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.
|
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
provider: falcon
model: Edison Scientific Literature
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start_time: '2026-03-21T13:54:47.142375'
end_time: '2026-03-21T14:07:36.612640'
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template_variables:
organism: PSEPK
gene_id: cheA
gene_symbol: cheA
uniprot_accession: Q88EW4
protein_description: 'RecName: Full=Chemotaxis protein CheA {ECO:0000256|ARBA:ARBA00021495};
EC=2.7.13.3 {ECO:0000256|ARBA:ARBA00012438};'
gene_info: Name=cheA {ECO:0000313|EMBL:AAN69917.1}; OrderedLocusNames=PP_4338 {ECO:0000313|EMBL:AAN69917.1};
organism_full: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB
11950 / KT2440).
protein_family: Not specified in UniProt
protein_domains: Bact_Chemotaxis_CheA. (IPR051315); CheA-like_dim. (IPR004105);
CheA-like_homodim_sf. (IPR037006); CheW-like_dom_sf. (IPR036061); CheW-lke_dom.
(IPR002545)
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citation_count: 31
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'cheA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene cheA (gene ID: cheA, UniProt: Q88EW4) in PSEPK.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'cheA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene cheA (gene ID: cheA, UniProt: Q88EW4) in PSEPK.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The UniProt accession Q88EW4 corresponds to Chemotaxis protein CheA (EC 2.7.13.3) encoded by cheA with ordered locus name PP_4338 in Pseudomonas putida KT2440; this locus is explicitly identified as cheA2 in KT2440 genetic work, which also distinguishes cheA1 (pp1492) and cheA3 (pp4988) paralogs. (lopezfarfan2019concentrationdependenteffect pages 5-6, lopezfarfan2019concentrationdependenteffect pages 3-5)
In KT2440, CheA2 (PP_4338) functions as the central histidine kinase of the canonical chemotaxis signaling pathway, required for chemotaxis to maize root exudates in quantitative capillary assays. (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11)
CheA is the dimeric histidine kinase at the core of bacterial chemotaxis pathways. It is activated/inhibited by chemoreceptor signaling complexes and initiates a phosphorylation cascade by autophosphorylation and phosphotransfer to response regulators (CheY, CheB). (muok2024unpackingalternativefeatures pages 2-4, vass2023analysisofchew‐like pages 1-3)
CheA catalyzes an ATP-dependent autophosphorylation on a conserved histidine in the P1 (Hpt/HPT) domain, driven by the P4 (ATP-binding catalytic) domain, and subsequently transfers the phosphoryl group to response regulators such as CheY (and typically CheB) as part of the chemotaxis two-component-like system. (muok2024unpackingalternativefeatures pages 2-4, vass2023analysisofchew‐like pages 1-3)
Direct biochemical evidence in P. putida shows purified CheA has strong [32P]ATPγP-dependent autophosphorylation and that addition of CheY yields CheY labeling with a reduction in CheA label, consistent with phosphate transfer from CheA to CheY. (he2025coordinatedregulationof pages 3-5)
A canonical CheA comprises five domains (P1–P5):
- P1 (Hpt/HPT): phosphoacceptor histidine-bearing domain
- P2: docking/binding of response regulators (CheY/CheB)
- P3: dimerization domain
- P4 (HATPase_c): ATP-binding/catalytic domain that phosphorylates P1
- P5 (CheW-like): coupling to receptors and CheW for array assembly
These functions and the five-domain model are summarized in authoritative recent reviews and are consistent with UniProt’s CheA-like/CheW-like domain annotations provided in the prompt. (muok2024unpackingalternativefeatures pages 2-4, he2025coordinatedregulationof pages 1-2)
CheA functions within chemosensory arrays (also called receptor arrays) made of chemoreceptors plus coupling proteins (CheW) and CheA. The core signaling unit (CSU) is commonly defined as one CheA dimer + two CheW + two receptor trimers-of-dimers, which then assemble into larger hexagonal lattices. (muok2024unpackingalternativefeatures pages 2-4)
Although the retrieved KT2440-specific texts did not directly image CheA2 localization, the conserved mechanism implies that KT2440 CheA2 operates at these membrane-proximal/polar chemosensory arrays to integrate receptor inputs and control downstream phosphorylation. (muok2024unpackingalternativefeatures pages 2-4)
