ConspectusIn the quest to understand prebiotic catalysis, different molecular entities, mainly minerals, metal ions, organic cofactors, and ribozymes, have been implied as key players. Of these, inorganic and organic cofactors have gained attention for their ability to catalyze a wide array of reactions central to modern metabolism and frequently participate in these reactions within modern enzymes. Nevertheless, bridging the gap between prebiotic and modern metabolism remains a fundamental question in the origins of life.In this Account, peptides are investigated as a potential bridge linking prebiotic catalysis by minerals/cofactors to enzymes that dominate modern life's chemical reactions. Before ribosomal synthesis emerged, peptides of random sequences were plausible on early Earth. This was made possible by different sources of amino acid delivery and synthesis, as well as their condensation under a variety of conditions. Early peptides and proteins probably exhibited distinct compositions, enriched in small aliphatic and acidic residues. An increase in abundance of amino acids with larger side chains and canonical basic groups was most likely dependent on the emergence of their more challenging (bio)synthesis. Pressing questions thus arise: how did this composition influence the early peptide properties, and to what extent could they contribute to early metabolism?Recent research from our group and colleagues shows that highly acidic peptides/proteins comprising only the presumably "early" amino acids are in fact competent at secondary structure formation and even possess adaptive folding characteristics such as spontaneous refoldability and chaperone independence to achieve soluble structures. Moreover, we showed that highly acidic proteins of presumably "early" composition can still bind RNA by utilizing metal ions as cofactors to bridge carboxylate and phosphoester functional groups. And finally, ancient organic cofactors were shown to be capable of binding to sequences from amino acids considered prebiotically plausible, supporting their folding properties and providing functional groups, which would nominate them as catalytic hubs of great prebiotic relevance.These findings underscore the biochemical plausibility of an early peptide/protein world devoid of more complex amino acids yet collaborating with other catalytic species. Drawing from the mechanistic properties of protein-cofactor catalysis, it is speculated here that the early peptide/protein-cofactor ensemble could facilitate a similar range of chemical reactions, albeit with lower catalytic rates. This hypothesis invites a systematic experimental test.Nonetheless, this Account does not exclude other scenarios of prebiotic-to-biotic catalysis or prioritize any specific pathways of prebiotic syntheses. The objective is to examine peptide availability, composition, and functional potential among the various factors involved in the emergence of early life.

Department of Cell Biology Faculty of Science Charles University Prague 12800 Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague 16610 Czech Republic

Zobrazit více v PubMed

Tretyachenko V.; Vymetal J.; Neuwirthova T.; Vondrasek J.; Fujishima K.; Hlouchova K. Modern and prebiotic amino acids support distinct structural profiles in proteins. Open Biology 2022, 12, 220040.10.1098/rsob.220040. PubMed DOI PMC

Makarov M.; Sanchez Rocha A. C.; Krystufek R.; Cherepashuk I.; Dzmitruk V.; Charnavets T.; Faustino A. M.; Lebl M.; Fujishima K.; Fried S. D.; Hlouchova K. Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability. J. Am. Chem. Soc. 2023, 145 (9), 5320–5329. 10.1021/jacs.2c12987. PubMed DOI PMC

Giacobelli V. G.; Fujishima K.; Lepsik M.; Tretyachenko V.; Kadava T.; Bednarova L.; Novak P.; Hlouchova K.; Makarov M. In vitro evolution reveals non-cationic protein – RNA interaction mediated by metal ions. Mol. Biol. Evol. 2022, 39, msac032.10.1093/molbev/msac032. PubMed DOI PMC

Sanchez Rocha A. C.; Makarov M.; Novotny M.; Hlouchova K. Coenzyme-Protein Interactions since Early Life. eLife 2024, 13, RP94174.10.7554/eLife.94174.1. DOI

Hiller D. A.; Strobel S. A. The chemical versatility of RNA. Philosophical Transactions of the Royal Society B: Biological Sciences 2011, 366 (1580), 2929–35. 10.1098/rstb.2011.0143. PubMed DOI PMC

