生物多样性 ›› 2017, Vol. 25 ›› Issue (1): 94-106.doi: 10.17520/biods.2016260

• • 上一篇    

遗传密码子的起源——从能量转化到信息化

谢平*   

  1. 中国科学院水生生物研究所, 武汉 430072
  • 收稿日期:2016-09-14 接受日期:2016-10-05 出版日期:2017-01-20
  • 通讯作者: 谢平

The origin of genetic codes: from energy transformation to informatiza- tion

Ping Xie   

  1. Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072
  • Received:2016-09-14 Accepted:2016-10-05 Online:2017-01-20

大自然将奥秘或法则隐匿于一套密码之中, 藉此创作出数以千万计的物种, 之后又将其销毁, 周而复始, 生生不息……虽然遗传密码子的破译已过去了半个多世纪, 但对它的起源人们依然一无所知, 有人甚至宣称这是不可知的, 还有一些人则认为它源自外来的设计。生命/遗传密码子的起源被誉为现代生命科学的最大谜团之一, 但它却关乎人们对生命本质与演化的认知。关于遗传密码子的起源, 已提出了各式各样的假说, 如凝固事件假说、立体化学假说、共进化假说、综合进化假说, 等等。但这些假说有两个致命缺陷: 首先, 没有哪一个能解释为何遗传密码子要如此演化; 其次, 都未从生化系统演化的视角来予以解释(部分与整体的关系)。近年, 虽然对密码子变异或可塑性及其与氨基酸分配的关系等研究很多, 但在密码子起源方面几乎没有取得实质性进展。本文从密码子与生化系统的内在关联之中探寻它们可能的协同演化机理, 认为遗传密码是原始细胞从能量转化到信息化演化过程的产物, 而三磷酸腺苷(ATP)扮演了最重要的角色。本文提出的“ATP中心假说”认为, ATP既是能量的载体, 也是信息的载体, 在核酸和蛋白质之间搭起了桥梁, 是遗传密码子出现的始作俑者: (a)ATP是光能转化成化学能的终端; (b)导演了一系列的生化循环(如卡尔文循环、糖酵解和三羧酸循环等)及令人眼花缭乱的元素重组; (c)它通过自身的转化与缩合将错综复杂的生命过程信息化——筛选出用4种碱基编码20多种氨基酸的三联体密码子系统(43 = 64, 还有相当大的编码冗余), 精巧地构建了一套遗传信息的保存、复制、转录和翻译以及多肽链的生产体系; (d)演绎出蛋白质与核酸互为因果的反馈体系, 并在个体生存的方向性筛选中, 构筑了对细胞内成百上千种同步发生的生化反应进行秩序化管控(自组织)的复杂体系与规则, 最终建立起个性生命的同质化传递机制——遗传。当然, 未来还需要更多的实验证据来验证这一假说。

关键词: 遗传密码的起源, ATP中心假说, 光合介导, 信息化, 结构化, 同质性个体

It is a miracle of nature that a set of genetic codes have assembled tens of millions of different species on the earth. However, no one knows exactly how these genetic codes came into being. Many biologists hold the pessimistic view that an exact reconstruction of the process of code construction may never be possible. It is even believed that the origin of the genetic code is unknowable, as there is no trace in physics or chemistry of the control of chemical reactions by a sequence of any sort or of a code between sequences. Many papers have been published with titles indicating that they explore the origin of the genetic code, but in actuality the content deals only with its evolution. More than half a century has passed since the discovery of genetic codes, but their origin is still one of the greatest mysteries in the modern life sciences. Are the genetic codons really unknowable? Do they require external design? So far, several hypotheses have been proposed to explain the origin of the genetic code, including the frozen accident hypothesis, stereochemical hypothesis, co-evolution hypothesis, and synthetic hypothesis. These hypotheses suffer from two fatal defects: first, none can explain satisfactorily why the genetic codes evolved, and second, none has explained the origin of genetic codes from that of the biochemical system (a relation of part to whole). In other words, all of these hypotheses completely overlooked the coevolution of genetic codes with the biochemical system. In recent decades, very little definitive progress has been made, although intensive studies have focused on variation or flexibility of the codes and possible rules of codon allocations to amino acids. This paper is aimed to explore the secrets of coevolution between the codon and the biochemical system. The genetic codes were likely an evolutionary product of primordial cells from energy transformation to informatization when ATP played a crucial role. Here, we present an ATP-centric hypothesis aimed at exploring the hidden primordial world inspiring the origin of genetic codes. We examined how and why ATP is at the heart of the extant biochemical system, and how the genetic codes came into being with the evolution of the biochemical system driven by photosynthesis. ATP, carriers of both energy and information, provide a bridge between amino acids and proteins, and are most likely the initiator of the genetic codes. In short, the energetic ATP together with its derivatives could randomly extend chains of both polynucleotides and polypeptides, which made it possible to establish or fix chemical relations between sequences of nucleotides in polynucleotides and amino acids in polypeptides from their numerous random combinations through a feedback mechanism (selection of cellular survival); and technically, photosynthesis, a goal-oriented process, enabled various biotic factors or reactions (ATP, lipid vesicle, informatization, structuralization, homogenous individual, individuality, survival, etc.) to be integrated into an operating system of genetic codes. It is challenging to crack the mystery of genetic codes, but sophisticated experimental evidence are needed in the future.

