Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli

Abstract

BackgroundThe alarmone (p)ppGpp mediates a global reprogramming of gene expression upon nutrient limitation and other stresses to cope with these unfavorable conditions. Synthesis of (p)ppGpp is, in most bacteria, controlled by RelA/SpoT (Rsh) proteins. The role of (p)ppGpp has been characterized primarily in Escherichia coli and several Gram-positive bacteria. Here, we report the first in-depth analysis of the (p)ppGpp-regulon in an α-proteobacterium using a high-resolution tiling array to better understand the pleiotropic stress phenotype of a relA/rsh mutant.ResultsWe compared gene expression of the Rhizobium etli wild type and rsh (previously rel) mutant during exponential and stationary phase, identifying numerous (p)ppGpp targets, including small non-coding RNAs. The majority of the 834 (p)ppGpp-dependent genes were detected during stationary phase. Unexpectedly, 223 genes were expressed (p)ppGpp-dependently during early exponential phase, indicating the hitherto unrecognized importance of (p)ppGpp during active growth. Furthermore, we identified two (p)ppGpp-dependent key regulators for survival during heat and oxidative stress and one regulator putatively involved in metabolic adaptation, namely extracytoplasmic function sigma factor EcfG2/PF00052, transcription factor CH00371, and serine protein kinase PrkA.ConclusionsThe regulatory role of (p)ppGpp in R. etli stress adaptation is far-reaching in redirecting gene expression during all growth phases. Genome-wide transcriptome analysis of a strain deficient in a global regulator, and exhibiting a pleiotropic phenotype, enables the identification of more specific regulators that control genes associated with a subset of stress phenotypes. This work is an important step toward a full understanding of the regulatory network underlying stress responses in α-proteobacteria.

The Stringent Response Controls Catalases in Pseudomonas aeruginosa and Is Required for Hydrogen Peroxide and Antibiotic Tolerance

“…Additionally, we and others have recently shown that SR inactivation in P. aeruginosa led to increased oxidant susceptibility (33,57). Conversely, (p)ppGpp accumulation has been associated with oxidative stress tolerance in Streptococcus mutans (58), and transcriptomic studies of (p)ppGpp-regulated genes in Rhizobium etli identified several genes involved in oxidative stress resistance (59).…”

Physiology and transcriptome of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 after long-term starvation

“…One important gene that showed increased expression after long-term starvation was the gene encoding a homologue of the (p)ppGpp synthase gene. (p)ppGpp is known as a master regulator of gene expression during stress conditions (Atkinson et al, 2011) and is required for regulation of gene expression during starvation or the non-growing state of cells in a number of bacteria including E. coli and Rhizobium etli (Traxler et al, 2008;Vercruysse et al, 2011). Starved cells of LH128 also expressed genes that encode RNases, such as RNaseE, which degrade rRNA during starvation stress.…”

The Bacterial Alarmone (p)ppGpp Activates the Type III Secretion System in Erwinia amylovora

“…In E. coli, accumulation of ppGpp activates LEE gene expression and increases bacterial adherence (32). In plant-associated pseudomonads and rhizobia, ppGpp affects epiphytic fitness, biocontrol activity, biofilm formation, and hydrogen peroxide and antibiotic tolerance, as well as nodulation (33)(34)(35)(36). In plant-pathogenic bacteria, ppGpp is required for cell wall-degrading enzyme production, quorum sensing signal degradation, and Ti plasmid transfer (37)(38)(39).…”