Periplasmic [NiFe] hydrogenase large subunit (hynA1/DVU_1922) catalyzing H2 oxidation with cytochrome c3 as the physiological electron acceptor. This enzyme is part of the hydrogen-cycling machinery that couples periplasmic H2 oxidation to dissimilatory sulfate reduction in D. vulgaris Hildenborough. The large subunit contains the bimetallic [NiFe] active site with CO and CN ligands on Fe, while the small subunit (HynB) provides the Fe-S cluster relay for electron transfer to cytochrome c3. The heterodimer is exported to the periplasm via the Tat pathway, with the small subunit carrying the twin-arginine signal peptide.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0008901
ferredoxin hydrogenase activity
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: This annotation assigns ferredoxin hydrogenase activity based on InterPro domain matching (IPR018194). However, the physiological electron acceptor for this periplasmic [NiFe] hydrogenase is cytochrome c3, not ferredoxin. The GO term GO:0008901 describes the reaction "2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2" which is the H2 evolution direction with ferredoxin as electron donor - opposite to the physiological function of this uptake hydrogenase. Deep research summaries indicate that periplasmic [NiFe] hydrogenases in Desulfovibrio transfer electrons primarily to tetraheme cytochrome c3.
Reason: The annotation is based on domain similarity but assigns an incorrect electron partner (ferredoxin) and incorrect reaction direction (H2 production vs uptake). D. vulgaris Hildenborough periplasmic [NiFe] hydrogenases function as H2 uptake enzymes with cytochrome c3 as the immediate acceptor. "Periplasmic electron transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171)" as summarized in the deep research report. The more appropriate term is GO:0047806 (cytochrome-c3 hydrogenase activity) which describes the correct reaction with the physiological acceptor.
Proposed replacements:
cytochrome-c3 hydrogenase activity
Supporting Evidence:
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
Electron acceptors and redox partners: Periplasmic electron transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171) at high cellular abundance, which can mediate rapid electron transfer to the high-molecular-mass cytochrome (Hmc) transmembrane complex
|
|
GO:0016151
nickel cation binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This annotation correctly identifies nickel binding based on InterPro domain matching for the [NiFe] hydrogenase large subunit (IPR001501, IPR018194). The large subunit contains the bimetallic [NiFe] active site where Ni is coordinated by conserved cysteine residues. UniProt annotation shows Ni(2+) binding sites at positions 80, 83, and 545 of this protein. The [NiFe] center is essential for catalytic activity.
Reason: [NiFe] hydrogenases are defined by their bimetallic active site containing nickel and iron. "The [NiFe] active sites contain a heterobimetallic Ni-Fe center with diatomic ligands (CO and CN-) on Fe" (deep research). UniProt structural annotation confirms multiple Ni(2+) binding residues in this protein. This is a core functional property of all [NiFe] hydrogenases.
Supporting Evidence:
UniProt:Q72AS0
BINDING 80 /ligand="Ni(2+)" /ligand_id="ChEBI:CHEBI:49786" /evidence="ECO:0000256|PIRSR:PIRSR601501-1"
|
|
GO:0016491
oxidoreductase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: This is a generic annotation based on UniProt keyword mapping (KW-0560: Oxidoreductase). While technically correct - hydrogenases are oxidoreductases that catalyze H2 + A = 2H+ + AH2 - this term is too general and provides no specific information about the enzyme's function. More specific child terms are available and already annotated (GO:0047806 cytochrome-c3 hydrogenase activity).
Reason: Although this term is very general, it is not incorrect. The enzyme is indeed an oxidoreductase (EC 1.12.2.1). Since more specific annotations exist (GO:0047806), this general term provides hierarchical coverage without being misleading. The presence of more specific terms means this annotation adds little information but also does no harm.
Supporting Evidence:
UniProt:Q72AS0
EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159}
|
|
GO:0042597
periplasmic space
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: This cellular component annotation correctly identifies periplasmic localization based on UniProt subcellular location vocabulary mapping. D. vulgaris Hildenborough possesses multiple periplasmic [NiFe] hydrogenases that oxidize H2 in the periplasm and transfer electrons to the periplasmic cytochrome c3 pool. The heterodimeric enzyme is exported to the periplasm via the Tat (twin-arginine translocase) pathway.
Reason: Periplasmic localization is strongly supported by multiple lines of evidence. The genome analysis "showed multiple periplasmic NiFe hydrogenases" in D. vulgaris Hildenborough (deep research). The Tat export pathway for periplasmic hydrogenases is summarized in the deep research report. UniProt annotation states "Periplasm {ECO:0000256|ARBA:ARBA00004418}".
Supporting Evidence:
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
Localization: The periplasm is the site of H2 oxidation in DvH; periplasmic [NiFe] hydrogenases deliver electrons into the periplasmic cytochrome network. Genome analysis explicitly highlighted multiple periplasmic NiFe hydrogenases initiating energy transduction.
UniProt:Q72AS0
SUBCELLULAR LOCATION: Periplasm {ECO:0000256|ARBA:ARBA00004418}
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: This generic annotation for metal ion binding is derived from UniProt keyword mapping (KW-0479: Metal-binding). While technically accurate - the enzyme binds Ni, Fe, and Mg - this term is too general. More specific metal binding terms (GO:0016151 nickel cation binding) are already annotated and more informative.
