Origins of Life and Evolution of Biospheres

, Volume 48, Issue 2, pp 223–243 | Cite as

In the Beginning was a Mutualism - On the Origin of Translation

  • Marko Vitas
  • Andrej Dobovišek
Evolution of the Genetic Code


The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.


Origins of life Chemical evolution RNA world hypothesis Cytochrome P450 Genetic code Translation 



We would like to sincerely thank everyone who directly or indirectly contributed to the creation of this work. In particular, we would like to thank Michael J. Russell and André Brack for their critical reading of the manuscript and their useful suggestions. We would also like to thank Marko Dolinar, David H. Mathews, Peter F. Stadler, Nita Sahai, Alexei A. Sharov, Aaron Burton, Karo Michaelian, Aleksandar Simeonov, Günther Witzany and Andrew Robinson for the productive discussions and for providing us with valuable clues on references. A special thanks is acknowledged also to Robert Root-Bernstein for a clue regarding transfer factors. We also appreciate Aljaž Bolta’s help in the form of assistance in the preparation of the figures. Andrej Dobovišek acknowledges the financial support from the Slovenian Research Agency (research core funding No. P1-0055).

Compliance with Ethical Standards

Conflict of Interest

The authors declare no competing financial interest.


  1. Adamala K, Anella F, Wieczorek R, Stano P, Chiarabelli C, Luisi PL (2014) Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach. Comput Struct Biotechnol J 9:1–10. CrossRefGoogle Scholar
  2. Adami C (2015) Information-theoretic considerations concerning the origin of life. Orig Life Evol Biosph 45:309–317. PubMedCrossRefGoogle Scholar
  3. Annila A, Baverstock K (2014) Genes without prominence: a reappraisal of the foundations of biology. J R Soc Interface 11:20131017. PubMedPubMedCentralCrossRefGoogle Scholar
  4. Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, Gossett JJ, Lie L, Bowman JC, O’Neill E, Bernier CR, Hud NV, Wartell RM, Harvey SC, Williams LD (2012) RNA folding and catalysis mediated by iron (II). PLoS One 7:e38024. PubMedPubMedCentralCrossRefGoogle Scholar
  5. Balke D, Kuss A, Müller S (2016) Landmarks in the evolution of (t)-RNAs from the origin of life up to their present role in human cognition. Life 6:4–13. CrossRefGoogle Scholar
  6. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Ǻ resolution. Science 289:905–920. PubMedCrossRefGoogle Scholar
  7. Baymann F, Lebrun E, Brugna M, Schoepp-Cothenet B, Guidici-Oritconi MT, Nitschke W (2003) The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. Phil Tran R Soc B 358:267–274. CrossRefGoogle Scholar
  8. Beckwith SVW, Sargent AI (1996) Circumstellar disks and the search for neighbouring planetary systems. Nature 383:139–144. PubMedCrossRefGoogle Scholar
  9. Bowman JC, Hud NV, Williams LD (2015) The ribosome challenge to the RNA world. J Mol Evol 80:143–161. PubMedCrossRefGoogle Scholar
  10. Brack A (2007) From interstellar amino acids to prebiotic catalytic peptides: a review. Chem Biodivers 4:665–679. PubMedCrossRefGoogle Scholar
  11. Brack A (2010) Origin of life. In: Encyclopedia of life sciences. John Wiley & Sons, Ltd. (eds), Wiley, Ltd. Chichester.
