Interrelations between the nucleotide context of human start AUG codon, N-end amino acids of the encoded protein and initiation of translation.

It is known that the recognition of AUG triplet by eukaryotic ribosomes as a translation start site strongly depends on its nucleotide context. However, the relative significance of different context positions is not fully clear. In particular, it concerns the role of 3'-end part of the context located at the beginning of the protein-coding sequence. The significant bias observed in nucleotide frequencies in positions +4, +5, +6 (corresponding to the second codon of CDS) could result from different reasons and their contribution to start codon recognition and initiation of translation is under discussion. In this study, we conducted a comparative computational analysis of the human mRNA samples containing different nucleotides (adenine, guanine or pyrimidine) in the essential context position -3. It was found that the presence of G in position +4 could be important for the context variant GnnAUG but not for AnnAUG. Interestingly, the second position of proteins encoded by mRNAs with AnnAUG context variant was specifically and significantly enriched with serine whereas the presence of GnnAUG context also correlated with a higher occurrence of alanine and glycine. It is likely that the efficiency of translation initiation process can depend on the interplay between 5'-context part, 3'-context part and the type of amino acid in the second position of the encoded protein.