HbpA (Hydrophobic protein A) is a small, non-catalytic accessory scaffoldin from Clostridium cellulovorans. It contains a single cohesin domain for recruiting dockerin-bearing enzymes and an SLH-like (surface layer homology) module for cell surface attachment. Located within the cbpA/cellulosomal gene cluster (Clocel_2820), HbpA functions as an accessory component of the cellulosome system, contributing to enzyme recruitment and cell surface anchoring. Unlike the primary scaffoldin CbpA, HbpA has only one cohesin and appears to play a supplementary organizational role.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000272
polysaccharide catabolic process
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This annotation is incorrect. HbpA is a non-catalytic scaffoldin-like protein that organizes enzymes but does not itself catalyze polysaccharide catabolism. Like CbpA, it should not be annotated with catalytic process terms.
Reason: HbpA has no catalytic domain. It is a structural/organizational protein that recruits enzymes via its cohesin domain but does not directly participate in polysaccharide breakdown.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
Acts as a small scaffoldin/accessory scaffoldin that can recruit dockerin-bearing enzymes
|
|
GO:0030246
carbohydrate binding
|
IEA
GO_REF:0000002 |
UNDECIDED |
Summary: This annotation is questionable. While UniProt shows CBM2/CBM3 superfamily hits, the curated literature emphasizes the cohesin and SLH-like modules rather than a validated carbohydrate-binding module. The CBM signal may reflect distant homology.
Reason: The CBM annotation is inconsistent with experimental literature which describes HbpA as having cohesin and SLH-like domains. Until direct carbohydrate binding is validated, this annotation should be treated with caution.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
A CBM2/3 superfamily signal exists in UniProt but has not been emphasized experimentally for HbpA
|
|
GO:0043263
cellulosome
|
TAS
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md |
NEW |
Summary: HbpA is a cellulosome-associated accessory scaffoldin encoded within the cbpA/cellulosomal gene cluster.
Reason: HbpA is part of the cellulosome system with its cohesin domain recruiting dockerin-bearing enzymes into the complex.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
HbpA (UniProt Q9RGE7), a hydrophobic protein of Clostridium cellulovorans, is a small, cellulosome-associated scaffoldin-like component
|
|
GO:0005576
extracellular region
|
TAS
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md |
NEW |
Summary: HbpA is secreted and functions extracellularly, associated with the cell surface via its SLH-like module.
Reason: HbpA is secreted to the extracellular space where it associates with the cell surface and participates in cellulosome organization.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
Secreted, extracellular; SLH/S-layer-like modules mediate association with the cell surface
|
|
GO:0044575
cellulosome assembly
|
TAS
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md |
NEW |
Summary: HbpA contributes to cellulosome assembly by recruiting dockerin-bearing enzymes via its cohesin domain.
Reason: As an accessory scaffoldin, HbpA's primary function is organizing the cellulosome by binding dockerin-containing catalytic subunits.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
Accessory scaffoldin role—recruiting dockerin-bearing glycoside hydrolases via its cohesin
|
|
GO:1990308
type-I dockerin domain binding
|
TAS
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md |
NEW |
Summary: HbpA contains a cohesin domain that binds type I dockerins on cellulolytic enzymes, enabling cellulosome assembly.
Reason: The cohesin domain mediates Ca2+-dependent binding to dockerin-bearing enzymes, which is the primary molecular function of HbpA.
Supporting Evidence:
file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
Cohesin–dockerin binding is Ca2+-dependent and highly specific
|
Q: What is the binding specificity of HbpA's cohesin domain for different dockerins?
Q: Does HbpA have validated carbohydrate-binding function or is the CBM annotation an artifact?
Experiment: Direct binding assays to test whether HbpA binds cellulose or other carbohydrates through its putative CBM domain.
Hypothesis: The CBM superfamily annotation may reflect distant structural homology rather than functional carbohydrate binding activity.
Experiment: Gene knockout studies of hbpA to assess its contribution to cellulosome assembly and cellulolytic activity.
Hypothesis: HbpA may provide supplementary enzyme recruitment capacity that enhances cellulosome function under certain conditions.
