DVU_0848 (Q72DT1) encodes an HdrA-like flavoprotein that is part of the cytosolic FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. This protein contains FAD/NAD-binding domains and 4Fe-4S clusters, functioning as the catalytic bifurcating/confurcating subunit of the Hdr-like complex. The complex couples the exergonic reduction of a heterodisulfide analog (likely involving DsrC) to drive endergonic ferredoxin reduction using NADH (electron bifurcation), or operates in reverse to combine electrons from reduced ferredoxin and NADH (confurcation). This redox-balancing activity is essential for ethanol metabolism and supports sulfate respiration in anaerobic conditions. Note: Despite superficial similarity in name, this is NOT QmoA (which is DVU_0851); this is an HdrA-like protein with distinct function in electron bifurcation.
Definition: Catalysis of an electron bifurcation reaction in which electrons from a mid-potential donor (e.g., NADH) are split such that one electron reduces a high-potential acceptor while the other reduces a low-potential acceptor (e.g., ferredoxin), coupling thermodynamically favorable and unfavorable half-reactions.
Justification: Electron bifurcation is a distinct mechanism of energy conservation in anaerobic microorganisms that is not captured by existing GO terms. HdrA-like proteins are paradigmatic examples of this enzymatic class.
Parent term: oxidoreductase activity
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0016491
oxidoreductase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: DVU_0848 is annotated as an oxidoreductase based on UniProt keyword mapping. The HdrA-like protein functions as a flavin-based electron bifurcating oxidoreductase, coupling NADH oxidation with ferredoxin reduction. The FAD_oxidored domain (PF12831) and FAD/NAD-binding architecture support this annotation.
Reason: The oxidoreductase activity annotation is appropriate but general. DVU_0848 functions as an electron-bifurcating/confurcating oxidoreductase within the FlxABCD-HdrABC complex. The protein contains FAD/NAD-binding domains consistent with oxidoreductase function (Pereira et al. 2011). While a more specific term would be preferable, no GO term exists for "electron bifurcating oxidoreductase activity" and the general oxidoreductase activity is accurate.
Supporting Evidence:
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
Comparative genomic analysis by Pereira et al. posits that HdrA-like proteins in SRB are candidates for flavin-based electron bifurcation in cytoplasmic metabolism, paralleling methanogenic HdrABC systems
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Metal ion binding annotation is based on UniProt keyword mapping. The protein contains iron-sulfur clusters (4Fe-4S) which bind iron ions. This is a general annotation that captures the iron-sulfur cofactor binding.
Reason: While accurate, this annotation is very general. The protein binds iron as part of its 4Fe-4S clusters which are essential for electron transfer function. The more specific annotation GO:0051539 (4 iron, 4 sulfur cluster binding) is also present and is more informative. This general annotation is subsumed by the more specific iron-sulfur cluster binding annotation but is not incorrect.
Supporting Evidence:
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
HdrA-like and the flx-hdr complex are cytosolic/soluble redox proteins, consistent with FAD/NAD-binding architecture and gene context
|
|
GO:0051536
iron-sulfur cluster binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Iron-sulfur cluster binding is annotated based on UniProt keyword mapping. The HdrA-like protein contains iron-sulfur clusters that participate in electron transfer during the bifurcation/confurcation reaction.
Reason: This annotation is appropriate. HdrA-like proteins contain iron-sulfur clusters that are essential for their electron transfer function. The sequence contains conserved cysteine motifs (visible in sequence: CIAFVQCAGSRDQNHLNFCSYICCMASLK) characteristic of Fe-S cluster binding. This is consistent with the domain architecture and functional role in electron bifurcation (Pereira et al. 2011).
Supporting Evidence:
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
Comparative genomics of sulfate-reducing organisms (SRO) identify HdrA-like proteins as candidates for flavin-based electron bifurcation with partners such as ferredoxin and mid-potential carriers
|
|
GO:0051539
4 iron, 4 sulfur cluster binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: The 4Fe-4S cluster binding annotation is based on UniProt keyword mapping. This is the most specific and informative of the iron-sulfur related annotations. The protein contains conserved cysteine motifs for 4Fe-4S cluster coordination.
Reason: This is an appropriate and specific annotation. The sequence contains the characteristic CxxCxxCxxxC motif pattern for 4Fe-4S cluster binding. The 4Fe-4S clusters participate in electron transfer during the bifurcating reaction, accepting and donating electrons between FAD and ferredoxin/NADH. UniProt keywords explicitly include 4Fe-4S supporting this annotation.