  12. Brandman R, Brandman Y, Pande VS (2012) Sequence coevolution between RNA and protein characterized by mutual information between residue triplets. PLoS One 7:e30022. PubMedPubMedCentralCrossRefGoogle Scholar
  13. Caetano-Anollés G, Caetano-Anollés D (2015) Computing the origin and evolution of the ribosome from its structure - uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 13:427–447. PubMedPubMedCentralCrossRefGoogle Scholar
  14. Caetano-Anollés D, Caetano-Anollés G (2017) Commentary: history of the ribosome and the origin of translation. Front Mol Biosci 3:1–3. CrossRefGoogle Scholar
  15. Cafferty BJ, Fialho DM, Khanam J, Krishnamurthy R, Hud NV (2016) Spontaneous formation and base pairing of plausible prebiotic nucleotides in water. Nat Commun 7:11328. PubMedPubMedCentralCrossRefGoogle Scholar
  16. Callahan MP, Smith KE, Cleaves HJ II, Ruzicka J, Stern JC, Glavin DP, House CH, Dworkin JP (2011) Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci U S A 108:13995–13998. PubMedPubMedCentralCrossRefGoogle Scholar
  17. Carter CW Jr, Wolfenden R (2015) tRNA acceptor stem and anticodon bases form independent codes related to protein folding. Proc Natl Acad Sci U S A 112:7489–7494. PubMedPubMedCentralCrossRefGoogle Scholar
  18. Cech TR (2000) The ribosome is a ribozyme. Science 289:878–879. PubMedCrossRefGoogle Scholar
  19. Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77–93. PubMedCrossRefGoogle Scholar
  20. Cleaves HJ, Chalmers JH, Lazcano A, Miller SL, Bada JL (2008) A reassessment of prebiotic organic synthesis in neutral planetary atmospheres. Orig Life Evol Biosph 38:105–115. PubMedCrossRefGoogle Scholar
  21. Copley SD, Smith E, Morowitz HJ (2007) The origin of the RNA world: co-evolution of genes and metabolism. Bioorg Chem 35:430–443. PubMedCrossRefGoogle Scholar
  22. Corliss JB (1986) On the creation of living cells in submarine hot spring flow reactors: attractors and bifurcations in the natural hierarchy dissipative systems. Orig Life Evol Biosph 19:381–382. CrossRefGoogle Scholar
  23. Corliss JB, Baross JA, Hoffman SE (1981) An hypothesis concerning the relationships between submarine hot springs and the origin of life on earth. Oceanol Acta, Proccedings of 26th international geological congress, Paris, July 7-17, 1980, pp 59–69Google Scholar
  24. Cupal J, Kopp S, Stadler PF (2000) RNA shape space topology. Artif Lif 6:3–23. CrossRefGoogle Scholar
  25. Dalai P, Kaddour H, Sahai N (2016) Incubating life: prebiotic sources of organics for the origin of life. Elements 12:401–406CrossRefGoogle Scholar
  26. Deamer D (2009) First life, and next life. Synthetic biology is a new field, but it’s centered on an old question: how did life begin? Technol Rev 112:66–73Google Scholar
  27. Deamer D, Dworkin JP, Sandford SA, Bernstein MP, Allamandola LJ (2002) The first cell membranes. Astrobiology 2:371–381. PubMedCrossRefGoogle Scholar
  28. Dixon B (1994) Power unseen, how microbes rule the world. W.H. Freeman and company, New YorkGoogle Scholar
  29. Dutta D, Ghosh DK, Mishra AK, Samanta TB (1983) Induction of benz[a]pyren hydroxylase in Aspergillus ochraceus TS: evidences of multiple forms of cytochrome P-450. Biochem Biophys Res Commun 115:692–699. PubMedCrossRefGoogle Scholar
  30. de Duve C (1995) The beginnings of life on earth. Am Sci 83:428–437Google Scholar
  31. de Duve C (1998) Clues from present - day biology: the tioester world. In: Brack A (ed) The molecular origins of life. Cambridge University Press, Cambridge, pp 219–236CrossRefGoogle Scholar
  32. de Duve C (2003) A research proposal on the origin of life. Orig Life Evol Biosph 33:559–574. PubMedCrossRefGoogle Scholar
  33. Ehrenfreund P, Rasmussen S, Cleaves J, Chen L (2006) Experimentally tracing the key steps in the origin of life: the aromatic world. Astrobiology 6:490–520. PubMedCrossRefGoogle Scholar
