Studies on genomic organization, gene order, and recombination in prokaryotes, concentrating on members of the Thermotogales, an order of hyperthermophilic bacteria

Comparative genomic analyses of prokaryotes reveal extensive variation in gene content among organisms classified as the same, or closely related, "species". Strains of the same species, as defined by SSU rRNA, can contain 0 to 25% strain-specific genes. Prokaryotic genome plasticity allows for gene shuffling within a genome, along with lateral gene transfer, potentially disrupting conserved gene clusters or operons.; This thesis examined a range of strains from the order Thermotogales at specific areas of the genome to look for rearrangements and unsual features, using Thermotoga maritima MSB8 as a comparison point. A long walk PCR technique revealed gene content downstream of prfA, which codes for a conserved protein release factor. In T. maritima MSB8 and several related taxa, two different flagellar protein gene clusters were found, revealing recombination and different gene histories than the SSU rRNA gene, while maintaining the overall structure of the cluster. Analysis of several clusters of ribosomal protein genes, using genome comparison utilities and sequence analysis from the Thermotogales, reveals gene histories that differ from the SSU rRNA gene, and shuffling of clusters throughout bacteria and archaea. However, in spite of recombination, higher order cluster structure is maintained.; Spatial autocorrelation analysis, most often used for biogeographic studies, was adapted for a novel use in circular prokaryotic genomes, to assess the distribution of functional gene categories within genomes. Because only one Thermotogales genome sequence is available (T. maritima MSB8), 26 additional bacterial strains, from six species groups, were used to examine functional genomic architecture. Of particular interest was the distribution of ORFans (orphaned open reading frames), which are hypothetical genes with no known function. In T. maritima MSB8, and one other strain, Chlamydia pneumoniae AR39, hyperdispersal of true hypothetical proteins was observed, indicating that they were likely misannotated intervening sequence. Conserved hypothetical proteins in all strain groups except T. maritima MSB8 and Prochlorococcus marinus strains show clustered distributions, implying that they may code for functional clusters not yet discovered, but maintained within strain groups. The random distributions within T. maritima MSB8 and P. marinus strains likely result from gene insertions and recombinations within existing functional clusters.