FliA (sigma-28, sigma^F) is an alternative sigma factor belonging to the sigma-70 family that directs RNA polymerase to flagellar gene promoters in D. vulgaris Hildenborough. As the master regulator of late flagellar gene expression (class III/IV genes), FliA controls transcription of genes encoding flagellin (fliC), hook-associated proteins, motor components (motAB), and chemotaxis machinery. FliA activity is regulated by the anti-sigma factor FlgM, which sequesters FliA in the cytoplasm until hook-basal body (HBB) assembly is complete; upon HBB completion, FlgM is secreted through the flagellar type III export apparatus, releasing FliA to drive late gene expression. Deletion of fliA in D. vulgaris results in severe motility defects, defective/truncated flagella, and loss of biofilm formation capacity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:2000142
regulation of DNA-templated transcription initiation
|
IEA
GO_REF:0000108 |
ACCEPT |
Summary: FliA (sigma-28) regulates transcription initiation by directing RNA polymerase to sigma-28-dependent promoters of late flagellar genes. The annotation to "regulation of DNA-templated transcription initiation" is accurate since sigma factors specifically function in transcription initiation rather than elongation. However, this term is generic and does not capture the flagellar-specific function.
Reason: This annotation correctly reflects that FliA functions in regulation of transcription initiation. Sigma factors are initiation factors that promote attachment of RNA polymerase to specific promoter sequences and are released after initiation (UniProt Q726C4). While a more specific term involving flagellar regulation would be ideal, no such term exists in GO. The IEA annotation via logical inference (GO_REF:0000108) is appropriate.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA is an alternative sigma factor that associates with RNA polymerase core in the cytosol to initiate transcription from sigma-28 promoters
|
|
GO:0003677
DNA binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: FliA/sigma-28 contains conserved sigma-70 regions 2 and 4 that mediate DNA element recognition at promoters. While sigma factors do not bind DNA autonomously, they confer DNA-binding specificity when combined with RNA polymerase core to form the holoenzyme. The annotation is technically correct but somewhat imprecise.
Reason: The DNA binding annotation is acceptable because sigma factors confer DNA-binding specificity to the RNAP holoenzyme by recognizing specific promoter elements. FliA contains the characteristic sigma-70 region 2 and region 4 domains (IPR007627, IPR007630) that recognize the -10 and -35 promoter elements respectively. The sigma-28 promoter consensus is approximately TAAA-N15-GCCGATAA.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA contains conserved sigma-70 regions that mediate promoter recognition and RNA polymerase core binding, with regions 2 and 4 central to DNA element recognition
|
|
GO:0003700
DNA-binding transcription factor activity
|
IEA
GO_REF:0000120 |
MODIFY |
Summary: This annotation characterizes FliA as a DNA-binding transcription factor. While sigma factors do regulate transcription and confer promoter specificity, the term "DNA-binding transcription factor activity" is typically used for sequence-specific DNA-binding proteins that directly bind DNA and regulate transcription of target genes. Sigma factors function differently - they bind RNA polymerase core and confer promoter specificity to the holoenzyme.
Reason: The term "DNA-binding transcription factor activity" (GO:0003700) is not the most precise term for sigma factors. GO:0016987 (sigma factor activity) is the more appropriate molecular function term that specifically describes the mechanism by which sigma factors promote transcription initiation. This annotation should be replaced with the more specific sigma factor activity term.
Proposed replacements:
sigma factor activity
|
|
GO:0003899
DNA-directed RNA polymerase activity
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This annotation incorrectly attributes RNA polymerase catalytic activity to FliA. Sigma factors do not possess RNA polymerase enzymatic activity themselves; rather, they are regulatory subunits that associate with the RNA polymerase core enzyme (alpha2-beta-beta') to direct promoter recognition. The catalytic activity resides in the core enzyme subunits, not the sigma factor.
Reason: FliA is a sigma factor, not an RNA polymerase enzyme. Sigma factors function by binding to the RNA polymerase core to form a holoenzyme and directing it to specific promoters; they do not possess catalytic polymerase activity. This annotation appears to be an over-annotation based on InterPro domain associations (GO_REF:0000002). The UniProt record correctly identifies Q726C4 as "RNA polymerase sigma factor" not as RNA polymerase itself. This distinction is critical for accurate functional annotation.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA is an alternative sigma factor that associates with RNA polymerase core in the cytosol to initiate transcription from sigma-28 promoters
|
|
GO:0006352
DNA-templated transcription initiation
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: FliA is directly involved in DNA-templated transcription initiation as it binds RNA polymerase core and directs the holoenzyme to sigma-28-dependent promoters of late flagellar genes. Upon promoter recognition and initiation, sigma factors are released from the elongating polymerase.
Reason: This biological process annotation is accurate. Sigma factors function specifically in transcription initiation - they bind RNAP core to form the holoenzyme, recognize and bind promoter sequences, facilitate open complex formation, and are released after initiation. FliA participates in transcription initiation of late flagellar genes including flagellin, hook-associated proteins, motor components, and chemotaxis genes.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA (sigma-28) directs transcription of the late (class III/IV) flagellar regulon, which typically includes flagellin (fliC), hook-associated proteins, motor components (e.g., motAB), and chemotaxis genes
|
|
GO:0006355
regulation of DNA-templated transcription
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: FliA clearly functions in regulation of transcription as it controls expression of late flagellar genes. This annotation is accurate but somewhat general - FliA specifically regulates transcription initiation rather than elongation or other aspects of transcription.
