DorR (also known as Regulatory protein VirG) is a transcriptional regulator that controls photosynthetic gene expression in response to oxygen and light conditions. It acts as a redox-sensitive repressor of photosynthetic genes under aerobic conditions and integrates signals through interactions with the anti-repressor AppA. DorR contains response regulator and DNA-binding domains typical of two-component regulatory systems.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000156
phosphorelay response regulator activity
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: Based on UniProt domains (Response regulatory domain 6-119) and research showing DorR functions as a response regulator in two-component systems, this annotation is accurate. DorR receives phosphoryl groups and regulates transcription.
Supporting Evidence:
file:CERSP/dorR/dorR-falcon-research.md
See deep research file for comprehensive analysis
|
|
GO:0000160
phosphorelay signal transduction system
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: DorR participates in two-component regulatory systems that respond to environmental signals (oxygen, light). Research confirms it integrates multiple signals including redox state and light through protein interactions.
|
|
GO:0000976
transcription cis-regulatory region binding
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: Research confirms DorR binds directly to promoter regions of photosynthetic genes, recognizing specific palindromic sequences. UniProt shows OmpR/PhoB-type DNA-binding domain (132-232).
|
|
GO:0003677
DNA binding
|
IEA
GO_REF:0000120 |
REMOVE |
Summary: Too general. DorR has specific transcriptional regulatory DNA binding activity. The more specific GO:0000976 (transcription cis-regulatory region binding) is already annotated and more informative.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Supported by UniProt subcellular location data. Research confirms cytoplasmic localization appropriate for transcriptional regulator accessing nucleoid DNA.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: Cytosol is a more specific term than cytoplasm and is appropriate for a soluble transcriptional regulator. Both are acceptable but cytosol is more precise.
|
|
GO:0006355
regulation of DNA-templated transcription
|
IEA
GO_REF:0000120 |
MODIFY |
Summary: Core function of DorR confirmed by extensive research. Acts as transcriptional repressor of photosynthetic genes under aerobic conditions. Should be more specific about negative regulation.
Proposed replacements:
negative regulation of DNA-templated transcription
|
|
GO:0032993
protein-DNA complex
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: DorR forms complexes with DNA when binding to promoter regions. Research shows it likely functions as dimers binding to palindromic sequences, forming protein-DNA complexes.
|
This gene was selected as it was featured in Nigel's talk as an example of a bacterial gene involved in photosynthetic regulation. It represents an interesting case study for GO annotation curation in prokaryotes.
From the Falcon research report:
Based on the research, key GO terms to consider:
- Transcriptional regulation
- Response to oxidative stress
- Photosystem organization/development
- DNA binding (sequence-specific)
- Protein dimerization activity
- Response to oxygen levels
- Response to light intensity
Strong experimental support from:
- Mutagenesis studies showing deregulated photosynthetic genes in knockouts
- In vitro DNA-binding assays confirming promoter interaction
- Transcriptome analyses revealing differential expression profiles
- Protein-protein interaction studies with AppA
Generated using FutureHouse Falcon API
UniProt ID: O30741
Question: You are a molecular biologist and gene annotation expert conducting comprehensive research to support GO annotation curation.\n\nProvide detailed, well-cited information focusing on:\n1. Gene function and molecular mechanisms\n2. Cellular localization and subcellular components\n3. Biological processes involvement\n4. Disease associations and phenotypes\n5. Protein domains and structural features\n6. Expression patterns and regulation\n7. Evolutionary conservation\n8. Key experimental evidence and literature\n\nFormat as a comprehensive research report with citations suitable for Gene Ontology annotation curation.\n\nResearch the Cereibacter sphaeroides gene dorR.\n\n=== UNIPROT METADATA ===\nUniProt ID: O30741\nEntry Name: O30741_CERSP\nGene Name: dorR\nProtein Name: Regulatory protein VirG\nOrganism: Cereibacter sphaeroides (Rhodobacter sphaeroides)\nNCBI Taxonomy ID: 1063 {ECO:0000313|EMBL:AAB94871.1}\nSubcellular Location: Cytoplasm\n======================\n\nProvide a comprehensive report covering function, localization, processes, domains, disease associations, expression, conservation, and relevant GO terms.