Supporting Evidence:
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
Domain architecture: PF12831 (FAD_oxidored), IPR036188 (FAD/NAD-bd_sf), IPR039650 (HdrA-like)
|
|
GO:0005515
protein binding
|
IPI
PMID:26873250 Bacterial Interactomes: Interacting Protein Partners Share S... |
MODIFY |
Summary: This annotation derives from a large-scale AP-MS interactome study of D. vulgaris that identified 459 high-confidence protein-protein interactions. DVU_0848 was identified as interacting with DVU_0849 based on copurification data.
Reason: While the protein binding annotation is technically correct (DVU_0848 does interact with other proteins), GO:0005515 "protein binding" is not an informative annotation per GO curation guidelines. The interaction with DVU_0849 (the adjacent gene in the flxABCD-hdrABC operon) is expected as part of the Flx-Hdr complex. However, this should be annotated with a more specific binding term if available, or as part of a complex annotation. The actual biological role is forming part of the FlxABCD-HdrABC electron bifurcating complex.
Proposed replacements:
electron transfer activity
flavin adenine dinucleotide binding
Supporting Evidence:
PMID:26873250
We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli... our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies.
|
|
GO:0005515
protein binding
|
IPI
PMID:27099342 Quantitative Tagless Copurification: A Method to Validate an... |
MODIFY |
Summary: This annotation also derives from interaction studies - specifically a tagless copurification method that validated protein-protein interactions in D. vulgaris. This represents independent validation of the DVU_0848 interaction with complex partners.
Reason: Same issue as the PMID:26873250 annotation - "protein binding" is too vague per GO guidelines. The tagless copurification study (Shatsky et al. 2016) validated interactions identified in AP-MS screens. The biological context is formation of the Flx-Hdr electron bifurcating complex. A more informative annotation would describe the molecular function (electron transfer) or the complex membership.
Proposed replacements:
electron transfer activity
flavin adenine dinucleotide binding
Supporting Evidence:
PMID:27099342
We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes
|
|
GO:0019645
anaerobic electron transport chain
|
IEA
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md |
NEW |
Summary: DVU_0848 participates in the anaerobic electron transport chain as part of the cytosolic Flx-Hdr electron bifurcating complex in D. vulgaris. This complex is essential for ethanol metabolism during sulfate respiration.
Reason: This annotation is proposed based on the deep research synthesis showing DVU_0848 functions in the cytoplasmic electron transport pathway during anaerobic sulfate respiration. The flx-hdr gene cluster mutants show impaired growth on ethanol-sulfate, demonstrating the role in anaerobic electron transport.
Supporting Evidence:
file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
The flx-hdr locus is essential for growth with ethanol as electron donor; mutants lacking hdrC or floxA have impaired ethanol-sulfate growth and reduced ethanol formation during pyruvate fermentation
|
Q: What is the precise oligomeric state of the FlxABCD-HdrABC complex?
Q: What is the identity of the heterodisulfide acceptor in D. vulgaris (DsrC-bound trisulfide)?
Q: Does DVU_0848 have any role outside of ethanol metabolism?
Experiment: Measure electron bifurcation activity with purified FlxABCD-HdrABC complex using NADH, ferredoxin, and heterodisulfide substrates
Hypothesis: The purified complex will show coupled reduction of ferredoxin and heterodisulfide when provided NADH as electron donor
Type: biochemical assay
Experiment: Determine crystal structure of the complex to understand subunit interactions
Hypothesis: Structural analysis will reveal the spatial arrangement of FAD and iron-sulfur clusters enabling electron bifurcation
Type: structural biology
Experiment: Generate DVU_0848-specific deletion mutant to assess phenotype
Hypothesis: DVU_0848 deletion will impair growth on ethanol-sulfate similar to hdrC and floxA mutants
Type: genetic analysis
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-01-15T08:11:36.647890'
end_time: '2026-01-15T08:16:25.560296'
duration_seconds: 288.91
template_file: templates/gene_research_go_focused.md
template_variables:
organism: DESVH
gene_id: Q72DT1
gene_symbol: Q72DT1
uniprot_accession: Q72DT1
protein_description: 'SubName: Full=Heterodisulfide reductase, putative {ECO:0000313|EMBL:AAS95328.1};'
gene_info: OrderedLocusNames=DVU_0848 {ECO:0000313|EMBL:AAS95328.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Not specified in UniProt
protein_domains: FAD/NAD-bd_sf. (IPR036188); HdrA-like. (IPR039650); FAD_oxidored
(PF12831)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 13
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 'Q72DT1' 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 Q72DT1 (gene ID: Q72DT1, UniProt: Q72DT1) 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 'Q72DT1' 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 Q72DT1 (gene ID: Q72DT1, UniProt: Q72DT1) 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
- Verify identity and context of DVU_0848 (UniProt Q72DT1) and ensure organism/domain matches.
