Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates
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Models of competitive template replication, although basic for replicator dynamics and primordial evolution, have not yet taken different sequences explicitly into account, neither have they analyzed the effect of resource partitioning (feeding on different resources) on coexistence. Here we show by analytical and numerical calculations that Gause's principle of competitive exclusion holds for template replicators if resources (nucleotides) affect growth linearly and coexistence is at fixed point attractors. Cases of complementary or homologous pairing between building blocks with parallel or antiparallel strands show no deviation from the rule that the nucleotide compositions of stably coexisting species must be different and there cannot be more coexisting replicator species than nucleotide types. Besides this overlooked mechanism of template coexistence we show also that interesting sequence effects prevail as parts of sequences that are copied earlier affect coexistence more strongly due to the higher concentration of the corresponding replication intermediates. Template and copy always count as one species due their constraint of strict stoichiometric coupling. Stability of fixed-point coexistence tends to decrease with the length of sequences, although this effect is unlikely to be detrimental for sequences below 100 nucleotides. In sum, resource partitioning (niche differentiation) is the default form of competitive coexistence for replicating templates feeding on a cocktail of different nucleotides, as it may have been the case in the RNA world. Our analysis of different pairing and strand orientation schemes is relevant for artificial and potentially astrobiological genetics.
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In standard resource-regulated template replication, a complementary pair of sequences counts as a single replicator, not solitary strands.
“Note that in the “standard”, resource-regulated dynamics of template replication with a detailed chemical kinetics (per base elongation of sequences) a complementary pair of sequences counts as a single replicator, not the solitary strands.”
From Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems (2017) · cites this paper as [16]
Four different nucleotides can maintain coexistence of four complementary pairs of strands.
“Consequently, four different nucleotides can maintain the coexistence of four complementary pairs of strands [16].”
From Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems (2017) · cites this paper as [16]
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Cites
Selforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788 · see citing works
THE MAJOR TRANSITIONS OF EVOLUTION
Leigh, E. G., Smith, J. M., & Szathmáry, E. (1995) · Evolution · doi:10.1111/j.1558-5646.1995.tb04464.x · Cited by 3,432 · see citing works
Self-citationGauze, G. F. (1934) · doi:10.5962/bhl.title.4489 · Cited by 3,280 · see citing works
The Major Transitions in Evolution
Smith, J. M., & Szathmáry, E. (1997) · Oxford University Press eBooks · doi:10.1093/oso/9780198502944.001.0001 · Cited by 2,570 · see citing works
Self-citationHindmarsh, A. C., Brown, P. N., Grant, K. E., Lee, S. L., Serban, R., Shumaker, D. E., & Woodward, C. S. (2005) · ACM Transactions on Mathematical Software · doi:10.1145/1089014.1089020 · Cited by 2,551 · see citing works
Armstrong, R. A., & McGehee, R. (1980) · The American Naturalist · doi:10.1086/283553 · Cited by 1,016 · see citing works
A small catalytic oligoribonucleotide
Uhlenbeck, O. C. (1987) · Nature · doi:10.1038/328596a0 · Cited by 932 · see citing works
Community Equilibria and Stability, and an Extension of the Competitive Exclusion Principle
Levin, S. A. (1970) · The American Naturalist · doi:10.1086/282676 · Cited by 695 · see citing works
A Self‐Replicating Hexadeoxynucleotide
von Kiedrowski, G. (1986) · Angewandte Chemie International Edition in English · doi:10.1002/anie.198609322 · Cited by 583 · see citing works
Directed Evolution of Nucleic Acid Enzymes
Joyce, G. F. (2004) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.73.011303.073717 · Cited by 515 · see citing works
Spontaneous network formation among cooperative RNA replicators
Vaidya, N., Manapat, M. L., Chen, I. A., Xulvi-Brunet, R., Hayden, E. J., & Lehman, N. (2012) · Nature · doi:10.1038/nature11549 · Cited by 383 · see citing works
Swetina, J., & Schuster, P. M. (1982) · Biophysical Chemistry · doi:10.1016/0301-4622(82)87037-3 · Cited by 342 · see citing works
Minimal Replicator Theory I: Parabolic Versus Exponential Growth
von Kiedrowski, G. (1993) · Bioorganic Chemistry Frontiers · doi:10.1007/978-3-642-78110-0_4 · Cited by 212 · see citing works
Lee, J. F. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh094 · Cited by 188 · see citing works
Sub-exponential growth and coexistence of non-enzymatically replicating templates
Szathmáry, E., & Gladkih, I. (1989) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(89)80177-8 · Cited by 165 · see citing works
Self-citationKinetics of ribonucleic acid replication
Biebricher, C. Κ., Eigen, M., & Gardiner, W. C. (1983) · Biochemistry · doi:10.1021/bi00279a036 · Cited by 137 · see citing works
Kinetics of RNA replication: competition and selection among self-replicating RNA species
Biebricher, C. Κ., Eigen, M., & Gardiner, W. C. (1985) · Biochemistry · doi:10.1021/bi00344a037 · Cited by 95 · see citing works
Efforts toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs
Matsuda, S., Fillo, J. D., Henry, A. A., Rai, P., Wilkens, S. J., Dwyer, T. J., Geierstanger, B. H., Wemmer, D. E., Schultz, P. G., Spraggon, G., et al. (2007) · Journal of the American Chemical Society · doi:10.1021/ja072276d · Cited by 93 · 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
Kinetics of RNA replication: plus-minus asymmetry and annealing
Biebricher, C. Κ., Eigen, M., & Gardiner, W. C. (1984) · Biochemistry · doi:10.1021/bi00309a012 · Cited by 66 · see citing works
Megger, D. A., & Müller, J. (2009) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770903451579 · Cited by 64 · see citing works
Why are there four letters in the genetic alphabet?
