CelC (Endoglucanase C) is a glycoside hydrolase family 5 (GH5) enzyme that catalyzes the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin, and cereal beta-D-glucans (EC 3.2.1.4). CelC is a non-cellulosomal enzyme, lacking a dockerin domain and therefore does not integrate into the cellulosome complex. The 343 amino acid enzyme contains conserved active site residues typical of GH5 family members, with Gln-140 acting as proton donor and Glu-280 as nucleophile. The celC gene is part of a celC-glyR3-licA operon, with transcription regulated by the LacI-family repressor GlyR3, and induced by laminaribiose.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000272
polysaccharide catabolic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is a parent-level biological process term that correctly captures the catabolic activity of CelC. As an endoglucanase that breaks down cellulose (a polysaccharide), CelC is involved in polysaccharide catabolism. However, more specific child terms (GO:0030245 cellulose catabolic process) are also annotated and are more informative.
Reason: The annotation is accurate as cellulose is a polysaccharide and CelC participates in its degradation. This parent term complements the more specific cellulose catabolic process annotation. IEA evidence from InterPro domain and UniProtKB keyword mappings is appropriate for this general term.
|
|
GO:0004553
hydrolase activity, hydrolyzing O-glycosyl compounds
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This molecular function term is a parent term of cellulase activity (GO:0008810). It accurately describes the general catalytic mechanism of CelC, which hydrolyzes O-glycosyl bonds in cellulose.
Reason: As a GH5 family endoglucanase, CelC hydrolyzes O-glycosyl compounds (specifically beta-1,4-glucosidic bonds). The InterPro-based IEA annotation is accurate. This parent term is retained alongside the more specific cellulase activity term.
|
|
GO:0005576
extracellular region
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: CelC is classified as a non-cellulosomal enzyme that functions extracellularly. Deep research confirms CelC acts as a free extracellular enzyme rather than as part of the cellulosome complex [file:ACET2/celC/celC-deep-research-falcon.md].
Reason: Deep research supports extracellular localization. Non-cellulosomal hydrolytic enzymes in C. thermocellum function extracellularly in the milieu of plant biomass. While a signal peptide for CelC is expected for secretion, regulatory and operon studies explicitly classify CelC as non-cellulosomal, implying extracellular action as a free enzyme [file:ACET2/celC/celC-deep-research-falcon.md].
Supporting Evidence:
file:ACET2/celC/celC-deep-research-falcon.md
Non-cellulosomal hydrolytic enzymes in C. thermocellum function extracellularly in the milieu of plant biomass
|
|
GO:0005975
carbohydrate metabolic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This is a high-level biological process term that accurately but very broadly describes CelC function. The enzyme participates in carbohydrate metabolism through cellulose degradation.
Reason: While very general, this annotation is not incorrect. CelC is involved in carbohydrate metabolism via its cellulolytic activity. More specific child terms (cellulose catabolic process) provide better functional resolution. IEA from InterPro is reasonable for this broad term.
|
|
GO:0008422
beta-glucosidase activity
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: Beta-glucosidase activity (GO:0008422) is defined as catalysis of hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose. This is mechanistically distinct from cellulase/endoglucanase activity, which cleaves internal beta-1,4-glucosidic bonds. CelC is an ENDOglucanase, not an EXO-acting beta-glucosidase.
Reason: This annotation is incorrect. CelC (EC 3.2.1.4) is an endoglucanase that cleaves internal beta-1,4-glucosidic linkages in cellulose chains. Beta-glucosidase (EC 3.2.1.21) is a distinct enzyme class that removes terminal glucose residues. The TreeGrafter prediction appears to be based on broad sequence similarity within glycoside hydrolases but does not accurately reflect the specific enzymatic mechanism of CelC. UniProt clearly annotates CelC with EC 3.2.1.4 (cellulase), not EC 3.2.1.21 (beta-glucosidase).
|
|
GO:0008810
cellulase activity
|
IEA
GO_REF:0000003 |
ACCEPT |
Summary: Cellulase activity (GO:0008810) is defined as catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. This precisely matches the function of CelC as described in UniProt and confirmed by deep research [file:ACET2/celC/celC-deep-research-falcon.md].
Reason: This is the core molecular function annotation for CelC and is correctly assigned based on EC number mapping (EC:3.2.1.4). UniProt explicitly states that CelC catalyzes endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. The GH5 family classification and conserved active site residues (Gln-140 proton donor, Glu-280 nucleophile) support this annotation.
Supporting Evidence:
file:ACET2/celC/celC-deep-research-falcon.md
CelC is an endo-1,4-beta-glucanase that cleaves internal beta-1,4-glycosidic bonds in cellulose and related beta-glucans
|
|
GO:0009251
glucan catabolic process
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: Glucan catabolic process is a biological process term that describes the breakdown of glucans. Cellulose is a beta-1,4-glucan, so CelC participates in glucan catabolism through its cellulolytic activity.
