Noise propagation in an integrated model of bacterial gene expression and growth

PLoS Comput Biol. 2018 Oct 5;14(10):e1006386. doi: 10.1371/journal.pcbi.1006386. eCollection 2018 Oct.

Abstract

In bacterial cells, gene expression, metabolism, and growth are highly interdependent and tightly coordinated. As a result, stochastic fluctuations in expression levels and instantaneous growth rate show intricate cross-correlations. These correlations are shaped by feedback loops, trade-offs and constraints acting at the cellular level; therefore a quantitative understanding requires an integrated approach. To that end, we here present a mathematical model describing a cell that contains multiple proteins that are each expressed stochastically and jointly limit the growth rate. Conversely, metabolism and growth affect protein synthesis and dilution. Thus, expression noise originating in one gene propagates to metabolism, growth, and the expression of all other genes. Nevertheless, under a small-noise approximation many statistical quantities can be calculated analytically. We identify several routes of noise propagation, illustrate their origins and scaling, and establish important connections between noise propagation and the field of metabolic control analysis. We then present a many-protein model containing >1000 proteins parameterized by previously measured abundance data and demonstrate that the predicted cross-correlations between gene expression and growth rate are in broad agreement with published measurements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli / cytology
  • Escherichia coli / genetics*
  • Escherichia coli / growth & development*
  • Escherichia coli / metabolism
  • Gene Expression Regulation, Bacterial / genetics*
  • Genes, Bacterial / genetics*
  • Models, Biological*
  • Signal Processing, Computer-Assisted
  • Systems Biology

Grants and funding

LHJK was supported by the NWO (Nederlandse Organisatie voor Wetenschappelijk Onderzoek, www.nwo.nl) (Grant 022.005.023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.