EAGER: Exploratory Research in Accordion-Style Genome Dynamics

University Of Georgia Research Foundation Inc, Athens GA

Investigators

Abstract

Intellectual Merit In all organisms dynamic genetic changes can occur in which segments of the chromosome increase or decrease in copy relative to surrounding regions. Such expansion and contraction of the genome, termed "accordion-style dynamics," can play a critical role in adaptation and evolution. Although the process has many important biological implications, it is difficult to study. The difficulty in identifying specific genetic alteration stems from the transient and stochastic nature of the chromosomal changes and the variability of the events that occur in different cells of the population. This project will exploit special features of a soil bacterium, Acinetobacter baylyi ADP1, to facilitate experimental investigation. The high efficiency of natural transformation and recombination in this bacterium make it possible to design and engineer strains in which most cells of the population have multiple copies of the same segment of the chromosome arranged adjacent to each other in a high copy tandem array. These engineered strains can then serve as laboratory models to investigate the molecular details of the contribution of copy number change in adaptation and evolution. First, specific genes will be deleted from the genome. Next, other genes will be properly positioned such that they can substitute for the missing genes if the genome expands to place them in tandem arrays. In the restructured bacterial population, the large number of cells that have the same "expanded" version of the chromosome increase the opportunity for evolutionary processes to optimize new genetic and enzymatic activities. The restructured bacterial population also amplifies the signals that can be detected during experimentation such that the specific genetic changes can be much more readily observed. This research will involve testing specific gene sets to demonstrate that genomic expansion occurs as predicted. Having established the tandem arrays, it will be possible to vary the growth conditions for the bacteria to allow genetic evolution to be monitored and tested in a highly sensitive and reproducible manner. The advantages of developing a system that undergoes directed genetic expansion also include facilitating the bacterial production of important compounds for biotechnology and generating new enzymes with useful activities. Broader Impacts The manipulation and analysis of chromosomal rearrangements will contribute to efforts in the scientific community to take advantage of large scale DNA sequence data. In addition, ongoing programs at the University of Georgia will dovetail with this project to help broaden participation and increase diversity. Such programs include an NSF-supported Research Experiences for Undergraduate (REU) site program in prokaryotic biology. Research on the soil bacterium Acinetobacter baylyi ADP1 is also being integrated into an undergraduate lab course that uses authentic research projects to involve students in active learning and scientific engagement. High school students, undergraduates, and graduate students will participate in this project, and they will receive multidisciplinary training in genetics, biochemistry, and bioinformatics.