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

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Item Type:Article
Title:Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances
Creators Name:Chen, W.H. and van Noort, V. and Lluch-Senar, M. and Hennrich, M.L. and Wodke, J.A.H. and Yus, E. and Alibes, A. and Roma, G. and Mende, D.R. and Pesavento, C. and Typas, A. and Gavin, A.C. and Serrano, L. and Bork, P.
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 Genome, Bacterial Proteins, Base Sequence, Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Genomics, Molecular Sequence Annotation, Molecular Sequence Data, Mycoplasma pneumoniae, Post-Translational Protein Processing, Proteome, Proteomics, Systems Biology, Untranslated RNA
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:44
Number:3
Page Range:1192-1202
Date:18 February 2016
Official Publication:https://doi.org/10.1093/nar/gkw004
PubMed:View item in PubMed

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