hrvatski jezikClear Cookie - decide language by browser settings

Global shifts in genome and proteome composition are very tightly coupled

Brbić, Maria; Warnecke, Tobias; Kriško, Anita; Supek, Fran (2015) Global shifts in genome and proteome composition are very tightly coupled. Genome Biology and Evolution, 7 (6). pp. 1519-1532. ISSN 1759-6653

This is the latest version of this item.

[img]
Preview
PDF - Published Version - article
Available under License Creative Commons Attribution.

Download (1MB) | Preview

Abstract

The amino acid composition (AAC) of proteomes differs greatly between microorganisms and is associated with the environmental niche they inhabit, suggesting that these changes may be adaptive. Similarly, the oligonucleotide composition of genomes varies and may confer advantages at the DNA/RNA level. These influences overlap in protein-coding sequences, making it difficult to gauge their relative contributions. We disentangle these effects by systematically evaluating the correspondence between intergenic nucleotide composition, where protein-level selection is absent, the AAC, and ecological parameters of 909 prokaryotes. We find that G + C content, the most frequently used measure of genomic composition, cannot capture diversity in AAC and across ecological contexts. However, di-/trinucleotide composition in intergenic DNA predicts amino acid frequencies of proteomes to the point where very little cross-species variability remains unexplained (91% of variance accounted for). Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions. Upon factoring out oligonucleotide composition and phylogenetic inertia, the residual AAC is poorly predictive of the microbes’ ecological preferences, in stark contrast with the original AAC. Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome. Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome. We discuss these results in light of contravening evidence from biophysical data and further reading frame-specific analyses that suggest that adaptation takes place at the protein level.

Item Type: Article
Additional Information: This work was supported by the Mediterranean Institute for Life Sciences and Fondation Nelia et Amadeo Barletta (to M.B.and A.K.), by MRC core funding and an Imperial College Junior Research Fellowship (to T.W.), by FP7 FET grant ICT-2013-612944 MAESTRA (to F.S. and M.B.), by FP7 REGPOT grant InnoMol (to F.S.), by the Croatian Science Foundation grant HRZZ-9623 (to M.B.), and the Croatian Ministry of Science and Sport grant 098-0000000-3168 (to F.S.).
Uncontrolled Keywords: amino acid composition; oligonucleotide composition; intergenic DNA; ecological preferences; prokaryotic genome; fungal genome; support vector regression
Subjects: NATURAL SCIENCES > Biology
TECHNICAL SCIENCES > Computing > Artificial Intelligence
Divisions: Division of Electronics
Projects:
Project titleProject leaderProject codeProject type
Postupci strojnog učenja za dubinsku analizu složenih struktura podataka-DescriptiveInductionDragan GambergerIP-11-2013-9623HRZZ
Enhancement of the Innovation Potential in SEE through new Molecular Solutions in Research and Development-INNOMOLUNSPECIFIED316289EK
Learning from Massive, Incompletely annotated, and Structured Data-MAESTRAUNSPECIFIED612944EK
Strojno učenje prediktivnih modela u računalnoj biologijiTomislav Šmuc098-0000000-3168MZOS
Depositing User: Maria Brbić
Date Deposited: 09 Dec 2016 16:19
Last Modified: 14 Dec 2016 15:49
URI: http://fulir.irb.hr/id/eprint/3206
DOI: 10.1093/gbe/evv088

Available Versions of this Item

Actions (login required)

View Item View Item

Downloads

Downloads per month over past year