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protein_family: Not specified in UniProt
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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: P07598
• Protein Description: RecName: Full=Periplasmic [Fe] hydrogenase large subunit; EC=1.12.7.2; AltName: Full=Fe hydrogenlyase;
• Gene Information: Name=hydA; OrderedLocusNames=DVU_1769;
• 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: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); Cytosolic_Fe-S_CAF. (IPR050340); Fe_hydrogenase. (IPR009016); Fe_hydrogenase_lsu_C. (IPR004108)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "hydA" 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 'hydA' 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 hydA (gene ID: P07598, UniProt: P07598) 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: P07598
• Protein Description: RecName: Full=Periplasmic [Fe] hydrogenase large subunit; EC=1.12.7.2; AltName: Full=Fe hydrogenlyase;
• Gene Information: Name=hydA; OrderedLocusNames=DVU_1769;
• 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: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); Cytosolic_Fe-S_CAF. (IPR050340); Fe_hydrogenase. (IPR009016); Fe_hydrogenase_lsu_C. (IPR004108)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "hydA" 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 'hydA' 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 hydA (gene ID: P07598, UniProt: P07598) 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
- Verified target identity: hydA (DVU_1769) encodes the periplasmic [FeFe]-hydrogenase large subunit (HydA) in Desulfovibrio vulgaris Hildenborough; UniProt P07598 matches this description (completed).
- Collected and synthesized evidence on localization, catalysis, cofactors/domains, interaction partners and electron-transfer pathways, operon context, mutant phenotypes, kinetics/structure, and role in sulfate reduction.
- Added 2023–2024 contextual updates on hydrogen cycling in sulfate-reducing systems.

Comprehensive Research Report: hydA (DVU_1769; UniProt P07598) in Desulfovibrio vulgaris Hildenborough

Executive summary and definitions
- Identity: hydA (DVU_1769) encodes the large catalytic subunit of a dimeric periplasmic [FeFe]-hydrogenase (HydAB) in D. vulgaris Hildenborough. HydA harbors the H-cluster active site and multiple [4Fe–4S] clusters, whereas HydB is the small partner subunit of the periplasmic enzyme (HydAB) (barton2022electrontransportproteins pages 185-188, biosciences2022nataliepayne pages 68-71).
- Core reaction: reversible interconversion of molecular hydrogen and protons/electrons, 2 H+ + 2 e− ⇌ H2. In vivo, the periplasmic [FeFe]-hydrogenase primarily functions in H2 oxidation during sulfate respiration, with the direction depending on electron pressure and environmental context (biosciences2022nataliepayne pages 54-59, pollock1992molecularbiologyof pages 48-53).

Subcellular localization
- Periplasmic enzyme: Classical biochemical fractionation and spheroplast complementation established that key periplasmic hydrogenases in Desulfovibrio act in the periplasm with cytochrome c3, consistent with N‑terminal signal peptides driving export; HydAB in D. vulgaris Hildenborough is a periplasmic [FeFe]-hydrogenase (pollock1992molecularbiologyof pages 48-53, barton2022electrontransportproteins pages 185-188).

Reaction catalyzed and directionality; native electron partners
- Reaction: 2 H+ + 2 e− ⇌ H2. Periplasmic [FeFe]-hydrogenase can catalyze both H2 uptake and H2 evolution in vitro, but in sulfate-respiring conditions acts mainly as an H2-uptake enzyme that feeds electrons into the periplasmic c-type cytochrome network (e.g., TpI cytochrome c3), which then delivers electrons to membrane redox complexes for sulfate reduction (biosciences2022nataliepayne pages 68-71, biosciences2022nataliepayne pages 54-59).
- Kinetic directionality: High specific activities are measurable with artificial electron carriers (e.g., methyl viologen), with both uptake and evolution activities reported for D. vulgaris [FeFe]-hydrogenase; however, physiological electron acceptors are periplasmic cytochromes rather than MV (biosciences2022nataliepayne pages 68-71).

Cofactors, domains, and active site chemistry
- H-cluster: HydA contains the [FeFe]-hydrogenase H-cluster composed of a diiron center ligated to an atypical [4Fe–4S] subcluster. Two additional ferredoxin-like [4Fe–4S] clusters in HydA support intramolecular electron transfer to/from the H‑cluster (barton2022electrontransportproteins pages 185-188).
- Oxygen/ligand sensitivity: [FeFe]-hydrogenases are reversibly inhibited by CO and irreversibly damaged by O2 and NO; D. vulgaris Hyd forms an O2-protected inactive state (Hox(inact)/Hox(air)), with a model in which sulfide (H2S) binds the distal iron of the H-cluster to protect it, enabling reactivation upon reduction (biosciences2022nataliepayne pages 68-71).