Muchowska K. B.; Varma S. J.; Moran J. Nonenzymatic metabolic reactions and life’s origins. Chem. Rev. 2020, 120 (15), 7708–44. 10.1021/acs.chemrev.0c00191. PubMed DOI

Wieczorek R.; Adamala K.; Gasperi T.; Polticelli F.; Stano P. Small and random peptides: An unexplored reservoir of potentially functional primitive organocatalysts. The case of seryl-histidine. Life 2017, 7 (2), 19.10.3390/life7020019. PubMed DOI PMC

Stubbs R. T.; Yadav M.; Krishnamurthy R.; Springsteen G. A plausible metal-free ancestral analogue of the Krebs cycle composed entirely of α-ketoacids. Nat. Chem. 2020, 12 (11), 1016–22. 10.1038/s41557-020-00560-7. PubMed DOI PMC

Dherbassy Q.; Mayer R. J.; Muchowska K. B.; Moran J. Metal-Pyridoxal Cooperativity in Nonenzymatic Transamination. J. Am. Chem. Soc. 2023, 145 (24), 13357–13370. 10.1021/jacs.3c03542. PubMed DOI

Fischer J. D.; Holliday G. L.; Rahman S. A.; Thornton J. M. The structures and physicochemical properties of organic cofactors in biocatalysis. J. Mol. Biol. 2010, 403 (5), 803–24. 10.1016/j.jmb.2010.09.018. PubMed DOI

Alva V.; Söding J.; Lupas A. N. A vocabulary of ancient peptides at the origin of folded proteins. eLife 2015, 4, e0941010.7554/eLife.09410. PubMed DOI PMC

Kolodny R.; Nepomnyachiy S.; Tawfik D. S.; Ben-Tal N. Bridging themes: short protein segments found in different architectures. Mol. Biol. Evol. 2021, 38 (6), 2191–208. 10.1093/molbev/msab017. PubMed DOI PMC

Minami S.; Kobayashi N.; Sugiki T.; Nagashima T.; Fujiwara T.; Tatsumi-Koga R.; Chikenji G.; Koga N. Exploration of novel αβ-protein folds through de novo design. Nature Structural & Molecular Biology 2023, 30 (8), 1132–40. 10.1038/s41594-023-01029-0. PubMed DOI PMC

Bordin N.; Sillitoe I.; Lees J. G.; Orengo C. Tracing evolution through protein structures: nature captured in a few thousand folds. Frontiers in Molecular Biosciences. 2021, 8, 668184.10.3389/fmolb.2021.668184. PubMed DOI PMC

Chu X. Y.; Zhang H. Y. Cofactors as molecular fossils to trace the origin and evolution of proteins. ChemBioChem. 2020, 21 (22), 3161–8. 10.1002/cbic.202000027. PubMed DOI

Tokuriki N.; Tawfik D. S. Protein dynamism and evolvability. Science 2009, 324 (5924), 203–7. 10.1126/science.1169375. PubMed DOI

Goldman A. D.; Bernhard T. M.; Dolzhenko E.; Landweber L. F. LUCApedia: a database for the study of ancient life. Nucleic Acids Res. 2012, 41 (D1), D1079–82. 10.1093/nar/gks1217. PubMed DOI PMC

Goldman A. D.; Kacar B. Cofactors are remnants of life’s origin and early evolution. Journal of Molecular Evolution 2021, 89 (3), 127–33. 10.1007/s00239-020-09988-4. PubMed DOI PMC

Longo L. M.; Jabłońska J.; Vyas P.; Kanade M.; Kolodny R.; Ben-Tal N.; Tawfik D. S. On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment. eLife 2020, 9, e6441510.7554/eLife.64415. PubMed DOI PMC

Frenkel-Pinter M.; Samanta M.; Ashkenasy G.; Leman L. J. Prebiotic peptides: Molecular hubs in the origin of life. Chem. Rev. 2020, 120 (11), 4707–65. 10.1021/acs.chemrev.9b00664. PubMed DOI

Greenwald J.; Friedmann M. P.; Riek R. Amyloid aggregates arise from amino acid condensations under prebiotic conditions. Angew. Chem. 2016, 128 (38), 11781–5. 10.1002/ange.201605321. PubMed DOI