Reason: This annotation is correct. FliA regulates transcription of late flagellar genes by directing RNA polymerase to sigma-28-dependent promoters. The D. vulgaris fliA deletion mutant shows severe motility defects and defective flagella, demonstrating FliA's essential role in regulating expression of flagellar genes (Ray et al. 2014, Clark 2008).
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
D. vulgaris phenotypes: delta-fliA (DVU_3229) shows (i) severe motility defects on soft agar and wet mounts; (ii) defective or truncated flagella by TEM; (iii) failure to form biofilm under tested conditions
|
|
GO:0016987
sigma factor activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the core molecular function annotation for FliA. Sigma factor activity precisely describes FliA's function as a promoter specificity subunit that associates with RNA polymerase core and directs it to specific promoter sequences. FliA belongs to the sigma-70 family, specifically the FliA/WhiG clade (IPR012845).
Reason: This is the most accurate and informative molecular function annotation for FliA. GO:0016987 (sigma factor activity) precisely defines the mechanism by which FliA functions: it combines with RNA polymerase core to form a holoenzyme, confers promoter binding specificity, and is released after transcription initiation begins. This annotation is strongly supported by domain architecture (sigma-70 regions 2 and 4), family membership (FliA/WhiG subfamily), and functional evidence from D. vulgaris mutant studies.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA is an alternative sigma factor that associates with RNA polymerase core in the cytosol to initiate transcription from sigma-28 promoters
|
|
GO:1902208
regulation of bacterial-type flagellum assembly
|
IMP
PMID:24639670 Exploring the role of CheA3 in Desulfovibrio vulgaris Hilden... |
NEW |
Summary: FliA regulates late flagellar gene expression which is essential for flagellar assembly. Deletion of fliA in D. vulgaris results in defective or truncated flagella as shown by TEM (Ray et al. 2014).
Reason: This annotation is strongly supported by organism-specific experimental evidence. The delta-fliA mutant in D. vulgaris Hildenborough shows defective or truncated flagella by transmission electron microscopy, demonstrating that FliA is required for proper flagellar assembly. FliA regulates expression of late flagellar genes (class III/IV) including flagellin and hook-associated proteins that are essential for flagellum structure.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
the D. vulgaris delta-fliA mutant (DVU3229) for FliA, predicted to regulate flagella-related genes including cheA3, was defective both in flagellum formation and in forming the motility halos
PMID:24639670
Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility.
|
|
GO:0071973
bacterial-type flagellum-dependent cell motility
|
IMP
PMID:24639670 Exploring the role of CheA3 in Desulfovibrio vulgaris Hilden... |
NEW |
Summary: FliA is essential for motility in D. vulgaris. Delta-fliA mutants show severe motility defects in both soft agar assays and wet-mount microscopy (Ray et al. 2014, Clark 2008).
Reason: Direct experimental evidence from D. vulgaris Hildenborough demonstrates that fliA deletion results in severe motility defects. The delta-fliA mutant (JW9017) shows loss of motility on soft agar plates and in wet-mount assays. This phenotype is consistent with FliA's role in regulating late flagellar genes required for functional flagella and cell motility.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
D. vulgaris phenotypes: delta-fliA (DVU_3229) shows (i) severe motility defects on soft agar and wet mounts; (ii) defective or truncated flagella by TEM; (iii) failure to form biofilm under tested conditions
PMID:24639670
Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility.
|
|
GO:0005737
cytoplasm
|
IEA
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md |
NEW |
Summary: FliA is a cytoplasmic sigma factor that associates with RNA polymerase core in the cytosol. Its activity is regulated by the anti-sigma factor FlgM, which sequesters FliA in the cytoplasm until hook-basal body assembly is complete.
Reason: FliA functions in the cytoplasm where it associates with RNA polymerase core enzyme. Literature explicitly states FliA associates with RNA polymerase core in the cytosol. This localization is consistent with the function of sigma factors which must interact with cytoplasmic RNAP core to form the holoenzyme.
Supporting Evidence:
file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
FliA is an alternative sigma factor that associates with RNA polymerase core in the cytosol to initiate transcription from sigma-28 promoters
|
Q: What is the specific promoter sequence recognized by FliA in D. vulgaris? Is it similar to the consensus TAAA-N15-GCCGATAA found in other bacteria?
Q: Does D. vulgaris encode a FlgM anti-sigma factor ortholog, and if so, does it function similarly to regulate FliA activity?
Q: What is the complete FliA regulon in D. vulgaris? Which specific genes are transcribed from sigma-28-dependent promoters?
Experiment: ChIP-seq to identify FliA binding sites genome-wide in D. vulgaris and define the sigma-28 promoter consensus sequence for this organism.
Hypothesis: FliA binds to sigma-28-like promoter sequences upstream of late flagellar genes
Type: ChIP-seq
Experiment: RNA-seq comparing wild-type and delta-fliA strains to define the complete FliA regulon and identify all sigma-28-dependent genes.
