DVU_3336 is a KdpD-like sensory protein located in the kdp locus of D. vulgaris Hildenborough, positioned between kdpD and the structural kdpFABC genes. The protein contains an N-terminal KdpD sensor domain (IPR003852) and a C-terminal UspA stress-response domain (IPR006016), along with a P-loop NTPase fold. Critically, the catalytic histidine kinase domains (HisKA and HATPase_c) required for phosphotransfer activity are located on the adjacent DVU3335 gene, not on DVU_3336. This protein likely functions as a sensory/adapter component that participates in osmotic and K+ stress sensing, feeding into the KdpD/KdpE two-component regulatory system that controls expression of the high-affinity K+ transporter KdpFABC. The UspA domain suggests involvement in stress sensing, while the P-loop NTPase domain may enable nucleotide binding for signal modulation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: KdpD-like proteins are typically membrane-associated sensors in the two-component KdpD/KdpE system. The N-terminal KdpD domain (IPR003852) described in UniProt as "Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal" is typically membrane-associated. However, DVU_3336 lacks predicted transmembrane helices in its UniProt entry, and the membrane association is inferred by analogy rather than direct evidence (Freeman 2013).
Reason: Plasma membrane localization is consistent with the role of KdpD-like sensors, which function at the membrane interface to sense osmotic/K+ changes. While direct localization evidence for DVU_3336 is lacking, the TreeGrafter annotation based on phylogenetic inference (PANTHER:PTN008137371) supports membrane association. The KdpD domain in canonical systems requires membrane proximity for signal integration (Freeman 2013).
Supporting Evidence:
DOI:10.1371/journal.ppat.1003201
KdpD is a membrane-associated sensor histidine kinase
|
|
GO:0000155
phosphorelay sensor kinase activity
|
IEA
GO_REF:0000120 |
REMOVE |
Summary: This annotation is problematic. While DVU_3336 contains a KdpD N-terminal sensor domain (IPR003852), it LACKS the catalytic histidine kinase domains (HisKA/HATPase_c) required for actual kinase activity. Domain analysis shows DVU_3336 has only the sensory portion (aa 13-218) and a UspA domain (aa 243-357). The adjacent DVU3335 contains the conserved histidine kinase catalytic domains. The IEA annotation was generated from InterPro:IPR003852 combined with PANTHER, but this represents an over-annotation - having a sensor domain associated with kinases does not confer kinase activity itself.
Reason: DVU_3336 lacks the conserved histidine kinase catalytic domains (HisKA containing the phosphorylatable His residue, and HATPase_c for ATP binding/hydrolysis). Domain architecture shows only the N-terminal KdpD sensor domain (Pfam PF02702, aa 13-218) and UspA domain (Pfam PF00582, aa 243-357). The actual histidine kinase domains are on adjacent DVU3335 in DvH. Assigning kinase activity based on a sensor domain that is often found fused with kinase domains (in other organisms) but is separate in this operon organization is an over-annotation.
Supporting Evidence:
DOI:10.1371/journal.ppat.1003201
KdpD is a sensor histidine kinase
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
In DvH, the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene
|
|
GO:0000160
phosphorelay signal transduction system
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: DVU_3336 is located within the kdp locus and contains domains consistent with participation in the KdpD/KdpE phosphorelay signal transduction system. While it does not possess catalytic kinase activity itself, the KdpD sensor domain and UspA stress-sensing domain suggest it participates in sensing environmental signals (K+ limitation, osmotic stress) that are transduced through this system.
Reason: Involvement in phosphorelay signal transduction is appropriate even for non-catalytic components. The protein's location in the kdp operon, its KdpD sensor domain, and UspA domain all indicate participation in sensing and signal relay within the KdpD/KdpE two-component system. The term describes involvement in the process, not necessarily catalytic function.
Supporting Evidence:
DOI:10.1371/journal.ppat.1003201
KdpD/KdpE is a TCS that senses low external K+, high osmolarity (e.g., high Na+), and related stresses to induce expression of the high-affinity K+ pump KdpFABC
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
DVU_3336 is located within the kdp locus of DvH. Operon maps in DvH position DVU_3336 between kdpD and the structural kdpFABC genes
|
|
GO:0004673
protein histidine kinase activity
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This annotation is incorrect. It was assigned via InterPro:IPR003852 mapping, but IPR003852 is "Signal transduction histidine kinase KdpD N-terminal" - a SENSOR domain, not a catalytic kinase domain. The InterPro-to-GO mapping conflates the sensor domain with kinase activity because in many organisms these domains are fused on a single protein. In DVU_3336, only the sensor domain is present; the catalytic domains are on the adjacent DVU3335.
Reason: DVU_3336 lacks the HisKA domain containing the conserved phosphorylatable histidine residue and lacks the HATPase_c domain required for ATP hydrolysis and phosphotransfer. The protein is 379 aa with domains at positions 13-218 (KdpD N-terminal sensor) and 243-357 (UspA). There is no sequence region corresponding to histidine kinase catalytic function. This is a clear case of over-annotation where a sensory domain associated with kinases was incorrectly annotated as having kinase activity.
