Pseudogene repair driven by selection pressure applied in experimental evolution

We performed evolution of ∆menF∆entC strain of Escherichia coli K12 MG1655 to study how the system adapt to the loss of siderophore biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring. Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation. ALE is the acronym for adaptive laboratory evolution. ALE_39.91, ALE_29.82 and ALE_30.83 are the independent biological replicates of ∆menF∆entC which are evolved in our laboratory to study how the strains adapt to the loss of the menF and entC genes. Similarly, ALE_36.86, ALE_37.25 and ALE_38.28 are the independent biological replicates of ∆menF∆entC∆ubiC which are evolved in our laboratory to study how the strains adapt to the loss of the menF, entC and ubiC genes.

本研究对大肠杆菌（Escherichia coli）K12 MG1655的∆menF∆entC菌株开展适应性进化实验，旨在解析该系统应对铁载体生物合成通路缺失的适应机制。通过RNA测序（RNA-Seq）检测潜在的转录重编程事件。针对添加不同营养补充剂的大肠杆菌培养物开展生长实验，实验设置生物学重复。从对数生长期中期的培养物中提取总RNA，用于构建RNA测序文库。ALE为适应性实验室进化（adaptive laboratory evolution）的英文缩写。ALE_39.91、ALE_29.82与ALE_30.83为∆menF∆entC菌株的独立生物学重复株系，均由本实验室通过适应性进化获得，用于探究菌株缺失menF与entC基因后的适应机制。同理，ALE_36.86、ALE_37.25与ALE_38.28为∆menF∆entC∆ubiC菌株的独立生物学重复株系，同样由本实验室通过适应性进化获得，用于探究菌株缺失menF、entC与ubiC基因后的适应机制。