Potential Impact of Genetic-Code Mutations on Medicine and Health
Main Article Content
Abstract
The genetic code encoding amino acid sequences in ribosomal translation consists of an alphabet of 61 triplet codons for 20 amino acids and three chain termination signals. Basically the same universal code is employed by all organisms from the Last Universal Common Ancestor (LUCA)-proximal Methanobacter kandleri (Mka) to humans. This universal code, which has remained invariant for all living species, enables the transplantation of protein-coding genes between different species without loss of function, and constrains the chemical diversity of the encoded amino acids. Over the initial decades following the discovery of the code, its invariance coupled with the lack of any information regarding its origin have led to the view that the code might represent an inexplicable ‘frozen accident’ in the history of life. However, with the formulation of the coevolution theory of the genetic code and its multifaceted supporting evidence, this view has become untenable. Instead, the encoded amino acids are known to comprise two different classes: ten Class 1 amino acids available on prebiotic Earth were incorporated into the protocells as they evolved into life forms, while the ten Class 2 amino acids were produced by early life through biosynthesis. Thus, the later entry of the Class 2 amino acids identified them as end products of cellular evolution, which suggests the plausibility of continuing alterations of the encoded amino acids after an eons-long pause. Accordingly, attempts were made by our group to replace Trp by 4-fluroTrp (4FTrp) from the proteome of Bacillus subtilis. The targeted replacement obtained proved the inherent mutability of the code, and this has stimulated the development of a wide range of mutated codes through a variety of approaches. Hundreds of genetic code mutants have now been successfully isolated from microbes to animals, transforming the code from an immutable construct to a highly malleable molecular device. The effects of such new codes on medicine and health range from treatments for a variety of diseases to the alleviation of food crisis arising from the degradation of the environment and devastation due to natural disasters.
Article Details
How to Cite
WONG, Tze-Fei; XUE, Hong.
Potential Impact of Genetic-Code Mutations on Medicine and Health.
Medical Research Archives, [S.l.], v. 11, n. 8, aug. 2023.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/4331>. Date accessed: 13 may 2024.
doi: https://doi.org/10.18103/mra.v11i8.4331.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
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2. Baross JA, Hoffman SE. Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. Orig Life Evol Biosph. 1985;15(4):327-345. doi:10.1007/bf01808177.
3. Shock EL. Constraints on the origins of organic compounds in hydrothermal vent, Orig Life Evol Biosph. 1990; 20:331-367.
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5. Muchowska KB, Chevallot-Beroux E, Morana J. Recreating ancient metabolic pathways before enzymes. Bioorganic Med Chem. 2019;27(12):2292-2297. doi:10.1016/j.bmc.2019.03.012.
6. Lane N, Allen JF Martin W. How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays. 2010;32(4):271-280. doi:10.1002/bies.200900131.
7. Huber R, Kurr M, Jannasch HW, Stetter KO. A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110℃. Nature. 1989;342(6251):833-834. doi:10.1038/342833a0.
8. Xue H, Tong KL, Marck C, Grosjean H, Wong JTF. Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life. Gene. 2003;310:59-66. doi:10.1016/s0378-1119(03)00552-3.
9. Wong JTF, Ng SK, Mat WK, Hu T, Xue H. Coevolution theory of the genetic code at age forty: pathway to translation and synthetic life. Life. 2016;6(1):12. doi:10.3390/life6010012.
10. Long X, Xue H, Wong JTF. Descent of bacteria and eukarya from an archaeal root of life. Evol Bioinfor 2020; 16: 1-11.
11. Blank CE. Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. Archaea. 2012;2012:1-23. doi:10.1155/2012/843539.
12. Gilbert W. Origin of life: The RNA world. Nature. 1986;319(6055):618-618. doi:10.1038/319618a0.
13. Cech TR. Self-splicing of group I introns. Annu Rev Biochem. 1990;59(1):543-568. doi:10.1146/annurev.bi.59.070190.002551
14. Stairs S, Nikmal A, Bučar DK, Zheng SL, Szostak JW, Powner MW. Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides. Nat Commun s. 2017;8(1). doi:10.1038/ncomms15270.
15. Callahan MP, Smith KE, Cleaves HJ II, et al. Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci U S A 2011;108(34):13995-13998. doi:10.1073/pnas.1106493108.
16. Tjhung KF, Shokhirev MN, Horning DP, Joyce GF. An RNA polymerase ribozyme that synthesizes its own ancestor. Proc Natl Acad Sci USA. 2020;117(6):2906-2913. doi:10.1073/pnas.1914282117.
17. Orgel, L. E.Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol. 2004;39(2):99-123. doi:10.1080/10409230490460765.
18. Joyce GF, Orgel LE. Prospects for understanding the origin of the RNA World. In: Gesteland RF, Cech TR, Atkins JF, eds. The RNA World, Second Edition. Cold Spring Harbor Laboratory Press; 1999:49-77. doi:10.1017/S1355838299001259.
19. Wong JTF. Emergence of life: from functional RNA selection to natural selection and beyond. Front Biosci - Landmark. 2014;19(7):1117. doi:10.2741/4271.
20. Cech TR. Crawling out of the RNA World. Cell 2009; 136(4): 599-602. Doi.org/10.1016/jcell2009.02.0.
21. Wong JTF. Origin of genetically encoded protein synthesis: A model based on selection for RNA peptidation. Orig Life Evol Biosph. 1991;21(3):165-176. doi:10.1007/bf01809445.
