QmoC (DVU_0850) is the membrane-integral subunit C of the quinone-interacting membrane-bound oxidoreductase (QmoABC) complex in Desulfovibrio vulgaris Hildenborough. The Qmo complex functions as an electron transfer hub in dissimilatory sulfate reduction, transferring electrons from the menaquinone pool to adenylylsulfate (APS) reductase (AprAB). QmoC contains six transmembrane helices and a 4Fe-4S ferredoxin-type domain, serving as the membrane anchor that interfaces with the quinone pool. The protein is essential for the anaerobic electron transport chain during sulfate respiration, connecting cytoplasmic electron donors to the terminal reduction of sulfate. Proteomic and interactome studies in D. vulgaris have validated the physical interaction between the Qmo complex and APS reductase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: QmoC is the membrane-integral subunit of the QmoABC complex. UniProt Phobius predictions identify six transmembrane helices (aa 121-145, 165-186, 238-259, 279-297, 309-329, 341-362). Literature explicitly describes DVU0849-DVU0850 as encoding the quinone-interacting membrane-bound oxidoreductase complex. The deep research file confirms that the Qmo complex is membrane-associated and DVU_0850 is a membrane protein that interfaces with the quinone pool at the cytoplasmic membrane.
Reason: Multiple lines of evidence support plasma membrane localization. Phobius prediction of 6 TM helices, InterPro domains including transmembrane di-heme cytochromes (Gene3D 1.20.950.20), and literature explicitly describing Qmo as membrane-bound. This is a core localization for QmoC function.
Supporting Evidence:
DOI:10.1128/aem.01655-16
DVU0849-DVU0850 as coding for the quinone-interacting membrane-bound oxidoreductase complex (Qmo)
DOI:10.1128/aem.02469-07
heterodisulfide reductase complex (DVU0848 to DVU0850)
file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
The Qmo complex is membrane-associated; by inference and by the explicit characterization of DVU0849-DVU0850 as coding for the quinone-interacting membrane-bound oxidoreductase complex, DVU_0850 is a membrane protein.
|
|
GO:0016491
oxidoreductase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: QmoC is a subunit of the quinone-interacting membrane-bound oxidoreductase (Qmo) complex. The complex transfers electrons between the quinone pool and APS reductase during dissimilatory sulfate reduction. While this annotation is correct, it is quite broad for a protein with a specific role in electron transfer to APS reductase.
Reason: The annotation is accurate as QmoC is part of an oxidoreductase complex. UniProt keywords include "Oxidoreductase" and the protein belongs to the NarG-like superfamily (respiratory nitrate reductase-related). The term captures the general enzymatic category, though more specific terms for electron transfer activity could supplement this.
Supporting Evidence:
DOI:10.1128/aem.01655-16
quinone-interacting membrane-bound oxidoreductase complex
DOI:10.1002/pmic.200500930
DVU0848-DVU0850 with membrane electron-transfer roles consistent with energy metabolism in DvH
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: QmoC contains a 4Fe-4S ferredoxin-type domain (aa 61-86) and is predicted to bind iron. The protein has UniProt keywords for Iron, Iron-sulfur, and Metal-binding. This is a general parent term that is accurately applied.
Reason: The protein clearly binds metal ions through its iron-sulfur cluster. PROSITE patterns PS00198 and PS51379 identify 4Fe-4S binding sites. While more specific child terms (iron ion binding, 4Fe-4S cluster binding) are also annotated, retaining this parent term is appropriate for completeness.
Supporting Evidence:
UniProt:Q72DS9
DOMAIN 61..86 /note="4Fe-4S ferredoxin-type" /evidence="ECO:0000259|PROSITE:PS51379"
|
|
GO:0051536
iron-sulfur cluster binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: QmoC contains an experimentally predicted 4Fe-4S ferredoxin-type domain. InterPro domains include 4Fe4S_Fe-S-bd (IPR017896), 4Fe4S_Fe_S_CS (IPR017900), and HdrC_iron-sulfur_subunit (IPR051460). The Pfam domain Fer4_8 (PF13183) is also present.
Reason: Iron-sulfur cluster binding is a core functional property of QmoC. Multiple computational methods predict this binding capacity, which is essential for electron transfer function. This is supported by the more specific 4Fe-4S cluster binding annotation.