Hypothesis: FliA deletion will result in downregulation of late flagellar genes
Type: RNA-seq
Experiment: Complementation studies to confirm that the motility and flagellar defects in delta-fliA are specifically due to loss of FliA function.
Hypothesis: Expression of wild-type fliA will restore motility and flagellar assembly in delta-fliA mutants
Type: Genetic complementation
provider: falcon
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template_variables:
organism: DESVH
gene_id: Q726C4
gene_symbol: fliA
uniprot_accession: Q726C4
protein_description: 'RecName: Full=RNA polymerase sigma factor {ECO:0000256|RuleBase:RU362124};'
gene_info: Name=fliA {ECO:0000313|EMBL:AAS97699.1}; OrderedLocusNames=DVU_3229 {ECO:0000313|EMBL:AAS97699.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Belongs to the sigma-70 factor family.
protein_domains: RNA_pol_sigma-70_dom. (IPR014284); RNA_pol_sigma70. (IPR000943);
RNA_pol_sigma70_r2. (IPR007627); RNA_pol_sigma70_r4. (IPR007630); RNA_pol_sigma_FliA_WhiG.
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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 'fliA' 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 fliA (gene ID: Q726C4, UniProt: Q726C4) 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 'fliA' 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 fliA (gene ID: Q726C4, UniProt: Q726C4) 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 and verification
- Identity verification: The target is DVU_3229 (gene symbol fliA) from Desulfovibrio vulgaris Hildenborough, corresponding to UniProt Q726C4. Literature in D. vulgaris directly identifies DVU_3229 as fliA encoding a σ28/σ70-family alternative sigma factor (FliA) that regulates flagellar formation and motility, consistent with the sigma-70 FliA/WhiG subfamily domain architecture (regions 2 and 4) specified in UniProt (organism and gene context match) (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6, clark2008physiologicalanalysisof pages 149-154).
Research report: fliA (DVU_3229; UniProt Q726C4) in Desulfovibrio vulgaris Hildenborough (DESVH)
1) Key concepts and definitions
- Gene/protein and family: fliA encodes RNA polymerase sigma factor FliA (σ28), a member of the sigma-70 family, specifically the FliA/WhiG clade. FliA contains conserved sigma-70 regions that mediate promoter recognition and RNA polymerase core binding, with regions 2 and 4 central to DNA element recognition and anti-sigma interactions (general σ28 mechanistic features) (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 61-65).
- Functional class: FliA directs transcription of the “late” (class III/IV) flagellar regulon, which typically includes flagellin (fliC), hook-associated proteins, motor components (e.g., motAB), and chemotaxis genes in diverse bacteria (definition and examples from model systems) (smith2009regulationofthe pages 65-69, oladosu2024fliptheswitch pages 3-4).
- Promoter consensus: σ28-dependent promoters characteristically contain a −35/−10-like motif approximated by TAAA–N15–GCCGATAA in model organisms; this consensus encapsulates the sequence specificity recognized by FliA region 4 and region 2 analogs (smith2009regulationofthe pages 65-69).
2) Primary biological role and mechanism
- Primary role: FliA is an alternative sigma factor that associates with RNA polymerase core in the cytosol to initiate transcription from σ28 promoters, governing late stages of flagellar gene expression necessary for assembly of functional flagella and motility (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 61-65).
- Mechanistic integration with assembly: The FliA regulon is controlled by an export/assembly checkpoint. During hook–basal body (HBB) assembly, the anti-sigma factor FlgM sequesters FliA and inhibits σ28-dependent transcription. Upon HBB completion, FlgM is secreted through the flagellar type III export apparatus, relieving inhibition and allowing FliA-driven expression of late genes; FliA can also facilitate FlgM secretion and FlgM can stabilize σ28 against proteolysis (canonical mechanism) (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 69-73).
3) Organism-specific function in Desulfovibrio vulgaris Hildenborough
- Genetic identity and mutant phenotype: DVU_3229 (fliA) is present in the D. vulgaris Hildenborough genome. A ΔfliA mutant (JW9017) shows severe motility defects on soft agar and in wet-mount assays, and transmission electron microscopy indicates defective or truncated flagella under the conditions tested. These data directly implicate FliA in flagellar biogenesis and motility in D. vulgaris (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6).
- Biofilm and flagella linkage: Independent work in D. vulgaris reports that ΔfliA mutants lack functional flagella, are non-motile, and fail to form biofilm, consistent with a requirement for FliA-driven late flagellar gene expression to achieve functional flagellation and surface-associated behaviors in this anaerobe (clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154).
4) Cellular localization and action
- Localization: FliA functions in the cytosol, forming a holoenzyme with RNA polymerase to recognize σ28-type promoters. Its availability and activity are controlled by cytosolic sequestration with FlgM and release upon export-coupled checkpoints (mechanistic paradigm) (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 61-65).
5) Regulatory network and partners
- Anti-sigma factor: FlgM is the canonical anti-σ28 factor. It binds FliA (and can engage the holoenzyme) to block transcription until structural checkpoints trigger its secretion; this couples flagellar assembly status to late-gene transcription (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 69-73).