Higgs P. G.; Pudritz R. E. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 2009, 9 (5), 483–90. 10.1089/ast.2008.0280. PubMed DOI

Naraoka H.; Takano Y.; Dworkin J. P.; Oba Y.; Hamase K.; Furusho A.; Tsuda Y.; et al. Soluble organic molecules in samples of the carbonaceous asteroid (162173) Ryugu. Science 2023, 379 (6634), eabn903310.1126/science.abn9033. PubMed DOI

Pizzarello S.; Weber A. L. Prebiotic amino acids as asymmetric catalysts. Science 2004, 303 (5661), 1151–1151. 10.1126/science.1093057. PubMed DOI

Cornell C. E.; Black R. A.; Xue M.; Litz H. E.; Ramsay A.; Gordon M.; Mileant A.; Cohen Z. R.; Williams J. A.; Lee K. K.; Drobny G. P.; Keller S. L. Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proc. Natl. Acad. Sci. U. S. A. 2019, 116 (35), 17239–44. 10.1073/pnas.1900275116. PubMed DOI PMC

Burton A. S.; Stern J. C.; Elsila J. E.; Glavin D. P.; Dworkin J. P. Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites. Chem. Soc. Rev. 2012, 41 (16), 5459–72. 10.1039/c2cs35109a. PubMed DOI

Foden C. S.; Islam S.; Fernández-García C.; Maugeri L.; Sheppard T. D.; Powner M. W. Prebiotic synthesis of cysteine peptides that catalyze peptide ligation in neutral water. Science 2020, 370 (6518), 865–9. 10.1126/science.abd5680. PubMed DOI

Fried S. D.; Fujishima K.; Makarov M.; Cherepashuk I.; Hlouchova K. Peptides before and during the nucleotide world: An origins story emphasizing cooperation between proteins and nucleic acids. J. R. Soc., Interface 2022, 19 (187), 20210641.10.1098/rsif.2021.0641. PubMed DOI PMC

Weber A. L.; Miller S. L. Reasons for the occurrence of the twenty coded protein amino acids. Journal of Molecular Evolution. 1981, 17, 273–84. 10.1007/BF01795749. PubMed DOI

Parker E. T.; Cleaves H. J.; Callahan M. P.; Dworkin J. P.; Glavin D. P.; Lazcano A.; Bada J. L. Prebiotic synthesis of methionine and other sulfur-containing organic compounds on the primitive Earth: a contemporary reassessment based on an unpublished 1958 Stanley Miller experiment. Origins of Life and Evolution of Biospheres. 2011, 41, 201–12. 10.1007/s11084-010-9228-8. PubMed DOI PMC

Zaia D. A.; Zaia C. T.; De Santana H. Which amino acids should be used in prebiotic chemistry studies?. Origins of Life and Evolution of Biospheres 2008, 38, 469–88. 10.1007/s11084-008-9150-5. PubMed DOI

Frenkel-Pinter M.; Haynes J. W.; C M.; Petrov A. S.; Burcar B. T.; Krishnamurthy R.; Hud N. V.; Leman L. J.; Williams L. D. Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions. Proc. Natl. Acad. Sci. U. S. A. 2019, 116 (33), 16338–46. 10.1073/pnas.1904849116. PubMed DOI PMC

Longo L. M.; Despotović D.; Weil-Ktorza O.; Walker M. J.; Jabłońska J.; Fridmann-Sirkis Y.; Varani G.; Metanis N.; Tawfik D. S. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Proc. Natl. Acad. Sci. U. S. A. 2020, 117 (27), 15731–9. 10.1073/pnas.2001989117. PubMed DOI PMC

Forsythe J. G.; Yu S. S.; Mamajanov I.; Grover M. A.; Krishnamurthy R.; Fernández F. M.; Hud N. V. Ester-mediated amide bond formation driven by wet–dry cycles: A possible path to polypeptides on the prebiotic earth. Angew. Chem., Int. Ed. 2015, 54 (34), 9871–5. 10.1002/anie.201503792. PubMed DOI PMC

Copley S. D.; Smith E.; Morowitz H. J. A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (12), 4442–7. 10.1073/pnas.0501049102. PubMed DOI PMC