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template_file: templates/gene_research_go_focused.md
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gene_id: Q9RGE7
gene_symbol: hbpA
uniprot_accession: Q9RGE7
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gene_info: Name=hbpA {ECO:0000313|EMBL:AAF06108.1};
organism_full: Clostridium cellulovorans.
protein_family: Not specified in UniProt
protein_domains: CBM2/CBM3_carb-bd_dom_sf. (IPR008965); Cohesin_dom. (IPR002102);
Cohesin (PF00963)
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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 'hbpA' 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 hbpA (gene ID: Q9RGE7, UniProt: Q9RGE7) in CLOCL.
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 'hbpA' 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 hbpA (gene ID: Q9RGE7, UniProt: Q9RGE7) in CLOCL.
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 overview
- Objective 1 (identity verification): Completed. We verified that UniProt Q9RGE7 corresponds to hydrophobic protein A (HbpA) from Clostridium cellulovorans. Literature uses HbpA to denote a small, cellulosome-associated scaffoldin-like protein encoded in the cbpA/cellulosomal gene cluster. Domain expectations include one cohesin and an SLH-like module; UniProt adds a CBM2/CBM3 superfamily signal that may reflect distant homology. We explicitly avoided conflating with unrelated hbpA symbols (e.g., periplasmic heme-binding proteins) in other organisms (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
- Objective 2–5: Completed through literature synthesis and evidence gathering; results are reported below with citations.
Executive summary
HbpA (UniProt Q9RGE7), a hydrophobic protein of Clostridium cellulovorans, is a small, cellulosome-associated scaffoldin-like component encoded within the cbpA/cellulosome gene cluster. It contains a cohesin domain that can recruit dockerin-bearing enzymes and an SLH-like module that supports cell-surface association. Although the experimental base is deeper for the large scaffoldin CbpA, multiple sources place HbpA as an accessory scaffoldin that contributes to enzyme recruitment and possibly anchoring/attachment to cell surface and/or polysaccharide substrates. Recent literature specific to HbpA is sparse in 2023–2024; a 2025 CRISPR/Cas9 C. cellulovorans engineering study identifies hbpA (Clocel_2820) and clarifies locus context and domain architecture. Broader cellulosome principles—cohesin–dockerin specificity and Ca2+-dependence, extracellular localization, and S-layer-mediated attachment—provide strong mechanistic support for HbpA’s inferred function (demain2005cellulaseclostridiaand pages 7-9, demain2005cellulaseclostridiaand pages 9-10, doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
Artifact: concise identity/function summary
| Attribute | Summary | Key evidence |
|---|---|---|
| Identity (gene/protein) | Hydrophobic protein A (HbpA), small cellulosome-associated protein often annotated as Clocel_2820. | (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25) |
| Organism/strain | Clostridium cellulovorans (743B and related isolates reported in primary literature). | (doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25) |
| UniProt accession | Reported as Q9RGE7 for HbpA in the target specification (UniProt mapping consistent with literature locus annotations). | (schollkopf2025developmentofcrisprcas9 pages 22-25) |
| Genomic context (cluster/locus) | Located within the cbpA/cellulosomal gene cluster (adjacent to other scaffoldin/ cellulosome genes). | (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25) |
| Domain architecture | Contains a single cohesin module and an SLH-like (surface layer homology) module; UniProt annotations note CBM2/CBM3 superfamily hits (likely remote homology). | (doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25) |
| Predicted/known role | Acts as a small scaffoldin/accessory scaffoldin that can recruit dockerin-bearing enzymes and contribute to substrate or cell-surface attachment. | (doi2001theclostridiumcellulovorans pages 3-5, demain2005cellulaseclostridiaand pages 9-10) |
| Molecular interactions (cohesin–dockerin) | Expected to bind dockerin-containing glycoside hydrolases via its cohesin; interaction is Ca2+-dependent as for canonical cellulosomal cohesin–dockerin pairs. | (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26) |
| Localization | Secreted/extracellular and associated with the cell surface via SLH-like modules (cell-surface anchoring and substrate targeting). | (doi2001theclostridiumcellulovorans pages 3-5, demain2005cellulaseclostridiaand pages 9-10) |
| Experimental functional evidence | Reported enhancement/synergy of cellulosomal cellulase activity by HbpA in proteomic and functional studies; evidence is more limited than for major scaffoldins but consistent with accessory scaffoldin function. | (demain2005cellulaseclostridiaand pages 9-10, doi2001theclostridiumcellulovorans pages 3-5) |
| Recent developments (2023–2024) | Direct 2023–2024 publications specific to HbpA are scarce; most recent relevant work finds HbpA noted in genome/cluster annotations and is referenced in a CRISPR-Cas9 engineering report (2025) that maps HbpA (Clocel_2820) in the cellulosomal locus. | (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25) |
| Applications/implications | Relevant to engineering cellulosomes for biomass deconstruction (enzyme recruitment, substrate anchoring) and as a locus of interest for genetic modification to optimize cellulolytic complexes. | (demain2005cellulaseclostridiaand pages 7-9, doi2001theclostridiumcellulovorans pages 3-5) |
Table: Concise summary of identity, domain structure, location, function, evidence, and recent developments for Clostridium cellulovorans HbpA (UniProt Q9RGE7); useful as a quick-reference evidence-backed overview.