- Additional regulatory layers: In Pseudomonas, the HptB–HsbR–HsbA partner-switching system can antagonize FlgM-mediated sequestration of FliA, highlighting layered control beyond the core anti-sigma checkpoint; a FleQ-centered network integrates second messenger signaling and transcriptional regulation upstream of FliA-dependent genes (model system illustrating contemporary regulatory complexity) (oladosu2024fliptheswitch pages 3-4).
6) Conservation and comparative context
- Prevalence: A genomic survey cited in foundational work identified FliA/SigD orthologs across at least 552 genomes (≈300 species) predominantly in flagellated taxa, with notable lineage-specific absences (e.g., frequent lack in many α-Proteobacteria). This indicates widespread but non-universal conservation of σ28 across bacteria (smith2009regulationofthe pages 65-69).
- Phylogenetic variation: Comparative analyses show extensive diversity in flagellar regulatory architectures; some lineages lack FliA but regulate motility through σ70-type promoters and post-transcriptional mechanisms, underscoring that while the FlgM–FliA export-coupled checkpoint is common, alternatives exist (smith2009regulationofthe pages 69-73). Large-scale, recent mappings of flagellar components across thousands of genomes confirm that the presence of FliA varies and correlates with specific flagellar modules, reinforcing lineage-specific strategies for motility control (philip2025mappingtheloss pages 9-10).
7) Recent developments (2023–2024) relevant to σ28/FliA control
- Layered flagellar regulation interfacing with second messengers: Contemporary reviews in Pseudomonas detail how transcription factors (e.g., FleQ) and c-di-GMP-responsive circuits modulate the motility–biofilm switch and intersect with FlgM–FliA control, including partner-switching systems that influence σ28 activity. These works emphasize the modular, multi-signal integration around FliA-dependent late gene expression (Journal of Bacteriology, 2024; URL: https://doi.org/10.1128/jb.00365-23) (oladosu2024fliptheswitch pages 3-4).
- Systems/phylogenomic perspective: A 2025 systems-level mapping quantifies component distributions (including σ factors) across >11,000 genomes and correlates them with motility states, highlighting FliA’s heterogeneous distribution and its association with conserved flagellar modules; this provides updated comparative context even though not D. vulgaris–specific (The ISME Journal, 2025; URL: https://doi.org/10.1093/ismejo/wraf111) (philip2025mappingtheloss pages 9-10).
8) Current applications and real-world implications
- Motility and biofilm in SRB: In D. vulgaris, ΔfliA eliminates functional flagella, abrogates motility, and disrupts biofilm formation, directly tying FliA to phenotypes that influence surface colonization and community behaviors relevant to environmental persistence and engineered systems where sulfate-reducing bacteria operate (e.g., biofilms). These organism-specific data establish FliA as a lever for controlling motility-associated traits in this SRB (clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154).
9) Expert opinions and authoritative sources
- Canonical model: Foundational syntheses emphasize the export-coupled checkpoint integrating the flagellar type III secretion system with FliA and FlgM to ensure temporal control of late gene expression—an expert consensus model supported by multiple genetic and biochemical studies in diverse bacteria (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 69-73, smith2009regulationofthe pages 61-65).
- Modern perspectives: Recent field overviews in Pseudomonas integrate sigma-factor control with second-messenger signaling and partner-switching mechanisms, reflecting the prevailing expert view that FliA operates within multi-layered, signal-responsive networks (oladosu2024fliptheswitch pages 3-4).
10) Relevant statistics and data
- Conservation statistics: FliA/SigD reported across 552 genomes (≈300 species) in a survey of flagellated bacteria, with 83% of species lacking FliA/SigD belonging to α-Proteobacteria, illustrating uneven phylogenetic distribution (smith2009regulationofthe pages 65-69).
- D. vulgaris phenotypes: ΔfliA (DVU_3229) shows (i) severe motility defects on soft agar and wet mounts; (ii) defective or truncated flagella by TEM; (iii) failure to form biofilm under tested conditions—quantitative assay details provided in the primary organism-specific studies (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6, clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154).