Supporting Evidence:
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene
UniProt:Q725T9
Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: ARBA annotation for cytoplasm localization. KdpD-like sensors are membrane-associated but their cytoplasmic portions (including the UspA domain) extend into the cytoplasm. The UspA domain and P-loop NTPase region would be cytoplasmic. This is consistent with the dual annotation of plasma membrane and cytoplasm.
Reason: For membrane-associated signaling proteins, the cytoplasmic annotation captures the localization of the functional domains (KdpD sensor C-terminal region, UspA domain) that interact with cytoplasmic partners and nucleotides. The annotation is not contradictory with plasma membrane localization but rather complementary.
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Generic membrane annotation from InterPro:IPR003852 (KdpD N-terminal domain). This is consistent with the more specific plasma membrane annotation. KdpD-like proteins are membrane-associated sensors.
Reason: Membrane localization is consistent with KdpD-like sensors. While more specific than "plasma membrane" would be ideal, this general term is acceptable as a broader annotation alongside the more specific plasma membrane annotation. Both annotations capture the membrane association of this sensory protein.
|
|
GO:0016301
kinase activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: Annotation derived from UniProtKB keyword KW-0418 (Kinase). This keyword was likely assigned based on the protein name containing "histidine kinase domain" and the presence of KdpD-related domains. However, DVU_3336 lacks catalytic kinase domains - it has only sensory/regulatory domains.
Reason: DVU_3336 does not possess kinase activity. The "kinase" in the protein name refers to the type of signaling system (histidine kinase two-component system) it participates in, not its own enzymatic function. Domain analysis confirms absence of HisKA and HATPase_c catalytic domains. The P-loop NTPase fold present in the protein may bind ATP but does not confer kinase activity - it is a distinct nucleotide-binding fold found in many non-kinase proteins.
Supporting Evidence:
UniProt:Q725T9
Potassium channel histidine kinase domain protein/universal stress protein
|
|
GO:0016740
transferase activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: Annotation derived from UniProtKB keyword KW-0808 (Transferase). This is a parent term of kinase activity and was assigned for the same incorrect reason - the protein name and associated keywords suggest kinase function that the protein does not actually possess.
Reason: DVU_3336 is not a transferase. It lacks the catalytic domains required for phosphotransfer activity. This annotation cascades from the incorrect kinase-related keywords. The protein functions as a sensor/adapter in signal transduction, not as an enzyme catalyzing group transfer.
|
|
GO:0034220
monoatomic ion transmembrane transport
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: Annotation derived from UniProtKB keyword KW-0407 (Ion transport). This is incorrect - DVU_3336 is a sensor protein that participates in REGULATING ion transport (via the KdpD/KdpE system controlling KdpFABC), but it is NOT itself an ion transporter. The protein lacks transmembrane transporter domains. The "potassium channel" in the protein name refers to its role in sensing/ regulating potassium channel/transporter expression, not to being a channel itself.
Reason: DVU_3336 is NOT an ion transporter. It is a sensory protein that participates in the regulatory system controlling the high-affinity K+ transporter KdpFABC. The KdpFABC complex (encoded by separate genes) performs the actual ion transport. The keywords "Ion channel" and "Ion transport" in UniProt are misleading - they reflect the pathway context (kdp locus) rather than the protein's direct function. This is a clear over-annotation where regulatory components were annotated with the function they regulate.
Supporting Evidence:
DOI:10.1371/journal.ppat.1003201
KdpD/KdpE activates transcription of kdp genes... the high-affinity K+ pump KdpFABC
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
DVU_3336 likely participates in sensing and signaling that controls high-affinity K+ uptake via KdpFABC
|
|
GO:0005524
ATP binding
|
ISS
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md |
NEW |
Summary: DVU_3336 contains a P-loop NTPase domain (IPR027417) which is associated with nucleotide binding. This domain is distinct from the HATPase_c domain found in histidine kinases. The P-loop (Walker A motif) is a conserved nucleotide- binding element found in many ATP/GTP-binding proteins.
Reason: The presence of the P-loop NTPase domain (IPR027417) and Rossmann-like fold (IPR014729) strongly suggests ATP binding capability. This is a structural prediction based on conserved domain architecture. ATP binding by UspA-domain proteins and P-loop containing proteins is well documented. This annotation captures a likely molecular function that is not currently annotated.
Supporting Evidence:
UniProt:Q725T9
InterPro; IPR027417; P-loop_NTPase
|
|
GO:0006970
response to osmotic stress
|
ISS
file:DESVH/Q725T9/Q725T9-deep-research-falcon.md |
NEW |
Summary: The KdpD/KdpE system responds to osmotic stress and K+ limitation. DVU_3336 contains both a KdpD N-terminal sensor domain (osmosensitive K+ channel sensor) and a UspA domain. UspA domains are characteristic of universal stress proteins that respond to various stresses including osmotic stress.
Reason: The protein's domain architecture (osmosensitive KdpD sensor domain plus UspA stress domain) and operon context (kdp locus controlling K+ homeostasis under stress) strongly support involvement in osmotic stress response. The KdpD/KdpE system is a well-characterized osmotic stress response pathway, and DVU_3336 is positioned within this regulatory network.
Supporting Evidence:
DOI:10.1371/journal.ppat.1003201
KdpD/KdpE is a TCS that senses low external K+, high osmolarity (e.g., high Na+), and related stresses
UniProt:Q725T9
Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal
|
Q: What is the precise mechanism by which DVU_3336 and DVU3335 interact in D. vulgaris?