  34. El-Hani NC, Queiroz J, Emmeche C (2006) A semiotic analysis of the genetic information system. Semiotica 160:1–68. CrossRefGoogle Scholar
  35. Eschenmoser A (1988) Vitamin B12: experiments concerning the origin of its molecular structure. Angew Chem Int Ed 27:5–39. CrossRefGoogle Scholar
  36. Fan K, Wang W (2003) What is the minimum number of letters required to fold a protein? J Mol Biol 328:921–926. PubMedCrossRefGoogle Scholar
  37. Ferus M, Pietrucci F, Saitta AM, Knížek A, Kubelík P, Ivaneka O, Shestivska V, Civiša S (2017) Formation of nucleobases in a miller–Urey reducing atmosphere. Proc Natl Acad Sci U S A 114:4306–4311. PubMedPubMedCentralCrossRefGoogle Scholar
  38. Fox GE (2016) Origins and early evolution of the ribosome. In: Hernández G, Jagus R (eds) Evolution of the protein synthesis machinery and its regulation, springer international publishing Switzerland, pp 31–60CrossRefGoogle Scholar
  39. Fox S, Strasdeit H (2013) A possible prebiotic origin on volcanic islands of oligopyrrole-type photopigments and electron transfer cofactors. Astrobiology 13:578–595. PubMedCrossRefGoogle Scholar
  40. Fraix-Burnet D, Chattopadhyay T, Chattopadhyay AK, Davoust E, Thuillard M (2012) A six-parameter space to describe galaxy diversification. A & A 545:1–24. CrossRefGoogle Scholar
  41. Friedmann MP, Torbeev V, Zelenay V, Sobol A, Greenwald J, Riek R (2015) Towards prebiotic catalytic amyloids using high throughput screening. PLoS One 10:e0143948. PubMedPubMedCentralCrossRefGoogle Scholar
  42. Ghosh DK, Dutta D, Samanta TB, Mishra AK (1983) Microsomal benz[a]pyren hydrooxylase in Aspergillus ochraceus TS: assay and characterisation of the enzyme system. Biochem Biophys Res Commun 113:497–505. PubMedCrossRefGoogle Scholar
  43. Goodwin JT, Mehta AK, Lynn DG (2012) Digital and analog chemical evolution. Acc Chem Res 45:2189–2199. PubMedCrossRefGoogle Scholar
  44. Goodwin JT, Lynn DG, Burrows C, Walker S, Amin S, Armbrust EV (2014) Alternative chemistries of life, Empirical Approaches, A Report from a workshop on alternative chemistries of life: empirical approaches. Accessed 24 October 2014
  45. Gordon-Smith C (2011) Non-template molecules designed for open-ended evolution. In: Lenaerts T, Giacobini M, Bersini H, Bourgin P, Dorigo M, Doursat R (eds) Advances in artificial life ECAL, proceedings of the eleventh euorpean conference on the synthesis and simulation of living systems. Massachusetts Institute of Technology, USA, pp 268–275Google Scholar
  46. Gorlero M, Wieczorek R, Adamala K, Giorgi A, Schininá ME, Stano P, Luisi PL (2009) Ser-his catalyses the formation of peptides and PNAs. FEBS Lett 583:153–156. PubMedCrossRefGoogle Scholar
  47. Halevy I, Alesker M, Schuster EM, Popovitz-Biro R, Feldman Y (2017) A key role for green rust in the precambrian oceans and the genesis of iron formations. Nat Geosci 10:135–139. CrossRefGoogle Scholar
  48. Harish A, Caetano-Anolles G (2012) Ribosomal history reveals origins of modern protein synthesis. PLoS One 7:e32776. PubMedPubMedCentralCrossRefGoogle Scholar
  49. Higgs PG, Lehman N (2014) The RNA world: molecular cooperation at the origins of life. Nat Rev Genet 16:7–17. PubMedCrossRefGoogle Scholar
  50. Higgs PG, Pudritz RE (2009) A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9:483–490. PubMedCrossRefGoogle Scholar
  51. Ho BK, Dill KA (2006) Folding very short peptides using molecular dynamics. PLoS Comput Biol 2:e27. PubMedPubMedCentralCrossRefGoogle Scholar
  52. Hodgson GW, Ponnamperuma C (1968) Prebiotic porphyrin genesis: porphyrins from electric discharge in methane, ammonia and water vapour. Proc Natl Acad Sci U S A 59:22–28PubMedPubMedCentralCrossRefGoogle Scholar
  53. Hordijk W, Steel M (2014) Conditions for evolvability of autocatalytic sets: a formal example and analysis. Orig Life Evol Biosph 44:111–124. PubMedCrossRefGoogle Scholar
