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Prosdocimi F, de Farias ST. Major evolutionary transitions before cells: A journey from molecules to organisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:11-24. [PMID: 38971326 DOI: 10.1016/j.pbiomolbio.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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Janzen E, Shen Y, Vázquez-Salazar A, Liu Z, Blanco C, Kenchel J, Chen IA. Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes. Nat Commun 2022; 13:3631. [PMID: 35752631 PMCID: PMC9233669 DOI: 10.1038/s41467-022-31387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 06/16/2022] [Indexed: 11/24/2022] Open
Abstract
Systems of catalytic RNAs presumably gave rise to important evolutionary innovations, such as the genetic code. Such systems may exhibit particular tolerance to errors (error minimization) as well as coding specificity. While often assumed to result from natural selection, error minimization may instead be an emergent by-product. In an RNA world, a system of self-aminoacylating ribozymes could enforce the mapping of amino acids to anticodons. We measured the activity of thousands of ribozyme mutants on alternative substrates (activated analogs for tryptophan, phenylalanine, leucine, isoleucine, valine, and methionine). Related ribozymes exhibited shared preferences for substrates, indicating that adoption of additional amino acids by existing ribozymes would itself lead to error minimization. Furthermore, ribozyme activity was positively correlated with specificity, indicating that selection for increased activity would also lead to increased specificity. These results demonstrate that by-products of ribozyme evolution could lead to adaptive value in specificity and error tolerance.
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Affiliation(s)
- Evan Janzen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Yuning Shen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Celia Blanco
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Irene A Chen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
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