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gene_info: OrderedLocusNames=DVU_2291 {ECO:0000313|EMBL:AAS96764.1};
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protein_domains: ComplexI_49kDa-like. (IPR052197); NADH_Q_OxRdtase_suD. (IPR001135);
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: Q729Q8
• Protein Description: SubName: Full=Carbon monoxide-induced hydrogenase CooH, putative {ECO:0000313|EMBL:AAS96764.1};
• Gene Information: OrderedLocusNames=DVU_2291 {ECO:0000313|EMBL:AAS96764.1};
• 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
• Key Domains: ComplexI_49kDa-like. (IPR052197); NADH_Q_OxRdtase_suD. (IPR001135); Ni-dep_hyd_lsu. (IPR001501); NiFe-Hase_large. (IPR029014); Complex1_49kDa (PF00346)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "Q729Q8" matches the protein description above
2. Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'Q729Q8' 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

Research Target:

Please provide a comprehensive research report on the gene Q729Q8 (gene ID: Q729Q8, UniProt: Q729Q8) 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.

Output

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.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: Q729Q8
• Protein Description: SubName: Full=Carbon monoxide-induced hydrogenase CooH, putative {ECO:0000313|EMBL:AAS96764.1};
• Gene Information: OrderedLocusNames=DVU_2291 {ECO:0000313|EMBL:AAS96764.1};
• 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
• Key Domains: ComplexI_49kDa-like. (IPR052197); NADH_Q_OxRdtase_suD. (IPR001135); Ni-dep_hyd_lsu. (IPR001501); NiFe-Hase_large. (IPR029014); Complex1_49kDa (PF00346)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "Q729Q8" matches the protein description above
2. Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'Q729Q8' 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

Research Target:

Please provide a comprehensive research report on the gene Q729Q8 (gene ID: Q729Q8, UniProt: Q729Q8) 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.

Research plan status
- Objective 1 (identity verification): Completed. Q729Q8 maps to DVU_2291 (CooH) in Desulfovibrio vulgaris Hildenborough, with domains consistent with [NiFe]-hydrogenase large subunits (ComplexI_49kDa-like). (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15)
- Objectives 2–6 (evidence gathering and synthesis): Completed based on cited sources. (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15, sokolova2024exploitinghydrogenasesfor pages 1-2)
- Objective 7 (final report): Provided below.

Comprehensive research report: DVU_2291 (UniProt Q729Q8) — CooH in Desulfovibrio vulgaris Hildenborough

Key concepts and definitions
- Identity and organism: DVU_2291 encodes the large subunit (CooH) of a carbon monoxide-induced [NiFe]-hydrogenase in Desulfovibrio vulgaris Hildenborough (also referenced as Nitratidesulfovibrio/Desulfovibrio vulgaris). This assignment is supported by protein–protein interactomics and operon-context analyses in D. vulgaris Hildenborough. URL: https://doi.org/10.1371/journal.pone.0021470 (published Jun 30, 2011) (chhabra2011towardsarigorous pages 8-9).
- Protein family and domains: Bioinformatic annotations place DVU_2291 in the [NiFe]-hydrogenase large-subunit family (NiFe-Hase_large/Ni-dep_hyd_lsu) with a ComplexI_49kDa-like fold characteristic of group 4 (energy-converting) [NiFe]-hydrogenases, which typically form multi-subunit membrane-associated complexes. URL: https://doi.org/10.3389/fmicb.2011.00069 (published Mar 30, 2011) (pereira2011acomparativegenomic pages 14-15).

Operon architecture, regulation, and localization
- Operon context: In D. vulgaris Hildenborough, the Coo-type hydrogenase locus is organized as cooMKLXUH, encoding a membrane-linked, cytoplasmically oriented hydrogenase, while the carbon monoxide dehydrogenase (CODH) locus is in a separate region (cooFSCTJ). The arrangement suggests functional coupling between CODH (CooS) and the Coo hydrogenase, but with distinct operons; transcriptional control appears to involve the CO-sensing regulator CooA. URL: https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9).
- Subcellular localization: CooH (DVU_2291) is part of a membrane-bound complex oriented toward the cytoplasm, consistent with energy-conserving group 4 [NiFe]-hydrogenases. Such membrane association enables coupling of H2 interconversion to electron transport/ion translocation. URL: https://doi.org/10.1371/journal.pone.0021470 (2011); URL: https://doi.org/10.3389/fmicb.2011.00069 (2011) (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15).

