Hfq is a conserved bacterial RNA-binding protein of the Sm/Lsm (Sm-like) family that assembles into a homohexameric ring and acts as a global RNA chaperone in post-transcriptional gene regulation. It uses distinct RNA-binding surfaces (proximal, distal, and rim faces, plus a basic C-terminal region) to bind small regulatory RNAs (sRNAs) and mRNAs, accelerating sRNA-mRNA base pairing (matchmaking), remodeling RNA structure, protecting sRNAs from degradation, and modulating mRNA translation and stability. In Pseudomonas putida KT2440, Hfq is a central effector of carbon catabolite repression; together with the co-repressor Crc it binds A-rich catabolite-activity motifs near ribosome-binding sites to repress translation of catabolic mRNAs, and this repression is antagonized by the decoy sRNAs CrcZ and CrcY, which sequester Hfq/Crc. Hfq also contributes to the stability and processing of CrcZ. The protein acts in the cytoplasm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003723 RNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: RNA binding is the defining and well-established molecular function of Hfq, supported by its Sm/Lsm domain and extensive literature on sRNA/mRNA binding in Pseudomonas and other bacteria. Reason: Hfq is a canonical RNA-binding protein; this IEA term is correct and represents a core molecular function. A more specific child term (e.g. sRNA binding) could be added but the general term is accurate and should be retained. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: Hfq acts on cytoplasmic sRNAs and mRNAs and is a soluble intracellular RNA chaperone, consistent with cytosolic localization. Reason: Localization is inferred from function rather than KT2440-specific imaging, but cytosolic localization is well established for Hfq across bacteria and is consistent with its post-transcriptional regulatory role. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: Hfq is a post-transcriptional regulator acting on RNA, not a direct regulator of DNA-templated transcription. This InterPro2GO mapping mislocates Hfq's activity at the transcriptional level. Reason: Hfq does not bind DNA or directly regulate transcription initiation/elongation; its regulatory role is post-transcriptional (sRNA-mediated effects on translation and RNA stability). The more accurate term is ncRNA-mediated regulation of translation, which is already separately annotated. This generic transcription-regulation term is an over-broad/incorrect propagation and should be replaced. Proposed replacements: regulation of translation, ncRNA-mediated |
| GO:0043487 regulation of RNA stability | IEA GO_REF:0000118 | ACCEPT | Summary: Hfq binds and stabilizes sRNAs (protecting them from nucleases) and also promotes targeted decay of mRNAs, directly influencing RNA stability. In KT2440, Hfq increases the stability of the CrcZ sRNA. Reason: Regulation of RNA stability is a well-documented function of Hfq and is specifically supported in P. putida KT2440 (Hfq increases CrcZ stability). |
| GO:0045974 regulation of translation, ncRNA-mediated | IEA GO_REF:0000118 | ACCEPT | Summary: Hfq mediates sRNA-dependent regulation of mRNA translation, the central function of the protein. In KT2440 this includes Crc/Hfq translational repression of catabolic mRNAs and its antagonism by the sRNAs CrcZ/CrcY. Reason: This term precisely captures Hfq's core biological role as an sRNA-mediated post-transcriptional regulator of translation, strongly supported by Pseudomonas literature. |
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Download this section (compressed HTML)Q: Does P. putida KT2440 Hfq have direct experimental subcellular localization data (microscopy/fractionation) confirming cytosolic distribution?
Q: Beyond the CCR/Crc axis, which sRNA regulons (e.g. stress, iron, quorum sensing) does KT2440 Hfq control?
Experiment: CLIP-seq or RIL-seq in P. putida KT2440 to define the genome-wide Hfq-bound sRNA and mRNA interactome
Experiment: Phenotypic and transcriptomic comparison of an hfq deletion mutant under carbon-source shifts and envelope/oxidative stress to map the Hfq regulon
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