N6-methyladenosine-dependent regulation of bacterial development

该项目的总体目标是了解DNA自然发生的化学修饰如何影响信息处理和随后的细胞反应。所有生物体都含有DNA，DNA是作为生命蓝图的遗传物质。来自不同生物体的DNA，如细菌和人类，具有影响编码信息读取方式的化学修饰。一种这样的修饰是甲基腺苷。 甲基腺苷通常存在于细菌DNA中，可以通过改变被打开的基因来改变细胞处理信息的方式，这反过来又可以帮助细胞对营养物质可用性的变化做出反应。这项研究检测了一种以前未研究过的蛋白质，这种蛋白质在细菌中形成甲基腺苷。当这种蛋白质失活并且腺苷甲基化丢失时，细胞的基因活性发生实质性变化，从而影响细胞的发育和行为。这项研究通过确定甲基腺苷如何影响细菌发育，包括多细胞细菌结构的形成和可能影响抗生素耐药性的不同细胞类型，使社会受益。除了研究的好处，这个项目的进一步社会影响包括教学不断扩大的计算生物学领域的学生从社会经济上处于不利地位的背景。该项目的推广计划为密歇根州北方农村的高中生提供了使用作为本研究一部分开发的在线教育门户网站学习生物信息学入门的机会。此外，该项目还为本科和研究生阶段的下一代科学家提供了培训机会，他们将接受尖端测序方法和数据分析方法的专门培训。已知来自生命的所有三个领域的生物体的基因组以DNA甲基化的形式进行化学修饰。N6-甲基腺苷（m6 A）是在原核生物和一些真核生物基因组中检测到的一种修饰类型。虽然m6 A甲基转移酶，负责基因组m6 A的酶，发现在许多不同的细菌物种的m6 A的功能仍然在很大程度上未研究。该项目的目标是了解革兰氏阳性细菌枯草芽孢杆菌中基因组m6 A修饰的影响。最初的实验表明，从B.枯草芽孢杆菌基因组导致参与细菌发育过程的基因的表达。展望未来，该研究项目将研究m6 A影响参与细菌细胞发育转变的基因表达的机制。全球基因组学方法将用于确定细菌染色体结构，全基因组蛋白质景观和m6 A丢失后的基因表达差异。此外，有针对性的生化方法将被用来确定是否m6 A是必要的和足够的差异基因表达，并确定在DNA调控区的m6 A响应的因素。一旦完成，该项目将提供m6 A依赖的基因表达变化如何与细菌发育平台相互作用的机制理解。

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.