hfq (PA4944, Q9HUM0) notes

Identity

UniProt Q9HUM0 (Swiss-Prot, PE 1), RNA-binding protein Hfq, Sm-like homohexamer (HAMAP MF_00436).
PANTHER Hfq family; InterPro IPR005001.

Function

RNA chaperone that binds sRNAs and mRNAs [UniProt CC FUNCTION, HAMAP MF_00436].
Hfq affects about 5% of PAO1 transcripts; it stimulates rhlI translation indirectly by binding and
stabilising the regulatory RNA RsmY, which sequesters the translational repressor RsmA
[PMID:16468994 abstract "We demonstrate that Hfq binds to and stabilizes the regulatory RNA RsmY"; "an
alleviation of the negative effect of RsmA accounts for the observed stimulation of rhlI expression by
Hfq"]. Abstract only in the cache.
Hfq is the principal post-transcriptional regulator of carbon catabolite repression in PAO1: it binds
A-rich sequences in the amiE ribosome binding site and represses translation in vitro and in vivo; the
regulatory RNA CrcZ binds Hfq with high affinity and acts as a decoy that relieves repression
[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"; "CrcZ RNA acts as a decoy for Hfq"].

Annotation decisions

GO:0003723 RNA binding (IBA, IEA): ACCEPT, core MF.
GO:0005829 cytosol (IBA): ACCEPT.
GO:0043487 regulation of RNA stability (IMP PseudoCAP, IBA): ACCEPT; Hfq binding stabilises RsmY.
GO:0045974 regulation of translation, ncRNA-mediated (IDA PseudoCAP, IBA): ACCEPT. In the CrcZ paper
Hfq itself represses amiE translation and the ncRNA CrcZ titrates it; Hfq does the work of a
regulation in which an ncRNA is the modulating component. The E. coli co-seed (Hfq-dependent sRNA
regulation) is the canonical case.
GO:0006417 regulation of translation (IDA): MODIFY to GO:0017148 negative regulation of translation
(direct in vitro repression of amiE).
GO:0043609 regulation of carbon utilization (IDA): KEEP_AS_NON_CORE; Hfq directly represses
translation of catabolic mRNAs under CCR.
GO:0009372 quorum sensing (IMP): MARK_AS_OVER_ANNOTATED; effect on rhlI is indirect via RsmY/RsmA, and
Hfq is not a component of QS signalling.
GO:0006355 regulation of DNA-templated transcription (InterPro2GO IEA): REMOVE; Hfq acts
post-transcriptionally.

PseudoCAP IBA-seed assessment

PTN002164223 has 20 leaves (19 taxa, local PAINT leaf GAF 2026-10-28): Hfq of proteobacteria and of
Firmicutes (B. subtilis, S. aureus, Listeria, B. anthracis, C. botulinum), Aquifex, Thermotoga and
Leptospira.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002164223	GO:0043487 regulation of RNA stability	1 (sole)	20 (19 taxa)	GO:0043487, IMP, PMID:16468994 (PseudoCAP)	SOUND	Hfq binds RsmY and its loss destabilises RsmY; protecting a bound RNA from decay is Hfq's own chaperone activity, not a distant phenotype. Hfq-mediated sRNA protection and mRNA turnover are also established in E. coli. Caveat: in Firmicutes Hfq has weaker, often undetectable roles in sRNA regulation, so the term's transfer to those leaves is less certain, though the binding activity is conserved.
PTN002164223	GO:0045974 regulation of translation, ncRNA-mediated	2	20 (19 taxa)	GO:0045974, IDA, PMID:24945892 (PseudoCAP); co-seed E. coli Hfq P0A6X3	SOUND	Hfq represses amiE translation directly and the ncRNA CrcZ modulates it by sequestering Hfq. Same Firmicutes caveat.