Can TraDIS be used to understand Labortory evolution.

Long term laboratory-based evolution experiments are a powerful tool that are increasingly being used to study fundamental aspects of evolution and to identify genes that contribute to overall fitness under different conditions. However, even with automation, the time that they take to execute limits the extent to which evolution experiments can be used as part of a high throughput approach to understand the links between genotype and phenotype. Mutations that lead to genetic loss of function are frequently selected for in evolution experiments. Thus in principle these experiments could be done more rapidly by starting not with clonal isolates but with dense transposon libraries that will contain loss of function mutations in all non-essential genes. Here, we test this hypothesis by comparing the results of long term (5 month) evolution experiment, in which E. coli was grown with daily transfers in unbuffered LB starting at pH 4.5, with short term (5 and 10 day) experiments on a high density transposon library in the same strain and under the same conditions. We show that there is very significant overlap in the genes and pathways identified using the two methods. Use of this approach thus has the potential to significantly increase the throughput of laboratory-based evolution and enable rapid testing of a wide range of parameters that may have an impact on evolutionary trajectories.

基于实验室的长期进化实验是一类极具价值的研究工具，如今正愈发广泛地被用于探究进化的核心机制，以及鉴定在不同环境条件下对整体适应性具有贡献的基因。然而，即便实现自动化操作，这类实验的耗时瓶颈仍限制了其作为高通量研究手段的应用范围，难以充分支撑对基因型与表型之间关联机制的解析。在进化实验中，引发遗传功能丧失的突变往往会被正向筛选。因此从理论上讲，若摒弃以克隆分离株作为实验起始材料的方案，转而使用覆盖所有非必需基因功能丧失突变的高密度转座子文库，便可大幅缩短实验周期。本研究通过对比两组实验的结果验证该假说：其一为长期（5个月）进化实验，以大肠杆菌（E. coli）为研究对象，在初始pH 4.5的无缓冲LB培养基中每日传代培养；其二为短期（5天与10天）实验，采用同一菌株的高密度转座子文库，并在完全相同的培养条件下开展。结果表明，两种实验方法所鉴定得到的基因与通路存在高度显著的重叠。因此，该方法的应用有望显著提升实验室进化实验的通量，并可快速检测诸多可能影响进化轨迹的参数变量。