Biodiversity Science ›› 2017, Vol. 25 ›› Issue (1): 94-106.doi: 10.17520/biods.2016260

• Orginal Article • Previous Article    

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:2017-02-08

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

Fig. 1

Adenosine triphosphate (ATP). The removal of the terminal phosphoryl group (shaded pink) of ATP, by breakage of a phosphoanhydride bond, is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell (cited from Nelson & Cox, 2004)"

Fig. 2

A sketch of the ATP synthesis coupled with photosynthesis in the thylakoid membrane (cited from Taiz & Zeiger, 2010)"

Fig. 3

The triplet codes and pairing between tRNA anticodon and mRNA codon (modified from Baidu Baike)"

Fig. 4

ATP (a carrier of both energy and information) is at the center of the biochemical system in a modern cell. It provides a unique bridge among photosynthesis, metabolic pathways and genetic information."

Fig. 5

Structural comparison between DNA and RNA (cited from TutorVista.comTM)"

Fig. 6

Structural homology between chlorophyll and the heme of cytochrome. Decyclization occurred from magnesium porphyrin to iron porphyrin (marked with red color). Evolutionarily, the membrane-bound chlorophyll was likely a merge of phospholipid and porphyrin. Dashed blue lines with arrows indicate possible directions of evolution"

Fig. 7

A simplified conceptual model on the origin of the genetic code based on the photosynthesis-mediated and ATP-centric hypothesis. Dashed blue lines indicate evolutionary processes during pre-life period, while solid red lines denote processes or interactions from pre-life period to the present. Arrows indicate the direction of influences or actions."

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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