  54. Hordijk W, Steel M, Kauffman S (2012) The structure of autocatalytic sets: evolvability, enablement and emergence. Acta Biotheor 60:379–392. PubMedCrossRefGoogle Scholar
  55. Hsiao C, Williams LD (2009) A recurrent magnesium-binding motif provides a framework for ribosomal peptidyl transferase center. Nucleid Acids Res 37:3134–3142. CrossRefGoogle Scholar
  56. Hsiao C, Chou IC, Okafor CD, Bowman JC, O’Neill EB, Athavale SS, Petrov AS, Hud NV, Wartell RM, Harvey SC, Williams LD (2013) RNA with iron(II) as a cofactor catalyses electron transfer. Nat Chem 5:525–528. PubMedCrossRefGoogle Scholar
  57. Hud NV (2016) Our odyssey to find a plausible prebiotic path to RNA: the first twenty years. Synlett 28:36–55. CrossRefGoogle Scholar
  58. Hwang S (2012) Investigation of peptide folding by nuclear magnetic resonance spectroscopy. Dissertation, Texas A&M UniversityGoogle Scholar
  59. Ivica NA, Obermayer B, Campbell GW, Rajamani S, Gerland U, Chen IA (2013) The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability. J Mol Evol 77:55–63. PubMedCrossRefGoogle Scholar
  60. Jackson JB (2016) Natural pH gradients in hydrothermal alkali vents were unlikely to have played a role in the origin of life. J Mol Evol 83:1–11. PubMedPubMedCentralCrossRefGoogle Scholar
  61. Jadhav VR, Yarus M (2002) Coenzymes as co-ribozymes. Biochimie 84:877–888. PubMedCrossRefGoogle Scholar
  62. Jahn D, Moser J, Schubert WD, Heinz DW (2006) Transfer RNA-dependent aminolevulinic acid formation: structure and function of glutamyl-tRNA synthetase, reductase and glutamate-1-semialdehyde-2,1-aminomutase. In: Grimm B, Porra RJ, Rüdiger W, Scheer H (eds) Chlorophylls and bacteriochlorophylls: biochemistry, biophysics, functions and applications. Springer, Netherlands, pp 159–171CrossRefGoogle Scholar
  63. Johnson DBF, Wang L (2010) Imprints of the genetic code in the ribosome. Proc Natl Acad Sci U S A 107:8298–8303. PubMedPubMedCentralCrossRefGoogle Scholar
  64. Kaddour H, Sahai N (2014) Synergism and mutualism in non-enzymatic RNA polymerization. Life (Basel) 4:598–620. CrossRefGoogle Scholar
  65. Kappler A, Emerson D, Gralnick JA, Roden EE, Muehe EM (2015) Geomicrobiology of iron, In: Ehrlich HL, Newman DK, Kappler A (eds) Geomicrobiology, 6th edition, CRC Press, pp 343–399Google Scholar
  66. Kasting JF (1993) Earth’s early atmosphere. Science 259:920–926. PubMedCrossRefGoogle Scholar
  67. Kasting JF, Catling D (2003) Evolution of a habitable planet. Annu Rev Astron Astrophys 41:429–463. CrossRefGoogle Scholar
  68. Kasting JF, Howard MT (2006) Atmospheric composition and climate on the early earth. Phil Trans R Soc B 361:1733–1742. PubMedCrossRefGoogle Scholar
  69. Kauffman SA (1971) Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. J Cybern 1:71–96. CrossRefGoogle Scholar
  70. Kauffman S (2007) Question 1: origin of life and the living state. Orig Life Evol Biosph 37:315–322. PubMedCrossRefGoogle Scholar
  71. Keller MA, Turchyn AV, Ralser M (2014) Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean Ocean. Mol Syst Biol 10:725. PubMedPubMedCentralCrossRefGoogle Scholar
  72. Kelly SL, Kelly DE (2013) Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? Phil Trans R Soc B 368:20120476. PubMedCrossRefGoogle Scholar
  73. Knight R (2007) Reviewers’ comments: wolf YI, Koonin EV: on the origin of the translation system and the genetic code in the RNA world by means of natural selection, and sub functionalization. Biol Direct 2:1–25. CrossRefGoogle Scholar
  74. Kovacs NA, Petrov AS, Lanier KA, Williams LD (2017) Frozen in time: the history of proteins. Mol Biol Evol 34:1252–1260. PubMedPubMedCentralCrossRefGoogle Scholar
  75. Kurland CG (2010) The RNA dreamtime. Bioassays 32:866–871. CrossRefGoogle Scholar