Interaction partners and electron-transfer pathways to the membrane
- Periplasmic partners: Type I cytochrome c3 (TpI-c3) is the principal periplasmic electron carrier interacting with periplasmic hydrogenases, including the [FeFe]-hydrogenase; periplasmic hydrogenase + TpI-c3 restores lactate oxidation and sulfate reduction in D. vulgaris spheroplast systems (pollock1992molecularbiologyof pages 48-53, biosciences2022nataliepayne pages 54-59).
- Membrane conduits: Electrons from periplasmic carriers are shuttled to cytoplasmic sulfate-reduction enzymes via multiheme transmembrane complexes (Hmc, Tmc) and the quinone-interfacing Qrc complex, forming the periplasm-to-cytoplasm electron transfer path for energy conservation during sulfate reduction (biosciences2022nataliepayne pages 59-62, biosciences2022nataliepayne pages 54-59).

Genetic context and operon organization
- Dimeric enzyme genes: Periplasmic [FeFe]-hydrogenases in Desulfovibrio are typically encoded by hydAB, with hydA specifying the catalytic large subunit harboring Fe–S clusters and the H-cluster, and hydB encoding the small partner. This genomic arrangement is widespread in Desulfovibrio and includes D. vulgaris Hildenborough (barton2022electrontransportproteins pages 185-188). Specific operon neighbors/regulators for DVU_1769 were not resolved in the collected evidence.

Mutant phenotypes related to H2 cycling and lactate metabolism
- Hydrogenase- and c3-dependent lactate oxidation: Removal of periplasmic hydrogenases and TpI-c3 abolishes lactate-dependent sulfate reduction in D. vulgaris Hildenborough; complementation with periplasmic hydrogenases plus TpI-c3 partially restores activity, substantiating the hydrogen-cycling model for coupling lactate oxidation to sulfate reduction (biosciences2022nataliepayne pages 54-59).
- Cytochrome c3 (cycA) mutants: D. vulgaris Hildenborough cycA mutants cannot grow by H2 oxidation and show impaired sulfate reduction from pyruvate, shifting toward fermentation, highlighting the requirement of the periplasmic electron conduit for certain substrates (biosciences2022nataliepayne pages 59-62).

Kinetic and structural data specific to D. vulgaris [FeFe]-hydrogenase
- Activity and affinity: Reported values for D. vulgaris Hyd include high H2-uptake activity and a Km for H2 of roughly ~100 μM, consistent with operation at relatively elevated H2 partial pressures compared to high-affinity [NiFe] uptake hydrogenases (biosciences2022nataliepayne pages 68-71, barton2022electrontransportproteins pages 185-188).
- Inhibitor sensitivity: CO reversibly inhibits, O2 and NO irreversibly inactivate most [FeFe]-hydrogenases; D. vulgaris Hyd can form a recoverable O2‑protected state, likely via sulfide ligation at the distal Fe (biosciences2022nataliepayne pages 68-71).

Role in sulfate reduction and energy conservation
- Hydrogen cycling framework: In D. vulgaris Hildenborough, lactate oxidation yields reducing equivalents that can be partitioned to H2 via cytoplasmic/membrane hydrogenases; H2 diffuses to the periplasm, where HydAB (HydA/HydB) and other periplasmic hydrogenases oxidize H2, delivering electrons to TpI-c3 and then across the membrane (via Hmc/Tmc/Qrc) to the cytoplasmic sulfate-reduction pathway (APS reductase, dissimilatory sulfite reductase), thereby contributing to proton motive force and energy conservation (pollock1992molecularbiologyof pages 48-53, biosciences2022nataliepayne pages 54-59, biosciences2022nataliepayne pages 59-62).
- Substrate dependence and flexibility: Genetic and systems analyses indicate hydrogen cycling is more critical for pyruvate oxidation than for lactate oxidation, and that alternative electron-transfer routes can support growth depending on conditions, reflecting metabolic flexibility in SRB (biosciences2022nataliepayne pages 59-62).