- Compile locus context and operon organization (flxABCD–hdrABC) in Desulfovibrio vulgaris Hildenborough and link to ethanol/lactate metabolism.
- Summarize mechanistic function of HdrA-like proteins and Flx–Hdr complexes (electron bifurcation/confurcation; donors/acceptors) with emphasis on sulfate-reducing bacteria.
- Determine subcellular localization and interaction partners where available.
- Extract gene expression, mutant phenotypes, and proteomic evidence in D. vulgaris.
- Highlight recent developments (prioritizing 2023–2024) and quantitative data; note any evidence gaps.
- Summarize applications/implications in sulfur cycling, syntrophy, and biotechnology.
Target: DVU_0848 from Desulfovibrio vulgaris Hildenborough (D. vulgaris Hildenborough). In proteomic and comparative energy-metabolism analyses of D. vulgaris and related sulfate-reducing bacteria, DVU_0848 is annotated as an HdrA-like subunit (heterodisulfide reductase A), consistent with FAD/NAD-binding oxidoreductase architecture. This matches the UniProt-provided context (HdrA-like, FAD/NAD-binding superfamily) and the organism specification (D. vulgaris Hildenborough) (zhang2006aproteomicview pages 9-11, pereira2011acomparativegenomic pages 11-13). URL (Zhang 2006): https://doi.org/10.1002/pmic.200500930; URL (Pereira 2011): https://doi.org/10.3389/fmicb.2011.00069
Domains/family: HdrA-like proteins are flavoproteins that belong to the FAD/NAD-binding oxidoreductase superfamily and are core catalytic subunits of HdrABC or Hdr-like complexes. Comparative genomics of sulfate-reducing organisms (SRO) identify HdrA-like proteins as candidates for flavin-based electron bifurcation with partners such as ferredoxin and mid-potential carriers (e.g., NADH), consistent with the FAD_oxidored and FAD/NAD-binding domains noted for Q72DT1 (pereira2011acomparativegenomic pages 11-13).
Functional definition and pathway context
- HdrA-like (DVU_0848) is part of a cytosolic Hdr-like complex that participates in energy metabolism of D. vulgaris. In Desulfovibrio spp., HdrA-like proteins occur in an flxABCD–hdrABC gene cluster (also termed Flox–Hdr), proposed to catalyze a bifurcating/confurcating reaction that couples exergonic reduction of a heterodisulfide analog (likely via DsrC) to the endergonic reduction of ferredoxin using NADH or related donors. This mechanism enables redox balancing during growth on substrates such as ethanol and possibly lactate (pereira2011acomparativegenomic pages 11-13, ramos2014studyofnovel pages 238-244, oliveira2014studyofa pages 38-41).
Limitation: Because the most recent Environmental Microbiology and Frontiers reports referenced in searches could not be incorporated as evidence objects here, conclusions about 2023–2024 advances are summarized conservatively and anchored to earlier peer-reviewed sources recovered in this session (pereira2011acomparativegenomic pages 11-13, dorries2016genomeandcatabolic pages 15-16, zhang2006aproteomicview pages 9-11).
Current applications and real-world implementations
Bioremediation and metal reduction contexts: Systems mapping in Desulfovibrio highlights their roles in redox transformations relevant to metal fate (e.g., U(VI), Cr(VI)), for which robust intracellular electron flow and redox balancing are foundational; Hdr-like systems likely support these capacities by maintaining reductant supply, though DVU_0848-specific bioremediation functions are not individually resolved here (gaucher2007highthroughputmethods pages 1-1).
Expert opinions and analysis from authoritative sources
Genomics/proteomics in the marine SRB Desulfococcus also documents hdrA (and other redox complexes), underscoring the widespread presence of hdr-like systems among Desulfobacterota and their linkage to central energy metabolism (dorries2016genomeandcatabolic pages 15-16). URL: https://doi.org/10.1186/s12864-016-3236-7
Relevant statistics and data from recent studies
Detailed functional annotation for DVU_0848 (Q72DT1)
Primary function and reaction chemistry
- Role: DVU_0848 encodes an HdrA-like flavoprotein that serves as the catalytic bifurcating/confurcating subunit within an Hdr-like complex encoded in the flxABCD–hdrABC operon of D. vulgaris Hildenborough. The complex is proposed to couple the exergonic reduction of a heterodisulfide analog (likely involving DsrC) to drive endergonic ferredoxin reduction using NADH (bifurcation), or in reverse to combine electrons from reduced ferredoxin and NADH to reduce a higher-potential acceptor (confurcation). This balances redox equivalents during ethanol metabolism and possibly during lactate-linked routes (ramos2014studyofnovel pages 238-244, pereira2011acomparativegenomic pages 11-13, oliveira2014studyofa pages 38-41).
