dksA (PA4723) encodes the canonical RNA polymerase-binding transcription factor DksA of Pseudomonas aeruginosa, a small protein with an N-terminal coiled-coil and a C4 zinc finger. DksA does not bind DNA itself; it associates with RNA polymerase and, together with the alarmone (p)ppGpp, changes the kinetics of transcription initiation at target promoters. In P. aeruginosa it represses ribosomal RNA transcription in growing and starved cells, and it is found with RNA polymerase on rRNA promoters. Through these global effects it influences quorum-sensing signal production, virulence factor output, anaerobic respiration and antibiotic tolerance. A zinc-independent paralog, DksA2 (PA5536), can substitute for it under zinc limitation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002139169, whose sole seed is this gene's PseudoCAP IMP to negative regulation of DNA-templated transcription (PMID:15853892). The target in its own WITH/FROM is expected. Reason: DksA regulates transcription by acting on RNA polymerase; family members both repress (rRNA) and activate promoters, so the unsigned term is as precise as is warranted for the gene's overall role and for the node. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002139169 · PTN002139169 SUPPORTS TRANSFER 17 leaves (16 taxa) in the PAINT leaf GAF; DksA orthologs, the P. aeruginosa DksA2 paralog, and divergent Bacteroides and Streptomyces DksA-like proteins. UniProtKB:G3XD14 · dksA SUPPORTS TRANSFER The target's own IMP is the seed; expected, not circular. Supporting Evidence: PMID:15853892 DksA, a protein with pleiotropic effects, is a negative regulator of rRNA transcription both during exponential growth and stringent conditions PMID:21255113 DksA is a global transcriptional regulator that directly interacts with RNA polymerase (RNAP) and, in conjunction with an alarmone ppGpp, alters transcription initiation at target promoters. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP-derived subcellular location. Consistent with an RNA polymerase-associated factor. Reason: DksA acts on RNA polymerase at promoters in the bacterial cytoplasm (nucleoid); no more specific supported location term is needed. Supporting Evidence: PMID:15853892 Cell-fractionation and chromosome immunoprecipitation experiments demonstrate that DksA is associated with DNA, in particular with promoters of ribosomal genes in vivo. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: HAMAP/InterPro mapping from the C4 zinc finger (Cys111, Cys114, Cys132, Cys135). Reason: The canonical DksA has a structural C4 zinc finger, distinguishing it from the Zn-free DksA2 paralog; zinc binding is structural, not the regulatory activity itself. Supporting Evidence: PMID:21255113 DksA proteins studied to date contain a canonical Cys-4 Zn-finger motif thought to be essential for their proper folding and thus activity. |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000104 | MODIFY | Summary: UniRule electronic annotation. Correct but general. Reason: DksA regulates gene expression at the level of transcription initiation; the descendant GO:0006355, which the gene already carries by IBA, is the precise term. Proposed replacements: regulation of DNA-templated transcription Supporting Evidence: PMID:21255113 DksA is a global transcriptional regulator that directly interacts with RNA polymerase (RNAP) and, in conjunction with an alarmone ppGpp, alters transcription initiation at target promoters. |
| GO:0045861 negative regulation of proteolysis | IDA PMID:11160083 Inhibition of quorum sensing by a Pseudomonas aeruginosa dks... | REMOVE | Summary: PseudoCAP IDA from the paper in which multicopy dksA suppressed elastase production. Not a PAINT seed. Reason: The paper shows that overexpressed dksA lowers production of the secreted protease elastase, and the authors conclude that this is indirect, via reduced rhlI transcription and C4-HSL signal. Reduced production of a protease is not regulation of proteolysis, and the effect is not exerted by DksA on that process. Supporting Evidence: PMID:11160083 It therefore appears that dksA does not inhibit the expression of lasB and rhlAB directly but affects both elastase and rhamnolipid production indirectly by the inhibition of rhlI transcription, leading to reduced C 4 -HSL levels. |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:15853892 DksA represses ribosomal gene transcription in Pseudomonas a... | ACCEPT | Summary: PseudoCAP IMP; sole seed of the GO:0006355 IBD at PTN002139169. Reason: The dksA mutant overexpresses rRNA without a change in ppGpp, and DksA is found with RNAP on rRNA promoters in vivo and increases RNAP binding to them with ppGpp. This is direct support for DksA's own role in repressing rRNA transcription. Abstract only in the cache. Supporting Evidence: PMID:15853892 A dksA mutant overexpresses rRNA, without being affected in the production of ppGpp. PMID:15853892 DNA band shift experiments show that DksA, in synergy with ppGpp, increases the binding of RNAP to ribosomal promoters. |
| GO:0051055 negative regulation of lipid biosynthetic process | IDA PMID:11160083 Inhibition of quorum sensing by a Pseudomonas aeruginosa dks... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IDA; multicopy dksA reduced rhamnolipid production. Not a PAINT seed. Reason: The effect was seen only on overexpression and the authors attribute it to indirect inhibition of the rhl quorum-sensing system (rhlI transcription); rhamnolipid synthesis is a distant downstream output of a global transcription factor. Supporting Evidence: PMID:11160083 However, the production of rhamnolipid was reduced by 35% when dksA was overexpressed in PAO1 |
| GO:0070063 RNA polymerase binding | IDA PMID:21255113 Role of a Zn-independent DksA in Zn homeostasis and stringen... | ACCEPT | Summary: PseudoCAP IDA citing the DksA2 paper. RNA polymerase binding is DksA's core molecular function. Reason: DksA co-purifies with RNAP subunits in P. aeruginosa (PMID:15853892), and its regulatory activity works through RNAP. The cited paper's in vitro work, however, uses purified DksA2 (PA5536) with E. coli RNAP, so the reference appears to support the paralog rather than PA4723; the term itself is correct for this gene. Supporting Evidence: PMID:15853892 Moreover DksA can be copurified with RNAP subunits in vivo. PMID:21255113 DksA is a global transcriptional regulator that directly interacts with RNA polymerase (RNAP) |
| GO:1901857 positive regulation of cellular respiration | IMP PMID:18203836 Proteomic, microarray, and signature-tagged mutagenesis anal... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP from a signature-tagged mutagenesis screen in which dksA was required for anaerobic nitrate and nitrite respiration. Not a PAINT seed. Reason: The screen shows only that a mutant of a pleiotropic global regulator grows poorly by anaerobic respiration; it does not show that DksA regulates the respiratory machinery. Abstract only in the cache, so the full data could not be checked. Supporting Evidence: PMID:18203836 the cysG and dksA genes were found to be required for both anaerobic NO(3)(-) and NO(2)(-) respiration |
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Download this section (compressed HTML)Q: Does P. aeruginosa DksA also activate amino-acid biosynthesis promoters together with ppGpp, as in E. coli, which would make a positive-regulation annotation appropriate?
Experiment: In vitro transcription with purified P. aeruginosa RNAP, DksA and ppGpp on rrn and amino-acid biosynthesis promoters, compared with DksA2.
Type: in vitro transcription assay
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