1
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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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2
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Jeancolas C, Matsubara YJ, Vybornyi M, Lambert CN, Blokhuis A, Alline T, Griffiths AD, Ameta S, Krishna S, Nghe P. RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling. Chem Commun (Camb) 2021; 57:7517-7520. [PMID: 34235521 PMCID: PMC8320737 DOI: 10.1039/d1cc02290c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We demonstrate that a recombinase ribozyme achieves multiple functions in the same reaction network: self-reproduction, iterative elongation and circularization of other RNAs, leading to synthesis of diverse products predicted by a kinetic model. This shows that key mechanisms can be integrated and controlled toward Darwinian evolution in RNA reaction networks. The integration of self-reproduction and diversification mechanisms in RNA reaction networks paves the way for experimental tests of prebiotic evolution.![]()
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Affiliation(s)
- Cyrille Jeancolas
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France. and Laboratoire d'Anthropologie Sociale, Collège de France, 52 rue du Cardinal Lemoine, Paris 75005, France
| | - Yoshiya J Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bellary Road, Bangalore 560 065, Karnataka, India
| | - Mykhailo Vybornyi
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France.
| | - Camille N Lambert
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France.
| | - Alex Blokhuis
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France. and Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Thomas Alline
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France.
| | - Andrew D Griffiths
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France.
| | - Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bellary Road, Bangalore 560 065, Karnataka, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bellary Road, Bangalore 560 065, Karnataka, India
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231, Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, Paris 75005, France.
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3
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Pappas CG, Liu B, Marić I, Ottelé J, Kiani A, van der Klok ML, Onck PR, Otto S. Two Sides of the Same Coin: Emergence of Foldamers and Self-Replicators from Dynamic Combinatorial Libraries. J Am Chem Soc 2021; 143:7388-7393. [PMID: 33955219 PMCID: PMC8154527 DOI: 10.1021/jacs.1c00788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of molecules
and systems to make copies of themselves
and the ability of molecules to fold into stable, well-defined three-dimensional
conformations are of considerable importance in the formation and
persistence of life. The question of how, during the emergence of
life, oligomerization reactions become selective and channel these
reactions toward a small number of specific products remains largely
unanswered. Herein, we demonstrate a fully synthetic chemical system
where structurally complex foldamers and self-replicating assemblies
emerge spontaneously and with high selectivity from pools of oligomers
as a result of forming noncovalent interactions. Whether foldamers
or replicators form depends on remarkably small differences in building
block structures and composition and experimental conditions. We also
observed the dynamic transformation of a foldamer into a replicator.
These results show that the structural requirements/design criteria
for building blocks that lead to foldamers are similar to those that
lead to replicators. What determines whether folding or replication
takes place is not necessarily the type of noncovalent interaction,
but only whether they occur intra- or intermolecularly. This work
brings together, for the first time, the fields of replicator and
foldamer chemistry.
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Affiliation(s)
- Charalampos G Pappas
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bin Liu
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Marić
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Armin Kiani
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcus L van der Klok
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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4
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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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5
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Ameta S, Arsène S, Foulon S, Saudemont B, Clifton BE, Griffiths AD, Nghe P. Darwinian properties and their trade-offs in autocatalytic RNA reaction networks. Nat Commun 2021; 12:842. [PMID: 33558542 PMCID: PMC7870898 DOI: 10.1038/s41467-021-21000-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Discovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands of networks of RNAs that catalyze their own formation from fragments, and derive relationships between network topology and chemical composition. We find that strong variations arise from catalytic innovations perturbing weakly connected networks, and that growth increases with global connectivity. These rules imply trade-offs between reproduction and variation, and between compositional persistence and variation along trajectories of network complexification. Overall, connectivity in reaction networks provides a lever to balance variation (to explore chemical states) with reproduction and heredity (persistence being necessary for selection to act), as required for chemical evolution.
