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Scientific article
Open access
English

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

Published inNucleic Acids Research, vol. 44, no. 3, p. 1192-1202
Publication date2016
Abstract

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.

Keywords
  • Amino Acid Sequence
  • Bacterial Proteins/genetics/metabolism
  • Base Sequence
  • Cluster Analysis
  • Gene Expression Profiling/methods/statistics & numerical data
  • Gene Expression Regulation
  • Genome
  • Bacterial/genetics
  • Genomics/methods/statistics & numerical data
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Mycoplasma pneumoniae/genetics/metabolism
  • Protein Processing
  • Post-Translational
  • Proteome/genetics/metabolism
  • Proteomics/methods/statistics & numerical data
  • RNA
  • Untranslated/genetics
  • Systems Biology/methods/statistics & numerical data
Affiliation Not a UNIGE publication
Funding
  • European Commission - Quantitative understanding of a living system and its engineering as a cellular organelle [232913]
  • European Commission - Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine [634942]
Citation (ISO format)
CHEN, Wei-Hua et al. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. In: Nucleic Acids Research, 2016, vol. 44, n° 3, p. 1192–1202. doi: 10.1093/nar/gkw004
Main files (1)
Article (Published version)
Identifiers
ISSN of the journal0305-1048
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123downloads

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