Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Cell Syst. 2019 Aug 28;9(2):143-158.e13. doi: 10.1016/j.cels.2019.07.001. Epub 2019 Aug 21.

Abstract

Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium's annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria.

Keywords: Mycoplasma pneumoniae; gene regulatory network; systems biology; transcription; transcription factors; transcription regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling / methods
  • Gene Expression Regulation / genetics
  • Gene Expression Regulation, Bacterial / genetics*
  • Gene Regulatory Networks / genetics*
  • Genome, Bacterial / genetics
  • Models, Genetic
  • Mycoplasma pneumoniae / genetics*
  • Signal Transduction / genetics
  • Transcription Factors / genetics
  • Transcription, Genetic / genetics

Substances

  • Transcription Factors