In P. putida KT2440, three cheA paralogs are present (cheA1, cheA2, cheA3). Functional analyses support division of labor:
- cheA2 (PP_4338) is required for chemotaxis to maize root exudates (MRE)
- cheA1 aligns with a wsp-like pathway that modulates c-di-GMP/biofilm traits
- cheA3 showed no defect in the specific MRE chemotaxis assay and was described as similar to wild type under those conditions, with broader role unresolved
(lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11)
The key identity mapping—PP_4338 = cheA2—is explicitly stated in the KT2440 mutant construction methods and strain descriptions (including pp4338::km). (lopezfarfan2019concentrationdependenteffect pages 5-6, lopezfarfan2019concentrationdependenteffect pages 3-5)
In KT2440, a cheA2 mutant was reported to be entirely deficient in MRE chemotaxis, supporting CheA2 as the primary kinase in the chemotaxis (che) pathway for this cue. (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11)
In the same study, quantitative capillary assays provided CFU counts in the chemotaxis readout (means ± SD; replicated), demonstrating a measurable chemotactic response to MRE, though many effect sizes for genotype comparisons were presented in figures rather than fully tabulated in text. (lopezfarfan2019concentrationdependenteffect pages 11-12)
Transcriptional mapping in a KT2440 motility/chemotaxis region placed cheA in a cheYZA operon, i.e., transcriptional linkage with cheY and cheZ in at least one chemotaxis-associated operon context. This supports a functional module organization typical of chemotaxis systems. (navarro‐aviles2010physiologicalandtranscriptomic pages 1-2)
A 2025 study identified multiple CheA-interacting proteins and showed that at least two regulators, CsoR (a copper-binding repressor) and PhaD, can inhibit CheA autophosphorylation in vitro in a dose-dependent manner, without acting as ATPases, indicating direct modulation of CheA catalytic activity rather than ATP depletion. (he2025coordinatedregulationof pages 3-5, he2025coordinatedregulationof pages 5-8)
The study also reports a CheA-dependent chemorepellent response to copper and quantifies this behavior using response indices and tracking-based metrics; for example, perturbation of CsoR expression altered a response index (RI) from 0.373 ± 0.021 (vector control) to 0.428 ± 0.015 (pcsoR) and changed center-of-mass displacement (e.g., 21.77 ± 3.60 μm vs 13.85 ± 1.92 μm), illustrating how CheA activity integrates environmental stress sensing into motility behavior. (he2025coordinatedregulationof pages 11-13)
Recent authoritative work emphasizes that mechanistic understanding of CheA regulation requires treating CheA as part of a supramolecular array, not an isolated kinase.
- A 2024 Annual Review synthesizes evidence that the CSU architecture (CheA dimer, CheW, and receptor trimers-of-dimers) is the fundamental signaling unit and highlights alternative/expanded architectures across bacteria. (muok2024unpackingalternativefeatures pages 2-4)
- 2023 studies further advanced CSU structural models of native arrays and interactions among CheA domains within these assemblies, helping explain long-range coupling between ligand binding and CheA kinase activity. (tran2023bacterialchemoreceptorsignaling pages 12-15)
These developments support annotation of KT2440 CheA2 as a multi-domain kinase whose activity is controlled by array assembly and receptor state, and whose localization is expected to be array-associated. (muok2024unpackingalternativefeatures pages 2-4, tran2023bacterialchemoreceptorsignaling pages 12-15)
Comparative analyses show that although CheA is often described as five-domain, noncanonical architectures (e.g., loss of P2, acquisition of receiver domains, split proteins) are widespread across bacteria, which is important when interpreting paralogs (like cheA1–3) and predicting functional specialization. (berry2023diversityandevolution pages 34-41)
Chemotaxis toward root exudates is a key determinant of rhizosphere performance. In KT2440, signaling through both a chemotaxis-associated pathway (involving cheA2) and a wsp-like pathway (involving cheA1) was reported as important for efficient maize root colonization, indicating that CheA paralogs contribute to ecologically relevant host-association outcomes. (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11)
