CV_2726 (UniProt Q7NUH2) is a 147-amino acid MarR family transcriptional regulator encoded by the Chromobacterium violaceum ATCC 12472 genome. The protein consists entirely of an HTH marR-type domain (PROSITE PS50995) containing the characteristic winged helix-turn-helix DNA-binding fold. MarR (Multiple Antibiotic Resistance Regulator) family proteins are homodimeric transcription factors that typically function as repressors, binding palindromic DNA operator sequences of approximately 16-20 bp. Ligand binding or oxidative modification of conserved cysteines induces conformational changes that reduce DNA affinity, thereby derepressing target gene expression. No direct experimental characterization of CV_2726 has been reported. By analogy to well-characterized MarR family members in C. violaceum and other bacteria, CV_2726 likely regulates genes involved in stress adaptation, potentially including oxidative stress responses, xenobiotic metabolism, or virulence-associated pathways. The C. violaceum genome encodes multiple MarR paralogs, including the experimentally characterized OhrR, which controls organic hydroperoxide defense and virulence traits.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0003677
DNA binding
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: IEA annotation from UniRule transfer based on shared sequence features (UniRule UR000415606). CV_2726 contains a full-length HTH marR-type domain spanning the entire 147-residue protein, which is the hallmark DNA-binding domain of MarR family transcriptional regulators. The winged helix-turn-helix fold in MarR proteins contacts both the major and minor groove of palindromic DNA operators. This annotation is well supported by domain architecture and family-wide structural and biochemical evidence.
Reason: DNA binding is the defining activity of MarR family proteins. The complete HTH marR-type domain (IPR000835) spanning the full protein provides strong evidence for DNA-binding capability.
|
|
GO:0003700
DNA-binding transcription factor activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation from InterPro2GO mapping based on IPR000835 (HTH_MarR-typ) and IPR039422 (MarR/SlyA-like). MarR family proteins are well-established transcription factors that regulate gene expression by binding DNA operator sequences and modulating transcription of target genes. This is the core molecular function of the MarR family and the annotation is strongly supported by the conserved domain architecture.
Reason: DNA-binding transcription factor activity is the primary molecular function of MarR family proteins. The InterPro domain assignments IPR000835 and IPR039422 strongly support this annotation. This represents the most informative molecular function annotation for this protein.
|
|
GO:0006351
DNA-templated transcription
|
IEA
GO_REF:0000104 |
MARK AS OVER ANNOTATED |
Summary: IEA annotation from UniRule transfer. As a MarR family transcription factor, CV_2726 is directly involved in DNA-templated transcription by binding DNA operator regions and modulating RNA polymerase access. However, GO:0006351 (DNA-templated transcription) describes the core transcription process itself, while MarR proteins are regulators of transcription rather than components of the basal transcription machinery. GO:0006355 (regulation of DNA-templated transcription) is already annotated and is the more appropriate biological process term for a transcriptional regulator.
Reason: MarR family proteins regulate transcription but are not part of the basal transcription machinery. Annotating to GO:0006351 (DNA-templated transcription) is an over-annotation for a transcriptional regulator. The more appropriate annotation GO:0006355 (regulation of DNA-templated transcription) is already present.
|
|
GO:0006355
regulation of DNA-templated transcription
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: IEA annotation from combined automated methods (ARBA, InterPro, PANTHER, UniRule). Regulation of DNA-templated transcription is the defining biological process of MarR family proteins. These regulators bind palindromic operator sequences near promoters to repress or activate transcription of target genes, with DNA-binding affinity modulated by small molecule ligands or oxidative signals. This is well supported by the MarR domain architecture and extensive family-wide evidence.
Reason: Regulation of transcription is the core biological process for MarR family transcriptional regulators. This annotation is well supported by multiple independent electronic inference methods and is consistent with the conserved domain structure and family-wide functional characterization.
|
|
GO:0006950
response to stress
|
IEA
GO_REF:0000118 |
UNDECIDED |
Summary: IEA annotation from TreeGrafter phylogenetic inference (PANTHER PTN002109393). Many MarR family regulators are involved in stress responses, including oxidative stress, antibiotic resistance, and environmental adaptation. In C. violaceum, the experimentally characterized MarR paralog OhrR regulates organic hydroperoxide defense and virulence-related traits. However, specific stress response roles for CV_2726 have not been experimentally determined, and not all MarR family members regulate stress-responsive genes. Some regulate metabolic or biosynthetic pathways. The TreeGrafter phylogenetic placement suggests stress response involvement for this particular MarR subfamily.