Reason: The annotation is correct but redundant given the more specific GO:0016151 (nickel cation binding) annotation. The protein does bind multiple metal ions (Ni, Fe, Mg) at the active site and structural positions. UniProt shows binding sites for Ni(2+), Fe cation, and Mg(2+). While not maximally informative, this general annotation is not misleading.
Supporting Evidence:
UniProt:Q72AS0
Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|PIRSR:PIRSR601501-1}; Nickel {ECO:0000256|ARBA:ARBA00022596, ECO:0000256|PIRSR:PIRSR601501-1};
|
|
GO:0047806
cytochrome-c3 hydrogenase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the most accurate molecular function annotation for this enzyme. GO:0047806 describes "Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3" which matches the physiological function of periplasmic [NiFe] hydrogenases in Desulfovibrio species. The annotation is derived from RHEA:20625 and EC:1.12.2.1. Kinetic studies demonstrated that cytochrome c3 is the primary physiological acceptor for periplasmic hydrogenases.
Reason: This annotation captures the core molecular function of the enzyme. "Kinetic measurements in Desulfovibrio spp. show that the [NiFe] periplasmic hydrogenases reduce Hmc efficiently and that cytochrome c3 markedly accelerates Hmc reduction, positioning c3 as the principal immediate acceptor from hydrogenases" (Pereira et al. 1998). UniProt catalytic activity annotation confirms: "2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 H(+)". EC 1.12.2.1 (hydrogen:cytochrome-c3 oxidoreductase) is the assigned enzyme classification.
Supporting Evidence:
UniProt:Q72AS0
EC=1.12.2.1; Evidence={ECO:0000256|ARBA:ARBA00029307};
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
Biochemical/electrochemical analyses in Desulfovibrio emphasize cytochrome c3 as the principal physiological partner for periplasmic hydrogenases, accelerating electron delivery to transmembrane complexes like Hmc
|
|
GO:0019420
dissimilatory sulfate reduction
|
NAS
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md |
NEW |
Summary: This biological process annotation captures the pathway context in which hynA1 functions. The periplasmic [NiFe] hydrogenases provide electrons from H2 oxidation that feed into the cytoplasmic sulfate reduction pathway via membrane-spanning complexes. While hynA1 does not directly catalyze sulfate reduction, it is part of the electron transport chain that powers this process.
Reason: The role of periplasmic [NiFe] hydrogenases in dissimilatory sulfate reduction is well established. "Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic sulfate reduction" (deep research). This represents the core biological role of this enzyme in D. vulgaris energy metabolism. GO annotation guidelines support annotating enzymes to the biological process they contribute to even when they don't directly catalyze the terminal reaction.
Supporting Evidence:
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
Central role in sulfate respiration: Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic sulfate reduction and contributing to proton motive force via periplasmic proton release.
|
|
GO:0019645
anaerobic electron transport chain
|
NAS
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md |
NEW |
Summary: The periplasmic [NiFe] hydrogenase operates as part of the anaerobic electron transport chain in D. vulgaris, transferring electrons from H2 to cytochrome c3 and onward to membrane complexes (Hmc/Tmc) that link to cytoplasmic terminal reductases.
Reason: D. vulgaris is an obligate anaerobe and its periplasmic hydrogenases function in the context of anaerobic respiration. "Electrons are captured by tetraheme cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic H2 oxidation to cytoplasmic sulfate reduction" (deep research). This accurately describes participation in an anaerobic electron transport chain.
Supporting Evidence:
file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
In the hydrogen-cycling model, H2 produced (or supplied) is oxidized in the periplasm; electrons are captured by tetraheme cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic H2 oxidation to cytoplasmic sulfate reduction and proton motive force generation.
|
Q: What is the relative contribution of hynA1 vs the [NiFeSe] hydrogenase to H2 uptake under different growth conditions?
Q: Does hynA1 have any role in hydrogen production under certain physiological conditions?
Q: What is the kinetic preference of hynA1 for different cytochrome c3 isoforms?
Experiment: Deletion mutant phenotyping under H2/sulfate growth to quantify contribution to sulfate reduction
Hypothesis: hynA1 is required for efficient H2-dependent sulfate reduction under specific growth conditions.
Experiment: Comparative kinetic analysis with purified enzyme and different cytochrome acceptors
Hypothesis: HynA1 preferentially transfers electrons to specific cytochrome c3 isoforms.
Experiment: Expression analysis under syntrophic growth conditions
Hypothesis: hynA1 expression is upregulated during syntrophic growth where H2 is limiting.
