稳健性和可变性在遗传密码起源与进化中的作用。
The role of robustness and changeability on the origin and evolution of genetic codes.
作者信息
Maeshiro T, Kimura M
机构信息
Department 6, ATR Human Information Processing Research Laboratories, 2-2 Hikaridai, Seika, Soraku, Kyoto, 619-0237 Japan.
出版信息
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5088-93. doi: 10.1073/pnas.95.9.5088.
Abstract
We propose that an essential factor on the origin of genetic codes is a balanced accomplishment of robustness and changeability, two antithetical, but fundamental, properties for the survival and evolution of organisms. These measures are defined as the intrinsic properties of genetic codes. An evaluation of these properties explains the structural regularity of genetic codes, estimates the order of codon reassignment in deviant codes, and predicts the most probable deviant codes that exist. The enumeration of genetic codes that could have evolved from the standard genetic code under the selection pressure on robustness and changeability strongly limits the freedom of codon reassignments. The codon reassignments of all currently known deviant genetic codes belong to this predicted evolutionary path, and they generally give the highest improvements on robustness and changeability.
摘要
我们提出，遗传密码起源的一个关键因素是稳健性和可变性的平衡实现，这是生物体生存和进化的两个相反但基本的特性。这些特性被定义为遗传密码的内在属性。对这些属性的评估解释了遗传密码的结构规律性，估计了异常密码中密码子重新分配的顺序，并预测了可能存在的最可能的异常密码。在稳健性和可变性的选择压力下，从标准遗传密码进化而来的遗传密码的列举极大地限制了密码子重新分配的自由度。所有目前已知的异常遗传密码的密码子重新分配都属于这一预测的进化路径，并且它们通常在稳健性和可变性方面有最高的提升。
相似文献
1
The role of robustness and changeability on the origin and evolution of genetic codes.稳健性和可变性在遗传密码起源与进化中的作用。
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5088-93. doi: 10.1073/pnas.95.9.5088.
2
Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.遗传密码的进化：在崎岖的适应度景观中，随机密码针对翻译错误的稳健性进行的部分优化。
Biol Direct. 2007 Oct 23;2:24. doi: 10.1186/1745-6150-2-24.
3
Mitochondrial genetic codes evolve to match amino acid requirements of proteins.线粒体遗传密码不断进化以匹配蛋白质的氨基酸需求。
J Mol Evol. 2005 Jan;60(1):128-39. doi: 10.1007/s00239-004-0077-9.
4
A multiobjective approach to the genetic code adaptability problem.一种解决遗传密码适应性问题的多目标方法。
BMC Bioinformatics. 2015 Feb 19;16:52. doi: 10.1186/s12859-015-0480-9.
5
Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code.许多替代和理论遗传密码比标准遗传密码更能耐受氨基酸替换。
J Theor Biol. 2019 Mar 7;464:21-32. doi: 10.1016/j.jtbi.2018.12.030. Epub 2018 Dec 21.
6
Simulated evolution applied to study the genetic code optimality using a model of codon reassignments.模拟进化在重新分配密码子模型中用于研究遗传密码最优性。
BMC Bioinformatics. 2011 Feb 21;12:56. doi: 10.1186/1471-2105-12-56.
7
Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.扩展遗传密码为大肠杆菌对利福平耐药性创造了新的突变途径。
Mol Biol Evol. 2016 Aug;33(8):2054-63. doi: 10.1093/molbev/msw094. Epub 2016 May 9.
8
The neutral emergence of error minimized genetic codes superior to the standard genetic code.错误的中性出现使遗传密码优于标准遗传密码的情况降至最低。
J Theor Biol. 2016 Nov 7;408:237-242. doi: 10.1016/j.jtbi.2016.08.022. Epub 2016 Aug 17.
9
Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria.呼吸链复合物中适应性抗氧化蛋氨酸积累解释了线粒体中异常遗传密码的使用。
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16496-501. doi: 10.1073/pnas.0802779105. Epub 2008 Oct 22.
10
Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.基于比对和无比对的方法在核遗传密码和线粒体遗传密码之间的分裂处，与由终止密码子编码的氨基酸的实验数据相吻合。
Biosystems. 2018 May;167:33-46. doi: 10.1016/j.biosystems.2018.03.002. Epub 2018 Apr 3.
引用本文的文献
1
Robust genetic codes enhance protein evolvability.稳健的遗传密码增强了蛋白质的可进化性。
PLoS Biol. 2024 May 16;22(5):e3002594. doi: 10.1371/journal.pbio.3002594. eCollection 2024 May.
2
Phenotypic mutations contribute to protein diversity and shape protein evolution.表型突变有助于蛋白质多样性，并塑造蛋白质进化。
Protein Sci. 2022 Sep;31(9):e4397. doi: 10.1002/pro.4397.
