CAREER: Investigation of a Prion-based Metabolic Switch Driven by Cross-kingdom Chemical Communication

职业：跨界化学通讯驱动的基于朊病毒的代谢开关的研究

• 批准号: 1453762
• 负责人: Daniel Jarosz
• 金额: $ 80万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-15 至 2021-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1453762&HistoricalAwards=false
• 关键词: CAREER; Investigation; Prion; based; Metabolic

To survive in changing environments, organisms must acquire new traits. However, mechanisms that protect the genome generally limit genome modifications to small changes in DNA sequence. Given this paradox, how do organisms adapt to new conditions? One way to study this question is with prions. Prion proteins adopt multiple conformations (or shapes), and these unusual and diverse conformations drive a paradigm-shifting mode of inheritance that is based on changes in protein shape rather than changes in DNA sequence. Although best known as the cause of mad cow disease, the majority of the nearly two-dozen prions that have now been identified are benign or beneficial. One such prion, termed [GAR+], controls a fundamental decision in metabolism: whether to harvest energy by breaking down glucose in the absence of oxygen (fermentation) or to harvest energy through the breakdown of glucose (or other organic substrates)in the presence of oxygen (respiration). This metabolic switch between fermentation and respiration has been associated with a diverse array of disease states. It was recently discovered that many bacteria secrete small molecules that induce the [GAR+] prion in neighboring eukaryotic cells. Mathematical modeling suggests that both organisms derive benefit from this interaction in some circumstances. However, this interaction can disrupt industrially important fermentation processes and may be harmful to human health. The recent recognition that the microorganisms associated with an organism are often correlated with certain disease states suggests that lessons we learn from better understanding the interactions between prion proteins and bacteria will have broad significance. Therefore, this project will characterize the interactions between bacteria and yeast that result in prion acquisition, and work to identify the compound(s) produced by bacteria that induces the prion. The experimental methods and data analysis approaches developed will be useful for studying a variety of systems, and the results will be transmitted to the public through peer-reviewed publications and training of high school, undergraduate, and graduate students. Undergraduate and high school students and teachers will be introduced to the scientific process and will be taught how to design experiments in quantitative cell and molecular biology. High school students will be recruited for a "boot camp" style course that will include developing teaching modules, training of K-12 science teachers, and working with Stanford University's Center for Teaching and Learning. Undergraduate students will be recruited for the project from existing programs that focus on students from underrepresented backgrounds (including Stanford Amgen-SSRP Scholars Program). A two-week "Methods and Logic in Chemical and Systems Biology Boot Camp" for incoming graduate students will be developed which will teach inquiry-based learning and directly integrate concepts and experiments from the project.Adaptation to changing environments requires the rapid acquisition of new heritable traits, generally ascribed to mutations. However, epigenetic mechanisms can also generate phenotypic diversity among genetically identical cells. Among these mechanisms, self-perpetuating protein conformations, known as prions, are emerging as an important means of generating phenotypic diversity that is heritable from one generation to the next. Recent studies suggest that these elements are common in wild fungi, where they often confer adaptive traits. An ancient biological circuit in fungi and many other eukaryotes normally prevents the use of other carbon sources when glucose is present. The [GAR+] prion reverses yeast's strong glucose repression. Although organisms have largely been studied in isolation, in the wild they compete and cooperate in complex communities, and it was recently discovered that bacteria can secrete a chemical factor that elicits the [GAR+] appearance. This induction can provide strong benefits to yeast and bacteria alike. Bacteria benefit because [GAR+] yeast produce less ethanol, creating a less toxic environment. [GAR+] yeast benefit from enhanced growth on mixed carbon sources and greater longevity. Four specific aims will investigate this novel interspecies interaction and the ensuing heritable shift in metabolism: 1) Identify and characterize genes that control interspecies communication, 2) Identify the bacterial signal that induces the [GAR+] prion, 3) Investigate how [GAR+] influences cooperation and cheating in mixed populations, and 4) Characterize mechanisms that drive the [GAR+] metabolic switch using systems-level approaches. Although dozens of prions have been discovered in the past decade, we lack understanding of their physiological consequences and of factors that regulate their acquisition and loss. This research will employ novel methods to dramatically enhance our understanding of what is emerging as a conserved and fundamental biological process. The experimental methodology and data analysis platforms developed will be useful for studying a variety of systems, and will lead to new insights into how a prion can heritably transform one of the most fundamental decisions in metabolism, and in particular how such regulatory decisions can be fueled by cross-kingdom chemical communication.

