Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

Cell Rep. 2016 Oct 11;17(3):904-916. doi: 10.1016/j.celrep.2016.09.040.

Abstract

Bacterial protein synthesis is an essential, conserved, and environmentally responsive process. Yet, many of its components and dependencies remain unidentified. To address this gap, we used quantitative synthetic genetic arrays to map functional relationships among >48,000 gene pairs in Escherichia coli under four culture conditions differing in temperature and nutrient availability. The resulting data provide global functional insights into the roles and associations of genes, pathways, and processes important for efficient translation, growth, and environmental adaptation. We predict and independently verify the requirement of unannotated genes for normal translation, including a previously unappreciated role of YhbY in 30S biogenesis. Dynamic changes in the patterns of genetic dependencies across the four growth conditions and data projections onto other species reveal overarching functional and evolutionary pressures impacting the translation system and bacterial fitness, underscoring the utility of systematic screens for investigating protein synthesis, adaptation, and evolution.

Keywords: E. coli; conditional rewiring; double mutant; fitness; genetic interaction; growth; protein synthesis; ribosome biogenesis; synthetic genetic array; translational fidelity.

MeSH terms

  • Cells, Cultured
  • Environment
  • Epistasis, Genetic
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / metabolism*
  • Gene Regulatory Networks
  • Genetic Testing*
  • Protein Biosynthesis*

Substances

  • Escherichia coli Proteins