The purpose of this master's thesis was to determine the role of gene clusters, comprised of genes similar to susCD and genes coding for non-specific nucelases. The work was done on species of the genera Prevotella and Bacteroides, known for their ability to degrade and utilize various polysaccharides, which is most commonly achieved via PULs. Our work was focused on a variant of these clusters presumably targeting nucleic acids and the genes for saccharide degradation are replaced by nucleases. The work encompassed three major parts: bioinformatical overview, growth studies and RT-PCR to assess cluster activity. We searched for the presence of such clusters in the genomes of the Prevotella and Bacteroides genera. Using the Hungate technique we showed the ability of six chosen strains to grow in media with the addition of specific nucleosides, sugars (ribose, deoxyribose) and DNA or RNA. Expression of the putatively active clusters was monitored with by reverse transcription of the isolated RNA and real-time PCR. The clusters appear to be widely present as well as architecturally conserved and the tested strains have been able to grow on select media. Differences in the gene expression levels are noticable, but despite being unable to explain them completely, these conclusions show that the clusters might play an important role in both symbiotic rumen strains and potential pathogens from the oral cavity.
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