Global mistranslation increases cell survival under stress in Escherichia coli

Abstract

Mistranslation is typically deleterious for cells, although specific mistranslated proteins can confer a short-term benefit in a particular environment. However, given its large overall cost, the prevalence of high global mistranslation rates remains puzzling. Altering basal mistranslation levels of Escherichia coli in several ways, we show that generalized mistranslation enhances early survival under DNA damage, by rapidly activating the SOS response. Mistranslating cells maintain larger populations after exposure to DNA damage, and thus have a higher probability of sampling critical beneficial mutations. Both basal and artificially increased mistranslation increase the number of cells that are phenotypically tolerant and genetically resistant under DNA damage; they also enhance survival at high temperature. In contrast, decreasing the normal basal mistranslation rate reduces cell survival. This wideranging stress resistance relies on Lon protease, which is revealed as a key effector that induces the SOS response in addition to alleviating proteotoxic stress. The new links between error-prone protein synthesis, DNA damage, and generalised stress resistance indicate surprising coordination between intracellular stress responses and suggest a novel hypothesis to explain high global mistranslation rates. Author summaryCells make mistakes all the time. Protein synthesis is exceptionally error-prone, which is puzzling because such mistakes are usually harmful. Prior work shows that specific erroneous proteins can be beneficial under specific stresses. However, this cannot explain a high background error rate, because most mistakes will not be useful. We offer a solution to this conundrum: cells that make more mistakes accumulate a key quality-control enzyme, tripping the switch for a broad stress response (the "SOS" response, that repairs damaged DNA). In turn, this increases cell survival. The unexpected link between protein synthesis and DNA damage suggests surprising cross talk across important quality-control processes, and motivates a new hypothesis to explain how and why cells tolerate so many mistakes.

The Impact of Mistranslation on Phenotypic Variability and Fitness

“…8). Recently, using the same manipulations, we showed that global mistranslation increases survival under at least two stresses, DNA damage and high temperature (Samhita et al 2020). Together, these results show that mistranslation-induced variability has the potential to significantly alter ecological and evolutionary dynamics of populations.…”

“…For example, norleucine also inhibits DNA methylation and methionine biosynthesis (Bogosian et al 1989). To generate hyper-accurate ribosomes, we used a mutation that impacts population growth rate minimally (Samhita et al 2020), and the WT single cell data show tighter distributions for both division time and cell length as compared with their parent strains (Fig. 2b-c).…”

“…Initiator tRNA acts only at the first step of protein synthesis and has no substitute (Gualerzi and Pon 2015). Since the mutant carries ~25% of the WT initiator tRNA complement, it has a lower rate of protein synthesis, a ~20% slower growth rate than the WT (Samhita et al 2020), and mistranslates through non-AUG initiation (Samhita et al 2013). In contrast, to reduce mistranslation rates in the WT, we introduced a mutation (K42R) in the protein S12 that increases translation accuracy by reducing the frequency of decoding errors (Chumpolkulwong et al 2004).…”

“…We transferred this mutation into KL16 and KLΔZWV from the parent strain SS3242 obtained from CGSC, Yale university, via P1 transduction, generating strains KL(HA) and KLΔZWV(HA), referred to as WT(HA) and Mutant(HA) in the text. The mutation led to an ~10-fold increase in translation accuracy both in the WT and in the Mutant (Samhita et al 2020). For single-cell variability measurements, we used WT and mutant strains carrying a genomically encoded, constitutively expressed GFPmut2 allele tagged with a kanamycin resistance marker inserted between the genes aidB and yjfN, and expressed from a P5 promoter (gifted by Prof Bianca Sclavi, ENS, Paris).…”

“…We increased the basal level of mistranslation in wild type (WT) cells by introducing mutations or by changing the growth environment. Recently, we showed that generalised mistranslation increases mean population survival under specific stresses (Samhita et al 2020). However, we had not explored whether mistranslation generates phenotypic variability that influences both cell and population fitness, and in optimal as well as stressful environments.…”