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Pregled bibliografske jedinice broj: 765225

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled


Brbić, Maria; Warnecke, Tobias; Kriško, Anita; Supek, Fran
Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled // Genome Biology and Evolution, 7 (2015), 6; 1519-1532 doi:10.1093/gbe/evv088 (međunarodna recenzija, članak, znanstveni)


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Naslov
Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

Autori
Brbić, Maria ; Warnecke, Tobias ; Kriško, Anita ; Supek, Fran

Izvornik
Genome Biology and Evolution (1759-6653) 7 (2015), 6; 1519-1532

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
amino acid composition ; oligonucleotide composition ; intergenic DNA ; ecological preferences ; prokaryotic genome ; fungal genome ; support vector regression

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Matematika, Biologija, Računarstvo



POVEZANOST RADA


Projekti:
ICT-2013-612944
098-0000000-3168 - Strojno učenje prediktivnih modela u računalnoj biologiji (Šmuc, Tomislav, MZOS ) ( POIROT)
HRZZ-IP-2013-11-9623 - Postupci strojnog učenja za dubinsku analizu složenih struktura podataka (DescriptiveInduction) (Gamberger, Dragan, HRZZ - 2013-11) ( POIROT)

Ustanove:
Institut "Ruđer Bošković", Zagreb,
Mediteranski institut za istraživanje života

Profili:

Avatar Url Anita Kriško (autor)

Avatar Url Maria Brbić (autor)

Avatar Url Fran Supek (autor)

Citiraj ovu publikaciju:

Brbić, Maria; Warnecke, Tobias; Kriško, Anita; Supek, Fran
Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled // Genome Biology and Evolution, 7 (2015), 6; 1519-1532 doi:10.1093/gbe/evv088 (međunarodna recenzija, članak, znanstveni)
Brbić, M., Warnecke, T., Kriško, A. & Supek, F. (2015) Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled. Genome Biology and Evolution, 7 (6), 1519-1532 doi:10.1093/gbe/evv088.
@article{article, year = {2015}, pages = {1519-1532}, DOI = {10.1093/gbe/evv088}, keywords = {amino acid composition, oligonucleotide composition, intergenic DNA, ecological preferences, prokaryotic genome, fungal genome, support vector regression}, journal = {Genome Biology and Evolution}, doi = {10.1093/gbe/evv088}, volume = {7}, number = {6}, issn = {1759-6653}, title = {Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled}, keyword = {amino acid composition, oligonucleotide composition, intergenic DNA, ecological preferences, prokaryotic genome, fungal genome, support vector regression} }
@article{article, year = {2015}, pages = {1519-1532}, DOI = {10.1093/gbe/evv088}, keywords = {amino acid composition, oligonucleotide composition, intergenic DNA, ecological preferences, prokaryotic genome, fungal genome, support vector regression}, journal = {Genome Biology and Evolution}, doi = {10.1093/gbe/evv088}, volume = {7}, number = {6}, issn = {1759-6653}, title = {Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled}, keyword = {amino acid composition, oligonucleotide composition, intergenic DNA, ecological preferences, prokaryotic genome, fungal genome, support vector regression} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


Uključenost u ostale bibliografske baze podataka::


  • BIOSIS Previews (Biological Abstracts)
  • Zoological Record


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