Abstract
Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single –C=C bond and two nitrogen atoms in each heterocycle involved in C–N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of –C=O and/or –NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M–Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
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Achrainer F, Emel’yanenko VN, Tantawy W, Verevkin SP, Zipse H (2014) Transfer hydrogenation as a redox process in nucleotides. J Phys Chem B 118(35):10426–10429. https://doi.org/10.1021/jp507855k
Adande GR, Woolf NJ, Ziurys LM (2013) Observations of interstellar formamide: availability of a prebiotic precursor in the galactic habitable zone. Astrobiology 13(5):439–453. https://doi.org/10.1089/ast.2012.0912
Aldersley MF, Joshu PC, Price JD, Ferris JP (2011) The role of montmorillonite in its catalysis of RNA synthesis. Appl Clay Sci 54(1):1–14. https://doi.org/10.1016/j.clay.2011.06.011
Alvarez-Carreño C, Bacerra A, Lazcano A (2013) Norvaline and norleucine may have been more abundant protein components during early stages of cell evolution. Orig Life Evol Biosph 43(4–5):363–375. https://doi.org/10.1007/s11084-013-9344-3
Amend JP, Shock EL (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. Science 281(5383):1659–1662. https://doi.org/10.1126/science.281.5383.1659
Ardell DH (1998) On error minimization in sequential origin of the standard genetic code. J Mol Evol 47(1):1–13. https://doi.org/10.1007/PL00006356
Barrell BG, Bankier AT, Drouin J (1979) A different genetic code in human mitochondria. Nature 282(5735):189–194. https://doi.org/10.1038/282189a0
Brooks DJ , Fresco JR. (2003) Greater GNN pattern bias insequence elements encoding conserved residues of ancient proteins may be an indicator of amino acid composition of early proteins. Gene 303:177–185. https://doi.org/10.1016/s0378-1119(02)01176-9
Beaty DW, Buxbaum K, Meyer M, Barlow N, Boynton W, Clark B et al (2006) Findings of the Mars special regions Science analysis group. Astrobiology 6(5):677–732. https://doi.org/10.1089/ast.2006.6.677
Bera PP, Nuevo M, Materese CK, Sandford SA, Lee TJ (2016) Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life. J Chem Phys 144(14):144308. https://doi.org/10.1063/1.4945745
Bethe HA (1968) Energy production in stars. Science 161(3841):541–547. https://doi.org/10.1126/science.161.3841.541
Błażej P, Wnetrzak M, Mackiewicz D, Mackiewicz P (2019) The influence of different types of translational inaccuracies on the genetic code structure. BMC Bioinform 20(1):114. https://doi.org/10.1186/s12859-019-2661-4
Boyd RN, Kajino T, Onaka T (2011) Supernovae, neutrinos and the chirality of amino acids. Int J Mol Sci 12(6):3432–3444. https://doi.org/10.3390/ijms12063432
Brandenburg A (2019) The limited roles of autocatalysis and enantiomeric cross-inhibition in achieving homochirality in dilute systems. Orig Life Evol Biosph 49(1–2):49–60. https://doi.org/10.1007/s11084-019-09579-4
Burton AS, Stern JC, Elsila JE, Glavin DP, Dworkin JP (2012) Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites. Chem Soc Rev 41(16):5459–5472. https://doi.org/10.1039/c2cs35109a
Calvin M (1969) Chemical evolution: molecular evolutions towards the origin of living systems in the earth and elsewhere. Oxford University Press, New York
Caskey CT, Tompkins R, Scolnick E, Caryk T, Nirenberg MW (1968) Sequential translation of trinucleotide codons for the initiation and termination of protein synthesis. Science 162(3849):135–138. https://doi.org/10.1126/science.162.3849.135
Ciesla FJ, Sandford SA (2012) Organic synthesis via irradiation and warming of ice grains in the solar nebula. Science 336(6080):452–454. https://doi.org/10.1126/science.1217291
Copley SD, Smith E, Morowitz HJ (2005) A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc Natl Acad Sci USA 102(12):4442–4447. https://doi.org/10.1073/pnas.0501049102
