CheZ is the chemotaxis signal-terminating phosphatase of Pseudomonas putida KT2440. It accelerates the dephosphorylation of the phosphorylated response regulator CheY (CheY-P), the diffusible output of the chemotaxis two-component system. By lowering CheY-P levels, CheZ resets the signaling pathway after stimulation, controlling the proportion of phosphorylated CheY that reaches the flagellar motor and thereby tuning the balance between smooth swimming and reorientation (run/reversal-tumble bias). The protein belongs to the CheZ family (Pfam PF04344; InterPro IPR007439) of response-regulator aspartyl-phosphate phosphatases, which share a conserved C-terminal catalytic region acting on the phosphorylated aspartate of CheY. CheZ acts in the cytoplasm, typically as a homodimer, and in many bacteria is enriched at chemoreceptor/chemotaxis signaling clusters through interaction with other Che proteins. In P. putida KT2440 the gene (PP_4339) lies within a flagella-mediated swimming chemotaxis operon, where CheZ supports motile foraging through complex chemical environments such as the soil and rhizosphere.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0003824
catalytic activity
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: CheZ is a protein-aspartate (CheY-P) phosphatase; "catalytic activity" is correct but uninformatively general.
Reason: The InterPro2GO mapping assigns the root catalytic activity term, but CheZ has a well-defined, specific activity as a phosphoprotein phosphatase acting on phosphorylated CheY (an aspartyl-phosphate). UniProt itself maps the Protein phosphatase keyword for this entry to GO:0004721. Replace with the more specific molecular function term.
Proposed replacements:
phosphoprotein phosphatase activity
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: CheZ acts in the cytoplasm; consistent with UniProt subcellular location and the family's biology.
Reason: The UniProt record annotates Cytoplasm as the subcellular location, and CheZ-family phosphatases are soluble cytoplasmic proteins (acting on diffusible CheY-P, often enriched at cytoplasmic chemotaxis clusters). The IEA mapping from the Swiss-Prot subcellular location vocabulary is appropriate.
|
|
GO:0009288
bacterial-type flagellum
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: CheZ is a cytoplasmic signaling phosphatase, not a structural component of the flagellum.
Reason: This located_in annotation comes from an InterPro2GO mapping that conflates chemotaxis with the flagellar apparatus. CheZ is a soluble cytoplasmic enzyme that modulates the chemotaxis response regulator CheY; it is not a structural part of the bacterial-type flagellum and does not localize to the flagellar structure. The functional connection to motility is captured better by the chemotaxis process terms, and localization is already correctly represented by the cytoplasm annotation.
|
|
GO:0050920
regulation of chemotaxis
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: CheZ regulates chemotaxis by dephosphorylating CheY-P to terminate and reset the signaling output.
Reason: This is the core biological role of CheZ. By accelerating CheY-P dephosphorylation it controls the level of the chemotaxis output signal and thereby regulates chemotactic behavior. Supported by the conserved CheZ-family function and the UniProt FUNCTION annotation; the InterPro-based IEA is appropriate.
|
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.