1) Key concepts and definitions (with current understanding)
- Cellulosome: An extracellular, multi-enzyme complex that deconstructs plant cell walls. A noncatalytic scaffoldin presents multiple cohesins to recruit dockerin-bearing enzymes; many scaffoldins also include a cellulose-binding module (CBM) and interact with cell-surface S-layer anchors via SLH repeats. Cohesin–dockerin interactions are among the strongest noncovalent protein interactions and are Ca2+-dependent; EDTA can dissociate these interactions (Demain et al., Microbiol. Mol. Biol. Rev., 2005-03-01; https://doi.org/10.1128/mmbr.69.1.124-154.2005) (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31).
- Scaffoldin vs enzyme subunits: Scaffoldins (e.g., CbpA in C. cellulovorans) are noncatalytic organizers of the complex with multiple cohesins; enzyme subunits carry dockerins and may have their own CBMs. Anchoring occurs via S-layer-associated modules (SLH) that tether complexes to the cell surface (demain2005cellulaseclostridiaand pages 7-9, demain2005cellulaseclostridiaand pages 9-10).
- HbpA: Hydrophobic protein A from C. cellulovorans; a smaller, accessory scaffoldin-like protein encoded in the cellulosomal gene cluster, with one cohesin and an SLH-like module; implicated in recruiting enzymes and enhancing cellulosomal function (Doi & Tamaru, Chem. Record, 2001-01; https://doi.org/10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w; Schöllkopf, 2025) (doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
2) Domain architecture and relation to the cellulosome
- C. cellulovorans scaffoldin context (CbpA): CbpA (P170) comprises an N-terminal CBM (family 3), four modules with homology to SLH repeats, and nine cohesins; it is secreted and binds crystalline cellulose. Cohesins from CbpA bind dockerins of enzyme subunits; cohesin–cohesin interactions suggest multimerization into large assemblies (Doi & Tamaru, 2001) (doi2001theclostridiumcellulovorans pages 3-5).
- HbpA (Q9RGE7): Located in the cbpA/cellulosomal gene cluster (Clocel_2820), consists of one cohesin plus an SLH-like module. The SLH-like region implies potential cell-surface association; the cohesin suggests recruitment of dockerin-bearing enzymes following canonical cohesin–dockerin rules (Schöllkopf, 2025; Demain et al., 2005) (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25, demain2005cellulaseclostridiaand pages 7-9).
- CBM annotation note: UniProt lists CBM2/CBM3 superfamily signals for Q9RGE7; curated literature on HbpA emphasizes cohesin and SLH-like modules rather than a canonical CBM in HbpA, indicating that the CBM superfamily hit may reflect distant/structural homology rather than a validated CBM in HbpA (Schöllkopf, 2025; Doi & Tamaru, 2001) (schollkopf2025developmentofcrisprcas9 pages 22-25, doi2001theclostridiumcellulovorans pages 3-5).
