TABLE 2.
Variable CDSs in the Nordic group I Clostridium botulinum type B strains in relation to ATCC 3502 chromosomal and plasmid CDSsa
| CDS functional class | No. of CDSs present in cluster BI strains but not cluster BII strains | No. of CDSs present in cluster BII strains but not cluster BI strains | No. of CDSs missing from all type B strains studied | Total no. of CDSs present in ATCC 3502 chromosome and plasmid | No. (%) of discriminating CDSs in each functional classb |
|---|---|---|---|---|---|
| Cell processes | |||||
| Chemotaxis and mobility | 1 | 1 | 3 | 68 | 5 (7) |
| Chaperones | 15 | 0 (0) | |||
| Protection responses | 1 | 1 | 5 | 2 (40) | |
| Cell killing | 1 | 4 | 10 | 5 (50)* | |
| Detoxification | 2 | 11 | 2 (18) | ||
| Drug/analog sensitivity | 1 | 14 | 1 (7) | ||
| Radiation sensitivity | 1 | 0 (0) | |||
| Transport/binding proteins | 4 | 10 | 6 | 156 | 20 (13) |
| Amino acids and amines | 1 | 38 | 1 (3) | ||
| Cations | 3 | 36 | 3 (8) | ||
| Carbohydrates, organic acids, and alcohols | 1 | 35 | 1 (3) | ||
| Anions | 8 | 0 (0) | |||
| Other substances | 4 | 44 | 4 (10) | ||
| Adaptation | |||||
| Adaptations, atypical conditions | 8 | 0 (0) | |||
| Osmotic adaptation | 1 | 4 | 1 (25) | ||
| Fe storage | 5 | 36 | 5 (14) | ||
| Cell division | 23 | 0 (0) | |||
| Differentiation/sporulation | 5 | 2 | 81 | 7 (9) | |
| Macromolecule degradation | |||||
| Degradation of DNA | 10 | 0 (0) | |||
| Degradation of RNA | 1 | 9 | 1 (11) | ||
| Degradation of polysaccharides | 10 | 0 (0) | |||
| Degradation of proteins, peptides, glycoproteins | 1 | 5 | 50 | 6 (12) | |
| Macromolecule synthesis | 12 | 211 | 12 (6) | ||
| Amino acid biosynthesis | 54 | 0 (0) | |||
| Biosynthesis of cofactors, carriers | 1 | 3 | 1 | 86 | 5 (6) |
| Central intermediary metabolism | 1 | 1 | 109 | 2 (2) | |
| Degradation of small molecules | 86 | 0 (0) | |||
| Energy metabolism, carbon | 1 | 2 | 113 | 3 (3) | |
| Fatty acid biosynthesis | 6 | 18 | 6 (33) | ||
| Nucleotide biosynthesis | 24 | 0 (0) | |||
| Periplasmic/exported/lipoproteins | 1 | 8 | 1 (13) | ||
| Inner membrane | 2 | 4 | 2 (50) | ||
| Outer membrane constituents | 2 | 0 (0) | |||
| Surface polysaccharides and antigens | 1 | 13 | 40 | 14 (35)* | |
| Surface structures | 1 | 7 | 1 (14) | ||
| Gram-positive membrane | 1 | 14 | 11 | 281 | 26 (9) |
| Gram-positive exported protein/lipoprotein | 2 | 5 | 5 | 91 | 12 (13) |
| Gram-positive surface-anchored protein | 4 | 0 (0) | |||
| Gram-positive peptidoglycan, teichoic acid | 1 | 1 | 43 | 2 (5) | |
| Ribosome constituents | 1 | 2 | 63 | 3 (5) | |
| Horizontally acquired elements | |||||
| Phage-related functions and prophages | 1 | 4 | 111 | 166 | 116 (70)* |
| Plasmid-related functions | 4 | 5 | 4 (80)* | ||
| Transposon/IS element-related functions | 3 | 4 | 12 | 7 (58)* | |
| Pathogenicity | 1 | 1 | 16 | 2 (13) | |
| Regulation | 5 | 0 (0) | |||
| Two-component system | 2 | 1 | 74 | 3 (4) | |
| RNA polymerase core enzyme binding | 1 | 15 | 1 (7) | ||
| Defined regulatory families | |||||
| AsnC | 2 | 0 (0) | |||
| AraC | 2 | 4 | 24 | 6 (25)* | |
| GntR | 2 | 18 | 2 (11) | ||
| LacI | 2 | 0 (0) | |||
| LysR | 6 | 0 (0) | |||
| MarR | 1 | 12 | 1 (8) | ||
| TetR | 1 | 1 | 12 | 2 (17) | |
| DeoR | 5 | 0 (0) | |||
| LuxR (GerR) | 1 | 0 (0) | |||
| MerR | 1 | 10 | 1 (10) | ||
| ArsR | 1 | 5 | 1 (20) | ||
| PadR | 3 | 4 | 3 (75)* | ||
| Other regulatory proteins | 3 | 1 | 85 | 4 (5) | |
| Unknown function, conserved proteins | 3 | 26 | 48 | 642 | 77 (12) |
| Not classified | 1 | 14 | 15 | 383 | 30 (8) |
| Total | 17 | 128 | 268 | 3,421 | 413 (12) |
a
*, significant (P < 0.05) overrepresentation of a functional class as tested with one-sided Fisher's exact test.
b
The CDS functional classification is done according to data presented previously by Sebaihia et al. (27).