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Identifying Mutations that Promote Microbial Evolvability

识别促进微生物进化的突变

基本信息

批准号：
8413011
负责人：
Jeffrey Evan Barrick
金额：
$ 23.06万
依托单位：
UNIVERSITY OF TEXAS AT AUSTIN
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-03-01 至 2015-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8413011
关键词：
Affect Antibiotic Resistance Bacteria Biological Assay Biomedical Research Biotechnology Cell physiology Chemosensitization Chronic Coculture Techniques Collection Defect Disease Progression Environment Escherichia coli Event Evolution Frequencies Gene Amplification Gene Deletion Genetic Genetic Anticipation Genetic Drift Genome Genomic Instability Genotype Human Incidence Infection Instruction Knowledge Laboratories Lead Measures Metabolic Metabolism Microbe Microsatellite Repeats Modeling Molecular Mutation Organism Physiological Point Mutation Population Population Dynamics Population Genetics Relative (related person)Reporter Research Series Speed Statistical Methods Systems Biology Testing Time Variant abstracting case finding deep sequencing expectation experience fitness genome sequencing improved innovation mathematical model microbial microorganism pathogen research study simulation success trend

项目摘要

Evolvability describes an organism's capacity for producing descendants that are better adapted to a given environment. Mutations that elevate overall point mutation rates can make bacteria more evolvable under certain circumstances and consequently speed the progression of chronic infections and increase the incidence of antibiotic resistance. Little is currently known about how mutations affecting other cellular processes impact microbial evolvability or about how evolvability typically varies as microorganisms experience random mutations due to genetic drift or adapt by beneficial mutations to higher fitness. The proposed research systematically investigates how different kinds of mutations affect the evolvability of Escherichia coli in laboratory evolution experiments. The first aim is to test three strain series differing by predominantly deleterious, beneficial, or random mutations to establish baseline expectations. The second aim is to recover genotypes that eventually prevail over competitors of higher fitness because they are more evolvable by chronicling mutation dynamics in evolution experiments using deep sequencing, highthroughput genotyping, and deletion and microsatellite markers. The third aim is to construct chromosomal reporters with selectable markers for measuring gene amplification and deletion rates. These reporters will be used to isolate new kinds of genomic instability mutators and to examine whether a similar defect potentiated the evolution of a rare metabolic innovation in a 20-year evolution experiment. Throughout, evolvability will be measured on multiple time scales by comparing the initial divergence of marker trajectories in replicate evolution experiments to population genetic simulations and by performing co-culture competition assays between endpoint isolates and a reference strain. When a strain is found with unusually high or low evolvability, the causal mutation will be identified by genome re-sequencing, and its physiological consequences will be investigated to find out why it affects evolutionary potential.

可进化性描述了生物体产生后代的能力，这些后代更好地适应给定的环境。提高总体点突变率的突变可以使细菌在某些情况下，从而加速慢性感染的进展并增加抗生素耐药发生率。目前对突变如何影响其他细胞知之甚少过程影响微生物的进化性，或关于微生物的进化性通常是如何变化的经历遗传漂移导致的随机突变，或通过有益的突变适应更高的适应度。这项拟议的研究系统地研究了不同类型的突变是如何影响实验室进化实验中的大肠埃希氏菌。第一个目标是测试三个不同于主要是有害的、有益的或随机的突变以建立基线预期。第二目标是恢复最终战胜健康水平更高的竞争者的基因类型，因为它们更通过记录进化实验中的突变动态进行进化，使用深度测序，高通量基因分型、缺失和微卫星标记。第三个目标是构建染色体记者使用可选择的标记来测量基因扩增和缺失率。这些记者将用于分离新的基因组不稳定突变子，并检测类似的缺陷在20年的进化实验中强化了一种罕见的新陈代谢创新的进化。在整个过程中，进化性将在多个时间尺度上通过比较复制进化实验中的标记轨迹到群体遗传模拟，并通过执行终点分离株和参考菌株之间的共培养竞争分析。当发现一种带有异常高或低的进化性，原因突变将通过基因组重新测序来识别，其将对生理后果进行调查，以找出为什么它会影响进化潜力。

项目成果

期刊论文数量（20）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli.

DOI：
10.1534/g3.111.000406
发表时间：
2011-08-01
期刊：
G3 (Bethesda, Md.)
影响因子：
0
作者：
Wielgoss S;Barrick JE;Tenaillon O;Cruveiller S;Chane-Woon-Ming B;Médigue C;Lenski RE;Schneider D
通讯作者：
Schneider D

Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution.

基因组不稳定性介导贝氏不动杆菌 ADP1 在实验室进化过程中关键性状的丧失。

DOI：
10.1128/jb.02263-14
发表时间：
2015
期刊：
Journal of bacteriology
影响因子：
3.2
作者：
Renda,BrianA;Dasgupta,Aurko;Leon,Dacia;Barrick,JeffreyE
通讯作者：
Barrick,JeffreyE

Tempo and mode of genome evolution in a 50,000-generation experiment.

DOI：
10.1038/nature18959
发表时间：
2016-08-11
期刊：
Nature
影响因子：
64.8
作者：
Tenaillon O;Barrick JE;Ribeck N;Deatherage DE;Blanchard JL;Dasgupta A;Wu GC;Wielgoss S;Cruveiller S;Médigue C;Schneider D;Lenski RE
通讯作者：
Lenski RE

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.