Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness

Abstract

Summary Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically-identical population and facilitates its adaptation to changing environments.

Translational readthrough goes unseen by natural selection

“…Taken together with inference of presence and rate of TR, in 263 S.cerevisiae and S.pombe, our analyses suggest that TR is continuously present at a low 264 rate and not purged. This is in accordance with other studies that find continuous TR 265 to be heterogeneously present [26]. 266 Recently, TR has been suggested to be non-adaptive as its presence appear 267 stochastic [27].…”

“…Also 292 protein synthesis has been found to be heterogeneous and noisy [8,26], but also 293 harmful [39]. However, TR have been found to yield positive fitness effects for 294 microorganisms under stress, and plainly neutral in absence of stress [6,26]. We suggest 295 that the TR-yielded isoforms enrich the proteomic diversity by offering slight variants of 296 encoded proteins that may are readily available in sudden environmental shifts, which 297 has been suggested previously by others [8,34].…”

“…Translational and 25 transcriptional error rate is manifold higher than the genotypic error rate [1][2][3], i.e. the 26 error rate during DNA replication, which leads to heritable variation. Phenotypic 27 mutations have been suggested to act as intermediate stepping stones for traits not yet 28 encoded on the DNA level [4].…”

“…Overall transcriptional heterogeneity has been found to be beneficial in stressful 291 November 12, 2019 7/20 condition [36,37], and suggested to be an adaptive trait under selection [38]. Also 292 protein synthesis has been found to be heterogeneous and noisy [8,26], but also 293 harmful [39]. However, TR have been found to yield positive fitness effects for 294 microorganisms under stress, and plainly neutral in absence of stress [6,26].…”

Increased mistranslation protects E. coli from protein misfolding stress due to activation of a RpoS‐dependent heat shock response

“…Surprisingly, this protective heat shock response is dependent on the general stress response sigma factor, RpoS. This indicates a novel regulatory role for RpoS for mistranslation‐induced heat shock response activation and a second benefit RpoS provides due to increased mistranslation rates in addition to protection against oxidative stress .…”