| Claim/Observation | Evidence summary | Organism/Context (KT2440-specific vs general) | Year | Source (with URL) | Citation ID |
|---|---|---|---|---|---|
| UniProt Q88EW2 matches **cheY / PP_4340** in *Pseudomonas putida* KT2440 | KT2440 transcriptomic data explicitly annotate **PP_4340** as “Chemotaxis protein CheY” (gene **cheY**); the gene is part of a motility/chemotaxis region and is downregulated in a **fliA** mutant with fold change **−2.8** | KT2440-specific | 2010 | Navarro-Avilés & Van Dillewijn, DOI: https://doi.org/10.1111/j.1758-2229.2009.00084 | (pqac-00000000, pqac-00000003) |
| **PP_4340** likely lies in a local chemotaxis operon/gene neighborhood | The KT2440 study identifies a potential operon region **PP4340 to PP4338**, placing **cheY (PP_4340)** adjacent to other motility/chemotaxis genes | KT2440-specific | 2010 | Navarro-Avilés & Van Dillewijn, DOI: https://doi.org/10.1111/j.1758-2229.2009.00084 | (pqac-00000003) |
| CheY in KT2440 functions as a **chemosensory response regulator** downstream of CheA | In a KT2440 protein-engineering study, CheY is described as “a chemosensory response regulator in chemotaxis,” activated by phosphorylation from the upstream histidine kinase **CheA (PP_4338)**; photocrosslinking/proteomics supported a **CheY–CheA** interaction | KT2440-specific | 2022 | He et al., *ACS Synthetic Biology*, DOI: https://doi.org/10.1021/acssynbio.2c00325 | (pqac-00000004) |
| Core biochemical role: CheA transfers phosphate to CheY | Chemotaxis review states **CheA phosphorylates CheY**; a *P. putida* biochemical study shows radiolabeled phosphate transfer from phosphorylated CheA to CheY | General chemotaxis mechanism with *Pseudomonas* support | 2015; 2025 | Sampedro et al., https://doi.org/10.1111/1574-6976.12081; He et al., https://doi.org/10.7554/elife.100914.2 | (pqac-00000001, pqac-00000002) |
| Canonical output of CheY is control of the **flagellar motor** | Review states CheY transmits the chemotaxis signal to flagellar motors; this is the accepted functional role used to annotate Pseudomonas CheY proteins by homology | General, applicable to KT2440 by homology | 2015 | Sampedro et al., *FEMS Microbiology Reviews*, https://doi.org/10.1111/1574-6976.12081 | (pqac-00000002) |
| CheY-P is normally reset by **CheZ** phosphatase in canonical systems | The review notes **CheY-P dephosphorylation is performed by CheZ**, defining the transient nature of signaling output in canonical chemotaxis pathways | General | 2015 | Sampedro et al., *FEMS Microbiology Reviews*, https://doi.org/10.1111/1574-6976.12081 | (pqac-00000002) |
| Recent structural work shows CheY-P promotes **CW switching** by binding the C-ring | Structural studies show phosphorylated CheY binds the flagellar switch/C-ring, especially **FliM**, stabilizing the **clockwise (CW)** state and biasing motor rotation away from default **counterclockwise (CCW)** rotation | General mechanism | 2024 | Johnson et al., *Nature Microbiology*, https://doi.org/10.1038/s41564-024-01630-z | (pqac-00000005, pqac-00000007) |
| CheY binding site/mechanism involves **FliM/FliN** and likely remodels FliG-related interfaces | Review-level synthesis states CheY-P binds **FliM and FliN** at the motor base to raise CW bias; structural work places the phosphorylated residue near the **FliG/FliM** interface and supports conformational stabilization of the CW state | General mechanism | 2024 | Antani et al., https://doi.org/10.1146/annurev-chembioeng-100722-114625; Johnson et al., https://doi.org/10.1038/s41564-024-01630-z | (pqac-00000005, pqac-00000006) |
| Conserved phosphorylation site is **Asp57** in model CheY proteins | A 2024 structural study explicitly models the phosphorylated residue **D57** of CheY toward the FliG/FliM interface; this supports inference that KT2440 CheY, a canonical receiver-domain regulator, uses the conserved receiver Asp mechanism | General, strong homology-based inference for KT2440 | 2024 | Johnson et al., *Nature Microbiology*, https://doi.org/10.1038/s41564-024-01630-z | (pqac-00000005) |
| Motor switching is highly cooperative and sensitive to CheY-P levels | Review notes the motor response to CheY-P is sigmoidal with Hill coefficient about **10–20**, meaning small signaling changes can strongly alter CW/CCW bias | General quantitative mechanism | 2024 | Antani et al., https://doi.org/10.1146/annurev-chembioeng-100722-114625 | (pqac-00000006) |
| Structural stoichiometry supports a dedicated CheY-associated CW motor state | Cryo-EM study reports a **CW C-ring** with stoichiometry **34 FliG / 34 FliM / 102 FliN / 34 CheY** compared with a CCW C-ring lacking the CheY subring, supporting direct structural coupling of CheY binding to motor switching | General quantitative mechanism | 2024 | Tan et al., *Cell Research*, https://doi.org/10.1101/2024.04.30.591856 | (pqac-00000008) |
| Cellular localization of CheY is expected to be **cytoplasmic/diffusible**, acting at the pole-localized motor | CheY is described as a diffusible response regulator that carries signal from CheA to the flagellar motor; recent structural/mechanistic work places its action at the cytoplasmic **C-ring** of the motor. Direct localization for **KT2440 PP_4340** was not found in the retrieved papers | General mechanism; KT2440-specific localization remains indirect | 2015; 2024 | Sampedro et al., https://doi.org/10.1111/1574-6976.12081; Johnson et al., https://doi.org/10.1038/s41564-024-01630-z | (pqac-00000002, pqac-00000007) |


*Table: This table summarizes the strongest evidence linking UniProt Q88EW2 to cheY/PP_4340 in *Pseudomonas putida* KT2440 and places that evidence in the context of current CheY mechanism from recent structural and review literature. It is useful for separating direct KT2440-specific evidence from broader, well-supported functional inference.*