In higher eukaryotes, perhaps the most remarkable examples of stop codon readthrough and its biological consequences are provided by the Drosophila developmental mutants headcase (hdc) [13], [14], kelch [15], and out at first (oaf) [16].
Fitzpatrick et al. (2011) identified 376 examples of stop codon polymorphisms (SCPs), and reported these as subtractions.
In addition, in KCNB1 and NLRP10 examples of hotspot codon mutations were found, although the exact base changes were different from those seen in our discovery set data.
Scoring this group by the same criteria used for the predicted extensions, we identified 307 additional examples of stop codon readthrough (hereon referred to as 'novel extensions'; see example Figure 3F), including another example of double readthrough.
For example, optimization of codon usage within the coding sequence, by incorporating codons for the most abundant isoaccepting tRNA, is known to increase expression (Ikemura 1985).
Determining the role(s) of rare codons in protein biogenesis is complicated by literature reports that describe the negative effects of rare codon clusters, particularly at 5' termini [ 30], while also reporting examples of rare codons improving protein expression [ 31], increasing or altering protein activity [ 32] and being conserved through evolution [ 33].
Transitions between the high and low ranks often coincided with host territory borders, and seven examples of the codons diagnostic for host separation were presented (Fig. 3A).
Another notable example of biased codon usage is that the codon ATT (8.0%) is much more frequently used than ATC (0.7%) in the isoleucine family.
(A) An example of KRAS codon 12 and 13 direct sequencing analysis.
An example of stop codon read-through is the conserved plasmodium protein (PF13_0160), shown in Figure 9A.