Crick FHC (1968) The origin of the genetic code. J Mol Biol 38(3):367–379. https://doi.org/10.1016/0022-2836(68)90392-6
Crick FHC, Barnett L, Brenner S, Watts-Tobin RJ (1961) General nature of the genetic code for proteins. Nature 192(4809):1227–1232. https://doi.org/10.1038/1921227a0
da Silva MAR, Amaral LM, Szterner P (2011) Thermochemical study of 5-methyluracil, 6-methyluracil, and 5-nitrouracil. J Chem Thermodyn 43(12):1924–1927. https://doi.org/10.1016/j.jct.2011.06.023
Dawson RMC, Elliot DC, Elliot WH, Jones KM (1986) Data for biochemical research. Clarendon Press, Oxford
Di Giulio M (1989) Some aspects of the organization and evolution of the genetic code. J Mol Evol 29(3):191–201. https://doi.org/10.1007/bf02100202
Di Giulio M (2008) An extension of the coevolution theory of the origin of the genetic code. Biol Direct 3:37. https://doi.org/10.1186/1745-6150-3-37
Di Giulio M (2017) Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory. J Theor Biol 414:1–4. https://doi.org/10.1016/j.jtbi.2016.11.014
Doig AJ (2017) Frozen, but no accident—why the 20 standard amino acids were selected. FEBS J 284(9):1296–1305. https://doi.org/10.1111/febs.13982
Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58(10):465–523. https://doi.org/10.1007/BF00623322
Eigen M, Schuster P (1979) The hypercycle: a principle of natural self-organization. Springer-Verlag, Berlin, Heidelberg, New York
Emel’yanenko VN, Verevkin SP, Notario R (2015a) Thermochemistry of uracil and thymine revisited. J Chem Thermodyn 87:129–135. https://doi.org/10.1016/j.jct.2015.03.015
Emel’yanenko VN, Zaitsau DH, Shoifet E, Meurer F, Verevkin SP, Schick C, Held C (2015b) Benchmark thermochemistry for biologically relevant adenine and cytosine. A combined experimental and theoretical study. J Phys Chem A 119(37):9680–9691. https://doi.org/10.1021/acs.jpca.5b04753
Engel MH, Nagy B (1982) Distribution and enantiomeric composition of amino acids in the Murchison meteorite. Nature 296:837–840. https://doi.org/10.1038/296837a0
Famiano MA, Boyd RN, Kajino T, Onaka T, Mo Y (2018) Amino acid chiral selection via weak interactions in stellar environments: implications for the origin of life. Sci Rep 8:8033. https://doi.org/10.1038/s41598-018-27110-z
Fox RF (1988) Energy and the evolution of life. WH Freeman, New York
Francis BR (2013) Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 77(4):134–158. https://doi.org/10.1007/s00239-013-9567-y
Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47(3):238–248. https://doi.org/10.1007/PL00006381
Ganyecz A, Kallay M, Csontos J (2019) Thermochemistry of uracil, thymine, cytosine, and adenine. J Phys Chem A 123(18):4057–4067. https://doi.org/10.1021/acs.jpca.9b02061
Gaston MA, Zhang L, Green-Church KB, Krzycki JA (2011) The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471(7340):647–650. https://doi.org/10.1038/nature09918
Gilbert W (1986) The RNA world. Nature 319(6055):618. https://doi.org/10.1038/319618a0
Higgs (2009) A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct 4:16. https://doi.org/10.1186/1745-6150-4-16
Haig D, Hurst LD (1991) A quantitative measure of error minimization in the genetic code. J Mol Evol 33(5):412–417. https://doi.org/10.1007/pl00006591
Higgs PG, Lehman N (2015) The RNA world: molecular cooperation at the origins of life. Nat Rev Genet 16(1):7–17. https://doi.org/10.1038/nrg3841
Higgs PG, Pudritz RE (2009) A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9(5):483–490. https://doi.org/10.1089/ast.2008.0280
Hohn MJ, Palioura S, Su D, Yuan J, Söll D (2011) Genetic analysis of selenocysteine biosynthesis in the archaeon Methanococcus maripaludis. Mol Microbiol 81(1):249–258. https://doi.org/10.1111/j.1365-2958.2011.07690.x
Huber C, Eisenreich W, Hecht S, Wächtershäuser G (2003) A possible primordial peptide cycle. Science 301(5635):938–940. https://doi.org/10.1126/science.1086501