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Affiliation(s)
- Sandeep Ameta
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
| | - Simon Arsène
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Sophie Foulon
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Baptiste Saudemont
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Bryce E Clifton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew D Griffiths
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
| | - Philippe Nghe
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
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6
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From self-replication to replicator systems en route to de novo life. Nat Rev Chem 2020; 4:386-403. [PMID: 37127968 DOI: 10.1038/s41570-020-0196-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.
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7
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Arsène S, Ameta S, Lehman N, Griffiths AD, Nghe P. Coupled catabolism and anabolism in autocatalytic RNA sets. Nucleic Acids Res 2019; 46:9660-9666. [PMID: 29982824 PMCID: PMC6182175 DOI: 10.1093/nar/gky598] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/22/2018] [Indexed: 11/14/2022] Open
Abstract
The ability to process molecules available in the environment into useable building blocks characterizes catabolism in contemporary cells and was probably critical for the initiation of life. Here we show that a catabolic process in collectively autocatalytic sets of RNAs allows diversified substrates to be assimilated. We modify fragments of the Azoarcus group I intron and find that the system is able to restore the original native fragments by a multi-step reaction pathway. This allows in turn the formation of catalysts by an anabolic process, eventually leading to the accumulation of ribozymes. These results demonstrate that rudimentary self-reproducing RNA systems based on recombination possess an inherent capacity to assimilate an expanded repertoire of chemical resources and suggest that coupled catabolism and anabolism could have arisen at a very early stage in primordial living systems.
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Affiliation(s)
- Simon Arsène
- Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231 Chimie Biologie Innovation, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Sandeep Ameta
- Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231 Chimie Biologie Innovation, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Niles Lehman
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| | - Andrew D Griffiths
- Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231 Chimie Biologie Innovation, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- To whom correspondence should be addressed. Philippe Nghe: Tel: +33 140794586; Fax: +33 140794776; , Andrew D. Griffiths: Tel: +33 140794539; Fax: +33 140794776;
| | - Philippe Nghe
- Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231 Chimie Biologie Innovation, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- To whom correspondence should be addressed. Philippe Nghe: Tel: +33 140794586; Fax: +33 140794776; , Andrew D. Griffiths: Tel: +33 140794539; Fax: +33 140794776;
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8
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Villarreal LP, Witzany G. That is life: communicating RNA networks from viruses and cells in continuous interaction. Ann N Y Acad Sci 2019; 1447:5-20. [PMID: 30865312 DOI: 10.1111/nyas.14040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.
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Affiliation(s)
- Luis P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
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9
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Jayathilaka TS, Lehman N. Spontaneous Covalent Self-Assembly of the Azoarcus Ribozyme from Five Fragments. Chembiochem 2018; 19:217-220. [PMID: 29207206 DOI: 10.1002/cbic.201700591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Indexed: 01/04/2023]
Abstract
Spontaneous covalent assembly of short RNA fragments has been proposed as a plausible prebiotically relevant pathway to a self-reproducing system. We previously showed that the Azoarcus group I intron could self-assemble from four RNA fragments. Here, we extended this fragmentation to five RNAs that averaged <40 nucleotides in length. We optimized this reaction and showed that a dehydration-rehydration sequence was the most effective means to date to shift the self-assembly equilibrium from reactants to products.
