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Vitas M, Dobovišek A. Is Darwinian selection a retrograde driving force of evolution? Biosystems 2023; 233:105031. [PMID: 37734699 DOI: 10.1016/j.biosystems.2023.105031] [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: 05/01/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Modern science has still not provided a satisfactory empirical explanation for the increasing complexity of living organisms through evolutionary history. As no agreed-upon definitions of the complexity exist, the working definition of biological complexity has been formulated. There is no theoretical reason to expect evolutionary lineages to increase in complexity over time, and there is no empirical evidence that they do so. In our discussion we have assumed the hypothesis that at the origins of life, evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. We discuss the role of Darwinian selection in evolution and pose the hypothesis that Darwinian selection acts predominantly as a retrograde driving force of evolution. In this context we understand the term retrograde evolution as a degeneration of living systems from higher complexity towards living systems with lower complexity. With the proposed hypothesis we have closed the gap between Darwinism and Lamarckism early in the evolutionary process. By Lamarckism, the action of a special principle called complexification force is understood here rather than inheritance of acquired characteristics.
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Affiliation(s)
- Marko Vitas
- Laze pri Borovnici 38, 1353, Borovnica, Slovenia.
| | - Andrej Dobovišek
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 6B, 2000, Maribor, Slovenia.
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2
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Russell MJ. A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism. Front Microbiol 2023; 14:1145915. [PMID: 37275164 PMCID: PMC10236563 DOI: 10.3389/fmicb.2023.1145915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/22/2023] [Indexed: 06/07/2023] Open
Abstract
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
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Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, Torino, Italy
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3
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Goswami S, Reja A, Pal S, Singh A, Das D. Nonequilibrium Amyloid Polymers Exploit Dynamic Covalent Linkage to Temporally Control Charge-Selective Catalysis. J Am Chem Soc 2022; 144:19248-19252. [PMID: 36219699 DOI: 10.1021/jacs.2c09262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extant proteins exploit thermodynamically activated negatively charged coenzymes and hydrotropes to temporally access mechanistically important conformations that regulate vital biological functions, from metabolic reactions to expression modulation. Herein, we show that a short amyloid peptide can bind to a small molecular coenzyme by exploiting reversible covalent linkage to polymerize and access catalytically proficient nonequilibrium amyloid microphases. Subsequent hydrolysis of the activated coenzyme leads to depolymerization, realizing a variance of the surface charge of the assembly as a function of time. Such temporal change of surface charge dynamically modulates catalytic activities of the transient assemblies as observed in highly evolved modern-day biocatalysts.
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Affiliation(s)
- Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Abhishek Singh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
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4
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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5
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Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian block chain distributed ledger. Biosystems 2022; 220:104718. [PMID: 35803502 DOI: 10.1016/j.biosystems.2022.104718] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 12/26/2022]
Abstract
The digitization of inheritable information in the genome has been called the 'algorithmic take-over of biology'. The McClintock discovery that viral software based transposable elements that conduct cut-paste (transposon) and copy-paste (retrotransposon) operations are needed for genomic evolvability underscores the truism that only software can change software and also that viral hacking by internal and external bio-malware is the Achilles heel of genomic digital systems. There was a paradigm shift in genomic information processing with the Adaptive Immune System (AIS) 500 mya followed by the Mirror Neuron System (MNS), latterly mostly in primate brains, which reaches its apogee in human social cognition. The AIS and MNS involve distinctive Gödelian features of self-reference (Self-Ref) and offline virtual self-representation (Self-Rep) for complex self-other interaction with prodigious open-ended capacity for anticipative malware detection and novelty production within a unique blockchain distributed ledger (BCDL). The role of self-referential information processing, often considered to be central to the sentient self with origins in the immune system 'Thymic self', is shown to be part of the Gödel logic behind a generator-selector framework at a molecular level, which exerts stringent selection criteria to maintain genomic BCDL. The latter manifests digital and decentralized record keeping where no internal or external bio-malware can compromise the immutability of the life's building blocks and no novel blocks can be added that is not consistent with extant blocks. This is demonstrated with regard to somatic hypermutation with novel anti-body production in the face of external non-self antigen attacks.
