Gene Amplification: Acinetobacter baylyi as a bacterial model system

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AbstractThis project focuses on a new bacterial system for studying chromosomal rearrangements involving gene duplication and further amplification. Gene amplification, which is a common process in all organisms, has significant consequences. It is essential to evolution, genetic diversity, and the ability of organisms to adapt to variable environments. Gene amplification also contributes to serious problems such as drug resistance, cancer, and microbial virulence. Despite its importance, many aspects of gene amplification remain poorly understood. Unlike other types of genetic change, amplification is dynamic and reversible. It may leave no evidence of its position or frequency. In this research project, an unusual characteristic of a soil bacterium, Acinetobacter baylyi ADP1, facilitates the systematic study of gene amplification. The critical characteristic is that A. baylyi naturally takes up DNA from the environment with exceptionally high efficiency and incorporates it into the genome via homologous recombination. This natural competence for DNA uptake permits the use of a transformation assay to detect the precise endpoints of duplicated chromosomal regions in mutants that arise spontaneously. The DNA sequence of such duplication sites provides information about the underlying genetic recombination event. This project builds on intriguing results from initial studies in which a new type of position specific illegitimate recombination (PSIR) process was discovered. The PSIR events lack DNA features that characterize typical site-specific recombination. One objective of this project is to determine the mechanism of PSIR, which appears to be novel. Additionally, a genome-wide approach will be used to characterize spontaneous duplications. Important features of DNA that contribute to gene duplication will be investigated such as DNA sequence and genomic context. This strategy will improve our understanding of a fundamental, common and important genetic process.Broader Impacts. Students will be trained in important multidisciplinary areas that bridge genetics, physiology, biochemistry, and computation. The project is accessible to students at all levels and will involve undergraduate and graduate students. Additionally, a postdoctoral researcher will conduct related investigations and help mentor the project participants. Ongoing programs at the University of Georgia will enhance the opportunity to train a diverse group of scientists. Such programs include an NSF-supported Research Experiences for Undergraduate (REU) site program in prokaryotic biology. The long-term impact of this research has the potential to offset harmful effects of gene amplification through a better understanding of the underlying mechanisms. Moreover, gene amplification can be developed for beneficial biotechnology applications. Ideally, chromosomal gene amplification could be used for desired manipulations to avoid the problematic use of plasmids and antibiotic selections in genetic engineering. Furthermore, computational analyses of chromosomal rearrangements have predictive value that will expand the utility of DNA sequences deposited in databases.