The evolution of selfish genetic elements within bacterial genomes : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Molecular Evolution at Massey University, Auckland, New Zealand

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Genes that increase their copy number relative to that of the host genome are termed selfish. Selfish genes are found ubiquitously in bacterial genomes. Within genomes they can often be identified due to their repetitive nature. Short repetitive sequences such as repetitive extragenic palindromic (REP) sequences have been proposed to be selfish genetic elements. However, evidence for the selfishness of REPs is scarce due to the lack of knowledge about their origin, evolution and mechanisms of dispersal. Here, REPs are studied in the model bacterium Pseudomonas fluorescens SBW25. The evidence provided suggests that REPs are part of a greater mobile genetic element, which is termed REP doublet forming hairpins (REPINs). Subsequently, I investigate the cause of REPIN dispersal: a putative transposase. The transposase, named REP-associated tyrosine transposase (RAYT) shares essential motifs with the IS200 family of insertion sequences. However, unlike insertion sequences, RAYTs are found only as single copy genes. This indicates that RAYTs may not be entirely selfish; instead they may have been co-opted by the host to perform a beneficial function. Finally, two more repetitive sequence classes are studied in the SBW25 genome. Interestingly, both sequence classes consist of a protein coding sequence and a sequence that forms a stable secondary structure in single stranded DNA or RNA. This arrangement is reminiscent of bacterial toxin-antitoxin (TA) systems. Evidence from sequence analyses suggests that the repetitive nature of these elements in SBW25 may be the result of cooperation between REPINs or other replicative elements and the TA systems. The presented analyses show that despite the streamlined nature of bacterial genomes selfish genetic elements frequently arise, replicate and probably increase theirpersistence and spread through cooperation with addictive and duplicative elements respectively. persistence and spread through cooperation with addictive and duplicative elements respectively.
Content removed due to copyright restrictions: Bertels, F., & Rainey, P.B. (2011). Curiosities of REPINs and RAYTs. Mobile Genetic Elements, 1(4), 1-7. doi.:10.4161/mge.1.4.18610.
Bacterial genomes, Evolutionary genetics