Reason: This annotation is accurate. CelC breaks down cellulose, which is a glucan (polymer of glucose). The TreeGrafter annotation correctly infers this biological process from sequence homology to characterized cellulases.
|
|
GO:0009986
cell surface
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: Cell surface localization is characteristic of cellulosomal enzymes that attach via dockerin-cohesin interactions. However, CelC (A3DJ77) is explicitly classified as non-cellulosomal and lacks a dockerin domain, meaning it cannot attach to the CipA scaffoldin on the cell surface [file:ACET2/celC/celC-deep-research-falcon.md].
Reason: This annotation is incorrect for CelC. Deep research explicitly states that CelC is categorized as non-cellulosomal and acts as a free enzyme rather than a CipA-bound cellulosomal subunit. Regulatory and operon studies explicitly classify CelC as non-cellulosomal, implying absence of a dockerin module. Without a dockerin, CelC cannot bind to the CipA scaffoldin and would not be retained at the cell surface. CelC functions as a free extracellular enzyme, not a cell-surface-attached one.
Supporting Evidence:
file:ACET2/celC/celC-deep-research-falcon.md
CelC is categorized as non-cellulosomal in transcriptional/regulatory studies rather than a dockerin-bearing component
file:ACET2/celC/celC-deep-research-falcon.md
Regulatory and operon studies explicitly classify CelC as non-cellulosomal; this implies absence of a dockerin module and action as a free enzyme rather than as a CipA-bound cellulosomal subunit
|
|
GO:0016787
hydrolase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Hydrolase activity is a very broad molecular function term that encompasses all enzymes that catalyze hydrolysis reactions. CelC is a hydrolase that cleaves glycosidic bonds.
Reason: This annotation is correct but very general. CelC is indeed a hydrolase (it catalyzes hydrolysis of beta-1,4-glucosidic bonds). The annotation derives from UniProtKB keyword mapping. More specific child terms provide better functional characterization.
|
|
GO:0016798
hydrolase activity, acting on glycosyl bonds
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: This molecular function term specifies that CelC acts on glycosyl bonds, which is accurate. It is a parent term of cellulase activity.
Reason: CelC hydrolyzes glycosidic (glycosyl) bonds, specifically beta-1,4-glucosidic linkages. This annotation from UniProtKB keyword mapping correctly places CelC within the glycoside hydrolase functional category.
|
|
GO:0030245
cellulose catabolic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Cellulose catabolic process is the most specific and appropriate biological process term for CelC. It directly describes the enzyme's participation in cellulose degradation.
Reason: This is the core biological process annotation for CelC. As an endoglucanase that cleaves internal bonds in cellulose chains, CelC directly participates in cellulose catabolism. UniProt explicitly annotates CelC for the cellulose degradation pathway (UniPathway:UPA00696). This annotation is supported by both the EC number mapping and the UniProt pathway annotation.
Supporting Evidence:
UniProt:A3DJ77
Glycan metabolism; cellulose degradation
|
Q: What is the specific substrate preference of CelC - does it have higher activity on cellulose, lichenan, or mixed-linkage beta-glucans?
Q: Are there kinetic parameters (Km, kcat) available for purified CelC on carboxymethylcellulose or other defined substrates?
Experiment: Express recombinant A3DJ77 CelC and assay for endoglucanase activity using carboxymethyl cellulose (CMC) or other cellulosic substrates. Demonstration of endoglucanase activity would confirm the GO:0008810 annotation with experimental evidence.
Experiment: Test A3DJ77 CelC for beta-glucosidase activity using p-nitrophenyl-beta-D-glucoside as substrate. Lack of activity would support removal of the GO:0008422 annotation and confirm that CelC is strictly an endoglucanase.
Experiment: Perform substrate specificity profiling to determine whether CelC has preference for cellulose versus lichenan or other beta-glucans, given the operon context with licA and laminaribiose-mediated induction.
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2025-12-26T17:03:13.228189'
end_time: '2025-12-26T17:12:59.230585'
duration_seconds: 586.0
template_file: templates/gene_research_go_focused.md
template_variables:
organism: ACET2
gene_id: celC
gene_symbol: celC
uniprot_accession: A3DJ77
protein_description: 'RecName: Full=Endoglucanase C; EC=3.2.1.4; AltName: Full=Cellulase
C; AltName: Full=Endo-1,4-beta-glucanase C; Short=EgC;'
gene_info: Name=celC; OrderedLocusNames=Cthe_2807;
organism_full: Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322
/ NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Clostridium thermocellum).
protein_family: Belongs to the glycosyl hydrolase 5 (cellulase A) family.
protein_domains: Glyco_hydro_5. (IPR001547); Glyco_hydro_5_CS. (IPR018087); Glycoside_hydrolase_SF.
(IPR017853); Glycosyl_hydrolase_5. (IPR050386); Cellulase (PF00150)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 20
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 'celC' 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 celC (gene ID: celC, UniProt: A3DJ77) in ACET2.
