Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission

Lanzhou, China

Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission

Lanzhou, China
SEARCH FILTERS
Time filter
Source Type

Liu J.L.,Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission | Liu J.L.,Northwest University for Nationalities | Ma Y.H.,Centers for Disease Control and Prevention | Xu J.Y.,Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission | And 7 more authors.
Genetics and Molecular Research | Year: 2015

The mechanism of alternative AUG usage in foot-and-mouth disease virus is not completely understood. Using simple computational approaches, we evaluated the contributions of overall codon bias, quantitative codon bias, and %GC of the region between the two alternative AUGs, Region-La, as well as the nucleotide bias of the sequence context flanking each AUG with respect to translation initiation efficiency. For all serotypes of this virus, we found that only a small component of the effect of RNA secondary structure on ribosome scanning was due to the low %GC of Region-La. In addition, we found that the nucleotide bias of the context from position -4 to +6 flanking the AUG2nd had a negative correlation with the overall codon bias, and that a strong purine bias existed in this AUG2nd context. However, the quantitative codon bias of Region-La was seen to be significantly lower than that of Region-Lb (the sequence following AUG2nd) in all serotypes except SAT 1-3. Taken together, our results suggest that the low codon bias of Region-La might impair the translation initiation efficiency at the AUG1st in all serotypes except SAT 1-3, and the specific AUG2nd context might be used as a strong signal to initiate translation from the AUG2nd in all serotypes. © FUNPEC-RP.

Loading Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission collaborators
Loading Key Laboratory of Bioengineering and Biotechnology of the State Ethnic Affairs Commission collaborators