Verified target identity: The requested protein is CheZ (chemotaxis protein; CheY-P phosphatase) from Pseudomonas putida strain KT2440, encoded by cheZ / PP_4339, UniProt Q88EW3. In the KT2440 genome annotation, CheZ is explicitly described as a phosphatase regulating the activity of the chemotaxis response regulator CheY, and it is placed within a flagella-mediated swimming chemotaxis operon (PP4332–PP4340) in a larger flagellar gene cluster (PP4331–PP4397). (santos2004genomicfeaturesof pages 24-27)
Domain/family alignment check: The UniProt-provided family assignment (“Belongs to the CheZ family”; Chemotax_Pase_CheZ) is consistent with the conserved CheZ-family catalytic motif and mechanism described for CheZ homologs in multiple bacteria. (liu2018achezlike pages 2-4, lertsethtakarn2015helicobacterpylorichezhp pages 3-4)
Ambiguity risk note: “cheZ” is a widely used chemotaxis gene symbol across bacteria; all claims below are either (i) directly supported for KT2440 CheZ by the KT2440 genome-level source or (ii) explicitly labeled as inference from CheZ-family experimental literature (other organisms). (santos2004genomicfeaturesof pages 24-27, lertsethtakarn2015helicobacterpylorichezhp pages 3-4)
CheZ is the canonical response regulator phosphatase in many bacterial chemotaxis systems. Its core biochemical role is to dephosphorylate phosphorylated CheY (CheY-P), thereby terminating the output signal that controls flagellar motor switching. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, frederick2026alteringchemotaxisas pages 1-5)
In KT2440, this canonical relationship is explicitly stated: “The activity of the transducer CheY is regulated by the phosphatase CheZ.” (santos2004genomicfeaturesof pages 24-27)
Reaction (functional definition): CheZ catalyzes hydrolysis of the aspartyl-phosphate on CheY-P, regenerating unphosphorylated CheY and inorganic phosphate (conceptually: CheY~P + H2O → CheY + Pi). This activity accelerates the intrinsic autodephosphorylation of CheY-P. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, frederick2026alteringchemotaxisas pages 1-5)
Substrate specificity: Experimental studies of CheZ-family proteins show preferential action on chemotaxis response regulators rather than unrelated receiver domains. For example, a CheZ ortholog in Campylobacter jejuni (Cj0700) dephosphorylated CheY and interacted with chemotaxis-associated receiver domains (CheA-RR, CheV) but did not act on an unrelated response regulator (RacR), supporting pathway-focused substrate selection. (jama2023achezorthologue pages 16-19)
Species-dependent specialization: A CheZ-like phosphatase in Sinorhizobium meliloti (CheT) showed selectivity among paralogous CheY proteins, accelerating dephosphorylation of CheY1~P but not CheY2~P. This indicates that even within the CheZ family, substrate specificity can be tuned to particular CheY-like proteins in the organism. (agbekudzi2023similaritiesandvariations pages 88-92)
CheZ-family proteins share a conserved DXXXQ catalytic motif. Multiple experimental systems demonstrate that the corresponding Asp/Gln residues are required for phosphatase activity (e.g., Azorhizobium caulinodans CheZ Asp165/Gln169; Helicobacter pylori CheZHP D189/Q193). (liu2018achezlike pages 2-4, lertsethtakarn2015helicobacterpylorichezhp pages 4-6)
Mechanistically, CheZ’s active-site Asp and Gln promote dephosphorylation by positioning/activating water for nucleophilic attack on the phosphoryl group at the CheY active site (described for E. coli CheZ Asp143/Gln147). (frederick2026alteringchemotaxisas pages 1-5)
A conserved C-terminal CheY-P binding region (often described as the last ~12 amino acids) is important for activity in at least some CheZ-family members; in H. pylori CheZHP, the C-terminal 12-aa segment contributes to CheY-P binding and phosphatase function. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 4-6)
In KT2440, CheZ is located in a flagella-mediated swimming chemotaxis operon (PP4332–PP4340) within the larger flagellar gene region (PP4331–PP4397), consistent with a role in controlling swimming behavior via chemotaxis signaling. (santos2004genomicfeaturesof pages 24-27)
CheY phosphorylation state determines chemotaxis output (motor switching); CheZ lowers CheY-P levels and thereby resets signaling after stimulation. This “reset” role is essential for maintaining responsiveness to changing gradients and avoiding persistent output states. While this dynamic description is established largely in model systems, it matches KT2440’s explicit annotation of CheZ as the regulator of CheY activity. (santos2004genomicfeaturesof pages 24-27, frederick2026alteringchemotaxisas pages 1-5)
Direct KT2440 evidence gap: No KT2440-specific microscopy or fractionation evidence for CheZ localization was identified in the retrieved texts.
Best-supported inference from authoritative experimental literature: CheZ-family phosphatase activity is frequently spatially restricted in bacterial cells, which is proposed to prevent formation of whole-cell CheY-P gradients and to coordinate outputs. In E. coli, CheZ localizes to the chemotaxis signaling cluster via interaction with CheA/CheA-short (CheAs). In H. pylori, CheZHP localizes to a cell pole through a different partner (ChePep), showing that localization mechanisms can diverge while maintaining polar/clustered localization logic. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 7-9)
For KT2440 CheZ (Q88EW3), the most defensible annotation is therefore cytoplasmic with likely enrichment at chemotaxis/flagellar signaling regions (e.g., chemoreceptor arrays or motor-associated zones), but the precise anchoring partner(s) and pattern remain to be experimentally verified in P. putida. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, santos2004genomicfeaturesof pages 24-27)
Direct KT2440 evidence gap: No KT2440 cheZ knockout phenotype was found in the gathered primary texts.
