Biodiv Sci ›› 2017, Vol. 25 ›› Issue (1): 94-106. DOI: 10.17520/biods.2016260
• Forums • Previous Articles
Ping Xie
Received:
2016-09-14
Accepted:
2016-10-05
Online:
2017-01-20
Published:
2017-02-08
Ping Xie. The origin of genetic codes: from energy transformation to informatiza- tion[J]. Biodiv Sci, 2017, 25(1): 94-106.
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. 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. 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. |
No related articles found! |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||
Copyright © 2022 Biodiversity Science
Editorial Office of Biodiversity Science, 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: 010-62836137, 62836665 E-mail: biodiversity@ibcas.ac.cn