Supporting Evidence:
InterPro:IPR017896
4Fe4S_Fe-S-bd domain
InterPro:IPR051460
HdrC_iron-sulfur_subunit domain
|
|
GO:0051539
4 iron, 4 sulfur cluster binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: QmoC contains a defined 4Fe-4S ferredoxin-type domain at positions 61-86. This is supported by PROSITE pattern PS00198 (4FE4S_FER_1) and profile PS51379 (4FE4S_FER_2). The protein is also annotated with the helical ferredoxin InterPro domain (IPR009051).
Reason: This is a specific and accurate annotation. The 4Fe-4S cluster is essential for the electron transfer function of QmoC within the Qmo complex. Domain predictions from multiple sources (PROSITE, Pfam, InterPro) consistently identify this binding capacity.
Supporting Evidence:
PROSITE:PS00198
4FE4S_FER_1 pattern match
PROSITE:PS51379
4Fe-4S ferredoxin-type domain at positions 61-86
|
|
GO:0019645
anaerobic electron transport chain
|
ISS
DOI:10.1128/aem.01655-16 |
NEW |
Summary: The Qmo complex is part of the anaerobic electron transport chain in sulfate-reducing bacteria. It transfers electrons from the quinone pool to APS reductase during dissimilatory sulfate reduction.
Reason: This annotation captures the core biological process in which QmoC participates. The Qmo complex is explicitly part of the respiratory electron transport machinery during anaerobic sulfate respiration. Evidence from the deep research file and publications supports this role.
Supporting Evidence:
DOI:10.1128/aem.01655-16
DVU0849-DVU0850 expression was repressed alongside broader anaerobic respiration machinery
file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
DVU_0850 contributes at the membrane quinone interface (Qmo), while Hdr-Flx modules manage cytosolic redox coupling and low-potential electron supply.
|
|
GO:0019420
dissimilatory sulfate reduction
|
ISS
DOI:10.1128/aem.02469-07 |
NEW |
Summary: QmoC is essential for dissimilatory sulfate reduction by providing electrons to APS reductase, which catalyzes the first reductive step in the pathway (APS to sulfite).
Reason: This is the defining biological process for sulfate-reducing bacteria like D. vulgaris. The Qmo complex is positioned at a critical junction transferring electrons from the quinone pool to APS reductase. Proteomic evidence from PMID:27099342 confirms Qmo-AprA interaction.
Supporting Evidence:
DOI:10.1128/aem.02469-07
heterodisulfide reductase complex (DVU0848 to DVU0850) under cathodic growth, directly tying the DVU numbering to this organism
PMID:27099342
Qmo oxidoreductase and adenyl sulfate reductase alpha subunit
|
|
GO:0048038
quinone binding
|
ISS
DOI:10.1128/aem.01655-16 |
NEW |
Summary: As the membrane subunit of the quinone-interacting membrane-bound oxidoreductase complex, QmoC is expected to interact with the quinone pool (menaquinone in D. vulgaris).
Reason: The name "quinone-interacting membrane-bound oxidoreductase" explicitly indicates quinone interaction. QmoC is the membrane anchor subunit and thus the primary interface with the membrane-embedded quinone pool.
Supporting Evidence:
DOI:10.1128/aem.01655-16
quinone-interacting membrane-bound oxidoreductase complex (Qmo)
file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
As a Qmo membrane component, DVU_0850 interfaces with the membrane quinone pool
|
|
GO:0009055
electron transfer activity
|
ISS
DOI:10.1002/pmic.200500930 |
NEW |
Summary: QmoC participates in electron transfer from the quinone pool to APS reductase via its iron-sulfur clusters. This electron transfer activity is the primary molecular function of the Qmo complex.
Reason: The Qmo complex functions as an electron transfer module. QmoC with its 4Fe-4S cluster and membrane localization facilitates electron flow between the quinone pool and the soluble APS reductase complex. This is a more specific functional annotation than generic oxidoreductase.
Supporting Evidence:
DOI:10.1002/pmic.200500930
DVU0848-DVU0850 with membrane electron-transfer roles consistent with energy metabolism in DvH
|
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: DESVH
gene_id: Q72DS9
gene_symbol: Q72DS9
uniprot_accession: Q72DS9
protein_description: 'SubName: Full=Heterodisulfide reductase, transmembrane subunit,
putative {ECO:0000313|EMBL:AAS95330.1};'
gene_info: OrderedLocusNames=DVU_0850 {ECO:0000313|EMBL:AAS95330.1};
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: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); HdrC_iron-sulfur_subunit.
