Suppr超能文献

复杂代谢反应网络中的进化可塑性和创新。

Evolutionary plasticity and innovations in complex metabolic reaction networks.

机构信息

Department of Biochemistry, University of Zürich, Zürich, Switzerland.

出版信息

PLoS Comput Biol. 2009 Dec;5(12):e1000613. doi: 10.1371/journal.pcbi.1000613. Epub 2009 Dec 18.

Abstract

Genome-scale metabolic networks are highly robust to the elimination of enzyme-coding genes. Their structure can evolve rapidly through mutations that eliminate such genes and through horizontal gene transfer that adds new enzyme-coding genes. Using flux balance analysis we study a vast space of metabolic network genotypes and their relationship to metabolic phenotypes, the ability to sustain life in an environment defined by an available spectrum of carbon sources. Two such networks typically differ in most of their reactions and have few essential reactions in common. Our observations suggest that the robustness of the Escherichia coli metabolic network to mutations is typical of networks with the same phenotype. We also demonstrate that networks with the same phenotype form large sets that can be traversed through single mutations, and that single mutations of different genotypes with the same phenotype can yield very different novel phenotypes. This means that the evolutionary plasticity and robustness of metabolic networks facilitates the evolution of new metabolic abilities. Our approach has broad implications for the evolution of metabolic networks, for our understanding of mutational robustness, for the design of antimetabolic drugs, and for metabolic engineering.

摘要

基因组规模的代谢网络对于酶编码基因的消除具有高度的鲁棒性。它们的结构可以通过消除这些基因的突变和通过添加新的酶编码基因的水平基因转移而迅速进化。使用通量平衡分析,我们研究了代谢网络基因型的广阔空间及其与代谢表型的关系,即能够在可用碳源谱定义的环境中维持生命的能力。两种这样的网络通常在其大多数反应中都不同,并且很少有共同的必需反应。我们的观察结果表明,大肠杆菌代谢网络对突变的鲁棒性是具有相同表型的网络的典型特征。我们还证明,具有相同表型的网络形成了可以通过单个突变遍历的大集合,并且具有相同表型的不同基因型的单个突变可以产生非常不同的新表型。这意味着代谢网络的进化可塑性和鲁棒性促进了新代谢能力的进化。我们的方法对代谢网络的进化、对突变鲁棒性的理解、抗代谢药物的设计以及代谢工程都具有广泛的意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c9e1/2785887/3be1c508f4bd/pcbi.1000613.g001.jpg

相似文献

1
Evolutionary plasticity and innovations in complex metabolic reaction networks.
PLoS Comput Biol. 2009 Dec;5(12):e1000613. doi: 10.1371/journal.pcbi.1000613. Epub 2009 Dec 18.
2
Genotype networks, innovation, and robustness in sulfur metabolism.
BMC Syst Biol. 2011 Mar 7;5:39. doi: 10.1186/1752-0509-5-39.
3
Genotype networks in metabolic reaction spaces.
BMC Syst Biol. 2010 Mar 19;4:30. doi: 10.1186/1752-0509-4-30.
4
Superessential reactions in metabolic networks.
Proc Natl Acad Sci U S A. 2012 May 1;109(18):E1121-30. doi: 10.1073/pnas.1113065109. Epub 2012 Apr 16.
5
The molecular origins of evolutionary innovations.
Trends Genet. 2011 Oct;27(10):397-410. doi: 10.1016/j.tig.2011.06.002. Epub 2011 Aug 27.
6
Environmental versatility promotes modularity in genome-scale metabolic networks.
BMC Syst Biol. 2011 Aug 24;5:135. doi: 10.1186/1752-0509-5-135.
7
Adaptive Genetic Robustness of Escherichia coli Metabolic Fluxes.
Mol Biol Evol. 2016 May;33(5):1164-76. doi: 10.1093/molbev/msw002. Epub 2016 Jan 5.
8
Analysis on relationship between extreme pathways and correlated reaction sets.
BMC Bioinformatics. 2009 Jan 30;10 Suppl 1(Suppl 1):S58. doi: 10.1186/1471-2105-10-S1-S58.
10
Metabolic networks and their evolution.
Adv Exp Med Biol. 2012;751:29-52. doi: 10.1007/978-1-4614-3567-9_2.

引用本文的文献

2
Competition and cooperation: The plasticity of bacterial interactions across environments.
PLoS Comput Biol. 2025 Jul 24;21(7):e1013213. doi: 10.1371/journal.pcbi.1013213. eCollection 2025 Jul.
3
The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family.
bioRxiv. 2025 May 2:2025.01.28.635160. doi: 10.1101/2025.01.28.635160.
5
Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations.
PLoS Comput Biol. 2022 Nov 21;18(11):e1010710. doi: 10.1371/journal.pcbi.1010710. eCollection 2022 Nov.
6
What makes a reaction network "chemical"?
J Cheminform. 2022 Sep 19;14(1):63. doi: 10.1186/s13321-022-00621-8.
7
A synthetic synthesis to explore animal evolution and development.
Philos Trans R Soc Lond B Biol Sci. 2022 Jul 18;377(1855):20200517. doi: 10.1098/rstb.2020.0517. Epub 2022 May 30.
8
Clinically relevant mutations in core metabolic genes confer antibiotic resistance.
Science. 2021 Feb 19;371(6531). doi: 10.1126/science.aba0862.
9
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.
PLoS Comput Biol. 2021 Jan 19;17(1):e1008596. doi: 10.1371/journal.pcbi.1008596. eCollection 2021 Jan.
10
Quantum aspects of evolution: a contribution towards evolutionary explorations of genotype networks via quantum walks.
J R Soc Interface. 2020 Nov;17(172):20200567. doi: 10.1098/rsif.2020.0567. Epub 2020 Nov 11.

本文引用的文献

1
Abundant indispensable redundancies in cellular metabolic networks.
Genome Biol Evol. 2009 Apr 30;1:23-33. doi: 10.1093/gbe/evp002.
2
Latent evolutionary potentials under the neutral mutational drift of an enzyme.
HFSP J. 2007 May;1(1):67-78. doi: 10.2976/1.2739115/10.2976/1. Epub 2007 May 21.
3
Exposing the fitness contribution of duplicated genes.
Nat Genet. 2008 May;40(5):676-81. doi: 10.1038/ng.123. Epub 2008 Apr 13.
4
Predicting synthetic rescues in metabolic networks.
Mol Syst Biol. 2008;4:168. doi: 10.1038/msb.2008.1. Epub 2008 Feb 12.
6
Plasticity of genetic interactions in metabolic networks of yeast.
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2307-12. doi: 10.1073/pnas.0607153104. Epub 2007 Feb 6.
7
Robustness can evolve gradually in complex regulatory gene networks with varying topology.
PLoS Comput Biol. 2007 Feb 2;3(2):e15. doi: 10.1371/journal.pcbi.0030015.
8
Experimental and computational assessment of conditionally essential genes in Escherichia coli.
J Bacteriol. 2006 Dec;188(23):8259-71. doi: 10.1128/JB.00740-06. Epub 2006 Sep 29.
9
Using the topology of metabolic networks to predict viability of mutant strains.
Biophys J. 2006 Sep 15;91(6):2304-11. doi: 10.1529/biophysj.105.080572. Epub 2006 Jun 16.
10
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Mol Syst Biol. 2006;2:2006.0008. doi: 10.1038/msb4100050. Epub 2006 Feb 21.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验