PA3271 (mxtR) encodes MxtR, an orphan hybrid sensor histidine kinase of the inner membrane. The protein has an N-terminal domain of 13 transmembrane helices belonging to the sodium:solute symporter (SSF, SLC5) family, then a PAS-like domain, a HisKA dimerisation/phosphoacceptor domain (His808), an HATPase_c catalytic domain and a C-terminal receiver domain (Asp1090). It has no histidine phosphotransfer (HPt) domain. MxtR autophosphorylates in vitro, and ubiquinone inhibits the autophosphorylation, which suggests that it senses the respiratory or redox state. Loss of mxtR induces the LysR-type regulator MexT and its MexEF-OprN efflux pump. This delays expression of the 2-alkyl-4-quinolone (AQ) biosynthetic genes and of AQ-dependent virulence factors, so MxtR links environmental sensing to quorum-sensing signal production.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000155 phosphorelay sensor kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Sensor kinase activity by IBA from PTN001976860, seeded by M. tuberculosis SenX3, P. aeruginosa RpfC (PA1611) and MxtR itself. Reason: Agrees with the in vitro autophosphorylation of MxtR and its intact HisKA/HATPase architecture. SenX3 is an experimentally characterised sensor kinase, so the node does not rest on MxtR. MxtR among the sources reflects its own IDA. Supporting Evidence: PMID:22168309 Furthermore, we demonstrated that autophosphorylation of MxtR was inhibited by ubiquinone, the central electron carrier of respiration in in vitro experiments. |
| GO:0000155 phosphorelay sensor kinase activity | IDA PMID:22168309 An orphan sensor kinase controls quinolone signal production... | ACCEPT | Summary: PseudoCAP IDA, one of three seeds of the PTN001976860 IBD. The abstract states that MxtR autophosphorylation was measured in vitro and was inhibited by ubiquinone. Reason: The abstract positively reports an in vitro autophosphorylation assay, which is direct evidence of histidine kinase activity. Modulation by ubiquinone fits the sensor part of the definition. Phosphotransfer to a response regulator is not described in the abstract (full text not available), so the receiver-coupled part is inferred from the domain architecture. The seed is sound. Supporting Evidence: PMID:22168309 Furthermore, we demonstrated that autophosphorylation of MxtR was inhibited by ubiquinone, the central electron carrier of respiration in in vitro experiments. |
| GO:0000155 phosphorelay sensor kinase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Sensor kinase from the InterPro HisKA mapping; consistent. Reason: Same claim as the IDA and IBA rows. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt Pfam; PF00512; HisKA; 1. |
| GO:0000160 phosphorelay signal transduction system | IBA GO_REF:0000033 | ACCEPT | Summary: Phosphorelay signal transduction by IBA; consistent. Reason: MxtR is a hybrid HisKA-HATPase-REC kinase whose loss reprograms MexT expression, so it signals by phosphorelay. Supporting Evidence: PMID:22168309 In this study, we show that AQ production is modulated by an orphan P. aeruginosa sensor kinase. |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: Phosphorelay signal transduction from the receiver-domain mapping. Reason: Same claim as the IBA and ISS rows. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt Pfam; PF00072; Response_reg; 1. |
| GO:0000160 phosphorelay signal transduction system | ISS PMID:22168309 An orphan sensor kinase controls quinolone signal production... | ACCEPT | Summary: PseudoCAP ISS (with E. coli ArcB) for phosphorelay signal transduction. Reason: The similarity to the hybrid sensor kinase ArcB is sound, and the paper characterises MxtR as a sensor kinase. Supporting Evidence: PMID:22168309 In this study, we show that AQ production is modulated by an orphan P. aeruginosa sensor kinase. |
| GO:0004673 protein histidine kinase activity | IEA GO_REF:0000120 | TOO GENERAL | Summary: Protein histidine kinase activity from EC 2.7.13.3. Reason: Entailed by the accepted GO:0000155 phosphorelay sensor kinase activity (is_a GO:0004673). |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma membrane by IBA; consistent with the 13-helix N-terminal domain. Reason: Thirteen predicted TM helices plus cytoplasmic kinase and receiver domains place MxtR in the inner membrane. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt TRANSMEM 6..27 |