3) Primary function, interactions, and localization
- Function: Accessory scaffoldin role—recruiting dockerin-bearing glycoside hydrolases via its cohesin and contributing to cell-surface and/or substrate association via an SLH-like module. This is consistent with the established cellulosome architecture in clostridia and reported locus/domain features for HbpA (Demain et al., 2005; Doi & Tamaru, 2001; Schöllkopf, 2025) (demain2005cellulaseclostridiaand pages 7-9, doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
- Interactions: Cohesin–dockerin binding is Ca2+-dependent and highly specific by cohesin/dockerin type. This implies HbpA’s cohesin will select among the bacterium’s dockerin-bearing enzymes by type and sequence specificity (Demain et al., 2005; Gold 2007 overview of cohesin/docerin features) (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31).
- Localization: Secreted, extracellular; SLH/S-layer-like modules mediate association with the cell surface exterior to the peptidoglycan. In C. cellulovorans, SLH-like repeats in scaffoldin-related proteins tether the cellulosome to the cell envelope; complexes can be cell-associated during early growth and released later (Demain et al., 2005; Doi & Tamaru, 2001) (demain2005cellulaseclostridiaand pages 9-10, doi2001theclostridiumcellulovorans pages 3-5).
4) Experimental evidence connecting HbpA to cellulosome function
- Early biochemical/architectural evidence in C. cellulovorans focused on CbpA but established the functional framework: scaffoldin cohesins recruit enzymes to enable crystalline cellulose degradation that free enzymes cannot accomplish efficiently alone (Doi & Tamaru, 2001) (doi2001theclostridiumcellulovorans pages 3-5).
- HbpA locus/domain and accessory-scaffoldin characterization: A recent systems/genetic engineering paper (2025) on CRISPR/Cas9 in C. cellulovorans explicitly identifies hbpA (Clocel_2820) in the cbpA cluster and describes a one-cohesin plus SLH-like module architecture with affinity to cell wall and polysaccharides, supporting a cellulosome-associated role (Schöllkopf, 2025) (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
- General cohesin–dockerin and SLH principles underpin HbpA’s inferred activity: Ca2+-dependent binding, strong noncovalent interactions, and S-layer association are well established for clostridial cellulosomes (Demain et al., 2005; Gold 2007) (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31, demain2005cellulaseclostridiaand pages 9-10).
5) Recent developments and latest research (prioritize 2023–2024)
- Direct HbpA-focused publications in 2023–2024 are scarce in the accessible corpus here. However, a 2025 CRISPR/Cas9 genome editing study on C. cellulovorans catalogs hbpA (Clocel_2820) within the cellulosomal locus and details its domain architecture, creating a near-term platform for functional genetics on hbpA and related scaffoldins (Schöllkopf, 2025) (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
- Broader, transferable insights continue to emphasize extracellular assembly, SLH-mediated anchoring, and cohesin–dockerin specificity in clostridial cellulosomes, which are directly relevant to HbpA’s predicted activity (Demain et al., 2005; overview/proteomic principles in Gold, 2007) (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31, demain2005cellulaseclostridiaand pages 9-10).
6) Current applications and real-world implementations
- Consolidated bioprocessing and engineered cellulosomes: The scaffoldin/enzyme recruitment paradigm enables improved hydrolysis of crystalline cellulose and other recalcitrant substrates. Functional complementation studies in related systems show that engineered scaffoldins can assemble active complexes, underscoring the practical potential of manipulating scaffoldin components like HbpA for bioconversion (general principles and demonstrations summarized by Demain et al., 2005) (demain2005cellulaseclostridiaand pages 7-9).
- Targeting accessory scaffoldins: Given HbpA’s cohesin and SLH-like features and its location in the cellulosomal gene cluster, it represents a modifiable node to tune enzyme composition at the complex and attachment to biomass/cell surface, complementing established roles of the major scaffoldin CbpA (Doi & Tamaru, 2001; Schöllkopf, 2025) (doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
7) Expert opinions and analysis from authoritative sources
- Demain, Newcomb, and Wu (MMBR, 2005) synthesize foundational concepts: extracellular cellulosomes, Ca2+-dependent cohesin–dockerin pairing, strong affinity and specificity, and S-layer-mediated anchoring. These principles strongly support HbpA’s inferred role from its domains and locus (https://doi.org/10.1128/mmbr.69.1.124-154.2005) (demain2005cellulaseclostridiaand pages 7-9, demain2005cellulaseclostridiaand pages 9-10).
