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Huson D, Xavier JC, Steel M. Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry. J R Soc Interface 2024; 21:20230732. [PMID: 38774958 DOI: 10.1098/rsif.2023.0732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/18/2024] [Indexed: 07/31/2024] Open
Abstract
The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.
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Affiliation(s)
- Daniel Huson
- Institute for Bioinformatics and Medical Informatics, Tübingen University , Tübingen, Germany
| | - Joana C Xavier
- Department of Chemistry, Imperial College London , London, UK
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury , Christchurch, New Zealand
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2
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Csekő G, Horváth AK. Bromide Ion Impurity-Induced Reaction between Selenium(IV) and Acidic Bromate: Prototype of a Cycle with Autocatalytic Behavior. Inorg Chem 2024; 63:2053-2059. [PMID: 38227950 PMCID: PMC10828994 DOI: 10.1021/acs.inorgchem.3c03833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
The selenium(IV)-bromate reaction in an acidic medium using phosphoric acid/phosphate buffer was investigated by UV-vis spectroscopy monitoring the formation of bromine. In an excess of bromate, the absorbance-time curves measured at 450 nm display a characteristic sigmoidal shape having a fairly long induction period, while in the opposite case, when selenium(IV) species is used in excess, the measured data follow the rise and fall behavior. Depending on the excess of Se(IV) the final bromine-containing product is either an elementary bromine or bromide ion. Simultaneous evaluation of the measured kinetic traces clearly indicated that, surprisingly, no direct reaction takes place between the reactants. Instead of that, a trace amount of bromide ion impurity in the stock bromate solution is sufficient to drive the system via the oxidation of the bromide ion by bromate producing elementary bromine followed by the subsequent selenite-bromine reaction reestablishing the bromide ion to open a new cycle. As a result, the concentration of bromide ions increases in a sigmoidal fashion during the course of the reaction unless enough selenium(IV) species is present; hence, the overall synergetic effect observed is the autocatalytic rise of bromide ions. Therefore, the cycle mentioned above may be considered as a prototype of autocatalytic cycles. This observation prompted us to clarify the explicit difference between an autocatalytic cycle and an autocatalytic reaction.
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Affiliation(s)
- György Csekő
- Department of General and Inorganic
Chemistry, Faculty of Sciences, University
of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary
| | - Attila K. Horváth
- Department of General and Inorganic
Chemistry, Faculty of Sciences, University
of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary
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3
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Buhse T, Micheau JC. Spontaneous Emergence of Transient Chirality in Closed, Reversible Frank-like Deterministic Models. ORIGINS LIFE EVOL B 2022; 52:3-20. [PMID: 35680768 DOI: 10.1007/s11084-022-09621-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
Abstract
To explore abiotic theories related to the origin of biomolecular homochirality, we analyze two entirely reversible kinetic models composed of an enantioselective autocatalysis with limited stereoselectivity that is coupled to an enantiomeric mutual inhibition (Frank-like models). The two models differ in their autocatalytic steps in respect to the formation of monomer species in one model and of dimer species in the other. While fully reversible and running in a closed system, spontaneous mirror symmetry breaking (SMSB) gives rise to transient chiral excursions, even when starting from a strictly achiral situation. Before the SMSB, the two models differ in the main dissipative processes. At the SMSB, the entropy production rate reaches its maximum in both models. Here it is the enantioselective autocatalysis with retention of the winner enantiomer that dominates. During the terminal phase, the enantioselective autocatalysis with inversion prevails, while the entropy production rate vanishes, thus fulfilling the conditions of microscopic reversibility. SMSB does not occur if the autocatalytic rate constant is too strong or too weak. However, when the autocatalysis is relatively weak, the temporary chiral excursions last for long periods of time and could be the starting point of a cascade of asymmetric reactions. The realism of such Frank-like models is discussed from the viewpoint of their relevance to prebiotic chemistry.