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Affiliation(s)
- Tharuka S Jayathilaka
- Department of Chemistry, Portland State University, P. O. Box 751, Portland, OR, 97207, USA
| | - Niles Lehman
- Department of Chemistry, Portland State University, P. O. Box 751, Portland, OR, 97207, USA
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10
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Wang TP, Su YC, Chen Y, Severance S, Hwang CC, Liou YM, Lu CH, Lin KL, Zhu RJ, Wang EC. Corroboration of Zn( ii)–Mg( ii)-tertiary structure interplays essential for the optimal catalysis of a phosphorothiolate thiolesterase ribozyme. RSC Adv 2018; 8:32775-32793. [PMID: 35547718 PMCID: PMC9086351 DOI: 10.1039/c8ra05083j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
The TW17 ribozyme, a catalytic RNA selected from a pool of artificial RNA, is specific for the Zn2+-dependent hydrolysis of a phosphorothiolate thiolester bond. Here, we describe the organic synthesis of both guanosine α-thio-monophosphate and the substrates required for selecting and characterizing the TW17 ribozyme, and for deciphering the catalytic mechanism of the ribozyme. By successively substituting the substrate originally conjugated to the RNA pool with structurally modified substrates, we demonstrated that the TW17 ribozyme specifically catalyzes phosphorothiolate thiolester hydrolysis. Metal titration studies of TW17 ribozyme catalysis in the presence of Zn2+ alone, Zn2+ and Mg2+, and Zn2+ and [Co(NH3)6]3+ supported our findings that Zn2+ is absolutely required for ribozyme catalysis, and indicated that optimal ribozyme catalysis involves the presence of outer-sphere and one inner-sphere Mg2+. A survey of the TW17 ribozyme activity at various pHs revealed that the activity of the ribozyme critically depends on the alkaline conditions. Moreover, a GNRA tetraloop-containing ribozyme constructed with active catalysis in trans provided catalysis and multiple substrate turnover efficiencies significantly higher than ribozymes lacking a GNRA tetraloop. This research supports the essential roles of Zn2+, Mg2+, and a GNRA tetraloop in modulating the TW17 ribozyme structure for optimal ribozyme catalysis, leading also to the formulation of a proposed reaction mechanism for TW17 ribozyme catalysis. Zn(ii) and Mg(ii) and GAGA tetraloop in the ion atmosphere of the TW17 ribozyme is critical to optimal ribozyme catalysis at alkaline pH.![]()
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Affiliation(s)
- Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
- Kaohsiung Medical University Hospital
| | - Yu-Chih Su
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Yi Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Scott Severance
- Department of Molecular and Cellular Sciences
- Liberty University College of Osteopathic Medicine
- Lynchburg
- USA
| | - Chi-Ching Hwang
- Department of Biochemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Yi-Ming Liou
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Chia-Hui Lu
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Kun-Liang Lin
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Rui Jing Zhu
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Eng-Chi Wang
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
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11
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Staroseletz Y, Nechaev S, Bichenkova E, Bryce RA, Watson C, Vlassov V, Zenkova M. Non-enzymatic recombination of RNA: Ligation in loops. Biochim Biophys Acta Gen Subj 2017; 1862:705-725. [PMID: 29097301 DOI: 10.1016/j.bbagen.2017.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating. METHODS We report here on the study of recombination process modelled with two 96 nts RNA fragments. Detection of recombination products was performed with RT-PCR followed by TA-cloning and Sanger sequencing. RESULTS A wide range of recombinant products was detected. We found that (i) the most efficient ligation was observed for RNA species forming bulges or internal loops, with ligation partners located within the loop; (ii) a strong preference was observed for formation of a few types of major products with a large variety of minor products; (iii) ligation could occur with participation of either 2',3'-cyclophosphate or 5'-ppp; (iv) the presence of key reaction components, i.e. 5'ppp-RNAs, enabled the formation of additional types of product; (v) molecular dynamics simulations of one of the most abundant products suggests that the ligation results in a preferable formation of 2'-5'- rather than 3'-5'-linkages. CONCLUSIONS The study demonstrates regularities of new RNA molecules formation with non-enzymatic recombination process. GENERAL SIGNIFICANCE Our findings provide new data supporting the RNA World hypothesis and show the way of new RNA sequences emergence under prebiotic conditions.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Sergey Nechaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Elena Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Catherine Watson
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
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12
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Mathis C, Ramprasad SN, Walker SI, Lehman N. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation. Life (Basel) 2017; 7:life7040038. [PMID: 29035326 PMCID: PMC5745551 DOI: 10.3390/life7040038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/06/2017] [Accepted: 10/11/2017] [Indexed: 12/31/2022] Open
Abstract
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life.