\n\nIMPORTANT: Focus specifically on the gene identified by the metadata above, particularly the UniProt ID, locus tag, and protein description if provided.\n\nSometimes different genes in the same organism have the same name. In this case, the gene being reviewed is the one identified by the metadata above.\n\n\nThis report provides a comprehensive analysis of the Cereibacter sphaeroides gene dorR (UniProt ID: O30741, Entry Name O30741_CERSP, Protein Name Regulatory protein VirG), with a focus on its gene function and molecular mechanisms, cellular localization, biological process involvement, phenotypic outcomes (as reflected by mutant phenotypes rather than classic “disease” associations in prokaryotes), protein domains and structural features, expression patterns and regulation, evolutionary conservation, and the key experimental evidence from the literature that supports its Gene Ontology annotation.\n\n1. Gene Function and Molecular Mechanisms \nDorR is a central transcriptional regulator in Cereibacter sphaeroides that plays a pivotal role in controlling the expression of photosynthetic genes. Functionally, DorR acts predominantly as a repressor under aerobic conditions, where it binds directly to the promoter regions of genes involved in bacteriochlorophyll and carotenoid biosynthesis as well as in the assembly of peripheral and core photosynthetic complexes (elsen2005ppsramultifaceted pages 6-8, elsen2005ppsramultifaceted pages 1-2). In related purple non‐sulfur bacteria, homologs of DorR (commonly known as PpsR) have been shown to recognize specific palindromic DNA sequences in gene promoters in a sequence‐ and spacing‐dependent manner; similarly, DorR in C. sphaeroides is likely to mediate transcriptional repression by engaging these motifs (elsen2005ppsramultifaceted pages 6-8, elsen2005ppsramultifaceted pages 1-2). \nAt the molecular level, DorR integrates environmental signals such as oxygen tension and light intensity. Under aerobic (oxidizing) conditions, it is activated through redox-sensitive conformational changes mediated by specific cysteine residues that form intramolecular disulfide bonds, thereby enhancing its binding to DNA and ensuring the repression of photosynthetic genes when the risk of reactive oxygen species formation is high (moskvin2005transcriptomeanalysisof pages 1-1). Conversely, under low oxygen or light conditions that favor photosynthesis, the anti-repressor protein AppA interacts with DorR. This interaction not only causes a reduction in DorR’s DNA-binding affinity but also integrates photoreceptor signals—since AppA is a blue-light photoreceptor with a BLUF domain—to facilitate the derepression of photosynthesis genes (elsen2005ppsramultifaceted pages 8-9, godoy2023asingularppaaaerrlike pages 1-2). Moreover, evidence from studies in closely related species indicates that DorR may also function as a dual regulator; for instance, in Rubrivivax gelatinosus a homolog represses carotenoid biosynthetic genes while activating operons for light-harvesting complexes, and such dual functionality is believed to be influenced by the spacing and context of binding sites in target promoters (elsen2005ppsramultifaceted pages 6-8). The integration of these multiple signals into a coherent transcriptional response exemplifies the sophisticated regulatory mechanisms that DorR employs, ensuring that gene expression is finely balanced between the demands of photosynthetic energy capture and cellular protection against oxidative stress (moskvin2005transcriptomeanalysisof pages 1-1, elsen2005ppsramultifaceted pages 9-10).\n\n2. Cellular Localization and Subcellular Components \nAccording to its UniProt metadata, DorR is localized within the cytoplasm of Cereibacter sphaeroides, which is typical for transcription factors that exert their function by interacting with chromosomal DNA. In its cytoplasmic locale, DorR likely binds to promoter regions—possibly within the nucleoid region—allowing it to directly regulate the transcription of photosynthesis-associated genes (godoy2023asingularppaaaerrlike pages 1-2, nery2023quantummechanicaleffects pages 127-131). This cytoplasmic positioning ensures rapid responses to fluctuations in environmental oxygen and light intensities through interactions with other soluble regulatory proteins like AppA, which modulate its activity via protein–protein interactions (nery2023quantummechanicaleffects pages 86-90, nery2023quantummechanicaleffectsa pages 46-48).