TABLE 1.
Number of genes significantly up-regulated or down-regulated during growth in modified C medium versus unmodified C medium
| Gene code | Gene descriptiona (no. of genes in categoryb) | No. (%) of genes detected in C medium under the indicated conditionsc
|
|||
|---|---|---|---|---|---|
| pH 7.5
|
0.15 M NaCl
|
||||
| Up-regulated | Down-regulated | Up-regulated | Down-regulated | ||
| J | Translation (140) | 39 (27.8) | 5 (3.6) | 1 (0.7) | 7 (5) |
| K | Transcription (93) | 9 (9.7) | 9 (9.7) | 1 (1.1) | 4 (4.3) |
| L | Replication, recombination, and repair (95) | 6 (6.3) | 5 (5.3) | 1 (1.1) | 3 (3.2) |
| C | Energy production and conversion (57) | 5 (8.8) | 6 (10.5) | 10 (17.5) | 0 (0) |
| E | Amino acid transport and metabolism (99) | 8 (8.1) | 0 (0) | 1 (1.0) | 0 (0) |
| F | Nucleotide transport and metabolism (59) | 10 (16.9) | 1 (1.7) | 2 (3.4) | 0 (0) |
| G | Carbohydrate transport and metabolism (124) | 12 (9.7) | 12 (9.7) | 6 (4.8) | 8 (6.5) |
| H | Coenzyme transport and metabolism (34) | 3 (8.8) | 1 (2.9) | 1 (2.9) | 0 (0) |
| I | Lipid transport and metabolism (45) | 5 (11.1) | 2 (4.4) | 1 (2.2) | 1 (2.2) |
| Q | Secondary metabolite biosynthesis, transport, and catabolism (11) | 1 (9.1) | 0 (0) | 0 (0) | 1 (9.1) |
| D | Cell cycle control, mitosis, and meiosis (16) | 2 (12.5) | 0 (0) | 0 (0) | 0 (0) |
| M | Cell wall/membrane biogenesis (64) | 2 (3.1) | 2 (3.1) | 0 (0) | 0 (0) |
| O | Posttranslational modification, protein turnover, chaperones (50) | 2 (4) | 8 (16) | 0 (0) | 7 (14) |
| P | Inorganic ion transport and metabolism (58) | 2 (3.4) | 5 (8.6) | 0 (0) | 1 (1.7) |
| T | Signal transduction mechanisms (37) | 3 (8.1) | 2 (5.4) | 0 (0) | 0 (0) |
| U | Intracellular trafficking and secretion (14) | 2 (14.3) | 1 (7.1) | 0 (0) | 0 (0) |
| V | Defence mechanisms (36) | 4 (11.1) | 4 (11.1) | 3 (8.3) | 1 (2.8) |
| R | General function prediction only (137) | 10 (7.3) | 5 (3.6) | 3 (2.2) | 3 (2.2) |
| S | Function unknown (126) | 7 (5.6) | 16 (12.7) | 0 (0) | 2 (1.6) |
| None | Not in COGs (222) | 17 (7.7) | 31 (14) | 13 (5.9) | 11 (5) |
| Totald | 149 (9.8) | 115 (7.6) | 43 (2.8) | 49 (3.2) | |
Genes were categorized according to a functional classification, COGs (clusters of orthologous groups) (56).
Structural RNA genes (tRNA and rRNA) and phage genes were omitted for clarity.
Number of genes displaying statistically significant differential expression in the modified medium as opposed to unmodified medium fulfilling the following criteria: average severalfold change of at least ±2.0 and a false discovery rate in SAM (57) of 90th percentile = 0.1%. Percentages represent numbers of statistically significant genes versus the total number of genes assigned to the category.
Total number of genes in all categories, 1,517.