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Open Access Publications from the University of California

Examining the Role of Horizontal Gene Transfer on the Evolution of CRISPR-Cas

  • Author(s): O'Meara, Derek Miles
  • Advisor(s): Nunney, Leonard
  • et al.

CRISPR-Cas is a widespread bacterial genomic defense system characterized by its unique ability to “remember” nucleic acid sequences from invasive threats and provide future protection against these elements. CRISPR-Cas is found to have variable presence/absence throughout much of the bacterial Kingdom, even at the species level. This variability is presumably caused by a mix of both gain events, by which the system is passed horizontally from one bacterial genome to another, and loss events, by which CRISPR-Cas is removed from the bacterial genome driven either by a loss of selective pressure or active selection against the system. To further understand the evolution of CRISPR-Cas, this research was broken into three distinct chapters.

In the first chapter, a single bacterial species (Pseudomonas psychrotolerans) found to show variability in CRISPR-Cas presence was analyzed for evidence of both horizontal transfer and loss of the system by comparison of the bacterial phylogeny to the CRISPR-Cas phylogeny and through a search for recombination sites surrounding the CRISPR-Cas loci. Evidence indicated that there were multiple, independent losses of the CRISPR-Cas system from these strains of bacteria, potentially due to human driven changes in their environments. Further, homologous recombination was found to be responsible for multiple independent horizontal transfers of CRISPR-Cas between the related genomes.

The second chapter followed the next logical step in zooming out to the level of the Pseudomonas genus in search of recombination of CRISPR-Cas at the intraspecies and interspecies levels. It was found that while intraspecies recombination of CRISPR-Cas was prevalent (as seen in the first chapter), interspecies horizontal transfer appeared to only be a rare, founder-like process.

Branching away from these phylogenetic approaches, the third chapter instead focuses on identifying whether the CRISPR-Cas system imposes a cost on its bacterial genome by acting as a barrier towards the entry of potentially beneficial DNA. Through a phylogenetically constrained pairwise analysis of related CRISPR-Cas present and CRISPR-Cas absent bacterial strains from throughout the bacterial kingdom, a significant negative correlation was found between CRISPR-Cas presence and plasmid count.

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