Key result
The optimal nucleotide contexts flanking the start codons of foot-and-mouth disease virus RNA were identified as UUU AUG1st AAC and AAG AUG2nd GAA, which influence translation initiation efficiency.
The nucleotide contexts flanking the start codon can influence translation initiation efficiencies under the FMDV IRES-dependent mechanism.
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Optimal FMDV contexts may refine IRES translation models; leaves open applicability to antiviral design or human picornaviruses.
As for the alternative AUGs in foot-and-mouth disease virus (FMDV), nucleotide bias of the context flanking the AUG(2nd) could be used as a strong signal to initiate translation. To determine the role of the specific nucleotide context, dicistronic reporter constructs were engineered to contain different versions of nucleotide context linking between internal ribosome entry site (IRES) and downstream gene. The results indicate that under FMDV IRES-dependent mechanism, the nucleotide contexts flanking start codon can influence the translation initiation efficiencies. The most optimal sequences for both start codons have proved to be UUU AUG(1st) AAC and AAG AUG(2nd) GAA.
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X. et al. (2016) studied Foot-and-mouth disease virus (FMDV) translation. Nucleotide context flanking the start codon vs. Alternative nucleotide contexts was evaluated on Translation initiation efficiency (EGFP/CAT ratio). The optimal nucleotide contexts flanking the start codons of foot-and-mouth disease virus RNA were identified as UUU AUG1st AAC and AAG AUG2nd GAA, which influence translation initiation efficiency.
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