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Singh AY, Jain S. Multistable Protocells Can Aid the Evolution of Prebiotic Autocatalytic Sets. Life (Basel) 2023; 13:2327. [PMID: 38137928 PMCID: PMC10744544 DOI: 10.3390/life13122327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 12/24/2023] Open
Abstract
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model, the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division dynamics of the compartment. Bistability in the dynamics of the autocatalytic set results in a protocell that can exist with two distinct growth rates. Stochasticity in chemical reactions plays the role of mutations and causes transitions from one growth regime to another. We show that the system exhibits 'natural selection', where a 'mutant' protocell in which the autocatalytic set is active arises by chance in a population of inactive protocells, and then takes over the population because of its higher growth rate or 'fitness'. The work integrates three levels of dynamics: intracellular chemical, single protocell, and population (or ecosystem) of protocells.
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Affiliation(s)
- Angad Yuvraj Singh
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India;
| | - Sanjay Jain
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India;
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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2
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Gagnon JS, Hochberg D. Conditions for the origin of homochirality in primordial catalytic reaction networks. Sci Rep 2023; 13:9885. [PMID: 37336897 DOI: 10.1038/s41598-023-36852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/11/2023] [Indexed: 06/21/2023] Open
Abstract
We study the generation of homochirality in a general chemical model (based on the homogeneous, fully connected Smoluchowski aggregation-fragmentation model) that obeys thermodynamics and can be easily mapped onto known origin of life models (e.g. autocatalytic sets, hypercycles, etc.), with essential aspects of origin of life modeling taken into consideration. Using a combination of theoretical modeling and numerical simulations, we look for minimal conditions for which our general chemical model exhibits spontaneous mirror symmetry breaking. We show that our model spontaneously breaks mirror symmetry in various catalytic configurations that only involve a small number of catalyzed reactions and nothing else. Of particular importance is that mirror symmetry breaking occurs in our model without the need for single-step autocatalytis or mutual inhibition, which may be of relevance for prebiotic chemistry.
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Affiliation(s)
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir Km. 4, 28850, Torrejón de Ardóz, Madrid, Spain
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3
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Pavlinova P, Lambert CN, Malaterre C, Nghe P. Abiogenesis through gradual evolution of autocatalysis into template-based replication. FEBS Lett 2023; 597:344-379. [PMID: 36203246 DOI: 10.1002/1873-3468.14507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022]
Abstract
How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.
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Affiliation(s)
- Polina Pavlinova
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Camille N Lambert
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Christophe Malaterre
- Laboratory of Philosophy of Science (LAPS) and Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), Canada
| | - Philippe Nghe
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
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4
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Prosdocimi F, de Farias ST, José MV. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory Biosci 2022; 141:339-347. [PMID: 36042123 DOI: 10.1007/s12064-022-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
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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, 21.941-902, Rio de Janeiro, Brazil. .,Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
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5
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Ameta S, Matsubara YJ, Chakraborty N, Krishna S, Thutupalli S. Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems. Life (Basel) 2021; 11:308. [PMID: 33916135 PMCID: PMC8066523 DOI: 10.3390/life11040308] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Yoshiya J. Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560089, India
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Banwell EF, Piette BMAG, Taormina A, Heddle JG. Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator. Mol Biol Evol 2019; 35:404-416. [PMID: 29126321 PMCID: PMC5850689 DOI: 10.1093/molbev/msx292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Even the simplest organisms are too complex to have spontaneously arisen fully formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of evolution: the Initial Darwinian Ancestor. Here, we suggest that nucleopeptide reciprocal replicators could have carried out this important role and contend that this is the simplest way to explain extant replication systems in a mathematically consistent way. We propose short nucleic acid templates on which amino-acylated adapters assembled. Spatial localization drives peptide ligation from activated precursors to generate phosphodiester-bond-catalytic peptides. Comprising autocatalytic protein and nucleic acid sequences, this dynamical system links and unifies several previous hypotheses and provides a plausible model for the emergence of DNA and the operational code.
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Affiliation(s)
- Eleanor F Banwell
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - Anne Taormina
- Department for Mathematical Sciences, Durham University, Durham, United Kingdom
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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7
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Matsubara YJ, Kaneko K. Kinetic Selection of Template Polymer with Complex Sequences. PHYSICAL REVIEW LETTERS 2018; 121:118101. [PMID: 30265117 DOI: 10.1103/physrevlett.121.118101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/21/2018] [Indexed: 06/08/2023]
Abstract
The emergence and maintenance of polymers with complex sequences pose a major question in the study of the origin of life. To answer this, we study a model polymerization reaction, where polymers are synthesized by stepwise ligation from two types of monomers, catalyzed by a long polymer as a template. Direct stochastic simulation and dynamical systems analysis reveal that the most dominant polymer sequence in a population successively changes, depending on the flow rate of monomers to the system, with more complex sequences selected at a lower flow rate. We discuss the relevance of this kinetic sequence selection through nonequilibrium flow to the origin of complex polymers.