22. Wong JTF. A Co-Evolution theory of the genetic code. Proc Natl Acad Sci U S A. 1975;72(5):1909-1912. doi:10.1073/pnas.72.5.1909.
23. Wong JTF. Coevolution of genetic code and amino acid biosynthesis. Trends Biochem Sci. 1981;6:33-36. doi:10.1016/0968-0004(81)90013-x.
24. Pizzarello S. Meteorites and the chemistry that preceded life’s origin. In: Wong JTF, Lazcano A, eds. Prebiotic Evolution and Astrobiology. CRC Press; 2009:46-51. http://dx.doi.org/10.1201/9781498713986.
25. Kobayashi K, Kaneko T, Saito T, Oshima T. Amino acid formation in gas mixtures by high energy particle irradiation. Orig Life Evol Biosph. 1998;28(2):155-165. doi:10.1023/a:1006561217063.
26. Wong JTF, Bronskill PM. Inadequancy of prebiotic synthesis as origin of proteinous amino acids. J Mol Evol 1979; 13: 115-125.
27. Wong JTF. Membership mutation of the genetic code: loss of fitness by tryptophan. Proc Natl Acad Sci U S A. 1983; 80(20):6303-06. doi:10.1073/pnas.80.20.6303.
28. Mat WK, Xue H, Wong JTF. Genetic code mutations: The breaking of a three billion year invariance. PLoS ONE. 2010;5(8):e12206. doi:10.1371/journal.pone.0012206.
29. Wong JTF, Xue H. Synthetic genetic codes as the basis of synthetic life. In Chemical Synthetic Biology, Luisi PL, Chiarabelli C.eds. Wiley, New York2010; pp.178-199.
30. Hoesl MG, Budisa N. In vivo incorporation of multiple noncanonical amino acids into proteins. Angew Chemie Intern Ed 2011; doi.org/10.1002/anie.201005680.
31. Merkel L, Schauer M, Budisa N. et al. Parallel incorporation of different fluorinated amino acids: On the way to“Teflon” like proteins. ChemBioChem. 2010;11(11):1505-1507. doi:10.1002/cbic.201000295.
32. Thyer R, Shroff R, Klein DR, et al. Custom selenoprotein production enabled by laboratory evolution of recoded bacterial strains. Nat Biotechnol. 2018;36(7):624-631. doi:10.1038/nbt.4154.
33. Kwok Y, Wong JTF. Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes. Can J Biochem. 1980;58(3):213-218. doi:10.1139/080-029.
34. Furter R. Expansion of the genetic code: Site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci. 1998;7(2):419-426. doi:10.1002/pro.5560070223
35. Santoro SW, Anderson JC, Schultz PG et al. An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res. 2003;31(23):6700-6709. doi:10.1093/nar/gkg903.
36. Italia JS, Addy PS, Erickson SB et al. Mutually orthogonal nonsense -suppression systems for precise protein labelling at up to three distinct sites. J Am Chem Soc 2019; 141: 6204-6212.
37. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Church GM et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011; 333: 348-353.
38. Lummis SCR, Beene DL, Lee LW, Lester HA, Broadhurst RW, Dougherty DA. Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel, Nature 2005; 438: 248-252.
Doi: 10.1038/nature04130.
39. Bryson DI, Fan C, Guo LT, Miller C, Söll D, Liu DR. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat Chem Biol. 2017;13(12):1253-1260. doi:10.1038/nchembio.
40. Xue H, Wong JTF. Future of the genetic code. Life. 2017;7(1):10. doi:10.3390/life7010010.
41. Xi Z, Davis L, Baxter K, Tynan A, Goutou A, Greiss S. Using a quadruplet codon to expand the genetic code of an animal. Nucleic Acids Res. 2021;50(9):4801-4812. doi:10.1093/nar/gkab1168.
42. Mukai T, Hayashi A, Iraha F, et al. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res. 2010;38(22):8188-8195. doi:10.1093/nar/gkq707
43. Marlière P, Patrouix J, Döring V, et al. Chemical evolution of a bacterium’s genome. Angew Chemie Int Ed. 2011;50(31):7109-7114. doi:10.1002/anie.201100535.
44. Zhang Y, Lamb BM, Romesberg FE et al. A semisynthetic organism engineered for the stable expansion of the genetic alphabet. Proc Natl Acad Sci U S A. 2017;114(6):1317-1322. doi:10.1073/pnas.1616443114.
45. Hoshika S, Leal NA, Benner S.A. et al. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 2019;363(6429):884-887. doi:10.1126/science.aat0971.
46. Dunkelmann DL, Oehm SB, Chin JW. A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design. Nat Chem. 2021;13(11):1110-1117. doi:10.1038/s41557-021-00764-5
47. Axup JY, Bajjuri KM, Scultz PG et al. Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc Nat Acad Sci USA 2012; 109(40): 16101-16106.
48. Lu H, Zhou Q, Deshmukh V, et al. Targeting human C-type lectin-like molecule-1 (CLL1) with a bispecific antibody for immunotherapy of acute myeloid leukemia. Angew Chem Int Ed Engl. 2014;53(37):9841-9845. doi:10.1002/anie.201405353.
49. Rosenberg SA. IL-2: the first effective immunotherapy for human cancer. J Immunol. 2014;192(12):5451-5458. doi:10.4049/jimmunol.1490019.
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