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 'celC' 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 celC (gene ID: celC, UniProt: A3DJ77) in ACET2.
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 summary
- Objective 1 (identity check): Completed. Multiple sources concur that celC (locus Cthe_2807) in Acetivibrio thermocellus (syn. Clostridium thermocellum) encodes Endoglucanase C (CelC), a non-cellulosomal endoglucanase in the glycoside hydrolase system; it resides in a celCโglyR3โlicA gene cluster/operon and is repressed by a LacI-family regulator (GlyR3) that binds the celC promoter (organism, gene symbol, and function consistent with UniProt A3DJ77) (newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56, wilson2017lacitranscriptionalregulatory pages 1-3, newcomb2008transcriptionregulationof pages 19-23).
Comprehensive research report
1) Key concepts and definitions with current understanding
- Target identity and nomenclature: celC (Cthe_2807; Endoglucanase C, CelC) encodes an endo-1,4-ฮฒ-glucanase that acts on internal ฮฒ-1,4 linkages of cellulose (EC 3.2.1.4). In C. thermocellum, celC is part of a non-cellulosomal cellulase locus and is co-transcribed with a local LacI-family regulator gene (glyR3) and licA, an enzyme implicated in ฮฒ-glucan (lichenan) degradation (celCโglyR3โlicA operon) (Newcomb 2008; Applied and Environmental Microbiology 2017) (newcomb2008transcriptionregulationofa pages 47-56, wilson2017lacitranscriptionalregulatory pages 1-3, newcomb2008transcriptionregulationof pages 19-23). URL and date examples: AEM Mar 2017, https://doi.org/10.1128/aem.02751-16 (wilson2017lacitranscriptionalregulatory pages 1-3).
- Cellulosome context: C. thermocellum secretes large extracellular multi-enzyme complexes (cellulosomes) assembled on the CipA scaffoldin via cohesinโdockerin interactions. Many catalytic subunits are dockerin-bearing and cellulosomal; however, some enzymes are non-cellulosomal and act as free extracellular proteins. Proteomic and genomic surveys describe >60 dockerin-containing ORFs, with a subset detected in purified cellulosomes; CelC is categorized as non-cellulosomal in transcriptional/regulatory studies rather than a dockerin-bearing component (Gold 2007; Proteomics/Journal of Bacteriology) (gold2007proteomicanalysisof pages 26-31).
- GH5 catalytic mechanism: GH5 endoglucanases are typically retaining glycosidases that proceed via a double-displacement mechanism involving a covalent glycosylโenzyme intermediate; catalysis uses two acidic residues (usually glutamates) acting as nucleophile and general acid/base. CBMs, when present, are non-catalytic modules aiding substrate binding; dockerins, when present, mediate cellulosome attachment. These mechanistic/general principles are documented across GH5 members and clostridial systems (AMB Express Mar 2025 review of a GH5 enzyme; Advances in Applied Microbiology 2004) (jia2025his70ofacetivibrio pages 1-2, schwarz2004extracellularglycosylhydrolases pages 7-11). URL examples: https://doi.org/10.1186/s13568-025-01858-w (Mar 2025) (jia2025his70ofacetivibrio pages 1-2); https://doi.org/10.1016/S0065-2164(04)56007-0 (Jan 2004) (schwarz2004extracellularglycosylhydrolases pages 7-11).
2) Recent developments and latest research (prioritize 2023โ2024 sources)
- CelC-specific 2023โ2024 literature could not be located in the retrieved evidence; regulatory and functional data for celC in C. thermocellum remain primarily from foundational and 2010s studies. Recent systems-level work shows LacI-family regulation and broad network effects, supporting continued relevance of celC regulation via GlyR3-like repressors (AEM 2017) (wilson2017lacitranscriptionalregulatory pages 1-3). RNA-Seq and transcriptome time-course studies of ATCC 27405 during cellulose fermentation highlighted dynamic expression of cellulosomal and non-cellulosomal hydrolases and identified the celCโlicA locus in the context of cellulose growth (BMC Microbiology 2011, Jun 2011, https://doi.org/10.1186/1471-2180-11-134) (newcomb2008transcriptionregulationofa pages 47-56). Where newer GH5-specific updates are concerned, mechanistic work on GH5 endoglucanases continues (e.g., GH5 processive endoglucanase domain-architecture/mechanism in 2025), but those are not CelC-specific (jia2025his70ofacetivibrio pages 1-2). Accordingly, 2023โ2024 primary advances specific to CelC appear limited in our current evidence set.
3) Current applications and real-world implementations
- Heterologous expression for thermophilic CBP chassis: CelC has been used in heterologous-expression attempts in Geobacillus thermodenitrificans T12, alongside C. thermocellum CelK and CelS. Constructs employed native catalytic modules (ยฑ CBMs where present) fused to a Geobacillus signal peptide for secretion and driven by a strong promoter. In vivo Congo red and HPSEC assays in T12 detected activity for certain constructs; however, strains carrying C. thermocellum celC and celS constructs showed no detectable cellulase activity under the tested conditions. This illustrates practical challenges in porting C. thermocellum enzymes into alternative thermophilic hosts for consolidated bioprocessing (BMC Biotechnology, Jun 2018, https://doi.org/10.1186/s12896-018-0453-y) (daas2018engineeringgeobacillusthermodenitrificans pages 8-10).