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6
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Mahato C, Menon S, Singh A, Afrose SP, Mondal J, Das D. Short Peptide-based Cross-β Amyloids Exploit Dual Residues for Phosphoesterase like Activity. Chem Sci 2022; 13:9225-9231. [PMID: 36092997 PMCID: PMC9384705 DOI: 10.1039/d2sc03205h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/17/2022] [Indexed: 11/21/2022] Open
Abstract
Herein, we report that short peptides are capable of exploiting their anti-parallel registry to access cross-β stacks to expose more than one catalytic residue, exhibiting the traits of advanced binding pockets of enzymes. Binding pockets decorated with more than one catalytic residue facilitate substrate binding and process kinetically unfavourable chemical transformations. The solvent-exposed guanidinium and imidazole moieties on the cross-β microphases synergistically bind to polarise and hydrolyse diverse kinetically stable model substrates of nucleases and phosphatase. Mutation of either histidine or arginine results in a drastic decline in the rate of hydrolysis. These results not only support the argument of short amyloid peptides as the earliest protein folds but also suggest their interactions with nucleic acid congeners, foreshadowing the mutualistic biopolymer relationships that fueled the chemical emergence of life. Amyloid based short peptide assemblies use antiparallel registry to expose multiple catalytic residues to bind and cleave kinetically stable phosphoester bonds of nucleic acid congeners, foreshadowing interactions of protein folds with nucleic acids.![]()
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Affiliation(s)
- Chiranjit Mahato
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Sneha Menon
- Tata Institute of Fundamental Research Hyderabad Telangana 500046 India
| | - Abhishek Singh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad Telangana 500046 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
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7
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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8
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Prosdocimi F, de Farias ST. Life and living beings under the perspective of organic macrocodes. Biosystems 2021; 206:104445. [PMID: 34033908 DOI: 10.1016/j.biosystems.2021.104445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
A powerful and concise concept of life is crucial for studies aiming to understand the characteristics that emerged from an inorganic world. Among biologists, the most accepted argument define life under a top-down strategy by looking into the shared characteristics observed in all cellular organisms. This is often made highlighting (i) autonomy and (ii) evolutionary capacity as fundamental characteristics observed in all cellular organisms. Along the present work, we assume the framework of code biology considering that biology started with the emergence of the first organic code by self-organization. We reinforces that the conceptual structure of life should be reallocated from the ontology class of Matter to its sister class of Process. Along the emergence and early evolution of biological systems, biological codes changed from open systems of "naked" molecules (at the progenote era), to close, encapsulated systems (at the organismic era). Living beings appeared at the very moment when nucleic acids with coding properties became encapsulated. This led to the origin of viruses and, then, to the origin of cells. In this context, we propose that the single character that makes a clear distinction between the abiotic and the biotic world is the capacity to process organic codes. Thus, life appears with the self-assembly of a genetic code and evolves by the emergence of other overlapping codes. Once life has been clearly conceptualized, we go further to conceptualize organisms, parents, lineages, and species in terms of code biology.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK.
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9
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Affiliation(s)
- Dragana Despotovic
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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10
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Classification of the Biogenicity of Complex Organic Mixtures for the Detection of Extraterrestrial Life. Life (Basel) 2021; 11:life11030234. [PMID: 33809046 PMCID: PMC8001260 DOI: 10.3390/life11030234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/02/2021] [Accepted: 03/07/2021] [Indexed: 11/17/2022] Open
Abstract
Searching for life in the Universe depends on unambiguously distinguishing biological features from background signals, which could take the form of chemical, morphological, or spectral signatures. The discovery and direct measurement of organic compounds unambiguously indicative of extraterrestrial (ET) life is a major goal of Solar System exploration. Biology processes matter and energy differently from abiological systems, and materials produced by biological systems may become enriched in planetary environments where biology is operative. However, ET biology might be composed of different components than terrestrial life. As ET sample return is difficult, in situ methods for identifying biology will be useful. Mass spectrometry (MS) is a potentially versatile life detection technique, which will be used to analyze numerous Solar System environments in the near future. We show here that simple algorithmic analysis of MS data from abiotic synthesis (natural and synthetic), microbial cells, and thermally processed biological materials (lab-grown organisms and petroleum) easily identifies relational organic compound distributions that distinguish pristine and aged biological and abiological materials, which likely can be attributed to the types of compounds these processes produce, as well as how they are formed and decompose. To our knowledge this is the first comprehensive demonstration of the utility of this analytical technique for the detection of biology. This method is independent of the detection of particular masses or molecular species samples may contain. This suggests a general method to agnostically detect evidence of biology using MS given a sufficiently strong signal in which the majority of the material in a sample has either a biological or abiological origin. Such metrics are also likely to be useful for studies of possible emergent living phenomena, and paleobiological samples.