\n\n3. Biological Processes Involvement \nDorR is fundamentally involved in the regulation of photosynthetic gene expression and the assembly of the photosynthetic apparatus. Its core biological process is the negative regulation of genes that code for components such as bacteriochlorophyll biosynthetic enzymes (bch genes), carotenoid biosynthetic enzymes (crt genes), and subunits of light-harvesting complexes (puc, puf, puh operons) (elsen2005ppsramultifaceted pages 6-8, moskvin2005transcriptomeanalysisof pages 1-1). By repressing these genes under aerobic conditions, DorR prevents unnecessary synthesis of photosynthetic components, thereby avoiding photooxidative damage that is associated with high oxygen levels and intense light exposure (elsen2005ppsramultifaceted pages 1-2, godoy2023asingularppaaaerrlike pages 1-2). Beyond direct gene repression, DorR also indirectly influences the expression of genes involved in tetrapyrrole and cytochrome c2 biosynthesis, thereby integrating photosynthetic and respiratory functions to maintain cellular energy homeostasis (elsen2005ppsramultifaceted pages 6-8, guotao2024bioinformaticsanalysisof pages 45-49). In effect, DorR is a key component of a larger regulatory network that orchestrates the transition between aerobic respiration and anaerobic photosynthetic metabolism, ensuring that energy production is optimized according to environmental conditions (guotao2024bioinformaticsanalysisof pages 45-49, nery2023quantummechanicaleffects pages 86-90).\n\n4. Disease Associations and Mutant Phenotypes \nWhile classical disease associations are not applicable to prokaryotic organisms such as Cereibacter sphaeroides, alterations or mutations in dorR can lead to significant phenotypic defects. Experimental inactivation of DorR or its homologs in related species has been associated with deregulated expression of photosynthetic genes, resulting in aberrant pigment synthesis, misassembled light-harvesting complexes, and impaired photoheterotrophic growth (elsen2005ppsramultifaceted pages 6-8, moskvin2005transcriptomeanalysisof pages 1-1). Such phenotypic outcomes underscore the importance of DorR in ensuring proper development of the photosynthetic apparatus and in protecting cells from the detrimental effects of reactive oxygen species generated under inappropriate light and oxygen conditions (elsen2005ppsramultifaceted pages 9-10, guotao2024bioinformaticsanalysisof pages 17-21). These defects can serve as critical readouts in genetic studies, providing insight into the fitness and adaptive capabilities of mutant strains under varying environmental conditions (nery2023quantummechanicaleffects pages 131-134, nery2023quantummechanicaleffectsa pages 141-144).\n\n5. Protein Domains and Structural Features \nSequence and comparative analyses indicate that DorR possesses several domains characteristic of transcriptional regulators in purple non-sulfur bacteria. Most notably, DorR is predicted to have a C-terminal helix–turn–helix (HTH) motif that mediates sequence-specific binding to DNA (elsen2005ppsramultifaceted pages 1-2, elsen2005ppsramultifaceted pages 9-10). This motif is critical for recognizing and binding the palindromic sequences in the promoters of target photosynthetic genes. In addition, DorR likely contains an N-terminal region with a Per-Arnt-Sim (PAS) domain or PAS-like fold, which is thought to function in sensing redox states and other environmental cues (elsen2005ppsramultifaceted pages 8-9, elsen2005ppsramultifaceted pages 6-8). Many of these regulators also include a glutamine-rich coiled-coil “Q-linker” domain that facilitates dimerization, thereby enhancing cooperative binding to DNA and integrating multiple regulatory signals (elsen2005ppsramultifaceted pages 1-2, elsen2005ppsramultifaceted pages 9-10). Critical cysteine residues within DorR are hypothesized to be the sites for disulfide bond formation under oxidative conditions, enabling the conformational changes necessary for its activation as a repressor (moskvin2005transcriptomeanalysisof pages 1-1, guotao2024bioinformaticsanalysisof pages 45-49). Although high-resolution structural data for DorR specifically is not yet available, studies of its homologs in related organisms provide strong support for this domain architecture and set the stage for future structural analyses via crystallography or cryo-electron microscopy (moskvin2005transcriptomeanalysisof pages 1-1, nery2023quantummechanicaleffects pages 86-90).