Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG

Abstract

The Escherichia coli eukaryote-like serine/threonine kinase, encoded by yeaG, is expressed in response to diverse stresses, including nitrogen (N) starvation. A role for yeaG in bacterial stress response is unknown. Here we reveal for the first time that wild-type E. coli displays metabolic heterogeneity following sustained periods of N starvation, with the metabolically active population displaying compromised viability. In contrast, such heterogeneity in metabolic activity is not observed in an E. coli ∆yeaG mutant, which continues to exist as a single and metabolically active population and thus displays an overall compromised ability to survive sustained periods of N starvation. The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ. This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response. Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.

A role for a conserved kinase in the transcriptional control of methionine biosynthesis inEscherichia coliexperiencing sustained nitrogen starvation

“…S3 later). Intriguingly, although ΔyeaG bacteria contain significantly reduced intracellular levels of σ 38 under sustained N starvation (6), only a small subset (none at N-, and ~8% at N-24) of the σ 38regulon (as defined by (8)) was differentially expressed in ΔyeaG bacteria, suggesting that the dysregulation of expression of the σ 38 regulon is unlikely to contribute to the inability of the ΔyeaG bacteria to survive sustained N starvation ( Fig. S1).…”

“…RNA sequencing (RNA-seq). Cultures were grown as in (6) and sampled at the following time points: N+, when the OD 600nm = 0.3; N-, 20 minutes following N runout; and N-24, where bacteria were subjected to 24 hours of N starvation. Two biological replicates were taken for N+ and N-, and three for N-24.…”

“…Although the product of yeaH has no sequence or structural homology to any known protein, YeaG is a Hank's type kinase (11,12). In earlier work, we revealed that the viability of ΔyeaG Escherichia coli becomes significantly compromised only after 24 h under N starvation and thus proposed a role for YeaG in the adaptive response to sustained N starvation (6). Further, we showed that the intracellular concentration of RpoS (σ 38 ), the major bacterial sigma (σ) factor required for the transcription of general stress response genes, was decreased by more than 2-fold in ΔyeaG bacteria compared to the wild-type (6) and consequently suggested that ΔyeaG bacteria might be compromised to effectively adapt their transcriptional programme to survive a sustained period of time under N starvation.…”

“…One of the highly expressed operons during the initial adaptive response to N starvation consists of yeaG and yeaH. Both genes are conserved across several bacterial species, especially Enterobacteriaceae (5)(6)(7). They are also induced in response to diverse stresses (including low pH (8), high osmolarity (9), stationary phase (8) and low sulphur (10)), which suggests a wider importance of yeaG and yeaH and pathways affected by them in bacterial adaptive processes.…”

Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain

“…The eukaryotic like serine protein kinase, YeaG or stress kinase involved in stress adaptation of E . coli [46] is overexpressed. YeaG is highly conserved in other enterobacteria and contains AAA+ (ATPases Associated with diverse cellular Activities) and a P - loop NTPase domain.…”