E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli.
E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli.
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E Unibus Plurum：大肠杆菌中实验进化的多态性的基因组分析。
DOI：
10.1371/journal.pgen.1000713
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Rosenzweig F
中科院分区：
文献类型：
--
作者：
Kinnersley MA;Holben WE;Rosenzweig F
由单个克隆建立并在资源限制下繁殖的微生物种群可能会变得多态。我们试图阐明遗传机制，即在葡萄糖限制下，大肠杆菌中的多态进化并由于多个适应性克隆之间的交叉喂养而持续存在。除了显性克隆中29kb的缺失，没有大规模的基因组变化将进化克隆与它们的共同祖先区分开来。利用在葡萄糖限制下单独培养的共同进化克隆的转录图谱，我们发现了180个基因相对于在相似条件下生长的共同祖先在表达上发生了显着变化。其中90个基因在所有克隆中都有相似的表达，并且许多受影响的基因(如mglBAC、mglD和lamb)都在由CRP和/或rpos协调调控的操纵子中。虽然剩下的显著差异是克隆特异性的，但93%的表达差异是由大多数克隆显示的，其中许多克隆受全球调控因子CRP和CpxR的控制。当对共同培养的适应性克隆进行转录谱分析时，没有许多区别于分离培养的大多数克隆的表达差异，这表明CpxR可能被共培养中交叉饲养的菌株清除的溢出代谢物激活。相对于它们的共同祖先，适应性克隆之间的共同表达差异部分归因于反式作用全球调节因子rpos和顺式作用调节因子mglO的早期共同突变。差异克隆的基因表达差异可以部分解释为反式作用调节子MALT和glpK以及ACS顺式作用序列的突变。在创始人中，ACs(乙酰辅酶A合成酶)的顺式调节突变和glpR(甘油-3-磷酸抑制物)的结构突变可能有利于依靠溢出代谢物茁壮成长的专家的进化。后来出现的导致专业化的突变强调了这个系统中补偿性突变的重要性，而不是功能获得性突变的重要性。综上所述，这些发现强调了调控变化、创始人基因型和生物环境在微生物适应性进化中的重要性。无性生殖物种的实验进化表明，多种基因类型可以从一个单一祖先产生并稳定共存(E Unibus Plum)。虽然环境的异质性促进了这种现象，但这种现象也发生在简单、同质的环境中，提供了单一的限制性营养物质。我们试图发现使单个克隆建立的大肠杆菌种群成为由多个克隆组成的相互作用的群落的遗传机制。这一群体的创始人含有破坏醋酸盐和甘油代谢调节的突变，并可能有利于交叉喂养的进化。适应性克隆共享其他地方显示的顺式和反式调节突变，以增强葡萄糖限制下的适应性。区分适应性克隆和专家基础进化的某些突变是补偿性的，而不是功能获得，我们检测到的所有突变都导致了基因表达的变化，而不是蛋白质结构的变化。进化克隆相对于其共同祖先表现出共同的和克隆特有的基因表达变化；单独培养的显性克隆的基因表达模式不同于与以其溢出的代谢物为食的变异体培养时观察到的模式。这些发现阐明了方正基因、差异基因调控和生物环境在细菌适应性进化中所起的作用。
Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of the genes affected (e.g., mglBAC, mglD, and lamB) are in operons coordinately regulated by CRP and/or rpoS. While the remaining significant expression differences were clone-specific, 93% were exhibited by the majority clone, many of which are controlled by global regulators, CRP and CpxR. When transcriptional profiling was performed on adaptive clones cultured together, many expression differences that distinguished the majority clone cultured in isolation were absent, suggesting that CpxR may be activated by overflow metabolites removed by cross-feeding strains in co-culture. Relative to their common ancestor, shared expression differences among adaptive clones were partly attributable to early-arising shared mutations in the trans-acting global regulator, rpoS, and the cis-acting regulator, mglO. Gene expression differences that distinguished clones may in part be explained by mutations in trans-acting regulators malT and glpK, and in cis-acting sequences of acs. In the founder, a cis-regulatory mutation in acs (acetyl CoA synthetase) and a structural mutation in glpR (glycerol-3-phosphate repressor) likely favored evolution of specialists that thrive on overflow metabolites. Later-arising mutations that led to specialization emphasize the importance of compensatory rather than gain-of-function mutations in this system. Taken together, these findings underscore the importance of regulatory change, founder genotype, and the biotic environment in the adaptive evolution of microbes. Experimental evolution of asexual species has shown that multiple genotypes can arise from a single ancestor and stably coexist (e unibus plurum). Although facilitated by environmental heterogeneity, this phenomenon also occurs in simple, homogeneous environments provisioned with a single limiting nutrient. We sought to discover genetic mechanisms that enabled an E. coli population founded by a single clone to become an interacting community composed of multiple clones. The founder of this population contained mutations that impair regulation of acetate and glycerol metabolism and likely favored the evolution of cross-feeding. Adaptive clones share cis- and trans-regulatory mutations shown elsewhere to enhance fitness under glucose limitation. Certain mutations that distinguish adaptive clones and underlie evolution of specialists were compensatory rather than gain-of-function, and all that we detected resulted in gene expression changes rather than protein structure changes. Evolved clones exhibited both common and clone-specific gene expression changes relative to their common ancestor; the pattern of gene expression in the dominant clone cultured alone differed from the pattern observed when it was cultured with variants feeding on its overflow metabolites. These findings illuminate the roles played by founder genotype, differential gene regulation, and the biotic environment in the adaptive evolution of bacteria.
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DOI：
10.1073/pnas.37.3.146
发表时间：
1951-01-01
影响因子：
11.1
作者：
ATWOOD, KC;SCHNEIDER, LK;RYAN, FJ
通讯作者：
RYAN, FJ
影响因子：
3.3
作者：
DYKHUIZEN, D
通讯作者：
DYKHUIZEN, D
两个层面的进化：基因和形态。
影响因子：
9.8
作者：
Carroll, SB
通讯作者：
Carroll, SB
影响因子：
3.6
作者：
Browning, DF;Beatty, CM;Wolfe, AJ
通讯作者：
Wolfe, AJ
影响因子：
3.2
作者：
DARDONVILLE, B;RAIBAUD, O
通讯作者：
RAIBAUD, O