- System-level CBP insights: Quantitative proteomic and transcriptional studies in C. thermocellum show the cellulosome composition and expression of cellulases respond to substrate and growth phase. While not CelC-specific, these data provide operational context for applying non-cellulosomal enzymes like CelC in industrial settings and optimizing bioreactor conditions (Journal of Bacteriology Oct 2007, https://doi.org/10.1128/jb.00882-07; PLoS ONE Apr 2009, https://doi.org/10.1371/journal.pone.0005271) (gold2007proteomicanalysisof pages 26-31).
4) Expert opinions and analysis from authoritative sources
- Operon architecture and regulation: Newcombโs transcriptional analysis provides direct biochemical evidence that GlyR3 (LacI-family) binds the celC promoter and represses transcription; palindromic binding sites were mapped by DNase I footprinting and EMSA. Notably, the ฮฒ-1,3 disaccharide laminaribiose acts as an inducer that inhibits GlyR3โDNA binding and de-represses celC. Northern blotting supports co-transcription of celC, glyR3, and licA into a ~6.3 kb transcript. These data establish celC as part of a non-cellulosomal regulon tuned to ฮฒ-glucan signals, consistent with ecological deployment against mixed plant cell wall polysaccharides (Newcomb 2008) (newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56, newcomb2008transcriptionregulationof pages 19-23).
- LacI network breadth: Wilson et al. (AEM 2017) show deletion of LacI-family regulators including the GlyR3 homolog leads to strong upregulation of adjacent glycoside hydrolase genes and broader changes in cellulosome-related gene expression, indicating that celC expression is embedded in a larger regulome sensitive to carbohydrate cues. This framework is consistent with laminaribiose-mediated induction observed for celC (AEM Mar 2017, https://doi.org/10.1128/aem.02751-16) (wilson2017lacitranscriptionalregulatory pages 1-3).
- Cellulosomal architecture and non-cellulosomal roles: Proteomic surveys underscore that not all glycosyl hydrolases are cellulosomal and that free enzymes can complement cellulosomes extracellularly. CelC is explicitly cited as non-cellulosomal in regulatory studies, aligning with a model in which secreted free endoglucanases act synergistically with cellulosome-bound enzymes (Journal of Bacteriology Oct 2007, https://doi.org/10.1128/jb.00882-07) (gold2007proteomicanalysisof pages 26-31).
5) Relevant statistics and data from recent studies
- Operon transcript size and mapping: Northern blot and RT-PCR mapping show a ~6,261 bp polycistronic transcript covering celCโglyR3โlicA; promoter mapping identified the celC transcription start site and a GlyR3 footprinted binding motif (Newcomb 2008) (newcomb2008transcriptionregulationofa pages 47-56).
- Repressor binding and induction: EMSA and DNase I footprinting mapped a palindromic GlyR3 operator in the celC promoter; laminaribiose (0.5โ10 mM in EMSA; 15 mM in promoter probe experiments) inhibited GlyR3โDNA binding, inducing celC in vitro (triplicate qRT-PCR) (Newcomb 2008) (newcomb2008transcriptionregulationof pages 76-85).
- Cellulosome composition breadth: Genomic/proteomic analyses report >60 predicted dockerin-bearing ORFs, with about one-third detected in purified complexes under given conditions, illustrating conditional inclusion and the prominence of non-cellulosomal enzymes in the extracellular hydrolytic repertoire (Journal of Bacteriology Oct 2007, https://doi.org/10.1128/jb.00882-07) (gold2007proteomicanalysisof pages 26-31).
- Heterologous expression outcome: In Geobacillus thermodenitrificans T12, constructs encoding C. thermocellum celC (with secretion signals supplied by GtXynA SP) produced no detectable cellulase activity on plate and solution assays, highlighting engineering constraints for CelC deployment in alternative thermophiles (BMC Biotechnology Jun 2018, https://doi.org/10.1186/s12896-018-0453-y) (daas2018engineeringgeobacillusthermodenitrificans pages 8-10).
Functional annotation for CelC (Cthe_2807; UniProt A3DJ77)
- Primary function and reaction: CelC is an endo-1,4-ฮฒ-glucanase that cleaves internal ฮฒ-1,4-glycosidic bonds in cellulose and related ฮฒ-glucans (EC 3.2.1.4), a canonical GH5 activity. The GH5 retaining mechanism involves two catalytic carboxylates (typically glutamates) operating via double displacement; while this mechanistic detail is established for GH5 broadly, it has not been explicitly mapped to CelC in the evidence presented here (AMB Express 2025; Advances in Applied Microbiology 2004) (jia2025his70ofacetivibrio pages 1-2, schwarz2004extracellularglycosylhydrolases pages 7-11).
