Understanding Gene Regulatory Network Function During Stress Response Adaptation of an Archael Extremophile

了解古生菌极端微生物压力反应适应过程中的基因调控网络功能智力优势：尽管生命科学研究已经进入后基因组时代，但我们对地球上微生物生命的多样性仍然知之甚少。关于微生物极端微生物的信息尤其缺乏，这些微生物在生命极限、高压和高温下的深海热液喷口、饱和盐湖和极地冰盖中茁壮成长。这些生物中有许多属于第三生命领域--古生菌。尽管古生菌对全球碳循环和能源循环做出了重大贡献，但由于它们很难培养和基因操纵，对它们的研究仍然不足。这些微生物如何应对极端多变的环境？它们如何改变自己的遗传程序和新陈代谢途径，以适应和生存在地球上独特栖息地的变化？这些问题在今天尤其重要，因为气候变化迅速改变了全球维持生命的条件。这些变化对负责全球碳和能源循环的微生物群落的影响尚不清楚，但预计将对人类社会产生巨大影响。为了解决这些问题，这项拟议研究的长期目标是了解生物体如何在不断变化的环境条件下保持动态平衡。这一过程的中心是基因调控网络(GRN)，它由一组调控蛋白质组成，这些蛋白质对环境刺激做出反应，开启和关闭基因。一旦感觉到环境的变化，GRN就会促进产生蛋白质，修复损伤，将细胞恢复到健康状态，并为未来的压力条件做好准备。本研究中研究的盐生盐杆菌在高盐环境中生长旺盛。这种生物是一种应激反应专家，能够在光、热、氧和营养物质在极端盐分浓度下的每日强烈波动中在大盐湖生存。作为回应，生物体的新陈代谢在四种依赖光和氧的能量产生模式之间转换。这项拟议工作的目的是确定生物体如何利用GRN或基因电路来适应光线、氧气和营养物质的动态变化，以确保生存。这项研究将采用一种创新的系统生物学方法，将尖端的高通量实验技术与计算和统计建模相结合。盐生细菌是研究古极端细菌的一个很好的模式系统，因为它易于培养和基因操作。我们所了解到的关于盐杆菌遗传电路的知识将很容易应用于绘制其他古菌的遗传电路图。此外，它还将提供对微生物GRN动态和表达模式的更深层次的理解，以响应不断变化的环境条件。更广泛地说，这项研究的结果将为理解微生物能量生产和全球碳循环应对气候变化奠定基础。更广泛的影响：这项研究将有助于高中、本科和研究生层面的教育、培训和推广。具体地说，所有级别的学生都将有机会在数学和生物的界面上进行培训。首先，PI和实验室成员将为北卡罗来纳州科学与数学学校的学生教授为期一周的迷你课程，这是一所位于北卡罗来纳州达勒姆的公立高中，每年吸引来自北卡罗来纳州每个国会选区的尖子生。其次，将为北卡罗来纳州大学的本科生提供与该项目相关的外展研究机会，这些大学通过杜克大学(如北卡罗来纳州中央大学、费耶特维尔州立大学)现有的暑期项目为代表不足的群体提供服务。第三，该项目资助的一名研究生将接受下一代数学和生物交叉学科的培训。

Understanding gene regulatory network function during stress response adaptation of an archaeal extremophileIntellectual merit: Although life science research has entered the post-genomic era, we still understand little about the diversity of microbial life on earth. Information is particularly lacking on microbial extremophiles, which thrive at the limits of life, in deep-sea hydrothermal vents under high pressure and temperature, saturated salt lakes, and polar icecaps. Many of these organisms are members of the third domain of life, the archaea. Although archaea contribute substantially to global carbon and energy cycles, they remain understudied because they are difficult to culture and genetically manipulate. How do these microorganisms cope with an extreme and changing environment? How do they alter their genetic programs and metabolic pathways to adapt and survive changes in their unique habitats on earth? These questions are particularly relevant today, as climate change rapidly alters the conditions that support life across the globe. The impact of such changes on the microbial communities responsible for global carbon and energy cycling is unclear, but is expected to have enormous implications for human society. To address these issues, the long-term goal of the proposed research is to understand how organisms maintain homeostasis in the face of fluctuating environmental conditions. Central to this process are gene regulatory networks (GRNs) composed of groups of regulatory proteins that switch genes on and off in response to environmental stimuli. Upon sensing a change in the environment, GRNs promote the production proteins that repair damage, restore the cell to a healthy state and prepare it for future stress conditions. The Halobacterium salinarum studied in this research thrives in high salt environments. This organism is a stress response specialist, capable of surviving in the Great Salt Lake during strong daily fluctuations of light, heat, oxygen, and nutrients at extreme salt concentrations. In response, the organism shifts its metabolism between four light- and oxygen-dependent energy-generating modes. The aim of the proposed work is to determine how the organism uses GRNs,or gene circuitries, to adapt to the dynamic alterations in light, oxygen, and nutrients to ensure survival. This research will employ an innovative systems biology approach, which combines cutting-edge high throughput experimental techniques with computational and statistical modeling. Halobacterium is a good model system for studying archaeal extremophiles because it is easy to culture and genetically manipulate. What we learn about the genetic circuitry of Halobacterium will be readily applicable toward mapping the genetic circuits of other archaea. Moreover, it will provide a deeper understanding of the dynamics of microbial GRNs and expression patterns in response to changing environmental conditions. More generally, the outcome of this research will lay the foundation for understanding microbial energy production and global carbon cycling in response to climate change. Broader impacts:The research will contribute to education, training, and outreach at the high school, undergraduate, and graduate levels. Specifically, students at all levels will have training opportunities at the interface of mathematics and biology. First, the PI and lab members will teach a week-long mini course for students from North Carolina School of Science and Math, a public high school in Durham, NC that draws the top students each year from each of the congressional districts in North Carolina. Second, outreach research opportunities associated with the project will be provided for undergraduates from North Carolina universities that serve underrepresented groups through established summer programs at Duke (e.g. North Carolina Central University, Fayetteville State University). Third, a graduate student funded on the project will receive next generation interdisciplinary training at the interface of mathematics and biology.