Molecular Evolution of Numt, a Recent Transfer and Tandem Amplification of Mitochondrial DNA into the Nuclear Genome of the Domestic Cat (Felis catus)

Jose V. Lopez, Nova Southeastern University Oceanographic Center

UMI Number: 9528192

Abstract

Mitochondrial DNA (mtDNA) are functional cytoplasmic chromosomes, tracing origins to a symbiotic infection of eukaryotic cells by bacterial progenitors. As prescribed by the Serial Endosymbiosis Theory, symbionts have gradually transferred their genes to the nuclear genome that enable functional interaction. In this dissertation, a 7.9 kb transposition of a typically 17.0 kb mitochondrial genome to a specific chromosomal position in the domestic cat is reported. The integrated mtDNA has amplified about 38-76 times and now occurs as a "macrosatellite"-like tandem repeat with multiple length alleles resolved by pulse field gel electrophoresis (PFGE) segregating in cat populations. To examine the tempo and mode of evolution between different organelles, characterization of the complete 7946 bp nuclear mitochondrial DNA monomer, Numt, and cytoplasmic mtDNA (17,009 bp) sequences reveals about 95% similarity, which supports recent divergence within 1.8-2.0 MYA and the radiation of four modern species in genus Felis. The motif, (ACACACGT), appears imperfectly repeated at the deletion junction of the control region (CR), and a likely target for recombination. Simple repeats are also implicated in indel generation. Most substitutions between the cat homologues are attributable to accelerated cytoplasmic mtDNA evolution, yet maintain a uniform rate of synonymous substitutions between different mitochondrial genes. Results of ribonuclease protection assays on cellular RNA verify the lack of Numt-specific transcription and the appraisal of Numt as a molecular "fossil". Despite an elevated number of transversions and no increase in dA/dT content over cytoplasmic mtDNA, Numt resembles archetypal pseudogene evolution.

To place the felid data in the context of functional mitochondrial genomes, pairwise similarity comparisons of all 37 mtDNA coding genes and the CR among eight complete mitochondrial genomes of five placental mammals were performed. In carnivores, the ND4L and ATPase 6 genes exhibit higher sequence conservation, while cyt B shows accelerated divergence. Lastly, the occurrence of Numt-like loci in other exotic felids deviates from current phylogenetic predictions. To confirm homology with the F. catus Numt locus, a series of experiments was conducted to isolate chromosomal sequences directly flanking Numt-like loci. These observations provide an empirical glimpse of historic genomic events that may parallel the accommodation of organelles in eukaryotes.