Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions

PLoS Comput Biol. 2014 May 8;10(5):e1003602. doi: 10.1371/journal.pcbi.1003602. eCollection 2014 May.

Abstract

Bacteria often face complex environments. We asked how gene expression in complex conditions relates to expression in simpler conditions. To address this, we obtained accurate promoter activity dynamical measurements on 94 genes in E. coli in environments made up of all possible combinations of four nutrients and stresses. We find that the dynamics across conditions is well described by two principal component curves specific to each promoter. As a result, the promoter activity dynamics in a combination of conditions is a weighted average of the dynamics in each condition alone. The weights tend to sum up to approximately one. This weighted-average property, called linear superposition, allows predicting the promoter activity dynamics in a combination of conditions based on measurements of pairs of conditions. If these findings apply more generally, they can vastly reduce the number of experiments needed to understand how E. coli responds to the combinatorially huge space of possible environments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / physiology
  • Bacterial Proteins / physiology*
  • Cell Proliferation / physiology
  • Computer Simulation
  • Escherichia coli / cytology
  • Escherichia coli / physiology*
  • Gene Expression Regulation, Bacterial / physiology*
  • Linear Models
  • Models, Biological*
  • Promoter Regions, Genetic / physiology*
  • Stress, Physiological / physiology*

Substances

  • Bacterial Proteins

Grants and funding

This study was supported by the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement n° 249919 and by the Israel Science Foundation. UA is the incumbent of the Abisch-Frenkel Professorial Chair. JH acknowledges the support of the Swiss National Science Foundation (PBBSP3_146961) and of EMBO (ALTF 1160-2012). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.