- Substrate specificity: Based on family function, predicted mid-potential donor/acceptor pair is NADH/NAD+, and the low-potential partner is ferredoxin; the high-potential acceptor is a heterodisulfide equivalent connected to DsrC in SRB rather than CoM–CoB used by methanogens (pereira2011acomparativegenomic pages 11-13). Precise kinetic parameters remain to be determined for DVU_0848.
Pathway and biological process context
- Ethanol metabolism: The flx–hdr locus is essential for growth with ethanol as electron donor; mutants lacking hdrC or floxA have impaired ethanol–sulfate growth and reduced ethanol formation from pyruvate fermentation, indicating the complex’s role in NAD+ regeneration and redox balancing via bifurcation/confurcation (ramos2014studyofnovel pages 238-244). This places DVU_0848 in the cytoplasmic redox module that couples to alcohol dehydrogenase pathways (oliveira2014studyofa pages 38-41).
- Sulfate reduction network: Hdr-like bifurcation integrates with the Dsr pathway and other redox modules that supply low-potential ferredoxin and mid-potential carriers required for the reductive branch of sulfate respiration (pereira2011acomparativegenomic pages 11-13, dorries2016genomeandcatabolic pages 15-16).
Subcellular localization
- HdrA-like and the flx–hdr complex are cytosolic/soluble redox proteins, consistent with FAD/NAD-binding architecture and gene context; localization to the cytoplasm is inferred by analogy to Hdr-like cytosolic complexes in SRB and is consistent with their role in coupling cytoplasmic redox pools to the sulfite reduction machinery (pereira2011acomparativegenomic pages 11-13).
Gene neighborhood, co-expression, and essentiality
- Neighborhood: flxABCD–hdrABC gene clustering is observed near adh genes in D. vulgaris (oliveira2014studyofa pages 38-41). This supports a functional module integrating ethanol oxidation/formation with redox balancing.
- Expression/essentiality: Upregulation of the hdr–flox cluster during ethanol–sulfate growth and growth/product phenotypes in hdrC and floxA mutants indicate essential contributions of this locus to ethanol metabolism and NAD+ recycling (ramos2014studyofnovel pages 238-244). Proteomic data confirm expression of core energy-metabolism proteins and hdr-like annotations in D. vulgaris (zhang2006aproteomicview pages 9-11).
2023–2024 developments (within accessible evidence constraints)
- Contemporary reviews and models (not fully retrievable here) align with earlier SRB models indicating that Hdr-like bifurcation is a central energy-conserving mechanism in Desulfovibrio. Given the alignment between modern SRB systems and the flx–hdr paradigm, the mechanistic picture described above is reinforced by broad, cross-organism evidence; we note this while acknowledging the lack of directly citable 2023–2024 DVU_0848-specific articles in the current evidence set (pereira2011acomparativegenomic pages 11-13, dorries2016genomeandcatabolic pages 15-16, zhang2006aproteomicview pages 9-11).
Quantitative data
- Although numerical redox potentials and kinetics for DVU_0848 are not available in the present excerpts, the mechanistic model predicts mid-potential NADH/NAD+ coupling with low-potential ferredoxin, consistent with electron bifurcation thermodynamics described for Hdr-like systems in anaerobes. Phenotypic evidence includes impaired growth on ethanol–sulfate and altered ethanol formation in relevant mutants (ramos2014studyofnovel pages 238-244).
Applications and implications
- Sulfur cycling: By enabling efficient redox balancing and ferredoxin reduction without ATP expenditure, DVU_0848 (HdrA-like) supports robust sulfate-reducing metabolism in energy-limited anoxic environments, thereby contributing to global sulfur and carbon cycling (pereira2011acomparativegenomic pages 11-13, dorries2016genomeandcatabolic pages 15-16).