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template_variables:
organism: DESVH
gene_id: Q72AS0
gene_symbol: hynA-1
uniprot_accession: Q72AS0
protein_description: 'RecName: Full=Periplasmic [NiFe] hydrogenase large subunit
{ECO:0000256|ARBA:ARBA00074020}; EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159};
AltName: Full=NiFe hydrogenlyase large chain {ECO:0000256|ARBA:ARBA00083852};'
gene_info: Name=hynA-1 {ECO:0000313|EMBL:AAS96398.1}; OrderedLocusNames=DVU_1922
{ECO:0000313|EMBL:AAS96398.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit
protein_domains: Ni-dep_hyd_lsu. (IPR001501); Ni-dep_hyd_lsu_Ni_BS. (IPR018194);
NiFe-Hase_large. (IPR029014); NiFe/NiFeSe_hydrgnase_LSU. (IPR050867); NiFeSe_Hases
(PF00374)
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citation_count: 20
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 'hynA-1' 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 hynA-1 (gene ID: Q72AS0, UniProt: Q72AS0) 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 'hynA-1' 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 hynA-1 (gene ID: Q72AS0, UniProt: Q72AS0) 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 status: We verified identity and gathered targeted evidence on function, localization, partners, gene context, and metabolism, prioritizing authoritative sources and recent literature where available. Below is the research report with explicit citations.
Comprehensive research report: DVU_1922 (hynA-1; UniProt Q72AS0), periplasmic [NiFe] hydrogenase large subunit in Desulfovibrio vulgaris Hildenborough (DvH)
1) Key concepts and definitions with current understanding
• Identity and nomenclature: DVU_1922 encodes the large subunit of a periplasmic [NiFe] hydrogenase in D. vulgaris Hildenborough. DvH harbors multiple periplasmic [NiFe] hydrogenases and an expansive c-type cytochrome network supporting periplasmic H2 oxidation and energy conservation. Note that subunit naming in the literature is inconsistent across species (HynA vs HynB for large/small); the DvH locus DVU_1922 (hynA-1) is annotated as the large subunit in UniProt and fits the periplasmic [NiFe] uptake hydrogenase (group 1) paradigm (genome-wide context and periplasmic hydrogenase complement in DvH). (heidelberg2004thegenomesequence pages 2-3)
• Enzyme class and reaction: Periplasmic [NiFe] hydrogenases catalyze H2 ⇄ 2H+ + 2e−. As uptake hydrogenases (EC 1.12.2.1; hydrogen dehydrogenase (acceptor)), the physiological direction is H2 oxidation with electron transfer to periplasmic acceptors (e.g., c-type cytochromes), feeding membrane complexes that couple to sulfate reduction. [NiFe] active sites contain a heterobimetallic Ni–Fe center with diatomic ligands (CO and CN−) on Fe; activity typically requires reductive activation from Ni–A/Ni–B states. (biosciences2022nataliepayne pages 68-71, agrawal2005molecularbiologicaland pages 12-17)
• Cellular role and pathway context: In the hydrogen-cycling model, H2 produced (or supplied) is oxidized in the periplasm; electrons are captured by tetraheme cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic H2 oxidation to cytoplasmic sulfate reduction and proton motive force generation. (pereira1998electrontransferbetween pages 1-2, heidelberg2004thegenomesequence pages 2-3)
2) Recent developments and latest research (emphasis 2023–2024)
• Tat export mechanisms for periplasmic hydrogenases (2024): The twin-arginine translocase (Tat) exports folded cofactor-containing proteins to the periplasm via N‑terminal twin-arginine signal peptides. For periplasmic [NiFe] hydrogenases, export can occur as a heterodimer by a hitchhiker mechanism: the small subunit often bears the Tat signal peptide and a C‑terminal tail-anchor, delivering the large subunit to the periplasm in complex. This general mechanism underpins periplasmic localization and maturation/assembly of [NiFe] hydrogenases in bacteria, including Desulfovibrio species. (Gallego‑Parrilla et al., Microbiology, 2024; https://doi.org/10.1099/mic.0.001431) (gallegoparrilla2024identificationofnovel pages 1-2)
• Spectroscopy/maturation overviews (2024): Recent reviews synthesize advances in [NiFe] hydrogenase structure and maturation intermediates (e.g., HypCD scaffold and CN/CO ligand installation), reinforcing conserved features of the [NiFe] active site and maturation sequence (Fe(CN)2CO insertion prior to Ni) that apply to Desulfovibrio uptake enzymes. While not DvH-specific, these updates refine the mechanistic basis for DVU_1922 function. (overview, 2024) (agrawal2005molecularbiologicaland pages 12-17)
• Genome-scale functional context (foundational but still current): The DvH genome showed multiple periplasmic NiFe hydrogenases and a large c-type cytochrome network as a defining feature of DvH energy metabolism; this framework remains the basis for current models and is used in recent systems studies. (Heidelberg et al., Nature Biotechnol., 2004; https://doi.org/10.1038/nbt959) (heidelberg2004thegenomesequence pages 2-3)
3) Primary function, substrates, and electron acceptors
