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. The Hfq/Crc catabolite repression system is functionally conserved across the Pseudomonadaceae, including Azotobacter vinelandii.
| 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; P. putida Hfq binds CA-motif RNAs through its distal face. The term is accurate and core; no more specific GO term for A-rich motif binding exists, so it is retained as-is. Supporting Evidence: PMID:24803210 Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. PMID:27777366 In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. |
| 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: Not imaged in KT2440, but Hfq acts on translation initiation regions of mRNAs and is a soluble protein without membrane or secretion features; cytosolic localization is consistent with its function. Supporting Evidence: PMID:30758287 We describe high-resolution cryo-EM structures of the assembly of Hfq and Crc bound to the translation initiation site of a target mRNA. |
| 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 Supporting Evidence: PMID:27777366 In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. |
| 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). Supporting Evidence: PMID:27777366 In addition, we show that Crc and Hfq increase CrcZ stability, which supports the idea that these proteins can form a complex with CrcZ and protect it from degradation by RNases. |
| 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. Supporting Evidence: PMID:27777366 The effect of these two proteins is antagonized by the CrcZ and CrcY small RNAs (sRNAs), the levels of which vary greatly according to growth conditions. PMID:27777366 In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. file:PSEPK/hfq/hfq-deep-research-falcon.md A well-characterized, KT2440-relevant primary function of Hfq is its participation in **carbon catabolite repression (CCR)** in *Pseudomonas*, where Hfq cooperates with the translational co-repressor **Crc**. |
| GO:0030371 translation repressor activity | ISS PMID:34139006 Stabilization of Hfq-mediated translational repression by th... | NEW | Summary: Hfq binds A-rich catabolite-activity motifs at translation initiation regions of catabolic mRNAs and, with the co-repressor Crc, blocks their translation. Reason: Translational repression by Hfq/Crc is shown directly with in vitro translation and in vivo reporters for the P. aeruginosa ortholog (PMID:34139006); for P. putida Hfq, distal-face recognition of CA motifs is shown directly and repression is proposed (PMID:24803210), so the activity is transferred by sequence similarity (ISS), matching the crc review. Supporting Evidence: PMID:24803210 Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. PMID:27777366 In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. PMID:34139006 In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. |
| GO:0061985 carbon catabolite repression | IMP PMID:24803210 The Crc and Hfq proteins of Pseudomonas putida cooperate in ... | NEW | Summary: hfq mutants of P. putida are impaired in carbon catabolite repression to the same extent as crc mutants. Reason: Hfq performs the RNA-recognition step of the Crc/Hfq repression that implements carbon catabolite repression in pseudomonads. Supporting Evidence: PMID:24803210 Inactivation of the hfq or the crc gene impaired catabolite repression to a similar extent. PMID:27777366 The effect of these two proteins is antagonized by the CrcZ and CrcY small RNAs (sRNAs), the levels of which vary greatly according to growth conditions. file:PSEPK/hfq/hfq-deep-research-falcon.md A well-characterized, KT2440-relevant primary function of Hfq is its participation in **carbon catabolite repression (CCR)** in *Pseudomonas*, where Hfq cooperates with the translational co-repressor **Crc**. |
| GO:0017148 negative regulation of translation | ISS PMID:34139006 Stabilization of Hfq-mediated translational repression by th... | NEW | Summary: Hfq, with Crc, represses translation of catabolic mRNAs bearing A-rich catabolite-activity motifs. Reason: Translation repression by Hfq/Crc is shown directly for the P. aeruginosa ortholog and the same CA-motif complexes form with P. putida Hfq; this is the direct process of the Hfq/Crc repressor and is distinct from the broader ncRNA-mediated regulation term. Supporting Evidence: PMID:34139006 In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. PMID:27777366 In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. |
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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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