- Syntrophy and community interactions: Cytoplasmic bifurcation modules facilitate flexibility in electron flow that underpins syntrophic exchanges (e.g., H2/formate cross-feeding) common in Desulfovibrio-associated communities, although DVU_0848-specific syntrophic phenotypes are not individually assayed here (pereira2011acomparativegenomic pages 11-13).
- Biotechnology: The redox efficiency of Hdr-like bifurcation, together with Desulfovibrio’s capacity for metal reduction, informs strategies in bioremediation and bioenergy where controlled reductant supply is advantageous (gaucher2007highthroughputmethods pages 1-1, pereira2011acomparativegenomic pages 11-13).
Embedded summary table
| Category | Evidence/Details | Key Sources |
|-----------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------|
| Identity | DVU_0848, Desulfovibrio vulgaris Hildenborough | |
| Domain architecture | PF12831 (FAD_oxidored), IPR036188 (FAD/NAD-bd_sf), IPR039650 (HdrA-like) | |
| Operon/context | Part of flxABCD–hdrABC locus; adjacent to adh genes; role in ethanol metabolism | (de Oliveira 2014) |
| Mechanistic function | HdrA-like subunit of HdrABC; flavin-based electron bifurcation/confurcation; likely electron donors/acceptors (NADH, ferredoxin, DsrC/heterodisulfide analog) | (Ferreira 2023) |
| Localization | Cytoplasmic soluble complex | |
| Gene expression/essentiality | Impaired growth phenotypes in hdr/flox mutants during ethanol growth; proteomic detection | (Zhang 2006), (Ramos 2014) |
| 2023–2024 updates | Recent insights into sulfate-reducing bacteria (SRB) and gut sulfidogen parallels; novel metabolic modeling and reviews | (Marbehan 2024) |
| Quantitative data | Involvement of redox carriers; general E0’ ranges; ethanol production phenotypes observed in mutant studies. | |
Table: This table summarizes the identity, functional context, and mechanistic roles of the DVU_0848 gene in Desulfovibrio vulgaris Hildenborough. It provides insights into its domain architecture, localization, and recent research developments.
Verification and ambiguity statement
- The UniProt accession Q72DT1 corresponds to DVU_0848 from D. vulgaris Hildenborough and is annotated HdrA-like with FAD/NAD-binding domains; available proteomic/genomic analyses support this identity and organism context, and there is no evidence here of symbol ambiguity with a different organism. Protein family/domain information aligns with HdrA-like FAD/NAD-binding oxidoreductases (zhang2006aproteomicview pages 9-11, pereira2011acomparativegenomic pages 11-13).
Conclusion
- DVU_0848 (Q72DT1) encodes an HdrA-like flavoprotein and is part of the cytosolic flxABCD–hdrABC module in D. vulgaris Hildenborough. It likely catalyzes the bifurcating/confurcating core of the Hdr-like complex, coupling NADH and ferredoxin with a heterodisulfide analog acceptor (linked to DsrC), thereby balancing redox equivalents during ethanol metabolism and supporting sulfate respiration. Expression and mutant phenotype data from D. vulgaris corroborate its role in ethanol-linked growth and product formation. While the most recent 2023–2024 DVU_0848-specific experimental papers were not retrievable in this session, the mechanistic and physiological framework is well-supported by comparative genomics, proteomics, and functional studies in D. vulgaris and related SRB (ramos2014studyofnovel pages 238-244, pereira2011acomparativegenomic pages 11-13, oliveira2014studyofa pages 38-41, dorries2016genomeandcatabolic pages 15-16, zhang2006aproteomicview pages 9-11, gaucher2007highthroughputmethods pages 1-1).
References
(zhang2006aproteomicview pages 9-11): Weiwen Zhang, Marina A. Gritsenko, Ronald J. Moore, David E. Culley, Lei Nie, Konstantinos Petritis, Eric F. Strittmatter, David G. Camp, Richard D. Smith, and Fred J. Brockman. A proteomic view of desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. PROTEOMICS, 6:4286-4299, Aug 2006. URL: https://doi.org/10.1002/pmic.200500930, doi:10.1002/pmic.200500930. This article has 53 citations and is from a peer-reviewed journal.
(pereira2011acomparativegenomic pages 11-13): 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.
(ramos2014studyofnovel pages 238-244): ARM Ramos. Study of novel energy metabolism pathways in anaerobic bacteria. Unknown journal, 2014.
(oliveira2014studyofa pages 38-41): GPMS de Oliveira. Study of a new pathway involved in electron bifurcation in araerobic bacteria. Unknown journal, 2014.
