UC Berkeley

Organisms of all domains of life face a multitude of physiological stresses, ranging from metabolic stresses, such as limited nutrient availability, to predation by viruses. Bacteriophages (phages), the viruses of bacteria, are suspected to be the most abundant entity on the planet. As such, bacteria are faced with omnipresent predation by their phages and have evolved numerous distinct mechanisms to overcome phage infection. The identification and characterization of these bacterial immune systems has rapidly increased. It has become increasing appreciated that mobile genetic elements of bacteria, genomic loci capable of inter- and intra-genome transfer, are hotspots of these immune systems that inhibit bacteriophage infection. The relationship between the host bacterium, mobile genetic element, and infecting phage is highly convoluted, as each entity must sense and properly respond to another, tipping the complicated symbioses at play in their favor. In this work, we probed the interactions between Vibrio cholerae, its selfish mobile genetic elements, and the bacteriophage that prey upon V. cholerae at three distinct magnitudes: local transcriptional regulation, global transcriptional regulation, and cross-genome exchange between entities. First, we define a novel role for mobile genetic element encoded small RNAs in regulating the bacterial response to infection by phage. Prokaryotic small RNAs act as post-transcriptional regulators, altering the expression of a set of target transcripts by direct base pairing. Second, we investigated the regulation of mobile genetic element gene expression at the genomic scale, identifying global regulators involved in the regulation of V. cholerae mobile genetic elements. These global regulators act to control the activation of many mobile genetic elements simultaneously. We then leveraged our collection of co-isolated bacteria and phages to undertake a primarily bioinformatic analysis of the role that mobile selfish nuclease genes play in the conflict between phages, mobile genetic elements, and their hosts. The genetic exchange of these mobile nuclease genes is suggested to be a driving force of evolution between the entities. Broadly, this work investigates the local and global transcriptomic and genomic interactions between bacteria, their selfish mobile elements, and phages.