  76. Lanier KA, Petrov AS, Williams LD (2017a) The central symbiosis of molecular biology: molecules in mutualism. J Mol Evol 85:8–13. PubMedPubMedCentralCrossRefGoogle Scholar
  77. Lanier KA, Roy P, Schneider DM, Williams LD (2017b) Ancestral interactions of ribosomal RNA and ribosomal proteins. Biophys J 113:268–276. PubMedCrossRefPubMedCentralGoogle Scholar
  78. Lawrence HS, Borkowsky W (1983) A new basis for the immunoregulatory activities of transfer factor-an arcane dialect in the language of cells. Cell Immunol 82:102–116PubMedCrossRefGoogle Scholar
  79. Lehman N, Díaz Arenas C, White WA, Schmidt FJ (2011) Complexity through recombination: from chemistry to biology. Entropy 13:17–37. CrossRefGoogle Scholar
  80. Lehman N, Bernhard T, Larson BC, Robinson AJN, Southgate CCB (2014) Empirical demonstration of environmental sensing in catalytic RNA: evolution of interpretive behaviour at the origins of life. BMC Evol Biol 14:1–11. CrossRefGoogle Scholar
  81. Luisi PL (2006) The emergence of life, from chemical origins to synthetic biology. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  82. Lupas AN, Alva V (2017) Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins. J Struct Biol 198:74–81. PubMedCrossRefGoogle Scholar
  83. Martin W, Baross J, Kelley D, Russell MJ (2008) Hydrothermal vents and the origin of life. Nature 6:805–814. CrossRefGoogle Scholar
  84. Maynard Smith J, Szathmáry E (1995) The major evolutionary transitions. W.H. Freeman Spectrum, OxfordGoogle Scholar
  85. Melton DE, Swanner ED, Behrens S, Schmidt C, Kappler A (2014) The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol 12:797–808. PubMedCrossRefGoogle Scholar
  86. Michaelian K, Simeonov A (2015) Fundamental molecules of life are pigments which arose and co-evolved as a response to the thermodynamic imperative of dissipating the prevailing solar spectrum. Biogeosciences 12:4913–4937. CrossRefGoogle Scholar
  87. Miller SL (1953) The production of amino acids under possible primitive earth conditions. Science 117:528–529. PubMedCrossRefGoogle Scholar
  88. Miller SL (1998) The endogenous synthesis of organic compounds. In: Brack A (ed) The molecular origins of life. Cambridge University Press, Cambridge, pp 59–85CrossRefGoogle Scholar
  89. Milner-White EJ, Russell MJ (2008) Predicting peptide and protein conformations in early evolution. Biol Direct 3:1–9. CrossRefGoogle Scholar
  90. Milner-White EJ, Russell MJ (2011) Functional capabilities of the earliest peptides and the emergence of life. Genes 2:671–688. PubMedPubMedCentralCrossRefGoogle Scholar
  91. Moore PB, Steitz TA (2010) The roles of RNA in the synthesis of protein. Cold Spring Harb Perspect Biol 3:1–17. CrossRefGoogle Scholar
  92. Moore B, Katz N, Lake G, Dressler A, Oemler A (1996) Galaxy harassment and the evolution of clusters of galaxies. Nature 379:613–616. CrossRefGoogle Scholar
  93. Murphy M P, O'Neill LAJ (1997) What is life? The next fifty years. An introduction. In: Murphy MP, O' Neill LAJ (eds) What is life? The next fifty years, Cambridge University Press, Cambridge, pp 1–4Google Scholar
  94. Myles IA, Zhao M, Nardone G, Olano LR, Reckhow JD, Saleem D, Break TJ, Lionakis MS, Myers TG, Gardina PJ, Kirkpatrick CH, Holland SM, Datta SK (2016) CD8 + T cells produce a dialyzable antigen-specific activator of dendritic cells. J Leukoc Biol 100:1–14. CrossRefGoogle Scholar
  95. Nelson DR, Goldstone JV, Stegeman JJ (2013) The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. Phil Trans R Soc B 368:20120474. PubMedCrossRefGoogle Scholar
  96. Nitschke W, McGlynn SE, Milner-White EJ, Russell MJ (2013) On the antiquity of metalloenzymes and their substrates in bioenergetics. Biochim Biophys Acta 1827:871–881. PubMedCrossRefGoogle Scholar
  97. Noller HF (2012) Evolution of protein synthesis from an RNA world. Cold Spring Harb Perspect Biol 4:1–14. CrossRefGoogle Scholar