Strong inference from chemotaxis systems with validated CheZ loss-of-function:
Given KT2440’s operon context and explicit CheY regulatory annotation, a comparable prediction for P. putida KT2440 is that loss of cheZ would cause a strong swimming chemotaxis defect (altered run-reversal/tumble bias and impaired migration in gradient/soft-agar assays). This remains a prediction until directly measured in KT2440. (santos2004genomicfeaturesof pages 24-27, lertsethtakarn2015helicobacterpylorichezhp pages 4-6)
Quantitative catalytic effects can vary by organism and CheY substrate.
These values provide a quantitative family reference point for CheZ-like catalytic acceleration and substrate selection, but should not be assumed identical for KT2440 CheZ without direct kinetics. (agbekudzi2023similaritiesandvariations pages 88-92, santos2004genomicfeaturesof pages 24-27)
The H. pylori cheZHP deletion phenotype provides a concrete example of how loss of CheZ-family phosphatase activity shifts motility output: direction changes increased from ~21.6/min to ~48/min (~2.2×). (lertsethtakarn2015helicobacterpylorichezhp pages 4-6)
Protein-protein interactions can modulate CheZ activity; work cited within the CheZHP study notes that CheA-short can activate CheZ ~2.5-fold in the E. coli paradigm, highlighting that in vivo activity is not purely intrinsic catalysis but can be tuned by chemotaxis complex assembly. (lertsethtakarn2015helicobacterpylorichezhp pages 7-9)
A major 2024 Annual Review emphasizes that while the E. coli chemotaxis pathway serves as the canonical model, many bacteria possess alternative architectures and protein compositions, implying that CheZ function (and especially localization/complex integration) can be implemented in different organizational contexts across taxa. This directly supports caution when transferring detailed mechanistic assumptions to Pseudomonas without organism-specific evidence. (frederick2026alteringchemotaxisas pages 30-35)
A 2023 study/review of S. meliloti chemotaxis variation provides quantitative evidence that CheZ-family phosphatases can be selective among multiple CheY-like proteins and can have additional interaction partners (e.g., binding CheR with KD ~19 μM reported by microcalorimetry and formation of higher-order complexes), underscoring that CheZ-family roles may extend beyond a single simple phosphatase-substrate pair in some organisms. (agbekudzi2023similaritiesandvariations pages 92-97, agbekudzi2023similaritiesandvariations pages 88-92)
A 2023 preprint in C. jejuni provides evidence for CheZ-like activity in a lineage previously thought to lack canonical CheZ, reinforcing the point that distant CheZ homologs may be missed by simple annotation, and that conserved phosphatase activity can be retained even with low sequence identity. (jama2023achezorthologue pages 16-19)
Chemotaxis systems (including CheY/CheZ interactions) are increasingly used as components in biosensing concepts where bacterial accumulation reports chemical availability; split-fluorescent approaches explicitly use CheY–CheZ interaction as a readout of chemotaxis pathway activity in living cells (demonstrated in E. coli). While not specific to KT2440 CheZ, these approaches illustrate practical implementation of CheZ-mediated signaling state as a measurable output. (frederick2026alteringchemotaxisas pages 1-5)
For Pseudomonas putida, chemotaxis is an enabling trait for navigating complex soil/rhizosphere chemical landscapes. Genome-level organization indicates KT2440 invests in a large flagellar/chemotaxis gene complement (>50 genes for the flagellar system in the cited genome discussion), supporting a functional role for CheZ in environmental motility strategies. (santos2004genomicfeaturesof pages 24-27)
Protein name/function: Chemotaxis protein CheZ; CheY-P phosphatase (EC 3.1.3.-, response regulator phosphatase). (santos2004genomicfeaturesof pages 24-27, lertsethtakarn2015helicobacterpylorichezhp pages 3-4)
Primary substrate: CheY-P (chemotaxis response regulator). (santos2004genomicfeaturesof pages 24-27, frederick2026alteringchemotaxisas pages 1-5)