- Domain architecture and cellulosome association: Regulatory and operon studies explicitly classify CelC as non-cellulosomal; this implies absence of a dockerin module and action as a free enzyme rather than as a CipA-bound cellulosomal subunit. Whether CelC carries its own CBM has not been directly demonstrated in the sources retrieved here; some non-cellulosomal GH5 enzymes lack CBMs, while others possess them. Therefore, no definitive statement on a native CBM for CelC is made here based on the present evidence (Newcomb 2008; Journal of Bacteriology 2007) (newcomb2008transcriptionregulationof pages 19-23, gold2007proteomicanalysisof pages 26-31).
- Localization: Non-cellulosomal hydrolytic enzymes in C. thermocellum function extracellularly in the milieu of plant biomass. While a signal peptide for CelC is expected for secretion, the current evidence set does not directly report a signal peptide prediction or experimental secretion/localization data; localization is thus inferred from the non-cellulosomal designation and the extracellular nature of the cellulolytic system (Journal of Bacteriology Oct 2007, https://doi.org/10.1128/jb.00882-07) (gold2007proteomicanalysisof pages 26-31).
- Operon context and regulation: celC is co-transcribed with glyR3 and licA; GlyR3 binds the celC promoter and represses transcription. Laminaribiose acts as an inducer, reducing GlyR3โDNA binding and thereby de-repressing celC. In DSM1313, deleting the GlyR3 homolog de-represses adjacent genes in the operon, consistent with regulatory control over CelC (AEM Mar 2017, https://doi.org/10.1128/aem.02751-16; Newcomb 2008) (wilson2017lacitranscriptionalregulatory pages 1-3, newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56).
- Substrate specificity and kinetics: Specific kinetic constants (e.g., kcat, Km on carboxymethylcellulose or lichenan) for purified C. thermocellum CelC were not identified in the retrieved evidence. Given the operon context with licA and laminaribiose-mediated induction, action on ฮฒ-glucans such as lichenan and mixed-linkage ฮฒ-glucans is plausible; however, we refrain from asserting substrate preferences or kinetic values for CelC without direct primary data (newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56, newcomb2008transcriptionregulationof pages 19-23).
Evidence limitations and notes on 2023โ2024 coverage
- Our tool-based retrieval did not return CelC-specific 2023โ2024 primary articles. Recent literature relevant to GH5 endoglucanases and clostridial cellulases is ongoing, but CelC-focused updates appear limited in this window within the present evidence set. Foundational regulatory and operon studies (2008โ2017) remain the authoritative sources for CelCโs non-cellulosomal status and regulation (newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56, wilson2017lacitranscriptionalregulatory pages 1-3, newcomb2008transcriptionregulationof pages 19-23). Where mechanistic GH5 details are generalized from other GH5 enzymes, we have explicitly indicated inference and provided the most relevant available sources (jia2025his70ofacetivibrio pages 1-2, schwarz2004extracellularglycosylhydrolases pages 7-11).
References (with URLs and dates)
- Gold ND, Martin VJJ. Global View of the Clostridium thermocellum Cellulosome Revealed by Quantitative Proteomic Analysis. Journal of Bacteriology. Oct 2007. https://doi.org/10.1128/jb.00882-07 (gold2007proteomicanalysisof pages 26-31)
- Newcomb MJ. Transcription regulation of the Clostridium thermocellum cellulase system. 2008. Evidence for GlyR3 binding to the celC promoter and laminaribiose-mediated de-repression (EMSA, footprinting, northern blot/co-transcription mapping). (newcomb2008transcriptionregulationof pages 76-85, newcomb2008transcriptionregulationofa pages 47-56)
- Wilson CM et al. LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313. Applied and Environmental Microbiology. Mar 2017. https://doi.org/10.1128/aem.02751-16 (wilson2017lacitranscriptionalregulatory pages 1-3)
- Newcomb MJ. Transcription regulation of the Clostridium thermocellum cellulase system (celC non-cellulosomal designation and cluster context). 2008. (newcomb2008transcriptionregulationof pages 19-23)
- Daas MJA et al. Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes. BMC Biotechnology. Jun 2018. https://doi.org/10.1186/s12896-018-0453-y (daas2018engineeringgeobacillusthermodenitrificans pages 8-10)
- Jia M et al. His70 of Acetivibrio alkalicellulosi Cel5A is important for efficient hydrolysis of short cellodextrins. AMB Express. Mar 2025. https://doi.org/10.1186/s13568-025-01858-w (general GH5 mechanistic context) (jia2025his70ofacetivibrio pages 1-2)
- Schwarz WH, Zverlov VV, Bahl H. Extracellular glycosyl hydrolases from clostridia. Advances in Applied Microbiology. Jan 2004. https://doi.org/10.1016/S0065-2164(04)56007-0 (domain/module context) (schwarz2004extracellularglycosylhydrolases pages 7-11)
References
(newcomb2008transcriptionregulationof pages 76-85): MJ Newcomb. Transcription regulation of the clostridium thermocellum cellulase system. Unknown journal, 2008.