(IPR051460); Helical_ferredxn. (IPR009051); NarG-like_sf. (IPR036197)
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citation_count: 19
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 'Q72DS9' 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 Q72DS9 (gene ID: Q72DS9, UniProt: Q72DS9) 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 'Q72DS9' 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 Q72DS9 (gene ID: Q72DS9, UniProt: Q72DS9) in DESVH.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan
- Verified the target: UniProt accession Q72DS9 corresponds to the ordered locus DVU_0850 in Desulfovibrio vulgaris Hildenborough (DvH). Literature from DvH explicitly discusses the DVU0848–DVU0850 locus; however, sources differ on whether they refer to it as a heterodisulfide reductase-like (Hdr) locus or the quinone-interacting membrane oxidoreductase (Qmo) locus. We therefore treat DVU_0850 as a membrane subunit of the Qmo/Hdr-like electron transfer module and reconcile nomenclature conflicts with evidence. (caffrey2008geneexpressionby pages 4-5, gao2016antimicrobialeffectsof pages 14-16)
- Gathered recent (2023–2024) evidence on Hdr-like (Hdr–Flx) systems in DvH to place DVU_0850 in its energetic context. (marbehan2024combiningmetabolicflux pages 7-9)
- Integrated foundational proteomic/transcriptomic evidence that the DVU0848–DVU0850 region encodes a membrane electron-transfer complex relevant to sulfate respiration. (zhang2006aproteomicview pages 9-11, caffrey2008geneexpressionby pages 4-5, gao2016antimicrobialeffectsof pages 14-16)
Executive verification and ambiguity note
- Identity and organism: The correct context is Desulfovibrio vulgaris Hildenborough. Primary literature discussing gene expression in DvH explicitly references “heterodisulfide reductase complex (DVU0848 to DVU0850)” under cathodic growth, directly tying the DVU numbering to this organism (Applied and Environmental Microbiology, Apr 2008; URL: https://doi.org/10.1128/aem.02469-07). (caffrey2008geneexpressionby pages 4-5)
- Ambiguous nomenclature: In DvH literature, the DVU0848–DVU0850 operon is also referred to as the Qmo (quinone-interacting membrane oxidoreductase) complex; one study assessing antimicrobial stress explicitly notes DVU0849–DVU0850 as coding for the quinone-interacting membrane-bound oxidoreductase complex (Qmo) (Applied and Environmental Microbiology, Sep 2016; URL: https://doi.org/10.1128/aem.01655-16). Thus, DVU_0850 is best interpreted as the membrane subunit of the Qmo complex, even though some sources group it under “heterodisulfide reductase complex” terminology. (gao2016antimicrobialeffectsof pages 14-16, caffrey2008geneexpressionby pages 4-5)
1) Key concepts and definitions
- Qmo/Hdr-like membrane module: In sulfate-reducing bacteria, the QmoABC complex is a membrane-associated quinone-interacting oxidoreductase that channels reducing equivalents within the sulfate respiration electron transport chain. In DvH, DVU0849–DVU0850 are stated to encode components of the membrane-bound Qmo complex; DVU0848–DVU0850 are described collectively as a heterodisulfide reductase complex in one transcriptomic study, reflecting a historical annotation overlap between Hdr-like and Qmo modules. (Gao 2016 AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16; Caffrey 2008 AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07) (gao2016antimicrobialeffectsof pages 14-16, caffrey2008geneexpressionby pages 4-5)
- DVU_0850 (Q72DS9): Within this locus, DVU_0850 is the predicted transmembrane subunit, i.e., the membrane anchor of the Qmo/Hdr-like module. Proteomic work and locus-focused studies identify DVU0848–DVU0850 with membrane electron-transfer roles consistent with energy metabolism in DvH. (Zhang 2006 Proteomics, Aug 2006, https://doi.org/10.1002/pmic.200500930; Caffrey 2008 AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07) (zhang2006aproteomicview pages 9-11, caffrey2008geneexpressionby pages 4-5)
- Hdr-like electron bifurcation context: Separately from the Qmo module, DvH harbors Hdr–Flx-type complexes that perform flavin-based electron bifurcation/confurcation to balance redox and supply low-potential electrons (e.g., to ferredoxin and DsrC). A 2024 systems study in DvH explicitly references Hdr–Flx-mediated reoxidation of NADH via bifurcation to ferredoxin and DsrC, situating Hdr-like systems centrally in DvH bioenergetics. (Frontiers in Microbiology, Feb 2024, https://doi.org/10.3389/fmicb.2024.1336360) (marbehan2024combiningmetabolicflux pages 7-9)
2) Recent developments and latest research (prioritizing 2023–2024)