Reason: While many MarR family regulators are involved in stress responses, this is not universal for the family. Without experimental evidence or knowledge of the specific regulon controlled by CV_2726, it is uncertain whether this particular MarR protein regulates stress-responsive genes. The TreeGrafter phylogenetic inference provides some support, but the breadth of MarR family functions (stress, metabolism, virulence, biosynthesis) makes this annotation uncertain for this specific uncharacterized member.
|
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.
MarR Family: A large family of bacterial transcriptional regulators, originally named for the "Multiple antibiotic resistance Regulator" in Escherichia coli. MarR proteins commonly serve as repressors or dual-function transcription factors, modulating gene expression in response to environmental cues, toxins, metabolites, and oxidative stress. They are crucial for pathogen adaptation, stress resistance, and metabolic regulation (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2, beggs2020marrfamilyproteins pages 2-4).
Structural Features: MarR proteins are typically homodimeric, with a conserved winged helix-turn-helix (wHTH) DNA-binding domain. They recognize palindromic DNA sequences (~16–20 bp), often with additional specificity via the wing contacting the minor groove. Ligand binding (small molecule effectors or oxidative modification of cysteines) induces conformational changes that reduce DNA binding, derepressing target genes (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2, beggs2020marrfamilyproteins pages 2-4, nazaret2023marrfamilytranscriptional pages 2-4).
Stress Response and Virulence Regulation: Current studies on MarR family regulators in C. violaceum and other proteobacteria emphasize their roles in managing oxidative stress (e.g., peroxides/organic hydroperoxides), responding to environmental signals (phenolics, metals), and regulating key adaptations like virulence, exopolysaccharide synthesis, and aromatic compound degradation (nazaret2023marrfamilytranscriptional pages 4-6, previatomello2017globaltranscriptionalresponse pages 1-3).
Experimental Characterization: While direct experimental studies of Q7NUH2/CV_2726 are lacking, the MarR family member OhrR has been rigorously analyzed in C. violaceum. OhrR represses genes related to peroxide defense (notably ohrA) and c-di-GMP signaling; OhrR loss impairs virulence in animal models. These studies further support the family-level inference for Q7NUH2/CV_2726 regulatory roles (previatomello2017globaltranscriptionalresponse pages 1-3).
Primary Function: DNA-binding transcriptional regulator, most likely acting mainly as a repressor. The protein likely responds to small molecule ligands, oxidants, or metal ions, as is characteristic of MarR family members. Upon ligand binding or oxidative modification (e.g., cysteine oxidation), DNA affinity is lost, allowing expression of adjoining or regulon genes (nazaret2023marrfamilytranscriptional pages 1-2, nazaret2023marrfamilytranscriptional pages 2-4, nazaret2023marrfamilytranscriptional pages 4-6).
Regulated Pathways and Processes: By analogy to characterized MarR family proteins (including OhrR in C. violaceum), CV_2726 may be involved in:
Environmental adaptation in response to metals or organic contaminants
These roles are well-supported for MarR/OhrR regulators in bacteria and align with the domain structure of Q7NUH2 (nazaret2023marrfamilytranscriptional pages 4-6, previatomello2017globaltranscriptionalresponse pages 1-3).
Direct Evidence: No direct functional or mutational data exist for Q7NUH2/CV_2726. Thus, these functional annotations are based on high-confidence inference from conserved structure and regulatory logic within the MarR family (nazaret2023marrfamilytranscriptional pages 1-2, nazaret2023marrfamilytranscriptional pages 4-6).
A summary table is included below to consolidate available information, supporting evidence, and the degree of experimental or inferred status for Q7NUH2 in C. violaceum.