Q: Does DVU_3336 have any autonomous regulatory function, or does it strictly depend on DVU3335 for signal relay?
Q: What specific signals (K+ concentration, osmolarity) does the UspA domain of DVU_3336 sense?
Experiment: Deletion mutant of DVU_3336 to assess phenotype under K+ limitation and osmotic stress
Hypothesis: DVU_3336 deletion will impair osmotic stress response and K+ homeostasis
Experiment: Co-immunoprecipitation or bacterial two-hybrid to determine protein-protein interactions with DVU3335 and KdpE
Hypothesis: DVU_3336 physically interacts with DVU3335 to modulate histidine kinase activity
Experiment: ATP binding assays to confirm P-loop NTPase domain function
Hypothesis: The P-loop NTPase domain of DVU_3336 binds ATP
Experiment: Transcriptomic analysis of kdpFABC expression in DVU_3336 mutant background
Hypothesis: DVU_3336 is required for proper induction of kdpFABC under K+ limitation
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template_variables:
organism: DESVH
gene_id: Q725T9
gene_symbol: Q725T9
uniprot_accession: Q725T9
protein_description: 'SubName: Full=Potassium channel histidine kinase domain protein/universal
stress protein {ECO:0000313|EMBL:AAS97804.1};'
gene_info: OrderedLocusNames=DVU_3336 {ECO:0000313|EMBL:AAS97804.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Not specified in UniProt
protein_domains: Histidine_kinase_KdpD. (IPR052023); P-loop_NTPase. (IPR027417);
Rossmann-like_a/b/a_fold. (IPR014729); Sig_transdc_His_kinase_KdpD_N. (IPR003852);
UspA. (IPR006016)
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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 'Q725T9' 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 Q725T9 (gene ID: Q725T9, UniProt: Q725T9) in DESVH.
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 'Q725T9' 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 Q725T9 (gene ID: Q725T9, UniProt: Q725T9) in DESVH.
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.
Plan overview
We verified the identity and genomic context of DVU_3336 (UniProt Q725T9) in Desulfovibrio vulgaris Hildenborough (DvH), then searched for organism-specific and general evidence regarding KdpD/KdpE systems and UspA fusions. Evidence directly on DVU_3336 is sparse; most DvH-specific functional data in the Kdp region centers on the adjacent histidine kinase DVU3335. We therefore integrate (i) DvH genomic/operon context that places DVU_3336 within the kdp locus, (ii) annotations indicating UspA- and KdpD-like features on DVU_3336, and (iii) authoritative, mechanism-focused reviews of KdpD/KdpE that clarify functional expectations for KdpD-like proteins, while explicitly noting where inference (rather than DvH-specific experiment) is used.
Research report: DVU_3336 (Q725T9) in Desulfovibrio vulgaris Hildenborough
1) Key concepts and definitions with current understanding
- Identity and locus: DVU_3336 is located within the kdp locus of DvH. Operon maps in DvH position DVU_3336 between kdpD and the structural kdpFABC genes, indicating it is part of a K+ homeostasis region typically regulated by the KdpD/KdpE two-component system (TCS) (kdpD sensor histidine kinase and KdpE response regulator). This establishes strong genomic linkage of DVU_3336 to potassium transport and its regulation in DvH (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1).
- Domain-level expectation: An annotation block placing DVU_3336 within the kdp locus labels it as a “Potassium channel histidine kinase domain-containing protein/universal stress protein,” implying a KdpD-like architecture that often combines an N-terminal sensory region (frequently UspA-like) with the histidine kinase machinery somewhere in the kdp region. In DvH, the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene; DVU_3336’s annotation emphasizes the Usp-like/stress-sensing association within the operon context (zhou2017keymetabolitesand pages 13-14, mukhopadhyay2008vimssesppdecipheringb pages 1-1).
- KdpD/KdpE concept: Across bacteria, KdpD/KdpE is a TCS that senses low external K+, high osmolarity (e.g., high Na+), and related stresses to induce expression of the high-affinity K+ pump KdpFABC. KdpD is a membrane-associated sensor histidine kinase; KdpE is the response regulator that activates transcription of kdp genes. Accessory interactions (e.g., Usp-like domains and binding partners) modulate response to osmotic/K+ cues (Freeman 2013 PLoS Pathog, https://doi.org/10.1371/journal.ppat.1003201, published Mar 2013) (freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 3-4).
Interpretation for DVU_3336: DVU_3336 sits in the canonical kdp region in DvH and carries annotation consistent with a KdpD/UspA-associated sensor component. However, DvH-specific catalytic histidine kinase motifs are ascribed to DVU3335 in the same locus, suggesting DVU_3336 may function as a sensory/adapter element associated with KdpD-like regulation rather than being the catalytic kinase itself (mukhopadhyay2008vimssesppdecipheringb pages 1-1, zhou2017keymetabolitesand pages 13-14).
2) Recent developments and latest research (priority 2023–2024)
- Direct, recent (2023–2024) organism-specific experimental data for DVU_3336 were not recovered in the available evidence. Contemporary reviews continue to emphasize KdpD/KdpE as central to integrating K+ homeostasis with stress/virulence in diverse bacteria, with emphasis on multi-signal sensing and Usp-like modulators, but without DvH-specific updates for DVU_3336 in the retrieved materials (Freeman 2013 review remains a core reference) (freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 3-4).
