However, codons in position 101, in reference to the putative initiation codon, are generally ochre (UAA) or amber (UAG) stop codons, which are the most efficient stop codons, strongly suggest a possible termination of the ORF at this position.
AUG is not only the most frequently used initiation codon, but also the most efficient initiation codon in Escherichia coli [31] and Saccharomyces cerevisiae [32].
This hypothesis argues that the anticodon CAU would increase the translation initiation rate but decrease the translation elongation rate, because AUG is the most efficient initiation codon, while AUA is usually more frequently used in mitogenomes.
This result is largely consistent with the frequent assumption that in the set of genes with the highest expression levels the most translationally efficient codon dominates.
In E. coli, the most efficient non-AUG initiation codon is AUA and its rate of initiation is only 7.5% of AUG [31].
Previous studies have indicated that the upper limit for a 5′-UTR to allow usage of the leaderless translation pathway is around 5 nt, with most efficient translation when the start codon is directly at the 5′-terminus (Hering et al. 2009; Krishnan et al. 2010).
In brief, CAI measures how the codon usage of a given gene resembles the codon usage of the most highly expressed genes, because the latter are the most likely to adapt toward using translational efficient codons.
This most likely reflects adaptation toward using more translational efficient codons in the mitochondria.
Of the CGGN-type four-base codons, CGGA and CGGG were the most efficient ones for assigning the positions of nonnatural amino acids.
Raymond and Soriano also reported that the mouse codon-optimized FLP and ϕC31 recombinases, FLPo and ϕC31o, improved recombination efficiency to similar levels to that of Cre, which is the most efficient site-specific recombination system to mediate DNA recombination in vitro and in vivo[ 161].