Data and evidence table (with sources, URLs, and years)
| Topic | Organism/Scope | Key finding (1–2 sentences) | Source (journal/title with DOI/URL) | Year |
|---|---|---|---|---|
| DVU_3229 (fliA) mutant phenotype | Desulfovibrio vulgaris Hildenborough | Deletion of DVU_3229 (fliA) causes loss or truncation of flagella and severe motility defects on soft agar and in wet-mount assays. (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6) | Ray et al., Frontiers in Microbiology — https://doi.org/10.3389/fmicb.2014.00077 | 2014 |
| ΔfliA effects on motility/flagella/biofilm | Desulfovibrio vulgaris Hildenborough | ΔfliA mutants lack functional flagella, are non-motile, and show impaired biofilm formation; deletions may have polar effects on downstream genes. (clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154) | Clark 2008 (thesis/report) — NA | 2008 |
| Canonical FliA/FlgM export-coupled regulation | Broad bacterial models (e.g., H. pylori, E. coli) | FliA (σ28) directs late (class III/IV) flagellar genes; FlgM is an anti‑σ that is secreted via the flagellar export apparatus to relieve inhibition upon hook–basal‑body completion; promoter consensus TAAA–N15–GCCGATAA described. (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 69-73) | Smith 2009 review/paper — NA | 2009 |
| Regulatory layers and c-di-GMP integration | Pseudomonas aeruginosa (model for layered control) | Additional layers (e.g., HptB‑HsbR‑HsbA partner switching) can antagonize FlgM sequestration; FleQ links flagellar transcription to c‑di‑GMP signaling, illustrating multi‑layered control of FliA‑dependent genes. (oladosu2024fliptheswitch pages 3-4) | Oladosu et al., Journal of Bacteriology — https://doi.org/10.1128/jb.00365-23 | 2024 |
| Distribution and conservation of FliA | Large-scale bacterial phylogeny | Genome-wide mapping shows variable presence of FliA correlated with flagellar filament components; many lineages lack FliA despite other flagellar elements, indicating lineage-specific regulatory variation. (philip2025mappingtheloss pages 9-10) | Philip et al., The ISME Journal — https://doi.org/10.1093/ismejo/wraf111 | 2025 |
Table: Concise, source‑linked evidence for FliA (σ28) focusing on DVU_3229 in Desulfovibrio vulgaris Hildenborough and broader regulatory features; useful as a quick reference to primary findings and reviews cited in the report.
Notes on the promoter motif and domains
- Promoter: The σ28 motif TAAA–N15–GCCGATAA (−35/−10-like) is reported from model systems; while D. vulgaris–specific promoters were not delineated in the cited organism-specific studies, DVU_3229’s functional role in flagellar assembly and motility supports the inference that a σ28-like regulon exists in DVH (smith2009regulationofthe pages 65-69, ray2014exploringtherole pages 4-5, clark2008physiologicalanalysisof pages 149-154).
- Domains: Anti-sigma FlgM binding targets conserved σ28 surfaces overlapping with regions 2 and 4, explaining sequestration and modulation of holoenzyme stability; these mechanistic insights from model organisms are consistent with the family/domain annotations for Q726C4 (smith2009regulationofthe pages 65-69).
Citations with publication details
- Ray et al., Frontiers in Microbiology (2014). Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. DOI: 10.3389/fmicb.2014.00077. URL: https://doi.org/10.1101/2014.00077 (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6).
- Clark (2008). Physiological analysis of Desulfovibrio vulgaris Hildenborough under conditions relevant to the subsurface environment: Carbon and energy limitation and biofilm… (Thesis/report). URL: NA (clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154).
- Smith (2009). Regulation of the Helicobacter pylori RpoN regulon by the flagellar protein export apparatus (review/paper). URL: NA (smith2009regulationofthe pages 65-69, smith2009regulationofthe pages 69-73, smith2009regulationofthe pages 61-65).
- Oladosu et al., Journal of Bacteriology (2024). Flip the switch: FleQ and layered regulation of motility/biofilm; DOI: 10.1128/jb.00365-23. URL: https://doi.org/10.1128/jb.00365-23 (oladosu2024fliptheswitch pages 3-4).
- Philip et al., The ISME Journal (2025). Mapping the loss of flagellar motility across the tree of life; DOI: 10.1093/ismejo/wraf111. URL: https://doi.org/10.1093/ismejo/wraf111 (philip2025mappingtheloss pages 9-10).
Summary
- The fliA gene in D. vulgaris Hildenborough (DVU_3229; UniProt Q726C4) encodes a σ28/FliA sigma factor essential for late flagellar gene expression, functional flagella, motility, and biofilm formation under tested conditions. Its regulation is expected to conform to the canonical FlgM-mediated, export-coupled checkpoint observed broadly in bacteria, with emerging multi-layered controls exemplified in model systems. Comparative analyses underscore wide but uneven conservation of FliA across bacterial lineages. Together, organism-specific genetics and general mechanistic studies provide a coherent, well-supported functional annotation for Q726C4 as the flagellar sigma factor FliA in this sulfate-reducing bacterium (ray2014exploringtherole pages 4-5, ray2014exploringtherole pages 5-6, clark2008physiologicalanalysisof pages 135-139, clark2008physiologicalanalysisof pages 149-154, smith2009regulationofthe pages 65-69, oladosu2024fliptheswitch pages 3-4, smith2009regulationofthe pages 69-73).
References
(ray2014exploringtherole pages 4-5): Jayashree Ray, Kimberly L. Keller, Michela Catena, Thomas R. Juba, Marcin Zemla, Lara Rajeev, Bernhard Knierim, Grant M. Zane, Jarrod J. Robertson, Manfred Auer, Judy D. Wall, and Aindrila Mukhopadhyay. Exploring the role of chea3 in desulfovibrio vulgaris hildenborough motility. Frontiers in Microbiology, Mar 2014. URL: https://doi.org/10.3389/fmicb.2014.00077, doi:10.3389/fmicb.2014.00077. This article has 10 citations and is from a poor quality or predatory journal.
(ray2014exploringtherole pages 5-6): Jayashree Ray, Kimberly L. Keller, Michela Catena, Thomas R. Juba, Marcin Zemla, Lara Rajeev, Bernhard Knierim, Grant M. Zane, Jarrod J. Robertson, Manfred Auer, Judy D. Wall, and Aindrila Mukhopadhyay. Exploring the role of chea3 in desulfovibrio vulgaris hildenborough motility. Frontiers in Microbiology, Mar 2014. URL: https://doi.org/10.3389/fmicb.2014.00077, doi:10.3389/fmicb.2014.00077. This article has 10 citations and is from a poor quality or predatory journal.