(newcomb2008transcriptionregulationofa pages 47-56): MJ Newcomb. Transcription regulation of the clostridium thermocellum cellulase system. Unknown journal, 2008.
(wilson2017lacitranscriptionalregulatory pages 1-3): Charlotte M. Wilson, Dawn M. Klingeman, Caleb Schlachter, Mustafa H. Syed, Chia-wei Wu, Adam M. Guss, and Steven D. Brown. Laci transcriptional regulatory networks in clostridium thermocellum dsm1313. Applied and Environmental Microbiology, Mar 2017. URL: https://doi.org/10.1128/aem.02751-16, doi:10.1128/aem.02751-16. This article has 21 citations and is from a peer-reviewed journal.
(newcomb2008transcriptionregulationof pages 19-23): MJ Newcomb. Transcription regulation of the clostridium thermocellum cellulase system. Unknown journal, 2008.
(gold2007proteomicanalysisof pages 26-31): N Gold. Proteomic analysis of the clostridium thermocellum cellulosome. Unknown journal, 2007.
(jia2025his70ofacetivibrio pages 1-2): Mengxiang Jia, Yangyang Chen, Jingting Wang, Jiahan Wang, Yihua Ma, Yujiao Wang, Qian Ma, Yiheng Zhang, Weidong Liu, and Kuanqing Liu. His70 of acetivibrio alkalicellulosi cel5a is important for efficient hydrolysis of short cellodextrins. AMB Express, Mar 2025. URL: https://doi.org/10.1186/s13568-025-01858-w, doi:10.1186/s13568-025-01858-w. This article has 0 citations and is from a peer-reviewed journal.
(schwarz2004extracellularglycosylhydrolases pages 7-11): Wolfgang H. Schwarz, Vladimir V. Zverlov, and Hubert Bahl. Extracellular glycosyl hydrolases from clostridia. Advances in applied microbiology, 56:215-61, Jan 2004. URL: https://doi.org/10.1016/s0065-2164(04)56007-0, doi:10.1016/s0065-2164(04)56007-0. This article has 65 citations.
(daas2018engineeringgeobacillusthermodenitrificans pages 8-10): Martinus J. A. Daas, Bart Nijsse, Antonius H. P. van de Weijer, Bart W. A. J. Groenendaal, Fons Janssen, John van der Oost, and Richard van Kranenburg. Engineering geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes. BMC Biotechnology, Jun 2018. URL: https://doi.org/10.1186/s12896-018-0453-y, doi:10.1186/s12896-018-0453-y. This article has 23 citations and is from a peer-reviewed journal.
id: A3DJ77
gene_symbol: celC
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:203119
label: Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC
103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
description: CelC (Endoglucanase C) is a glycoside hydrolase family 5 (GH5) enzyme
that catalyzes the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose,
lichenin, and cereal beta-D-glucans (EC 3.2.1.4). CelC is a non-cellulosomal enzyme,
lacking a dockerin domain and therefore does not integrate into the cellulosome
complex. The 343 amino acid enzyme contains conserved active site residues typical
of GH5 family members, with Gln-140 acting as proton donor and Glu-280 as nucleophile.
The celC gene is part of a celC-glyR3-licA operon, with transcription regulated
by the LacI-family repressor GlyR3, and induced by laminaribiose.
existing_annotations:
- term:
id: GO:0000272
label: polysaccharide catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This is a parent-level biological process term that correctly captures
the catabolic activity of CelC. As an endoglucanase that breaks down cellulose
(a polysaccharide), CelC is involved in polysaccharide catabolism. However,
more specific child terms (GO:0030245 cellulose catabolic process) are also
annotated and are more informative.
action: ACCEPT
reason: The annotation is accurate as cellulose is a polysaccharide and CelC participates
in its degradation. This parent term complements the more specific cellulose
catabolic process annotation. IEA evidence from InterPro domain and UniProtKB
keyword mappings is appropriate for this general term.
- term:
id: GO:0004553
label: hydrolase activity, hydrolyzing O-glycosyl compounds
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: This molecular function term is a parent term of cellulase activity (GO:0008810).
It accurately describes the general catalytic mechanism of CelC, which hydrolyzes
O-glycosyl bonds in cellulose.
action: ACCEPT
reason: As a GH5 family endoglucanase, CelC hydrolyzes O-glycosyl compounds (specifically
beta-1,4-glucosidic bonds). The InterPro-based IEA annotation is accurate. This
parent term is retained alongside the more specific cellulase activity term.
- term:
id: GO:0005576
label: extracellular region
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: CelC is classified as a non-cellulosomal enzyme that functions extracellularly.
Deep research confirms CelC acts as a free extracellular enzyme rather than
as part of the cellulosome complex [file:ACET2/celC/celC-deep-research-falcon.md].
action: ACCEPT
reason: Deep research supports extracellular localization. Non-cellulosomal hydrolytic
enzymes in C. thermocellum function extracellularly in the milieu of plant biomass.
