sigma70_r2 |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro sigma-70 mapping to transcription initiation, the step at which sigma factors act. Reason: Sigma factors take part in initiation itself (promoter recognition and open complex formation); core process. Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/sigX/sigX-uniprot.txt PF04542; Sigma70_r2 |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PAINT IBD on PTN002455017 (8 seeds, including PvdS and AlgU). Regulation of transcription is true of every ECF sigma factor, and sigX sits inside the clade. Reason: Correct but general. A sigma factor regulates transcription at the initiation step, so the specific term GO:2000142 regulation of DNA-templated transcription initiation, which the gene already carries (IEA, GO_REF:0000108), is the right gene-level term. The node-level claim itself is sound and needs no change upstream. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002455017 Β· PTN002455017 SUPPORTS TRANSFER ECF sigma factor clade node (250 leaves, 29 taxa; 8 seeds: E. coli RpoE, V. cholerae RpoE, M. tuberculosis SigC/SigH/SigL/SigM, AlgU and PvdS). The node term is appropriate for the clade and the target is a bona fide member; only the granularity for this gene differs. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/sigX/sigX-uniprot.txt TIGR02937; sigma70-ECF |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro sigma-70 domain mapping to regulation of transcription. Reason: Correct but general; refined to the initiation-specific term the gene already carries, consistent with the IBA row. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: file:PSEAE/sigX/sigX-uniprot.txt PF04542; Sigma70_r2 |
| GO:0016987 sigma factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PAINT IBD on PTN002455017, the ECF sigma factor clade of PTHR43133 (16 seeds). sigX is a member of the clade, with the ECF sigma-70 domain architecture, and is itself one of the seeds, so its own appearance in WITH/FROM is expected, not circular. Reason: Core function. The IBD is well founded on several experimentally characterised ECF sigma factors (E. coli FecI, M. tuberculosis ECF sigmas, PvdS, AlgU with in vitro transcription evidence) and the target retains the sigma-70 region 4.2 module and ECF family membership. Supporting Evidence: file:PSEAE/sigX/sigX-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/sigX/sigX-uniprot.txt PF04542; Sigma70_r2 PMID:29729420 the iron starvation Ο (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFΟ AlgU, SigX and SbrI, and the unorthodox ΟVreI involved in the expression of virulence |
| GO:0016987 sigma factor activity | IDA PMID:10438740 Influence of a putative ECF sigma factor on expression of th... | ACCEPT | Summary: PseudoCAP IDA and seed. The abstract reports a sigX disruption and primer extension comparing mutant and wild-type RNA, which mapped a SigX-dependent oprF promoter of the ECF type. This supports sigma factor activity. Later ChIP-seq (PMID:24187091) confirms direct SigX occupancy of target promoters. Reason: Seed verdict SOUND: the paper supports sigma factor activity for this gene, and the term is the core molecular function. Supporting Evidence: PMID:10438740 monocistronic transcription of oprF occurs from two overlapping promoters, one that is SigX-dependent and resembles ECF sigma factor promoters in its minus-35 region PMID:24187091 the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) led to the identification of the DNA binding motif of SigX |
| GO:0030307 positive regulation of cell growth | IMP PMID:10438740 Influence of a putative ECF sigma factor on expression of th... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP positive regulation of cell growth. The phenotype is a reduced logarithmic-phase growth rate of the sigX mutant in rich medium, which oprF complementation did not rescue. That is a pleiotropic population growth-rate defect of a regulator mutant. GO:0030307 regulates cell growth, defined as the irreversible increase in size of a cell. Reason: An indirect pleiotropic phenotype annotated as a regulatory process, and the term (cell size growth) does not match a growth-rate defect. SigX's direct role is transcription of its envelope-related regulon (fatty acid synthesis, membrane fluidity), which explains the growth defect. Supporting Evidence: PMID:10438740 which included a markedly reduced logarithmic-phase growth rate in rich medium |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: Inferred from sigma factor activity by inter-ontology link; the regulatory process a sigma factor performs. Reason: Correct granularity for the process side of sigma factor activity; replacement target for the GO:0006355 rows. Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/sigX/sigX-uniprot.txt PF04542; Sigma70_r2 |
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Experiment: Purify SigX and test core RNAP binding and in vitro transcription from the SigX-dependent oprF promoter.
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