Biological process: Swimming chemotaxis signal termination/resetting by accelerating CheY-P dephosphorylation, thereby shaping flagellar motor switching behavior. (santos2004genomicfeaturesof pages 24-27, lertsethtakarn2015helicobacterpylorichezhp pages 4-6)
Cellular component/localization (best-supported): Cytoplasmic; likely recruited to chemotaxis clusters and/or polar signaling regions as in other bacteria, but KT2440-specific localization is currently unverified in the retrieved literature. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 7-9)
| Claim/Topic | Organism/Protein studied | Key quantitative/qualitative findings | Relevance to P. putida Q88EW3 (direct vs inferred) | Source |
|---|---|---|---|---|
| Gene identity and pathway placement | Pseudomonas putida KT2440 CheZ (PP_4339; UniProt Q88EW3) | KT2440 genome annotation places cheZ/PP_4339 in a flagella-mediated swimming chemotaxis operon (PP4332–PP4340; linked cluster PP4331–PP4397); text states “the activity of the transducer CheY is regulated by the phosphatase CheZ.” (santos2004genomicfeaturesof pages 24-27) | Direct evidence for correct gene/protein identity and chemotaxis role in KT2440 | dos Santos et al., 2004, doi: https://doi.org/10.1007/978-1-4419-9086-0_3 |
| Biochemical function | Canonical CheZ family; E. coli / H. pylori CheZ homologs | CheZ is the canonical CheY-P phosphatase in bacterial chemotaxis; it dephosphorylates phosphorylated CheY to terminate the signal. Conserved catalytic mechanism involves active-site Asp/Gln promoting hydrolysis of the aspartyl phosphate. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, frederick2026alteringchemotaxisas pages 1-5) | Inferred to Q88EW3 from family/domain conservation plus KT2440 genome annotation as CheZ | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086; Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |
| Substrate specificity | Campylobacter jejuni Cj0700 (CheZ ortholog) | Purified CheZ ortholog dephosphorylates CheY and interacts strongly with CheY; weaker interactions with CheA-RR and CheV were reported, while no activity on unrelated RR RacR was detected, indicating preference for chemotaxis response regulators rather than generic RRs. (jama2023achezorthologue pages 16-19) | Inferred: supports that CheZ-family enzymes such as Q88EW3 are primarily CheY-P phosphatases, though species-specific side-substrates may vary | Jama & Ketley, 2023, doi: https://doi.org/10.1101/2023.01.06.523011 |
| Catalytic residues / motif | Azorhizobium caulinodans CheZ; H. pylori CheZHP; CheZ family | CheZ-family phosphatases carry a conserved DXXXQ catalytic motif. In A. caulinodans, Asp165/Gln169 are conserved; in H. pylori, D189 and Q193 are required for activity; family summaries place the active site and CheY-P binding region in the C-terminal half. (liu2018achezlike pages 2-4, lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 4-6) | Inferred: Q88EW3 is annotated as CheZ-family/Chemotax_Pase_CheZ, so catalytic function is strongly supported by domain-level conservation | Liu et al., 2018, doi: https://doi.org/10.1128/AEM.01827-17; Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| CheY-P binding region | H. pylori CheZHP; CheZ family | A C-terminal ~12-aa CheY-P binding region is required for full phosphatase activity; the C-terminal half contains the catalytic residues and binding determinants. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 4-6) | Inferred to Q88EW3 from family-level conservation; direct binding-site mapping in KT2440 not found | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Pathway role | Canonical chemotaxis systems / KT2440 annotation | CheZ lowers intracellular CheY-P, thereby resetting pathway output and biasing motor behavior away from persistent reversal/tumble states; KT2440 annotation specifically links CheZ to regulation of CheY in the swimming chemotaxis operon. (santos2004genomicfeaturesof pages 24-27, lertsethtakarn2015helicobacterpylorichezhp pages 3-4, frederick2026alteringchemotaxisas pages 1-5) | Direct + inferred: direct for pathway membership in KT2440; inferred for detailed dynamic role from conserved mechanism | dos Santos et al., 2004, doi: https://doi.org/10.1007/978-1-4419-9086-0_3; Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |
| Localization | E. coli CheZ; H. pylori CheZHP | CheZ phosphatase activity is often spatially restricted. In E. coli, CheZ localizes to the chemotaxis cluster via CheA/CheAs; in H. pylori, CheZHP localizes to the pole via ChePep, with localization region mapped to aa ~40–241. Spatial restriction is proposed to prevent whole-cell CheY-P gradients. (lertsethtakarn2015helicobacterpylorichezhp pages 3-4, lertsethtakarn2015helicobacterpylorichezhp pages 7-9) | Inferred only: no direct localization study for KT2440 Q88EW3 found in gathered evidence | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Mutant phenotype | A. caulinodans CheZ | cheZ disruption abolishes chemotactic ring formation in soft agar while single-cell motility remains; complementation restores chemotaxis. This separates chemotaxis signaling from basal flagellar motility. (liu2018achezlike pages 2-4) | Inferred: strongly supports expected phenotype for KT2440 CheZ loss, but not directly tested here | Liu et al., 2018, doi: https://doi.org/10.1128/AEM.01827-17 |
| Mutant phenotype | H. pylori CheZHP | Full ΔcheZ mutant shows poor soft-agar migration and hyper-reversal behavior; direction changes increase about 2-fold from ~21.6/min (WT) to ~48/min (mutant), consistent with elevated CheY-P. Active-site mutants D189N/Q193R phenocopy the null. (lertsethtakarn2015helicobacterpylorichezhp pages 4-6) | Inferred: illustrates expected behavioral consequence of losing CheZ-family phosphatase activity | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Quantitative catalytic effect | Sinorhizobium meliloti CheT (CheZ-like phosphatase) | CheT accelerates dephosphorylation of CheY1~P 2-fold, reducing half-life from 26 s to 13 s; does not enhance dephosphorylation of CheY2~P, showing substrate selectivity. Binding: KD ~75 μM for CheY1 and ~2.9 μM for phosphomimic CheY1-BeF3−. (agbekudzi2023similaritiesandvariations pages 88-92) | Inferred: quantitative family benchmark for expected phosphatase behavior of Q88EW3, but kinetics may differ by species | Agbekudzi, 2023, no DOI URL available in gathered evidence |
| Quantitative activation / complex effects | E. coli / H. pylori CheZ family context | Interaction with CheA-short can activate CheZ about 2.5-fold in prior E. coli work cited within the H. pylori study; CheZ-family proteins are therefore modulated by pathway protein interactions as well as catalytic residues. (lertsethtakarn2015helicobacterpylorichezhp pages 7-9) | Inferred: suggests Q88EW3 activity may also be influenced by chemotaxis-complex interactions, but no KT2440-specific data found | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Alternative phosphatases / annotation context | Broad bacterial chemotaxis systems | CheZ is canonical, but some taxa use CheC/FliY/CheX instead; comparative genomics indicates Pseudomonas genomes are predominantly CheZ-only in the cited dataset (1,375 CheZ-only; 1 both; 1 CheX-only), supporting the expectation that CheZ is the principal chemotaxis phosphatase in pseudomonads. (frederick2026alteringchemotaxisas pages 30-35) | Inferred: supports uniqueness/centrality of CheZ for Pseudomonas chemotaxis, though not specific to KT2440 experiment | Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |
Table: This table compiles direct evidence for the identity and pathway placement of Pseudomonas putida KT2440 CheZ (PP_4339/Q88EW3) together with experimentally supported CheZ-family findings used to infer biochemical function, substrate specificity, localization logic, and likely phenotypes.
References
(santos2004genomicfeaturesof pages 24-27): Vitor A. P. Martins dos Santos, Kenneth N. Timmis, Burkhard Tümmler, and Christian Weinel. Genomic features of pseudomonas putida strain kt2440. ArXiv, pages 77-112, Jan 2004. URL: https://doi.org/10.1007/978-1-4419-9086-0_3, doi:10.1007/978-1-4419-9086-0_3. This article has 19 citations.
(liu2018achezlike pages 2-4): Xiaolin Liu, Wei Liu, Yu Sun, Chunlei Xia, Claudine Elmerich, and Zhihong Xie. A chez -like gene in azorhizobium caulinodans is a key gene in the control of chemotaxis and colonization of the host plant. Applied and Environmental Microbiology, Feb 2018. URL: https://doi.org/10.1128/aem.01827-17, doi:10.1128/aem.01827-17. This article has 37 citations and is from a peer-reviewed journal.