A soil microcosm study on a different P. putida strain (DLL-1) compared mutants and found that a cheA non-chemotaxis mutant (DAK) lost directed chemotaxis and showed reduced in-situ degradation performance for the hydrophobic pesticide methyl parathion (MP) relative to wild type, despite similar degradation in well-mixed liquid. For example, the cheA mutant degraded ~64.3–85.7% of MP in soil microcosms (reported 5-day endpoints), while both wild type and cheA mutant could degrade MP to nondetectable levels in ~18 h in shaken liquid medium, supporting the practical principle that chemotaxis enhances contact with poorly soluble substrates in heterogeneous environments. (guo2009comparisonofinsitu pages 1-2, guo2009comparisonofinsitu pages 4-5)
CheA2 (PP_4338; Q88EW4) is an ATP-dependent protein histidine kinase that autophosphorylates and transfers phosphoryl groups to chemotaxis response regulators (e.g., CheY), thereby controlling chemotactic motility in P. putida KT2440; genetically, CheA2 is essential for chemotaxis toward maize root exudates. (he2025coordinatedregulationof pages 3-5, lopezfarfan2019concentrationdependenteffect pages 1-2)
Chemotaxis signaling pathway (chemosensory array → CheA2 → CheY/CheB → flagellar motor/adaptation), contributing to environmental navigation and plant-root colonization. (muok2024unpackingalternativefeatures pages 2-4, lopezfarfan2019concentrationdependenteffect pages 1-2)
CheA2 is expected to localize to chemosensory receptor arrays/core signaling units (often polar, membrane-associated supramolecular assemblies) through interactions mediated by its P5/CheW-like region and CheW; this is strongly supported for bacterial chemotaxis systems generally, but direct imaging for KT2440 CheA2 was not captured in the retrieved KT2440-specific sources. (muok2024unpackingalternativefeatures pages 2-4, muok2024unpackingalternativefeatures media cd438e27)
KT2440 encodes three CheA paralogs. Functional attribution for PP_4338/Q88EW4 should be limited to cheA2 (chemotaxis-associated), not cheA1 (wsp-like, c-di-GMP/biofilm) or cheA3 (unclear/condition-dependent). (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 3-5)
| Topic | Key finding | Evidence/assay type | Organism/strain | Publication (authors/year) | URL/DOI | Citation context ID |
|---|---|---|---|---|---|---|
| Identity | UniProt Q88EW4 matches cheA2 / PP_4338 in Pseudomonas putida KT2440; the 2019 mutant construction paper explicitly states that PP_4338 is cheA2, distinguishing it from cheA1/PP_1492 and cheA3/PP_4988. | Targeted mutant construction by homologous recombination; strain table/genetic mapping | P. putida KT2440 | López-Farfán et al. 2019 | https://doi.org/10.3389/fmicb.2019.00078 | (lopezfarfan2019concentrationdependenteffect pages 5-6, lopezfarfan2019concentrationdependenteffect pages 3-5) |
| Reaction | CheA is the central chemotaxis histidine kinase that autophosphorylates using ATP and transfers phosphate to CheY; in vitro radiolabel assays showed strong CheA autophosphorylation and CheY labeling with reduced CheA label after CheY addition. | Purified-protein phosphotransfer assay with [32P]ATPγP, SDS-PAGE/autoradiography | P. putida KT2440 | He et al. 2025 | https://doi.org/10.7554/elife.100914.2 | (he2025coordinatedregulationof pages 3-5, he2025coordinatedregulationof pages 5-8) |
| Domains | CheA has the canonical five-domain architecture (P1–P5): P1/HPT phosphoacceptor, P2 CheY/CheB docking, P3 dimerization, P4 HATPase catalytic ATP-binding domain, P5 CheW-like receptor/CheW interaction domain; this matches UniProt and InterPro annotations for Q88EW4. | Domain mapping from reviews and truncation/interactor mapping in P. putida | P. putida KT2440; comparative bacterial systems | Berry et al. 2024; Muok et al. 2024; He et al. 2025 | https://doi.org/10.1128/spectrum.03464-23 ; https://doi.org/10.1146/annurev-micro-032421-110850 ; https://doi.org/10.7554/elife.100914.2 | (he2025coordinatedregulationof pages 1-2, he2025coordinatedregulationof pages 5-8, muok2024unpackingalternativefeatures pages 2-4, berry2024diversedomainarchitectures pages 12-13) |