- Electron bifurcation in DvH metabolism: Recent flux-modeling plus proteomics analyses emphasize the role of Hdr–Flx in reoxidizing NADH by bifurcating electrons to ferredoxin and DsrC, thereby supporting sulfate reduction under different substrate regimes. This frames Hdr-like systems as key flex points in DvH’s energetic economy. While these studies do not specifically dissect DVU_0850, they define the contemporary understanding of Hdr-like energy coupling that interfaces with membrane electron transfer, where Qmo resides. (Frontiers in Microbiology, Feb 2024, https://doi.org/10.3389/fmicb.2024.1336360) (marbehan2024combiningmetabolicflux pages 7-9)
- Operon-level response to stress: In antimicrobial stress experiments relevant to wastewater corrosion, DVU0849–DVU0850 (Qmo) expression was repressed alongside broader anaerobic respiration machinery, indicating the operon’s integration in respiratory energy conservation under environmental perturbations. This provides current applied evidence of operon regulation rather than direct biochemistry but reinforces the locus’ role in respiration. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (gao2016antimicrobialeffectsof pages 14-16)
3) Current applications and real-world implementations
- Environmental and industrial relevance: Because the DVU0848–DVU0850 locus (Qmo/Hdr-like) is integrated into sulfate respiration, it influences processes such as sulfide production implicated in biocorrosion and wastewater treatment challenges. Transcriptomic/proteomic studies of DvH under cathodic protection and antimicrobial treatments explicitly track this locus, underscoring its applied relevance in corrosion control and process microbiology. (AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07; AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (caffrey2008geneexpressionby pages 4-5, gao2016antimicrobialeffectsof pages 14-16)
4) Expert opinions and analysis from authoritative sources
- Operon identity reconciliation: The best-supported interpretation for DvH is that DVU0848–DVU0850 encode the QmoABC complex, with DVU_0850 as the membrane subunit (QmoC). The 2016 AEM study explicitly assigns DVU0849–DVU0850 to the Qmo complex and links their expression to anaerobic respiratory function. Earlier work employing the term “heterodisulfide reductase complex (DVU0848 to DVU0850)” likely reflects historical or functional grouping of electron-transfer modules in sulfate-respiring systems; however, “QmoABC” is the more precise designation for this operon in DvH. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16; AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07) (gao2016antimicrobialeffectsof pages 14-16, caffrey2008geneexpressionby pages 4-5)
- Cellular localization: The Qmo complex is membrane-associated; by inference and by the explicit characterization of DVU0849–DVU0850 as coding for the quinone-interacting membrane-bound oxidoreductase complex, DVU_0850 is a membrane protein. This supports localization at the cytoplasmic membrane interfacing with the quinone pool. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (gao2016antimicrobialeffectsof pages 14-16)
- Energetic role and Hdr–Flx linkage: Contemporary DvH research emphasizes Hdr–Flx complexes performing electron bifurcation to ferredoxin and DsrC. Although DVU_0850 (QmoC) is not itself the Hdr–Flx complex, both systems are components of the broader electron transport landscape that enables sulfate respiration. Integrating these points, DVU_0850 contributes at the membrane quinone interface (Qmo), while Hdr–Flx modules manage cytosolic redox coupling and low-potential electron supply. (Frontiers in Microbiology, Feb 2024, https://doi.org/10.3389/fmicb.2024.1336360) (marbehan2024combiningmetabolicflux pages 7-9)
5) Relevant statistics and data
- Global studies capturing the locus: Proteomic surveys detected and cataloged membrane and soluble proteins of DvH, supporting the presence and study of electron-transfer complexes like those encompassing DVU0848–DVU0850, though quantitative coverage is proteome-wide rather than DVU_0850-specific. (PROTEOMICS, Aug 2006, https://doi.org/10.1002/pmic.200500930) (zhang2006aproteomicview pages 9-11)
- Condition-dependent expression: Under antimicrobial free nitrous acid stress, genes encoding the quinone-interacting membrane-bound oxidoreductase complex (including DVU0849–DVU0850) were downregulated, indicating sensitivity of this respiratory node; while exact fold-changes are condition-specific and not reproduced here, the qualitative trend was reported. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (gao2016antimicrobialeffectsof pages 14-16)
Functional annotation for DVU_0850 (Q72DS9) in DvH: Synthesis