  98. Noller HF, Hoffarth V, Zimniak L (1992) Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416–1419. PubMedCrossRefGoogle Scholar
  99. Öberg KI, Guzmán VV, Furuya K, Qi C, Aikawa Y, Andrews SM, Loomis R, Wilner DJ (2015) The comet-like composition of a protoplanetary disk as revealed by complex cyanides. Nature 520:198–201. PubMedCrossRefGoogle Scholar
  100. Oda A, Fukuyoshi S (2015) Predicting three-dimensional conformations of peptides constructed of only glycine, alanine, aspartic acid, and valine. Orig Life Evol Biosph 45:183–193. PubMedCrossRefGoogle Scholar
  101. Okafor CD, Lanier KA, Petrov AS, Athavale S, Bowman JC, Hud NV, Williams LD (2017) Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event. Nucleic Acids Res 45:3634–3642. PubMedPubMedCentralCrossRefGoogle Scholar
  102. Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99–123. PubMedCrossRefGoogle Scholar
  103. Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, Williams LD (2014) Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci U S A 111:10251–10256. PubMedPubMedCentralCrossRefGoogle Scholar
  104. Petrov AS, Gulen B, Norris AM, Kovacs NA, Bernier CR, Lanier KA, Fox GE, Harvey SC, Wartell RM, Hud NV, Williams LD (2015) History of the ribosome and the origin of translation. Proc Natl Acad Sci U S A 112:15396–15401. PubMedPubMedCentralCrossRefGoogle Scholar
  105. Piast RW, Wieczorek R (2017) Origin of life and the phosphate transfer catalyst. Astrobiology 17:277–285. PubMedCrossRefGoogle Scholar
  106. Pizzarello S, Shock E (2010) The organic composition of carbonaceous meteorites: the evolutionary story ahead of biochemistry. Cold Spring Harb Perspect Biol 2:1–20. CrossRefGoogle Scholar
  107. Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1–17. PubMedCrossRefGoogle Scholar
  108. Poon LCH, Methot SP, Morabi-Pazooki W, Pio F, Bennet AJ, Sen D (2011) Guanine-rich RNAs and DNAs that bind heme robustly catalyze oxygen transfer reactions. J Am Chem Soc 133:1877–1884. PubMedCrossRefGoogle Scholar
  109. Pressman A, Blanco C, Chen IA (2015) The RNA world as a model system to study the origin of life. Curr Biol 25:953–963. CrossRefGoogle Scholar
  110. Pross A (2004) Causation and the origin of life. Metabolism or replication first? Origin Life Evol Biosph 34:307–321. CrossRefGoogle Scholar
  111. Pulido P, Perello C, Rodriguez-Concepcion M (2012) New insights into plant isoprenoid metabolism. Mol Plant 5:964–967. PubMedCrossRefGoogle Scholar
  112. Raag R, Whitlow M (1995) Single-chain Fvs. FASEB J 9:73–80PubMedCrossRefGoogle Scholar
  113. Raffaelli N (2011) Nicotinamide coenzyme synthesis: a case of ribonucleotide emergence or a byproduct of the RNA world? In: Egel R (ed) Origins of life: the primal self-organization. Springer-Verlag, Berlin, pp 185–208CrossRefGoogle Scholar
  114. Robinson A, Southgate C (2010) A general definition of interpretation and its application to origin of life research. Biol Philos 25:163–181. CrossRefGoogle Scholar
  115. Root-Bernstein M, Root-Bernstein R (2015) The ribosome as a missing link in the evolution of life. J Theor Biol 367:130–158. PubMedCrossRefGoogle Scholar
  116. Russell MJ, Hall AJ (2009) The hydrothermal source of energy and materials at the origin of life. In: Zaikowski L, Friedrich JM, Seidel SR (eds) Chemical evolution II: from the origins of life to modern society, ACS symposium series; American chemical society, Washington, pp 45–62Google Scholar
  117. Russell MJ, Nitschke W (2017) Methane: fFuel or exhaust at the emergence of life? Astrobiology 17:1053–1066. PubMedPubMedCentralCrossRefGoogle Scholar
  118. 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. CrossRefGoogle Scholar
  119. Russell MJ, Nitschke W, Branscomb E (2013) The inevitable journey to being. Phil Trans R Soc B 368:20120254. PubMedCrossRefGoogle Scholar
  120. Schönheit P, Buckel W, Martin WF (2016) On the origin of heterotrophy. Trends Microbiol 24:12–25. PubMedCrossRefGoogle Scholar