- Conclusion: Literature specifically resolving DVU_3336 function in 2023–2024 appears limited in the collected sources. Where needed below, we explicitly separate inference from confirmed experimental findings.
3) Current applications and real-world implementations
- In general, Kdp systems allow bacteria to maintain intracellular K+ under limiting or high-osmolarity conditions, supporting growth and stress tolerance. In DvH, the presence of an intact kdp locus (including DVU_3336) implies a role in adaptation to saline/nutrient shifts typical of subsurface and industrial environments where sulfate-reducing bacteria persist. Operon mapping in DvH supports this linkage, although functional dissection in DvH assigns the catalytic kinase domains to DVU3335 (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1).
- Practical implication: Regulation of K+ uptake via the kdp locus is expected to contribute to DvH tolerance to osmotic stress and shifting ion conditions that occur in bioremediation, wastewater systems, and petroleum infrastructure; this is consistent with the generalized roles of KdpD/KdpE systems in bacterial stress physiology (freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 3-4).
4) Expert opinions and analysis from authoritative sources
- Mechanistic model: Authoritative review emphasizes that KdpD integrates multiple inputs—K+ limitation, osmotic stress, and metabolic/host cues—and via KdpE activates kdpFABC transcription. Usp-like domains or Usp-binding partners interface with KdpD to scaffold/stimulate the signaling complex under osmotic stress (Freeman 2013 PLoS Pathog, https://doi.org/10.1371/journal.ppat.1003201) (freeman2013thekdpdkdpetwocomponent pages 6-7). This provides a mechanistic rationale for proteins annotated as “histidine kinase domain-containing/universal stress protein” within kdp loci, as seen for DVU_3336 in DvH (zhou2017keymetabolitesand pages 13-14, mukhopadhyay2008vimssesppdecipheringb pages 1-1).
- DvH genomic context and mutant work: DvH studies map the kdp region and identify two sensor-linked genes in the operon: kdpD (with canonical K+/Na+ sensing motifs) and DVU3335 (containing conserved histidine kinase domains). Operon-focused mutagenesis and phenotyping targeted this locus, though explicit DVU_3336 functional assays were not shown in the excerpts; one downstream locus (DVU3335) was used for insertional mutation and phenotyping (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1, mukhopadhyay2008vimssesppdecipheringc pages 1-1).
5) Relevant statistics and data from recent studies (DvH-specific where available)
- Operon structure and gene counts: DvH encodes many two-component systems (>70 predicted), with the kdp locus including kdpD, DVU_3336, DVU3335, and kdpFABC genes in proximity. Figures and captions place DVU_3336 within this region, supporting its inclusion in the K+-homeostasis regulon context (mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1, mukhopadhyay2008vimssesppdecipheringb pages 1-1).
- Mutant phenotype (adjacent kinase DVU3335): Insertional disruption within the downstream histidine kinase domain-containing gene (DVU3335) was examined; under defined lactate–sulfate conditions, growth differences versus wild type were not detected and upstream kdp gene expression remained similar by mRNA measurements in that condition. While not directly about DVU_3336, this highlights experimental attention on the kdp sensor-kinase region and suggests condition-dependence of phenotypes (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringc pages 1-1).
Functional synthesis for DVU_3336 (Q725T9) with strength-of-evidence notes
- Protein identity and organism: DVU_3336 (Q725T9) from Desulfovibrio vulgaris Hildenborough; positioned in the kdp operon. Verified in DvH operon maps (strong evidence, DvH-specific) (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1).
- Domains and architecture: Annotation indicates a “Potassium channel histidine kinase domain-containing protein/universal stress protein,” consistent with KdpD-like/UspA-associated sensory components. In DvH, the adjacent DVU3335 contains the conserved HisKA/HATPase_c catalytic kinase domains, suggesting DVU_3336 may primarily act as a sensor/adapter module within the operon (moderate evidence: DvH annotation plus general KdpD architecture; limited direct DVU_3336 domain mapping in retrieved texts) (zhou2017keymetabolitesand pages 13-14, mukhopadhyay2008vimssesppdecipheringb pages 1-1).
- Cellular localization: By analogy to KdpD, sensor components are membrane-associated; however, the DVU_3336-specific cellular localization is not directly demonstrated in the retrieved DvH texts. This is an inference based on KdpD-like function and operon context (inference supported by KdpD reviews) (freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 3-4).
- Pathway role: Part of the kdp operon that regulates high-affinity K+ uptake via KdpFABC in response to low K+ and osmotic stress; KdpD/KdpE is the canonical regulatory system. DVU_3336 is positioned within this regulatory/structural neighborhood, implying participation in potassium homeostasis signaling. Direct DVU_3336–KdpE coupling is not experimentally shown in the retrieved DvH-specific excerpts (strong contextual inference; no direct DVU_3336 functional assay extracted) (mukhopadhyay2008vimssesppdecipheringb pages 1-1, zhou2017keymetabolitesand pages 13-14, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 3-4).
