Genome Structure, Gene transfer and Innovation

Horizontal gene transfer (HGT) and mobile genetic elements have a profound impact on genome organization across the Tree of Life. This dissertation explores frequency of HGT of an intein. It also explores the relative timing of HGT events and how these HGT events have expanded preexisting metabolic pathways in the Thermotogae phylum.;Some examples of mobile genetic elements that affect genome organization are inteins, group I introns and group II introns. These mobile genetic elements are self-splicing; and, inteins and group I introns and are mobile by homing endonucleases. Group II introns are mobile either by a reverse transcriptase or endonuclease. A survey of proteins, invaded by inteins and introns, reveal group I introns and inteins are found in conserved sites while group II introns are not.;More specifically analyzing the inteins present in one insertion site of a protein family provides opportunities to understand the evolutionary history of an intein allele. The vacuolar and archaeal catalytic ATPase subunit protein family has been invaded by two different intein alleles (vma-a and vma-b). I show the vma-b inteins are frequently transferred and may have been transferred interdomain between the Archaea and Bacteria.;Large highways of HGT are a hallmark of the Thermotogae phylum. HGT from the Archaea and Firmicutes has left large signatures in the genome. When these genes arrived in the Thermotogae phylum is unknown. Evidence is provided in this thesis that strongly suggests these highways arrived later in the evolutionary history of the phylum after the speciation and divergence of the last common ancestor of the phylum.;Along the Firmicute highways of gene transfer a large number of genes, which allow for de novo vitamin B12 biosynthesis, arrived in the Thermosipho lineage and added onto the cobinamide salvage pathway. This large HGT expanded the existing pathway from synthesizing vitamin B 12 from partial B12 molecules to synthesizing B12 molecules from glutamate.;When closely related whole genomes of the Thermotoga genus are examined it becomes apparent that intragenus transfers involve information and storage genes and that inversion events were likely mediated by CRISPRS and transposons.