3
Increased RNA virus population diversity improves adaptability.病毒群体多样性增加可提高适应性。
Sci Rep. 2021 Mar 25;11(1):6824. doi: 10.1038/s41598-021-86375-z.
4
The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences.标准遗传密码有助于探索功能核苷酸序列的空间。
J Mol Evol. 2018 Jul;86(6):325-339. doi: 10.1007/s00239-018-9852-x. Epub 2018 Jun 29.
5
Phenotypic plasticity and modularity allow for the production of novel mosaic phenotypes in ants.表型可塑性和模块性使得蚂蚁能够产生新的镶嵌表型。
Evodevo. 2015 Dec 1;6:36. doi: 10.1186/s13227-015-0031-5. eCollection 2015.
6
Neutral and weakly nonneutral sequence variants may define individuality.中性和弱非中性序列变异可能定义个体性。
Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14255-60. doi: 10.1073/pnas.1216613110. Epub 2013 Aug 12.
7
The rules of variation: amino acid exchange according to the rotating circular genetic code.变则规则：氨基酸按照旋转循环遗传密码进行交换。
J Theor Biol. 2010 Jun 7;264(3):711-21. doi: 10.1016/j.jtbi.2010.03.046. Epub 2010 Apr 3.
8
Certain non-standard coding tables appear to be more robust to error than the standard genetic code.某些非标准编码表似乎比标准遗传密码更能抵抗错误。
J Mol Evol. 2010 Jan;70(1):13-28. doi: 10.1007/s00239-009-9303-9. Epub 2009 Dec 10.
9
Codon size reduction as the origin of the triplet genetic code.密码子大小缩减作为三联体遗传密码的起源。
PLoS One. 2009 May 27;4(5):e5708. doi: 10.1371/journal.pone.0005708.
10
A statistical analysis of the robustness of alternate genetic coding tables.对替代遗传编码表稳健性的统计分析。
Int J Mol Sci. 2008 May;9(5):679-697. doi: 10.3390/ijms9050679. Epub 2008 May 2.
本文引用的文献
1
Dramatic events in ciliate evolution: alteration of UAA and UAG termination codons to glutamine codons due to anticodon mutations in two Tetrahymena tRNAs.纤毛生物进化中的戏剧性事件：由于两种四膜虫 tRNA 的反密码子突变，UAA 和 UAG 终止密码子改变为谷氨酰胺密码子。
EMBO J. 1986 Jun;5(6):1307-11. doi: 10.1002/j.1460-2075.1986.tb04360.x.
2
Phylogenetic methods come of age: testing hypotheses in an evolutionary context.系统发育方法已然成熟：在进化背景下检验假设。
Science. 1997 Apr 11;276(5310):227-32. doi: 10.1126/science.276.5310.227.
3
Directional mutation pressure, mutator mutations, and dynamics of molecular evolution.定向突变压力、突变体突变与分子进化动力学
J Mol Evol. 1993 Aug;37(2):137-53. doi: 10.1007/BF02407349.
4
On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code.关于遗传密码进化中氨基酸间物理化学距离的优化
J Theor Biol. 1994 May 7;168(1):43-51. doi: 10.1006/jtbi.1994.1086.
5
Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates.灵长类非编码核苷酸序列中插入和缺失的进化速率。
Mol Biol Evol. 1994 May;11(3):504-12. doi: 10.1093/oxfordjournals.molbev.a040130.
6
Genetic code deviations in the ciliates: evidence for multiple and independent events.纤毛虫中的遗传密码偏差：多次独立事件的证据。
EMBO J. 1995 Jul 3;14(13):3262-7. doi: 10.1002/j.1460-2075.1995.tb07329.x.
7
Role of minimization of chemical distances between amino acids in the evolution of the genetic code.氨基酸之间化学距离最小化在遗传密码进化中的作用。
Proc Natl Acad Sci U S A. 1980 Feb;77(2):1083-6. doi: 10.1073/pnas.77.2.1083.
8
Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications.假基因中核苷酸替换所反映的点突变的非随机性及其进化意义。
J Mol Evol. 1984;21(1):58-71. doi: 10.1007/BF02100628.
9
Genetic code and optimal resistance to the effects of mutations.遗传密码与对突变效应的最佳抗性
Orig Life. 1984;14(1-4):579-88. doi: 10.1007/BF00933707.
10
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.大肠杆菌转移RNA丰度与其蛋白质基因中相应密码子出现情况之间的相关性：关于一种对大肠杆菌翻译系统而言最优的同义密码子选择的提议。
J Mol Biol. 1981 Sep 25;151(3):389-409. doi: 10.1016/0022-2836(81)90003-6.
Zotero 插件