| Characteristic | Summary for Q7NUH2 / CV_2726 | Evidence |
|---|---|---|
| Protein Name/ID | UniProt Q7NUH2; ordered locus name CV_2726; annotated as a probable transcriptional regulator, MarR family | UniProt-derived target description; genome-scale annotation of C. violaceum ATCC 12472 supports the presence of this locus in the sequenced strain (vasconcelos2003thecompletegenome pages 1-2, vasconcelos2003thecompletegenome pages 3-4) |
| Organism | Chromobacterium violaceum strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK | The complete genome sequence analyzed was from C. violaceum type strain ATCC 12472 (vasconcelos2003thecompletegenome pages 1-2) |
| Protein Family | MarR-family transcriptional regulator | MarR proteins are widespread bacterial transcription factors that generally act as repressors and often regulate stress-adaptive responses (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2) |
| Key Domains | HTH_MarR-typ; MarR/SlyA-like; winged helix-turn-helix DNA-binding fold; MarR_2/PF12802 | MarR proteins characteristically contain a winged helix-turn-helix DNA-binding domain plus helices involved in dimerization (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2, beggs2020marrfamilyproteins pages 2-4) |
| Predicted Molecular Function | Sequence-specific DNA-binding transcriptional regulator, most likely functioning primarily as a repressor that modulates transcription of neighboring or regulon genes in response to chemical/redox signals | MarR-family proteins commonly repress transcription until ligand binding or oxidation lowers DNA affinity and derepresses target genes (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 2-4, nazaret2023marrfamilytranscriptional pages 2-4) |
| DNA Binding Characteristics | Likely homodimeric DNA-binding protein recognizing palindromic operator DNA, typically ~16–20 bp; recognition helices contact adjacent major grooves and the wing can contact the minor groove | General MarR-family DNA-binding mode and operator architecture are well established from structural and biochemical studies (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2, beggs2020marrfamilyproteins pages 2-4) |
| Signal/Ligand Sensing | Exact ligand for CV_2726 is unknown; by family analogy it may respond to small molecules such as phenolics, antibiotics, metals, or redox-active/oxidative signals that alter DNA-binding affinity | MarR-family regulators sense phenolic compounds, antibiotics, urate, metals, and oxidants; signaling commonly occurs through allosteric ligand binding or cysteine oxidation (nazaret2023marrfamilytranscriptional pages 4-6, nazaret2023marrfamilytranscriptional pages 2-4) |
| Biological Processes Regulated | Specific regulon for CV_2726 has not been experimentally defined; by family inference likely involved in environmental stress adaptation, potentially including oxidative stress responses, aromatic/xenobiotic metabolism, metal response, or virulence-associated regulation | In C. violaceum, the MarR-family regulator OhrR controls peroxide defense genes and virulence-related traits, while broader MarR-family literature links these regulators to oxidative stress resistance, aromatic compound degradation, exopolysaccharide/virulence control, and adaptive signaling pathways (nazaret2023marrfamilytranscriptional pages 4-6, previatomello2017globaltranscriptionalresponse pages 1-3) |
| Subcellular Localization | Cytoplasmic DNA-binding regulator acting on chromosomal promoter/operator regions | MarR proteins act as intracellular transcription factors that bind target DNA in the bacterial cytoplasm/nucleoid compartment (nazaret2023marrfamilytranscriptional pages 1-2, beggs2020marrfamilyproteins pages 1-2) |
| Evidence Type (experimental vs inferred) | Direct evidence for Q7NUH2/CV_2726: genome annotation/domain-based assignment; no direct functional study identified for this specific protein. Strong inferred evidence from conserved MarR-family structure-function relationships and from experimentally characterized MarR regulators in C. violaceum such as OhrR | Annotation and genome evidence are direct for locus existence; function, ligand sensing, and pathway roles are inferred from family/domain conservation and organism-level MarR studies (vasconcelos2003thecompletegenome pages 1-2, nazaret2023marrfamilytranscriptional pages 1-2, previatomello2017globaltranscriptionalresponse pages 1-3) |
Table: This table summarizes what is known directly and what can be inferred for Q7NUH2/CV_2726 in Chromobacterium violaceum. It is useful because direct literature on this exact protein is limited, so the table distinguishes annotation-supported facts from family-based functional inference.
This report integrates current knowledge, recent literature, and direct experimental findings for MarR-family regulators in C. violaceum, supplemented by high-confidence family-wide inferences. For precise assignments regarding CV_2726 function, future dedicated mutational and biochemical studies are recommended.