| Localization | By current understanding, CheA localizes to chemosensory receptor arrays/core signaling units at the cell pole or membrane-proximal chemosensory arrays, where one CheA dimer associates with CheW and receptor trimers-of-dimers. Direct localization was not shown specifically for KT2440 PP_4338 in the retrieved KT2440 papers, so localization is inferred from conserved chemosensory architecture. | Structural reviews; cryo-ET/core signaling unit model | Comparative bacterial systems; inference for KT2440 CheA2 | Muok et al. 2024; Cassidy et al. 2023 | https://doi.org/10.1146/annurev-micro-032421-110850 ; https://doi.org/10.1128/mbio.00793-23 | (muok2024unpackingalternativefeatures media cd438e27, muok2024unpackingalternativefeatures pages 2-4, tran2023bacterialchemoreceptorsignaling pages 12-15) |
| Pathway context | KT2440 encodes three CheA paralogs with distinct pathway roles: cheA1 belongs to a wsp-like signaling cluster affecting c-di-GMP/biofilm, whereas cheA2 (PP_4338) belongs to the che/chemotaxis pathway and is required for maize root exudate chemotaxis; cheA3 remains less clearly assigned. | Mutant phenotyping; pathway inference from paralog-specific phenotypes | P. putida KT2440 | López-Farfán et al. 2019 | https://doi.org/10.3389/fmicb.2019.00078 | (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11) |
| Genomic context | A KT2440 motility/chemotaxis region places cheA in a cheYZA operon, indicating transcriptional linkage with cheY and cheZ in at least one chemotaxis-associated cluster. | RT-PCR transcriptional organization; transcriptomics | P. putida KT2440 | Navarro-Avilés & van Dillewijn 2010 | https://doi.org/10.1111/j.1758-2229.2009.00084 | (navarro‐aviles2010physiologicalandtranscriptomic pages 1-2) |
| Mutant phenotypes | cheA2/PP_4338 mutants abolish chemotaxis to maize root exudates, whereas cheA1 mutants show reduced c-di-GMP, increased swimming, and early biofilm defects; cheA3 is similar to wild type in the tested chemotaxis assay. | Quantitative capillary chemotaxis assays, c-di-GMP biosensor, swimming plates, biofilm assays | P. putida KT2440 | López-Farfán et al. 2019 | https://doi.org/10.3389/fmicb.2019.00078 | (lopezfarfan2019concentrationdependenteffect pages 1-2, lopezfarfan2019concentrationdependenteffect pages 10-11) |
| Regulation | CsoR and PhaD interact with CheA and inhibit CheA autophosphorylation; interaction mapping implicated the P1, P3, and P4 regions, with P3 contributing strongly. Copper weakens the CsoR–CheA interaction, relieving inhibition and altering chemotaxis behavior. | Pull-down/MS, bacterial two-hybrid, BiFC, MST, truncation analysis, autoradiography, semisolid chemotaxis assays | P. putida KT2440 | He et al. 2025 | https://doi.org/10.7554/elife.100914.2 | (he2025coordinatedregulationof pages 5-8, he2025coordinatedregulationof pages 3-5, he2025coordinatedregulationof pages 11-13, he2025coordinatedregulationof pages 1-2) |
| Applications | Chemotaxis signaling through CheA-like proteins contributes to root colonization in KT2440 and, in another P. putida strain, cheA-dependent chemotaxis improves in-situ pollutant biodegradation in soil even when degradation kinetics in well-mixed liquid are unchanged. | Competitive maize root colonization assays; soil microcosm biodegradation comparisons | P. putida KT2440; P. putida DLL-1/DAK | López-Farfán et al. 2019; Guo et al. 2009 | https://doi.org/10.3389/fmicb.2019.00078 ; https://doi.org/10.1016/j.ibiod.2009.01.008 | (lopezfarfan2019concentrationdependenteffect pages 10-11, lopezfarfan2019concentrationdependenteffect pages 11-12, guo2009comparisonofinsitu pages 1-2, guo2009comparisonofinsitu pages 4-5) |
| Quantitative notes | Reported quantitative values include root colonization inoculum starting at 50 ± 3% WT vs mutant, chemotaxis assay counts around 1960 ± 339 to 2133 ± 280 in the cited panel, and copper-repellent response indices such as 0.428 ± 0.015 vs 0.373 ± 0.021 under CsoR perturbation; many KT2440 effect sizes were figure-based rather than fully tabulated in text. | Replicated chemotaxis, colonization, and Cu-response measurements with statistics | P. putida KT2440 | López-Farfán et al. 2019; He et al. 2025 | https://doi.org/10.3389/fmicb.2019.00078 ; https://doi.org/10.7554/elife.100914.2 | (lopezfarfan2019concentrationdependenteffect pages 11-12, he2025coordinatedregulationof pages 11-13) |
Table: This table summarizes organism-specific and comparative evidence supporting the functional annotation of Pseudomonas putida KT2440 CheA2 (PP_4338; UniProt Q88EW4). It highlights identity verification, catalytic activity, domains, pathway assignment, mutant phenotypes, regulatory interactions, and application-relevant phenotypes with traceable context IDs.