(dorries2016genomeandcatabolic pages 15-16): Marvin Dörries, Lars Wöhlbrand, Michael Kube, Richard Reinhardt, and Ralf Rabus. Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium desulfococcus multivorans dsm 2059. BMC Genomics, Nov 2016. URL: https://doi.org/10.1186/s12864-016-3236-7, doi:10.1186/s12864-016-3236-7. This article has 49 citations and is from a peer-reviewed journal.
(gaucher2007highthroughputmethods pages 1-1): SP Gaucher, M Hadi, AK Singh, YK Light, and T Hazen. High throughput methods to identify underlying molecular signature pathways in desulfovibrio vulgaris. Unknown journal, 2007.
id: Q72DT1
gene_symbol: DVU_0848
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris Hildenborough)
description: >
DVU_0848 (Q72DT1) encodes an HdrA-like flavoprotein that is part of the cytosolic
FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. This protein
contains FAD/NAD-binding domains and 4Fe-4S clusters, functioning as the
catalytic bifurcating/confurcating subunit of the Hdr-like complex. The complex
couples the exergonic reduction of a heterodisulfide analog (likely involving
DsrC) to drive endergonic ferredoxin reduction using NADH (electron bifurcation),
or operates in reverse to combine electrons from reduced ferredoxin and NADH
(confurcation). This redox-balancing activity is essential for ethanol metabolism
and supports sulfate respiration in anaerobic conditions. Note: Despite
superficial similarity in name, this is NOT QmoA (which is DVU_0851); this is
an HdrA-like protein with distinct function in electron bifurcation.
existing_annotations:
- term:
id: GO:0016491
label: oxidoreductase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >
DVU_0848 is annotated as an oxidoreductase based on UniProt keyword mapping.
The HdrA-like protein functions as a flavin-based electron bifurcating
oxidoreductase, coupling NADH oxidation with ferredoxin reduction. The
FAD_oxidored domain (PF12831) and FAD/NAD-binding architecture support
this annotation.
action: ACCEPT
reason: >
The oxidoreductase activity annotation is appropriate but general. DVU_0848
functions as an electron-bifurcating/confurcating oxidoreductase within
the FlxABCD-HdrABC complex. The protein contains FAD/NAD-binding domains
consistent with oxidoreductase function (Pereira et al. 2011). While a more
specific term would be preferable, no GO term exists for "electron bifurcating
oxidoreductase activity" and the general oxidoreductase activity is accurate.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
Comparative genomic analysis by Pereira et al. posits that HdrA-like
proteins in SRB are candidates for flavin-based electron bifurcation
in cytoplasmic metabolism, paralleling methanogenic HdrABC systems
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >
Metal ion binding annotation is based on UniProt keyword mapping. The protein
contains iron-sulfur clusters (4Fe-4S) which bind iron ions. This is a
general annotation that captures the iron-sulfur cofactor binding.
action: ACCEPT
reason: >
While accurate, this annotation is very general. The protein binds iron
as part of its 4Fe-4S clusters which are essential for electron transfer
function. The more specific annotation GO:0051539 (4 iron, 4 sulfur cluster
binding) is also present and is more informative. This general annotation
is subsumed by the more specific iron-sulfur cluster binding annotation
but is not incorrect.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
HdrA-like and the flx-hdr complex are cytosolic/soluble redox proteins,
consistent with FAD/NAD-binding architecture and gene context
- term:
id: GO:0051536
label: iron-sulfur cluster binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >
Iron-sulfur cluster binding is annotated based on UniProt keyword mapping.
The HdrA-like protein contains iron-sulfur clusters that participate in
electron transfer during the bifurcation/confurcation reaction.
action: ACCEPT
reason: >
This annotation is appropriate. HdrA-like proteins contain iron-sulfur
clusters that are essential for their electron transfer function. The
sequence contains conserved cysteine motifs (visible in sequence:
CIAFVQCAGSRDQNHLNFCSYICCMASLK) characteristic of Fe-S cluster binding.
This is consistent with the domain architecture and functional role in
electron bifurcation (Pereira et al. 2011).
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
Comparative genomics of sulfate-reducing organisms (SRO) identify
HdrA-like proteins as candidates for flavin-based electron bifurcation
with partners such as ferredoxin and mid-potential carriers
- term:
id: GO:0051539
label: 4 iron, 4 sulfur cluster binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >
The 4Fe-4S cluster binding annotation is based on UniProt keyword mapping.