- Doi & Tamaru (Chem. Record, 2001) provide primary data on C. cellulovorans scaffoldin architecture, binding functions, and necessity of scaffoldin-enzyme complexes for crystalline cellulose breakdown; these data anchor the interpretation of HbpA as a smaller scaffoldin/accessory component (https://doi.org/10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w) (doi2001theclostridiumcellulovorans pages 3-5).
8) Relevant statistics and data from recent studies
- Cellulosome size and composition: Extracellular complexes commonly in the 2–6 MDa range, built on scaffoldins with multiple cohesins; in C. cellulovorans, the primary scaffoldin (CbpA) carries nine cohesins, one CBM (family 3), and multiple SLH-like modules (Demain et al., 2005; Doi & Tamaru, 2001) (demain2005cellulaseclostridiaand pages 7-9, doi2001theclostridiumcellulovorans pages 3-5).
- Binding and assembly parameters: Cohesin–dockerin interactions require Ca2+; EDTA chelation disrupts assembly; dockerins feature two Ca2+-binding loop-helix motifs; cohesins adopt beta-sandwich folds mediating high-affinity binding through hydrophobic contacts and conserved residues (Demain et al., 2005; Gold 2007) (demain2005cellulaseclostridiaand pages 7-9, gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31).
Mandatory verification and ambiguity note
- Symbol/organism verification: The hbpA discussed here is from Clostridium cellulovorans (Q9RGE7). We did not use literature on other hbpA genes (e.g., heme-binding proteins in Gram-negative bacteria), which are unrelated (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
- Domain consistency: The cohesin and SLH-like modules for HbpA are consistent across sources; a CBM2/3 superfamily signal exists in UniProt but has not been emphasized experimentally for HbpA, so its presence should be treated cautiously until validated (Schöllkopf, 2025; Doi & Tamaru, 2001) (schollkopf2025developmentofcrisprcas9 pages 22-25, doi2001theclostridiumcellulovorans pages 3-5).
Bibliographic notes (URLs and dates from accessible sources)
- Demain AL, Newcomb M, Wu JHD. Cellulase, clostridia, and ethanol. Microbiol. Mol. Biol. Rev. 2005-03-01. URL: https://doi.org/10.1128/mmbr.69.1.124-154.2005 (demain2005cellulaseclostridiaand pages 7-9).
- Doi RH, Tamaru Y. The Clostridium cellulovorans cellulosome: an enzyme complex with plant cell wall degrading activity. Chem. Record. 2001-01. URL: https://doi.org/10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w (doi2001theclostridiumcellulovorans pages 3-5).
- Gold N. Proteomic analysis of the Clostridium thermocellum cellulosome. 2007. General architecture overview applicable to clostridial cellulosomes; journal metadata unavailable in the retrieved excerpt (gold2007proteomicanalysisof pages 22-26, gold2007proteomicanalysisof pages 26-31).
- Schöllkopf AI. Development of CRISPR-Cas9 gene editing systems for the genetic engineering of Clostridium cellulovorans 743B. 2025. Locus/domain description of hbpA (Clocel_2820) and related scaffoldins; publication details not fully specified in the retrieved excerpt (schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
Conclusions
The balance of evidence supports HbpA (Q9RGE7) as a small, accessory scaffoldin-like component of the C. cellulovorans cellulosome, comprising one cohesin and an SLH-like module. It is secreted and associates with the cell surface, recruiting dockerin-bearing enzymes and contributing to substrate/cell attachment. While high-resolution, HbpA-specific studies in 2023–2024 are limited, its genetic context, domain composition, and established cellulosome principles provide a coherent functional model that is actionable for metabolic engineering and consolidated bioprocessing applications (demain2005cellulaseclostridiaand pages 7-9, demain2005cellulaseclostridiaand pages 9-10, doi2001theclostridiumcellulovorans pages 3-5, schollkopf2025developmentofcrisprcas9 pages 22-25, schollkopf2025developmentofcrisprcas9a pages 22-25).
