Identifying Mutations that Promote Microbial Evolvability

描述（由申请人提供）：进化能力描述生物体产生后代的能力，这些后代更好地适应给定的环境。随着时间的推移，细菌的慢性感染可能会被突变体控制，因为这些菌株的突变率升高使它们更容易进化。目前对影响其他细胞过程的突变如何影响微生物的可进化性以及在微生物对新环境的长期适应过程中，可进化性在每个突变步骤中是如何变化的知之甚少。拟议的项目包括三个综合研究，旨在确定促进微生物进化的突变。首先，突变积累系将用于建立适应度变化对大肠杆菌菌株相对进化性影响的基线预期。接下来，将重建20年大肠杆菌长期进化实验中的突变历史，以寻找最终成功的突变例子，因为它们相对于竞争基因型增加了可进化性。最后，功能基因组学技术将用于筛选大肠杆菌基因缺失和过表达菌株的文库，以寻找在不同环境下增加可进化性的遗传变化。在这一过程的每一步，标记分化实验将根据测试基因型的局部适应度景观提供一致的可进化性测量。前瞻性的实验设计将进行比较，数据将在这些研究中使用一套共同的群体遗传学模型和模拟来解释。目前，我正在研究大肠杆菌基因调控与可进化性之间的关系，大肠杆菌基因组减少的实验进化，以及使用终止密码子避免来预测基因的必要性。我还扩展了Avida人工生命平台，以研究具有复杂遗传调控的自我复制计算机程序的可进化性。

DESCRIPTION (provided by applicant): Evolvability describes an organism's capacity for producing descendants that are better adapted to a given environment. Chronic infections of bacteria can become dominated by mutators over time because the elevated mutation rates of these strains make them more evolvable. Little is currently known about how mutations affecting other cellular processes impact microbial evolvability and about how evolvability changes at each mutational step during the prolonged adaptation of a microorganism to a novel environment. The proposed project consists of three integrated studies that aim to identify mutations that promote microbial evolvability. First, mutation accumulation lines will be used to establish baseline expectations for the effects of fitness changes on the relative evolvability of Escherichia coli strains. Next, the histories of mutations in a twenty-year E. coli long-term evolution experiment will be reconstructed to search for examples of mutations that were ultimately successful because they increased evolvability relative to competing genotypes. Finally, functional genomics techniques will be used to screen libraries of E. coli gene deletion and overexpression strains for genetic changes that increase evolvability with respect to different environments. At each step in this process, marker divergence experiments will provide a consistent measure of evolvability in terms of the local fitness landscape of a test genotype. Prospective experimental designs will be compared and data will be interpreted throughout these studies using a common set of population genetics models and simulations. Currently, I am investigating relationships between genetic regulation and evolvability in E. coli, the experimental evolution of E. coli with reduced genomes, and using pretermination codon avoidance to predict gene essentiality. I am also extending the Avida artificial life platform to enable studies of the evolvability of self-replicating computer progams exhibiting complex genetic regulation. Relevance: Understanding what kinds of mutations are likely to affect the evolvability of microorganisms has implications for holding the progression of chronic infections and the responses of pathogen populations to new therapeutic pressures in check. Methods for engineering more evolvable domesticated microbes would also be useful for green chemistry, renewable bioenergy, and biotechnology applications related to medicine.