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Affiliation(s)
- Yoshiya J Matsubara
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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8
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Veldhuis MP, Berg MP, Loreau M, Olff H. Ecological autocatalysis: a central principle in ecosystem organization? ECOL MONOGR 2018. [DOI: 10.1002/ecm.1292] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michiel P. Veldhuis
- Groningen Institute for Evolutionary Life Sciences; University of Groningen; P.O. Box 11103 9700CC Groningen The Netherlands
| | - Matty P. Berg
- Groningen Institute for Evolutionary Life Sciences; University of Groningen; P.O. Box 11103 9700CC Groningen The Netherlands
- Department of Ecological Science; Vrije Universiteit; De Boelelaan 1085 1081 HV Amsterdam The Netherlands
| | - Michel Loreau
- Centre for Biodiversity Theory and Modeling, Theoretical and Experimental Ecology Station; CNRS and Paul Sabatier University; 09200 Moulis France
| | - Han Olff
- Groningen Institute for Evolutionary Life Sciences; University of Groningen; P.O. Box 11103 9700CC Groningen The Netherlands
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9
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Matsubara YJ, Kaneko K. Optimal size for emergence of self-replicating polymer system. Phys Rev E 2016; 93:032503. [PMID: 27078401 DOI: 10.1103/physreve.93.032503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 11/07/2022]
Abstract
A biological system consists of a variety of polymers that are synthesized from monomers by catalysis, which exists only for some long polymers. It is important to elucidate the emergence and sustenance of such autocatalytic polymerization. We analyze here the stochastic polymerization reaction dynamics to investigate the transition time from a state with almost no catalysts to a state with sufficient catalysts. We found an optimal volume that minimizes this transition time, which agrees with the inverse of the catalyst concentration at the unstable fixed point that separates the two states, as is theoretically explained. Relevance to the origin of life is also discussed.
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Affiliation(s)
- Yoshiya J Matsubara
- Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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10
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Deshpande A, Gopalkrishnan M. Autocatalysis in reaction networks. Bull Math Biol 2014; 76:2570-95. [PMID: 25245394 DOI: 10.1007/s11538-014-0024-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 09/04/2014] [Indexed: 11/24/2022]
Abstract
The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions. The idea is that if all reactions are reversible in a weak sense, then no species can go extinct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of critical siphons, with a view toward the persistence conjecture. We introduce the notions of "drainable" and "self-replicable" (or autocatalytic) siphons. We show that: Every minimal critical siphon is either drainable or self-replicable; reaction networks without drainable siphons are persistent; and nonautocatalytic weakly reversible networks are persistent. Our results clarify that the difficulties in proving the persistence conjecture are essentially due to competition between drainable and self-replicable siphons.
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Affiliation(s)
- Abhishek Deshpande
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, India,
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11
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Pereira JA. Transient and sustained elementary flux mode networks on a catalytic string-based chemical evolution model. Biosystems 2014; 122:38-54. [PMID: 24971802 DOI: 10.1016/j.biosystems.2014.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 05/10/2014] [Accepted: 06/23/2014] [Indexed: 11/26/2022]
Abstract
Theoretical models designed to test the metabolism-first hypothesis for prebiotic evolution have yield strong indications about the hypothesis validity but could sometimes use a more extensive identification between model objects and real objects towards a more meaningful interpretation of results. In an attempt to go in that direction, the string-based model SSE ("steady state evolution") was developed, where abstract molecules (strings) and catalytic interaction rules are based on some of the most important features of carbon compounds in biological chemistry. The system is open with a random inflow and outflow of strings but also with a permanent string food source. Although specific catalysis is a key aspect of the model, used to define reaction rules, the focus is on energetics rather than kinetics. Standard energy change tables were constructed and used with standard formation reactions to track energy flows through the interpretation of equilibrium constant values. Detection of metabolic networks on the reaction system was done with elementary flux mode (EFM) analysis. The combination of these model design and analysis options enabled obtaining metabolic and catalytic networks showing several central features of biological metabolism, some more clearly than in previous models: metabolic networks with stepwise synthesis, energy coupling, catalysts regulation, SN2 coupling, redox coupling, intermediate cycling, coupled inverse pathways (metabolic cycling), autocatalytic cycles and catalytic cascades. The results strongly suggest that the main biological metabolism features, including the genotype-phenotype interpretation, are caused by the principles of catalytic systems and are prior to modern genetic systems principles. It also gives further theoretical support to the thesis that the basic features of biologic metabolism are a consequence of the time evolution of a random catalyst search working on an open system with a permanent food source. The importance of the food source characteristics and evolutionary possibilities are discussed.
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Affiliation(s)
- José A Pereira
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto, Portugal; REQUIMTE/CEQUP - Centro de Química da Universidade do Porto, R. D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal.
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