  121. Sen D, Poon LCH (2011) RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean? Crit Rev Biochem Mol Biol 46:478–492. PubMedCrossRefGoogle Scholar
  122. Sephton MA (2002) Organic compounds in carbonaceous meteorites. Nat Prod Rep 19:292–311PubMedCrossRefGoogle Scholar
  123. Shapiro R (2000) A replicator was not involved in the origin of life. IUBMB Life 49:173–176. PubMedCrossRefGoogle Scholar
  124. Shapiro R (2007) A simpler origin for life. Sci Am 296:46–53PubMedCrossRefGoogle Scholar
  125. Shapiro JA (2014) Physiology of the read–write genome. J Physiol 592:2319–2341. PubMedPubMedCentralCrossRefGoogle Scholar
  126. Shapiro JA (2016a) Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol 52:1–17. PubMedCrossRefGoogle Scholar
  127. Shapiro JA (2016b) The basic concept of the read-write genome: mini-review on cell-mediated DNA modification. Biosystems 140:35–37. PubMedCrossRefGoogle Scholar
  128. Sharov AA (2009) Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life. Int J Mol Sci 10:1838–1852. PubMedPubMedCentralCrossRefGoogle Scholar
  129. Sharov AA (2016) Coenzyme world model of the origin of life. Biosystems 144:8–17. PubMedPubMedCentralCrossRefGoogle Scholar
  130. Shaw GH (2008) Earth’s atmosphere – hadean to early proterozoic. Chem Erde 68:235–264. CrossRefGoogle Scholar
  131. Shi Z, C Olson CA, Rose GD, Baldwin RL, Kallenbach NL (2002) Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci U S A 99:9190–9195. PubMedPubMedCentralCrossRefGoogle Scholar
  132. Simionescu CI, Simionescu BC, Mora R, Leancâ M (1978) Porphyrin-like compounds genesis under simulated abiotic conditions. Orig Life Evol Biosph 9:103–114. CrossRefGoogle Scholar
  133. Škrlj N, Dolinar M (2014) New engineered antibodies against prions. Bioengineered 5(1):10–14. PubMedCrossRefGoogle Scholar
  134. Škrlj N, Čurin Šerbec V, Dolinar M (2010) Single-chain Fv antibody fragments retain binding properties of the monoclonal antibody raised against peptide P1 of the human prion protein. Appl Biochem Biotechnol 160:1808–1821. PubMedCrossRefGoogle Scholar
  135. Smith JE, Mowles AK, Mehta AK, Lynn DG (2014) Looked at life from both sides now. Life 4:887–902. PubMedPubMedCentralCrossRefGoogle Scholar
  136. Sousa FL, Hordijk W, Steel M, Martin WF (2015) Autocatalytic sets in E. coli metabolism. J Syst Chem 6:1–21. CrossRefGoogle Scholar
  137. Spitzer J, Pielak GJ, Poolman B (2015) Emergence of life: physical chemistry changes the paradigm. Biol Direct 10:1–15. CrossRefGoogle Scholar
  138. Stryer L (1988) Biochemistry (3rd edition). W.H. Freeman and company, New York, pp 906–910Google Scholar
  139. Su F, Takaya N, Shoun H (2004) Nitrous oxide-forming codenitrification catalyzed by cytochrome P450nor. Biosci Biotechnol Biochem 68:473–475. PubMedCrossRefGoogle Scholar
  140. Szathmáry E (2015) Toward major evolutionary transitions theory 2.0. Proc Natl Acad Sci U.S.A. 112:10104–10111. PubMedPubMedCentralCrossRefGoogle Scholar
  141. Szathmáry E, Maynard Smith J (1995) The major evolutionary transitions. Nature 374:227–232. PubMedCrossRefGoogle Scholar
  142. Taran O, Chen C, Omosun TO, Hsieh M-C, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG (2017) Expanding the informational chemistries of life: peptide/RNA networks. Philos Trans A Math Phys Eng Sci 28:20160356. CrossRefGoogle Scholar
  143. Tashiro T, Ishida A, Hori M, Igisu M, Koike M, Méjean P, Takahata N, Sano Y, Komiya T (2017) Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada. Nature 549:516–518. PubMedCrossRefGoogle Scholar
  144. Tessera M (2011) Origin of evolution versus origin of life: a shift of paradigm. Int J Mol Sci 12:3445–3458. PubMedPubMedCentralCrossRefGoogle Scholar
  145. Ts’o POP (1974) Bases, nucleosides, and nucleotides. In: Ts’o POP (ed) Basic principles in nucleic acid chemistry. Academic Press, New York, pp 453–584CrossRefGoogle Scholar