- Primary role (inferred): DVU_0850 encodes the membrane subunit of the QmoABC complex (QmoC), a quinone-interacting, membrane-bound oxidoreductase that participates in the sulfate respiration electron transport chain. This is supported by explicit assignment of DVU0849–DVU0850 to Qmo and by the historical grouping of DVU0848–DVU0850 under a heterodisulfide reductase-like complex in DvH. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16; AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07) (gao2016antimicrobialeffectsof pages 14-16, caffrey2008geneexpressionby pages 4-5)
- Substrates/electron carriers (inferred system-level): As a Qmo membrane component, DVU_0850 interfaces with the membrane quinone pool; specific redox partners for DVU_0850 are not resolved in the provided texts, but the complex is placed among anaerobic respiration machinery impacted during stress. (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (gao2016antimicrobialeffectsof pages 14-16)
- Localization: Cytoplasmic membrane (membrane-bound Qmo complex). (AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (gao2016antimicrobialeffectsof pages 14-16)
- Pathway context: Sulfate respiration with contemporary DvH models emphasizing concurrent Hdr–Flx-type electron bifurcation to ferredoxin and DsrC to balance redox and drive dissimilatory sulfate reduction. DVU_0850’s Qmo role is complementary to these cytosolic Hdr–Flx modules in the overall electron-transport architecture. (Frontiers in Microbiology, Feb 2024, https://doi.org/10.3389/fmicb.2024.1336360) (marbehan2024combiningmetabolicflux pages 7-9)
Limitations and cautions
- Ambiguity persists in historical annotations: One transcriptomic study describes DVU0848–DVU0850 as a “heterodisulfide reductase complex,” while another explicitly assigns DVU0849–DVU0850 to the Qmo complex. Given the direct Qmo assignment and common usage in SRB literature, we prioritize “QmoABC (DVU0848–DVU0850)” nomenclature, with DVU_0850 as QmoC. (AEM, Apr 2008, https://doi.org/10.1128/aem.02469-07; AEM, Sep 2016, https://doi.org/10.1128/aem.01655-16) (caffrey2008geneexpressionby pages 4-5, gao2016antimicrobialeffectsof pages 14-16)
- Domain-level details and specific catalytic residues for DVU_0850 were not provided in the accessed texts. Where necessary, function has been inferred from operon context and membrane complex assignments within DvH. (gao2016antimicrobialeffectsof pages 14-16, caffrey2008geneexpressionby pages 4-5)
Cited sources
- Caffrey SM et al. Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions. Applied and Environmental Microbiology. 2008-04; URL: https://doi.org/10.1128/aem.02469-07. (caffrey2008geneexpressionby pages 4-5)
- Gao S-H et al. Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete. Applied and Environmental Microbiology. 2016-09; URL: https://doi.org/10.1128/aem.01655-16. (gao2016antimicrobialeffectsof pages 14-16)
- Marbehan X et al. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Frontiers in Microbiology. 2024-02; URL: https://doi.org/10.3389/fmicb.2024.1336360. (marbehan2024combiningmetabolicflux pages 7-9)
- Zhang W et al. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. PROTEOMICS. 2006-08; URL: https://doi.org/10.1002/pmic.200500930. (zhang2006aproteomicview pages 9-11)
References
(caffrey2008geneexpressionby pages 4-5): Sean M. Caffrey, Hyung Soo Park, Jenny Been, Paul Gordon, Christoph W. Sensen, and Gerrit Voordouw. Gene expression by the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough grown on an iron electrode under cathodic protection conditions. Applied and Environmental Microbiology, 74:2404-2413, Apr 2008. URL: https://doi.org/10.1128/aem.02469-07, doi:10.1128/aem.02469-07. This article has 42 citations and is from a peer-reviewed journal.
(gao2016antimicrobialeffectsof pages 14-16): Shu-Hong Gao, Jun Yuan Ho, Lu Fan, David J. Richardson, Zhiguo Yuan, and Philip L. Bond. Antimicrobial effects of free nitrous acid on desulfovibrio vulgaris: implications for sulfide-induced corrosion of concrete. Applied and Environmental Microbiology, 82:5563-5575, Sep 2016. URL: https://doi.org/10.1128/aem.01655-16, doi:10.1128/aem.01655-16. This article has 54 citations and is from a peer-reviewed journal.
(marbehan2024combiningmetabolicflux pages 7-9): Xavier Marbehan, Magali Roger, Frantz Fournier, Pascale Infossi, Emmanuel Guedon, Louis Delecourt, Régine Lebrun, Marie-Thérèse Giudici-Orticoni, and Stéphane Delaunay. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of desulfovibrio vulgaris hildenborough. Frontiers in Microbiology, Feb 2024. URL: https://doi.org/10.3389/fmicb.2024.1336360, doi:10.3389/fmicb.2024.1336360. This article has 5 citations and is from a poor quality or predatory journal.