(lertsethtakarn2015helicobacterpylorichezhp pages 3-4): Paphavee Lertsethtakarn, Michael R. Howitt, Juan Castellon, Manuel R. Amieva, and Karen M. Ottemann. Helicobacter pylori chezhp and chepep form a novel chemotaxis‐regulatory complex distinct from the core chemotaxis signaling proteins and the flagellar motor. Molecular Microbiology, 97:1063-1078, Sep 2015. URL: https://doi.org/10.1111/mmi.13086, doi:10.1111/mmi.13086. This article has 41 citations and is from a domain leading peer-reviewed journal.
(frederick2026alteringchemotaxisas pages 1-5): Abigael Frederick, Carolina Lopes, Ben Fulton, Yuhsun Huang, Ram Podicheti, Douglas Rusch, George Minasov, Ludmilla Shuvalova, Karla J. F. Satchell, and Dean A. Rowe-Magnus. Altering chemotaxis as a strategy to enhance the foraging range of motility-restricted bacteria. Communications Biology, Jan 2026. URL: https://doi.org/10.1038/s42003-025-09475-w, doi:10.1038/s42003-025-09475-w. This article has 0 citations and is from a peer-reviewed journal.
(jama2023achezorthologue pages 16-19): Abdullahi S. Jama and Julian M. Ketley. A chez orthologue in campylobacter jejuni plays a role in chemotaxis through conserved phosphatase activity. bioRxiv, Jan 2023. URL: https://doi.org/10.1101/2023.01.06.523011, doi:10.1101/2023.01.06.523011. This article has 0 citations.
(agbekudzi2023similaritiesandvariations pages 88-92): A Agbekudzi. Similarities and variations of the enterobacterial chemotaxis paradigm in sinorhizobium meliloti. Unknown journal, 2023.
(lertsethtakarn2015helicobacterpylorichezhp pages 4-6): Paphavee Lertsethtakarn, Michael R. Howitt, Juan Castellon, Manuel R. Amieva, and Karen M. Ottemann. Helicobacter pylori chezhp and chepep form a novel chemotaxis‐regulatory complex distinct from the core chemotaxis signaling proteins and the flagellar motor. Molecular Microbiology, 97:1063-1078, Sep 2015. URL: https://doi.org/10.1111/mmi.13086, doi:10.1111/mmi.13086. This article has 41 citations and is from a domain leading peer-reviewed journal.
(lertsethtakarn2015helicobacterpylorichezhp pages 7-9): Paphavee Lertsethtakarn, Michael R. Howitt, Juan Castellon, Manuel R. Amieva, and Karen M. Ottemann. Helicobacter pylori chezhp and chepep form a novel chemotaxis‐regulatory complex distinct from the core chemotaxis signaling proteins and the flagellar motor. Molecular Microbiology, 97:1063-1078, Sep 2015. URL: https://doi.org/10.1111/mmi.13086, doi:10.1111/mmi.13086. This article has 41 citations and is from a domain leading peer-reviewed journal.
(frederick2026alteringchemotaxisas pages 30-35): Abigael Frederick, Carolina Lopes, Ben Fulton, Yuhsun Huang, Ram Podicheti, Douglas Rusch, George Minasov, Ludmilla Shuvalova, Karla J. F. Satchell, and Dean A. Rowe-Magnus. Altering chemotaxis as a strategy to enhance the foraging range of motility-restricted bacteria. Communications Biology, Jan 2026. URL: https://doi.org/10.1038/s42003-025-09475-w, doi:10.1038/s42003-025-09475-w. This article has 0 citations and is from a peer-reviewed journal.
