RUI: Characterizing the Role of Regulatory Genes in Adaptive Evolution to Complex Environments

这项工作将描述进化的基本机制，不仅可以更好地理解进化过程，而且最终可以预测进化结果。研究人员将使用实验进化，这是一种在严格条件下在实验室中进化生物的技术，允许PI探索有关进化过程的基本问题。这一过程将使PI了解有利突变的作用，包括影响其他基因表达的基因。这些类型的突变可能对处于变化环境中的生物体特别有利。这项工作将与西班牙裔和少数民族服务机构（HSI和MSI）的本科生和硕士生合作进行，其中近90%的学生来自STEM领域代表性不足的群体。此外，PI将把这个项目整合到她的高年级微生物学课程中，作为每年24-48名本科生的真实研究经验，并与K-12教育工作者开展与这个项目相关的推广活动。通过这些方式，这项研究将有助于增加进入STEM管道的学生的多样性，并让他们为STEM领域的角色做好更好的准备。基因调控的变化是进化的驱动力。当比较不同物种时，顺式调节元件通常是进化变化的原因，而当生物体需要适应变化的环境时，反式调节元件通常会改变。对微生物的实验进化研究已经开始探索这些因子的作用，但通常是在不变的环境中，功能或顺式调节变化将受到青睐。PI将通过关注在两个调控基因cytR和sspA中鉴定的突变来探索反式调控元件中的突变在适应异质环境中发挥的作用，这两个基因在复杂培养基中的大肠杆菌长期培养物中具有适应性。为了表征它们在适应中的作用，PI将首先将适应性基因型与群体的转录组相关联，以鉴定基因表达变化，并确定哪些变化赋予适应性表型。然后，PI将对突变细胞进行实验性进化，以确定这些突变如何改变细胞可以用来适应异质环境的进化途径。了解这些类型的调节变化如何影响适应将有助于对进化原理的基本理解。

This work will characterize a fundamental mechanism of evolution, not only leading to a better understanding of the evolutionary process, but eventually allowing for prediction of evolutionary outcomes. The investigators will use experimental evolution, a technique where organisms are evolved in the laboratory under strict conditions, allowing the PI to probe basic questions about the evolutionary process. This process will allow the PI to understand the role of advantageous mutations, including in genes that affect expression of other genes. These types of mutations may be particularly advantageous for organisms in changing environments. This work will be performed in collaboration with undergraduate and master's students at a Hispanic and Minority Serving Institution (HSI and MSI), where almost 90% of students are from groups underrepresented in STEM fields. Further, the PI will integrate this project into her upper division microbiology course as an authentic research experience for 24-48 undergraduate students per year, and perform outreach activities related to this project with K-12 educators. In these ways, the research will help to increase the diversity of students entering the STEM pipeline and leave them better prepared for roles in STEM fields.Changes in gene regulation are a driving force for evolution. Cis regulatory elements are often the cause of evolutionary change when comparing different species, whereas trans regulatory elements are often altered when organisms need to adapt to changing environments. Experimental evolution studies with microbes have begun to probe the role of these factors, but often in unchanging environments where either functional or cis regulatory changes would be favored. The PI will explore the role mutations in trans regulatory elements play in adaptation to a heterogeneous environment by focusing on mutations identified in two regulatory genes, cytR and sspA, that they have shown are adaptive in long-term cultures of Escherichia coli in complex media. To characterize their role in adaptation, the PI will first correlate the adaptive genotype with the transcriptome of the population to identify gene expression changes, and determine which of those changes confer the adaptive phenotype. The PI will then perform experimental evolution on mutant cells to determine how these mutations may change the evolutionary pathways cells can use to adapt to a heterogeneous environment. Understanding how these types of regulatory changes affect adaptation will contribute to the fundamental understanding of evolutionary principles.