• Catalytic reaction: H2 + acceptor(ox) → 2H+ + acceptor(red). The periplasmic [NiFe] hydrogenase large subunit (DVU_1922) houses the [NiFe] active site that oxidizes H2; its physiological activity is H2 uptake rather than proton reduction under standard growth conditions. (biosciences2022nataliepayne pages 68-71)
• Electron acceptors and redox partners: Periplasmic electron transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171) at high cellular abundance, which can mediate rapid electron transfer to the high-molecular-mass cytochrome (Hmc) transmembrane complex; Tmc is a related transmembrane complex also implicated in periplasm-to-cytoplasm electron flow. Kinetic measurements in Desulfovibrio spp. show that the [NiFe] periplasmic hydrogenases reduce Hmc efficiently and that cytochrome c3 markedly accelerates Hmc reduction, positioning c3 as the principal immediate acceptor from hydrogenases. (Pereira et al., 1998; Heidelberg et al., 2004; JBIC 1998 https://doi.org/10.1007/s007750050259; Nat. Biotechnol. 2004 https://doi.org/10.1038/nbt959) (pereira1998electrontransferbetween pages 1-2, heidelberg2004thegenomesequence pages 2-3, pereira1998electrontransferbetween pages 2-3)
• Subunit architecture and electron relay: Periplasmic [NiFe] hydrogenases are heterodimers; the large subunit contains the [NiFe] site while the small subunit carries an Fe–S cluster chain for electron transfer to c-type cytochromes. Biochemical characterizations show high H2 affinity (e.g., Km ~9 µM) and high uptake activities, consistent with the role as an H2-oxidizing enzyme. (biosciences2022nataliepayne pages 68-71)
4) Subcellular localization and maturation/trafficking
• Localization: The periplasm is the site of H2 oxidation in DvH; periplasmic [NiFe] hydrogenases deliver electrons into the periplasmic cytochrome network. Genome analysis explicitly highlighted multiple periplasmic NiFe hydrogenases initiating energy transduction. (Heidelberg et al., 2004) (heidelberg2004thegenomesequence pages 2-3)
• Export pathway: [NiFe] hydrogenases destined for the periplasm are exported as folded cofactor-containing complexes via the Tat pathway. The small subunit typically harbors the twin‑arginine (RR) signal peptide; export can occur with the large subunit as a hitchhiker. Tail-anchored Tat substrates that interact with hydrogenase modules are widely observed. (Gallego‑Parrilla et al., 2024) (gallegoparrilla2024identificationofnovel pages 1-2)
• Maturation: The [NiFe] center is assembled by the Hyp machinery (HypC/D/E/F scaffold and CN/CO installation) prior to Ni insertion into the apo‑large subunit; reductive activation is often required to relieve the Ni‑A/Ni‑B states. These maturation steps, while generalized, apply to Desulfovibrio periplasmic enzymes. (agrawal2005molecularbiologicaland pages 12-17)
5) Gene context and regulation/expression
• Gene neighborhood and operon logic: In Desulfovibrio, periplasmic [NiFe] hydrogenases are encoded as large and small subunits with adjacent genes. Although individual locus maps vary and the literature sometimes swaps HynA/HynB labels across species, DVU_1922 corresponds to the large subunit and functions with its cognate small subunit, together forming the periplasmic uptake complex that interfaces with c-type cytochromes. (genome context and hydrogenase complement) (heidelberg2004thegenomesequence pages 2-3)
• Expression patterns across energy conditions: Transcriptome analyses in DvH demonstrate substrate-dependent regulation of hydrogenases. Growth with H2/sulfate strongly induces periplasmic hydrogenases (notably the [NiFeSe] type), while multiple hydrogenase-linked pathways are engaged under lactate, pyruvate, and thiosulfate growth. These data support flexible deployment of hydrogenases according to electron donor availability and redox conditions. (Pereira et al., Antonie van Leeuwenhoek, 2008; https://doi.org/10.1007/s10482-007-9212-0) (pereira2008energymetabolismin pages 1-6)
• Kinetic/biophysical activation: Periplasmic [NiFe] hydrogenases often require pre-reduction (e.g., H2 or dithionite) to achieve maximal activity from their resting oxidized (Ni‑A/Ni‑B) states, a property noted in Desulfovibrio species and consistent with enzyme handling in vitro. (pereira1998electrontransferbetween pages 2-3, biosciences2022nataliepayne pages 68-71)
6) Roles in energy metabolism and ecology (applications/implementations)
• Central role in sulfate respiration: Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic sulfate reduction and contributing to proton motive force via periplasmic proton release. This architecture underlies the hydrogen-cycling model and remains a cornerstone of DvH bioenergetics. (pereira1998electrontransferbetween pages 1-2, heidelberg2004thegenomesequence pages 2-3, pereira2008energymetabolismin pages 1-6)
• Syntrophy and community interactions: The hydrogen-cycling framework supports syntrophic exchanges where H2 serves as an interspecies electron carrier; DvH periplasmic hydrogenases enable H2 uptake from partners and redistribute electrons into sulfate reduction pathways. (pereira1998electrontransferbetween pages 1-2, biosciences2022nataliepayne pages 59-62)