| GO:0007165 signal transduction | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic signal transduction. Reason: Entailed by the accepted phosphorelay signal transduction system. |
| GO:0009927 histidine phosphotransfer kinase activity | IBA GO_REF:0000033 | REMOVE | Summary: Histidine phosphotransfer (HPt) activity by IBA from PTN001976860, seeded by E. coli RcsD and yeast S000001409. MxtR has no HPt domain. Reason: GO:0009927 describes the phospho-His intermediate (HPt) that shuttles phosphate from a hybrid kinase's receiver to a response regulator. RcsD carries such a domain. MxtR's domain content (InterPro, Pfam, SMART: SSF, PAS, HisKA, HATPase_c, REC) has no HPt module, so it cannot be its own phosphotransfer intermediate and must pass phosphate to an unidentified HPt or regulator. The node term does not suit the HPt-less members of the clade. The node-level GO_CENTRAL defect for this IBD is recorded once, on PA1611 (genes/PSEAE/PA1611), which receives the same IBA and also lacks an HPt domain. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN001976860 · PTN001976860 SUPPORTS SOURCE BUT NOT TARGET Hybrid-kinase node; HPt activity belongs to members with an HPt domain (RcsD), not to HPt-less hybrids such as MxtR. UniProtKB:P39838 · E. coli RcsD SUPPORTS SOURCE BUT NOT TARGET RcsD has an HPt domain; MxtR does not. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt SMART; SM00448; REC; 1. |
| GO:0016020 membrane | IEA GO_REF:0000120 | TOO GENERAL | Summary: Generic membrane. Reason: Entailed by the accepted plasma membrane row (GO:0005886 is_a GO:0016020). |
| GO:0016301 kinase activity | IEA GO_REF:0000104 | TOO GENERAL | Summary: Generic kinase activity. Reason: Entailed by the accepted phosphorelay sensor kinase activity. |
| GO:0016740 transferase activity | IEA GO_REF:0000104 | TOO GENERAL | Summary: Generic transferase activity. Reason: Entailed by the accepted phosphorelay sensor kinase activity. |
| GO:0016772 transferase activity, transferring phosphorus-containing groups | IEA GO_REF:0000002 | TOO GENERAL | Summary: Transferase activity, transferring phosphorus-containing groups. Reason: Entailed by the accepted phosphorelay sensor kinase activity. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Transporter activity mapped from the N-terminal sodium:solute symporter (SSF) domain. Reason: The SSF-family membrane domain is real, but MxtR has no known transported substrate. In this sensor kinase the domain may sense rather than transport. A transporter activity inferred only from the family signature overstates what is known. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt InterPro; IPR001734; Na/solute_symporter. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Transmembrane transport from the SSF domain mapping. Reason: Same basis as the transporter activity row; no transport by MxtR has been shown. Supporting Evidence: file:PSEAE/PA3271/PA3271-uniprot.txt InterPro; IPR001734; Na/solute_symporter. |
| GO:1900376 regulation of secondary metabolite biosynthetic process | IMP PMID:22168309 An orphan sensor kinase controls quinolone signal production... | KEEP AS NON CORE | Summary: Regulation of secondary metabolite (AQ) biosynthesis. The mxtR mutant overexpresses MexT/MexEF-OprN, which delays AQ biosynthetic gene expression. Reason: A regulation term from mutant evidence is appropriate. The effect is indirect (through MexT and efflux), so it is downstream of the core signalling function. Supporting Evidence: PMID:22168309 Thereby, overexpression of the MexT-regulated MexEF-OprN efflux pump led to a delayed expression of the AQ biosynthetic genes and of AQ-dependent virulence factors. |
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Download this section (compressed HTML)Q: Which HPt protein and response regulator receive phosphate from MxtR, given that it lacks an HPt domain and is an orphan kinase?
Q: Does the N-terminal SSF (SLC5) domain of MxtR transport a solute, or does it serve only as a sensory module?
Experiment: Test in vitro phosphotransfer from MxtR to candidate HPt proteins and response regulators, and assay transport by the isolated SSF domain in proteoliposomes.
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