- Stress/osmotic regulation: General KdpD systems respond to low external K+, increased osmolarity, and related stresses, often involving Usp-like interactions. DvH kdp locus mapping and the DVU_3336 annotation (Usp-related) support a role in stress signaling, but DVU_3336-specific stress assays are not shown in the excerpts (general mechanism evidence; DvH-specific operon context) (zhou2017keymetabolitesand pages 13-14, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 3-4, mukhopadhyay2008vimssesppdecipheringb pages 1-1).
Critical verification and limitations
- The target gene/protein identity matches: DVU_3336 in DvH (Hildenborough strain) corresponds to UniProt Q725T9 and is annotated in the kdp locus as a potassium channel histidine kinase domain/universal stress protein—consistent with the user-provided UniProt context (supported by DvH operon maps and locus annotations) (mukhopadhyay2008vimssesppdecipheringb pages 1-1, zhou2017keymetabolitesand pages 13-14, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1).
- Ambiguity and literature limitation: The literature specific to DVU_3336 is limited in the retrieved sources; more detailed experimental work in DvH centers on the adjacent kinase DVU3335. Therefore, aspects of DVU_3336’s precise biochemical activity, membrane topology, and direct regulatory partners in DvH are inferred from KdpD/KdpE paradigm and genomic context rather than demonstrated with DVU_3336-specific assays in these texts (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringc pages 1-1, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 6-7).
Recommendations for future clarification
- Targeted genetics/phenotyping of DVU_3336 (e.g., deletion or domain truncation) under low-K+ and osmotic upshift, combined with kdpFABC transcriptional reporters, could directly test DVU_3336’s role in Kdp signaling.
- Proteomics of membrane fractions and crosslinking/immunoprecipitation to determine DVU_3336 interactions with DVU3335 (kinase) and the response regulator would refine placement within the signaling cascade.
Key sources and availability
- Freeman ZN, Dorus S, Waterfield NR. The KdpD/KdpE Two-Component System: Integrating K+ Homeostasis and Virulence. PLoS Pathog. 2013;9(3):e1003201. URL: https://doi.org/10.1371/journal.ppat.1003201 (published Mar 2013) (freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 3-4).
- DvH kdp operon mapping and locus context including DVU_3336 and DVU3335: multiple excerpts presenting gene order and sensor-kinase assignments (2008) (mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1).
- DvH annotation block placing DVU_3336 as potassium channel histidine kinase domain/universal stress protein adjacent to kdpFABC (2017) (zhou2017keymetabolitesand pages 13-14).
Conclusion
DVU_3336 (Q725T9) in DvH is embedded in the kdp operon and annotated as a potassium channel histidine kinase domain-containing/universal stress protein, consistent with a KdpD/UspA-associated sensory role. The conserved catalytic histidine kinase domains in this locus are attributed to the adjacent DVU3335 gene in DvH. By analogy to KdpD/KdpE systems, DVU_3336 likely participates in sensing and signaling that controls high-affinity K+ uptake via KdpFABC under low-K+ and osmotic stress conditions, but DVU_3336-specific mechanistic and localization data remain to be demonstrated directly in DvH in the retrieved sources (zhou2017keymetabolitesand pages 13-14, mukhopadhyay2008vimssesppdecipheringb pages 1-1, mukhopadhyay2008vimssesppdeciphering pages 1-1, mukhopadhyay2008vimssesppdecipheringa pages 1-1, freeman2013thekdpdkdpetwocomponent pages 7-8, freeman2013thekdpdkdpetwocomponent pages 6-7, freeman2013thekdpdkdpetwocomponent pages 3-4).
References
(mukhopadhyay2008vimssesppdecipheringb pages 1-1): A Mukhopadhyay. Vimss espp: deciphering the roles of two-component systems in desulfovibrio vulgaris hildenborough. Unknown journal, 2008.
(mukhopadhyay2008vimssesppdeciphering pages 1-1): A Mukhopadhyay. Vimss espp: deciphering the roles of two-component systems in desulfovibrio vulgaris hildenborough. Unknown journal, 2008.
(mukhopadhyay2008vimssesppdecipheringa pages 1-1): A Mukhopadhyay. Vimss espp: deciphering the roles of two-component systems in desulfovibrio vulgaris hildenborough. Unknown journal, 2008.
(zhou2017keymetabolitesand pages 13-14): A Zhou, R Lau, R Baran, J Ma, F Von Netzer, and W Shi. Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium desulfovibrio vulgaris. mbio 8: e01780-17. Unknown journal, 2017.
(freeman2013thekdpdkdpetwocomponent pages 6-7): Zoë N. Freeman, Steve Dorus, and Nicholas R. Waterfield. The kdpd/kdpe two-component system: integrating k+ homeostasis and virulence. PLoS Pathogens, 9:e1003201, Mar 2013. URL: https://doi.org/10.1371/journal.ppat.1003201, doi:10.1371/journal.ppat.1003201. This article has 200 citations and is from a highest quality peer-reviewed journal.
(freeman2013thekdpdkdpetwocomponent pages 7-8): Zoë N. Freeman, Steve Dorus, and Nicholas R. Waterfield. The kdpd/kdpe two-component system: integrating k+ homeostasis and virulence. PLoS Pathogens, 9:e1003201, Mar 2013. URL: https://doi.org/10.1371/journal.ppat.1003201, doi:10.1371/journal.ppat.1003201. This article has 200 citations and is from a highest quality peer-reviewed journal.