• Corrosion and metal reduction: The DvH genome analysis connected periplasmic hydrogenases and c-type cytochromes to U(VI) and Cr(VI) reduction, processes relevant to bioremediation and to microbially influenced corrosion (MIC) in industrial systems. Periplasmic H2 oxidation and sulfide production from sulfate reduction are implicated in MIC phenotypes. (Heidelberg et al., 2004; Nat. Biotechnol. https://doi.org/10.1038/nbt959) (heidelberg2004thegenomesequence pages 2-3)
7) Expert opinions and authoritative analyses
• Hydrogenase–cytochrome wiring: Biochemical/electrochemical analyses in Desulfovibrio emphasize cytochrome c3 as the principal physiological partner for periplasmic hydrogenases, accelerating electron delivery to transmembrane complexes like Hmc; this perspective, grounded in kinetic data, is widely adopted in authoritative reviews and remains the consensus for DvH. (Pereira et al., JBIC 1998; https://doi.org/10.1007/s007750050259) (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 2-3)
• Systems view: The DvH genome study articulated hydrogenase redundancy and specialization within a dense periplasmic redox network, a view that continues to inform current systems microbiology work on sulfate reducers and their environmental roles. (Heidelberg et al., Nat. Biotechnol. 2004; https://doi.org/10.1038/nbt959) (heidelberg2004thegenomesequence pages 2-3)
• Protein export and assembly (2024 perspective): Modern Tat-pathway analyses underscore the hitchhiker export of periplasmic hydrogenase heterodimers and identify additional tail-anchored electron transfer proteins integrated by Tat, reinforcing the periplasmic orientation and assembly dependencies of hydrogenase complexes. (Gallego‑Parrilla et al., Microbiology, 2024; https://doi.org/10.1099/mic.0.001431) (gallegoparrilla2024identificationofnovel pages 1-2)
8) Relevant statistics and data from recent and classic studies
• Kinetic properties: Representative periplasmic [NiFe] hydrogenases (Desulfovibrio spp.) exhibit high H2 affinity (Km ~9 µM) and high H2-uptake activities (>200 U/mg) under activating conditions; the same enzymes can evolve H2 in vitro, but H2 presence inhibits proton reduction, supporting in vivo uptake function. (biosciences2022nataliepayne pages 68-71)
• Electron transfer preferences: Comparative kinetics revealed that [NiFe] hydrogenases reduce Hmc faster than [Fe]-hydrogenase does, and cytochrome c3 markedly accelerates Hmc reduction for all hydrogenases tested, quantifying c3’s role as an electron-transfer mediator in the periplasm. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 2-3)
• Network architecture: DvH encodes multiple periplasmic NiFe hydrogenases and several c3-type cytochromes including DVU3171 (TpIc3), providing quantitative network redundancy at the gene level for periplasmic electron transfer. (heidelberg2004thegenomesequence pages 2-3)
9) Gene symbol ambiguity check (mandated)
• The symbol “hynA-1” has been used inconsistently across Desulfovibrio species to denote either the large or small subunit. For DvH DVU_1922, UniProt Q72AS0 explicitly annotates hynA-1 as the large subunit of a periplasmic [NiFe] hydrogenase. All evidence and organismal context above refer to D. vulgaris Hildenborough; no switch to another organism was made. Where literature uses differing labels (HynA vs HynB), we treat DVU_1922 as the large subunit consistent with UniProt and the DvH genome context. (heidelberg2004thegenomesequence pages 2-3)
Conclusion and functional annotation summary
• DVU_1922 (hynA-1; UniProt Q72AS0) encodes the large subunit of a periplasmic [NiFe] uptake hydrogenase that oxidizes H2 (EC 1.12.2.1) and transfers electrons primarily to tetraheme cytochrome c3, which relays them to membrane complexes (Hmc/Tmc) to drive sulfate respiration. The enzyme functions in the periplasm, is exported via the Tat pathway as part of a heterodimer with a Tat‑signal‑bearing small subunit, and requires the canonical Hyp maturation machinery for active-site assembly and reductive activation. Its activity underpins DvH energy conservation, syntrophic H2 uptake, and environmental processes including metal reduction and MIC. (pereira1998electrontransferbetween pages 1-2, gallegoparrilla2024identificationofnovel pages 1-2, heidelberg2004thegenomesequence pages 2-3, pereira1998electrontransferbetween pages 2-3, biosciences2022nataliepayne pages 68-71, agrawal2005molecularbiologicaland pages 12-17, pereira2008energymetabolismin pages 1-6)
References
(heidelberg2004thegenomesequence pages 2-3): John F Heidelberg, Rekha Seshadri, Shelley A Haveman, Christopher L Hemme, Ian T Paulsen, James F Kolonay, Jonathan A Eisen, Naomi Ward, Barbara Methe, Lauren M Brinkac, Sean C Daugherty, Robert T Deboy, Robert J Dodson, A Scott Durkin, Ramana Madupu, William C Nelson, Steven A Sullivan, Derrick Fouts, Daniel H Haft, Jeremy Selengut, Jeremy D Peterson, Tanja M Davidsen, Nikhat Zafar, Liwei Zhou, Diana Radune, George Dimitrov, Mark Hance, Kevin Tran, Hoda Khouri, John Gill, Terry R Utterback, Tamara V Feldblyum, Judy D Wall, Gerrit Voordouw, and Claire M Fraser. The genome sequence of the anaerobic, sulfate-reducing bacterium desulfovibrio vulgaris hildenborough. Nature Biotechnology, 22:554-559, May 2004. URL: https://doi.org/10.1038/nbt959, doi:10.1038/nbt959. This article has 783 citations and is from a highest quality peer-reviewed journal.