Szathmáry, E. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1231 · Cited by 62 · see citing works
Self-citationA trinucleotide can promote metal ion-dependent specific cleavage of RNA.
Kazakov, S. A., & 幹, 直. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.17.7939 · Cited by 60 · see citing works
The meaning of a minuscule ribozyme
Yarus, M. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0139 · Cited by 44 · see citing works
Meyer, A. J., Ellefson, J. W., & Ellington, A. D. (2012) · Accounts of Chemical Research · doi:10.1021/ar200325v · Cited by 39 · see citing works
Coexistence of competing stage-structured populations
Fujiwara, M., Pfeiffer, G., Boggess, M., Day, S., & Walton, J. R. (2011) · Scientific Reports · doi:10.1038/srep00107 · Cited by 29 · see citing works
Community Dynamics in a Homogeneous Environment
Hallam, T. G. (1986) · Biomathematics · doi:10.1007/978-3-642-69888-0_10 · Cited by 25 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- [5]Spiegelman S (1970) Extracellular evolution of replicating molecules, New York: Rockefeller University Press. pp. 927–945.
- [10]von Kiedrowski G (1986) A self-replicating hexadeoxy nucleotide. Angewandte Chemie International Edition in English 25: 932– 935.
- [27]Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, et al (2005) SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers. ACM Transactions on Mathematical Software 31: 363– 396.
Cited by
Sorted by citations
The dynamics of the RNA world: insights and challenges
Kun, Á., Szilágyi, A., Könnyű, B., Boza, G., Zachar, I., & Szathmáry, E. (2015) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12700 · Cited by 65 · see citing works
Self-citationEcology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems
Szilágyi, A., Zachar, I., Scheuring, I., Kun, Á., Könnyű, B., & Czárán, T. (2017) · Life · doi:10.3390/life7040048 · Cited by 44 · see citing works
“) Furthermore, the determination of coexisting species (and hence their number) may be also complicated (as is the case for replicating nucleotide sequences, where a complementary pair of strands counts as a single replicator instead of two [16].”
BackgroundSelf-citationCzárán, T., Könnyű, B., & Szathmáry, E. (2015) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2015.06.002 · Cited by 37 · see citing works
Self-citationEvolution of Functional Diversification within Quasispecies
Colizzi, E. S., & Hogeweg, P. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu150 · Cited by 23 · see citing works
Szilágyi, A., Könnyű, B., & Czárán, T. (2020) · Scientific Reports · doi:10.1038/s41598-019-56986-8 · Cited by 13 · see citing works
Self-citationEleveld, M., Geiger, Y., Wu, J., Kiani, A., Schaeffer, G., & Otto, S. (2024) · Nature Chemistry · doi:10.1038/s41557-024-01664-0 · Cited by 12 · see citing works
Maintenance of Genetic Information in the First Ribocell
Kun, Á. (2021) · Wiley eBooks · doi:10.1002/9783527814527.ch14 · Cited by 6 · see citing works
Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world
Wu, S., Yu, C., Zhang, W., Yin, S., Chen, Y., Feng, Y., & Ma, W. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172702 · Cited by 4 · see citing works
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism
Vörös, D., Könnyű, B., & Czárán, T. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008634 · Cited by 4 · see citing works
Paczkó, M., Szathmáry, E., & Szilágyi, A. (2024) · eLife · doi:10.7554/elife.93208 · Cited by 3 · see citing works
Self-citationStruggle for Existence: the models for Darwinian and non-Darwinian selectionPreprint
Karev, G. P., & Berezovskaya, F. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1812.03048
Inhomogeneous logistic equations and models for Darwinian and non-Darwinian evolution
Kareva, I., & Karev, G. P. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814368-1.00007-2
(2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814368-1.09992-6
Paczkó, M., Szathmáry, E., & Szilágyi, A. (2024) · eLife · doi:10.7554/elife.93208.1
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- Authors
- Szilágyi, A., Zachar, I., & Szathmáry, E.
- Affiliations
- Eötvös Loránd University (HU)
- Parmenides Foundation (DE)
- Corresponding author
- Szathmáry, Eörs
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-08-22
- Volume
- 9
- Issue
- 8
- Pages
- e1003193
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3749944
- OpenAlex
- W2080813513
- Cited by
- 17
- References
- 27
- Citations by year
- 2024: 5 · 2023: 1 · 2021: 2 · 2020: 1 · 2019: 2 · 2018: 1 · 2017: 2 · 2015: 2 · 2014: 1
- FWCI
- 0.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ELTE Digital Institutional Repository (EDIT) (Eötvös Loránd University) (submittedVersion, other-oa)
- Figshare (submittedVersion, cc-by)
- Funders
- Nemzeti Kutatási és Technológiai Hivatal (KCKHA005, NAP 2005/KCKHA005)
- FP7 Ideas: European Research Council (294332)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- template replication, resource partitioning, niche differentiation, fixed-point attractors, nucleotide composition, RNA world, order effects, strand orientation, replication intermediates, sequence length
- MeSH terms
- Computer Simulation, Gene Expression Regulation, Interleukin-3, Models, Genetic, Monte Carlo Method, Recombinant Fusion Proteins, RNA, Messenger, Stochastic Processes, Models, Statistical, Cluster Analysis, Granulocyte Colony-Stimulating Factor, Computational Biology, GATA2 Transcription Factor
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