References
(schollkopf2025developmentofcrisprcas9 pages 22-25): AI Schöllkopf. Development of crispr-cas9 gene editing systems for the genetic engineering of clostridium cellulovorans 743b. Unknown journal, 2025.
(schollkopf2025developmentofcrisprcas9a pages 22-25): AI Schöllkopf. Development of crispr-cas9 gene editing systems for the genetic engineering of clostridium cellulovorans 743b. Unknown journal, 2025.
(demain2005cellulaseclostridiaand pages 7-9): Arnold L. Demain, Michael Newcomb, and J. H. David Wu. Cellulase, clostridia, and ethanol. Microbiology and Molecular Biology Reviews, 69:124-154, Mar 2005. URL: https://doi.org/10.1128/mmbr.69.1.124-154.2005, doi:10.1128/mmbr.69.1.124-154.2005. This article has 1268 citations and is from a domain leading peer-reviewed journal.
(demain2005cellulaseclostridiaand pages 9-10): Arnold L. Demain, Michael Newcomb, and J. H. David Wu. Cellulase, clostridia, and ethanol. Microbiology and Molecular Biology Reviews, 69:124-154, Mar 2005. URL: https://doi.org/10.1128/mmbr.69.1.124-154.2005, doi:10.1128/mmbr.69.1.124-154.2005. This article has 1268 citations and is from a domain leading peer-reviewed journal.
(doi2001theclostridiumcellulovorans pages 3-5): Roy H. Doi and Yutaka Tamaru. The clostridium cellulovorans cellulosome: an enzyme complex with plant cell wall degrading activity. Chemical record, 1 1:24-32, Jan 2001. URL: https://doi.org/10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w, doi:10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w. This article has 144 citations and is from a peer-reviewed journal.
(gold2007proteomicanalysisof pages 22-26): N Gold. Proteomic analysis of the clostridium thermocellum cellulosome. Unknown journal, 2007.
(gold2007proteomicanalysisof pages 26-31): N Gold. Proteomic analysis of the clostridium thermocellum cellulosome. Unknown journal, 2007.
id: Q9RGE7
gene_symbol: hbpA
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:1493
label: Clostridium cellulovorans
description: >-
HbpA (Hydrophobic protein A) is a small, non-catalytic accessory scaffoldin from
Clostridium cellulovorans. It contains a single cohesin domain for recruiting
dockerin-bearing enzymes and an SLH-like (surface layer homology) module for cell
surface attachment. Located within the cbpA/cellulosomal gene cluster (Clocel_2820),
HbpA functions as an accessory component of the cellulosome system, contributing to
enzyme recruitment and cell surface anchoring. Unlike the primary scaffoldin CbpA,
HbpA has only one cohesin and appears to play a supplementary organizational role.
aliases:
- hydrophobic protein A
- accessory scaffoldin
existing_annotations:
- term:
id: GO:0000272
label: polysaccharide catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation is incorrect. HbpA is a non-catalytic scaffoldin-like protein
that organizes enzymes but does not itself catalyze polysaccharide catabolism.
Like CbpA, it should not be annotated with catalytic process terms.
action: REMOVE
reason: >-
HbpA has no catalytic domain. It is a structural/organizational protein that
recruits enzymes via its cohesin domain but does not directly participate in
polysaccharide breakdown.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "Acts as a small scaffoldin/accessory scaffoldin that can recruit dockerin-bearing enzymes"
- term:
id: GO:0030246
label: carbohydrate binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation is questionable. While UniProt shows CBM2/CBM3 superfamily hits,
the curated literature emphasizes the cohesin and SLH-like modules rather than
a validated carbohydrate-binding module. The CBM signal may reflect distant homology.
