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On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli


Supek, Fran; Šmuc, Tomislav
On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli // Genetics, 185 (2010), 1129-1134 doi:10.1534/genetics.110.115477 (međunarodna recenzija, članak, znanstveni)


Naslov
On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli

Autori
Supek, Fran ; Šmuc, Tomislav

Izvornik
Genetics (0016-6731) 185 (2010); 1129-1134

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

Ključne riječi
Codon bias; mRNA secondary structure; protein translation; heterologous expression; Escherichia coli

Sažetak
A recent investigation concluded that codon bias did not affect expression of green fluorescent protein (GFP) variants in Escherichia coli, while stability of an mRNA secondary structure near the 5' end played a dominant role. We demonstrate that combining the two variables using regression trees or support vector regression yields a biologically plausible model with better support in the GFP dataset and in other experimental data: codon usage is relevant for protein levels if the 5' mRNA structures are not strong. Natural E. coli genes had weaker 5' mRNA structures than the examined set of GFP variants, and did not exhibit a correlation between the folding free energy of 5' mRNA structures and protein expression.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo, Biotehnologija



POVEZANOST RADA


Projekt / tema
00980501
098-0000000-3168 - Strojno učenje prediktivnih modela u računalnoj biologiji (Tomislav Šmuc, )

Ustanove
Institut "Ruđer Bošković", Zagreb

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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