1
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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2
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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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3
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Frenkel-Pinter M, Haynes JW, Mohyeldin AM, C M, Sargon AB, Petrov AS, Krishnamurthy R, Hud NV, Williams LD, Leman LJ. Mutually stabilizing interactions between proto-peptides and RNA. Nat Commun 2020; 11:3137. [PMID: 32561731 PMCID: PMC7305224 DOI: 10.1038/s41467-020-16891-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
The close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay W Haynes
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ahmad M Mohyeldin
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Martin C
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alyssa B Sargon
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton S Petrov
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramanarayanan Krishnamurthy
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Loren Dean Williams
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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4
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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5
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Lancet D, Segrè D, Kahana A. Twenty Years of "Lipid World": A Fertile Partnership with David Deamer. Life (Basel) 2019; 9:E77. [PMID: 31547028 PMCID: PMC6958426 DOI: 10.3390/life9040077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Daniel Segrè
- Bioinformatics Program, Department of Biology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
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6
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Exploration of RNA Sequence Space in the Absence of a Replicase. J Mol Evol 2018; 86:264-276. [PMID: 29748740 DOI: 10.1007/s00239-018-9846-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/04/2018] [Indexed: 12/29/2022]
Abstract
It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed. An initial 20-mer served as a seed and was subjected to 180 min of simultaneous ligation and degradation. The seed RNA rapidly disappeared and was replaced by an increasing number and variety of both larger and smaller variants. Variants of 40-80 residues were consistently seen, typically representing 2-4% of the unique sequences. In a second experiment with four individual 9-mers, numerous variants were again produced. These included variants of the individual 9-mers as well as sequences that contained sequence segments from two or more 9-mers. In both cases, the RNA products lack large numbers of point mutations but instead incorporate additions and subtractions of fragments of the original RNAs. The system demonstrates that if such equilibrium were established in a prebiotic world it would result in significant exploration of RNA sequence space and likely increased complexity. It remains to be seen if the variety of products produced is affected by the presence of small peptide oligomers.
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7
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Danchin A. Archives or Palimpsests? Bacterial Genomes Unveil a Scenario for the Origin of Life. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot.2007.2.1.52] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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8
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Egel R. Origins and emergent evolution of life: the colloid microsphere hypothesis revisited. ORIGINS LIFE EVOL B 2014; 44:87-110. [PMID: 25208738 DOI: 10.1007/s11084-014-9363-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 08/14/2014] [Indexed: 11/28/2022]
Abstract
Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life's complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative 'protolife' communities, in which 'protoplasmic continuity' was maintained throughout a graded series of 'proto-biofilms', 'protoorganisms' and 'protocells' toward modern life. The proneness of organic microspheres to merge back into the bulk of sessile films by spontaneous fusion can have made large populations promiscuous from the beginning, which was important for the speed of collective evolution early on. In this protein-centered scenario, the emergent coevolution of uncoded peptides, metabolic cofactors and oligoribonucleotides was primarily optimized for system-supporting catalytic capabilities arising from nonribosomal peptide synthesis and nonreplicative ribonucleotide polymerization, which in turn incorporated other reactive micromolecular organics as vitamins and cofactors into composite macromolecular colloid films and microspheres. Template-dependent replication and gene-encoded protein synthesis emerged as secondary means for further optimization of overall efficieny later on. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark,
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9
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Boison D, Sandau US, Ruskin DN, Kawamura M, Masino SA. Homeostatic control of brain function - new approaches to understand epileptogenesis. Front Cell Neurosci 2013; 7:109. [PMID: 23882181 PMCID: PMC3712329 DOI: 10.3389/fncel.2013.00109] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/22/2013] [Indexed: 12/31/2022] Open
Abstract
Neuronal excitability of the brain and ongoing homeostasis depend not only on intrinsic neuronal properties, but also on external environmental factors; together these determine the functionality of neuronal networks. Homeostatic factors become critically important during epileptogenesis, a process that involves complex disruption of self-regulatory mechanisms. Here we focus on the bioenergetic homeostatic network regulator adenosine, a purine nucleoside whose availability is largely regulated by astrocytes. Endogenous adenosine modulates complex network function through multiple mechanisms including adenosine receptor-mediated pathways, mitochondrial bioenergetics, and adenosine receptor-independent changes to the epigenome. Accumulating evidence from our laboratories shows that disruption of adenosine homeostasis plays a major role in epileptogenesis. Conversely, we have found that reconstruction of adenosine's homeostatic functions provides new hope for the prevention of epileptogenesis. We will discuss how adenosine-based therapeutic approaches may interfere with epileptogenesis on an epigenetic level, and how dietary interventions can be used to restore network homeostasis in the brain. We conclude that reconstruction of homeostatic functions in the brain offers a new conceptual advance for the treatment of neurological conditions which goes far beyond current target-centric treatment approaches.
