Bacterial diversity has always been associated with micro-evolutionary events such as horizontal gene transfer and DNA mutations. Such events influence the rapid evolution of bacteria as a result of the environmental conditions which they encounter. They further establish beneficial phenotypic effects that allow bacteria to specialize in new habitats. Due to the increase in number of bacterial genomic sequences, studying microbial evolution has been made possible, and the impact of micro-evolution on bacterial diversity is becoming more apparent. To gain biological information from this ever increasing genomic data, a variety of computational tools are required. This thesis therefore, focuses on the development and application of computational approaches to identify genomic regions of divergence which have resulted from horizontal gene transfer or small mutational changes. The first and major part of the thesis describes the application of DNA patterns, termed oligonucleotide signatures to identify horizontally acquired genomic regions in prokaryotes. These DNA patterns are demonstrated to differentiate between signatures of the core genome and those which have been acquired through horizontal transfer events. DNA patterns are further demonstrated to: reveal the distribution patterns of horizontally acquired genomic elements, determine their acquisition periods, and predict their putative donor organisms. The second part of the thesis focuses on the evaluation of modern short read sequence data of geographically unrelated Pseudomonas aeruginosa to study their intraclonal genomic diversity. The work described in the thesis was purely in silico driven and performed at Hannover Medical School and the Bioinformatics and Computation Biology Unit at the University of Pretoria. / Thesis (PhD)--University of Pretoria, 2013. / gm2014 / Biochemistry / unrestricted

Durante a anidrobiose (um estado ametabólico muito estável), o nematóide Panagrolaimus superbus tolera vários tipos de estresses físicos. A fim de melhor compreender essa extremotolerância, P. superbus foi submetido a regimes de hiperaceleração (RHA) de até 400.000 x g. Surpreendentemente, foi observado que esse verme tolera a exposição à RHA tanto dessecado (i.e., em anidrobiose) como hidratado. Para verificar se esse fenômeno era específico para essa espécie ou algo observável em outros organismos, os mesmos procedimentos experimentais foram realizados no organismo modelo Caenorhabditis elegans. Intrigantemente, C. elegans também mostrou o mesmo perfil de sobrevivência. Ademais, o desenvolvimento, comportamento, morfologia e crescimento populacional desse nematóide também foram analisados após a exposição ao RHA, não sendo observada quaisquer mudanças nesses parâmetros em função da exposição à hipergravidade. Em seguida, foram realizadas buscas (tBLASTn) no genoma de C. elegans por homólogos de genes relacionados ao gravitropismo que são naturalmente encontrados em plantas. Essa busca resultou nos genes dnj- 16 (homólogo ao ARG1), ipla-1 (homólogo ao SGR2) e uma sequência não caracterizada (homóloga a TWD1). Especial atenção foi despendida ao gene dnj-16, uma vez que é o mais conservado entre eles. As análises de RT-qPCR revelaram que o dnj-16 é ligeiramente regulado para baixo durante o RHA, o que não era esperado caso ele possuísse função semelhante ao seu homólogo em plantas. A análise do estado metabólico desse nematoide durante o RHA lançou luz sobre os dados de RT-qPCR, mostrando que a queda na expressão de dnj-16 é provavelmente devida à centrifugação. Posteriormente, diversas análises in silico foram realizadas a fim de caracterizar o gene dnj-16 e a sua respectiva proteína. Inicialmente, a análise comparativa dos domínios DnaJ, transmembrana e coiled coil das proteínas dnj-16, ARG1, ARL1 e ARL2 apontou para uma grande semelhança não apenas na sequência como na estrutura dessas proteínas. Essa grande similaridade motivou análises para desvendar o papel e a origem do gene dnj-16. Três hipóteses ((i) homologia, (ii) convergência e (iii) transferência gênica horizontal (TGH)) foram consideradas na investigação desse intrigante gene. Os resultados obtidos nas análises in silico apontaram para uma TGH mediada por RNA, potencialmente ocorrida a 1325 m.a., como a hipótese mais plausível para explicar a origem de dnj-16 e algumas espécies parasitas do gênero Phytophthora como prováveis mediadores dessa transferência. Dessa forma, os dados apresentados nessa tese mostram pela primeira vez que C. elegans é tolerante a RHA ordens de magnitude mais altas do que se pensava serem compatíveis com a vida multicelular. Além disso, os dados sugerem que dnj-16 foi transferido horizontalmente de plantas para nematoides e que a ultracentrifugação leva a uma redução no metabolismo de C. elegans, o que ajudaria a explicar a sua sobrevivência sob tal condição extrema. Por fim, o conjunto de dados desse trabalho representa contribuições originais para a compreenção da biologia, da genética e da evolução de C. elegans. / During anhydrobiosis (a very stable ametabolic state), the nematode Panagrolaimus superbus tolerates many types of physical stresses. In order to better understand this extremotolerance, P. superbus underwent hyperacceleration regimes (RHA) of up to 400,000 x g. Surprisingly, it was observed that this worm tolerated RHA exposure both dried (i.e., during anhydrobiosis) and hydrated. In order to verify if this phenomenon was specific for this species or something observable in other organisms, the same experimental procedures were performed in the model organism Caenorhabditis elegans. Intriguingly, C. elegans also showed the same survival profile. In addition, the development, behavior, morphology and population growth of this nematode were also analyzed after the exposure to RHA and no changes were observed in these parameters due to the hypergravity exposure. Thereafter, searches (tBLASTn) were performed on C. elegans genome by homologs of gravitropism related genes that are naturally found in plants. These searches resulted in the genes dnj-16 (homologous to ARG1), ipla-1 (homologous to SGR2) and an uncharacterized sequence (homologous to TWD1). Special attention was given to dnj-16 gene, since it is the most conserved among them. RT-qPCR analyzes revealed that dnj-16 is slightly down regulated during RHA, which was not expected if it had similar function to its homologue in plants. Analysis of the metabolic status of this nematode during RHA shed light on the RT-qPCR data, showing that the decrease in dnj-16 expression was probably due to centrifugation. Subsequently, several in silico analyzes were performed in order to characterize the dnj-16 gene and its respective protein. Initially, the comparative analyzis of the DnaJ, transmembrane and coiled coil domains of dnj-16, ARG1, ARL1 and ARL2 proteins pointed to a great similarity not only in the sequence as well as in the structure of these proteins. This great similarity motivated analyzes in order to uncover the real nature of the dnj-16 gene. Three hypotheses ((i) homology, (ii) convergence and (iii) horizontal gene transfer (HGT)) were considered in the investigation of this intriguing gene. The results obtained in the in silico analyzes indicated an RNA mediated TGH, potentially occurred 1325 my (millions of years), as the most plausible hypothesis to explain the origin of dnj-16 and some parasitic species of the Phytophthora genus as probable mediators of this transference. Therefore, data presented in this thesis show for the first time that C. elegans tolerates RHA of magnitude orders higher than it was thought to be compatible with multicellular life. In addition, the data suggest that dnj-16 was transferred horizontally from plants to nematodes and that ultracentrifugation leads to a reduction in C. elegans metabolism, which would help explain its survival under such extreme condition. Finally, the data set of this work represent original contributions to the understanding of the C. elegans\' biology, genetics and evolution.

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