The following retrieved figure crops illustrate (i) the chemotaxis core signaling unit and (ii) the CheA P1–P5 domain architecture used throughout this report. (muok2024unpackingalternativefeatures media cd438e27, muok2024unpackingalternativefeatures media 770fbb22)
Some KT2440 phenotype effect sizes (e.g., exact fold-changes in c-di-GMP fluorescence, swim halo diameters, biofilm biomass, and competitive colonization ratios) were reported primarily in figures/supplements and were not fully extractable from the provided text excerpts; the qualitative genotype-to-function mapping remains strongly supported. (lopezfarfan2019concentrationdependenteffect pages 10-11, lopezfarfan2019concentrationdependenteffect pages 11-12)
References
(lopezfarfan2019concentrationdependenteffect pages 5-6): Diana López-Farfán, José A. Reyes-Darias, Miguel A. Matilla, and Tino Krell. Concentration dependent effect of plant root exudates on the chemosensory systems of pseudomonas putida kt2440. Frontiers in Microbiology, Jan 2019. URL: https://doi.org/10.3389/fmicb.2019.00078, doi:10.3389/fmicb.2019.00078. This article has 76 citations and is from a peer-reviewed journal.
(lopezfarfan2019concentrationdependenteffect pages 3-5): Diana López-Farfán, José A. Reyes-Darias, Miguel A. Matilla, and Tino Krell. Concentration dependent effect of plant root exudates on the chemosensory systems of pseudomonas putida kt2440. Frontiers in Microbiology, Jan 2019. URL: https://doi.org/10.3389/fmicb.2019.00078, doi:10.3389/fmicb.2019.00078. This article has 76 citations and is from a peer-reviewed journal.
(lopezfarfan2019concentrationdependenteffect pages 1-2): Diana López-Farfán, José A. Reyes-Darias, Miguel A. Matilla, and Tino Krell. Concentration dependent effect of plant root exudates on the chemosensory systems of pseudomonas putida kt2440. Frontiers in Microbiology, Jan 2019. URL: https://doi.org/10.3389/fmicb.2019.00078, doi:10.3389/fmicb.2019.00078. This article has 76 citations and is from a peer-reviewed journal.
(lopezfarfan2019concentrationdependenteffect pages 10-11): Diana López-Farfán, José A. Reyes-Darias, Miguel A. Matilla, and Tino Krell. Concentration dependent effect of plant root exudates on the chemosensory systems of pseudomonas putida kt2440. Frontiers in Microbiology, Jan 2019. URL: https://doi.org/10.3389/fmicb.2019.00078, doi:10.3389/fmicb.2019.00078. This article has 76 citations and is from a peer-reviewed journal.
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(vass2023analysisofchew‐like pages 1-3): Luke R. Vass, Robert B. Bourret, and Clay A. Foster. Analysis of
(he2025coordinatedregulationof pages 3-5): Meina He, Yongxin Tao, Kexin Mu, Haoqi Feng, Ying Fan, Tong Liu, Qiaoyun Huang, Yujie Xiao, and Wenli Chen. Coordinated regulation of chemotaxis and resistance to copper by csor in pseudomonas putida. Jan 2025. URL: https://doi.org/10.7554/elife.100914.2, doi:10.7554/elife.100914.2. This article has 4 citations.
(he2025coordinatedregulationof pages 1-2): Meina He, Yongxin Tao, Kexin Mu, Haoqi Feng, Ying Fan, Tong Liu, Qiaoyun Huang, Yujie Xiao, and Wenli Chen. Coordinated regulation of chemotaxis and resistance to copper by csor in pseudomonas putida. Jan 2025. URL: https://doi.org/10.7554/elife.100914.2, doi:10.7554/elife.100914.2. This article has 4 citations.
