TABLE 3.
Expression of SOS regulated genes increases in response to a single site-specific double-strand break in B. subtilis
| Genea | Function or element | Fold change (Q value, %)b
|
|
|---|---|---|---|
| I-SceI + xylose vs ΔI-SceI + xylose | I-SceI + xylose vs I-SceI (no xylose) | ||
| yneB | Site-specific recombinase | 9.7 (1.3) | 7.7 (1.6) |
| yneA | Cell division inhibitor | 5.5 (1.3) | 4.6 (1.6) |
| msmE | Multiple sugar binding protein | 5.1 (1.3) | 2.9 (1.6) |
| dinB | Nuclease inhibitor | 4.4 (1.3) | 3.4 (1.6) |
| i_aprX_ymaC | Alkaline serine protease | 3.7 (1.3) | 2.6 (1.6) |
| yhaZ | Alkylation repair | 3.6 (1.3) | 2.8 (1.6) |
| lexA | Transcriptional repressor of SOS | 2.6 (1.3) | 2.4 (1.6) |
| recA | Homologous recombination | 2.2 (1.3) | ND |
| xkdF | PBSX | 3.3 (1.3) | ND |
| xkdM | PBSX | 3.2 (1.3) | ND |
| xkdV | PBSX | 3.0 (1.3) | ND |
| xkdE | PBSX | 2.9 (1.3) | ND |
| xkdN | PBSX | 2.7 (1.3) | ND |
| xkdG | PBSX | 2.6 (1.3) | ND |
| xhlA | PBSX | 2.5 (1.3) | ND |
| xkdJ | PBSX | 2.5 (1.3) | ND |
| xkdP | PBSX | 2.5 (1.3) | ND |
| xkdH | PBSX | 2.4 (1.3) | ND |
| i_xylB_yncB | Xylulose kinase | ND | 62 (1.6) |
| ptsG | Glucose transport/phosphorylation | ND | 24.3 (1.6) |
| xynB | Xylan β-1,4-xylosidase | ND | 12 (1.6) |
| xylA | Xylose isomerase | ND | 20.1 (1.6) |
a
“i” indicates “intergenic region.”
b
The Q value is the rate of false-positive discovery. A Q value of 1% means that 1 out of 100 is likely to be false positive. The list of genes in this table reflects the significantly upregulated genes that were identified. The gene tagC was induced 1.8-fold in the microarray when comparing I-SceI + xylose with ΔI-SceI + xylose (data not shown). Raw microarray data are available at NCBI GEO (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE13694. Gene names are from http://genolist.pasteur.fr/SubtiList/. ND, not determined.