Catalytic activity, cofactors, and maturation (current understanding)
- Catalytic role: As a [NiFe]-hydrogenase large subunit, CooH houses the heterobimetallic Ni–Fe active site that catalyzes the reversible interconversion between H2 and protons/electrons. In the context of CO metabolism, CooH is proposed to receive low-potential electrons generated by CODH (CooS) oxidation of CO, using them to produce H2 (i.e., CO oxidation linked to H2 evolution) or to feed electrons into respiratory modules, depending on physiological conditions. URL: https://doi.org/10.1371/journal.pone.0021470 (2011); URL: https://doi.org/10.3389/fmicb.2011.00069 (2011) (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15).
- Active-site chemistry: Contemporary reviews emphasize that [NiFe]-hydrogenases share a conserved Ni–Fe(CN)2CO cofactor coordinated by cysteine residues, with outer-sphere protein environment tuning oxygen tolerance, catalytic bias (oxidation vs evolution), and reversibility. While these reviews are not DVU_2291-specific, they define the mechanistic framework applicable to CooH. URL: https://doi.org/10.1039/d4sc00691g (published Mar 22, 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2).

Interactions and protein partnerships
- Interacting subunits and partners: Affinity pulldown experiments in D. vulgaris Hildenborough identified co-purification of CooU with CooH under the conditions tested, supporting assembly of at least part of the CooMKLXUH complex. The study also observed association of CooH with DsrC (DVU_2776), a central electron-transfer protein in sulfate reduction, via detection of a modified DsrC peptide in the pulldown, suggesting physiological electron-transfer connectivity. URL: https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9).
- CODH linkage: Genomic neighborhood and regulatory evidence imply functional association of the Coo hydrogenase with the CODH (CooS)-containing locus, though the two operons are distinct; in other bacteria, analogous complexes physically couple CODH and hydrogenase for CO-driven H2 evolution, supporting a similar model in D. vulgaris. URL: https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9).

Physiological role and pathway context in CO metabolism
- CO metabolism model: In carboxydotrophic contexts, CODH (CooS) oxidizes CO to CO2, generating reduced electron carriers (e.g., ferredoxin) that can be directed to the Coo hydrogenase (CooMKLXUH) for H2 production or routed into respiratory chains. This scheme aligns with the separation yet coordinated regulation of CODH and CooH operons and the detection of partial complex assembly. URL: https://doi.org/10.1371/journal.pone.0021470 (2011); URL: https://doi.org/10.3389/fmicb.2011.00069 (2011) (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15).

Current applications and real-world implementations (hydrogenase field, 2023–2024 focus)
- Biocatalytic hydrogenations and cofactor recycling: Recent work highlights practical deployment of [NiFe]-hydrogenases for H2-driven biocatalysis, including NAD(P)H recycling and site-separated hydrogenation cascades on conductive supports, offering greener alternatives to precious-metal catalysis. These developments demonstrate how hydrogenases’ H2 activation can be wired to reduction reactions relevant to synthesis and manufacturing. URL: https://doi.org/10.1039/d4cc04525d (published Oct 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2).
- Tuning catalytic properties by outer-sphere effects: 2024 expert review outlines how modifications to residues and second-sphere features modulate O2 sensitivity, catalytic bias, and reversibility of [NiFe]-hydrogenases, guiding enzyme selection and engineering for applications (e.g., O2-tolerant, high-affinity, or production-biased catalysts). URL: https://doi.org/10.1039/d4sc00691g (published Mar 22, 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2).

Expert opinions and analysis
- Network-level insights in D. vulgaris Hildenborough: The affinity-purification interactome underscores the presence of two membrane-bound cytoplasmically oriented hydrogenases, including the Coo-type, and suggests specialized electron-transfer routes tied to oxidoreductases and sulfate reduction machinery, including a putative role for CooH in CO-responsive energy metabolism. URL: https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9).
- Comparative metabolism perspective: Comparative genomics of sulfate-reducing bacteria indicates common deployment of complex I homologs, Rnf, and Ech/Coo-type hydrogenases for energy conservation, supporting the inference that DVU_2291 functions within a membrane-associated electron-transport framework in D. vulgaris. URL: https://doi.org/10.3389/fmicb.2011.00069 (2011) (pereira2011acomparativegenomic pages 14-15).
- Application-focused expert view (2023–2024): Hydrogenase researchers emphasize the promise of [NiFe]-hydrogenases as industrial biocatalysts due to selectivity for H2 activation and emerging strategies for oxygen tolerance and catalytic tuning, informing future translation of Coo-type enzymes where expression/stability can be achieved. URLs: https://doi.org/10.1039/d4cc04525d (Oct 2024); https://doi.org/10.1039/d4sc00691g (Mar 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2).