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(navarro‐aviles2010physiologicalandtranscriptomic pages 1-2): G Navarro‐Avilés and P Van Dillewijn. Physiological and transcriptomic characterization of a flia mutant of pseudomonas putida kt2440. Unknown journal, 2010. URL: https://doi.org/10.1111/j.1758-2229.2009.00084, doi:10.1111/j.1758-2229.2009.00084.
(he2025coordinatedregulationof pages 5-8): Meina He, Yongxin Tao, Kexin Mu, Haoqi Feng, Ying Fan, Tong Liu, Qiaoyun Huang, Yujie Xiao, and Wenli Chen. Coordinated regulation of chemotaxis and resistance to copper by csor in pseudomonas putida. Jan 2025. URL: https://doi.org/10.7554/elife.100914.2, doi:10.7554/elife.100914.2. This article has 4 citations.
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(berry2024diversedomainarchitectures pages 12-13): Marissa A. Berry, Ekaterina P. Andrianova, and Igor B. Zhulin. Diverse domain architectures of chea histidine kinase, a central component of bacterial and archaeal chemosensory systems. Jan 2024. URL: https://doi.org/10.1128/spectrum.03464-23, doi:10.1128/spectrum.03464-23. This article has 8 citations and is from a domain leading peer-reviewed journal.
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PP_4338; the KT2440cheA2 [UniProt:Q88EW4 "OrderedLocusNames=PP_4338"]a cheA2 mutant was entirely deficient in MRE
chemotaxis [DOI:10.3389/fmicb.2019.00078 "a cheA2 mutant was entirely deficient in MRE chemotaxis"].cheA1 affected c-di-GMP andcheA2 mapped to the classical chemotaxis pathwayprotein histidine kinase activity, phosphorelay signal transduction
system, and chemotaxis; demote or remove broader parent terms likephosphorelay sensor kinase activity, transferase activity, transferring
phosphorus-containing groups, and signal transduction.id: Q88EW4
gene_symbol: cheA
product_type: PROTEIN
aliases:
- PP_4338
- cheA2
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
/ KT2440)
description: 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.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings:
- statement: InterPro mappings recover the broad conserved chemotaxis and phosphorelay
context for CheA-family histidine kinases, but they also seed very broad parent
terms that should be reviewed for redundancy.
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings:
- statement: Combined automated methods recover the kinase activity of CheA, but
the broader phosphorelay sensor kinase term is less specific than protein histidine
kinase activity for this gene.
- id: UniProt:Q88EW4
title: UniProt entry Q88EW4 for Pseudomonas putida KT2440 chemotaxis protein CheA
findings:
- statement: UniProt identifies Q88EW4 as chemotaxis protein CheA and states that
it is autophosphorylated and can transfer phosphate to CheB or CheY.
supporting_text: >-
RecName: Full=Chemotaxis protein CheA...CheA is autophosphorylated; it can
transfer its phosphate group to either CheB or CheY.
- statement: The sequence carries an HPt domain, a histidine kinase region, and
a CheW-like domain, with a phosphohistidine annotated at residue 49.
- id: DOI:10.3389/fmicb.2019.00078
title: Concentration Dependent Effect of Plant Root Exudates on the Chemosensory
Systems of Pseudomonas putida KT2440
findings:
- statement: The KT2440 study identifies PP_4338 as cheA2 and reports that a cheA2
mutant is entirely deficient in maize root exudate chemotaxis.
- statement: The same study separates cheA paralog roles, with cheA1 affecting c-di-GMP
and biofilm formation while cheA2 maps to the canonical chemotaxis pathway.
- id: file:PSEPK/cheA/cheA-deep-research-falcon.md
title: Falcon deep research report for cheA in Pseudomonas putida KT2440
findings:
- statement: Synthesizes KT2440 cheA2 literature, conserved CheA domain architecture,
and recent chemosensory-system reviews into a curation-focused assessment of
core versus over-broad GO terms.
existing_annotations:
- term:
id: GO:0000155
label: phosphorelay sensor kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: MARK_AS_OVER_ANNOTATED
reason: Retaining the broader phosphorelay sensor kinase term adds little beyond
the specific protein histidine kinase annotation and obscures the more informative
catalytic term.
supported_by:
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: GO:0000155 is broader than GO:0004673 and becomes redundant
when the child protein histidine kinase term is already present.
