Genome-Wide Screening with Hydroxyurea Reveals a Link between Nonessential Ribosomal Proteins and Reactive Oxygen Species Production

We performed a screening of hydroxyurea (HU)-sensitive mutants using a single-gene-deletion mutant collection in Escherichia coli. HU inhibits ribonucleotide reductase (RNR), which leads to arrest of the replication fork. Surprisingly, the wild-type was less resistant to HU than the average for the Keio Collection. Respiration-defective mutants were significantly more resistant to HU, suggesting that the generation of reactive oxygen species (ROS) contributes to cell death. High-throughput screening revealed that 15 mutants were completely sensitive on plates containing 7.5 mM HU. Unexpectedly, translation-related mutants based on COG categorization were the most enriched, and three of them were deletion mutants of nonessential ribosomal proteins (L1, L32, and L36). We found that, in these mutants, an increased membrane stress response was provoked, resulting in increased ROS generation. The addition of OH radical scavenger thiourea rescued the HU sensitivity of these mutants, suggesting that ROS generation is the direct cause of cell death. Conversely, both the deletion of rpsF and the deletion of rimK, which encode S6 and S6 modification enzymes, respectively, showed an HU-resistant phenotype. These mutants increased the copy number of the p15A-based plasmid and exhibited reduced basal levels of SOS response. The data suggest that nonessential proteins indirectly affect the DNA-damaging process.