The overall goal of this project is to understand how naturally occurring chemical modifications of DNA influence information processing and the subsequent cellular response. All living organisms contain DNA, the genetic material that serves as the blueprint for life. DNA from diverse organisms, such as bacteria and humans, has chemical modifications that affect how the encoded information is read. One such modification is methyladenosine. Methyladenosine is commonly found in bacterial DNA and can change how cells process information by altering the genes that are switched on, which in turn can help the cell respond to changes in nutrient availability. This research examines a previously unstudied protein that forms methyladenosine in bacteria. When this protein is inactive and adenosine methylation is lost, cells undergo substantial changes in gene activity that affect how the cells develop and behave. This research benefits society by determining how methyladenosine influences bacterial development, including the formation of multicellular bacterial structures and distinct cell types that can affect antibiotic resistance. In addition to the research benefits, further societal impacts of this project include teaching the expanding field of computational biology to students from socioeconomically disadvantaged backgrounds. The project's outreach initiative provides high school students in rural Northern Michigan with the opportunity to learn introductory bioinformatics using an online educational portal developed as part of this research. Further, this project provides training opportunities for the next generation of scientists at both the undergraduate and graduate levels with specialized training in cutting edge sequencing approaches and methods of data analysis.
The genomes of organisms from all three domains of life are known to harbor chemical modifications in the form of DNA methylation. N6-methyladenosine (m6A) is a type of modification detected in prokaryotic and some eukaryotic genomes. Although m6A methyltransferases, the enzymes responsible for genomic m6A, are found in many diverse bacterial species the function of m6A remains largely unstudied. The goal of this project is to understand the effects of genomic m6A modifications in the Gram-positive bacterium Bacillus subtilis. Initial experiments have shown that elimination of m6A from the B. subtilis genome results in the expression of genes involved in bacterial developmental processes. Moving forward, this research project will investigate the mechanism by which m6A affects the expression of genes involved in bacterial cell developmental transitions. Global genomics approaches will be used to determine the differences in bacterial chromosome structure, genome-wide protein landscapes, and gene expression upon loss of m6A. Further, targeted biochemical approaches will be used to determine if m6A is necessary and sufficient for differential gene expression and to identify the factors that respond to m6A in DNA regulatory regions. Once complete, this project will provide a mechanistic understanding for how m6A-dependent changes in gene expression interface with bacterial developmental platforms.