- term:
id: GO:0004673
label: protein histidine kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.'
action: ACCEPT
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.
supported_by:
- reference_id: UniProt:Q88EW4
supporting_text: CheA is autophosphorylated; it can transfer its phosphate group
to either CheB or CheY.
- reference_id: UniProt:Q88EW4
supporting_text: >-
-!- CATALYTIC ACTIVITY: Reaction=ATP + protein L-histidine = ADP +
protein N-phospho-L- histidine.; EC=2.7.13.3;
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: CheA is the central histidine kinase of the canonical chemotaxis
phosphorelay in KT2440.
- term:
id: GO:0016772
label: transferase activity, transferring phosphorus-containing groups
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MARK_AS_OVER_ANNOTATED
reason: The broader transferase term is redundant once the specific protein histidine
kinase activity is retained.
supported_by:
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: GO:0016772 is a very broad parent term and does not add useful
specificity beyond protein histidine kinase activity.
- term:
id: GO:0000160
label: phosphorelay signal transduction system
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: UniProt:Q88EW4
supporting_text: CheA is autophosphorylated; it can transfer its phosphate group
to either CheB or CheY.
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: CheA is the central histidine kinase of the canonical chemotaxis
phosphorelay in KT2440.
- term:
id: GO:0006935
label: chemotaxis
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: ACCEPT
reason: The KT2440 cheA2 mutant phenotype directly connects this paralog to the
canonical chemotaxis pathway rather than only to generic signaling.
supported_by:
- reference_id: DOI:10.3389/fmicb.2019.00078
supporting_text: a cheA2 mutant was entirely deficient in MRE chemotaxis
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: PP_4338/Q88EW4 is the CheA paralog for the flagellar chemotaxis
pathway rather than the Wsp-like surface signaling pathway.
- term:
id: GO:0007165
label: signal transduction
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MARK_AS_OVER_ANNOTATED
reason: GO:0007165 is a very high-level parent of the more informative phosphorelay
and chemotaxis terms already present for this gene.
supported_by:
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: GO:0007165 is a broad parent term and does not add useful specificity
once phosphorelay signal transduction system and chemotaxis are retained.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: KEEP_AS_NON_CORE
reason: The annotation is not wrong, but it is too generic to represent the most
informative localization context for the chemotaxis machinery.
supported_by:
- reference_id: UniProt:Q88EW4
supporting_text: GO; GO:0005737; C:cytoplasm; IEA:InterPro
- reference_id: file:PSEPK/cheA/cheA-deep-research-falcon.md
supporting_text: 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.
core_functions:
- description: CheA is the chemotaxis histidine kinase of the KT2440 chemosensory
phosphorelay. It autophosphorylates on histidine and transfers phosphate to downstream
response regulators such as CheY and CheB to couple chemoreceptor input to chemotactic
behavior.
molecular_function:
id: GO:0004673
label: protein histidine kinase activity
directly_involved_in:
- id: GO:0000160
label: phosphorelay signal transduction system
- id: GO:0006935
label: chemotaxis
supported_by:
- reference_id: UniProt:Q88EW4
supporting_text: Involved in the transmission of sensory signals from the chemoreceptors
to the flagellar motors.
- reference_id: UniProt:Q88EW4
supporting_text: CheA is autophosphorylated; it can transfer its phosphate group
to either CheB or CheY.
- reference_id: DOI:10.3389/fmicb.2019.00078
supporting_text: a cheA2 mutant was entirely deficient in MRE chemotaxis
proposed_new_terms: []
suggested_questions:
- question: Which KT2440 response regulators are the dominant in vivo phospho-acceptors
for PP_4338/CheA during chemotaxis under rhizosphere conditions?
experts:
- Tino Krell
- Miguel A Matilla
- Jose A Reyes-Darias
- question: How are signaling duties partitioned among the three KT2440 CheA paralogs
across defined attractants and surface-associated states?
experts:
- Tino Krell
- Miguel A Matilla
- question: Does PP_4338 form stable polar chemosensory arrays with specific MCP and
CheW partners in KT2440, and how condition-dependent is that assembly?
experts:
- Tino Krell
suggested_experiments:
- description: 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.
experiment_type: biochemical phosphotransfer assay
- description: 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.
experiment_type: comparative mutant phenotyping
- description: 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.
experiment_type: live-cell localization microscopy