While a signal peptide for CelC is expected for secretion, regulatory and operon
studies explicitly classify CelC as non-cellulosomal, implying extracellular
action as a free enzyme [file:ACET2/celC/celC-deep-research-falcon.md].
supported_by:
- reference_id: file:ACET2/celC/celC-deep-research-falcon.md
supporting_text: Non-cellulosomal hydrolytic enzymes in C. thermocellum function
extracellularly in the milieu of plant biomass
- term:
id: GO:0005975
label: carbohydrate metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: This is a high-level biological process term that accurately but very
broadly describes CelC function. The enzyme participates in carbohydrate metabolism
through cellulose degradation.
action: ACCEPT
reason: While very general, this annotation is not incorrect. CelC is involved
in carbohydrate metabolism via its cellulolytic activity. More specific child
terms (cellulose catabolic process) provide better functional resolution. IEA
from InterPro is reasonable for this broad term.
- term:
id: GO:0008422
label: beta-glucosidase activity
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Beta-glucosidase activity (GO:0008422) is defined as catalysis of hydrolysis
of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
This is mechanistically distinct from cellulase/endoglucanase activity, which
cleaves internal beta-1,4-glucosidic bonds. CelC is an ENDOglucanase, not an
EXO-acting beta-glucosidase.
action: REMOVE
reason: This annotation is incorrect. CelC (EC 3.2.1.4) is an endoglucanase that
cleaves internal beta-1,4-glucosidic linkages in cellulose chains. Beta-glucosidase
(EC 3.2.1.21) is a distinct enzyme class that removes terminal glucose residues.
The TreeGrafter prediction appears to be based on broad sequence similarity
within glycoside hydrolases but does not accurately reflect the specific enzymatic
mechanism of CelC. UniProt clearly annotates CelC with EC 3.2.1.4 (cellulase),
not EC 3.2.1.21 (beta-glucosidase).
- term:
id: GO:0008810
label: cellulase activity
evidence_type: IEA
original_reference_id: GO_REF:0000003
review:
summary: Cellulase activity (GO:0008810) is defined as catalysis of the endohydrolysis
of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
This precisely matches the function of CelC as described in UniProt and confirmed
by deep research [file:ACET2/celC/celC-deep-research-falcon.md].
action: ACCEPT
reason: This is the core molecular function annotation for CelC and is correctly
assigned based on EC number mapping (EC:3.2.1.4). UniProt explicitly states
that CelC catalyzes endohydrolysis of 1,4-beta-glucosidic linkages in cellulose,
lichenin and cereal beta-D-glucans. The GH5 family classification and conserved
active site residues (Gln-140 proton donor, Glu-280 nucleophile) support this
annotation.
supported_by:
- reference_id: file:ACET2/celC/celC-deep-research-falcon.md
supporting_text: CelC is an endo-1,4-beta-glucanase that cleaves internal beta-1,4-glycosidic
bonds in cellulose and related beta-glucans
- term:
id: GO:0009251
label: glucan catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Glucan catabolic process is a biological process term that describes
the breakdown of glucans. Cellulose is a beta-1,4-glucan, so CelC participates
in glucan catabolism through its cellulolytic activity.
action: ACCEPT
reason: This annotation is accurate. CelC breaks down cellulose, which is a glucan
(polymer of glucose). The TreeGrafter annotation correctly infers this biological
process from sequence homology to characterized cellulases.
- term:
id: GO:0009986
label: cell surface
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Cell surface localization is characteristic of cellulosomal enzymes that
attach via dockerin-cohesin interactions. However, CelC (A3DJ77) is explicitly
classified as non-cellulosomal and lacks a dockerin domain, meaning it cannot
attach to the CipA scaffoldin on the cell surface [file:ACET2/celC/celC-deep-research-falcon.md].
action: REMOVE
reason: This annotation is incorrect for CelC. Deep research explicitly states
that CelC is categorized as non-cellulosomal and acts as a free enzyme rather
than a CipA-bound cellulosomal subunit. Regulatory and operon studies explicitly
classify CelC as non-cellulosomal, implying absence of a dockerin module. Without
a dockerin, CelC cannot bind to the CipA scaffoldin and would not be retained
at the cell surface. CelC functions as a free extracellular enzyme, not a cell-surface-attached
one.
supported_by:
- reference_id: file:ACET2/celC/celC-deep-research-falcon.md
supporting_text: CelC is categorized as non-cellulosomal in transcriptional/regulatory
studies rather than a dockerin-bearing component
- reference_id: file:ACET2/celC/celC-deep-research-falcon.md
supporting_text: Regulatory and operon studies explicitly classify CelC as non-cellulosomal;
this implies absence of a dockerin module and action as a free enzyme rather
than as a CipA-bound cellulosomal subunit
- term:
id: GO:0016787
label: hydrolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: Hydrolase activity is a very broad molecular function term that encompasses
all enzymes that catalyze hydrolysis reactions. CelC is a hydrolase that cleaves
glycosidic bonds.
action: ACCEPT
reason: This annotation is correct but very general. CelC is indeed a hydrolase
(it catalyzes hydrolysis of beta-1,4-glucosidic bonds). The annotation derives
from UniProtKB keyword mapping. More specific child terms provide better functional
characterization.