Bilus M.; Semanjski M.; Mocibob M.; Zivkovic I.; Cvetesic N.; Tawfik D. S.; Toth-Petroczy A.; Macek B.; Gruic-Sovulj I. On the mechanism and origin of isoleucyl-tRNA synthetase editing against norvaline. J. Mol. Biol. 2019, 431 (6), 1284–97. 10.1016/j.jmb.2019.01.029. PubMed DOI

Jabłońska J.; Longo L. M.; Tawfik D. S.; Gruic-Sovulj I. The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation. bioRxiv 2022, 10.1101/2022.06.09.495570. DOI

Ozturk S. F.; Bhowmick D. K.; Kapon Y.; Sang Y.; Kumar A.; Paltiel Y.; Naaman R.; Sasselov D. D. Chirality-induced avalanche magnetization of magnetite by an RNA precursor. Nature Communications. 2023, 14 (1), 6351.10.1038/s41467-023-42130-8. PubMed DOI PMC

Deng M.; Yu J.; Blackmond D. G. Symmetry breaking and chiral amplification in prebiotic ligation reactions. Nature. 2024, 626 (8001), 1019–24. 10.1038/s41586-024-07059-y. PubMed DOI

Brack A.; Orgel L. E. β structures of alternating polypeptides and their possible prebiotic significance. Nature 1975, 256 (5516), 383–7. 10.1038/256383a0. PubMed DOI

Lupas A. N.; Alva V. Ribosomal proteins as documents of the transition from unstructured (poly) peptides to folded proteins. J. Struct. Biol. 2017, 198 (2), 74–81. 10.1016/j.jsb.2017.04.007. PubMed DOI

Rout S. K.; Friedmann M. P.; Riek R.; Greenwald J. A prebiotic template-directed peptide synthesis based on amyloids. Nat. Commun. 2018, 9 (1), 234.10.1038/s41467-017-02742-3. PubMed DOI PMC

Tretyachenko V.; Vymětal J.; Bednárová L.; Kopecký V. Jr.; Hofbauerová K.; Jindrová H.; Hubálek M.; Souček R.; Konvalinka J.; Vondrášek J.; Hlouchová K. Random protein sequences can form defined secondary structures and are well-tolerated in vivo. Sci. Rep. 2017, 7 (1), 15449.10.1038/s41598-017-15635-8. PubMed DOI PMC

Despotović D.; Longo L. M.; Aharon E.; Kahana A.; Scherf T.; Gruic-Sovulj I.; Tawfik D. S. Polyamines mediate folding of primordial hyperacidic helical proteins. Biochemistry 2020, 59 (46), 4456–62. 10.1021/acs.biochem.0c00800. PubMed DOI PMC

Wang M. S.; Hoegler K. J.; Hecht M. H. Unevolved de novo proteins have innate tendencies to bind transition metals. Life 2019, 9 (1), 8.10.3390/life9010008. PubMed DOI PMC

Milner-White E. J.; Russell M. J. Functional capabilities of the earliest peptides and the emergence of life. Genes 2011, 2 (4), 671–88. 10.3390/genes2040671. PubMed DOI PMC

van Der Gulik P.; Massar S.; Gilis D.; Buhrman H.; Rooman M. The first peptides: the evolutionary transition between prebiotic amino acids and early proteins. J. Theor. Biol. 2009, 261 (4), 531–9. 10.1016/j.jtbi.2009.09.004. PubMed DOI

Szostak J. W. The eightfold path to non-enzymatic RNA replication. Journal of Systems Chemistry 2012, 3, 2.10.1186/1759-2208-3-2. DOI

Hsiao C.; Mohan S.; Kalahar B. K.; Williams L. D. Peeling the onion: ribosomes are ancient molecular fossils. Mol. Biol. Evol. 2009, 26 (11), 2415–25. 10.1093/molbev/msp163. PubMed DOI

Blanco C.; Bayas M.; Yan F.; Chen I. A. Analysis of evolutionarily independent protein-RNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios. Curr. Biol. 2018, 28 (4), 526–37. 10.1016/j.cub.2018.01.014. PubMed DOI