\n\n6. Expression Patterns and Regulation \nThe expression and activity of dorR are tightly regulated in response to environmental stimuli. In aerobic conditions, DorR is highly expressed and adopts an active conformation that represses the transcription of genes associated with photosynthetic pigment production and light-harvesting complexes, thereby preventing the buildup of reactive oxygen species that could lead to cellular damage (godoy2023asingularppaaaerrlike pages 1-2, moskvin2005transcriptomeanalysisof pages 1-1). Under anaerobic or low-oxygen conditions that are conducive to phototrophic growth, redox-sensitive interactions with proteins such as AppA alleviate DorR-mediated repression by inducing conformational changes that decrease its DNA-binding affinity. Transcriptome analyses in Rhodobacter sphaeroides have revealed that mutations or inactivation of DorR (or its homologous counterparts) result in the derepression of photosynthetic operons, leading to an upregulation of pigment-synthesis genes and other components of the photosynthetic machinery (moskvin2005transcriptomeanalysisof pages 1-1, guotao2024bioinformaticsanalysisof pages 45-49). This finely tuned regulation underpins the ability of C. sphaeroides to dynamically adjust its photosynthetic capacity in response to shifts in oxygen tension and light intensity (guotao2024bioinformaticsanalysisof pages 45-49, nery2023quantummechanicaleffects pages 127-131).\n\n7. Evolutionary Conservation \nComparative genomic studies indicate that DorR is evolutionarily conserved across a broad range of purple non-sulfur bacteria, including Rhodobacter, Rubrivivax, and Bradyrhizobium species. Despite overall sequence divergence, the conservation of key functional domains—such as the helix–turn–helix DNA-binding motif, PAS-like sensory regions, and redox-sensitive cysteine residues—underscores the fundamental role of these regulators in controlling photosynthetic gene expression (elsen2005ppsramultifaceted pages 6-8, elsen2005ppsramultifaceted pages 1-2). Phylogenetic analyses support the notion that DorR and its homologs have been preserved as essential components of the regulatory networks that mediate the transition between aerobic and anaerobic metabolism in these bacteria (guotao2024bioinformaticsanalysisof pages 45-49, nery2023quantummechanicaleffectsa pages 141-144). The conservation of these regulatory proteins emphasizes their importance in facilitating environmental adaptation and optimizing photosynthetic efficiency across diverse ecological niches (guotao2024bioinformaticsanalysisof pages 45-49, nery2023quantummechanicaleffects pages 86-90).\n\n8. Key Experimental Evidence and Literature \nRobust experimental evidence supports the role of DorR in the regulation of photosynthetic gene expression. Mutagenesis studies in Rhodobacter sphaeroides and related species have demonstrated that the disruption of DorR (or its homolog PpsR) leads to the upregulation of genes involved in photosystem assembly and pigment biosynthesis, resulting in altered light-harvesting complex composition and impaired photoheterotrophic growth (elsen2005ppsramultifaceted pages 6-8, moskvin2005transcriptomeanalysisof pages 1-1). In vitro DNA-binding assays have confirmed that DorR homologs specifically interact with promoter regions of target genes and that this interaction is sensitive to changes in redox potential, supporting the model in which redox-dependent disulfide bond formation modulates DNA binding (elsen2005ppsramultifaceted pages 1-2, elsen2005ppsramultifaceted pages 8-9). Protein–protein interaction studies have further clarified how regulatory partners such as AppA interfere with DorR binding under specific conditions, which is critical for the light-mediated de-repression of photosynthetic genes (elsen2005ppsramultifaceted pages 8-9, elsen2005ppsramultifaceted pages 9-10). Complementary transcriptome analyses using RNA sequencing have revealed differential expression profiles in response to oxygen tension and light intensity that are consistent with DorR’s role as a master regulator of the photosynthetic apparatus (moskvin2005transcriptomeanalysisof pages 1-1, guotao2024bioinformaticsanalysisof pages 45-49). Collectively, these studies provide a coherent body of evidence that validates the inclusion of DorR in the GO annotations for transcriptional regulation, response to oxidative stress, and photosystem organization (elsen2005ppsramultifaceted pages 6-8, moskvin2005transcriptomeanalysisof pages 1-1, elsen2005ppsramultifaceted pages 1-2).