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11
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Functional characterization of the ATPase-like activity displayed by a catalytic amyloid. Biochim Biophys Acta Gen Subj 2020; 1865:129729. [PMID: 32916204 DOI: 10.1016/j.bbagen.2020.129729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/17/2020] [Accepted: 09/04/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND Amyloids are highly ordered polypeptide aggregates stabilized by a beta-sheet structural core. Though classically associated to pathology, reports on novel functional roles of these proteins have increasingly emerged in the past decade. Moreover, the recent discovery that amyloids formed with rationally designed small peptides can exhibit catalytic reactivity has opened up new opportunities in both biology and biotechnology. The observed activities typically require the binding of divalent metals, giving rise to active metal-amyloid complexes. METHODS Peptide (SDIDVFI) was aggregated in vitro. The structure of the self-assembled species was analyzed using fluorescence, transmission electron microscopy, circular dichroism and computational modeling. A kinetic characterization of the emerging catalytic activity was performed. RESULTS The peptide self-assembled into canonical amyloids that exhibited catalytic activity towards hydrolysis of the phosphoanhydride bonds of adenosine triphosphate (ATP), partially mimicking an ATPase-like enzyme. Both amyloid formation and activity are shown to depend on manganese (Mn2+) binding. The activity was not restricted to ATP but also affected all other ribonucleotides (GTP, CTP and UTP). Peptides carrying a single aspartate exhibited a similar activity. CONCLUSIONS The phosphoanhydride bonds appear as the main specificity target of the Mn2+-amyloid complex. A single aspartate per peptide is sufficient to enable the hydrolytic activity. GENERAL SIGNIFICANCE Catalytic amyloids are shown for the first time to catalyze the hydrolysis of all four ribonucleotides. Our results should contribute towards understanding the biological implications of amyloid-mediated reactivity as well as in the design of future catalytic amyloids for biotechnological applications.
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Chatterjee A, Afrose SP, Ahmed S, Venugopal A, Das D. Cross-β amyloid nanotubes for hydrolase-peroxidase cascade reactions. Chem Commun (Camb) 2020; 56:7869-7872. [PMID: 32154814 DOI: 10.1039/d0cc00279h] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, we report the catalytic potential of short peptide based cross-β amyloid nanotubes with surface exposed histidine capable of binding hemin and showing facile cascade reactions, playing the dual roles of hydrolases and peroxidases, two of the most important classes of enzymes in extant biology. The activity of these simple systems exceeded those of modern and larger proteins like cytochrome C and hemoglobin. Further, evidence suggested that these self-assembled nanotubes foreshadow the process of intermediate channeling, a feature seen in the case of advanced enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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13
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
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14
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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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15
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020; 59:4329-4334. [PMID: 31920004 DOI: 10.1002/anie.201914633] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Indexed: 12/25/2022]
Abstract
Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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16
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Saha B, Chatterjee A, Reja A, Das D. Condensates of short peptides and ATP for the temporal regulation of cytochrome c activity. Chem Commun (Camb) 2019; 55:14194-14197. [PMID: 31702760 DOI: 10.1039/c9cc07358b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein, we report the generation of simple condensates of short peptides with ATP, which are spatiotemporally formed under dissipative conditions created in presence of ATP-ase. These coacervates could imbibe cytochrome c and temporally modulate a redox reaction catalyzed by the entrapped protein, thus mimicking the advanced functional machinery of transient intercellular membraneless condensates of large proteins and RNA.
