The RpoH (σ) Regulon and Its Role in Essential Cellular Functions, Starvation Survival, and Antibiotic Tolerance

The bacterial heat-shock response is regulated by the alternative sigma factor, σ (RpoH), which responds to misfolded protein stress and directs the RNA polymerase to the promoters for genes required for protein refolding or degradation. In , RpoH is essential for viability under laboratory growth conditions. Here, we used a transcriptomics approach to identify the genes of the RpoH regulon, including RpoH-regulated genes that are essential for . We placed the gene under control of the arabinose-inducible P promoter, then deleted the chromosomal allele. This allowed transcriptomic analysis of the RpoH (σ) regulon following a short up-shift in the cellular concentration of RpoH by arabinose addition, in the absence of a sudden change in temperature. The ∆ (P-) strain grew in the absence of arabinose, indicating that some expression occurred without arabinose induction. When arabinose was added, the mRNA abundance of ∆ (P-) measured by RT-qPCR increased five-fold within 15 min of arabinose addition. Transcriptome results showed that genes required for protein repair or degradation are induced by increased RpoH levels, and that many genes essential for growth are induced by RpoH. Other stress response genes induced by RpoH are involved in damaged nucleic acid repair and in amino acid metabolism. Annotation of the hypothetical proteins under RpoH control included proteins that may play a role in antibiotic resistances and in non-ribosomal peptide synthesis. Phenotypic analysis of ∆ (P-) showed that it is impaired in its ability to survive during starvation compared to the wild-type strain. ∆ (P-) also had increased sensitivity to aminoglycoside antibiotics, but not to other classes of antibiotics, whether cultured planktonically or in biofilms. The enhanced aminoglycoside sensitivity of the mutant strain may be due to indirect effects, such as the build-up of toxic misfolded proteins, or to the direct effect of genes, such as aminoglycoside acetyl transferases, that are regulated by RpoH. Overall, the results demonstrate that RpoH regulates genes that are essential for viability of , that it protects from damage from aminoglycoside antibiotics, and that it is required for survival during nutrient-limiting conditions.