References
(vasconcelos2003thecompletegenome pages 1-2): A. Vasconcelos, D. F. Almeida, M. Hungria, C. T. Guimarães, R. Antônio, F. Almeida, L. G. Almeida, R. Almeida, J. Alves-Gomes, Elizabeth M. Mazoni Andrade, J. Araripe, Magnólia Araújo, S. Astolfi-Filho, V. Azevedo, A. J. Baptista, L. A. Bataus, J. Batista, A. Beló, C. Berg, M. Bogo, S. Bonatto, J. Bordignon, Marcelo M. Macedo Brigidom, C. Brito, M. Brocchi, H. A. Burity, A. Camargo, D. D. Cardoso, N. Carneiro, D. Carraro, C. Carvalho, J. Cascardo, B. Cavada, L. M. O. Chueire, T. Creczynski-Pasa, Nivaldo C. Costa Da Cunha-Junior, N. J. Fagundes, Clarissa Lima Falão, F. Fantinatti, I. Farias, M. Felipe, Lilian Pereira Ferrari, J. Ferro, M. Ferro, G. Franco, N. S. A. Freitas, L. R. Furlan, R. Gazzinelli, E. Gomes, P. Gonçalves, T. B. Grangeiro, D. Grattapaglia, E. Grisard, E. S. Hanna, S. N. Jardim, J. Laurino, Lélia Cristina Tenório Leoi, L. F. A. Lima, M. F. Loureiro, M. D. C. C. P. Lyra, H. Madeira, G. Manfio, A. Maranhão, W. Martins, S. Mauro, S. R. B. Medeiros, R. V. Meissner, M. A. Moreira, F. F. Nascimento, M. Nicolás, J. G. Oliveira, S. Oliveira, Roger F. C. Paixão, J. A. Parente, F. Pedrosa, Sergio Danilo Junho Penat, J. Pereira, M. Pereira, Luciana Santos Rodrigues Costa Pinto, Luciano Da SilvaPinto, J. Porto, D. P. Potrich, C. E. Ramalho-Neto, A. Reis, Liu U. Rigo, Edson Rondinelli, Elen Bethleen Pedraça do Santos, F. Santos, M. Schneider, H. Seuánez, Ana Maria Rodrigues da Silva, Artur Silva, D. W. Silva, Rosane Silva, I. C. Simões, Daniel Simon, C. M. Soares, and R. B. Soares. The complete genome sequence of chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. Proceedings of the National Academy of Sciences of the United States of America, 100:11660-11665, Sep 2003. URL: https://doi.org/10.1073/pnas.1832124100, doi:10.1073/pnas.1832124100. This article has 398 citations and is from a highest quality peer-reviewed journal.
(vasconcelos2003thecompletegenome pages 3-4): A. Vasconcelos, D. F. Almeida, M. Hungria, C. T. Guimarães, R. Antônio, F. Almeida, L. G. Almeida, R. Almeida, J. Alves-Gomes, Elizabeth M. Mazoni Andrade, J. Araripe, Magnólia Araújo, S. Astolfi-Filho, V. Azevedo, A. J. Baptista, L. A. Bataus, J. Batista, A. Beló, C. Berg, M. Bogo, S. Bonatto, J. Bordignon, Marcelo M. Macedo Brigidom, C. Brito, M. Brocchi, H. A. Burity, A. Camargo, D. D. Cardoso, N. Carneiro, D. Carraro, C. Carvalho, J. Cascardo, B. Cavada, L. M. O. Chueire, T. Creczynski-Pasa, Nivaldo C. Costa Da Cunha-Junior, N. J. Fagundes, Clarissa Lima Falão, F. Fantinatti, I. Farias, M. Felipe, Lilian Pereira Ferrari, J. Ferro, M. Ferro, G. Franco, N. S. A. Freitas, L. R. Furlan, R. Gazzinelli, E. Gomes, P. Gonçalves, T. B. Grangeiro, D. Grattapaglia, E. Grisard, E. S. Hanna, S. N. Jardim, J. Laurino, Lélia Cristina Tenório Leoi, L. F. A. Lima, M. F. Loureiro, M. D. C. C. P. Lyra, H. Madeira, G. Manfio, A. Maranhão, W. Martins, S. Mauro, S. R. B. Medeiros, R. V. Meissner, M. A. Moreira, F. F. Nascimento, M. Nicolás, J. G. Oliveira, S. Oliveira, Roger F. C. Paixão, J. A. Parente, F. Pedrosa, Sergio Danilo Junho Penat, J. Pereira, M. Pereira, Luciana Santos Rodrigues Costa Pinto, Luciano Da SilvaPinto, J. Porto, D. P. Potrich, C. E. Ramalho-Neto, A. Reis, Liu U. Rigo, Edson Rondinelli, Elen Bethleen Pedraça do Santos, F. Santos, M. Schneider, H. Seuánez, Ana Maria Rodrigues da Silva, Artur Silva, D. W. Silva, Rosane Silva, I. C. Simões, Daniel Simon, C. M. Soares, and R. B. Soares. The complete genome sequence of chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. Proceedings of the National Academy of Sciences of the United States of America, 100:11660-11665, Sep 2003. URL: https://doi.org/10.1073/pnas.1832124100, doi:10.1073/pnas.1832124100. This article has 398 citations and is from a highest quality peer-reviewed journal.
