通过定向进化探索蛋白质适应度景观。
Exploring protein fitness landscapes by directed evolution.
作者信息
Romero Philip A, Arnold Frances H
机构信息
Division of Chemistry and Chemical Engineering, 21041, California Institute of Technology, Pasadena, California 91125, USA.
出版信息
Nat Rev Mol Cell Biol. 2009 Dec;10(12):866-76. doi: 10.1038/nrm2805.
Abstract
Directed evolution circumvents our profound ignorance of how a protein's sequence encodes its function by using iterative rounds of random mutation and artificial selection to discover new and useful proteins. Proteins can be tuned to adapt to new functions or environments by simple adaptive walks involving small numbers of mutations. Directed evolution studies have shown how rapidly some proteins can evolve under strong selection pressures and, because the entire 'fossil record' of evolutionary intermediates is available for detailed study, they have provided new insight into the relationship between sequence and function. Directed evolution has also shown how mutations that are functionally neutral can set the stage for further adaptation.
摘要
定向进化通过随机突变和人工选择的迭代轮次来发现新的有用蛋白质，从而规避了我们对蛋白质序列如何编码其功能的极度无知。通过涉及少量突变的简单适应性进化过程，蛋白质可以被调整以适应新功能或新环境。定向进化研究表明，在强大的选择压力下，一些蛋白质能够多么迅速地进化，而且由于进化中间体的完整“化石记录”可供详细研究，这些研究为序列与功能之间的关系提供了新的见解。定向进化还表明，功能中性的突变如何能够为进一步的适应性变化奠定基础。
相似文献
1
Exploring protein fitness landscapes by directed evolution.通过定向进化探索蛋白质适应度景观。
Nat Rev Mol Cell Biol. 2009 Dec;10(12):866-76. doi: 10.1038/nrm2805.
2
How proteins adapt: lessons from directed evolution.蛋白质如何适应：定向进化的经验教训。
Cold Spring Harb Symp Quant Biol. 2009;74:41-6. doi: 10.1101/sqb.2009.74.046. Epub 2010 Apr 22.
3
In the light of directed evolution: pathways of adaptive protein evolution.鉴于定向进化：适应性蛋白质进化的途径。
Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1(Suppl 1):9995-10000. doi: 10.1073/pnas.0901522106. Epub 2009 Jun 15.
4
Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.适应性增强进化过程中中性突变的分子钟
PLoS Genet. 2015 Jul 15;11(7):e1005392. doi: 10.1371/journal.pgen.1005392. eCollection 2015 Jul.
5
Shifting Fitness and Epistatic Landscapes Reflect Trade-offs along an Evolutionary Pathway.适应性转移与上位性景观反映了进化路径上的权衡。
J Mol Biol. 2016 Jul 3;428(13):2730-43. doi: 10.1016/j.jmb.2016.04.033. Epub 2016 May 10.
6
Rational evolutionary design: the theory of in vitro protein evolution.理性进化设计：体外蛋白质进化理论
Adv Protein Chem. 2000;55:79-160. doi: 10.1016/s0065-3233(01)55003-2.
7
Contingency and chance erase necessity in the experimental evolution of ancestral proteins.偶然和机遇在祖先蛋白质的实验进化中消除了必然性。
Elife. 2021 Jun 1;10:e67336. doi: 10.7554/eLife.67336.
8
Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races.抗病毒限制的突变弹性有利于灵长类动物 TRIM5α 在宿主-病毒进化军备竞赛中。
Elife. 2020 Sep 15;9:e59988. doi: 10.7554/eLife.59988.
9
Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes.在崎岖的地形上获得更高的适应性：反转突变为 NK 适应性景观中的更适应的适应性峰开辟了通道。
PLoS Comput Biol. 2022 Oct 31;18(10):e1010647. doi: 10.1371/journal.pcbi.1010647. eCollection 2022 Oct.
10
Colloquium papers: Adaptive landscapes and protein evolution.学术研讨会论文：适应性景观与蛋白质进化
Proc Natl Acad Sci U S A. 2010 Jan 26;107 Suppl 1(Suppl 1):1747-51. doi: 10.1073/pnas.0906192106. Epub 2009 Sep 30.
引用本文的文献
1
Combing Directed Enzyme Evolution with Metabolic Engineering to Develop Efficient Microbial Cell Factories.将定向酶进化与代谢工程相结合以开发高效的微生物细胞工厂。
Chem Bio Eng. 2025 May 1;2(8):449-459. doi: 10.1021/cbe.5c00002. eCollection 2025 Aug 28.
2
Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function.蛋白质催化中的动态能量转换：从布朗运动到酶功能
Comput Struct Biotechnol J. 2025 Jul 30;27:3337-3369. doi: 10.1016/j.csbj.2025.07.050. eCollection 2025.