Key words: origin of genetic codes, ATP-centric hypothesis, photosynthesis-mediated, informatization, structuralization, homogenous individual

图1

三磷酸腺苷(ATP)的结构, 通过磷酸酐键的断裂移去ATP末端的磷酸基团将释放高的能量, 这在细胞中与许多吸能反应相耦联(如粉色区域所示)(引自Nelson & Cox, 2004)"

图2

在内囊体膜上, 与光合作用耦联的ATP合成示意图(引自Taiz & Zeiger, 2010)"

图3

三联体密码表以及tRNA的反密码子和mRNA的密码子的配对(修改自百度百科)"

图4

作为能量和信息载体的ATP在现代细胞中位于生化系统的中心, 在光合作用、代谢通路和遗传信息之间架起了桥梁"

图5

脱氧核糖核酸(DNA)和核糖核酸(RNA)基本结构的比较(引自TutorVista.comTM)"

图6

叶绿素与细胞色素的血红素辅基之间在结构上的相似性。在从镁卟啉到铁卟啉的转变中发生了去环化作用(红色标记位置)。从进化上来看, 膜耦联的叶绿素分子可能由磷脂与卟啉环加合而成。带箭头的蓝色虚线表示可能的演化方向"

图7

密码子的起源——光合作用介导的ATP中心假说(ATP-centered hypothesis)示意图。蓝色虚线表示前生命期的演化过程, 红色实线表示演化或作用从前生命期一直延续到生命期。箭头表示作用或影响方向。"