Recent statistics and data
- Pulldown interactomics in D. vulgaris: Experimental co-purification of CooU with CooH and detection of DsrC peptides provide direct evidence for complex assembly and potential electron-transfer connections in vivo; the study also reports that some membrane subunits are under-represented due to extraction limitations, a common caveat in membrane-complex proteomics. URL: https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9).
- Field-wide performance indicators: 2024 reviews summarize productivities and operational contexts for hydrogenase-enabled hydrogenations and cofactor recycling, though enzyme-specific turnover numbers depend on the scaffold and configuration; these reviews serve as authoritative summaries for technology readiness and performance benchmarks. URL: https://doi.org/10.1039/d4cc04525d (Oct 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2).

Conclusions
- DVU_2291 (Q729Q8) in D. vulgaris Hildenborough encodes CooH, the large subunit of a CO-induced [NiFe]-hydrogenase that is part of a membrane-bound, cytoplasmically oriented multi-subunit complex (CooMKLXUH). Genomic organization indicates coordination with a separate CODH operon (cooFSCTJ) under CO-responsive regulation (CooA). Pulldown evidence supports interaction with CooU and association with DsrC, situating CooH at a nexus of CO oxidation, hydrogen metabolism, and energy conservation. While organism-specific kinetic parameters are not reported in the retrieved sources, current hydrogenase research provides a strong mechanistic and applied framework for understanding and potentially exploiting this enzyme system. URLs: https://doi.org/10.1371/journal.pone.0021470 (2011); https://doi.org/10.3389/fmicb.2011.00069 (2011); https://doi.org/10.1039/d4cc04525d (2024); https://doi.org/10.1039/d4sc00691g (2024) (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15, sokolova2024exploitinghydrogenasesfor pages 1-2).

Embedded summary artifact
| Category | Key finding | Evidence/source (with URL and publication date) | Notes |
|---|---|---|---|
| Identity / organism mapping | DVU_2291 encodes the carbon monoxide-induced hydrogenase large subunit (CooH); UniProt Q729Q8; organism Desulfovibrio vulgaris Hildenborough | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9) | Confirms locus identity and annotation as CooH in D. vulgaris Hildenborough. |
| Domain / family | Annotated as NiFe-hydrogenase large subunit (NiFe-Hase_large) and ComplexI_49kDa-like (PF00346/IPR001501/IPR029014/IPR052197) | Pereira et al., Frontiers in Microbiology (Mar 2011): https://doi.org/10.3389/fmicb.2011.00069 (2011) (pereira2011acomparativegenomic pages 14-15) | Domain assignments consistent with group-4/energy-converting [NiFe]-hydrogenase large subunits (bioinformatic inference). |
| Operon context | CooH resides in a Coo-type hydrogenase locus (CooMKLXUH) distinct from the CODH-containing cooFSCTJ region; operon appears CO-responsive and linked to CooA regulation | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9) | Indicates physical/genomic separation of hydrogenase and CODH operons but regulatory/functional linkage via CO sensing. |
| Localization | Membrane-bound, cytoplasmically oriented hydrogenase complex (membrane association predicted/observed in proteomics) | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9); Pereira et al., Front. Microbiol. (Mar 2011): https://doi.org/10.3389/fmicb.2011.00069 (2011) (pereira2011acomparativegenomic pages 14-15) | Membrane association supports role in energy conservation and coupling to quinone/ion-translocating systems. |
| Interaction partners | CooU co-purified with CooH in pulldown experiments; proteomics detected association with DsrC (post-translationally modified peptide observed) | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9) | Experimental pulldowns recovered partial complex (membrane components may be underrepresented due to extraction). |
| Physiological / pathway role | Proposed role in CO oxidation → electron transfer to hydrogenase to produce H2 (CO-oxidation linked H2 evolution), likely functioning with CODH (CooS) and electron carriers | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9); Pereira et al., Front. Microbiol. (Mar 2011): https://doi.org/10.3389/fmicb.2011.00069 (2011) (pereira2011acomparativegenomic pages 14-15) | Functional assignment supported by operon context and comparative genomics; direct enzymatic assays for DVU_2291 not reported in these sources. |
| Omics induction / expression | Coo (DVU2286–DVU2291) described as CO-induced; proteomics/PPI data and prior transcriptomic/proteomic studies indicate inducible expression under relevant conditions | Chhabra et al., PLoS ONE (Jun 2011): https://doi.org/10.1371/journal.pone.0021470 (2011) (chhabra2011towardsarigorous pages 8-9) | Omics evidence supports CO-responsive regulation; specific fold-changes and condition details are reported in targeted transcriptomic/proteomic studies (see cited works). |
| Applications & 2024 developments | NiFe hydrogenases (including Coo-type conceptual relatives) are being adapted for H2-driven biocatalysis, cofactor recycling, and energy conversion; recent reviews highlight strategies for coupling hydrogenase H2 oxidation to synthetic reductions (2024) | Sokolova & Vincent, Chem. Commun. (Oct 2024): https://doi.org/10.1039/d4cc04525d (Oct 2024) (sokolova2024exploitinghydrogenasesfor pages 1-2) | Contemporary applications emphasize NiFe hydrogenases for H2-based biocatalysis and cofactor recycling; organism-specific engineering/characterization needed for DVU_2291 utility. |