(clark2008physiologicalanalysisof pages 149-154): ME Clark. Physiological analysis of desulfovibrio vulgaris hildenborough under conditions relevant to the subsurface environment: carbon and energy limitation and biofilm …. Unknown journal, 2008.
(smith2009regulationofthe pages 65-69): TG Smith. Regulation of the helicobacter pylori rpon regulon by the flagellar protein export apparatus. Unknown journal, 2009.
(smith2009regulationofthe pages 61-65): TG Smith. Regulation of the helicobacter pylori rpon regulon by the flagellar protein export apparatus. Unknown journal, 2009.
(oladosu2024fliptheswitch pages 3-4): Victoria I. Oladosu, Soyoung Park, and Karin Sauer. Flip the switch: the role of fleq in modulating the transition between the free-living and sessile mode of growth in pseudomonas aeruginosa. Journal of Bacteriology, Mar 2024. URL: https://doi.org/10.1128/jb.00365-23, doi:10.1128/jb.00365-23. This article has 26 citations and is from a peer-reviewed journal.
(smith2009regulationofthe pages 69-73): TG Smith. Regulation of the helicobacter pylori rpon regulon by the flagellar protein export apparatus. Unknown journal, 2009.
(clark2008physiologicalanalysisof pages 135-139): ME Clark. Physiological analysis of desulfovibrio vulgaris hildenborough under conditions relevant to the subsurface environment: carbon and energy limitation and biofilm …. Unknown journal, 2008.
(philip2025mappingtheloss pages 9-10): Jamiema Sara Philip, Sehhaj Grewal, Jacob Scadden, Caroline Puente-Lelievre, Nicholas J. Matzke, Luke McNally, and Matthew AB Baker. Mapping the loss of flagellar motility across the tree of life. The ISME Journal, Jan 2025. URL: https://doi.org/10.1093/ismejo/wraf111, doi:10.1093/ismejo/wraf111. This article has 2 citations.
id: Q726C4
gene_symbol: fliA
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris Hildenborough)
description: >-
FliA (sigma-28, sigma^F) is an alternative sigma factor belonging to the sigma-70
family
that directs RNA polymerase to flagellar gene promoters in D. vulgaris Hildenborough.
As the master regulator of late flagellar gene expression (class III/IV genes),
FliA
controls transcription of genes encoding flagellin (fliC), hook-associated proteins,
motor components (motAB), and chemotaxis machinery. FliA activity is regulated by
the
anti-sigma factor FlgM, which sequesters FliA in the cytoplasm until hook-basal
body
(HBB) assembly is complete; upon HBB completion, FlgM is secreted through the flagellar
type III export apparatus, releasing FliA to drive late gene expression. Deletion
of
fliA in D. vulgaris results in severe motility defects, defective/truncated flagella,
and loss of biofilm formation capacity.
existing_annotations:
- term:
id: GO:2000142
label: regulation of DNA-templated transcription initiation
evidence_type: IEA
original_reference_id: GO_REF:0000108
review:
summary: >-
FliA (sigma-28) regulates transcription initiation by directing RNA polymerase
to sigma-28-dependent promoters of late flagellar genes. The annotation to
"regulation of DNA-templated transcription initiation" is accurate since sigma
factors specifically function in transcription initiation rather than elongation.
However, this term is generic and does not capture the flagellar-specific
function.
action: ACCEPT
reason: >-
This annotation correctly reflects that FliA functions in regulation of transcription
initiation. Sigma factors are initiation factors that promote attachment of
RNA
polymerase to specific promoter sequences and are released after initiation
(UniProt Q726C4). While a more specific term involving flagellar regulation
would
be ideal, no such term exists in GO. The IEA annotation via logical inference
(GO_REF:0000108) is appropriate.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
- term:
id: GO:0003677
label: DNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
FliA/sigma-28 contains conserved sigma-70 regions 2 and 4 that mediate DNA
element
recognition at promoters. While sigma factors do not bind DNA autonomously,
they
confer DNA-binding specificity when combined with RNA polymerase core to form
the
holoenzyme. The annotation is technically correct but somewhat imprecise.
action: ACCEPT
reason: >-
The DNA binding annotation is acceptable because sigma factors confer DNA-binding
specificity to the RNAP holoenzyme by recognizing specific promoter elements.
FliA
contains the characteristic sigma-70 region 2 and region 4 domains (IPR007627,
IPR007630) that recognize the -10 and -35 promoter elements respectively.
The
sigma-28 promoter consensus is approximately TAAA-N15-GCCGATAA.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA contains conserved sigma-70 regions that mediate
promoter recognition and RNA polymerase core binding, with regions 2 and
4 central to DNA element recognition"
- term:
id: GO:0003700
label: DNA-binding transcription factor activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This annotation characterizes FliA as a DNA-binding transcription factor.