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Affiliation(s)
- Baishakhi Saha
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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17
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Cleaves HJ, Butch C, Burger PB, Goodwin J, Meringer M. One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. J Chem Inf Model 2019; 59:4266-4277. [PMID: 31498614 DOI: 10.1021/acs.jcim.9b00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological functions and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids both in vivo and in vitro; yet despite remarkable advances over the last few decades, much remains unknown regarding which structures are compatible with molecular information storage. Chemical space describes the structures and properties of molecules that could exist within a given molecular formula or other classification system. Using structure generation methods, we explore nucleic acid analogues within the formula ranges BC3-7H5-15O2-4 and BC3-6H5-15N1-2O0-4, where B is a recognition element (e.g., a nucleobase). Other restrictions included two obligatory points of attachment for inclusion into a linear polymer and substructures predicting chemical stability. These sets contain 86,007 (CHO) and 75,309 (CHNO) compositionally isomeric structures, representing 706,568 CHO and 454,422 CHNO stereoisomers, that diversely and densely occupy this space. These libraries point toward there being large spaces of unexplored chemistry relevant to pharmacology and biochemistry and efforts to understand the origins of life.
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Affiliation(s)
- Henderson James Cleaves
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Institute for Advanced Study , Princeton , New Jersey 08540 , United States.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States
| | - Christopher Butch
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States.,Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Pieter Buys Burger
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Jay Goodwin
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Markus Meringer
- German Aerospace Center (DLR) , Earth Observation Center (EOC) , Münchner Straße 20 , 82234 Oberpfaffenhofen-Wessling , Germany
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18
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Doran D, Abul‐Haija YM, Cronin L. Emergence of Function and Selection from Recursively Programmed Polymerisation Reactions in Mineral Environments. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- David Doran
- School of ChemistryUniversity of Glasgow Glasgow G12 8QQ UK
| | | | - Leroy Cronin
- School of ChemistryUniversity of Glasgow Glasgow G12 8QQ UK
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19
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Doran D, Abul-Haija YM, Cronin L. Emergence of Function and Selection from Recursively Programmed Polymerisation Reactions in Mineral Environments. Angew Chem Int Ed Engl 2019; 58:11253-11256. [PMID: 31206983 PMCID: PMC6772075 DOI: 10.1002/anie.201902287] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/21/2019] [Indexed: 01/06/2023]
Abstract
Living systems are characterised by an ability to sustain chemical reaction networks far-from-equilibrium. It is likely that life first arose through a process of continual disruption of equilibrium states in recursive reaction networks, driven by periodic environmental changes. Herein, we report the emergence of proto-enzymatic function from recursive polymerisation reactions using amino acids and glycolic acid. Reactions were kept out of equilibrium by diluting products 9:1 in fresh starting solution at the end of each recursive cycle, and the development of complex high molecular weight species is explored using a new metric, the Mass Index, which allows the complexity of the system to be explored as a function of cycle. This process was carried out on a range of different mineral environments. We explored the hypothesis that disrupting equilibrium via recursive cycling imposes a selection pressure and subsequent boundary conditions on products. After just four reaction cycles, product mixtures from recursive reactions exhibit greater catalytic activity and truncation of product space towards higher-molecular-weight species compared to non-recursive controls.
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Affiliation(s)
- David Doran
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Leroy Cronin
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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20
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Wagner N, Hochberg D, Peacock-Lopez E, Maity I, Ashkenasy G. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life (Basel) 2019; 9:life9020045. [PMID: 31163645 PMCID: PMC6617095 DOI: 10.3390/life9020045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/05/2022] Open
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra Ajalvir Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
- Present address: Institute for Macromolecular Chemistry, Albert Ludwigs University of Freiburg, D-79104 Freiburg, Germany.
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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21
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Vitas M, Dobovišek A. Towards a General Definition of Life. ORIGINS LIFE EVOL B 2019; 49:77-88. [PMID: 31222432 DOI: 10.1007/s11084-019-09578-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/04/2019] [Indexed: 01/18/2023]
Abstract
A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA's working definition of life, which postulates that life is a "self-sustaining chemical system capable of Darwinian evolution". The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.