(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.
id: Q72DS9
gene_symbol: qmoC
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Desulfovibrio vulgaris Hildenborough
description: >-
QmoC (DVU_0850) is the membrane-integral subunit C of the quinone-interacting
membrane-bound oxidoreductase (QmoABC) complex in Desulfovibrio vulgaris
Hildenborough. The Qmo complex functions as an electron transfer hub in
dissimilatory sulfate reduction, transferring electrons from the menaquinone
pool to adenylylsulfate (APS) reductase (AprAB). QmoC contains six
transmembrane helices and a 4Fe-4S ferredoxin-type domain, serving as the
membrane anchor that interfaces with the quinone pool. The protein is
essential for the anaerobic electron transport chain during sulfate
respiration, connecting cytoplasmic electron donors to the terminal
reduction of sulfate. Proteomic and interactome studies in D. vulgaris
have validated the physical interaction between the Qmo complex and APS
reductase.
existing_annotations:
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: >-
QmoC is the membrane-integral subunit of the QmoABC complex. UniProt
Phobius predictions identify six transmembrane helices (aa 121-145,
165-186, 238-259, 279-297, 309-329, 341-362). Literature explicitly
describes DVU0849-DVU0850 as encoding the quinone-interacting
membrane-bound oxidoreductase complex. The deep research file confirms
that the Qmo complex is membrane-associated and DVU_0850 is a membrane
protein that interfaces with the quinone pool at the cytoplasmic membrane.
action: ACCEPT
reason: >-
Multiple lines of evidence support plasma membrane localization.
Phobius prediction of 6 TM helices, InterPro domains including
transmembrane di-heme cytochromes (Gene3D 1.20.950.20), and literature
explicitly describing Qmo as membrane-bound. This is a core localization
for QmoC function.
supported_by:
- reference_id: DOI:10.1128/aem.01655-16
supporting_text: >-
DVU0849-DVU0850 as coding for the quinone-interacting membrane-bound
oxidoreductase complex (Qmo)
- reference_id: DOI:10.1128/aem.02469-07
supporting_text: >-
heterodisulfide reductase complex (DVU0848 to DVU0850)
- reference_id: file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
supporting_text: >-
The Qmo complex is membrane-associated; by inference and by the
explicit characterization of DVU0849-DVU0850 as coding for the
quinone-interacting membrane-bound oxidoreductase complex,
DVU_0850 is a membrane protein.
- term:
id: GO:0016491
label: oxidoreductase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
QmoC is a subunit of the quinone-interacting membrane-bound oxidoreductase
(Qmo) complex. The complex transfers electrons between the quinone pool
and APS reductase during dissimilatory sulfate reduction. While this
annotation is correct, it is quite broad for a protein with a specific
role in electron transfer to APS reductase.
action: ACCEPT
reason: >-
The annotation is accurate as QmoC is part of an oxidoreductase complex.
UniProt keywords include "Oxidoreductase" and the protein belongs to
the NarG-like superfamily (respiratory nitrate reductase-related).
The term captures the general enzymatic category, though more specific
terms for electron transfer activity could supplement this.
supported_by:
- reference_id: DOI:10.1128/aem.01655-16
supporting_text: >-
quinone-interacting membrane-bound oxidoreductase complex
- reference_id: DOI:10.1002/pmic.200500930
supporting_text: >-
DVU0848-DVU0850 with membrane electron-transfer roles consistent
with energy metabolism in DvH
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
QmoC contains a 4Fe-4S ferredoxin-type domain (aa 61-86) and is predicted
to bind iron. The protein has UniProt keywords for Iron, Iron-sulfur,
and Metal-binding. This is a general parent term that is accurately
applied.
action: ACCEPT
reason: >-
The protein clearly binds metal ions through its iron-sulfur cluster.
PROSITE patterns PS00198 and PS51379 identify 4Fe-4S binding sites.
While more specific child terms (iron ion binding, 4Fe-4S cluster binding)
are also annotated, retaining this parent term is appropriate for
completeness.
supported_by:
- reference_id: UniProt:Q72DS9
supporting_text: >-
DOMAIN 61..86 /note="4Fe-4S ferredoxin-type"
/evidence="ECO:0000259|PROSITE:PS51379"
- term:
id: GO:0051536
label: iron-sulfur cluster binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
QmoC contains an experimentally predicted 4Fe-4S ferredoxin-type domain.
