和百欧博伟生物一起探索大肠杆菌基因组演化的速度和模式！
中国微生物菌种查询网 / 2018-12-05 09:25:32
大肠杆菌的主要基因型包括：与基因重组相关的基因型（如recA、recB和recC等）、与甲基化相关的基因型（如dam、dcm、mcrA、mcrB和C、mrr和hsdM等）、与点突变相关的基因型（如mutS、mutT、dut、ung和uvrB等）、与核酸内切酶相关的基因型（如hsdR、hsdS和endA等）、与终止密码子相关的基因型（如supE和supF）、与抗药性相关的基因型（gyrA、rpsl和Tn5等）及其他与能量代谢、氨基酸代谢、维生素代谢等相关的基因型。基因工程中，经常使用的大肠杆菌几乎都来自于K-12菌株，也使用由B株和C株来源的大肠杆菌。
大肠杆菌克隆的基因组分别在2,000代、5,000代、10,000代、15,000代、20,000代和 40,000代后被取样。适应性的发展加速极快，但基因组演化在20,000代几乎是不变的。这样的一致性被认为是中性演化的特点，但来自几个方面的证据都表明，这些突变大部分都是有益的。这个种群后来突变速度加快，并且积累了数百个另外的、以中性为特征的突变。显然，基因组演化和适应性演化之间的耦合是一个复杂的问题。
原始出处：
Nature 461, 1243-1247 (29 October 2009) | doi:10.1038/nature08480
Genome evolution and adaptation in a long-term experiment with Escherichia coli
Jeffrey E. Barrick1,7, Dong Su Yu2,3,7, Sung Ho Yoon2, Haeyoung Jeong2, Tae Kwang Oh2,4, DominIQue Schneider5, Richard E. Lenski1 & Jihyun F. Kim2,6
1 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
2 Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea
3 Department of Computer Science and Engineering, Chungnam National University, Yuseong, Daejeon 305-764, Korea
4 21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon 305-806, Korea
5 Institut Jean Roget, Laboratoire Adaptation et Pathogénie des Microorganismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble cedex 9, France
6 Functional Genomics Program, School of Science, University of Science and Technology, Yuseong, Daejeon 305-333, Korea
7 These authors contributed equally to this work.
Correspondence to: Richard E. Lenski1Jihyun F. Kim2,6 Correspondence and requests for materials should be addressed to R.E.L. or J.F.K.
The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.