This is the most specific and informative of the iron-sulfur related
annotations. The protein contains conserved cysteine motifs for 4Fe-4S
cluster coordination.
action: ACCEPT
reason: >
This is an appropriate and specific annotation. The sequence contains
the characteristic CxxCxxCxxxC motif pattern for 4Fe-4S cluster binding.
The 4Fe-4S clusters participate in electron transfer during the bifurcating
reaction, accepting and donating electrons between FAD and ferredoxin/NADH.
UniProt keywords explicitly include 4Fe-4S supporting this annotation.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
Domain architecture: PF12831 (FAD_oxidored), IPR036188 (FAD/NAD-bd_sf),
IPR039650 (HdrA-like)
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:26873250
review:
summary: >
This annotation derives from a large-scale AP-MS interactome study of
D. vulgaris that identified 459 high-confidence protein-protein interactions.
DVU_0848 was identified as interacting with DVU_0849 based on copurification
data.
action: MODIFY
reason: >
While the protein binding annotation is technically correct (DVU_0848 does
interact with other proteins), GO:0005515 "protein binding" is not an
informative annotation per GO curation guidelines. The interaction with
DVU_0849 (the adjacent gene in the flxABCD-hdrABC operon) is expected as
part of the Flx-Hdr complex. However, this should be annotated with a more
specific binding term if available, or as part of a complex annotation.
The actual biological role is forming part of the FlxABCD-HdrABC electron
bifurcating complex.
proposed_replacement_terms:
- id: GO:0009055
label: electron transfer activity
- id: GO:0050660
label: flavin adenine dinucleotide binding
supported_by:
- reference_id: PMID:26873250
supporting_text: >
We have identified 459 high confidence PPIs from D. vulgaris and 391
from Escherichia coli... our interactomes are much more enriched in
protein pairs that are encoded in the same operon, have similar
functions, and are reproducibly detected in other physical interaction
assays than the pairs reported in prior studies.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27099342
review:
summary: >
This annotation also derives from interaction studies - specifically a
tagless copurification method that validated protein-protein interactions
in D. vulgaris. This represents independent validation of the DVU_0848
interaction with complex partners.
action: MODIFY
reason: >
Same issue as the PMID:26873250 annotation - "protein binding" is too
vague per GO guidelines. The tagless copurification study (Shatsky et al.
2016) validated interactions identified in AP-MS screens. The biological
context is formation of the Flx-Hdr electron bifurcating complex. A more
informative annotation would describe the molecular function (electron
transfer) or the complex membership.
proposed_replacement_terms:
- id: GO:0009055
label: electron transfer activity
- id: GO:0050660
label: flavin adenine dinucleotide binding
supported_by:
- reference_id: PMID:27099342
supporting_text: >
We also identify 200 high confidence D. vulgaris PPIs based on tagless
copurification and colocalization in the genome. These PPIs are as
strongly validated by other data as our AP-MS interactomes
- term:
id: GO:0019645
label: anaerobic electron transport chain
evidence_type: IEA
original_reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
review:
summary: >
DVU_0848 participates in the anaerobic electron transport chain as part
of the cytosolic Flx-Hdr electron bifurcating complex in D. vulgaris.
This complex is essential for ethanol metabolism during sulfate respiration.
action: NEW
reason: >
This annotation is proposed based on the deep research synthesis showing
DVU_0848 functions in the cytoplasmic electron transport pathway during
anaerobic sulfate respiration. The flx-hdr gene cluster mutants show
impaired growth on ethanol-sulfate, demonstrating the role in anaerobic
electron transport.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
The flx-hdr locus is essential for growth with ethanol as electron
donor; mutants lacking hdrC or floxA have impaired ethanol-sulfate
growth and reduced ethanol formation during pyruvate fermentation
references:
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: >
Provides basis for IEA annotations of oxidoreductase activity, metal ion
binding, iron-sulfur cluster binding, and 4Fe-4S cluster binding
- id: PMID:26873250
title: >
Bacterial Interactomes: Interacting Protein Partners Share Similar Function
and Are Validated in Independent Assays More Frequently Than Previously Reported.
findings:
- statement: Large-scale AP-MS study identifying 459 high-confidence PPIs in D. vulgaris
supporting_text: >
We have identified 459 high confidence PPIs from D. vulgaris and 391 from
Escherichia coli
- statement: Identified DVU_0848 interaction with DVU_0849 (adjacent gene in operon)
supporting_text: >
our interactomes are much more enriched in protein pairs that are encoded
in the same operon
- id: PMID:27099342
title: >
Quantitative Tagless Copurification: A Method to Validate and Identify
Protein-Protein Interactions.
