SG: Origin and Evolutionary History of Gene Transfer Agents in Marine Bacteria

Dartmouth College, Hanover NH

Investigators

Abstract

Exchange of genes is an important evolutionary process that occurs at high frequency within microbial populations, allowing them to adapt quickly to changing environmental conditions. Acquisition of resistance to antibiotics in bacteria is one of the many ways in which such gene swapping impacts society. Because of the potentially tremendous benefit to their survival, bacteria have developed a large arsenal of mechanisms for gene trade. One enigmatic gene exchange mechanism involves shuttling genes packaged in particles (so-called Gene Transfer Agents) that resemble bacterial viruses. This raises many questions about the origin and functionality of this mechanism. How beneficial is it to exchange genes this way? Do Gene Transfer Agents represent former viruses that were "domesticated" by bacteria? Bacterial viruses are numerically the most abundant organisms on Earth. Could many of these viruses in fact be Gene Transfer Agents? Answers to these questions will advance our understanding of how gene exchange contributes to bacterial adaptation. Because of accumulating evidence that Gene Transfer Agents are of use to a microbial population as a whole rather than to an individual cell, this project will also advance our knowledge on the origin and maintenance of cooperation, a long-standing mystery of evolutionary biology. Since bacteria and viruses are key players in all Earth environments, including human bodies, the project will benefit both the scientific community and broader society. Researchers at Dartmouth College will investigate the above questions via computational analyses of genetic information from marine bacteria. Those bacteria are key players in Earth's nutrient cycling and ocean habitability. Genes encoding Gene Transfer Agents (GTAs) will be identified and extracted from bacterial genomes and oceanic metagenomes. These GTAs will then be rigorously compared to similar genes from bacterial viruses. The comparison will assess the GTA's evolutionary relationship to viruses and the selective pressure exerted on their genes by bacterial hosts. Given the recent discovery of the GTA system and its resemblance to actual viruses, many true GTAs in available genomic sequences could be mistakenly annotated as integrated bacterial viruses. To address this important issue, the researchers will develop a novel bioinformatic method that aims to successfully distinguish Gene Transfer Agents from their viral counterparts. Ultimately, this cross-disciplinary project will contribute to better understanding of oceanic and global elemental cycles and of adaptive evolutionary processes that drive bacterial populations in marine and other environments. The data sets and computer programs generated in this project will be shared with scientific community.