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Affiliation(s)
- Thomas Buhse
- Centro de Investigaciones Químicas - IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62209, Cuernavaca, Morelos, Mexico.
| | - Jean-Claude Micheau
- Laboratoire des IMRCP, Université Paul Sabatier, UMR au CNRS No. 5623, F-31062, Toulouse Cedex, France.
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4
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Fried SD, 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; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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5
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Branca M, Calvet C, Limoges B, Mavré F. Specific Versus Non-specific Response in Exponential Molecular Amplification from Cross-Catalysis: Modeling the Influence of Background Amplifications on the Analytical Performances. Chemphyschem 2021; 22:1611-1621. [PMID: 34038617 DOI: 10.1002/cphc.202100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Indexed: 11/05/2022]
Abstract
Molecule based signal amplifications relying on an autocatalytic process may represent an ideal strategy for the development of ultrasensitive analytical or bioanalytical assays, the main reason being the exponential nature of the amplification. However, to take full advantage of such amplification rates, high stability of the starting co-reactants is required in order to avoid any undesirable background amplification. Here, on the basis of a simple kinetic model of cross-catalysis including a certain degree of intrinsic instability of co-reactants, we highlight the key parameters governing the analytical response of the system and discuss the analytical performances that are expected from a given kinetic set. In particular, we show how the detection limit is directly related to the relative instability of reactants within each catalytic loop. The model is validated with an experimental dataset and is intended to serve as a guide in the design and optimization of autocatalytic molecular-based amplification systems with improved analytical performances.
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Affiliation(s)
- Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
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6
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Horváth AK. Correct classification and identification of autocatalysis. Phys Chem Chem Phys 2021; 23:7178-7189. [PMID: 33734272 DOI: 10.1039/d1cp00224d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is generally accepted that autocatalysis is a kinetic phenomenon, where a product of a reacting system functions as a catalyst. Consequently, the reaction proceeds faster upon adding the corresponding product to the unreacted mixture of reactants providing an unequivocal possibility of how a system may be identified either experimentally or theoretically as an autocatalysis. Once this is approved, it often results in sigmoidal concentration-time profiles, though it is neither a necessary nor sufficient prerequisite because appropriate mechanistic and parametric conditions must be met to give rise to the appearance of this kinetic feature. Several mass action type kinetic models producing sigmoidal concentration-time profiles are systematically analyzed to clarify their correct characterization and classification. This procedure has led us to refine the definitions of autocatalysis and autocatalyst. A kinetic phenomenon where a product of the overall chemical event serves as a catalyst for at least one of its subsystems or for the whole system itself is called autocatalysis. This definition makes it clear that in the case of autocatalysis, the concentration of autocatalyst necessarily increases during the course of any real overall chemical or biochemical reaction. The way it is achieved thereby provides a suitable tool to classify autocatalytic processes by their elucidated and fine mechanistic details.
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Affiliation(s)
- Attila K Horváth
- Department of Inorganic Chemistry, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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7
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Abstract
Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution.
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8
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Wołos A, Roszak R, Żądło-Dobrowolska A, Beker W, Mikulak-Klucznik B, Spólnik G, Dygas M, Szymkuć S, Grzybowski BA. Synthetic connectivity, emergence, and
self-regeneration in the network of prebiotic
chemistry. Science 2020; 369:369/6511/eaaw1955. [DOI: 10.1126/science.aaw1955] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
The challenge of prebiotic chemistry is to
trace the syntheses of life’s key building blocks
from a handful of primordial substrates. Here we
report a forward-synthesis algorithm that
generates a full network of prebiotic chemical
reactions accessible from these substrates under
generally accepted conditions. This network
contains both reported and previously unidentified
routes to biotic targets, as well as plausible
syntheses of abiotic molecules. It also exhibits
three forms of nontrivial chemical emergence, as
the molecules within the network can act as
catalysts of downstream reaction types; form
functional chemical systems, including
self-regenerating cycles; and produce surfactants
relevant to primitive forms of biological
compartmentalization. To support these claims,
computer-predicted, prebiotic syntheses of several
biotic molecules as well as a multistep,
self-regenerative cycle of iminodiacetic acid were
validated by experiment.
