和百歐博偉生物一起探索大腸桿菌基因組演化的速度和模式！
中國微生物菌種查詢網(wǎng) / 2018-12-05 09:25:32
大腸桿菌的主要基因型包括：與基因重組相關(guān)的基因型（如recA、recB和recC等）、與甲基化相關(guān)的基因型（如dam、dcm、mcrA、mcrB和C、mrr和hsdM等）、與點(diǎn)突變相關(guān)的基因型（如mutS、mutT、dut、ung和uvrB等）、與核酸內(nèi)切酶相關(guān)的基因型（如hsdR、hsdS和endA等）、與終止密碼子相關(guān)的基因型（如supE和supF）、與抗藥性相關(guān)的基因型（gyrA、rpsl和Tn5等）及其他與能量代謝、氨基酸代謝、維生素代謝等相關(guān)的基因型。基因工程中，經(jīng)常使用的大腸桿菌幾乎都來自于K-12菌株，也使用由B株和C株來源的大腸桿菌。
大腸桿菌克隆的基因組分別在2,000代、5,000代、10,000代、15,000代、20,000代和 40,000代后被取樣。適應(yīng)性的發(fā)展加速極快，但基因組演化在20,000代幾乎是不變的。這樣的一致性被認(rèn)為是中性演化的特點(diǎn)，但來自幾個方面的證據(jù)都表明，這些突變大部分都是有益的。這個種群后來突變速度加快，并且積累了數(shù)百個另外的、以中性為特征的突變。顯然，基因組演化和適應(yīng)性演化之間的耦合是一個復(fù)雜的問題。
原始出處：
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.