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Affiliation(s)
- Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute Portland, OR, USA
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10
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Sankaran N. How the discovery of ribozymes cast RNA in the roles of both chicken and egg in origin-of-life theories. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2012; 43:741-750. [PMID: 22886071 DOI: 10.1016/j.shpsc.2012.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 06/10/2012] [Accepted: 06/24/2012] [Indexed: 06/01/2023]
Abstract
Scientific theories about the origin-of-life theories have historically been characterized by the chicken-and-egg problem of which essential aspect of life was the first to appear, replication or self-sustenance. By the 1950s the question was cast in molecular terms and DNA and proteins had come to represent the carriers of the two functions. Meanwhile, RNA, the other nucleic acid, had played a capricious role in origin theories. Because it contained building blocks very similar to DNA, biologists recognized early that RNA could store information in its linear sequences. With the discovery in the 1980s that RNA molecules were capable of biological catalysis, a function hitherto ascribed to proteins alone, RNA took on the role of the single entity that could act as both chicken and egg. Within a few years of the discovery of these catalytic RNAs (ribozymes) scientists had formulated an RNA World hypothesis that posited an early phase in the evolution of life where all key functions were performed by RNA molecules. This paper traces the history the role of RNA in origin-of-life theories with a focus on how the discovery of ribozymes influenced the discourse.
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Affiliation(s)
- Neeraja Sankaran
- History of Science, Technology & Medicine Underwood International College, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul 120-749, Republic of Korea.
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11
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Fishkis M. Emergence of self-reproduction in cooperative chemical evolution of prebiological molecules. ORIGINS LIFE EVOL B 2011; 41:261-75. [PMID: 20811777 DOI: 10.1007/s11084-010-9220-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 07/07/2010] [Indexed: 01/19/2023]
Abstract
The paper presents a model of coevolution of short peptides (P) and short oligonucleotides (N) at an early stage of chemical evolution leading to the origin of life. The model describes polymerization of both P and N types of molecules on mineral surfaces in aqueous solution at moderate temperatures. It is assumed that amino acid and nucleotide monomers were available in a prebiotic milieu, that periodic variation in environmental conditions between dry/warm and wet/cool took place and that energy sources were available for the polymerization. An artificial chemistry approach in combination with agent-based modeling was used to explore chemical evolution from an initially random mixture of monomers. It was assumed that the oligonucleotides could serve as templates for self-replication and for translation of peptide compositional sequences, and that certain peptides could serve as weak catalysts. Important features of the model are the short lengths of the peptide and oligonucleotide molecules that prevent an error catastrophe caused by copying errors and a finite diffusion rate of the molecules on a mineral surface that prevents excessive development of parasitism. The result of the simulation was the emergence of self-replicating molecular systems consisting of peptide catalysts and oligonucleotide templates. In addition, a smaller but significant number of molecules with alternative compositions also survived due to imprecise reproduction and translation of templates providing variability for further evolution. In a more general context, the model describes not only peptide-oligonucleotide molecular systems, but any molecular system containing two types of polymer molecules: one of which serves as templates and the other as catalysts.The presented coevolutionary system suggests a possible direction towards finding the origin of molecular functionality in a prebiotic environment.
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Affiliation(s)
- Maya Fishkis
- Evolving Systems Technology, 95 Hawkfield Crescent, Calgary, Alberta, Canada.
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12
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Griffith RW. A specific scenario for the origin of life and the genetic code based on peptide/oligonucleotide interdependence. ORIGINS LIFE EVOL B 2009; 39:517-31. [PMID: 19468859 DOI: 10.1007/s11084-009-9169-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 04/05/2009] [Indexed: 10/20/2022]
Abstract
Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and translation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface.
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Affiliation(s)
- Robert W Griffith
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, 02747, USA.
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13
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Kashiwagi N, Furuta H, Ikawa Y. Primitive templated catalysis of a peptide ligation by self-folding RNAs. Nucleic Acids Res 2009; 37:2574-83. [PMID: 19264804 PMCID: PMC2677871 DOI: 10.1093/nar/gkp111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA–polypeptide complexes (RNPs), which play various roles in extant biological systems, have been suggested to have been important in the early stages of the molecular evolution of life. At a certain developmental stage of ancient RNPs, their RNA and polypeptide components have been proposed to evolve in a reciprocal manner to establish highly elaborate structures and functions. We have constructed a simple model system, from which a cooperative evolution system of RNA and polypeptide components could be developed. Based on the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides. We have designed an RNA molecule possessing two peptide binding sites that capture the two peptides. This designed RNA can also accelerate the peptide ligation. The resulting ligated peptide, which has two RNA-binding sites, can in turn function as a trans-acting factor that enhances the endonuclease activity catalyzed by the designed RNA.
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Affiliation(s)
- Norimasa Kashiwagi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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14
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Fishkis M. Steps towards the formation of a protocell: the possible role of short peptides. ORIGINS LIFE EVOL B 2007; 37:537-53. [PMID: 17874202 DOI: 10.1007/s11084-007-9111-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 08/15/2007] [Indexed: 10/22/2022]
Abstract
The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.
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Affiliation(s)
- Maya Fishkis
- Evolving Systems Technology, 95 Hawkfield Crescent NW, Calgary, Alberta, Canada.