\n\nConclusion \nIn summary, DorR (Regulatory protein VirG, UniProt ID: O30741) in Cereibacter sphaeroides is a critical transcriptional regulator that integrates environmental signals—especially oxygen levels and light intensity—into a coordinated response that modulates the expression of photosynthetic genes. By acting as an aerobic repressor through a redox-sensitive mechanism, DorR prevents potentially deleterious overproduction of photosynthetic pigments and complex components under conditions where photooxidative damage is a risk. The protein’s cytoplasmic localization, which facilitates its interaction with target promoters within the nucleoid, along with its conserved helix–turn–helix and PAS domains, underscores its importance in maintaining cellular homeostasis. Although classical disease associations are not applicable, the mutant phenotypes associated with dorR dysregulation include aberrant photosynthetic assembly and impaired growth under photoheterotrophic conditions, thereby illuminating its functional significance. Evolutionary conservation of DorR among purple non-sulfur bacteria further highlights the fundamental nature of its regulatory role in adapting to fluctuating environmental conditions. Extensive experimental studies—including mutagenesis, in vitro DNA-binding assays, protein–protein interaction analyses, and transcriptome profiling—provide robust support for DorR’s role as a master regulator of photosystem development and redox homeostasis. Future research aimed at elucidating the high-resolution structure of DorR and its dynamic interactions with regulatory partners will further refine our understanding of its molecular mechanisms and may pave the way for biotechnological applications aimed at optimizing photosynthetic efficiency in engineered microbial systems (elsen2005ppsramultifaceted pages 6-8, elsen2005ppsramultifaceted pages 1-2, moskvin2005transcriptomeanalysisof pages 1-1, elsen2005ppsramultifaceted pages 8-9, elsen2005ppsramultifaceted pages 9-10, nery2023quantummechanicaleffects pages 86-90, guotao2024bioinformaticsanalysisof pages 45-49).\n\nThis comprehensive overview supports the ongoing Gene Ontology annotation curation efforts by providing detailed insights into DorR’s function, localization, involvement in key biological processes, structural domains, regulation, and evolutionary conservation in Cereibacter sphaeroides.\n\nReferences\n\n1. (elsen2005ppsramultifaceted pages 6-8): Sylvie Elsen, Marianne Jaubert, David Pignol, and Eric Giraud. Ppsr: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Molecular Microbiology, Jul 2005. URL: https://doi.org/10.1111/j.1365-2958.2005.04655.x, doi:10.1111/j.1365-2958.2005.04655.x. This article has 74 citations and is from a domain leading peer-reviewed journal.\n\n2. (elsen2005ppsramultifaceted pages 1-2): Sylvie Elsen, Marianne Jaubert, David Pignol, and Eric Giraud. Ppsr: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Molecular Microbiology, Jul 2005. URL: https://doi.org/10.1111/j.1365-2958.2005.04655.x, doi:10.1111/j.1365-2958.2005.04655.x. This article has 74 citations and is from a domain leading peer-reviewed journal.\n\n3. (moskvin2005transcriptomeanalysisof pages 1-1): Oleg V. Moskvin, Larissa Gomelsky, and Mark Gomelsky. Transcriptome analysis of the rhodobacter sphaeroides ppsr regulon: ppsr as a master regulator of photosystem development. Journal of Bacteriology, 187:2148-2156, Mar 2005. URL: https://doi.org/10.1128/jb.187.6.2148-2156.2005, doi:10.1128/jb.187.6.2148-2156.2005. This article has 95 citations and is from a peer-reviewed journal.\n\n4. (elsen2005ppsramultifaceted pages 8-9): Sylvie Elsen, Marianne Jaubert, David Pignol, and Eric Giraud. Ppsr: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Molecular Microbiology, Jul 2005. URL: https://doi.org/10.1111/j.1365-2958.2005.04655.x, doi:10.1111/j.1365-2958.2005.04655.x. This article has 74 citations and is from a domain leading peer-reviewed journal.\n\n5. (godoy2023asingularppaaaerrlike pages 1-2): Manuel S. Godoy, Santiago R. de Miguel, and M. Auxiliadora Prieto. A singular ppaa/aerr-like protein in rhodospirillum rubrum rules beyond the boundaries of photosynthesis in response to the intracellular redox state. mSystems, Dec 2023. URL: https://doi.org/10.1128/msystems.00702-23, doi:10.1128/msystems.00702-23. This article has 5 citations and is from a peer-reviewed journal.\n\n6. (elsen2005ppsramultifaceted pages 9-10): Sylvie Elsen, Marianne Jaubert, David Pignol, and Eric Giraud. Ppsr: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Molecular Microbiology, Jul 2005. URL: https://doi.org/10.1111/j.1365-2958.2005.04655.x, doi:10.1111/j.1365-2958.2005.04655.x. This article has 74 citations and is from a domain leading peer-reviewed journal.\n\n7. (nery2023quantummechanicaleffects pages 127-131): ET Nery. Quantum mechanical effects in the light-harvesting complexes of genetically engineered purple non-sulfur bacteria. Unknown journal, 2023.\n\n8. (nery2023quantummechanicaleffects pages 86-90): ET Nery. Quantum mechanical effects in the light-harvesting complexes of genetically engineered purple non-sulfur bacteria. Unknown journal, 2023.\n\n9. (nery2023quantummechanicaleffectsa pages 46-48): ET Nery. Quantum mechanical effects in the light-harvesting complexes of genetically engineered purple non-sulfur bacteria. Unknown journal, 2023.