The mitochondrial genomes (mt-genomes) of animals are very compact in structure, encoding thirteen protein genes involved in the production of ATP, and the key components of the translation system to express these proteins. The mitochondrial expression system, which functions separately from that of the nucleus, shows characteristics of both prokaryotic and eukaryotic expression systems, and has diverged greatly from that currently observed in the closest living relatives of mitochondria, the a-proteobacteria. Current understanding of transcript maturation is that large multi-gene transcripts are processed by the removal of intervening tRNA genes, leaving behind RNA templates to be matured into the functional mRNAs and rRNAs. One of the most striking features of insect mt-genomes has been the apparent replacement of a start codon with a stop codon for the essential mitochondrial gene cytochrome c oxidase subunit 1 (coxl). When first observed in Drosophila, Clary and Wolstenholme proposed a highly unusual four-base "ATAA" start codon. With the expanded sampling of mitochondrial sequence across the various insect orders, the data does not support the use of this aberrant initiation for coxl. At the initiation of this study, the diversity of insect groups represented by complete mt-genome sequence was very poor. To address this deficit, I undertook sequencing projects to increase the number of insect orders represented in the mitochondrial sequence databases. I report the complete mt-genome sequences for two insects, the spittlebug Philaenus spumarius, and the giant stonefly Pteronarcys princeps. The sequences are annotated and compared to other insect mt-genomes in the sequence databases. I report the cDNA sequences of Drosophila melanogaster mitochondrial mRNAs, rRNA subunits, and a population of pre-mRNA molecules that are intermediates of the RNA processing system. Models to explain mitochondrial transcript maturation in light of these new observations are proposed. Comparative analyses were undertaken to apply the information gained from the mitochondrial transcripts of D. melanogaster to the mitochondrial structure and annotations of mt-genomes from the other insects. These analyses suggest a 5' specific modification to the tRNA punctuation model for insect mitochondria. This modification may represent a further evolutionary simplification of the mitochondrial expression system.
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