Kelley DS, Karson JA, Blackman DK, Früh-Green GL, Butterfield DA, Lilley MD et al (2001) An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30°N. Nature 412(6843):145–149. https://doi.org/10.1038/35084000
Kirklin DR, Domalski ES (1983) Enthalpy of combustion of adenine. J Chem Thermodyn 15(10):941–947. https://doi.org/10.1016/0021-9614(83)90127-1
Kirklin DR, Domalski ES (1984) Enthalpy of combustion of purine. J Chem Thermodyn 16(7):633–641. https://doi.org/10.1016/0021-9614(84)90043-0
Kitadai N (2015) Energetics of amino acid synthesis in alkaline hydrothermal environments. Orig Life Evol Biosph 45(4):377–409. https://doi.org/10.1007/s11084-015-9428-3
Knight RD, Landweber LE (2000) The early evolution of the genetic code. Cell 101(6):569–572. https://doi.org/10.1016/s0092-8674(00)80866-1
Koonin EV, Novozhilov AS (2017) Origin and evolution of the universal genetic code. Annu Rev Genet 51(1):45–62. https://doi.org/10.1146/annurev-genet-120116-024713
Krishnamurthy R (2012) Role of pKa of nucleobases in the origins of chemical evolution. Acc Chem Res 45(12):2035–2044. https://doi.org/10.1021/ar200262x
Kuiper GP (1949) The law of planetary and satellite distances. Astrophys J 109:308–313. https://doi.org/10.1086/145133
Kun A, Radványi A (2018) The evolution of the genetic code: impasses and challenges. Biosystems 164:217–225. https://doi.org/10.1016/j.biosystems.2017.10.006
LaRowe DE, Regnier P (2008) Thermodynamic potential for the abiotic synthesis of adenine, cytosine, guanine, thymine, uracil, ribose, and deoxyribose in hydrothermal systems. Orig Life Evol Biosph 38(5):383–397. https://doi.org/10.1007/s11084-008-9137-2
Marshall RE, Caskey CT, Nirenberg M (1967) Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA. Science 155(3764):820–826. https://doi.org/10.1126/science.155.3764.820
Martin A, McMinn A (2018) Sea ice, extremophiles and life on extra-terrestrial ocean worlds. Int J Astrobiol 17(1):1–16. https://doi.org/10.1017/S1473550416000483
Martin W, Russel MJ (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc Lond B 362(1486):1887–1926. https://doi.org/10.1098/rstb.2006.1881
Massey SE (2016) The neutral emergence of error minimized genetic codes superior to the standard genetic code. J Theor Biol 408:237–242. https://doi.org/10.1016/j.jtbi.2016.08.022
Materese CK, Nuevo M, Bera PP, Lee TJ, Sandford SA (2013) Thymine and other prebiotic molecules produced from the ultraviolet photo-irradiation of pyrimidine in simple astrophysical ice analogs. Astrobiology 13(10):948–962. https://doi.org/10.1089/ast.2013.1044
Materese CK, Nuevo M, Sandford SA (2017) The formation of nucleobases from the ultraviolet photo-irradiation of purine in simple astrophysical ice analogues. Astrobiology 17(8):761–770. https://doi.org/10.1089/ast.2016
McCutcheon JP, McDonald BR, Moran NA (2009) Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet 5(7):e1000565. https://doi.org/10.1371/journal.pgen.100056
McKay CP (2016) Titan as the abode of life. Life 6(1):8. https://doi.org/10.3390/life6010008
Metzler DE (1977) Biochemistry. The chemical reactions of living cells, vol 1. Academic Press, New York, London
Miller SL (1953) Production of some organic compounds under possible primitive earth conditions. J Am Chem Soc 77(9):2351–2361. https://doi.org/10.1021/ja01614a001
Miller SL, Bada JL (1988) Submarine hot springs and the origin of life. Nature 334(6183):609–611. https://doi.org/10.1038/334609a0
Miller SL, Orgel LE (1974) The origins of life on the earth. Prentice-Hall, Englewood Cliffs, New Jersey
Mojzsis SJ, Brasser R, Kelly NM, Abramov O, Werner SC (2019) Onset of giant planet migration before 4480 million years ago. Astrophys J 881:44. https://doi.org/10.3847/1538-4357/ab2c03
Morgens DW, Cavalcanti ARO (2013) An alternative look at code evolution: using non-canonical codes to evaluate adaptive and historic models for the origin of the genetic code. J Mol Evol 76:71–80. https://doi.org/10.1007/s00239-013-9542-7