action: UNDECIDED
reason: >-
The CBM annotation is inconsistent with experimental literature which describes
HbpA as having cohesin and SLH-like domains. Until direct carbohydrate binding
is validated, this annotation should be treated with caution.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "A CBM2/3 superfamily signal exists in UniProt but has not been emphasized experimentally for HbpA"
# NEW ANNOTATIONS
- term:
id: GO:0043263
label: cellulosome
evidence_type: TAS
original_reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
review:
summary: >-
HbpA is a cellulosome-associated accessory scaffoldin encoded within the
cbpA/cellulosomal gene cluster.
action: NEW
reason: >-
HbpA is part of the cellulosome system with its cohesin domain recruiting
dockerin-bearing enzymes into the complex.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "HbpA (UniProt Q9RGE7), a hydrophobic protein of Clostridium cellulovorans, is a small, cellulosome-associated scaffoldin-like component"
- term:
id: GO:0005576
label: extracellular region
evidence_type: TAS
original_reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
review:
summary: >-
HbpA is secreted and functions extracellularly, associated with the cell surface
via its SLH-like module.
action: NEW
reason: >-
HbpA is secreted to the extracellular space where it associates with the cell
surface and participates in cellulosome organization.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "Secreted, extracellular; SLH/S-layer-like modules mediate association with the cell surface"
- term:
id: GO:0044575
label: cellulosome assembly
evidence_type: TAS
original_reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
review:
summary: >-
HbpA contributes to cellulosome assembly by recruiting dockerin-bearing enzymes
via its cohesin domain.
action: NEW
reason: >-
As an accessory scaffoldin, HbpA's primary function is organizing the cellulosome
by binding dockerin-containing catalytic subunits.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "Accessory scaffoldin role—recruiting dockerin-bearing glycoside hydrolases via its cohesin"
- term:
id: GO:1990308
label: type-I dockerin domain binding
evidence_type: TAS
original_reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
review:
summary: >-
HbpA contains a cohesin domain that binds type I dockerins on cellulolytic
enzymes, enabling cellulosome assembly.
action: NEW
reason: >-
The cohesin domain mediates Ca2+-dependent binding to dockerin-bearing enzymes,
which is the primary molecular function of HbpA.
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "Cohesin–dockerin binding is Ca2+-dependent and highly specific"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
title: Deep research summary for Q9RGE7/hbpA
findings:
- statement: HbpA is a non-catalytic accessory scaffoldin
supporting_text: "Acts as a small scaffoldin/accessory scaffoldin that can recruit dockerin-bearing enzymes"
- statement: HbpA contains one cohesin and an SLH-like module
supporting_text: "Contains a single cohesin module and an SLH-like (surface layer homology) module"
- statement: HbpA is part of the cellulosome system
supporting_text: "HbpA is a small, cellulosome-associated scaffoldin-like component encoded within the cbpA/cellulosome gene cluster"
core_functions:
- description: >-
HbpA is a non-catalytic accessory scaffoldin that recruits dockerin-bearing
cellulolytic enzymes via its cohesin domain, contributing to cellulosome
assembly and organization.
molecular_function:
id: GO:1990308
label: type-I dockerin domain binding
directly_involved_in:
- id: GO:0044575
label: cellulosome assembly
locations:
- id: GO:0005576
label: extracellular region
in_complex:
id: GO:0043263
label: cellulosome
supported_by:
- reference_id: file:CLOCL/Q9RGE7/Q9RGE7-deep-research-falcon.md
supporting_text: "Accessory scaffoldin role—recruiting dockerin-bearing glycoside hydrolases via its cohesin"
proposed_new_terms: []
suggested_questions:
- question: >-
What is the binding specificity of HbpA's cohesin domain for different dockerins?
experts: []
- question: >-
Does HbpA have validated carbohydrate-binding function or is the CBM annotation an artifact?
experts: []
suggested_experiments:
- description: >-
Direct binding assays to test whether HbpA binds cellulose or other carbohydrates
through its putative CBM domain.
hypothesis: >-
The CBM superfamily annotation may reflect distant structural homology rather than
functional carbohydrate binding activity.
- description: >-
Gene knockout studies of hbpA to assess its contribution to cellulosome assembly
and cellulolytic activity.
hypothesis: >-
HbpA may provide supplementary enzyme recruitment capacity that enhances
cellulosome function under certain conditions.