Ribozyme Catalysis of Metabolism in the RNA World
Abstract
In vitro selection has proven to be a useful means of explore the molecules and catalysts that may have existed in a primoridal ‘RNA world’. By selecting binding species (aptamers) and catalysts (ribozymes) from random sequence pools, the relationship between biopolymer complexity and function can be better understood, and potential evolutionary transitions between functional molecules can be charted. In this review, we have focused on several critical events or transitions in the putative RNA world: RNA self‐replication; the synthesis and utilization of nucleotide‐based cofactors; acyl‐transfer reactions leading to peptide and protein synthesis; and the basic metabolic pathways that are found in modern living systems.
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Today, RNA serves as the sole genetic molecule in many viruses.
“Today, RNA serves as the sole genetic molecule in many viruses, and the number of reactions catalyzed by RNA enzymes (“ribozymes”) is ever increasing (Doudna and Cech, 2002; Chen et al., 2007).”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Chen et al., 2007
The number of reactions catalyzed by RNA enzymes (ribozymes) is ever increasing.
“Today, RNA serves as the sole genetic molecule in many viruses, and the number of reactions catalyzed by RNA enzymes (“ribozymes”) is ever increasing (Doudna and Cech, 2002; Chen et al., 2007).”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Chen et al., 2007
Cites
The antiquity of RNA-based evolution.
Joyce, G. F. (2002) · Nature · doi:10.1038/418214a · Cited by 1,070 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension.
Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1060786 · Cited by 768 · see citing works
RNA, the first macromolecular catalyst: the ribosome is a ribozyme
Steitz, T. A., & Moore, P. B. (2003) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(03)00169-5 · Cited by 319 · see citing works
Autocatalytic synthesis of a tetranucleotide analogue
Zielinski, W. S., & Orgel, L. E. (1987) · Nature · doi:10.1038/327346a0 · Cited by 310 · see citing works
Peptide bond formation by in vitro selected ribozymes
Zhang, B., & Cech, T. R. (1997) · Nature · doi:10.1038/36375 · Cited by 299 · see citing works
A self-replicating ligase ribozyme
Paul, N., & Joyce, G. F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202471099 · Cited by 264 · see citing works
Selection of RNA amide synthases
Wiegand, T. W., Janssen, R. C., & Eaton, B. E. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90223-4 · Cited by 153 · see citing works
An in vitro evolved precursor tRNA with aminoacylation activity
Saito, H., Kourouklis, D., & Suga, H. (2001) · The EMBO Journal · doi:10.1093/emboj/20.7.1797 · Cited by 145 · see citing works
Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers
Held, D. M., Travis Greathouse, S., Agrawal, A., & Burke, D. H. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2481-y · Cited by 41 · see citing works
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RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code
Yarus, M., Widmann, J. J., & Knight, R. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9270-1 · Cited by 198 · see citing works
Domagal-Goldman, S. D., Wright, K. E., Domagal-Goldman, S. D., Wright, K. E., Adamala, K., Arina de la Rubia, L., Bond, J., Dartnell, L. R., Goldman, A. D., Lynch, K., et al. (2016) · Astrobiology · doi:10.1089/ast.2015.1460 · Cited by 136 · see citing works
“Today, RNA serves as the sole genetic molecule in many viruses, and the number of reactions catalyzed by RNA enzymes (‘‘ribozymes’’) is ever increasing (Doudna and Cech, 2002; Chen et al., 2007).”
Coenzymes and their role in the evolution of life
Kirschning, A. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.201914786 · Cited by 107 · see citing works
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life
Wong, J., Ng, S.-K., Mat, W.-K., Hu, T., & Xue, H. (2016) · Life · doi:10.3390/life6010012 · Cited by 93 · see citing works
Welcome home, systems chemists
von Kiedrowski, G., Otto, S., & Herdewijn, P. (2010) · Journal of Systems Chemistry · doi:10.1186/1759-2208-1-1 · Cited by 102 · see citing works
Rapid and simple ribozymic aminoacylation using three conserved nucleotides
Chumachenko, N. V., Novikov, Y., & Yarus, M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja809419f · Cited by 68 · see citing works
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life
Hoeppner, M. P., Gardner, P. P., & Poole, A. M. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002752 · Cited by 62 · see citing works
Coupled catabolism and anabolism in autocatalytic RNA sets
Arsène, S., Ameta, S., Lehman, N., Griffiths, A. D., & Nghe, P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky598 · Cited by 57 · see citing works
The structural basis of RNA-catalyzed RNA polymerization
Shechner, D. M., & Bartel, D. P. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2107 · Cited by 48 · see citing works
Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway
Yadav, M., Pulletikurti, S., Yerabolu, J. R., & Krishnamurthy, R. (2022) · Nature Chemistry · doi:10.1038/s41557-021-00878-w · Cited by 48 · see citing works
Evolution of the division of labor between genes and enzymes in the RNA world
Boza, G., Szilágyi, A., Kun, Á., Santos, M., & Szathmáry, E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003936 · Cited by 36 · see citing works
Könnyű, B., & Czárán, T. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-204 · Cited by 25 · see citing works
Characterization of the B6.61 polymerase ribozyme accessory domain
Wang, Q. S., Cheng, L. K. L., & Unrau, P. J. (2011) · RNA · doi:10.1261/rna.2495011 · Cited by 24 · see citing works
Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme
Akoopie, A., & Müller, U. F. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp00672h · Cited by 16 · see citing works
Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides
Yao, C., & Müller, U. F. (2011) · RNA · doi:10.1261/rna.2726811 · Cited by 8 · see citing works
- Authors
- Chen, X., Li, N., & Ellington, A. D.
- Affiliations
- The University of Texas at Austin (US)
- Venue
- Chemistry & Biodiversity
- Publisher
- Wiley
- Published
- 2007-04
- Volume
- 4
- Issue
- 4
- Pages
- 633-655
- ISSN
- 1612-1872 (ISSN-L)
- 1612-1880
- OpenAlex
- W1984319638
- Cited by
- 196
- References
- 10
- Citations by year
- 2026: 8 · 2025: 7 · 2024: 6 · 2023: 8 · 2022: 12 · 2021: 11 · 2020: 7 · 2019: 9 · 2018: 6 · 2017: 1 · 2016: 12 · 2015: 10 · 2014: 8 · 2013: 5 · 2012: 12
- FWCI
- 1.50
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Chemistry & Biodiversity (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- ribozymes, RNA world, in vitro selection, aptamers, RNA self-replication, nucleotide cofactors, acyl transfer, peptide synthesis, protein synthesis, origin of life, metabolic pathways, evolutionary transitions
- MeSH terms
- Base Sequence, Catalysis, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Protein Biosynthesis, RNA, Catalytic
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