Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Nucleic Acids Res. 2016 Feb 18;44(3):1192-202. doi: 10.1093/nar/gkw004. Epub 2016 Jan 14.


We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated '-omics' data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Cluster Analysis
  • Gene Expression Profiling / methods
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation
  • Genome, Bacterial / genetics*
  • Genomics / methods*
  • Genomics / statistics & numerical data
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Mycoplasma pneumoniae / genetics*
  • Mycoplasma pneumoniae / metabolism*
  • Protein Processing, Post-Translational
  • Proteome / genetics
  • Proteome / metabolism
  • Proteomics / methods*
  • Proteomics / statistics & numerical data
  • RNA, Untranslated / genetics
  • Systems Biology / methods
  • Systems Biology / statistics & numerical data


  • Bacterial Proteins
  • Proteome
  • RNA, Untranslated