Nirenberg MW, Matthaei JH (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci USA 47(10):1588–1602. https://doi.org/10.1073/pnas.47.10.1588
Novozhilov AS, Koonin EV (2009) Exceptional error minimization in putative primordial genetic code. Biol Direct 4:44. https://doi.org/10.1186/1745-6150-4-44
Nucleic acids from A to Z. A Concise Encyclopedia (2008) WILEY-VCH Verlag Gmb H & Co. KGaA, FRG
Orgel LE (1968) Evolution of the genetic apparatus. J Mol Biol 38(3):381–393. https://doi.org/10.1016/0022-2836(68)90393-8
Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39(2):99–123. https://doi.org/10.1080/10409230490460765
Orό J, Kimball AP (1961) Synthesis of purines under possible primitive earth conditions, I. Adenine from hydrogen cyanide. Arch Biochem Biophys 94(2):217–227. https://doi.org/10.1016/0003-9861(61)90033-9
Patel BH, Percivalle C, Ritson DJ, Duffy CD, Sutherland JD (2015) Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism. Nat Chem 7(4):301–307. https://doi.org/10.1038/nchem.2202
Pauling L, Pauling P (1975) Chemistry. Freeman WH and Company, San Francisco
Pavlov A, Cheptsov V, Tsurcov D, Lomasov V, Frolov D, Vasiliev G (2019) Survival of radioresistant bacteria on Europa’s surface after pulse ejection of subsurface ocean water. Geosciences 9(1):9. https://doi.org/10.3390/geosciences9010009
Pearce BKD, Pudritz RE (2015) Seeding the pregenetic earth: meteoritic abundances of nucleobases and potential reaction pathways. Astrophys J 807:85. https://doi.org/10.1088/0004-637X/807/1/85
Pelc SR, Welton MGE (1966) Stereochemical relation between coding triplets and amino acids. Nature 209(5026):868–870. https://doi.org/10.1038/209868a0
Pinčák R, Bartoš E (2020) Chemical evolution of protein folding in amino acids. Chem Phys 537:110856. https://doi.org/10.1016/j.chemphys.2020.110856
Pinčák R, Bartoš E (2021) The role of codons during a natural selection. Chem Phys 540:110986. https://doi.org/10.1016/j.chemphys.2020.110986
Pino S, Sponer JE, Costanzo G, Saladino R, Di Mauro E (2015) From formamide to RNA the path is tenuous but continuous. Life 5(1):372–384. https://doi.org/10.3390/life5010372
Polyansky AA, Zagrovic B (2013) Evidence of direct complementary interactions between messenger RNAs and their cognate proteins. Nucleic Acids Res 41(18):8434–8443. https://doi.org/10.1093/nar/gkt618
Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459(7244):239–242. https://doi.org/10.1038/nature08013
Rodin AS, Szathmary E, Rodin SN (2011) On origin of genetic code and tRNA before translation. Biol Direct 6:14. https://doi.org/10.1186/1745-6150-6-14
Rogalski M, Karcher D, Bock R (2008) Superwobbling facilitates translation with reduced tRNA sets. Nat Struct Mol Biol 15(2):192–198. https://doi.org/10.1038/nsmb.1370
Rosen G (1999) Molecular content relations in the genetic code. Phys Lett A 253:354–357. https://doi.org/10.1016/S0375-9601(99)00075-4
Ruiz-Mirazo K, Briones C, de la Escosura A (2014) Prebiotic systems chemistry: new perspectives for the origins of life. Chem Rev 114(1):285–366. https://doi.org/10.1021/cr2004844
Russell MJ (2018) Green rust: the simple organizing ‘Seed’ of all life? Life 8(3):35. https://doi.org/10.3390/life8030035
Russell MJ, Hall AJ (1997) The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J Geol Soc Lond 154(3):377–402. https://doi.org/10.1144/gsjgs.154.3.0377
Russell MJ, Kanik I (2010) Why does life start, what does it do, where will it be, and how might we find it? J Cosmol 5:1008–1039
Russell MJ, Daniel RM, Hall AJ, Sherringham JA (1994) A hydrothermally precipitated catalytic iron sulphide membrane as a first step toward life. J Mol Evol 39:231–243. https://doi.org/10.1007/BF00160147
Russell MJ, Hall HJ, Martin W (2010) Serpentinization as a source of energy at the origin of life. Geobiology 8(5):355–371. https://doi.org/10.1111/j.1472-4669.2010.00249.x