(agbekudzi2023similaritiesandvariations pages 92-97): A Agbekudzi. Similarities and variations of the enterobacterial chemotaxis paradigm in sinorhizobium meliloti. Unknown journal, 2023.
id: Q88EW3
gene_symbol: cheZ
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
CheZ is the chemotaxis signal-terminating phosphatase of Pseudomonas putida
KT2440. It accelerates the dephosphorylation of the phosphorylated response
regulator CheY (CheY-P), the diffusible output of the chemotaxis two-component
system. By lowering CheY-P levels, CheZ resets the signaling pathway after
stimulation, controlling the proportion of phosphorylated CheY that reaches the
flagellar motor and thereby tuning the balance between smooth swimming and
reorientation (run/reversal-tumble bias). The protein belongs to the CheZ
family (Pfam PF04344; InterPro IPR007439) of response-regulator
aspartyl-phosphate phosphatases, which share a conserved C-terminal catalytic
region acting on the phosphorylated aspartate of CheY. CheZ acts in the
cytoplasm, typically as a homodimer, and in many bacteria is enriched at
chemoreceptor/chemotaxis signaling clusters through interaction with other Che
proteins. In P. putida KT2440 the gene (PP_4339) lies within a
flagella-mediated swimming chemotaxis operon, where CheZ supports motile
foraging through complex chemical environments such as the soil and rhizosphere.
existing_annotations:
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
CheZ is a protein-aspartate (CheY-P) phosphatase; "catalytic activity" is
correct but uninformatively general.
action: MODIFY
reason: >-
The InterPro2GO mapping assigns the root catalytic activity term, but CheZ
has a well-defined, specific activity as a phosphoprotein phosphatase
acting on phosphorylated CheY (an aspartyl-phosphate). UniProt itself maps
the Protein phosphatase keyword for this entry to GO:0004721. Replace with
the more specific molecular function term.
proposed_replacement_terms:
- id: GO:0004721
label: phosphoprotein phosphatase activity
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
CheZ acts in the cytoplasm; consistent with UniProt subcellular location
and the family's biology.
action: ACCEPT
reason: >-
The UniProt record annotates Cytoplasm as the subcellular location, and
CheZ-family phosphatases are soluble cytoplasmic proteins (acting on
diffusible CheY-P, often enriched at cytoplasmic chemotaxis clusters). The
IEA mapping from the Swiss-Prot subcellular location vocabulary is
appropriate.
- term:
id: GO:0009288
label: bacterial-type flagellum
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: >-
CheZ is a cytoplasmic signaling phosphatase, not a structural component of
the flagellum.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This located_in annotation comes from an InterPro2GO mapping that conflates
chemotaxis with the flagellar apparatus. CheZ is a soluble cytoplasmic
enzyme that modulates the chemotaxis response regulator CheY; it is not a
structural part of the bacterial-type flagellum and does not localize to
the flagellar structure. The functional connection to motility is captured
better by the chemotaxis process terms, and localization is already
correctly represented by the cytoplasm annotation.
- term:
id: GO:0050920
label: regulation of chemotaxis
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
CheZ regulates chemotaxis by dephosphorylating CheY-P to terminate and
reset the signaling output.
action: ACCEPT
reason: >-
This is the core biological role of CheZ. By accelerating CheY-P
dephosphorylation it controls the level of the chemotaxis output signal and
thereby regulates chemotactic behavior. Supported by the conserved
CheZ-family function and the UniProt FUNCTION annotation; the InterPro-based
IEA is appropriate.
core_functions:
- description: >-
Acts as the chemotaxis signal-terminating phosphatase, accelerating
dephosphorylation of the phosphorylated response regulator CheY (CheY-P) to
reset the chemotaxis signaling output and regulate flagellar motor switching.
supported_by:
- reference_id: PMID:12534463
supporting_text: >-
UniProt FUNCTION for Q88EW3, from the KT2440 genome paper - "Plays an
important role in bacterial chemotaxis signal transduction pathway by
accelerating the dephosphorylation of phosphorylated CheY (CheY-P)."
full_text_unavailable: true
molecular_function:
id: GO:0004721
label: phosphoprotein phosphatase activity
locations:
- id: GO:0005737
label: cytoplasm
directly_involved_in:
- id: GO:0050920
label: regulation of chemotaxis
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
findings: []
- id: PMID:12534463
title: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
findings:
- statement: >-
Source of the UniProt FUNCTION annotation; CheZ (PP_4339) is placed in the
flagella-mediated swimming chemotaxis gene region of the KT2440 genome and
functions to regulate CheY by accelerating CheY-P dephosphorylation.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
PMID 12534463 is the KT2440 complete genome paper (Nelson et al., Environ
Microbiol 2002), cited as reference [1] in the UniProt record for Q88EW3.
It establishes gene identity and chemotaxis-operon context.