Recent developments and latest research (2023–2024) contextualizing hydA
- Community-level H2 flux control: In a 4-member synthetic community including D. vulgaris, sulfate addition shifted electron fluxes by enhancing sulfate reduction and intensifying competition for H2 between D. vulgaris and a hydrogenotrophic methanogen, reducing methane output; this underscores SRB as key H2 sinks in sulfate-replete environments and situational H2 producers in sulfate limitation—contexts where HydAB function as an H2-oxidizing periplasmic enzyme is central (Wang et al., 2023, mBio; URL: https://doi.org/10.1128/mbio.03189-22, published Apr 2023) (wang2023crossfeedingscompetitionand pages 1-2).
- Essentiality is environment dependent: A 2023 network/text-mining study in SRB highlights that hydrogenase genes tend to be in the pangenome “shell” rather than the persistent core, indicating conditional essentiality dependent on H2 availability and growth conditions; this aligns with observations that the HydAB pathway is critical under specific electron-donor/acceptor regimes (Saxena et al., 2023, Frontiers in Microbiology; URL: https://doi.org/10.3389/fmicb.2023.1086021, published Apr 2023) (saxena2023integrationoftext pages 13-15).
- Mechanistic and classification context: Contemporary syntheses emphasize complementary roles of [FeFe] and [NiFe]/[NiFeSe] hydrogenases—[FeFe] with higher activities but lower O2 tolerance and higher H2 Km (∼100 μM for D. vulgaris Hyd), versus [NiFe] uptake enzymes with high H2 affinity—explaining partitioning of H2 oxidation duties under varying H2 levels and redox stresses in SRB (2022 synthesis; URL: https://doi.org/10.1007/978-3-030-96703-1_4, published Jan 2022) (barton2022electrontransportproteins pages 185-188, biosciences2022nataliepayne pages 68-71).

Current applications and real-world implementations
- Biogeochemical and engineered consortia: SRB participation in anaerobic communities modulates methane yields from complex substrates by contesting H2 with methanogens—a lever for engineered bioprocesses (e.g., waste-to-energy, anaerobic digestion) and for interpreting in situ geochemical H2 sinks; community experiments and modeling quantify these flux reallocations under sulfate amendment (Wang et al., 2023, mBio; URL: https://doi.org/10.1128/mbio.03189-22) (wang2023crossfeedingscompetitionand pages 1-2).
- Conceptual frameworks for energy conservation: Unified models integrating hydrogen cycling and direct electron transfer routes (via menaquinone and membrane complexes) guide metabolic engineering or control strategies in SRB-rich systems, with HydAB functioning as a key periplasmic H2-oxidation module when H2 is available (biosciences2022nataliepayne pages 59-62, biosciences2022nataliepayne pages 54-59).

Expert opinions and authoritative syntheses
- Classic and modern views: Foundational analyses articulated hydrogen cycling in Desulfovibrio and demonstrated periplasmic hydrogenase–cytochrome c3 coupling via spheroplast experiments (Pollock, 1992; URL: https://doi.org/10.11575/prism/15124) (pollock1992molecularbiologyof pages 48-53). Updated syntheses emphasize the diversity and localization of Desulfovibrio hydrogenases and the mechanistic underpinnings of [FeFe] catalysis and inhibition relevant to SRB physiology (Barton & Fauque, 2022; URL: https://doi.org/10.1007/978-3-030-96703-1_4) (barton2022electrontransportproteins pages 185-188), with additional summaries of physiological partitioning among hydrogenase classes and protective inactivation states (biosciences2022nataliepayne pages 68-71).

Relevant quantitative data and statistics
- Enzyme properties: D. vulgaris periplasmic [FeFe]-hydrogenase exhibits a Km for H2 ≈ 100 μM and very high turnover in H2 uptake assays; it is reversibly inhibited by CO and forms an O2-protected inactive state thought to involve sulfide ligation to the H‑cluster (biosciences2022nataliepayne pages 68-71, barton2022electrontransportproteins pages 185-188).
- System-level flux control: Sulfate addition to a defined synthetic community shifted electron fluxes away from methanogenesis toward sulfate reduction and increased H2 competition with D. vulgaris as a dominant H2 sink, as measured by integrated metaproteomics/metabolite profiling and stoichiometric modeling (Wang et al., 2023; URL: https://doi.org/10.1128/mbio.03189-22) (wang2023crossfeedingscompetitionand pages 1-2).

Ambiguity and nomenclature note
- hydA is a widely used symbol for [FeFe]-hydrogenase catalytic subunits across bacteria and eukaryotes; here, hydA refers specifically to DVU_1769 in D. vulgaris Hildenborough, the periplasmic [FeFe]-hydrogenase large subunit corresponding to UniProt P07598. All evidence and interpretations above are constrained to this organism/protein context (barton2022electrontransportproteins pages 185-188, biosciences2022nataliepayne pages 68-71).

Knowledge gaps and future directions
- Operon/regulatory context for DVU_1769 in D. vulgaris Hildenborough, the full set of native physiological electron partners and complex formation dynamics with TpI‑c3 and membrane conduits (Qrc/Tmc/Hmc), and condition-specific essentiality remain priority areas for targeted genetic/biochemical work, building on community-level and systems observations (wang2023crossfeedingscompetitionand pages 1-2, saxena2023integrationoftext pages 13-15, biosciences2022nataliepayne pages 59-62).