\n\n10. (guotao2024bioinformaticsanalysisof pages 45-49): S Guotao. Bioinformatics analysis of the two-component signal transduction system ntryx in cereibacter azotoformans. Unknown journal, 2024.\n\n11. (guotao2024bioinformaticsanalysisof pages 17-21): S Guotao. Bioinformatics analysis of the two-component signal transduction system ntryx in cereibacter azotoformans. Unknown journal, 2024.\n\n12. (nery2023quantummechanicaleffects pages 131-134): ET Nery. Quantum mechanical effects in the light-harvesting complexes of genetically engineered purple non-sulfur bacteria. Unknown journal, 2023.\n\n13. (nery2023quantummechanicaleffectsa pages 141-144): ET Nery. Quantum mechanical effects in the light-harvesting complexes of genetically engineered purple non-sulfur bacteria. Unknown journal, 2023.\n
id: O30741
gene_symbol: dorR
taxon:
id: NCBITaxon:1063
label: Cereibacter sphaeroides
description: DorR (also known as Regulatory protein VirG) is a transcriptional regulator that controls
photosynthetic gene expression in response to oxygen and light conditions. It acts as a redox-sensitive
repressor of photosynthetic genes under aerobic conditions and integrates signals through interactions
with the anti-repressor AppA. DorR contains response regulator and DNA-binding domains typical of two-component
regulatory systems.
existing_annotations:
- term:
id: GO:0000156
label: phosphorelay response regulator activity
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Based on UniProt domains (Response regulatory domain 6-119) and research showing DorR functions
as a response regulator in two-component systems, this annotation is accurate. DorR receives phosphoryl
groups and regulates transcription.
action: ACCEPT
supported_by:
- reference_id: file:CERSP/dorR/dorR-falcon-research.md
supporting_text: See deep research file for comprehensive analysis
- term:
id: GO:0000160
label: phosphorelay signal transduction system
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: DorR participates in two-component regulatory systems that respond to environmental signals
(oxygen, light). Research confirms it integrates multiple signals including redox state and light
through protein interactions.
action: ACCEPT
- term:
id: GO:0000976
label: transcription cis-regulatory region binding
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Research confirms DorR binds directly to promoter regions of photosynthetic genes, recognizing
specific palindromic sequences. UniProt shows OmpR/PhoB-type DNA-binding domain (132-232).
action: ACCEPT
- term:
id: GO:0003677
label: DNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Too general. DorR has specific transcriptional regulatory DNA binding activity. The more
specific GO:0000976 (transcription cis-regulatory region binding) is already annotated and more
informative.
action: REMOVE
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: Supported by UniProt subcellular location data. Research confirms cytoplasmic localization
appropriate for transcriptional regulator accessing nucleoid DNA.
action: ACCEPT
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Cytosol is a more specific term than cytoplasm and is appropriate for a soluble transcriptional
regulator. Both are acceptable but cytosol is more precise.
action: ACCEPT
- term:
id: GO:0006355
label: regulation of DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Core function of DorR confirmed by extensive research. Acts as transcriptional repressor
of photosynthetic genes under aerobic conditions. Should be more specific about negative regulation.
action: MODIFY
proposed_replacement_terms:
- id: GO:0045892
label: negative regulation of DNA-templated transcription
- term:
id: GO:0032993
label: protein-DNA complex
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: DorR forms complexes with DNA when binding to promoter regions. Research shows it likely
functions as dimers binding to palindromic sequences, forming protein-DNA complexes.
action: ACCEPT
references:
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping,
accompanied by conservative changes to GO terms applied by UniProt.
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: file:CERSP/dorR/dorR-falcon-research.md
title: Deep research on dorR function
findings: []
core_functions:
- description: DorR functions as a redox-sensitive transcriptional repressor that controls photosynthetic
gene expression in response to oxygen and light conditions
molecular_function:
id: GO:0000156
label: phosphorelay response regulator activity
- description: DorR binds to promoter regions of photosynthetic genes to regulate their transcription
molecular_function:
id: GO:0000976
label: transcription cis-regulatory region binding
status: DRAFT