While
sigma factors do regulate transcription and confer promoter specificity, the
term
"DNA-binding transcription factor activity" is typically used for sequence-specific
DNA-binding proteins that directly bind DNA and regulate transcription of
target
genes. Sigma factors function differently - they bind RNA polymerase core
and
confer promoter specificity to the holoenzyme.
action: MODIFY
reason: >-
The term "DNA-binding transcription factor activity" (GO:0003700) is not the
most
precise term for sigma factors. GO:0016987 (sigma factor activity) is the
more
appropriate molecular function term that specifically describes the mechanism
by
which sigma factors promote transcription initiation. This annotation should
be
replaced with the more specific sigma factor activity term.
proposed_replacement_terms:
- id: GO:0016987
label: sigma factor activity
- term:
id: GO:0003899
label: DNA-directed RNA polymerase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation incorrectly attributes RNA polymerase catalytic activity to
FliA.
Sigma factors do not possess RNA polymerase enzymatic activity themselves;
rather,
they are regulatory subunits that associate with the RNA polymerase core enzyme
(alpha2-beta-beta') to direct promoter recognition. The catalytic activity
resides
in the core enzyme subunits, not the sigma factor.
action: REMOVE
reason: >-
FliA is a sigma factor, not an RNA polymerase enzyme. Sigma factors function
by
binding to the RNA polymerase core to form a holoenzyme and directing it to
specific
promoters; they do not possess catalytic polymerase activity. This annotation
appears
to be an over-annotation based on InterPro domain associations (GO_REF:0000002).
The
UniProt record correctly identifies Q726C4 as "RNA polymerase sigma factor"
not as
RNA polymerase itself. This distinction is critical for accurate functional
annotation.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
- term:
id: GO:0006352
label: DNA-templated transcription initiation
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
FliA is directly involved in DNA-templated transcription initiation as it
binds
RNA polymerase core and directs the holoenzyme to sigma-28-dependent promoters
of late flagellar genes. Upon promoter recognition and initiation, sigma factors
are released from the elongating polymerase.
action: ACCEPT
reason: >-
This biological process annotation is accurate. Sigma factors function specifically
in transcription initiation - they bind RNAP core to form the holoenzyme,
recognize
and bind promoter sequences, facilitate open complex formation, and are released
after initiation. FliA participates in transcription initiation of late flagellar
genes including flagellin, hook-associated proteins, motor components, and
chemotaxis genes.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA (sigma-28) directs transcription of the late (class
III/IV) flagellar regulon, which typically includes flagellin (fliC),
hook-associated proteins, motor components (e.g., motAB), and chemotaxis
genes"
- term:
id: GO:0006355
label: regulation of DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
FliA clearly functions in regulation of transcription as it controls expression
of late flagellar genes. This annotation is accurate but somewhat general
- FliA
specifically regulates transcription initiation rather than elongation or
other
aspects of transcription.
action: ACCEPT
reason: >-
This annotation is correct. FliA regulates transcription of late flagellar
genes
by directing RNA polymerase to sigma-28-dependent promoters. The D. vulgaris
fliA
deletion mutant shows severe motility defects and defective flagella, demonstrating
FliA's essential role in regulating expression of flagellar genes (Ray et
al. 2014,
Clark 2008).
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "D. vulgaris phenotypes: delta-fliA (DVU_3229) shows (i)
severe motility defects on soft agar and wet mounts; (ii) defective or
truncated flagella by TEM; (iii) failure to form biofilm under tested
conditions"
- term:
id: GO:0016987
label: sigma factor activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This is the core molecular function annotation for FliA. Sigma factor activity
precisely describes FliA's function as a promoter specificity subunit that
associates with RNA polymerase core and directs it to specific promoter sequences.
FliA belongs to the sigma-70 family, specifically the FliA/WhiG clade (IPR012845).
action: ACCEPT
reason: >-
This is the most accurate and informative molecular function annotation for
FliA.
GO:0016987 (sigma factor activity) precisely defines the mechanism by which
FliA
functions: it combines with RNA polymerase core to form a holoenzyme, confers
promoter binding specificity, and is released after transcription initiation
begins.
This annotation is strongly supported by domain architecture (sigma-70 regions
2
and 4), family membership (FliA/WhiG subfamily), and functional evidence from
D. vulgaris mutant studies.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
# Proposed new annotations based on literature evidence
- term:
id: GO:1902208
label: regulation of bacterial-type flagellum assembly
evidence_type: IMP
original_reference_id: PMID:24639670
review:
summary: >-
FliA regulates late flagellar gene expression which is essential for flagellar
assembly. Deletion of fliA in D. vulgaris results in defective or truncated
flagella
as shown by TEM (Ray et al. 2014).
action: NEW
reason: >-
This annotation is strongly supported by organism-specific experimental evidence.
The delta-fliA mutant in D. vulgaris Hildenborough shows defective or truncated
flagella by transmission electron microscopy, demonstrating that FliA is required
for proper flagellar assembly. FliA regulates expression of late flagellar
genes
(class III/IV) including flagellin and hook-associated proteins that are essential
for flagellum structure.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "the D. vulgaris delta-fliA mutant (DVU3229) for FliA,
predicted to regulate flagella-related genes including cheA3, was defective
both in flagellum formation and in forming the motility halos"
- reference_id: PMID:24639670
supporting_text: Exploring the role of CheA3 in Desulfovibrio vulgaris
Hildenborough motility.