  146. Turk RM, Chumachenko NV, Yarus M (2010) Multiple translational products from a five-nucleotide ribozyme. Proc Natl Acad Sci U S A 107:4585–4589. PubMedPubMedCentralCrossRefGoogle Scholar
  147. Turner DH, Mathews DH (2010) NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res 38:280–282. CrossRefGoogle Scholar
  148. Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N (2012) Spontaneous network formation among cooperative RNA replicators. Nature 491:72–77. PubMedCrossRefGoogle Scholar
  149. Vasas V, Fernando C, Santos M, Kauffman S, Szathmáry E (2012) Evolution before genes. Biol Direct 7:1–14. PubMedPubMedCentralCrossRefGoogle Scholar
  150. Venkateswarlu K, Marsh RM, Faber B, Kelly SL (1996) Investigation of cytochrome P450 mediated benzo[a]pirene hydroxylation in Aspergillus fumigatus. J Chem Tech Biotechnol 66:139–144.;2-D CrossRefGoogle Scholar
  151. Villarreal LP, Witzany G (2015) When competing viruses unify: evolution, conservation, and plasticity of genetic identities. J Mol Evol 80:305–318. PubMedCrossRefGoogle Scholar
  152. Vitas M (2011) On the theory of species evolution through natural selection. Original title: O teoriji razvoja vrst s pomočjo naravne selekcije. Apokalipsa: revija za preboj v živo kulturo 152:113–122Google Scholar
  153. Vitas M, Dobovišek A (2014) Evolution, transposition, transformation and flow of information. Anali Pazu 4:66–74Google Scholar
  154. Vitas M, Dobovišek A (2017) On a quest of reverse translation. Found Chem 19:139–155. CrossRefGoogle Scholar
  155. Viza D, Fudenberg HH, Palareti A, Ablashi D, De Vinci C, Pizza G (2013) Transfer factor: an overlooked potential for the prevention and treatment of infectious diseases. Folia Biol (Praha) 59:53–67Google Scholar
  156. Wachowius F, Attwater J, Holliger P (2017) Nucleic acids: function and potential for abiogenesis. Q Rev Biophys 50:e4. PubMedCrossRefGoogle Scholar
  157. Wächtershäuser G (1998) Origin of life in an iron – sulfur world. In: Brack A (ed) The molecular origins of life. Cambridge University Press, Cambridge, pp 206–218CrossRefGoogle Scholar
  158. Wächtershäuser G (2006) From volcanic origins of chemoautotrophic life to bacteria, archaea and eukarya. Phil Trans R Soc B 361:1787–1808. PubMedCrossRefGoogle Scholar
  159. White HB 3rd (1976) Coenzymes as fossils of an earlier metabolic state. J Mol Evol 7:101–104PubMedCrossRefGoogle Scholar
  160. Wieczorek R, Dörr M, Chotera A, Luisi PL, Monnard PA (2013) Formation of RNA phosphodiester bond by histidine-containing dipeptides. Chembiochem 14:217–223. PubMedCrossRefGoogle Scholar
  161. Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P (2017) Small and random peptides: an unexplored reservoir of potentially functional primitive organocatalysts. The case of seryl-histidine. Life 7:1–24. CrossRefGoogle Scholar
  162. Wills PR, Carter CW Jr (2018) Insuperable problems of the genetic code initially emerging in an RNA world. Biosystems 164:155–166. PubMedCrossRefGoogle Scholar
  163. Witzany G (2017) Two genetic codes: repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives. Commun Integr Biol 10:e1297352. PubMedPubMedCentralCrossRefGoogle Scholar
  164. Yarus M (2010) Getting past the RNA world: the initial Darwinian ancestor. Cold Spring Harb Perspect Biol 1:1–8. CrossRefGoogle Scholar
  165. Yarus M (2011) The meaning of a minuscule ribozyme. Phil Trans R Soc B 366:2902–2909. PubMedCrossRefGoogle Scholar
  166. Yeates JAM, Lehman N (2016) RNA networks at the origins of life. Biochemist 38:8–12Google Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Marko Vitas
    • 1
  • Andrej Dobovišek
    • 2
  1. 1.BorovnicaSlovenia
  2. 2.Faculty of Natural Sciences and MathematicsUniversity of MariborMariborSlovenia

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