Journal
NUCLEIC ACIDS RESEARCH
Volume 44, Issue 3, Pages 1192-1202Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw004
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Funding
- European Research Council under the European Union's Seventh Framework Programme (FP7)/ERC [232913]
- Spanish Ministry of Economy and Competitiveness
- 'Centro de Excelencia Severo Ochoa' [SEV-2012-0208]
- European Union's Horizon research and innovation program [634942]
- European Research council (ERC) [232913]
- Fundacion Marcelino Botin
- Spanish Ministerio de Economia y Competitividad [BIO2007-61762]
- ISCIII, Subdireccion General de evaluacion y fomento de la investigacion [PI10/01702]
- European Research Council (ERC) [232913] Funding Source: European Research Council (ERC)
- ICREA Funding Source: Custom
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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.
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