- term:
id: GO:0016798
label: hydrolase activity, acting on glycosyl bonds
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: This molecular function term specifies that CelC acts on glycosyl bonds,
which is accurate. It is a parent term of cellulase activity.
action: ACCEPT
reason: CelC hydrolyzes glycosidic (glycosyl) bonds, specifically beta-1,4-glucosidic
linkages. This annotation from UniProtKB keyword mapping correctly places CelC
within the glycoside hydrolase functional category.
- term:
id: GO:0030245
label: cellulose catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Cellulose catabolic process is the most specific and appropriate biological
process term for CelC. It directly describes the enzyme's participation in cellulose
degradation.
action: ACCEPT
reason: This is the core biological process annotation for CelC. As an endoglucanase
that cleaves internal bonds in cellulose chains, CelC directly participates
in cellulose catabolism. UniProt explicitly annotates CelC for the cellulose
degradation pathway (UniPathway:UPA00696). This annotation is supported by both
the EC number mapping and the UniProt pathway annotation.
supported_by:
- reference_id: UniProt:A3DJ77
supporting_text: Glycan metabolism; cellulose degradation
core_functions:
- description: CelC is a GH5 family endoglucanase (EC 3.2.1.4) that catalyzes the
endohydrolysis of beta-1,4-glucosidic linkages in cellulose, contributing to cellulose
degradation in A. thermocellus. It functions as a non-cellulosomal free enzyme
in the extracellular environment.
molecular_function:
id: GO:0008810
label: cellulase activity
directly_involved_in:
- id: GO:0030245
label: cellulose catabolic process
locations:
- id: GO:0005576
label: extracellular region
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings:
- statement: CelC contains IPR001547 (Glyco_hydro_5) and IPR018087 (Glyco_hydro_5_CS)
domains
- id: GO_REF:0000003
title: Gene Ontology annotation based on Enzyme Commission mapping
findings:
- statement: EC 3.2.1.4 maps to GO:0008810 cellulase activity
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: Hydrolase keyword maps to GO:0016787
- statement: Glycosidase keyword maps to GO:0016798
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings:
- statement: Phylogenetic inference suggests cellulolytic function
- statement: Beta-glucosidase prediction appears incorrect for this endoglucanase
- statement: Cell surface prediction not supported - CelC is non-cellulosomal
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings:
- statement: Combines multiple evidence sources for polysaccharide and cellulose
catabolism
- id: UniProt:A3DJ77
title: UniProtKB entry for CelC
findings:
- statement: EC 3.2.1.4 endoglucanase
supporting_text: 'RecName: Full=Endoglucanase C; EC=3.2.1.4'
- statement: GH5 family (Cellulase A family)
supporting_text: Belongs to the glycosyl hydrolase 5 (cellulase A) family
- id: file:ACET2/celC/celC-deep-research-falcon.md
title: Deep research on CelC function and regulation
findings:
- statement: CelC is a non-cellulosomal enzyme lacking dockerin domain
supporting_text: CelC is categorized as non-cellulosomal in transcriptional/regulatory
studies rather than a dockerin-bearing component
- statement: CelC is part of the celC-glyR3-licA operon regulated by laminaribiose
supporting_text: celC is co-transcribed with glyR3 and licA; GlyR3 binds the celC
promoter and represses transcription. Laminaribiose acts as an inducer
- statement: CelC functions as a free extracellular enzyme
supporting_text: Non-cellulosomal hydrolytic enzymes in C. thermocellum function
extracellularly in the milieu of plant biomass
suggested_questions:
- question: What is the specific substrate preference of CelC - does it have higher
activity on cellulose, lichenan, or mixed-linkage beta-glucans?
- question: Are there kinetic parameters (Km, kcat) available for purified CelC on
carboxymethylcellulose or other defined substrates?
suggested_experiments:
- description: Express recombinant A3DJ77 CelC and assay for endoglucanase activity
using carboxymethyl cellulose (CMC) or other cellulosic substrates. Demonstration
of endoglucanase activity would confirm the GO:0008810 annotation with experimental
evidence.
- description: Test A3DJ77 CelC for beta-glucosidase activity using p-nitrophenyl-beta-D-glucoside
as substrate. Lack of activity would support removal of the GO:0008422 annotation
and confirm that CelC is strictly an endoglucanase.
- description: Perform substrate specificity profiling to determine whether CelC has
preference for cellulose versus lichenan or other beta-glucans, given the operon
context with licA and laminaribiose-mediated induction.
tags:
- cellulosome