Sabbah R (1980) Thermodynamique de composes azotes. V. Etude thermochimiqye de la cytosine. Thermochim Acta 35(1):73–77. https://doi.org/10.1016/0040-6031(80)85023-4
Saladino R, Crestini C, Pino S, Costanzo G, Di Mauro E (2012) Formamide and the origin of life. Phys Life Rev 9(1):84–104. https://doi.org/10.1016/j.plrev.2011.12.002
Saladino R, Carota E, Botta G, Kapralov M, Tomoshenko GN, Rozanov AY, Krasavin E, Di Mauro E (2015) Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. Proc Natl Acad Sci USA 112(21):E2746-2755. https://doi.org/10.1073/pnas.1422225112
Saralov AI (2019a) Adaptivity of archaeal and bacterial extremophiles. Microbiology 88(4):379–401. https://doi.org/10.1134/S0026261719040106 (Russian text Mikrobiologia)
Saralov AI (2019b) Selection factors for the protobiomonomers at the origin of genetic code. Intl J Appl Fund Res 10(2):243–249. https://doi.org/10.17513/mjpfi.12900 (Russian text)
Saralov AI (2020) Calculaton of combustion enthalpies amino acids and nucleobases according to their element composition and structure. Int J Appl Fund Res 3:113–121. https://doi.org/10.17513/mjpfi.13045 (Russian text)
Satzger H, Townsend D, Zgierski MZ, Patchkovskii S, Ullrich S, Stolov A (2006) Primary processes underlying the photostability of isolated DNA bases: adenine. Proc Natl Acad Sci USA 103(27):10196–10201. https://doi.org/10.1073/pnas.0602663103
Schmidt OJ (1944) Meteorite theory of the origin of the Earth and planets. DAN USSR 45:222–233 (Russian text)
Schulze-Makuch D, Airo A, Schirmack J (2017) The adaptability of life on earth and the diversity of planetary habitats. Front Microbiol 8:2011. https://doi.org/10.3389/fmicb.2017.02011
Sczepanski JT, Joyce GF (2014) A cross-chiral RNA polymerase ribozyme. Nature 515(7527):440–442. https://doi.org/10.1038/nature13900
Sella G, Ardell DH (2006) The coevolution of genes and genetic codes: Crick’s frozen accident revisited. J Mol Evol 63(3):297–313. https://doi.org/10.1007/s00239-004-0176-7
Sengupta S, Higgs PG (2005) A unified model of codon reassignment in alternative genetic codes. Genetics 170(2):831–840. https://doi.org/10.1534/genetics.104.037887
Sengupta S, Higgs PG (2015) Pathways of genetic code evolution in ancient and modern organisms. J Mol Evol 80(5–6):229–243. https://doi.org/10.1007/s00239-015-9686-8
Shimoyama A, Ponnamperuma C, Yanai K (1979) Amino acids in the Yamato carbonaceous chondrite from Antarctica. Nature 282(5737):394–396. https://doi.org/10.1038/282394a0
Siddiqui KS, Williams TJ, Wilkins D, Yau S, Allen MA, Brown MV, Lauro FM, Cavicchioli R (2013) Psychrophiles. Annu Rev Earth Planet Sci 41:87–115. https://doi.org/10.1146/annurev-earth-040610-133514
Sleep NH, Meibom A, Fridriksson T, Coleman RG, Bird DK (2004) H2-rich fluids from serpentinization: geochemical and biotic implications. Proc Natl Acad Sci USA 101(35):12818–12823. https://doi.org/10.1073/pnas.0405289101
Stiehler RD, Huffman HM (1935) Thermal data. IV. The heats of combustion of adenine, hypoxanthine, guanine, xanthine, uric acid, allantoin and alloxan. J Am Chem Soc 57(9):1734–1740. https://doi.org/10.1021/ja01312a071
Szathmary E (1993) Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc Natl Acad Sci USA 90(21):9916–9920. https://doi.org/10.1073/pnas.90.21.9916
Szathmary E (1999) The origin of the genetic code: amino acids as cofactors in an RNA World. Trends Genet 15(6):223–229. https://doi.org/10.1016/s0168-9525(99)01730-8
Tamura K (2008) Origin of amino acid homochirality: relationship with the RNA world and origin of tRNA aminoacylation. Biosystems 92(1):91–98. https://doi.org/10.1016/j.biosystems.2007.12.005
Taylor FJR, Coates D (1989) The code within the codons. Biosystems 22(3):177–187. https://doi.org/10.1016/0303-2647(89)90059-2
Trifonov EN (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261(1):139–151. https://doi.org/10.1016/S0378-1119(00)00476-5
Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22(1):1–11. https://doi.org/10.1080/07391102.2004.10506975