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Affiliation(s)
- Cole Mathis
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287, USA.
| | - Sanjay N Ramprasad
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97202, USA.
| | - Sara Imari Walker
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287, USA.
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA.
| | - Niles Lehman
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97202, USA.
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13
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Yeates JAM, Nghe P, Lehman N. Topological and thermodynamic factors that influence the evolution of small networks of catalytic RNA species. RNA (NEW YORK, N.Y.) 2017; 23:1088-1096. [PMID: 28389432 PMCID: PMC5473143 DOI: 10.1261/rna.061093.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative interactions into full-length ribozymes to investigate the dynamics of small (three- and four-membered) networks. We focused on the influence of a three-membered core network on the incorporation of additional nodes, and on the degree and direction of connectivity as single new nodes are added to this core. We confirmed experimentally the predictions that additional links to a core should enhance overall network growth rates, but that the directionality of the link (a "giver" or a "receiver") impacts the growth of the core itself. Additionally, we used a simple mathematical model based on the first-order effects of lower-level interactions to predict the growth of more complex networks, and find that such a model can, to a first approximation, predict the ordinal rankings of nodes once a steady-state distribution has been reached.
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Affiliation(s)
- Jessica A M Yeates
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Philippe Nghe
- Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), PSL Research University, CNRS UMR 8231, 75231 Paris, France
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
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14
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Group I Intron Internal Guide Sequence Binding Strength as a Component of Ribozyme Network Formation. Molecules 2016; 21:molecules21101293. [PMID: 27689977 PMCID: PMC6274277 DOI: 10.3390/molecules21101293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 11/17/2022] Open
Abstract
Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (KD) between the 3-nucleotide internal guide sequence (IGS) of one ribozyme and its complement in another is correlated to the catalytic ability of the ribozyme. This work demonstrates that one can begin to deconstruct the thermodynamic basis of information in prebiotic RNA systems.
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15
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Yeates JAM, Hilbe C, Zwick M, Nowak MA, Lehman N. Dynamics of prebiotic RNA reproduction illuminated by chemical game theory. Proc Natl Acad Sci U S A 2016; 113:5030-5. [PMID: 27091972 PMCID: PMC4983821 DOI: 10.1073/pnas.1525273113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.
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Affiliation(s)
| | - Christian Hilbe
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Martin Zwick
- Systems Science Graduate Program, Portland State University, Portland, OR 97207
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, OR 97207;
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16
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Colizzi ES, Hogeweg P. Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation. PLoS Comput Biol 2016; 12:e1004902. [PMID: 27120344 PMCID: PMC4847872 DOI: 10.1371/journal.pcbi.1004902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/07/2016] [Indexed: 11/19/2022] Open
Abstract
In a prebiotic RNA world, parasitic behaviour may be favoured because template dependent replication happens in trans, thus being altruistic. Spatially extended systems are known to reduce harmful effects of parasites. Here we present a spatial system to show that evolution of replication is (indirectly) enhanced by strong parasites, and we characterise the phase transition that leads to this mode of evolution. Building on the insights of this analysis, we identify two scenarios, namely periodic disruptions and longer replication time-span, in which speciation occurs and an evolved parasite-like lineage enables the evolutionary increase of replication rates in replicators. Finally, we show that parasites co-evolving with replicators are selected to become weaker, i.e. worse templates for replication when the duration of replication is increased. We conclude that parasites may not be considered a problem for evolution in a prebiotic system, but a degree of freedom that can be exploited by evolution to enhance the evolvability of replicators, by means of emergent levels of selection. The RNA world is a stage of evolution that preceded cellular life. In this world, RNA molecules would both replicate other RNAs and behave as templates for replication. A known evolutionary problem of this world is that selection should favour parasitic templates that do not replicate others, because they would be replicated the most. A possible solution to this problem comes from spatial self-organisation: local accumulation of parasites lead to their own local extinction, which leaves empty space for replicators to invade. We show that the spatial organisation generated by interacting replicators and parasites sets the (spatial) conditions that enhance replicase activity when parasites are stronger. Moreover, we find that the co-evolution of replicators and parasites is severely constrained by the type of spatial patterns they form, and we explore this feedback between evolution and self-organisation. We conclude that spatial self-organisation may have played a prominent role in prebiotic evolution.
