Non-AUG initiation codon and downstream inframe AUG in Pyrococcus Horikoshii: Evaluating two hypotheses

Non-AUG initiation codons in protein-coding genes in Pyrococcus horikoshii are associated with the presence of a downstream inframe AUG typically at the 4th codon, i.e., at the 9^th nucleotide site when the 1^st coding nucleotide is labeled 0. Here we report that the presence of this downstream codon depends not only on the presence/absence of the initiation AUG, but also on the strength of binding between the Shine-Dalgarno (SD) sequence in the 5´-UTR of mRNA and the anti-SD sequence in the 16S rRNA. Weak binding significantly increases the likelihood of having the downstream AUG. Genes with a GUG initiation codon have weaker binding and a high proportion of them have the downstream AUG. Deviation of the SD sequence from the optimal location also appears to increase the likelihood of the downstream AUG.