InterPro domains include 4Fe4S_Fe-S-bd (IPR017896), 4Fe4S_Fe_S_CS
(IPR017900), and HdrC_iron-sulfur_subunit (IPR051460). The Pfam domain
Fer4_8 (PF13183) is also present.
action: ACCEPT
reason: >-
Iron-sulfur cluster binding is a core functional property of QmoC.
Multiple computational methods predict this binding capacity, which is
essential for electron transfer function. This is supported by the
more specific 4Fe-4S cluster binding annotation.
supported_by:
- reference_id: InterPro:IPR017896
supporting_text: >-
4Fe4S_Fe-S-bd domain
- reference_id: InterPro:IPR051460
supporting_text: >-
HdrC_iron-sulfur_subunit domain
- term:
id: GO:0051539
label: 4 iron, 4 sulfur cluster binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
QmoC contains a defined 4Fe-4S ferredoxin-type domain at positions 61-86.
This is supported by PROSITE pattern PS00198 (4FE4S_FER_1) and profile
PS51379 (4FE4S_FER_2). The protein is also annotated with the helical
ferredoxin InterPro domain (IPR009051).
action: ACCEPT
reason: >-
This is a specific and accurate annotation. The 4Fe-4S cluster is
essential for the electron transfer function of QmoC within the Qmo
complex. Domain predictions from multiple sources (PROSITE, Pfam,
InterPro) consistently identify this binding capacity.
supported_by:
- reference_id: PROSITE:PS00198
supporting_text: >-
4FE4S_FER_1 pattern match
- reference_id: PROSITE:PS51379
supporting_text: >-
4Fe-4S ferredoxin-type domain at positions 61-86
- term:
id: GO:0019645
label: anaerobic electron transport chain
evidence_type: ISS
original_reference_id: DOI:10.1128/aem.01655-16
review:
summary: >-
The Qmo complex is part of the anaerobic electron transport chain in
sulfate-reducing bacteria. It transfers electrons from the quinone pool
to APS reductase during dissimilatory sulfate reduction.
action: NEW
reason: >-
This annotation captures the core biological process in which QmoC
participates. The Qmo complex is explicitly part of the respiratory
electron transport machinery during anaerobic sulfate respiration.
Evidence from the deep research file and publications supports this role.
supported_by:
- reference_id: DOI:10.1128/aem.01655-16
supporting_text: >-
DVU0849-DVU0850 expression was repressed alongside broader anaerobic
respiration machinery
- reference_id: file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
supporting_text: >-
DVU_0850 contributes at the membrane quinone interface (Qmo), while
Hdr-Flx modules manage cytosolic redox coupling and low-potential
electron supply.
- term:
id: GO:0019420
label: dissimilatory sulfate reduction
evidence_type: ISS
original_reference_id: DOI:10.1128/aem.02469-07
review:
summary: >-
QmoC is essential for dissimilatory sulfate reduction by providing
electrons to APS reductase, which catalyzes the first reductive step
in the pathway (APS to sulfite).
action: NEW
reason: >-
This is the defining biological process for sulfate-reducing bacteria
like D. vulgaris. The Qmo complex is positioned at a critical junction
transferring electrons from the quinone pool to APS reductase.
Proteomic evidence from PMID:27099342 confirms Qmo-AprA interaction.
supported_by:
- reference_id: DOI:10.1128/aem.02469-07
supporting_text: >-
heterodisulfide reductase complex (DVU0848 to DVU0850) under cathodic
growth, directly tying the DVU numbering to this organism
- reference_id: PMID:27099342
supporting_text: >-
Qmo oxidoreductase and adenyl sulfate reductase alpha subunit
- term:
id: GO:0048038
label: quinone binding
evidence_type: ISS
original_reference_id: DOI:10.1128/aem.01655-16
review:
summary: >-
As the membrane subunit of the quinone-interacting membrane-bound
oxidoreductase complex, QmoC is expected to interact with the quinone
pool (menaquinone in D. vulgaris).
action: NEW
reason: >-
The name "quinone-interacting membrane-bound oxidoreductase" explicitly
indicates quinone interaction. QmoC is the membrane anchor subunit and
thus the primary interface with the membrane-embedded quinone pool.
supported_by:
- reference_id: DOI:10.1128/aem.01655-16
supporting_text: >-
quinone-interacting membrane-bound oxidoreductase complex (Qmo)
- reference_id: file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
supporting_text: >-
As a Qmo membrane component, DVU_0850 interfaces with the membrane
quinone pool
- term:
id: GO:0009055
label: electron transfer activity
evidence_type: ISS
original_reference_id: DOI:10.1002/pmic.200500930
review:
summary: >-
QmoC participates in electron transfer from the quinone pool to APS
reductase via its iron-sulfur clusters. This electron transfer activity
is the primary molecular function of the Qmo complex.
action: NEW
reason: >-
The Qmo complex functions as an electron transfer module. QmoC with
its 4Fe-4S cluster and membrane localization facilitates electron
flow between the quinone pool and the soluble APS reductase complex.