(nazaret2023marrfamilytranscriptional pages 1-2): Fanny Nazaret, Geneviève Alloing, Karine Mandon, and Pierre Frendo. Marr family transcriptional regulators and their roles in plant-interacting bacteria. Microorganisms, 11:1936, Jul 2023. URL: https://doi.org/10.3390/microorganisms11081936, doi:10.3390/microorganisms11081936. This article has 15 citations.
(beggs2020marrfamilyproteins pages 1-2): Grace A. Beggs, Richard G. Brennan, and Mehreen Arshad. Marr family proteins are important regulators of clinically relevant antibiotic resistance. Protein Science, 29:647-653, Nov 2020. URL: https://doi.org/10.1002/pro.3769, doi:10.1002/pro.3769. This article has 84 citations and is from a peer-reviewed journal.
(beggs2020marrfamilyproteins pages 2-4): Grace A. Beggs, Richard G. Brennan, and Mehreen Arshad. Marr family proteins are important regulators of clinically relevant antibiotic resistance. Protein Science, 29:647-653, Nov 2020. URL: https://doi.org/10.1002/pro.3769, doi:10.1002/pro.3769. This article has 84 citations and is from a peer-reviewed journal.
(nazaret2023marrfamilytranscriptional pages 2-4): Fanny Nazaret, Geneviève Alloing, Karine Mandon, and Pierre Frendo. Marr family transcriptional regulators and their roles in plant-interacting bacteria. Microorganisms, 11:1936, Jul 2023. URL: https://doi.org/10.3390/microorganisms11081936, doi:10.3390/microorganisms11081936. This article has 15 citations.
(nazaret2023marrfamilytranscriptional pages 4-6): Fanny Nazaret, Geneviève Alloing, Karine Mandon, and Pierre Frendo. Marr family transcriptional regulators and their roles in plant-interacting bacteria. Microorganisms, 11:1936, Jul 2023. URL: https://doi.org/10.3390/microorganisms11081936, doi:10.3390/microorganisms11081936. This article has 15 citations.
(previatomello2017globaltranscriptionalresponse pages 1-3): Maristela Previato-Mello, Diogo de Abreu Meireles, Luis Eduardo Soares Netto, and José Freire da Silva Neto. Global transcriptional response to organic hydroperoxide and the role of ohrr in the control of virulence traits in chromobacterium violaceum. Infection and Immunity, Aug 2017. URL: https://doi.org/10.1128/iai.00017-17, doi:10.1128/iai.00017-17. This article has 33 citations and is from a peer-reviewed journal.
id: Q7NUH2
gene_symbol: Q7NUH2
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:243365
label: Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG
213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)
description: >-
CV_2726 (UniProt Q7NUH2) is a 147-amino acid MarR family transcriptional regulator
encoded by the Chromobacterium violaceum ATCC 12472 genome. The protein consists
entirely of an HTH marR-type domain (PROSITE PS50995) containing the characteristic
winged helix-turn-helix DNA-binding fold. MarR (Multiple Antibiotic Resistance
Regulator) family proteins are homodimeric transcription factors that typically
function as repressors, binding palindromic DNA operator sequences of approximately
16-20 bp. Ligand binding or oxidative modification of conserved cysteines induces
conformational changes that reduce DNA affinity, thereby derepressing target gene
expression. No direct experimental characterization of CV_2726 has been reported.
By analogy to well-characterized MarR family members in C. violaceum and other
bacteria, CV_2726 likely regulates genes involved in stress adaptation, potentially
including oxidative stress responses, xenobiotic metabolism, or virulence-associated
pathways. The C. violaceum genome encodes multiple MarR paralogs, including the
experimentally characterized OhrR, which controls organic hydroperoxide defense
and virulence traits.
existing_annotations:
- term:
id: GO:0003677
label: DNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: enables
review:
summary: IEA annotation from UniRule transfer based on shared sequence features
(UniRule UR000415606). CV_2726 contains a full-length HTH marR-type domain
spanning the entire 147-residue protein, which is the hallmark DNA-binding
domain of MarR family transcriptional regulators. The winged helix-turn-helix
fold in MarR proteins contacts both the major and minor groove of palindromic
DNA operators. This annotation is well supported by domain architecture and
family-wide structural and biochemical evidence.
action: ACCEPT
reason: DNA binding is the defining activity of MarR family proteins. The complete
HTH marR-type domain (IPR000835) spanning the full protein provides strong
evidence for DNA-binding capability.