(freeman2013thekdpdkdpetwocomponent pages 3-4): Zoë N. Freeman, Steve Dorus, and Nicholas R. Waterfield. The kdpd/kdpe two-component system: integrating k+ homeostasis and virulence. PLoS Pathogens, 9:e1003201, Mar 2013. URL: https://doi.org/10.1371/journal.ppat.1003201, doi:10.1371/journal.ppat.1003201. This article has 200 citations and is from a highest quality peer-reviewed journal.
(mukhopadhyay2008vimssesppdecipheringc pages 1-1): A Mukhopadhyay. Vimss espp: deciphering the roles of two-component systems in desulfovibrio vulgaris hildenborough. Unknown journal, 2008.
id: Q725T9
gene_symbol: DVU_3336
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris Hildenborough
description: >-
DVU_3336 is a KdpD-like sensory protein located in the kdp locus of D. vulgaris Hildenborough,
positioned between kdpD and the structural kdpFABC genes. The protein contains an N-terminal
KdpD sensor domain (IPR003852) and a C-terminal UspA stress-response domain (IPR006016),
along with a P-loop NTPase fold. Critically, the catalytic histidine kinase domains (HisKA
and HATPase_c) required for phosphotransfer activity are located on the adjacent DVU3335
gene, not on DVU_3336. This protein likely functions as a sensory/adapter component that
participates in osmotic and K+ stress sensing, feeding into the KdpD/KdpE two-component
regulatory system that controls expression of the high-affinity K+ transporter KdpFABC.
The UspA domain suggests involvement in stress sensing, while the P-loop NTPase domain
may enable nucleotide binding for signal modulation.
existing_annotations:
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: >-
KdpD-like proteins are typically membrane-associated sensors in the two-component
KdpD/KdpE system. The N-terminal KdpD domain (IPR003852) described in UniProt as
"Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal"
is typically membrane-associated. However, DVU_3336 lacks predicted transmembrane
helices in its UniProt entry, and the membrane association is inferred by analogy
rather than direct evidence (Freeman 2013).
action: ACCEPT
reason: >-
Plasma membrane localization is consistent with the role of KdpD-like sensors,
which function at the membrane interface to sense osmotic/K+ changes. While direct
localization evidence for DVU_3336 is lacking, the TreeGrafter annotation based
on phylogenetic inference (PANTHER:PTN008137371) supports membrane association.
The KdpD domain in canonical systems requires membrane proximity for signal
integration (Freeman 2013).
supported_by:
- reference_id: DOI:10.1371/journal.ppat.1003201
supporting_text: "KdpD is a membrane-associated sensor histidine kinase"
- term:
id: GO:0000155
label: phosphorelay sensor kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This annotation is problematic. While DVU_3336 contains a KdpD N-terminal sensor
domain (IPR003852), it LACKS the catalytic histidine kinase domains (HisKA/HATPase_c)
required for actual kinase activity. Domain analysis shows DVU_3336 has only the
sensory portion (aa 13-218) and a UspA domain (aa 243-357). The adjacent DVU3335
contains the conserved histidine kinase catalytic domains. The IEA annotation
was generated from InterPro:IPR003852 combined with PANTHER, but this represents
an over-annotation - having a sensor domain associated with kinases does not
confer kinase activity itself.
action: REMOVE
reason: >-
DVU_3336 lacks the conserved histidine kinase catalytic domains (HisKA containing
the phosphorylatable His residue, and HATPase_c for ATP binding/hydrolysis).
Domain architecture shows only the N-terminal KdpD sensor domain (Pfam PF02702,
aa 13-218) and UspA domain (Pfam PF00582, aa 243-357). The actual histidine
kinase domains are on adjacent DVU3335 in DvH. Assigning kinase activity based
on a sensor domain that is often found fused with kinase domains (in other
organisms) but is separate in this operon organization is an over-annotation.
supported_by:
- reference_id: DOI:10.1371/journal.ppat.1003201
supporting_text: "KdpD is a sensor histidine kinase"
- reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
supporting_text: "In DvH, the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene"
- term:
id: GO:0000160
label: phosphorelay signal transduction system
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
DVU_3336 is located within the kdp locus and contains domains consistent with
participation in the KdpD/KdpE phosphorelay signal transduction system. While
it does not possess catalytic kinase activity itself, the KdpD sensor domain
and UspA stress-sensing domain suggest it participates in sensing environmental
signals (K+ limitation, osmotic stress) that are transduced through this system.
action: ACCEPT
reason: >-
Involvement in phosphorelay signal transduction is appropriate even for non-catalytic
components. The protein's location in the kdp operon, its KdpD sensor domain, and
UspA domain all indicate participation in sensing and signal relay within the
KdpD/KdpE two-component system. The term describes involvement in the process,
not necessarily catalytic function.
supported_by:
- reference_id: DOI:10.1371/journal.ppat.1003201
supporting_text: "KdpD/KdpE is a TCS that senses low external K+, high osmolarity (e.g., high Na+), and related stresses to induce expression of the high-affinity K+ pump KdpFABC"
- reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
supporting_text: "DVU_3336 is located within the kdp locus of DvH. Operon maps in DvH position DVU_3336 between kdpD and the structural kdpFABC genes"
- term:
id: GO:0004673
label: protein histidine kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation is incorrect. It was assigned via InterPro:IPR003852 mapping,
but IPR003852 is "Signal transduction histidine kinase KdpD N-terminal" - a
SENSOR domain, not a catalytic kinase domain. The InterPro-to-GO mapping
conflates the sensor domain with kinase activity because in many organisms
these domains are fused on a single protein. In DVU_3336, only the sensor
domain is present; the catalytic domains are on the adjacent DVU3335.
