The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in Escherichia coli

Thomas Ferenci,Beny Spira,Thu Betteridge,Heloisa Filus Galbiati,Katherine Phan

doi:10.1186/1471-2180-11-62

Abstract

BackgroundSigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions. Both ppGpp and the sigma factor σS (RpoS) are potentially subject to variability across the species Escherichia coli. To find out the extent of strain variation we measured the level of RpoS and ppGpp using 31 E. coli strains from the ECOR collection and one reference K-12 strain.ResultsNine ECORs had highly deleterious mutations in rpoS, 12 had RpoS protein up to 7-fold above that of the reference strain MG1655 and the remainder had comparable or lower levels. Strain variation was also evident in ppGpp accumulation under carbon starvation and spoT mutations were present in several low-ppGpp strains. Three relationships between RpoS and ppGpp levels were found: isolates with zero RpoS but various ppGpp levels, strains where RpoS levels were proportional to ppGpp and a third unexpected class in which RpoS was present but not proportional to ppGpp concentration. High-RpoS and high-ppGpp strains accumulated rpoS mutations under nutrient limitation, providing a source of polymorphisms.ConclusionsThe ppGpp and σS variance means that the expression of genes involved in translation, stress and other traits affected by ppGpp and/or RpoS are likely to be strain-specific and suggest that influential components of regulatory networks are frequently reset by microevolution. Different strains of E. coli have different relationships between ppGpp and RpoS levels and only some exhibit a proportionality between increasing ppGpp and RpoS levels as demonstrated for E. coli K-12.

Highlights

Sigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions
We demonstrate here that strain variation in ppGpp is one of several factors that contribute to the difference in the level of sS across the species E. coli and discuss the polymorphisms at the core of bacterial regulation
The goal of this study is three-fold: to provide evidence that rpoS polymorphism and variation in sS levels are widespread in the species E. coli; to show that the genes that control ppGpp synthesis and degradation are subject to variation and to demonstrate that the different levels of RpoS are at least partially dependent on variability of endogenous ppGpp

Summary

Introduction

Sigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions. Both ppGpp and the sigma factor sS (RpoS) are potentially subject to variability across the species Escherichia coli. Sigma factors direct RNA polymerase to various sets of promoters, and are at the centre of complex networks regulating gene expression in bacteria such as Escherichia coli [1,2]. We approach this question by measuring the concentration the cell, as ppGpp increases by several-fold the cellular concentration of sS during nutritional stress or in the stationary phase. PpGpp is intertwined with rpoS regulation and here we investigate the conservation of the level of these regulators across the species E. coli

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