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小突变在抗生素抗性酶中提供适应性益处。

Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme.

机构信息

Laboratory of Genetics, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, The Netherlands.

Institute for Translational Vaccinology, 3721MA Bilthoven, The Netherlands.

出版信息

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12773-12778. doi: 10.1073/pnas.1712999114. Epub 2017 Nov 13.

Abstract

Populations with large mutation supplies adapt via the "greedy" substitution of the fittest genotype available, leading to fast and repeatable short-term responses. At longer time scales, smaller mutation supplies may in theory lead to larger improvements when distant high-fitness genotypes more readily evolve from lower-fitness intermediates. Here we test for long-term adaptive benefits from small mutation supplies using in vitro evolution of an antibiotic-degrading enzyme in the presence of a novel antibiotic. Consistent with predictions, large mutant libraries cause rapid initial adaptation via the substitution of cohorts of mutations, but show later deceleration and convergence. Smaller libraries show on average smaller initial, but also more variable, improvements, with two lines yielding alleles with exceptionally high resistance levels. These two alleles share three mutations with the large-library alleles, which are known from previous work, but also have unique mutations. Replay evolution experiments and analyses of the adaptive landscape of the enzyme suggest that the benefit resulted from a combination of avoiding mutational cohorts leading to local peaks and chance. Our results demonstrate adaptive benefits from limited mutation supplies on a rugged fitness landscape, which has implications for artificial selection protocols in biotechnology and argues for a better understanding of mutation supplies in clinical settings.

摘要

具有大量突变供应的种群通过“贪婪”地替换最适合的基因型来适应,从而导致快速且可重复的短期响应。在更长的时间尺度上,当来自低适应度中间状态的更远高适应度基因型更容易进化时,较小的突变供应理论上可能会带来更大的改进。在这里,我们使用新型抗生素存在的情况下,通过体外进化抗生素降解酶来测试小突变供应的长期适应性益处。与预测一致,大型突变文库通过突变群的替换导致快速的初始适应,但随后会减速和收敛。较小的文库平均初始改进较小,但也更具可变性,两条线产生了具有异常高抗性水平的等位基因。这两个等位基因与来自之前工作的大文库等位基因共享三个突变,但也有独特的突变。重演进化实验和酶适应性景观的分析表明,这种好处来自于避免导致局部峰值和机会的突变群的组合。我们的结果表明,在崎岖的适应度景观上,有限的突变供应具有适应性益处,这对生物技术中的人工选择方案具有重要意义,并呼吁更好地理解临床环境中的突变供应。

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本文引用的文献

1
Competition along trajectories governs adaptation rates towards antimicrobial resistance.
Nat Ecol Evol. 2016 Nov 21;1(1):7. doi: 10.1038/s41559-016-0007.
2
Evolutionary Trajectories to Antibiotic Resistance.
Annu Rev Microbiol. 2017 Sep 8;71:579-596. doi: 10.1146/annurev-micro-090816-093813. Epub 2017 Jul 11.
3
Mistranslation can enhance fitness through purging of deleterious mutations.
Nat Commun. 2017 May 19;8:15410. doi: 10.1038/ncomms15410.
4
Genotypic Complexity of Fisher's Geometric Model.
Genetics. 2017 Jun;206(2):1049-1079. doi: 10.1534/genetics.116.199497. Epub 2017 Apr 26.
5
Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase.
Mol Biol Evol. 2017 May 1;34(5):1040-1054. doi: 10.1093/molbev/msx053.
6
Tempo and mode of genome evolution in a 50,000-generation experiment.
Nature. 2016 Aug 11;536(7615):165-70. doi: 10.1038/nature18959. Epub 2016 Aug 1.
8
How mutational epistasis impairs predictability in protein evolution and design.
Protein Sci. 2016 Jul;25(7):1260-72. doi: 10.1002/pro.2876. Epub 2016 Jan 22.
10
Methods for the directed evolution of proteins.
Nat Rev Genet. 2015 Jul;16(7):379-94. doi: 10.1038/nrg3927. Epub 2015 Jun 9.

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