References with URLs and publication dates (cited above)
- Wang D. et al. Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane. mBio. Published Apr 2023. URL: https://doi.org/10.1128/mbio.03189-22 (wang2023crossfeedingscompetitionand pages 1-2)
- Saxena P. et al. Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria. Frontiers in Microbiology. Published Apr 2023. URL: https://doi.org/10.3389/fmicb.2023.1086021 (saxena2023integrationoftext pages 13-15)
- Barton L.L., Fauque G.D. Electron Transport Proteins and Cytochromes. In: Sulfate-Reducing Bacteria and Archaea. Published Jan 2022. URL: https://doi.org/10.1007/978-3-030-96703-1_4 (barton2022electrontransportproteins pages 185-188)
- Pollock W.B.R. Molecular biology of c-type cytochromes from Desulfovibrio vulgaris Hildenborough. Thesis/Monograph. Published Jan 1992. URL: https://doi.org/10.11575/prism/15124 (pollock1992molecularbiologyof pages 48-53)
- ISM Biosciences (compiled excerpts summarizing Desulfovibrio hydrogenases, 2022; includes mechanistic/kinetic notes and models). Publication date 2022; URL not specified in excerpt (biosciences2022nataliepayne pages 59-62, biosciences2022nataliepayne pages 68-71, biosciences2022nataliepayne pages 131-133, biosciences2022nataliepayne pages 54-59).

Citations in text correspond to context IDs: ().

References

1. (barton2022electrontransportproteins pages 185-188): Larry L. Barton and Guy D. Fauque. Electron transport proteins and cytochromes. Sulfate-Reducing Bacteria and Archaea, pages 173-244, Jan 2022. URL: https://doi.org/10.1007/978-3-030-96703-1_4, doi:10.1007/978-3-030-96703-1_4. This article has 1 citations.

2. (biosciences2022nataliepayne pages 68-71): ISM BiosCiences. Natalie payne. Unknown journal, 2022.

3. (biosciences2022nataliepayne pages 54-59): ISM BiosCiences. Natalie payne. Unknown journal, 2022.

4. (pollock1992molecularbiologyof pages 48-53): W. Brent R. Pollock. Molecular biology of c-type cytochromes from the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough. Other, Jan 1992. URL: https://doi.org/10.11575/prism/15124, doi:10.11575/prism/15124. This article has 3 citations.

5. (biosciences2022nataliepayne pages 59-62): ISM BiosCiences. Natalie payne. Unknown journal, 2022.

6. (wang2023crossfeedingscompetitionand pages 1-2): Dongyu Wang, Kristopher A. Hunt, Pieter Candry, Xuanyu Tao, Neil Q. Wofford, Jizhong Zhou, Michael J. McInerney, David A. Stahl, Ralph S. Tanner, Aifen Zhou, Mari Winkler, and Chongle Pan. Cross-feedings, competition, and positive and negative synergies in a four-species synthetic community for anaerobic degradation of cellulose to methane. mBio, Apr 2023. URL: https://doi.org/10.1128/mbio.03189-22, doi:10.1128/mbio.03189-22. This article has 18 citations and is from a domain leading peer-reviewed journal.

7. (saxena2023integrationoftext pages 13-15): Priya Saxena, Shailabh Rauniyar, Payal Thakur, Ram Nageena Singh, Alain Bomgni, Mathew O. Alaba, Abhilash Kumar Tripathi, Etienne Z. Gnimpieba, Carol Lushbough, and Rajesh Kumar Sani. Integration of text mining and biological network analysis: identification of essential genes in sulfate-reducing bacteria. Frontiers in Microbiology, Apr 2023. URL: https://doi.org/10.3389/fmicb.2023.1086021, doi:10.3389/fmicb.2023.1086021. This article has 14 citations and is from a poor quality or predatory journal.

8. (biosciences2022nataliepayne pages 131-133): ISM BiosCiences. Natalie payne. Unknown journal, 2022.

Citations

1. biosciences2022nataliepayne pages 68-71
2. barton2022electrontransportproteins pages 185-188
3. biosciences2022nataliepayne pages 54-59
4. biosciences2022nataliepayne pages 59-62
5. wang2023crossfeedingscompetitionand pages 1-2
6. saxena2023integrationoftext pages 13-15
7. pollock1992molecularbiologyof pages 48-53
8. biosciences2022nataliepayne pages 131-133
9. Fe
10. FeFe
11. 4Fe–4S
12. NiFe
13. NiFeSe
14. https://doi.org/10.1128/mbio.03189-22,
15. https://doi.org/10.3389/fmicb.2023.1086021,
16. https://doi.org/10.1007/978-3-030-96703-1_4,
17. https://doi.org/10.1128/mbio.03189-22
18. https://doi.org/10.11575/prism/15124
19. https://doi.org/10.1007/978-3-030-96703-1_4
20. https://doi.org/10.3389/fmicb.2023.1086021
21. https://doi.org/10.1007/978-3-030-96703-1_4,
22. https://doi.org/10.11575/prism/15124,