N6-methyladenosine-dependent regulation of bacterial development

该项目的总体目标是了解自然发生的DNA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，这种遗传物质是生命的蓝图。来自不同生物（如细菌和人类）的DNA具有化学修饰，影响编码信息的读取方式。其中一种修饰是甲基腺苷。甲基腺苷通常存在于细菌DNA中，可以通过改变打开的基因来改变细胞处理信息的方式，这反过来可以帮助细胞对营养可用性的变化做出反应。这项研究检测了一种以前未被研究过的蛋白质，这种蛋白质在细菌中形成甲基腺苷。当这种蛋白质失去活性，腺苷甲基化丧失时，细胞的基因活性就会发生实质性的变化，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不同的细胞类型，从而影响抗生素耐药性，从而造福社会。除了研究效益之外，这个项目的进一步社会影响还包括向来自社会经济不利背景的学生教授不断扩大的计算生物学领域。该项目的推广活动为密歇根州北部农村地区的高中生提供了学习生物信息学入门的机会，他们可以使用作为该项研究的一部分而开发的在线教育门户网站。此外，该项目还为本科生和研究生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。已知来自所有三个生命领域的生物体的基因组都以DNA甲基化的形式进行化学修饰。n6 -甲基腺苷（m6A）是一种在原核生物和一些真核生物基因组中检测到的修饰类型。尽管在许多不同的细菌物种中都发现了m6A甲基转移酶（负责基因组m6A的酶），但m6A的功能在很大程度上仍未被研究。这个项目的目标是了解基因组m6A修饰在革兰氏阳性细菌枯草芽孢杆菌中的作用。最初的实验表明，从枯草芽孢杆菌基因组中去除m6A会导致参与细菌发育过程的基因的表达。下一步，本研究项目将研究m6A影响细菌细胞发育转变相关基因表达的机制。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基因表达在m6A缺失时的差异。此外，靶向生化方法将用于确定m6A对于差异基因表达是否必要和充分，并确定DNA调控区域对m6A作出反应的因素。一旦完成，该项目将为m6a依赖性基因表达变化如何与细菌发育平台相结合提供机制理解。

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.