cheA encodes the chemotaxis histidine kinase CheA of Pseudomonas putida KT2440. The protein is a 747 aa phosphorelay kinase with an N-terminal HPt domain, a central histidine kinase ATPase/dimerization region, and a C-terminal CheW-like domain. In KT2440 literature this locus corresponds to PP_4338/cheA2, the CheA paralog assigned to the canonical chemotaxis pathway rather than the Wsp-like c-di-GMP signaling branch. Its core role is to relay chemoreceptor input by autophosphorylating on histidine and transferring phosphate to response regulators such as CheY and CheB, thereby controlling chemotaxis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000155 phosphorelay sensor kinase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: This annotation captures the general CheA-like phosphorelay kinase role, but it is broader than the more specific child term GO:0004673 protein histidine kinase activity, which is also already present for this gene. Reason: Retaining the broader phosphorelay sensor kinase term adds little beyond the specific protein histidine kinase annotation and obscures the more informative catalytic term. Supporting Evidence: file:PSEPK/cheA/cheA-deep-research-falcon.md GO:0000155 is broader than GO:0004673 and becomes redundant when the child protein histidine kinase term is already present. |
| GO:0004673 protein histidine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the best existing molecular-function term for cheA. UniProt assigns the canonical CheA chemistry: ATP-dependent autophosphorylation on histidine followed by phosphotransfer to downstream response regulators. Reason: Protein histidine kinase activity precisely captures the catalytic role of CheA in the chemotaxis phosphorelay and is supported by conserved domain architecture, phosphohistidine annotation, and the established CheA reaction. Supporting Evidence: UniProt:Q88EW4 CheA is autophosphorylated; it can transfer its phosphate group to either CheB or CheY. UniProt:Q88EW4 -!- CATALYTIC ACTIVITY: Reaction=ATP + protein L-histidine = ADP + protein N-phospho-L- histidine.; EC=2.7.13.3; file:PSEPK/cheA/cheA-deep-research-falcon.md CheA is the central histidine kinase of the canonical chemotaxis phosphorelay in KT2440. |
| GO:0016772 transferase activity, transferring phosphorus-containing groups | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This annotation is technically true for a histidine kinase, but it is a very broad parent term that adds no information beyond GO:0004673. Reason: The broader transferase term is redundant once the specific protein histidine kinase activity is retained. Supporting Evidence: file:PSEPK/cheA/cheA-deep-research-falcon.md GO:0016772 is a very broad parent term and does not add useful specificity beyond protein histidine kinase activity. |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: This is an appropriate core biological-process term for cheA because the protein is the autophosphorylating histidine kinase that relays sensory input to CheY/CheB response regulators. Reason: The phosphorelay system is the direct mechanistic context of CheA function, and this term is specific enough to retain as a core process annotation. Supporting Evidence: UniProt:Q88EW4 CheA is autophosphorylated; it can transfer its phosphate group to either CheB or CheY. file:PSEPK/cheA/cheA-deep-research-falcon.md CheA is the central histidine kinase of the canonical chemotaxis phosphorelay in KT2440. |
| GO:0006935 chemotaxis | IEA GO_REF:0000002 | ACCEPT | Summary: Chemotaxis is a core process annotation for this locus. The strongest species-specific evidence in KT2440 shows that PP_4338/cheA2 is required for chemotaxis toward maize root exudates. Reason: The KT2440 cheA2 mutant phenotype directly connects this paralog to the canonical chemotaxis pathway rather than only to generic signaling. Supporting Evidence: DOI:10.3389/fmicb.2019.00078 a cheA2 mutant was entirely deficient in MRE chemotaxis file:PSEPK/cheA/cheA-deep-research-falcon.md PP_4338/Q88EW4 is the CheA paralog for the flagellar chemotaxis pathway rather than the Wsp-like surface signaling pathway. |
| GO:0007165 signal transduction | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This term is true but too broad. CheA participates specifically in phosphorelay signaling for chemotaxis, which is already captured by more informative child terms. Reason: GO:0007165 is a very high-level parent of the more informative phosphorelay and chemotaxis terms already present for this gene. Supporting Evidence: file:PSEPK/cheA/cheA-deep-research-falcon.md GO:0007165 is a broad parent term and does not add useful specificity once phosphorelay signal transduction system and chemotaxis are retained. |
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Cytoplasm is acceptable as a broad localization because CheA is a soluble signaling kinase rather than a transmembrane receptor. However, this term does not capture the membrane-proximal chemosensory array context in which the protein actually operates. Reason: The annotation is not wrong, but it is too generic to represent the most informative localization context for the chemotaxis machinery. Supporting Evidence: UniProt:Q88EW4 GO; GO:0005737; C:cytoplasm; IEA:InterPro file:PSEPK/cheA/cheA-deep-research-falcon.md The safest curation decision is to keep cytoplasm as a non-core location rather than assert a more specific cell-pole or membrane-complex term. |
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Download this section (compressed HTML)Q: Which KT2440 response regulators are the dominant in vivo phospho-acceptors for PP_4338/CheA during chemotaxis under rhizosphere conditions?
Suggested experts: Tino Krell, Miguel A Matilla, Jose A Reyes-Darias
Q: How are signaling duties partitioned among the three KT2440 CheA paralogs across defined attractants and surface-associated states?
Suggested experts: Tino Krell, Miguel A Matilla
Q: Does PP_4338 form stable polar chemosensory arrays with specific MCP and CheW partners in KT2440, and how condition-dependent is that assembly?
Suggested experts: Tino Krell
Experiment: Purify PP_4338/CheA and test ATP-dependent autophosphorylation plus phosphotransfer to candidate KT2440 CheY and CheB proteins.
Hypothesis: PP_4338 is the cognate chemotaxis histidine kinase that directly transfers phosphate to the canonical chemotaxis response regulators.
Type: biochemical phosphotransfer assay
Experiment: Compare cheA1, cheA2, and cheA3 single and combinatorial mutants across defined attractants, root-exudate mixtures, motility, and root-colonization assays.
Hypothesis: cheA2 carries the core flagellar chemotaxis pathway, while the other paralogs control distinct surface-sensing or c-di-GMP-linked signaling branches.
Type: comparative mutant phenotyping
Experiment: Tag PP_4338 with a minimally perturbing fluorescent marker and image its localization relative to chemoreceptor arrays during planktonic and rhizosphere-like growth.
Hypothesis: The core chemotaxis CheA paralog forms membrane-proximal polar signaling arrays whose abundance changes with environmental context.
Type: live-cell localization microscopy
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