Table: Summary table of key findings, primary evidence (URLs and dates), and notes for DVU_2291 (CooH) in Desulfovibrio vulgaris Hildenborough, useful for quick reference when writing the comprehensive report. Sources cited are from the retrieved context (chhabra2011towardsarigorous pages 8-9, pereira2011acomparativegenomic pages 14-15, sokolova2024exploitinghydrogenasesfor pages 1-2).

References

1. (chhabra2011towardsarigorous pages 8-9): Swapnil R. Chhabra, Marcin P. Joachimiak, Christopher J. Petzold, Grant M. Zane, Morgan N. Price, Sonia A. Reveco, Veronica Fok, Alyssa R. Johanson, Tanveer S. Batth, Mary Singer, John-Marc Chandonia, Dominique Joyner, Terry C. Hazen, Adam P. Arkin, Judy D. Wall, Anup K. Singh, and Jay D. Keasling. Towards a rigorous network of protein-protein interactions of the model sulfate reducer desulfovibrio vulgaris hildenborough. PLoS ONE, 6:e21470, Jun 2011. URL: https://doi.org/10.1371/journal.pone.0021470, doi:10.1371/journal.pone.0021470. This article has 16 citations and is from a peer-reviewed journal.

2. (pereira2011acomparativegenomic pages 14-15): Inês A. Cardoso Pereira, Ana Raquel Ramos, Fabian Grein, Marta Coimbra Marques, Sofia Marques da Silva, and Sofia Santos Venceslau. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Frontiers in Microbiology, Mar 2011. URL: https://doi.org/10.3389/fmicb.2011.00069, doi:10.3389/fmicb.2011.00069. This article has 418 citations and is from a poor quality or predatory journal.

3. (sokolova2024exploitinghydrogenasesfor pages 1-2): Daria Sokolova and Kylie A. Vincent. Exploiting hydrogenases for biocatalytic hydrogenations. Chemical Communications (Cambridge, England), 60:13667-13677, Oct 2024. URL: https://doi.org/10.1039/d4cc04525d, doi:10.1039/d4cc04525d. This article has 11 citations.

Citations

1. chhabra2011towardsarigorous pages 8-9
2. pereira2011acomparativegenomic pages 14-15
3. sokolova2024exploitinghydrogenasesfor pages 1-2
4. NiFe
5. https://doi.org/10.1371/journal.pone.0021470
6. https://doi.org/10.3389/fmicb.2011.00069
7. https://doi.org/10.1039/d4sc00691g
8. https://doi.org/10.1039/d4cc04525d
9. https://doi.org/10.1371/journal.pone.0021470,
10. https://doi.org/10.3389/fmicb.2011.00069,
11. https://doi.org/10.1039/d4cc04525d,