title: Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection.
abstract: 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 AUG(2nd) had a negative correlation with the overall codon bias, and that a strong purine bias existed in this AUG(2nd)context. However, the quantitative codon bias of Region-La was seen to be significantly lower than that of Region-Lb (the sequence following AUG(2nd)) 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 AUG(1st) in all serotypes except SAT 1-3, and the specific AUG(2nd) context might be used as a strong signal to initiate translation from the AUG(2nd) in all serotypes.
authors.affiliation: Key Laboratory of Bioengineering & Biotechnology of the State Ethnic Affairs Commission, Lanzhou, China.|College of Life Science and Engineering, Northwest University for Nationalities, Engineering & Technology Research Center for Animal Cells, Gansu, China.
authors.forename: J L
authors.initials: JL
authors.lastname: Liu
authors.affiliation: Gansu Province Center for Disease Prevention and Control, Lanzhou, Gansu, China.
authors.forename: Y H
authors.initials: YH
authors.lastname: Ma
authors.affiliation: Key Laboratory of Bioengineering & Biotechnology of the State Ethnic Affairs Commission, Lanzhou, China.|College of Life Science and Engineering, Northwest University for Nationalities, Engineering & Technology Research Center for Animal Cells, Gansu, China.
authors.forename: J Y
authors.initials: JY
authors.lastname: Xu
authors.affiliation: Key Laboratory of Bioengineering & Biotechnology of the State Ethnic Affairs Commission, Lanzhou, China.|College of Life Science and Engineering, Northwest University for Nationalities, Engineering & Technology Research Center for Animal Cells, Gansu, China.
authors.forename: Y X
authors.initials: YX
authors.lastname: Chen
authors.affiliation: Key Laboratory of Bioengineering & Biotechnology of the State Ethnic Affairs Commission, Lanzhou, China.|College of Life Science and Engineering, Northwest University for Nationalities, Engineering & Technology Research Center for Animal Cells, Gansu, China.
authors.forename: S E
authors.initials: SE
authors.lastname: Chen
authors.affiliation: Key Laboratory of Bioengineering & Biotechnology of the State Ethnic Affairs Commission, Lanzhou, China.|College of Life Science and Engineering, Northwest University for Nationalities, Engineering & Technology Research Center for Animal Cells, Gansu, China.
authors.forename: Z R
authors.initials: ZR
authors.lastname: Ma
mesh_terms: D001482:Base Composition; D018387:Codon, Initiator; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D010442:Peptide Chain Initiation, Translational; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D012270:Ribosomes
chemical_list: D018387:Codon, Initiator; D012333:RNA, Messenger; D012367:RNA, Viral