This is a more specific functional annotation than generic oxidoreductase.
supported_by:
- reference_id: DOI:10.1002/pmic.200500930
supporting_text: >-
DVU0848-DVU0850 with membrane electron-transfer roles consistent
with energy metabolism in DvH
core_functions:
- description: >-
QmoC is part of the QmoABC complex that transfers electrons from the
menaquinone pool to APS reductase during dissimilatory sulfate reduction.
The 4Fe-4S cluster serves as the electron relay.
molecular_function:
id: GO:0009055
label: electron transfer activity
directly_involved_in:
- id: GO:0019420
label: dissimilatory sulfate reduction
- id: GO:0019645
label: anaerobic electron transport chain
locations:
- id: GO:0005886
label: plasma membrane
supported_by:
- reference_id: DOI:10.1002/pmic.200500930
supporting_text: >-
DVU0848-DVU0850 with membrane electron-transfer roles consistent
with energy metabolism in DvH
- reference_id: PMID:27099342
supporting_text: >-
Qmo oxidoreductase and adenyl sulfate reductase alpha subunit
references:
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:15077118
title: >-
The genome sequence of the anaerobic, sulfate-reducing bacterium
Desulfovibrio vulgaris Hildenborough
findings:
- statement: >-
Genome sequence of D. vulgaris Hildenborough reveals network of
c-type cytochromes and novel energy metabolism pathways
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.
- id: DOI:10.1128/aem.02469-07
title: >-
Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris
Hildenborough grown on an iron electrode under cathodic protection conditions
findings:
- statement: >-
DVU0848-DVU0850 described as heterodisulfide reductase complex,
upregulated under cathodic growth conditions
- id: DOI:10.1128/aem.01655-16
title: >-
Antimicrobial effects of free nitrous acid on Desulfovibrio vulgaris:
implications for sulfide-induced corrosion of concrete
findings:
- statement: >-
DVU0849-DVU0850 explicitly assigned to the Qmo (quinone-interacting
membrane-bound oxidoreductase) complex
- statement: >-
Qmo expression repressed under antimicrobial stress alongside
anaerobic respiration machinery
- id: DOI:10.1002/pmic.200500930
title: >-
A proteomic view of Desulfovibrio vulgaris metabolism as determined by
liquid chromatography coupled with tandem mass spectrometry
findings:
- statement: >-
Proteomic detection of membrane and soluble proteins including
electron-transfer complexes in DVU0848-DVU0850 region
- id: DOI:10.3389/fmicb.2024.1336360
title: >-
Combining metabolic flux analysis with proteomics to shed light on the
metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough
findings:
- statement: >-
Contemporary understanding of Hdr-Flx electron bifurcation in DvH
bioenergetics, complementary to Qmo membrane electron transfer
- id: PMID:27099342
title: >-
Quantitative Tagless Copurification: A Method to Validate and Identify
Protein-Protein Interactions.
findings:
- statement: >-
Physical interaction between Qmo oxidoreductase and adenyl sulfate
reductase alpha subunit validated by tagless co-purification
supporting_text: >-
many PPIs identified at high confidence by the tagless method but not
by our AP-MS screen are supported by physical interaction data from
another species: e.g. the interaction between flagella proteins FliS
and FlaB1; formate dehydrogenase and a formate dehydrogenase formation
protein; HypD and HypE hydrogenase maturation proteins;
phosphoribosylformylglycinamidine synthases I and II; and Qmo
oxidoreductase and adenyl sulfate reductase alpha subunit
- id: file:DESVH/Q72DS9/Q72DS9-deep-research-falcon.md
title: >-
Deep research report on Q72DS9 (qmoC) function in D. vulgaris
findings:
- statement: >-
DVU_0850 encodes the membrane subunit of the QmoABC complex (QmoC),
a quinone-interacting, membrane-bound oxidoreductase