为了在不断变化的环境中生存，生物体必须获得新的特征。然而，保护基因组的机制通常将基因组修饰限制在DNA序列的微小变化。面对这种矛盾，生物如何适应新的环境？ 研究这个问题的一种方法是用朊病毒。 朊病毒蛋白采用多种构象（或形状），这些不寻常的和不同的构象驱动了一种基于蛋白质形状变化而不是DNA序列变化的遗传模式。虽然最为人所知的是疯牛病的原因，但现在已经确定的近20种朊病毒中的大多数都是良性或有益的。一种称为[GAR+]的朊病毒控制着代谢中的一个基本决定：是在没有氧气的情况下通过分解葡萄糖（发酵）来收获能量，还是在有氧气的情况下通过分解葡萄糖（或其他有机底物）来收获能量（呼吸）。 发酵和呼吸之间的这种代谢转换与多种疾病状态有关。 最近发现，许多细菌分泌小分子，在邻近的真核细胞中诱导[GAR+]朊病毒。数学模型表明，在某些情况下，两种生物都从这种相互作用中获益。然而，这种相互作用会破坏工业上重要的发酵过程，并可能对人类健康有害。最近认识到，与生物体相关的微生物通常与某些疾病状态相关，这表明我们从更好地理解朊病毒蛋白和细菌之间的相互作用中吸取的教训将具有广泛的意义。 因此，本项目将描述导致朊病毒获得的细菌和酵母之间的相互作用，并致力于鉴定由细菌产生的诱导朊病毒的化合物。 开发的实验方法和数据分析方法将有助于研究各种系统，其结果将通过同行评审的出版物和高中，本科和研究生的培训传递给公众。 本科生和高中学生和教师将被介绍到科学的过程，并将被教导如何设计定量细胞和分子生物学实验。 高中生将被招募参加一个“靴子训练营”式的课程，其中包括开发教学模块，培训K-12科学教师，并与斯坦福大学的教学中心合作。 本科生将从现有的项目中招募，这些项目侧重于来自代表性不足背景的学生（包括斯坦福大学安进-SSRP学者项目）。 将为即将入学的研究生开发一个为期两周的“化学和系统生物学的方法和逻辑靴子营”，这将教授基于探究的学习，并直接整合项目中的概念和实验。适应不断变化的环境需要快速获得新的遗传特征，通常归因于突变。然而，表观遗传机制也可以在遗传相同的细胞中产生表型多样性。在这些机制中，自我永存的蛋白质构象，称为朊病毒，正在成为产生表型多样性的重要手段，这种多样性可以从一代遗传到下一代。最近的研究表明，这些元素在野生真菌中很常见，它们通常赋予适应性特征。 当葡萄糖存在时，真菌和许多其他真核生物中的古老生物回路通常会阻止其他碳源的使用。[GAR+]朊病毒逆转了酵母对葡萄糖的强烈抑制。虽然生物体在很大程度上被孤立地研究，但在野外，它们在复杂的群落中竞争和合作，最近发现细菌可以分泌一种化学因子来消除[GAR+]的出现。这种诱导可以为酵母和细菌提供强大的益处。细菌受益，因为[GAR+]酵母产生更少的乙醇，创造一个毒性较小的环境。[GAR+]酵母受益于混合碳源的增强生长和更长的寿命。四个具体目标将研究这种新的种间相互作用和随之而来的代谢遗传转变：1）识别和表征控制种间交流的基因，2）识别诱导[GAR+]朊病毒的细菌信号，3）调查[GAR+]如何影响混合种群中的合作和欺骗，和4）使用系统水平方法表征驱动[GAR+]代谢开关的机制。 尽管在过去的十年中已经发现了数十种朊病毒，但我们对其生理后果以及调节其获得和丧失的因素缺乏了解。这项研究将采用新的方法，以大大提高我们对什么是新兴的保守和基本的生物过程的理解。开发的实验方法和数据分析平台将有助于研究各种系统，并将导致对朊病毒如何遗传地改变代谢中最基本的决定之一的新见解，特别是这种调控决定如何通过跨王国的化学通讯来推动。