Botulinum Neurotoxin (BoNT) Resource Guide

BoNT Genes

Protein aggregates referred to as progenitor toxins or toxin complexes secrete botulinum neurotoxins. These aggregates comprise neurotoxin plus a set of seven toxin associated proteins (TAPs). TAPs include non-toxic non-hemagglutinin proteins (NTNH) and hemagglutinins (HA). As seen in Table 1 from Hines et al. 2005, PMID: 16085839, a number of proteins known to form protein aggregates have been identified for the seven botulinum serotypes.

Neurotoxins, designated BoNT/A to BoNT/G, are synthesized as single polypeptides. Proteolytic activation yields N-terminal light chain (Lc) and C-terminal heavy chain (Hc) polypeptides connected by disulfide bonds. Genes encoding neurotoxin proteins reside on the Clostridium botulinum chromosome (types A, B, F), bacteriophages (types C, D, E) and plasmid (type G).

NCBI Queries for BoNT Gene Sequences

Lists of gene-specific and gene-related nucleotide and protein sequences can be retrieved from NCBI's Nucleotide database by text searches based on the protein or gene name for the Clostridium botulinum genes.

Click on the provided links, below, to view the results for each gene. Each query is presented with the associated Gene Symbol, Putative Identification, NCBI Search String, NCBI Protein Link, NCBI Nucleotide Link and Pathema Annotation Link.

Clostridium botulinum Genes

Clostridium botulinum genes including BoNT genes involved in cellular processes such as pathogenesis, germination, toxin production and resistance are presented here by Serotype (A-G), Gene Symbol, PubMed ID, Protein Accession, Nucleotide Accession and Source Strain. Clostridium botulinum strains are linked to the corresponding Strain entry on the BoNT_strains page.

Pathema's Annotated BoNT Genes

Detailed results of Pathema's annotation of Clostridium botulinum can be found at the Clostridium botulinum Hall strain A Genome Page. You can also navigate directly to subsets of Pathema's annotated genes by the links provided below.

• Protein coding genes
  • Genes assigned a role category
  • Conserved hypothetical genes
  • Hypothetical genes
• tRNA genes
• rRNA genes

Genes involved in specific Role Categories can be viewed at Pathema's Role Categories Search page including Amino acid biosynthesis, Cellular processing, Energy metabolism, Protein synthesis and Transcription searches. Here, we provide links to a subset of toxin-related Role Category links.

• Pathogenesis
• Sporulation and germination
• Toxin production and resistance

Genome Annotation Data for Clostridium botulinum Genomes

Genome annotation data for Clostridium botulinum genome was obtained from the Entrez Genome database at NCBI. Genome Name, the associated RefSeq Accession linked to a graphical display of the genome annotation, and the Number of Annotated Genes linked to NCBI's Entrez Gene database are presented. Additional genome-related information on the corresponding Pathema Genome Pages can be viewed by clicking on the Genome Name link.

Synthetic Genes

The difficulty and high costs involved in culturing large quantities of toxin-producing Clostridium botulinum and the danger involved in working with highly toxic components such as formalin have led to the use of synthetic genes in new vaccine development. Due to rare codons and AT rich base compositions in naturally occurring clostridial DNA, synthetic genes are constructed for optimal expression in heterologous expression systems such as E. coli and yeast (Byrne MP and LA Smith 2000, PMID: 11086225).

Synthetically constructed genes are presented with their Synthetic Gene Name, Gene Source (N-terminal catalytic endopeptidase domain (light chain, Lc), translocation domain (HN or H1 of heavy chain, Hc) and the C-terminal binding domain (HC or H2 of heavy chain, Hc)), PubMed ID, Nucleotide Accession and Expression System.

Pathema's Genome Tools and Resources

Navigate to Pathema's Clostridium botulinum Resource Page to view Genome Annotation-related information including links to pre-computed Searches, Pathema's Genome Tools, Comparative Analysis resources and gene-specific information.

• Searches (Search Pathema for genes, genomes, sequence regions, and evidence)
  • Annotation Search Tool
  • GenBank Search Tool
  • EC Number Search Tool
  • Gene Ontology Search Tool
  • Role Category Search
  • Protein Motif Search Tool
  • Position Search/Segment Retrieval


• Genome Tools (Explore organism lists, summary information and analysis for Clostridium botulinum genomes)
  • All Genes in a Genome List
  • Role Category Pie Chart
  • DNA Molecule Information
  • KEGG Pathway Display
  • Genome Browser Front Page
  • Region View Search
  • Restriction Digest Tool
  • Pseudo 2D Gel
  • Codon Usage Table


• Lists (Select and download gene, evidence, and genomic element lists)
  • Role Categories
  • RNA List
  • Intergenic Regions Display
  • InterRNA Regions Display