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Affiliation(s)
- Enrico Sandro Colizzi
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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17
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Witzany G. The biocommunication method: On the road to an integrative biology. Commun Integr Biol 2016; 9:e1164374. [PMID: 27195071 PMCID: PMC4857777 DOI: 10.1080/19420889.2016.1164374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 02/06/2023] Open
Abstract
Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory could translate empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology.
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18
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Abstract
Construction of long RNAs can be achieved in vitro by using ribozymes to recombine shorter RNAs. This can be a useful technique to prepare RNAs when the final product is either very long or contains chemical modifications that are difficult to incorporate using standard in vitro transcription techniques. Here, we describe the use of the Azoarcus group I intron ribozyme to recombine shorter RNAs into longer ones. This ribozyme is a generalized RNA recombinase ribozyme that operates rapidly and with high efficiency.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, 751, Portland, OR, 97207, USA,
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19
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Abstract
The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core. The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching.
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20
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Vaidya N, Walker SI, Lehman N. Recycling of informational units leads to selection of replicators in a prebiotic soup. ACTA ACUST UNITED AC 2013; 20:241-52. [PMID: 23438753 DOI: 10.1016/j.chembiol.2013.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/30/2012] [Accepted: 01/03/2013] [Indexed: 11/15/2022]
Abstract
Prebiotic chemical reactions would have been greatly aided by a process whereby living materials could have been recycled under conditions of limiting resources. Recombination of RNA fragments is a viable means of recycling but has not been demonstrated. Using systems based on the Azoarcus group I intron ribozyme, computational Monte Carlo studies indicate that a moderate level of recycling activity, spontaneous or catalyzed, leads to the most robust selection scenarios. It is interesting that recycling leads to a threshold effect where a dominant species suddenly jumps to fixation. In conjunction, laboratory studies with the Azoarcus ribozyme corroborate these results, showing that mixtures of scrambled and/or deleteriously mutated molecules can recycle their component fragments to generate fully functional recombinase ribozymes. These studies highlight the importance of recombination and recycling jointly in the advent of living systems.
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Affiliation(s)
- Nilesh Vaidya
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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21
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Spontaneous network formation among cooperative RNA replicators. Nature 2012; 491:72-7. [PMID: 23075853 DOI: 10.1038/nature11549] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 09/06/2012] [Indexed: 12/16/2022]
Abstract
The origins of life on Earth required the establishment of self-replicating chemical systems capable of maintaining and evolving biological information. In an RNA world, single self-replicating RNAs would have faced the extreme challenge of possessing a mutation rate low enough both to sustain their own information and to compete successfully against molecular parasites with limited evolvability. Thus theoretical analyses suggest that networks of interacting molecules were more likely to develop and sustain life-like behaviour. Here we show that mixtures of RNA fragments that self-assemble into self-replicating ribozymes spontaneously form cooperative catalytic cycles and networks. We find that a specific three-membered network has highly cooperative growth dynamics. When such cooperative networks are competed directly against selfish autocatalytic cycles, the former grow faster, indicating an intrinsic ability of RNA populations to evolve greater complexity through cooperation. We can observe the evolvability of networks through in vitro selection. Our experiments highlight the advantages of cooperative behaviour even at the molecular stages of nascent life.