(biosciences2022nataliepayne pages 68-71): ISM BiosCiences. Natalie payne. Unknown journal, 2022.
(agrawal2005molecularbiologicaland pages 12-17): AG Agrawal. Molecular biological and spectroscopic characterisation of the -hydrogenase from desulfovibrio vulgaris. Unknown journal, 2005.
(pereira1998electrontransferbetween pages 1-2): Inês A. C. Pereira, Célia V. Romão, António V. Xavier, J. LeGall, and Miguel Teixeira. Electron transfer between hydrogenases and mono- and multiheme cytochromes in desulfovibrio ssp. JBIC Journal of Biological Inorganic Chemistry, 3:494-498, Oct 1998. URL: https://doi.org/10.1007/s007750050259, doi:10.1007/s007750050259. This article has 103 citations.
(gallegoparrilla2024identificationofnovel pages 1-2): José Jesús Gallego-Parrilla, Emmanuele Severi, Govind Chandra, and Tracy Palmer. Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase. Microbiology, Feb 2024. URL: https://doi.org/10.1099/mic.0.001431, doi:10.1099/mic.0.001431. This article has 5 citations and is from a peer-reviewed journal.
(pereira1998electrontransferbetween pages 2-3): Inês A. C. Pereira, Célia V. Romão, António V. Xavier, J. LeGall, and Miguel Teixeira. Electron transfer between hydrogenases and mono- and multiheme cytochromes in desulfovibrio ssp. JBIC Journal of Biological Inorganic Chemistry, 3:494-498, Oct 1998. URL: https://doi.org/10.1007/s007750050259, doi:10.1007/s007750050259. This article has 103 citations.
(pereira2008energymetabolismin pages 1-6): Patrícia M. Pereira, Qiang He, Filipa M. A. Valente, António V. Xavier, Jizhong Zhou, Inês A. C. Pereira, and Ricardo O. Louro. Energy metabolism in desulfovibrio vulgaris hildenborough: insights from transcriptome analysis. Antonie van Leeuwenhoek, 93:347-362, May 2008. URL: https://doi.org/10.1007/s10482-007-9212-0, doi:10.1007/s10482-007-9212-0. This article has 95 citations.
(biosciences2022nataliepayne pages 59-62): ISM BiosCiences. Natalie payne. Unknown journal, 2022.
id: Q72AS0
gene_symbol: hynA1
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris Hildenborough)
description: >-
Periplasmic [NiFe] hydrogenase large subunit (hynA1/DVU_1922) catalyzing H2 oxidation
with cytochrome c3 as the physiological electron acceptor. This enzyme is part of
the hydrogen-cycling machinery that couples periplasmic H2 oxidation to dissimilatory
sulfate reduction in D. vulgaris Hildenborough. The large subunit contains the
bimetallic [NiFe] active site with CO and CN ligands on Fe, while the small subunit
(HynB) provides the Fe-S cluster relay for electron transfer to cytochrome c3. The
heterodimer is exported to the periplasm via the Tat pathway, with the small subunit
carrying the twin-arginine signal peptide.
existing_annotations:
- term:
id: GO:0008901
label: ferredoxin hydrogenase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation assigns ferredoxin hydrogenase activity based on InterPro domain
matching (IPR018194). However, the physiological electron acceptor for this
periplasmic [NiFe] hydrogenase is cytochrome c3, not ferredoxin. The GO term
GO:0008901 describes the reaction "2 reduced ferredoxin + 2 H+ = 2 oxidized
ferredoxin + H2" which is the H2 evolution direction with ferredoxin as electron
donor - opposite to the physiological function of this uptake hydrogenase.
Deep research summaries indicate that periplasmic [NiFe] hydrogenases in
Desulfovibrio transfer electrons primarily to tetraheme cytochrome c3.
action: MODIFY
reason: >-
The annotation is based on domain similarity but assigns an incorrect electron
partner (ferredoxin) and incorrect reaction direction (H2 production vs uptake).
D. vulgaris Hildenborough periplasmic [NiFe] hydrogenases function as H2 uptake
enzymes with cytochrome c3 as the immediate acceptor. "Periplasmic electron
transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171)" as
summarized in the deep research report. The more appropriate term is GO:0047806
(cytochrome-c3 hydrogenase activity) which describes the correct reaction with
the physiological acceptor.
proposed_replacement_terms:
- id: GO:0047806
label: cytochrome-c3 hydrogenase activity
additional_reference_ids:
- PMID:15077118
supported_by:
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Electron acceptors and redox partners: Periplasmic electron transfer proceeds
primarily to tetraheme cytochrome c3 (TpIc3; DVU3171) at high cellular abundance,
which can mediate rapid electron transfer to the high-molecular-mass cytochrome
(Hmc) transmembrane complex
- term:
id: GO:0016151
label: nickel cation binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation correctly identifies nickel binding based on InterPro domain
matching for the [NiFe] hydrogenase large subunit (IPR001501, IPR018194). The
large subunit contains the bimetallic [NiFe] active site where Ni is coordinated
by conserved cysteine residues. UniProt annotation shows Ni(2+) binding sites at
positions 80, 83, and 545 of this protein. The [NiFe] center is essential for
catalytic activity.
