Horizontal gene transfer is the process by which genes are disseminated between different microbes in nature. This process is central to the ability of microbes to rapidly evolve new traits and has been linked to the spread of drug resistance and pathogenesis in humans, livestock, and agriculture. However, basic determinants that govern how genes spread in natural environments are not well characterized. This work utilizes a systems and synthetic biology approach to experimentally probe the underlying rules that determine the horizontal dissemination of genes between diverse bacteria species. A foundational idea is that gene regulation is an important driver in gene transfer. Results from this work will shed new light on a fundamental property of microbial evolution and address critical knowledge gaps for understanding the propagation of genetic material in natural and man-made environments. This endeavor will also lead to the characterization of genetic parts that will be useful for engineering a variety of microbes relevant in areas of biotechnology, biomaterials, and biofuels. These new insights can lead to improved strategies to contain the spread of problematic genetic materials that may lead to diseases in humans, livestock and crops, as well as those that alter the natural ecosystem in undesirable ways. This research will also provide creative educational and training opportunities for students from high school and regional undergraduate institutions with a diverse student population.

Technical Abstract

Recent sequencing efforts have highlighted the significance of horizontal gene transfer (HGT) in shaping microbial evolution. However, systems-level principles that govern the transfer and assimilation of foreign DNA into new hosts remain largely unexplored. An important corollary is that foreign regulatory elements that determine the level of transcription and translation for downstream protein-coding sequences may play a key role in HGT. Poorly expressed or translated foreign genes will not be beneficial to the receiving microbe and will be lost, while deregulated genes with abnormally high levels of expression are also selected against as they cause unnecessary resource burdens on the host. Therefore, the "Goldilocks" window of regulatory compatibility between donor and recipient microbes may be a significant and thus far underappreciated determinant in HGT. This NSF CAREER project aims to develop a systems and synthetic biology research program to answer key questions in this area. The proposal aims to determine whether compatibility of cis-regulatory elements in the donor DNA and the recipient's regulatory machinery is a key determinant of HGT and genomic acquisition of new DNA. This proposal aims to develop high-throughput methods using DNA library synthesis and sequencing to measure transcriptional and translational activity of tens of thousands of horizontally acquired regulatory elements. This proposal also aims to understand the regulatory barriers of HGT in diverse bacterial systems and identify strategies by which promiscuous mobile DNA such as conjugative plasmids and transposons are able to overcome such barriers to function in different species.

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
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David Rockcliffe
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Columbia University
New York
United States
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