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Self-Replication Reactions Dependent on Tertiary Interaction Motifs in an RNA Ligase Ribozyme. J Mol Evol 2011; 73:221-9. [DOI: 10.1007/s00239-011-9471-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/24/2011] [Indexed: 11/26/2022]
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23
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Wu M, Higgs PG. Comparison of the roles of nucleotide synthesis, polymerization, and recombination in the origin of autocatalytic sets of RNAs. ASTROBIOLOGY 2011; 11:895-906. [PMID: 22059642 DOI: 10.1089/ast.2011.0679] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ribozymes that act as polymerases and nucleotide synthases are known experimentally, even though no fully self-replicating system has yet been found. If the RNA World hypothesis is true, ribozymes must have arisen initially from within a random abiotic polymerization system. To investigate the origin of the RNA world, we studied a mathematical model of a chemical reaction system describing RNA polymerization. It is supposed that, in absence of ribozymes, polymerization occurs at a small spontaneous rate, and that in the presence of polymerase ribozymes, polymerization occurs at a faster rate that is proportional to the ribozyme concentration. Chains must be longer than a minimum threshold length in order to have the possibility of acting as ribozymes. The reaction system has two stable states that we term dead and living. The dead state is controlled by the small spontaneous rate and has negligible concentration of ribozymes. The living state has high concentration of ribozymes, and the reaction rates are determined by the ribozymes; thus, the system is autocatalytic. Concentration fluctuations in a finite volume can cause a transition to occur from the dead to the living state, that is, an origin of life occurs within this model. We also consider ribozymes that catalyze nucleotide synthesis. We show that living and dead states arise in the presence of synthase ribozymes in the same way as for polymerases. It has been proposed that recombination reactions are a way of generating long RNA chains in the early stages of life. We show that if the possibility of random reversible recombination reactions is added to our model, this does not lead to an increase in long polymer concentration. Thus, if recombination is fully reversible, there is no autocatalytic state controlled by recombination. Nevertheless, recombination can play an important role in ribozyme synthesis if there is an additional process that keeps the recombination reactions out of equilibrium. We modeled a case studied experimentally in which building block strands of moderate length associate due to RNA secondary structure formation. A recombination reaction then occurs between these strands to form a longer sequence that catalyzes its own formation via the recombination reaction. This system has an autocatalytic state, and it is possible for it to arise within our random polymerization system. If complexes formed by associations of shorter strands can act as catalysts without the requirement that the strands be covalently linked, this would alleviate the need for synthesis of very long strands; hence, it makes the emergence of an autocatalytic system from an abiotic random polymerization system much more likely.
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Affiliation(s)
- Meng Wu
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
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24
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Abstract
How life emerged on this planet is one of the most important and fundamental questions of science. Although nearly all details concerning our origins have been lost in the depths of time, there is compelling evidence to suggest that the earliest life might have exploited the catalytic and self-recognition properties of RNA to survive. If an RNA based replicating system could be constructed in the laboratory, it would be much easier to understand the challenges associated with the very earliest steps in evolution and provide important insight into the establishment of the complex metabolic systems that now dominate this planet. Recent progress into the selection and characterization of ribozymes that promote nucleotide synthesis and RNA polymerization are discussed and outstanding problems in the field of RNA-mediated RNA replication are summarized.
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Affiliation(s)
- Leslie K L Cheng
- Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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25
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Vaidya N, Lehman N. One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence. Nucleic Acids Res 2009; 37:3981-9. [PMID: 19406926 PMCID: PMC2709566 DOI: 10.1093/nar/gkp271] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/31/2009] [Accepted: 04/10/2009] [Indexed: 11/26/2022] Open
Abstract
Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5' end of the molecule, and added back exogenously in trans. The presence of GUG triplets in non-covalent fragments of the ribozyme allow trans-splicing to occur in both a reverse splicing assay and a covalent self-assembly assay in which the internal guide sequence (IGS)-less ribozyme can put itself together from two of its component pieces. Analysis of these reactions indicates that a single RNA fragment can perform up to three distinct roles in a reaction: behaving as a portion of a catalyst, behaving as a substrate, and providing an exogenous IGS. This property of RNA to be multifunctional in a single reaction pathway bolsters the probability that a system of self-replicating molecules could have existed in an RNA world during the origins of life on the Earth.