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Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, 1353 Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Taborska ulica 6b, 2000, Maribor, Slovenia
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22
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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23
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Bai Y, Chotera A, Taran O, Liang C, Ashkenasy G, Lynn DG. Achieving biopolymer synergy in systems chemistry. Chem Soc Rev 2018; 47:5444-5456. [PMID: 29850753 DOI: 10.1039/c8cs00174j] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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24
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Chotera A, Sadihov H, Cohen-Luria R, Monnard PA, Ashkenasy G. Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras. Chemistry 2018; 24:10128-10135. [PMID: 29732630 DOI: 10.1002/chem.201800500] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Indexed: 01/24/2023]
Abstract
Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.
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Affiliation(s)
- Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Hava Sadihov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Pierre-Alain Monnard
- Institute for Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
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25
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Vitas M, Dobovišek A. In the Beginning was a Mutualism - On the Origin of Translation. ORIGINS LIFE EVOL B 2018; 48:223-243. [PMID: 29713988 DOI: 10.1007/s11084-018-9557-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
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Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
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26
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Emergence of native peptide sequences in prebiotic replication networks. Nat Commun 2017; 8:434. [PMID: 28874657 PMCID: PMC5585222 DOI: 10.1038/s41467-017-00463-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.The synthesis of biopolymers in living cells is perfected by complex machinery, however this was not the case on early Earth. Here the authors show the role of non-enzymatic replication in the enrichment of certain products within prebiotically relevant mixtures.
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27
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Omosun TO, Hsieh MC, Childers WS, Das D, Mehta AK, Anthony NR, Pan T, Grover MA, Berland KM, Lynn DG. Catalytic diversity in self-propagating peptide assemblies. Nat Chem 2017; 9:805-809. [DOI: 10.1038/nchem.2738] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/03/2023]
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28
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Design of multi-phase dynamic chemical networks. Nat Chem 2017; 9:799-804. [DOI: 10.1038/nchem.2737] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/08/2023]
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29
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Liu Y, Lehn JM, Hirsch AKH. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers. Acc Chem Res 2017; 50:376-386. [PMID: 28169527 PMCID: PMC5332124 DOI: 10.1021/acs.accounts.6b00594] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 12/18/2022]
Abstract
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular biodynamers are commonly produced in aqueous media under mild or even physiological conditions to suit their biorelated applications. In contrast to static biopolymers emphasizing structural stability and unity by using irreversible covalent bonds, molecular biodynamers are seeking relative structural adaptability and diversity through the formation of reversible covalent bonds. Based on these considerations, molecular biodynamers are capable of reorganizing their monomers, generating, identifying, and amplifying the fittest structures in response to environmental factors. Hence, molecular biodynamers have received considerable research attention over the past decades. Accordingly, the construction of molecular biodynamers through equilibrium polymerization of nucleobase-, carbohydrate- or amino-acid-based monomers can lead to the fabrication of dynamic analogues of nucleic acids (DyNAs), polysaccharides (glycodynamers), or proteins (dynamic proteoids), respectively. In this Account, we summarize recent advances in developing different types of molecular biodynamers as structural or functional biomimetics of biopolymers, including DyNAs, glycodynamers, and dynamic proteoids. We introduce how chemists utilize various reversible reactions to generate molecular biodynamers with specific sequences and well-ordered structures in aqueous medium. We also discuss and list their potential applications in various research fields, such as drug delivery, drug discovery, gene sensing, cancer diagnosis, and treatment.
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Affiliation(s)
- Yun Liu
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jean-Marie Lehn
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée
Gaspard Monge, Strasbourg 67000, France
| | - Anna K. H. Hirsch
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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30
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Davies PCW, Walker SI. The hidden simplicity of biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:102601. [PMID: 27608530 DOI: 10.1088/0034-4885/79/10/102601] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Life is so remarkable, and so unlike any other physical system, that it is tempting to attribute special factors to it. Physics is founded on the assumption that universal laws and principles underlie all natural phenomena, but is it far from clear that there are 'laws of life' with serious descriptive or predictive power analogous to the laws of physics. Nor is there (yet) a 'theoretical biology' in the same sense as theoretical physics. Part of the obstacle in developing a universal theory of biological organization concerns the daunting complexity of living organisms. However, many attempts have been made to glimpse simplicity lurking within this complexity, and to capture this simplicity mathematically. In this paper we review a promising new line of inquiry to bring coherence and order to the realm of biology by focusing on 'information' as a unifying concept.
