hfq (PA4944) encodes the Sm-like RNA chaperone Hfq of Pseudomonas aeruginosa, a homohexameric RNA-binding protein that binds small regulatory RNAs and A-rich sequences in mRNAs. Hfq stabilises regulatory RNAs such as RsmY, which titrates the translational repressor RsmA, and so indirectly raises translation of quorum-sensing genes such as rhlI. It is the principal post-transcriptional effector of carbon catabolite repression, binding the ribosome binding site of catabolic mRNAs such as amiE and blocking their translation; the regulatory RNA CrcZ, induced when preferred carbon sources run out, sequesters Hfq and relieves repression. Through these activities Hfq affects a large fraction of the transcriptome, including virulence and quorum-sensing outputs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003723 RNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002164223 (E. coli Hfq seed). Core activity. Reason: P. aeruginosa Hfq binds RsmY, CrcZ and the amiE ribosome binding site; RNA binding by Hfq is conserved across the family. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002164223 · PTN002164223 SUPPORTS TRANSFER UniProtKB:P0A6X3 · E. coli Hfq SUPPORTS TRANSFER Supporting Evidence: PMID:24945892 Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE PMID:16468994 We demonstrate that Hfq binds to and stabilizes the regulatory RNA RsmY |
| GO:0045974 regulation of translation, ncRNA-mediated | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002164223, seeded by E. coli Hfq and this gene's PseudoCAP IDA (PMID:24945892). Reason: Hfq-dependent sRNA control of translation is the canonical Hfq role, and in PAO1 Hfq represses amiE translation in a regulation that the ncRNA CrcZ modulates by sequestering Hfq. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002164223 · PTN002164223 SUPPORTS TRANSFER 20 leaves (19 taxa); transfer to Firmicutes Hfq, whose sRNA roles are weaker, is less certain. UniProtKB:P0A6X3 · E. coli Hfq SUPPORTS TRANSFER UniProtKB:Q9HUM0 · hfq SUPPORTS TRANSFER The target's own IDA is a co-seed; expected, not circular. Supporting Evidence: PMID:24945892 Moreover, we present evidence that the regulatory RNA CrcZ binds to and sequesters Hfq, which in turn results in translation of Hfq-regulated mRNAs. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002164223 (E. coli Hfq seed). Reason: Hfq acts on mRNAs and sRNAs at the ribosome binding site in the cytosol; consistent with its translational repression of amiE. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN002164223 · PTN002164223 SUPPORTS TRANSFER UniProtKB:P0A6X3 · E. coli Hfq SUPPORTS TRANSFER Supporting Evidence: PMID:24945892 Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE, and to repress translation in vitro and in vivo. |
| GO:0043487 regulation of RNA stability | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002164223, whose sole seed is this gene's PseudoCAP IMP (PMID:16468994). The target in its own WITH/FROM is expected. Reason: Hfq binds and stabilises the regulatory RNA RsmY; protection of bound RNAs from decay is a direct consequence of Hfq's chaperone activity and is also well established for E. coli Hfq. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002164223 · PTN002164223 SUPPORTS TRANSFER 20 leaves (19 taxa); Firmicutes leaves are the least certain. UniProtKB:Q9HUM0 · hfq SUPPORTS TRANSFER The target's own IMP is the seed; expected, not circular. Supporting Evidence: PMID:16468994 We demonstrate that Hfq binds to and stabilizes the regulatory RNA RsmY |
| GO:0003723 RNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro mapping from the Hfq signature. Reason: As for the IBA row with the same term; direct RNA binding is shown in PAO1. Supporting Evidence: PMID:24945892 Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the Hfq family signature. Reason: Hfq acts post-transcriptionally, by binding RNAs to control their stability and translation. Transcriptome changes in the hfq mutant are explained by RNA-level control (for example, Hfq does not control lasR or lasI but stimulates rhlI translation via RsmY). The InterPro2GO mapping of a transcription term to the Hfq family is not supported for this gene. Supporting Evidence: PMID:16468994 However, Hfq considerably stimulated translation of the rhlI gene, encoding the synthetase of the autoinducer N-Butyryl-homoserine lactone (C4-HSL). |
| GO:0006417 regulation of translation | IDA PMID:24945892 Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa ... | MODIFY | Summary: PseudoCAP IDA; Hfq represses amiE translation in vitro and in vivo. Correct but general. Reason: The paper shows Hfq blocking translation initiation of amiE in vitro and in vivo, so the signed child GO:0017148 is the precise term. Proposed replacements: negative regulation of translation Supporting Evidence: PMID:24945892 Given that Hfq blocked translation initiation of amiE mRNA by binding to A-rich stretches encompassing the RBS |
| GO:0009372 quorum sensing | IMP PMID:16468994 Hfq-dependent alterations of the transcriptome profile and e... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP; the hfq mutant has lower rhlI translation and C4-HSL levels. Not a PAINT seed. Reason: Hfq is not a component of quorum-sensing signalling; it raises rhlI translation indirectly by stabilising RsmY, which titrates the repressor RsmA. Reduced autoinducer in the mutant is a downstream consequence of RNA-level regulation by a global post-transcriptional regulator. Abstract only. Supporting Evidence: PMID:16468994 an alleviation of the negative effect of RsmA accounts for the observed stimulation of rhlI expression by Hfq |
| GO:0043487 regulation of RNA stability | IMP PMID:16468994 Hfq-dependent alterations of the transcriptome profile and e... | ACCEPT | Summary: PseudoCAP IMP; sole seed of the GO:0043487 IBD at PTN002164223. Reason: The paper shows that Hfq binds RsmY and that RsmY is stabilised by Hfq; the stabilising effect is the direct result of Hfq binding the RNA, not a downstream phenotype. Abstract only in the cache. Supporting Evidence: PMID:16468994 We demonstrate that Hfq binds to and stabilizes the regulatory RNA RsmY |
| GO:0043609 regulation of carbon utilization | IDA PMID:24945892 Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa ... | KEEP AS NON CORE | Summary: PseudoCAP IDA; Hfq is the principal post-transcriptional regulator of carbon catabolite repression in PAO1. Reason: Hfq directly represses translation of catabolic and transport mRNAs during CCR, so the regulation of carbon utilization is exerted through its own activity; it is one physiological context of the core translational-repression function. Supporting Evidence: PMID:24945892 In this study the RNA chaperone Hfq was identified as the principle post-transcriptional regulator of CCR in PAO1. |
| GO:0045974 regulation of translation, ncRNA-mediated | IDA PMID:24945892 Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa ... | ACCEPT | Summary: PseudoCAP IDA; co-seed (with E. coli Hfq) of the GO:0045974 IBD at PTN002164223. Reason: Hfq represses amiE translation by binding its RBS, and the regulatory RNA CrcZ controls this by titrating Hfq; Hfq-dependent translational repression in vitro was relieved by CrcZ but not by a non-specific competitor RNA. Hfq does the work in a translational regulation in which an ncRNA is the modulating component. Supporting Evidence: PMID:24945892 In contrast, the mRNA was translated in the presence of CrcZ (Figure 5B, lanes 5 and 6), whereas the Hfq-mediated translational repression was not relieved in the presence of the non-specific competitor RNA RsmZ |
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Download this section (compressed HTML)Q: Does Hfq stabilise RsmY by protecting it from RNase E cleavage, and does the same mechanism hold for the other Hfq-bound sRNAs of PAO1?
Experiment: Measure RsmY and CrcZ half-lives after rifampicin in wild type, hfq distal- and proximal-face mutants and an RNase E temperature-sensitive background.
Type: RNA decay assay
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