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Affiliation(s)
| | - Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
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26
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Hayden EJ, von Kiedrowski G, Lehman N. Systems chemistry on ribozyme self-construction: evidence for anabolic autocatalysis in a recombination network. Angew Chem Int Ed Engl 2008; 47:8424-8. [PMID: 18780409 DOI: 10.1002/anie.200802177] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eric J Hayden
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
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27
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Lehman N. A recombination-based model for the origin and early evolution of genetic information. Chem Biodivers 2008; 5:1707-17. [PMID: 18816523 DOI: 10.1002/cbdv.200890159] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recombination is the exchange of groups of subunits between two entities. It is argued here that this process was central to the origin of life, because it allowed for the creation of useful information from a random pool of linear polymers. The length distribution of such a pool could be broadened if these polymers, such as RNA strands, have the capability of interacting and performing a cross-strand nucleophilic attack of a hydroxy group on a phosphate. Both the formation of stable secondary structures such as stem-loops and selection for self-replication can operate to push the equilibrium length distribution of the pool to longer and more catalytically proficient oligomers. There is empirical and theoretical support for these operations. Finally, in a collection of recombining linear oligomers, the advent of short recognition sequences that favor certain interactions over others, the property of a genotypic 'self' could develop, which later can shed its collective nature and be subject to Darwinian evolution. This could have given rise to true replicase enzymes, for example.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA.
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28
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Systems Chemistry on Ribozyme Self-Construction: Evidence for Anabolic Autocatalysis in a Recombination Network. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Ellington AD, Chen X, Robertson M, Syrett A. Evolutionary origins and directed evolution of RNA. Int J Biochem Cell Biol 2008; 41:254-65. [PMID: 18775793 DOI: 10.1016/j.biocel.2008.08.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/16/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
In vitro selection experiments show first and foremost that it is possible that functional nucleic acids can arise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove to be robust binding species and catalysts, indicating that it may have been possible to transition from even the earliest self-replicators to a nascent, RNA-catalyzed metabolism. Because of the diversity of aptamers and ribozymes that can be selected, it is possible to construct a 'fossil record' of the evolution of the RNA world, with in vitro selected catalysts filling in as doppelgangers for molecules long gone. In this way a plausible pathway from simple oligonucleotide replicators to genomic polymerases can be imagined, as can a pathway from basal ribozyme activities to the ribosome. Most importantly, though, in vitro selection experiments can give a true and quantitative idea of the likelihood that these scenarios could have played out in the RNA world. Simple binding species and catalysts could have evolved into other structures and functions. As replicating sequences grew longer, new, more complex functions or faster catalytic activities could have been accessed. Some activities may have been isolated in sequence space, but others could have been approached along large, interconnected neutral networks. As the number, type, and length of ribozymes increased, RNA genomes would have evolved and eventually there would have been no area in a fitness landscape that would have been inaccessible. Self-replication would have inexorably led to life.
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Affiliation(s)
- Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States.
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30
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Glansdorff N, Xu Y, Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 2008; 3:29. [PMID: 18613974 PMCID: PMC2478661 DOI: 10.1186/1745-6150-3-29] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 07/09/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario. RESULTS LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection. CONCLUSION Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound. REVIEWERS This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.
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Affiliation(s)
- Nicolas Glansdorff
- JM Wiame Research Institute for Microbiology and Vrije Universiteit Brussel, 1 ave E. Gryzon, B-1070 Brussels, Belgium.
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