Table 1. Genes identified in Tn-seq analysis of cells surviving replication arrest in the absence of DNA damage.
| Gene | Function | Log2 FC, Tn-seqa | Survival of null mutantsb | Strainb |
|---|---|---|---|---|
| DNA repair and recombination | ||||
| polA | DNA polymerase I | -6.51 | 0.06 (0.01) | LSF41 |
| recU | Holliday junction-specific endonuclease | -2.46 | 0.22 (0.09) | GP891 |
| recN | recognition of DNA double strand breaks | -1.65 | 0.14 (0.08) | LSF298 |
| addA | ATP-dependent deoxyribonuclease subunit A | -1.55 | 0.10 (0.06) | LSF253 |
| nfo | endonuclease IV | -1.11 | ND | |
| recJ | 5’-3’ exonuclease | 1.04 | 12 (1.7) | LSF200 |
| walJ | metallo-β-lactamase/ 5’-3’ exonuclease | 1.29 | 2.89 (0.07) | BKE40370 |
| Prophages | ||||
| yonH | unknown function (SPß) | 1.09 | 1.6 (0.3)c | LSF203 |
| yoyI | transmembrane protein (SPß) | 1.24 | ||
| xkdC | unknown function (PBSX) | 1.39 | 1.9 (0.1)d | LSF204 |
| xkdB | protein with LexA-type HTH domain (PBSX) | 1.46 | ||
| xpf | positive control sigma-like factor (PBSX) | 1.47 | ||
| Iron-Sulfur and oxidative homeostasis | ||||
| rex | redox-sensing transcriptional repressor | -1.24 | ND | |
| nadC | nicotinate-nucleotide pyrophosphorylase | 1.39 | ND | |
| nadA | quinolinate synthetase | 1.47 | ND | |
| defB | peptide deformylase | 1.64 | ND | |
| nifS | cysteine desulfurase | 1.84 | ND | |
| nadB | L-aspartate oxidase | 2.03 | ND | |
| Cell wall and membrane | ||||
| ltaS | polyglycerolphosphate lipoteichoic acid synthase | -1.79 | ND | |
| rseP | inner membrane zinc metalloprotease | -1.68 | ND | |
| oppA | oligopeptide ABC transporter binding lipoprotein | -1.67 | 0.21 (0.07) | JRL131 |
| ponA | peptidoglycan glycosyltransferase | -1.43 | 0.11 (0.03) | CMJ293 |
| oppB | oligopeptide ABC transporter permease | -1.40 | 0.3 (0.11) | JRL189 |
| ydiL | membrane protease | -1.05 | ND | |
| cwlO | secreted cell wall DL-endopeptidase | 1.10 | 2.2 (0.4) | CMJ374 |
| Other | ||||
| hrcA | heat-inducible transcription repressor | -1.93 | 0.26 (0.09) | LSF233 |
| bkdB | E2 subunit, lipoamide acyltransferase | -1.43 | ND | |
| speE | spermidine synthase | -1.38 | 0.3 (0.15) | LSF20 |
| yutD | unknown function | -1.12 | ND | |
| ytpQ | unknown function | -1.10 | ND | |
| argG | argininosuccinate synthase | 1.07 | ND | |
| ywdH | aldehyde dehydrogenase | 1.08 | ND | |
| yoaQ | unknown function | 1.25 | ND | |
| ycgE | transcriptional regulator | 1.39 | 4 (2) | LSF444 |
| argH | argininosuccinate lyase | 1.42 | ND | |
a Log2 FC: Log2 of the ratio of normalized number of insertions from the Tn-seq analyses in the indicated gene 4 h after removal of HPUra compared to that of cells that had not been treated with HPUra.
b Survival after HPUra treatment of defined null mutants (strain numbers listed) relative to that of the isogenic parental strain, with one standard deviation of the mean in parenthesis.
c Sensitivity of a strain devoid of SPß was used, rather than individual yonH and yoyI mutants.
d Sensitivity of a strain devoid of PBSX was used, rather than individual xkdC, xkdB, and xpf mutants.