action: REMOVE
reason: >-
DVU_3336 lacks the HisKA domain containing the conserved phosphorylatable
histidine residue and lacks the HATPase_c domain required for ATP hydrolysis
and phosphotransfer. The protein is 379 aa with domains at positions 13-218
(KdpD N-terminal sensor) and 243-357 (UspA). There is no sequence region
corresponding to histidine kinase catalytic function. This is a clear case
of over-annotation where a sensory domain associated with kinases was
incorrectly annotated as having kinase activity.
supported_by:
- reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
supporting_text: "the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene"
- reference_id: UniProt:Q725T9
supporting_text: "Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
ARBA annotation for cytoplasm localization. KdpD-like sensors are membrane-associated
but their cytoplasmic portions (including the UspA domain) extend into the cytoplasm.
The UspA domain and P-loop NTPase region would be cytoplasmic. This is consistent
with the dual annotation of plasma membrane and cytoplasm.
action: ACCEPT
reason: >-
For membrane-associated signaling proteins, the cytoplasmic annotation captures
the localization of the functional domains (KdpD sensor C-terminal region, UspA
domain) that interact with cytoplasmic partners and nucleotides. The annotation
is not contradictory with plasma membrane localization but rather complementary.
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Generic membrane annotation from InterPro:IPR003852 (KdpD N-terminal domain).
This is consistent with the more specific plasma membrane annotation. KdpD-like
proteins are membrane-associated sensors.
action: ACCEPT
reason: >-
Membrane localization is consistent with KdpD-like sensors. While more specific
than "plasma membrane" would be ideal, this general term is acceptable as a
broader annotation alongside the more specific plasma membrane annotation.
Both annotations capture the membrane association of this sensory protein.
- term:
id: GO:0016301
label: kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
Annotation derived from UniProtKB keyword KW-0418 (Kinase). This keyword was
likely assigned based on the protein name containing "histidine kinase domain"
and the presence of KdpD-related domains. However, DVU_3336 lacks catalytic
kinase domains - it has only sensory/regulatory domains.
action: REMOVE
reason: >-
DVU_3336 does not possess kinase activity. The "kinase" in the protein name
refers to the type of signaling system (histidine kinase two-component system)
it participates in, not its own enzymatic function. Domain analysis confirms
absence of HisKA and HATPase_c catalytic domains. The P-loop NTPase fold
present in the protein may bind ATP but does not confer kinase activity -
it is a distinct nucleotide-binding fold found in many non-kinase proteins.
supported_by:
- reference_id: UniProt:Q725T9
supporting_text: "Potassium channel histidine kinase domain protein/universal stress protein"
- term:
id: GO:0016740
label: transferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
Annotation derived from UniProtKB keyword KW-0808 (Transferase). This is a
parent term of kinase activity and was assigned for the same incorrect reason -
the protein name and associated keywords suggest kinase function that the
protein does not actually possess.
action: REMOVE
reason: >-
DVU_3336 is not a transferase. It lacks the catalytic domains required for
phosphotransfer activity. This annotation cascades from the incorrect
kinase-related keywords. The protein functions as a sensor/adapter in
signal transduction, not as an enzyme catalyzing group transfer.
- term:
id: GO:0034220
label: monoatomic ion transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
Annotation derived from UniProtKB keyword KW-0407 (Ion transport). This is
incorrect - DVU_3336 is a sensor protein that participates in REGULATING
ion transport (via the KdpD/KdpE system controlling KdpFABC), but it is NOT
itself an ion transporter. The protein lacks transmembrane transporter domains.
The "potassium channel" in the protein name refers to its role in sensing/
regulating potassium channel/transporter expression, not to being a channel
itself.
action: REMOVE
reason: >-
DVU_3336 is NOT an ion transporter. It is a sensory protein that participates
in the regulatory system controlling the high-affinity K+ transporter KdpFABC.
The KdpFABC complex (encoded by separate genes) performs the actual ion
transport. The keywords "Ion channel" and "Ion transport" in UniProt are
misleading - they reflect the pathway context (kdp locus) rather than the
protein's direct function. This is a clear over-annotation where regulatory
components were annotated with the function they regulate.
supported_by:
- reference_id: DOI:10.1371/journal.ppat.1003201
supporting_text: "KdpD/KdpE activates transcription of kdp genes... the high-affinity K+ pump KdpFABC"
- reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
supporting_text: "DVU_3336 likely participates in sensing and signaling that controls high-affinity K+ uptake via KdpFABC"
- term:
id: GO:0005524
label: ATP binding
evidence_type: ISS
original_reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
review:
summary: >-
DVU_3336 contains a P-loop NTPase domain (IPR027417) which is associated with
nucleotide binding. This domain is distinct from the HATPase_c domain found
in histidine kinases. The P-loop (Walker A motif) is a conserved nucleotide-
binding element found in many ATP/GTP-binding proteins.