1 Atkins JF, Gesteland RF, Cech TR (2011) RNA Worlds: from Life’s Origins to Diversity in Gene Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2 Baranov PV, Atkins JF, Yordanova MM (2015) Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nature Reviews Genetics, 16, 517-529.
3 Baranov PV, Venin M, Provan G (2009) Codon size reduction as the origin of the triplet genetic code. PLoS ONE, 4, e5708.
4 Crick FH (1968) The origin of the genetic code. Journal of Molecular Biology, 38, 367-379.
5 Dong XC, Zhou MY, Zhong C, Yang B, Shen N, Ding JP (2010) Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase. Nucleic Acids Research, 38, 1401-1412.
6 Eigen M, Schuster P (1979) The Hypercycle, A Principle of Natural Self-Organization. Springer-Verlag, Berlin.
7 Freeland SJ, Wu T, Keulmann N (2003) The case for an error minimizing standard genetic code. Origins of Life and Evolution of Biospheres, 33, 457-477.
8 Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Research, 17, 405-412.
9 Jee J, Sundstrom A, Massey SE, Mishra B (2013) What can information-asymmetric games tell us about the context of Crick’s “frozen accident”? Journal of the Royal Society Interface, 10, 20130614.
10 Knight RD, Freeland SJ, Landweber LF (1999) Selection, history and chemistry: the three faces of the genetic code. Trends in Biochemical Sciences, 24, 241-247.
11 Leslie M (2009) On the origin of photosynthesis. Science, 323, 1286-1287.
12 Nelson DL, Cox MM (2004) Lehninger Principles of Biochemistry, 4th edn. W. H. Freeman and Company, New York.
13 Ohama T, Inagaki Y, Bessho Y, Osawa S (2008) Evolving genetic code. Proceedings of the Japan Academy, Series B: Physical and Biological Sciences, 84, 58-74.
14 Polyansky AA, Hlevnjak M, Zagrovic B (2013) Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code. RNA Biology, 10, 1248-1254.
15 Radzicka A, Wolfenden R (1995) A proficient enzyme. Science, 267, 90-93.
16 Rauchfuss H (2008) Chemical Evolution and the Origin of Life. Springer-Verlag, Berlin, Heidelberg.
17 Sciarrino A, Sorba P (2013) Codon-anticodon interaction and the genetic code evolution. Biosystems, 111, 175-180.
18 Sella G, Ardell DH (2006) The coevolution of genes and genetic codes: Crick’s frozen accident revisited. Journal of Molecular Evolution, 63, 297-313.
19 Sengupta S, Higgs PG (2015) Pathways of genetic code evolution in ancient and modern organisms. Journal of Molecular Evolution, 80, 229-243.
20 Taiz L, Zeiger E (2010) Plant Physiology, 4th edn. Sinauer Associates, Sunderland, MA.
21 Tlusty T (2008) Rate-distortion scenario for the emergence and evolution of noisy molecular codes. Physical Review Letters, 100, 392-396.
22 Umena Y, Kawakami K, Shen JR, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature, 473, 55-60.
23 Woese CR (1967) The Genetic Code: The Molecular Basis for Genetic Expression. Harper & Row, New York.
24 Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC (1966) On the fundamental nature and evolution of the genetic code. Cold Spring Harbor Symposium on Quantitative Biology, 31, 723-736.
25 Wong JT (1975) A co-evolution theory of the genetic code. Proceedings of the National Academy of Sciences, USA, 72, 1909-1912.
26 Wu HL, Bagby S, van den Elsen JMH (2005) Evolution of the genetic triplet code via two types of doublet codons. Journal of Molecular Evolution, 61, 54-64.
27 Xiao JF, Yu J (2009) New arrangement of genetic codes with discussion on their origin. Science in China Series C: Life Sciences, 39, 717-726. (in Chinese)
[肖景发, 于军 (2009) 遗传密码的新排列和起源探讨. 中国科学C辑: 生命科学 , 39, 717-726].
28 Xiao J, Yu J (2007) A scenario on the stepwise evolution of the genetic code. Genomics Proteomics & Bioinformatics, 5, 143-151.
29 Xie P (2014) The Aufhebug and Breakthrough of the Theories on the Origin and Evolution of Life. Science Press, Beijing. (in Chinese)
[谢平 (2014) 生命的起源——进化理论之扬弃与革新: 哲学中的生命, 生命中的哲学. 科学出版社, 北京.]
30 Yarus M, Widmann JJ, Knight R (2009) RNA-amino acid binding: a stereochemical era for the genetic code. Journal of Molecular Evolution, 69, 406-429.
31 Yockey HP (2005) Information Theory, Evolution, and the Origin of Life. Cambridge University Press, Cambridge.
32 Yu J (2007) An evolutionary scenario for the origin of the genetic code. Communications of Chinese-American Chemical Society, 3, 3-7.
33 ZhaoYF, Cao PS (1994) Phosphoryl amino acids: common origin for nucleic acids and protein. Journal of Biological Physics, 20, 283-287.
34 Zhao YF, Cao PS (1996) Basic models of chemical evolution of life: the minimum evolving system. In: Chemical Evolution: Physics of Origin of Life (eds Chela-Flores J, Raulin F), pp. 279-285. Kluwer Academic Publishers, Netherlands.
35 Zhao YF, Ju Y, Li YM, Wang Q, Yin YW, Tan B (1995) Self-activation of N-phosphoamino acids and N-phosphodipeptides in oligopeptide formation. International Journal of Protein Research, 45, 514-518.
36 Zhou WH, Ju Y, Zhao YF, Wang QG, Luo GA (1996) Simultaneous formation of peptides and nucleotides from N-phosphpthreonine. Origins of Life and Evolution of Biospheres, 26, 547-560.
37 Zimmer C (2009) On the origin of life on earth. Science, 323, 198-199.
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