action: ACCEPT
reason: >-
[NiFe] hydrogenases are defined by their bimetallic active site containing nickel
and iron. "The [NiFe] active sites contain a heterobimetallic Ni-Fe center with
diatomic ligands (CO and CN-) on Fe" (deep research). UniProt structural annotation
confirms multiple Ni(2+) binding residues in this protein. This is a core functional
property of all [NiFe] hydrogenases.
supported_by:
- reference_id: UniProt:Q72AS0
supporting_text: >-
BINDING 80 /ligand="Ni(2+)" /ligand_id="ChEBI:CHEBI:49786" /evidence="ECO:0000256|PIRSR:PIRSR601501-1"
- term:
id: GO:0016491
label: oxidoreductase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This is a generic annotation based on UniProt keyword mapping (KW-0560: Oxidoreductase).
While technically correct - hydrogenases are oxidoreductases that catalyze
H2 + A = 2H+ + AH2 - this term is too general and provides no specific information
about the enzyme's function. More specific child terms are available and already
annotated (GO:0047806 cytochrome-c3 hydrogenase activity).
action: ACCEPT
reason: >-
Although this term is very general, it is not incorrect. The enzyme is indeed an
oxidoreductase (EC 1.12.2.1). Since more specific annotations exist (GO:0047806),
this general term provides hierarchical coverage without being misleading. The
presence of more specific terms means this annotation adds little information but
also does no harm.
supported_by:
- reference_id: UniProt:Q72AS0
supporting_text: >-
EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159}
- term:
id: GO:0042597
label: periplasmic space
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
This cellular component annotation correctly identifies periplasmic localization
based on UniProt subcellular location vocabulary mapping. D. vulgaris Hildenborough
possesses multiple periplasmic [NiFe] hydrogenases that oxidize H2 in the periplasm
and transfer electrons to the periplasmic cytochrome c3 pool. The heterodimeric
enzyme is exported to the periplasm via the Tat (twin-arginine translocase) pathway.
action: ACCEPT
reason: >-
Periplasmic localization is strongly supported by multiple lines of evidence.
The genome analysis "showed multiple periplasmic NiFe hydrogenases" in D. vulgaris
Hildenborough (deep research). The Tat export pathway for periplasmic hydrogenases
is summarized in the deep research report. UniProt annotation states "Periplasm
{ECO:0000256|ARBA:ARBA00004418}".
additional_reference_ids:
- PMID:15077118
supported_by:
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Localization: The periplasm is the site of H2 oxidation in DvH; periplasmic
[NiFe] hydrogenases deliver electrons into the periplasmic cytochrome network.
Genome analysis explicitly highlighted multiple periplasmic NiFe hydrogenases
initiating energy transduction.
- reference_id: UniProt:Q72AS0
supporting_text: >-
SUBCELLULAR LOCATION: Periplasm {ECO:0000256|ARBA:ARBA00004418}
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This generic annotation for metal ion binding is derived from UniProt keyword
mapping (KW-0479: Metal-binding). While technically accurate - the enzyme binds
Ni, Fe, and Mg - this term is too general. More specific metal binding terms
(GO:0016151 nickel cation binding) are already annotated and more informative.
action: ACCEPT
reason: >-
The annotation is correct but redundant given the more specific GO:0016151
(nickel cation binding) annotation. The protein does bind multiple metal ions
(Ni, Fe, Mg) at the active site and structural positions. UniProt shows binding
sites for Ni(2+), Fe cation, and Mg(2+). While not maximally informative, this
general annotation is not misleading.
supported_by:
- reference_id: UniProt:Q72AS0
supporting_text: >-
Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|PIRSR:PIRSR601501-1};
Nickel {ECO:0000256|ARBA:ARBA00022596, ECO:0000256|PIRSR:PIRSR601501-1};
- term:
id: GO:0047806
label: cytochrome-c3 hydrogenase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This is the most accurate molecular function annotation for this enzyme. GO:0047806
describes "Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ +
ferrocytochrome c3" which matches the physiological function of periplasmic
[NiFe] hydrogenases in Desulfovibrio species. The annotation is derived from
RHEA:20625 and EC:1.12.2.1. Kinetic studies demonstrated that cytochrome c3 is
the primary physiological acceptor for periplasmic hydrogenases.
action: ACCEPT
reason: >-
This annotation captures the core molecular function of the enzyme. "Kinetic
measurements in Desulfovibrio spp. show that the [NiFe] periplasmic hydrogenases
reduce Hmc efficiently and that cytochrome c3 markedly accelerates Hmc reduction,
positioning c3 as the principal immediate acceptor from hydrogenases" (Pereira
et al. 1998). UniProt catalytic activity annotation confirms: "2 Fe(III)-[cytochrome
c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 H(+)". EC 1.12.2.1 (hydrogen:cytochrome-c3
oxidoreductase) is the assigned enzyme classification.