action: NEW
reason: >-
The presence of the P-loop NTPase domain (IPR027417) and Rossmann-like fold
(IPR014729) strongly suggests ATP binding capability. This is a structural
prediction based on conserved domain architecture. ATP binding by UspA-domain
proteins and P-loop containing proteins is well documented. This annotation
captures a likely molecular function that is not currently annotated.
supported_by:
- reference_id: UniProt:Q725T9
supporting_text: "InterPro; IPR027417; P-loop_NTPase"
- term:
id: GO:0006970
label: response to osmotic stress
evidence_type: ISS
original_reference_id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
review:
summary: >-
The KdpD/KdpE system responds to osmotic stress and K+ limitation. DVU_3336
contains both a KdpD N-terminal sensor domain (osmosensitive K+ channel sensor)
and a UspA domain. UspA domains are characteristic of universal stress proteins
that respond to various stresses including osmotic stress.
action: NEW
reason: >-
The protein's domain architecture (osmosensitive KdpD sensor domain plus UspA
stress domain) and operon context (kdp locus controlling K+ homeostasis under
stress) strongly support involvement in osmotic stress response. The KdpD/KdpE
system is a well-characterized osmotic stress response pathway, and DVU_3336
is positioned within this regulatory network.
supported_by:
- reference_id: DOI:10.1371/journal.ppat.1003201
supporting_text: "KdpD/KdpE is a TCS that senses low external K+, high osmolarity (e.g., high Na+), and related stresses"
- reference_id: UniProt:Q725T9
supporting_text: "Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings:
- statement: Several annotations derived from IPR003852 (KdpD N-terminal sensor domain) incorrectly assign kinase activity to a sensory domain
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: Keywords "Kinase", "Transferase", and "Ion transport" led to over-annotations
- statement: The protein name containing "histidine kinase domain" was incorrectly interpreted as the protein having kinase activity
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings:
- statement: Cytoplasm annotation is appropriate for the cytoplasmic portions of this membrane-associated protein
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings:
- statement: Plasma membrane annotation is phylogenetically supported
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings:
- statement: Phosphorelay signal transduction system annotation is appropriate
- statement: Phosphorelay sensor kinase activity annotation is incorrect due to lack of catalytic domains
- id: DOI:10.1371/journal.ppat.1003201
title: "The KdpD/KdpE Two-Component System: Integrating K+ Homeostasis and Virulence"
findings:
- statement: Authoritative review of KdpD/KdpE function and mechanism
- statement: Clarifies that KdpD is the membrane sensor and KdpE is the response regulator
- statement: KdpD integrates multiple signals including K+ limitation and osmotic stress
- id: PMID:15077118
title: "The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough"
findings: []
- id: file:DESVH/Q725T9/Q725T9-deep-research-falcon.md
title: Deep research report on DVU_3336 (Q725T9) function
findings:
- statement: DVU_3336 is located within the kdp locus of DvH between kdpD and the structural kdpFABC genes
supporting_text: "DVU_3336 is located within the kdp locus of DvH. Operon maps in DvH position DVU_3336 between kdpD and the structural kdpFABC genes"
- statement: The conserved histidine kinase catalytic domains are on the adjacent DVU3335 gene, not DVU_3336
supporting_text: "In DvH, the conserved histidine kinase catalytic domains are explicitly assigned to the adjacent DVU3335 gene"
- id: UniProt:Q725T9
title: UniProt entry for Q725T9 (DVU_3336)
findings:
- statement: DVU_3336 contains KdpD N-terminal sensor domain and UspA domain
supporting_text: "Signal transduction histidine kinase osmosensitive K+ channel sensor N-terminal"
core_functions:
- description: >-
DVU_3336 participates in the KdpD/KdpE phosphorelay system as a sensory/adapter
component. It contains domains for environmental sensing (KdpD N-terminal sensor,
UspA) but relies on the adjacent DVU3335 for actual histidine kinase catalytic activity.
molecular_function:
id: GO:0005524
label: ATP binding
directly_involved_in:
- id: GO:0000160
label: phosphorelay signal transduction system
- id: GO:0006970
label: response to osmotic stress
locations:
- id: GO:0005886
label: plasma membrane
suggested_questions:
- question: What is the precise mechanism by which DVU_3336 and DVU3335 interact in D. vulgaris?
- question: Does DVU_3336 have any autonomous regulatory function, or does it strictly depend on DVU3335 for signal relay?
- question: What specific signals (K+ concentration, osmolarity) does the UspA domain of DVU_3336 sense?
suggested_experiments:
- description: Deletion mutant of DVU_3336 to assess phenotype under K+ limitation and osmotic stress
hypothesis: DVU_3336 deletion will impair osmotic stress response and K+ homeostasis
- description: Co-immunoprecipitation or bacterial two-hybrid to determine protein-protein interactions with DVU3335 and KdpE
hypothesis: DVU_3336 physically interacts with DVU3335 to modulate histidine kinase activity
- description: ATP binding assays to confirm P-loop NTPase domain function
hypothesis: The P-loop NTPase domain of DVU_3336 binds ATP
- description: Transcriptomic analysis of kdpFABC expression in DVU_3336 mutant background
hypothesis: DVU_3336 is required for proper induction of kdpFABC under K+ limitation