Di Giulio M. On the RNA world: evidence in favor of an early ribonucleopeptide world. Journal of Molecular Evolution 1997, 45, 571–8. 10.1007/PL00006261. PubMed DOI

Kirschning A. Coenzymes and their role in the evolution of life. Angew. Chem., Int. Ed. 2021, 60 (12), 6242–69. 10.1002/anie.201914786. PubMed DOI PMC

Cvjetan N.; Schuler L. D.; Ishikawa T.; Walde P. Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate. ACS omega 2023, 8 (45), 42878–99. 10.1021/acsomega.3c05915. PubMed DOI PMC

White H. B. Coenzymes as fossils of an earlier metabolic state. Journal of Molecular Evolution 1976, 7, 101–4. 10.1007/BF01732468. PubMed DOI

Longo L. M.; Petrović D.; Kamerlin S. C.; Tawfik D. S. Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proc. Natl. Acad. Sci. U. S. A. 2020, 117 (10), 5310–8. 10.1073/pnas.1911742117. PubMed DOI PMC

Longo L. M.; Hirai H.; McGlynn S. E. An evolutionary history of the CoA-binding protein Nat/Ivy. Protein Sci. 2022, 31 (12), e446310.1002/pro.4463. PubMed DOI PMC

Holliday G. L.; Mitchell J. B.; Thornton J. M. Understanding the functional roles of amino acid residues in enzyme catalysis. J. Mol. Biol. 2009, 390 (3), 560–77. 10.1016/j.jmb.2009.05.015. PubMed DOI

Bonfio C.; Mansy S. S. The chemical roots of iron–sulfur dependent metabolism. Biochemistry 2017, 56 (40), 5225–6. 10.1021/acs.biochem.7b00842. PubMed DOI

Vázquez-Salazar A.; Becerra A.; Lazcano A. Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines. PloS one 2018, 13 (4), e019634910.1371/journal.pone.0196349. PubMed DOI PMC

Lou Y.; Zhang B.; Ye X.; Wang Z. G. Self-assembly of the de novo designed peptides to produce supramolecular catalysts with built-in enzyme-like active sites: a review of structure-activity relationship. Materials Today Nano 2023, 21, 100302.10.1016/j.mtnano.2023.100302. DOI

Weber A. L.; Pizzarello S. The peptide-catalyzed stereospecific synthesis of tetroses: A possible model for prebiotic molecular evolution. Proceedings of the National Academy of Sciences. 2006, 103 (34), 12713–7. 10.1073/pnas.0602320103. PubMed DOI PMC

Yu J.; Jones A. X.; Legnani L.; Blackmond D. G. Prebiotic access to enantioenriched glyceraldehyde mediated by peptides. Chemical Science. 2021, 12 (18), 6350–4. 10.1039/D1SC01250A. PubMed DOI PMC

Rufo C. M.; Moroz Y. S.; Moroz O. V.; Stöhr J.; Smith T. A.; Hu X.; DeGrado W. F.; Korendovych I. V. Short peptides self-assemble to produce catalytic amyloids. Nature Chemistry. 2014, 6 (4), 303–9. 10.1038/nchem.1894. PubMed DOI PMC

Makarov M.; Meng J.; Tretyachenko V.; Srb P.; Březinová A.; Giacobelli V. G.; Bednárová L.; Vondrášek J.; Dunker A. K.; Hlouchová K. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Sci. 2021, 30 (5), 1022–34. 10.1002/pro.4068. PubMed DOI PMC

Krishnamurthy R. Systems chemistry in the chemical origins of life: the 18th camel paradigm. J. Syst. Chem. 2020, 8, 40–62.

Preiner M.; Asche S.; Becker S.; Betts H. C.; Boniface A.; Camprubi E.; Xavier J. C.; et al. The future of origin of life research: bridging decades-old divisions. Life 2020, 10 (3), 20.10.3390/life10030020. PubMed DOI PMC

Jia T. Z. Primitive membraneless compartments as a window into the earliest cells. Biophysical Reviews 2023, 15 (6), 1897–900. 10.1007/s12551-023-01135-9. PubMed DOI PMC