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15
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Kooijman SALM, Troost TA. Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory. Biol Rev Camb Philos Soc 2007; 82:113-42. [PMID: 17313526 DOI: 10.1111/j.1469-185x.2006.00006.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.
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Affiliation(s)
- S A L M Kooijman
- Department of Theoretical Biology Vrije Universiteit, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
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16
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Abstract
What was the first living molecule--RNA or protein? This question embodies the major disagreement in studies on the origin of life. The fact that in contemporary cells RNA polymerase is a protein and peptidyl transferase consists of RNA suggests the existence of a mutual catalytic dependence between these two kinds of biopolymers. I suggest that this dependence is a 'frozen accident', a remnant from the first living system. This system is proposed to be a combination of an RNA molecule capable of catalyzing amino acid polymerization and the resulting protein functioning as an RNA-dependent RNA polymerase. The specificity of the protein synthesis is thought to be achieved by the composition of the surrounding medium and the specificity of the RNA synthesis--by Watson-Crick base pairing. Despite its apparent simplicity, the system possesses a great potential to evolve into a primitive ribosome and further to life, as it is seen today. This model provides a possible explanation for the origin of the interaction between nucleic acids and protein. Based on the suggested system, I propose a new definition of life as a system of nucleic acid and protein polymerases with a constant supply of monomers, energy and protection.
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Affiliation(s)
- V Kunin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Smith JV. Biochemical evolution. I. Polymerization On internal, organophilic silica surfaces of dealuminated zeolites and feldspars. Proc Natl Acad Sci U S A 1998; 95:3370-5. [PMID: 9520372 PMCID: PMC19842 DOI: 10.1073/pnas.95.7.3370] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Catalysis at mineral surfaces might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and photochemical gas reactions. Many ideas are implausible in detail because the proposed mineral surfaces strongly prefer water and other ionic species to organic ones. The molecular sieve silicalite (Union Carbide; = Al-free Mobil ZSM-5 zeolite) has a three-dimensional, 10-ring channel system whose electrically neutral Si-O surface strongly adsorbs organic species over water. Three -O-Si tetrahedral bonds lie in the surface, and the fourth Si-O points inwards. In contrast, the outward Si-OH of simple quartz and feldspar crystals generates their ionic organophobicity. The ZSM-5-type zeolite mutinaite occurs in Antarctica with boggsite and tschernichite (Al-analog of Mobil Beta). Archean mutinaite might have become de-aluminated toward silicalite during hot/cold/wet/dry cycles. Catalytic activity of silicalite increases linearly with Al-OH substitution for Si, and Al atoms tend to avoid each other. Adjacent organophilic and catalytic Al-OH regions in nanometer channels might have scavenged organic species for catalytic assembly into specific polymers protected from prompt photochemical destruction. Polymer migration along weathered silicic surfaces of micrometer-wide channels of feldspars might have led to assembly of replicating catalytic biomolecules and perhaps primitive cellular organisms. Silica-rich volcanic glasses should have been abundant on the early Earth, ready for crystallization into zeolites and feldspars, as in present continental basins. Abundant chert from weakly metamorphosed Archaean rocks might retain microscopic clues to the proposed mineral adsorbent/catalysts. Other framework silicas are possible, including ones with laevo/dextro one-dimensional channels. Organic molecules, transition-metal ions, and P occur inside modern feldspars.
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Affiliation(s)
- J V Smith
- Department of Geophysical Sciences and Center for Advanced Radiation Sources, 5734 S. Ellis Avenue, University of Chicago, Chicago, IL 60637, USA
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Lahav N, Nir S. Emergence of template-and-sequence-directed (TSD) syntheses: I. A bio-geochemical model. ORIGINS LIFE EVOL B 1997; 27:377-95. [PMID: 11536830 DOI: 10.1023/a:1006588421147] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A biogeochemical model for the evolution of template-and-sequence-directed (TSD) syntheses of biological templates (proto-RNAs) and catalysts (peptides) is described. A fluctuating environment characterized by hydrating (cool) and dehydrating (warm) phases with cycles of consecutive organic reactions, as well as a constant supply of the polymeric building blocks is assumed. The scenario starts with the catalyzed formation of a primordial population of small random peptides, based on the relatively-ineffective mineral catalysts. The resulting peptides initiate a catalytic takeover process, during which the catalytic functions are gradually taken over by peptides. The evolution of TSD peptides is based on a combination of Lahav's (1991) co-evolution and Moller and Janssen's (1990) specific recognition sites hypotheses. During the emergence of TSD systems the fraction of TSD peptides and proto-RNA constituents rises from almost insignificance to dominance in a TSD Reactions Takeover. The TSD system is characterized by autocatalysis, positive feedback loops and a primordial genetic code. The model is the basis for a computer program (Part II of present series).
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Affiliation(s)
- N Lahav
- The Hebrew University of Jerusalem, The Faculty of Agriculture, Rehovot, Israel
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Linguistics of biomolecules and the protein-first hypothesis for the origins of cells. J Biol Phys 1995. [DOI: 10.1007/bf00700436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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