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Affiliation(s)
- Agnieszka Wołos
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Rafał Roszak
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | | | - Wiktor Beker
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Barbara Mikulak-Klucznik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Grzegorz Spólnik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Mirosław Dygas
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Sara Szymkuć
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
- Center for Soft and Living Matter of
Korea’s Institute for Basic Science (IBS), Ulsan,
South Korea
- Department of Chemistry, Ulsan
National Institute of Science and Technology,
Ulsan, South Korea
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9
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An ecological framework for the analysis of prebiotic chemical reaction networks. J Theor Biol 2020; 507:110451. [PMID: 32800733 DOI: 10.1016/j.jtbi.2020.110451] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/18/2020] [Accepted: 08/09/2020] [Indexed: 01/29/2023]
Abstract
It is becoming widely accepted that very early in life's origin, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this possibility, we formalize the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. To capture the idea that life-like chemical systems are maintained out of equilibrium by fluxes of energy-rich food chemicals, we model chemical ecosystems in well-mixed compartments that are subject to constant dilution by a solution with a fixed concentration of input chemicals. Modelling all chemical reactions as fully reversible, we show that seeding an autocatalytic cycle with tiny amounts of one or more of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding justifies drawing an instructive analogy between an autocatalytic cycle and a biological species. We extend this finding to show that pairs of autocatalytic cycles can exhibit competitive, predator-prey, or mutualistic associations just like biological species. Furthermore, when there is stochasticity in the environment, particularly in the seeding of autocatalytic cycles, chemical ecosystems can show complex dynamics that can resemble evolution. The evolutionary character is especially clear when the network architecture results in ecological precedence, which makes a system's trajectory historically contingent on the order in which cycles are seeded. For all its simplicity, the framework developed here helps explain the onset of adaptive evolution in prebiotic chemical reaction networks, and can shed light on the origin of key biological attributes such as thermodynamic irreversibility and genetic encoding.
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10
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de la Escosura A. The Informational Substrate of Chemical Evolution: Implications for Abiogenesis. Life (Basel) 2019; 9:E66. [PMID: 31398942 PMCID: PMC6789672 DOI: 10.3390/life9030066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.
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Affiliation(s)
- Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma of Madrid, Cantoblanco Campus, 28049 Madrid, Spain.
- Department of Organic Chemistry, Institute for Advanced Research in Chemistry (IAdChem), Cantoblanco Campus, 28049 Madrid, Spain.
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11
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Possible Roles of Amphiphilic Molecules in the Origin of Biological Homochirality. Symmetry (Basel) 2019. [DOI: 10.3390/sym11080966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A review. The question of homochirality is an intriguing problem in the field of chemistry, and is deeply related to the origin of life. Though amphiphiles and their supramolecular assembly have attracted less attention compared to biomacromolecules such as RNA and proteins, the lipid world hypothesis sheds new light on the origin of life. This review describes how amphiphilic molecules are possibly involved in the scenario of homochirality. Some prebiotic conditions relevant to amphiphilic molecules will also be described. It could be said that the chiral properties of amphiphilic molecules have various interesting features such as compositional information, spontaneous formation, the ability to exchange components, fission and fusion, adsorption, and permeation. This review aims to clarify the roles of amphiphiles regarding homochirality, and to determine what kinds of physical properties of amphiphilic molecules could have played a role in the scenario of homochirality.
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12
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Pallu J, Rabin C, Creste G, Branca M, Mavré F, Limoges B. Exponential Molecular Amplification by H
2
O
2
‐Mediated Autocatalytic Deprotection of Boronic Ester Probes to Redox Cyclers. Chemistry 2019; 25:7534-7546. [DOI: 10.1002/chem.201900627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 02/23/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Justine Pallu
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Charlie Rabin
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Geordie Creste
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Mathieu Branca
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
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