Understanding Horizontal Gene Transfer in Bacteria and Archaea: Units of Transfer and Modes of Integration

University Of Connecticut, Storrs CT

Investigators

Abstract

One of the most important, but poorly understood, drivers of microbial evolution is horizontal gene transfer (HGT), when whole genes or large gene fragments are passed along between two bacterial cells, sometimes representing different species. Understanding how HGT occurs may shed light on the adaptation of microbes to new ecological niches, evolution and spread of antibiotic resistance genes, the rise of emerging pathogens, and competition between microbes. The outcomes of the proposed research will include new computational methods and techniques for analyzing HGT events, open-source software tools for use by biologists, and valuable new insights into different types of HGT events in oceanic bacteria. The project will train three PhD students and at least three undergraduate students in interdisciplinary research skills. The project will also introduce several high-school students to bioinformatics research and provide training to several high-school science teachers on computational molecular evolution. Research results will also be integrated into graduate and undergraduate level classroom teaching. The project focuses on two fundamental properties of HGTs. The first property deals with the 'mode' of an HGT event, which defines whether the transferred gene is 'additive' or 'replacing', i.e., whether it adds itself as a new gene to the recipient genome or replaces an existing homologous gene. The second property concerns the units of HGT events, i.e., whether the HGT event involved a gene fragment, entire gene, several genes, or entire operons. The project entails development of new, broadly applicable, computational methods to infer the modes and units of HGT events, application of these methods to microbial genome datasets to investigate the frequencies and roles of the different modes and units of HGT events in various evolutionary scenarios, and testing of specific hypotheses relating these properties of HGT events to evolutionary divergence, HGT integration mechanism, and gene function.