Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

PLoS Biol. 2021 Dec 17;19(12):e3001491. doi: 10.1371/journal.pbio.3001491. eCollection 2021 Dec.

Abstract

Although it is well appreciated that gene expression is inherently noisy and that transcriptional noise is encoded in a promoter's sequence, little is known about the extent to which noise levels of individual promoters vary across growth conditions. Using flow cytometry, we here quantify transcriptional noise in Escherichia coli genome-wide across 8 growth conditions and find that noise levels systematically decrease with growth rate, with a condition-dependent lower bound on noise. Whereas constitutive promoters consistently exhibit low noise in all conditions, regulated promoters are both more noisy on average and more variable in noise across conditions. Moreover, individual promoters show highly distinct variation in noise across conditions. We show that a simple model of noise propagation from regulators to their targets can explain a significant fraction of the variation in relative noise levels and identifies TFs that most contribute to both condition-specific and condition-independent noise propagation. In addition, analysis of the genome-wide correlation structure of various gene properties shows that gene regulation, expression noise, and noise plasticity are all positively correlated genome-wide and vary independently of variations in absolute expression, codon bias, and evolutionary rate. Together, our results show that while absolute expression noise tends to decrease with growth rate, relative noise levels of genes are highly condition-dependent and determined by the propagation of noise through the gene regulatory network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli / genetics*
  • Escherichia coli Proteins / genetics
  • Gene Expression / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Bacterial / genetics*
  • Gene Regulatory Networks / genetics
  • Genes, Reporter / genetics
  • Promoter Regions, Genetic / genetics*
  • Transcriptome / genetics

Substances

  • Escherichia coli Proteins

Grants and funding

This work was partly funded by the Werner Siemens Stiftung through a fellowhip to AU, the Swiss National Science Foundation SystemsX.ch StoNets grant, and the Swiss National Science Foundation grant 31003A_159673 to EvN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.