- term:
id: GO:0071973
label: bacterial-type flagellum-dependent cell motility
evidence_type: IMP
original_reference_id: PMID:24639670
review:
summary: >-
FliA is essential for motility in D. vulgaris. Delta-fliA mutants show severe
motility defects in both soft agar assays and wet-mount microscopy (Ray et
al. 2014,
Clark 2008).
action: NEW
reason: >-
Direct experimental evidence from D. vulgaris Hildenborough demonstrates that
fliA
deletion results in severe motility defects. The delta-fliA mutant (JW9017)
shows
loss of motility on soft agar plates and in wet-mount assays. This phenotype
is
consistent with FliA's role in regulating late flagellar genes required for
functional flagella and cell motility.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "D. vulgaris phenotypes: delta-fliA (DVU_3229) shows (i)
severe motility defects on soft agar and wet mounts; (ii) defective or
truncated flagella by TEM; (iii) failure to form biofilm under tested
conditions"
- reference_id: PMID:24639670
supporting_text: Exploring the role of CheA3 in Desulfovibrio vulgaris
Hildenborough motility.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
review:
summary: >-
FliA is a cytoplasmic sigma factor that associates with RNA polymerase core
in the cytosol. Its activity is regulated by the anti-sigma factor FlgM, which
sequesters FliA in the cytoplasm until hook-basal body assembly is complete.
action: NEW
reason: >-
FliA functions in the cytoplasm where it associates with RNA polymerase core
enzyme. Literature explicitly states FliA associates with RNA polymerase core
in the cytosol. This localization is consistent with the function of sigma
factors which must interact with cytoplasmic RNAP core to form the holoenzyme.
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms
findings: []
- id: GO_REF:0000108
title: Automatic assignment of GO terms using logical inference, based on
inter-ontology links
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:24639670
title: "Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility"
full_text_unavailable: true
findings: []
- id: PMID:15077118
title: "The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio
vulgaris Hildenborough"
full_text_unavailable: true
findings: []
- id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
title: Deep research summary for Q726C4 (FliA) in D. vulgaris Hildenborough
findings:
- statement: FliA (sigma-28) is an alternative sigma factor that directs
transcription of late flagellar genes
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
- statement: delta-fliA mutants show defective flagella and motility
defects
supporting_text: "D. vulgaris phenotypes: delta-fliA (DVU_3229) shows (i)
severe motility defects on soft agar and wet mounts; (ii) defective or truncated
flagella by TEM; (iii) failure to form biofilm under tested conditions"
- statement: FliA contains sigma-70 regions 2 and 4 for promoter
recognition
supporting_text: "FliA contains conserved sigma-70 regions that mediate promoter
recognition and RNA polymerase core binding, with regions 2 and 4 central
to DNA element recognition"
core_functions:
- description: >-
FliA is an alternative sigma factor (sigma-28/sigma^F) that associates with
RNA
polymerase core enzyme to form a holoenzyme and directs it to sigma-28-dependent
promoters of late flagellar genes. Contains conserved sigma-70 regions 2 and
4
(IPR007627, IPR007630) that recognize -10 and -35 promoter elements respectively.
molecular_function:
id: GO:0016987
label: sigma factor activity
directly_involved_in:
- id: GO:2000142
label: regulation of DNA-templated transcription initiation
- id: GO:1902208
label: regulation of bacterial-type flagellum assembly
- id: GO:0071973
label: bacterial-type flagellum-dependent cell motility
locations:
- id: GO:0005737
label: cytoplasm
supported_by:
- reference_id: file:DESVH/Q726C4/Q726C4-deep-research-falcon.md
supporting_text: "FliA is an alternative sigma factor that associates with
RNA polymerase core in the cytosol to initiate transcription from sigma-28
promoters"
proposed_new_terms: []
suggested_questions:
- question: >-
What is the specific promoter sequence recognized by FliA in D. vulgaris?
Is it similar to the consensus TAAA-N15-GCCGATAA found in other bacteria?
- question: >-
Does D. vulgaris encode a FlgM anti-sigma factor ortholog, and if so,
does it function similarly to regulate FliA activity?
- question: >-
What is the complete FliA regulon in D. vulgaris? Which specific genes
are transcribed from sigma-28-dependent promoters?
suggested_experiments:
- description: >-
ChIP-seq to identify FliA binding sites genome-wide in D. vulgaris and
define the sigma-28 promoter consensus sequence for this organism.
experiment_type: ChIP-seq
hypothesis: FliA binds to sigma-28-like promoter sequences upstream of late
flagellar genes
- description: >-
RNA-seq comparing wild-type and delta-fliA strains to define the complete
FliA regulon and identify all sigma-28-dependent genes.
experiment_type: RNA-seq
hypothesis: FliA deletion will result in downregulation of late flagellar
genes
- description: >-
Complementation studies to confirm that the motility and flagellar
defects in delta-fliA are specifically due to loss of FliA function.
experiment_type: Genetic complementation
hypothesis: Expression of wild-type fliA will restore motility and flagellar
assembly in delta-fliA mutants