additional_reference_ids:
- PMID:15077118
supported_by:
- reference_id: UniProt:Q72AS0
supporting_text: >-
EC=1.12.2.1; Evidence={ECO:0000256|ARBA:ARBA00029307};
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Biochemical/electrochemical analyses in Desulfovibrio emphasize cytochrome c3 as
the principal physiological partner for periplasmic hydrogenases, accelerating
electron delivery to transmembrane complexes like Hmc
- term:
id: GO:0019420
label: dissimilatory sulfate reduction
evidence_type: NAS
original_reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
review:
summary: >-
This biological process annotation captures the pathway context in which hynA1
functions. The periplasmic [NiFe] hydrogenases provide electrons from H2 oxidation
that feed into the cytoplasmic sulfate reduction pathway via membrane-spanning
complexes. While hynA1 does not directly catalyze sulfate reduction, it is part
of the electron transport chain that powers this process.
action: NEW
reason: >-
The role of periplasmic [NiFe] hydrogenases in dissimilatory sulfate reduction
is well established. "Periplasmic H2 oxidation via [NiFe] hydrogenases provides
electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling
to cytoplasmic sulfate reduction" (deep research). This represents the core
biological role of this enzyme in D. vulgaris energy metabolism.
GO annotation guidelines support annotating enzymes to the biological process they
contribute to even when they don't directly catalyze the terminal reaction.
additional_reference_ids:
- PMID:15077118
supported_by:
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Central role in sulfate respiration: Periplasmic H2 oxidation via [NiFe]
hydrogenases provides electrons to the periplasmic cytochrome pool and
inner-membrane complexes, coupling to cytoplasmic sulfate reduction and
contributing to proton motive force via periplasmic proton release.
- term:
id: GO:0019645
label: anaerobic electron transport chain
evidence_type: NAS
original_reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
review:
summary: >-
The periplasmic [NiFe] hydrogenase operates as part of the anaerobic electron
transport chain in D. vulgaris, transferring electrons from H2 to cytochrome c3
and onward to membrane complexes (Hmc/Tmc) that link to cytoplasmic terminal
reductases.
action: NEW
reason: >-
D. vulgaris is an obligate anaerobe and its periplasmic hydrogenases function
in the context of anaerobic respiration. "Electrons are captured by tetraheme
cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules),
linking periplasmic H2 oxidation to cytoplasmic sulfate reduction" (deep research).
This accurately describes participation in an anaerobic electron transport chain.
supported_by:
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
In the hydrogen-cycling model, H2 produced (or supplied) is oxidized in the
periplasm; electrons are captured by tetraheme cytochrome c3 and relayed to
inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic
H2 oxidation to cytoplasmic sulfate reduction and proton motive force generation.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
title: Deep research report on Q72AS0
findings: []
- id: PMID:15077118
title: The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio
vulgaris Hildenborough
findings:
- statement: Genome analysis highlights a c-type cytochrome network connecting
multiple periplasmic hydrogenases and formate dehydrogenases in energy metabolism
supporting_text: >-
genome sequence reveals a network of novel c-type cytochromes, connecting multiple
periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy
metabolism.
- statement: Gene arrangement and inferred localization support an expanded hydrogen-cycling
model for energy efficiency in D. vulgaris
supporting_text: >-
provides a basis for proposing an expansion to the 'hydrogen-cycling' model for
increasing energy efficiency in this bacterium.
core_functions:
- description: >-
Periplasmic [NiFe] hydrogenase that oxidizes H2 and transfers electrons to
cytochrome c3 for anaerobic respiration.
supported_by:
- reference_id: UniProt:Q72AS0
supporting_text: >-
CATALYTIC ACTIVITY: Reaction=2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3]
+ 2 H(+); EC=1.12.2.1
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Biochemical/electrochemical analyses in Desulfovibrio emphasize cytochrome c3 as
the principal physiological partner for periplasmic hydrogenases, accelerating
electron delivery to transmembrane complexes like Hmc
- reference_id: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md
supporting_text: >-
Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the
periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic
sulfate reduction and proton motive force generation.
molecular_function:
id: GO:0047806
label: cytochrome-c3 hydrogenase activity
directly_involved_in:
- id: GO:0019645
label: anaerobic electron transport chain
- id: GO:0019420
label: dissimilatory sulfate reduction
locations:
- id: GO:0042597
label: periplasmic space
proposed_new_terms: []
suggested_questions:
- question: What is the relative contribution of hynA1 vs the [NiFeSe] hydrogenase
to H2 uptake under different growth conditions?
- question: Does hynA1 have any role in hydrogen production under certain physiological
conditions?
- question: What is the kinetic preference of hynA1 for different cytochrome c3
isoforms?
suggested_experiments:
- description: Deletion mutant phenotyping under H2/sulfate growth to quantify contribution
to sulfate reduction
hypothesis: hynA1 is required for efficient H2-dependent sulfate reduction under
specific growth conditions.
- description: Comparative kinetic analysis with purified enzyme and different cytochrome
acceptors
hypothesis: HynA1 preferentially transfers electrons to specific cytochrome c3
isoforms.
- description: Expression analysis under syntrophic growth conditions
hypothesis: hynA1 expression is upregulated during syntrophic growth where H2 is
limiting.