Trifonov EN, Kirzhner A, Kirzhner VM, Berezovsky IN (2001) Distinct stages of protein evolution as suggested by protein sequence analysis. J Mol Evol 53(4–5):394–401. https://doi.org/10.1007/s002390010229
Tupper AS, Pudritz RE, Higgs PG (2020) Can the RNA world still function without cytidine? Mol Biol Evol 37(1):71–83. https://doi.org/10.1093/molbev/msz200
Turanov AA, Lobanov AV, Fomenko DE, Morrison HG, Sogin ML, Klobutcher LA, Hatfield DL, Gladyshev VN (2009) Genetic code supports targeted insertion of two amino acids by one codon. Science 323(5911):259–261. https://doi.org/10.1126/science.1164748
Urey HC (1951) The origin and development of the earth and other terrestrial planets. Geochim Cosmochim Acta 1:209–277. https://doi.org/10.1016/0016-7037(51)90001-4
Urey HC (1962) Evidence regarding the origin of the earth. Geochim Cosmochim Acta 26:1–13. https://doi.org/10.1016/0016-7037(62)90002-9
Valley JW, Peck WH, King EM (2002) A cool early earth. Geology 30(4):351–354. https://doi.org/10.1130/0091-7613(2002)030%3c0351:ACEE%3e2.0.CO;2
Wächtershäuser G (1988) Before enzymes and templates: theory of surface metabolism. Microbiol Rec 52(4):452–484. https://doi.org/10.1128/mmbr.52.4.452-484.1988
Wächtershäuser G (2007) On the chemistry and evolution of the pioneer organism. Chem Biodivers 4(4):584–602. https://doi.org/10.1002/cbdv.200790052
Wilson SR, Watson ID, Malcolm GN (1979) Enthalpies of formation of solid cytosine, l-histidine, and uracil. J Chem Thermodyn 11(9):911–912. https://doi.org/10.1016/0021-9614(79)90073-9
Woese CR (1965) The genetic code: the molecular basis for genetic expression. Harper and Row, New York
Woese CR, Dugre SA, Dugre DH, Kando M, Saxinger WC (1966) On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol 31:723–736. https://doi.org/10.1101/sqb.1966.031.01.093
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87(12):4576–4579. https://doi.org/10.1073/pnas.87.12.4576
Woese CR, Olsen GJ, Ibba M, Söll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64:202–236. https://doi.org/10.1128/mmbr.64.1.202-236.2000
Wolf YI, Koonin EV (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2:14. https://doi.org/10.1186/1745-6150-2-14
Wong JT-F (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 72(5):1909–1912. https://doi.org/10.1073/pnas.72.5.1909
Wong JT-F (2014) Emergence of life: from functional RNA selection to natural selection and beyond. Front Biosci (Landmark Ed) 19:1117–1150. https://doi.org/10.2741/4271
Wong JT-F, Ng S-K, Mat W-K, Hu T, Xue H (2016) Coevolution theory of the genetic code at age forty: pathway to translation and synthetic life. Life 6(1):12. https://doi.org/10.3390/life6010012
Yang CM (2005) On the structural regularity in nucleobases and amino acids and relationship to the origin and evolution of the genetic code. Orig Life Evol Biosph 35(3):275–295. https://doi.org/10.10007/s11084-005-1078-4
Yarus M (2017) The genetic code and RNA-amino acid affinities. Life 7(2):13. https://doi.org/10.3390/life7020013
Yarus M, Widmann JJ, Knight R (2009) RNA-amino acid binding: a stereochemical era for the genetic code. J Mol Evol 69(5):406–429. https://doi.org/10.1007/s00239-009-9270-1
Zahonova K, Kostugov AY, Sevcikova T, Yurchenko V, Elias M (2016) An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Curr Biol 26(17):2364–2369. https://doi.org/10.1016/j.cub.2016.06.064
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I to thank two anonymous reviewers for their constructive comments, which helped to improve the manuscript. This study was performed as part of a State Assignment Project, Reg. No. NIOKTR AAAA-A19-119112290008-4.
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Saralov, A.I. Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code. Acta Biotheor 69, 745–767 (2021). https://doi.org/10.1007/s10441-021-09420-4
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DOI: https://doi.org/10.1007/s10441-021-09420-4