- term:
id: GO:0003700
label: DNA-binding transcription factor activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: IEA annotation from InterPro2GO mapping based on IPR000835 (HTH_MarR-typ)
and IPR039422 (MarR/SlyA-like). MarR family proteins are well-established
transcription factors that regulate gene expression by binding DNA operator
sequences and modulating transcription of target genes. This is the core
molecular function of the MarR family and the annotation is strongly supported
by the conserved domain architecture.
action: ACCEPT
reason: DNA-binding transcription factor activity is the primary molecular function
of MarR family proteins. The InterPro domain assignments IPR000835 and IPR039422
strongly support this annotation. This represents the most informative molecular
function annotation for this protein.
- term:
id: GO:0006351
label: DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: involved_in
review:
summary: IEA annotation from UniRule transfer. As a MarR family transcription factor,
CV_2726 is directly involved in DNA-templated transcription by binding DNA
operator regions and modulating RNA polymerase access. However, GO:0006351
(DNA-templated transcription) describes the core transcription process itself,
while MarR proteins are regulators of transcription rather than components of
the basal transcription machinery. GO:0006355 (regulation of DNA-templated
transcription) is already annotated and is the more appropriate biological
process term for a transcriptional regulator.
action: MARK_AS_OVER_ANNOTATED
reason: MarR family proteins regulate transcription but are not part of the basal
transcription machinery. Annotating to GO:0006351 (DNA-templated transcription)
is an over-annotation for a transcriptional regulator. The more appropriate
annotation GO:0006355 (regulation of DNA-templated transcription) is already
present.
- term:
id: GO:0006355
label: regulation of DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: IEA annotation from combined automated methods (ARBA, InterPro, PANTHER,
UniRule). Regulation of DNA-templated transcription is the defining biological
process of MarR family proteins. These regulators bind palindromic operator
sequences near promoters to repress or activate transcription of target genes,
with DNA-binding affinity modulated by small molecule ligands or oxidative
signals. This is well supported by the MarR domain architecture and extensive
family-wide evidence.
action: ACCEPT
reason: Regulation of transcription is the core biological process for MarR family
transcriptional regulators. This annotation is well supported by multiple
independent electronic inference methods and is consistent with the conserved
domain structure and family-wide functional characterization.
- term:
id: GO:0006950
label: response to stress
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: involved_in
review:
summary: IEA annotation from TreeGrafter phylogenetic inference (PANTHER PTN002109393).
Many MarR family regulators are involved in stress responses, including oxidative
stress, antibiotic resistance, and environmental adaptation. In C. violaceum,
the experimentally characterized MarR paralog OhrR regulates organic hydroperoxide
defense and virulence-related traits. However, specific stress response roles
for CV_2726 have not been experimentally determined, and not all MarR family
members regulate stress-responsive genes. Some regulate metabolic or biosynthetic
pathways. The TreeGrafter phylogenetic placement suggests stress response
involvement for this particular MarR subfamily.
action: UNDECIDED
reason: While many MarR family regulators are involved in stress responses, this
is not universal for the family. Without experimental evidence or knowledge
of the specific regulon controlled by CV_2726, it is uncertain whether this
particular MarR protein regulates stress-responsive genes. The TreeGrafter
phylogenetic inference provides some support, but the breadth of MarR family
functions (stress, metabolism, virulence, biosynthesis) makes this annotation
uncertain for this specific uncharacterized member.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000104
title: Electronic Gene Ontology annotations created by transferring manual GO annotations
between related proteins based on shared sequence features
findings: []
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
core_functions:
- description: MarR family DNA-binding transcription factor that regulates gene expression
by binding palindromic operator DNA sequences near target gene promoters. Functions
as a homodimer using the winged helix-turn-helix domain for sequence-specific DNA
recognition. Likely acts primarily as a transcriptional repressor whose DNA-binding
affinity is modulated by small molecule ligands or oxidative signals, leading to
derepression of target genes under specific environmental conditions. The specific
regulon and inducing signals for CV_2726 have not been experimentally determined.
molecular_function:
id: GO:0003700
label: DNA-binding transcription factor activity
directly_involved_in:
- id: GO:0006355
label: regulation of DNA-templated transcription