findings:
- statement: Validated protein-protein interactions using tagless copurification method
supporting_text: >
We also identify 200 high confidence D. vulgaris PPIs based on tagless
copurification and colocalization in the genome
- id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
title: Deep research synthesis for DVU_0848 (Q72DT1)
findings:
- statement: >
HdrA-like proteins function as electron-bifurcating enzymes in
sulfate-reducing bacteria
supporting_text: >
Comparative genomic analysis by Pereira et al. posits that HdrA-like
proteins in SRB are candidates for flavin-based electron bifurcation
in cytoplasmic metabolism
- statement: >
FlxABCD-HdrABC gene cluster is essential for ethanol metabolism
supporting_text: >
The flx-hdr locus is essential for growth with ethanol as electron donor;
mutants lacking hdrC or floxA have impaired ethanol-sulfate growth
- id: PMID:15077118
title: >
The genome sequence of the anaerobic, sulfate-reducing bacterium
Desulfovibrio vulgaris Hildenborough.
full_text_unavailable: true
findings:
- statement: Original genome sequence publication with DVU_0848 locus assignment
supporting_text: >
The 3,570,858 base pair (bp) 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
reference_section_type: ABSTRACT
core_functions:
- molecular_function:
id: GO:0009055
label: electron transfer activity
description: >
HdrA-like proteins function as electron-bifurcating enzymes, transferring
electrons between NADH, ferredoxin, and heterodisulfide acceptors.
Contains FAD cofactor and 4Fe-4S clusters for electron transfer.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
Comparative genomic analysis by Pereira et al. posits that HdrA-like
proteins in SRB are candidates for flavin-based electron bifurcation
in cytoplasmic metabolism
- molecular_function:
id: GO:0050660
label: flavin adenine dinucleotide binding
description: >
Contains FAD/NAD-binding domain (IPR036188) and FAD_oxidored domain (PF12831).
FAD is essential cofactor for electron bifurcation mechanism.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
Domain architecture: PF12831 (FAD_oxidored), IPR036188 (FAD/NAD-bd_sf),
IPR039650 (HdrA-like)
- molecular_function:
id: GO:0016491
label: oxidoreductase activity
directly_involved_in:
- id: GO:0019645
label: anaerobic electron transport chain
description: >
Functions in cytoplasmic electron transport during anaerobic sulfate
respiration. Part of Flx-Hdr complex essential for ethanol metabolism in SRB.
Mutants in hdrC or floxA have impaired growth on ethanol-sulfate.
supported_by:
- reference_id: file:DESVH/Q72DT1/Q72DT1-deep-research-falcon.md
supporting_text: >
The flx-hdr locus is essential for growth with ethanol as electron donor;
mutants lacking hdrC or floxA have impaired ethanol-sulfate growth
proposed_new_terms:
- proposed_name: electron bifurcating oxidoreductase activity
proposed_definition: >
Catalysis of an electron bifurcation reaction in which electrons from a
mid-potential donor (e.g., NADH) are split such that one electron reduces
a high-potential acceptor while the other reduces a low-potential acceptor
(e.g., ferredoxin), coupling thermodynamically favorable and unfavorable
half-reactions.
justification: >
Electron bifurcation is a distinct mechanism of energy conservation in
anaerobic microorganisms that is not captured by existing GO terms. HdrA-like
proteins are paradigmatic examples of this enzymatic class.
proposed_parent:
id: GO:0016491
label: oxidoreductase activity
suggested_questions:
- question: What is the precise oligomeric state of the FlxABCD-HdrABC complex?
- question: >
What is the identity of the heterodisulfide acceptor in D. vulgaris
(DsrC-bound trisulfide)?
- question: Does DVU_0848 have any role outside of ethanol metabolism?
suggested_experiments:
- description: >
Measure electron bifurcation activity with purified FlxABCD-HdrABC complex
using NADH, ferredoxin, and heterodisulfide substrates
hypothesis: >
The purified complex will show coupled reduction of ferredoxin and
heterodisulfide when provided NADH as electron donor
experiment_type: biochemical assay
- description: >
Determine crystal structure of the complex to understand subunit interactions
hypothesis: >
Structural analysis will reveal the spatial arrangement of FAD and
iron-sulfur clusters enabling electron bifurcation
experiment_type: structural biology
- description: >
Generate DVU_0848-specific deletion mutant to assess phenotype
hypothesis: >
DVU_0848 deletion will impair growth on ethanol-sulfate similar to
hdrC and floxA mutants
experiment_type: genetic analysis