3
CRISPR/Cas system-guided plasmid mutagenesis without sequence restriction.CRISPR/Cas系统引导的无序列限制的质粒诱变
Fundam Res. 2022 Jul 15;5(4):1481-1487. doi: 10.1016/j.fmre.2022.06.017. eCollection 2025 Jul.
4
PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context.PreMode通过对蛋白质序列和结构背景进行深度图表示学习来预测错义变体的作用模式。
Nat Commun. 2025 Aug 5;16(1):7189. doi: 10.1038/s41467-025-62318-4.
5
Considering Metabolic Context in Enzyme Evolution and Design.酶进化与设计中的代谢背景考量
Biochemistry. 2025 Aug 19;64(16):3495-3507. doi: 10.1021/acs.biochem.5c00165. Epub 2025 Aug 5.
6
Directed evolution of α-ketoisovalerate decarboxylase for improved isobutanol and 3-methyl-1-butanol production in cyanobacteria.用于提高蓝细菌中异丁醇和3-甲基-1-丁醇产量的α-酮异戊酸脱羧酶的定向进化
Biotechnol Biofuels Bioprod. 2025 Jul 31;18(1):84. doi: 10.1186/s13068-025-02687-6.
7
Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.通过结构动力学进行蛋白质催化：酶系统中能量转换的全面分析及其计算局限性
Pharmaceuticals (Basel). 2025 Jun 24;18(7):951. doi: 10.3390/ph18070951.
8
Efficient biodegradation and upcycling of polyethylene terephthalate mediated by cell-factories.细胞工厂介导的聚对苯二甲酸乙二酯的高效生物降解及升级再造
Front Microbiol. 2025 Jul 2;16:1599470. doi: 10.3389/fmicb.2025.1599470. eCollection 2025.
9
A generalized platform for artificial intelligence-powered autonomous enzyme engineering.用于人工智能驱动的自主酶工程的通用平台。
Nat Commun. 2025 Jul 1;16(1):5648. doi: 10.1038/s41467-025-61209-y.
10
Generating combinatorial diversity via engineered V(D)J-like recombination in Saccharomyces cerevisiae.通过酿酒酵母中工程化的V(D)J样重组产生组合多样性。
Nat Commun. 2025 Jul 1;16(1):5688. doi: 10.1038/s41467-025-61206-1.
本文引用的文献
1
Evolution and speciation on holey adaptive landscapes.多孔适应景观中的进化和物种形成。
Trends Ecol Evol. 1997 Aug;12(8):307-12. doi: 10.1016/S0169-5347(97)01098-7.
2
Stability effects of mutations and protein evolvability.突变的稳定性效应与蛋白质的进化能力
Curr Opin Struct Biol. 2009 Oct;19(5):596-604. doi: 10.1016/j.sbi.2009.08.003. Epub 2009 Sep 16.
3
Protein sectors: evolutionary units of three-dimensional structure.蛋白质结构域：三维结构的进化单元。
Cell. 2009 Aug 21;138(4):774-86. doi: 10.1016/j.cell.2009.07.038.
4
Constructing and exploiting the fluorescent protein paintbox (Nobel Lecture).构建与利用荧光蛋白颜料盒（诺贝尔演讲）
Angew Chem Int Ed Engl. 2009;48(31):5612-26. doi: 10.1002/anie.200901916.
5
In the light of directed evolution: pathways of adaptive protein evolution.鉴于定向进化：适应性蛋白质进化的途径。
Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1(Suppl 1):9995-10000. doi: 10.1073/pnas.0901522106. Epub 2009 Jun 15.
6
Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies.来自两种不同定向进化策略的产生具有改进底物特异性突变体的酶残基分布。
Protein Eng Des Sel. 2009 Jul;22(7):401-11. doi: 10.1093/protein/gzp020. Epub 2009 Jun 5.
7
Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting.通过荧光激活细胞分选对正交核苷类似物激酶进行定向进化。
Nucleic Acids Res. 2009 Jul;37(13):4472-81. doi: 10.1093/nar/gkp400. Epub 2009 May 27.
8
Latent evolutionary potentials under the neutral mutational drift of an enzyme.一种酶在中性突变漂变下的潜在进化潜力。
HFSP J. 2007 May;1(1):67-78. doi: 10.2976/1.2739115/10.2976/1. Epub 2007 May 21.
9
Protein dynamism and evolvability.蛋白质的动态性与可进化性。
Science. 2009 Apr 10;324(5924):203-7. doi: 10.1126/science.1169375.
10
A family of thermostable fungal cellulases created by structure-guided recombination.通过结构引导重组产生的一族热稳定真菌纤维素酶。
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5610-5. doi: 10.1073/pnas.0901417106. Epub 2009 Mar 23.
Zotero 插件