Recoding of translation in turtle mitochondrial genomes: Programmed frameshift mutations and evidence of a modified genetic code

A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing the polyadenylated mRNA in the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in the mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the common nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises revealed general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker’s sideneck turtle (Macrochelodina parkeri), the first known example of this in vertebrate mitochondria.