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Pregled bibliografske jedinice broj: 512434

Proteome sequence features carry signatures of the environmental niche of prokaryotes


Smole, Zlatko; Nikolić, Nela; Supek, Fran; Šmuc, Tomislav; Sbalzarini, Ivo; Kriško, Anita
Proteome sequence features carry signatures of the environmental niche of prokaryotes // Bmc evolutionary biology, 11 (2011), 26, 10 doi:10.1186/1471-2148-11-26 (međunarodna recenzija, članak, znanstveni)


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Naslov
Proteome sequence features carry signatures of the environmental niche of prokaryotes

Autori
Smole, Zlatko ; Nikolić, Nela ; Supek, Fran ; Šmuc, Tomislav ; Sbalzarini, Ivo ; Kriško, Anita

Izvornik
Bmc evolutionary biology (1471-2148) 11 (2011); 26, 10

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

Ključne riječi
halophiles ; thermophiles ; proteome ; archaea ; bacteria ; amino acid composition

Sažetak
Prokaryotic environmental adaptations occur at different levels within cells to ensure the preservation of genome integrity, proper protein folding and function as well as membrane fluidity. Although specific composition and structure of cellular components suitable for the variety of extreme conditions has already been postulated, a systematic study describing such adaptations has not yet been performed. We therefore explored whether the environmental niche of a prokaryote could be deduced from the sequence of its proteome. Finally, we aimed at finding the precise differences between proteome sequences of prokaryotes from different environments. We analyzed the proteomes of 192 prokaryotes from different habitats. We collected detailed information about the optimal growth conditions of each microorganism. Furthermore, we selected 42 physico-chemical properties of amino acids and computed their values for each proteome. Further, on the same set of features we applied two fundamentally different machine learning methods, Support Vector Machines and Random Forests, to successfully classify between bacteria and archaea, halophiles and non-halophiles, as well as mesophiles, thermophiles and mesothermophiles. Finally, we performed feature selection by using Random Forests. To our knowledge, this is the first time that three different classification cases (domain of life, halophilicity and thermophilicity) of proteome adaptation are successfully performed with the same set of 42 features. The characteristic features of a specific adaptation constitute a signature that may help understanding the mechanisms of adaptation to extreme environments.

Izvorni jezik
Engleski

Znanstvena područja
Biologija



POVEZANOST RADA


Projekt / tema
098-0000000-3168 - Strojno učenje prediktivnih modela u računalnoj biologiji (Tomislav Šmuc, )

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

Profili:

Avatar Url Anita Kriško (autor)

Avatar Url Fran Supek (autor)

Avatar Url Tomislav Šmuc (autor)

Citiraj ovu publikaciju

Smole, Zlatko; Nikolić, Nela; Supek, Fran; Šmuc, Tomislav; Sbalzarini, Ivo; Kriško, Anita
Proteome sequence features carry signatures of the environmental niche of prokaryotes // Bmc evolutionary biology, 11 (2011), 26, 10 doi:10.1186/1471-2148-11-26 (međunarodna recenzija, članak, znanstveni)
Smole, Z., Nikolić, N., Supek, F., Šmuc, T., Sbalzarini, I. & Kriško, A. (2011) Proteome sequence features carry signatures of the environmental niche of prokaryotes. Bmc evolutionary biology, 11, 26, 10 doi:10.1186/1471-2148-11-26.
@article{article, year = {2011}, pages = {10}, DOI = {10.1186/1471-2148-11-26}, chapter = {26}, keywords = {halophiles, thermophiles, proteome, archaea, bacteria, amino acid composition}, journal = {Bmc evolutionary biology}, doi = {10.1186/1471-2148-11-26}, volume = {11}, issn = {1471-2148}, title = {Proteome sequence features carry signatures of the environmental niche of prokaryotes}, keyword = {halophiles, thermophiles, proteome, archaea, bacteria, amino acid composition}, chapternumber = {26} }

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


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