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Affiliation(s)
- Paul C W Davies
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA
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31
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Ivnitski D, Amit M, Silberbush O, Atsmon-Raz Y, Nanda J, Cohen-Luria R, Miller Y, Ashkenasy G, Ashkenasy N. The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils. Angew Chem Int Ed Engl 2016; 55:9988-92. [DOI: 10.1002/anie.201604833] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Denis Ivnitski
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Moran Amit
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Ohad Silberbush
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yoav Atsmon-Raz
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- Department of Biological Science; University of Calgary, Center of Molecular Simulation; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
| | - Jayanta Nanda
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Rivka Cohen-Luria
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yifat Miller
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; 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
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
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32
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Ivnitski D, Amit M, Silberbush O, Atsmon-Raz Y, Nanda J, Cohen-Luria R, Miller Y, Ashkenasy G, Ashkenasy N. The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Denis Ivnitski
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Moran Amit
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Ohad Silberbush
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yoav Atsmon-Raz
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- Department of Biological Science; University of Calgary, Center of Molecular Simulation; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
| | - Jayanta Nanda
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Rivka Cohen-Luria
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yifat Miller
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; 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
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Piao X, Xia X, Mao J, Bong D. Peptide Ligation and RNA Cleavage via an Abiotic Template Interface. J Am Chem Soc 2015; 137:3751-4. [PMID: 25747470 DOI: 10.1021/jacs.5b00236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xijun Piao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Xin Xia
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Gonzalez-Burgos M, Latorre-Sanchez A, Pomposo JA. Advances in single chain technology. Chem Soc Rev 2015; 44:6122-42. [DOI: 10.1039/c5cs00209e] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review summarizes the recent advances in single chain technology for the construction of soft nano-objects via chain compaction, and their envisioned applications.
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Affiliation(s)
- Marina Gonzalez-Burgos
- Centro de Física de Materiales (CSIC, UPV/EHU) – Materials Physics Center
- E-20018 San Sebastián
- Spain
- Departamento de Física de Materiales
- Universidad del País Vasco (UPV/EHU)
| | - Alejandro Latorre-Sanchez
- Centro de Física de Materiales (CSIC, UPV/EHU) – Materials Physics Center
- E-20018 San Sebastián
- Spain
- Departamento de Física de Materiales
- Universidad del País Vasco (UPV/EHU)
| | - José A. Pomposo
- Centro de Física de Materiales (CSIC, UPV/EHU) – Materials Physics Center
- E-20018 San Sebastián
- Spain
- Departamento de Física de Materiales
- Universidad del País Vasco (UPV/EHU)
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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Liang C, Ni R, Smith JE, Childers WS, Mehta AK, Lynn DG. Kinetic Intermediates in Amyloid Assembly. J Am Chem Soc 2014; 136:15146-9. [DOI: 10.1021/ja508621b] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chen Liang
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Rong Ni
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Jillian E. Smith
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
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Russell MJ, Barge LM, Bhartia R, Bocanegra D, Bracher PJ, Branscomb E, Kidd R, McGlynn S, Meier DH, Nitschke W, Shibuya T, Vance S, White L, Kanik I. The drive to life on wet and icy worlds. ASTROBIOLOGY 2014; 14:308-43. [PMID: 24697642 PMCID: PMC3995032 DOI: 10.1089/ast.2013.1110] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/02/2014] [Indexed: 05/22/2023]
Abstract
This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).
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Dunn IS. Are molecular alphabets universal enabling factors for the evolution of complex life? ORIGINS LIFE EVOL B 2013; 43:445-64. [PMID: 24510462 DOI: 10.1007/s11084-014-9354-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
Abstract
Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers. In contrast, much less detailed focus has been directed towards the potential universal need for molecular alphabets in constituting complex chemically-based life, and the implications of such a requirement. To analyze this, emphasis here is placed on the generalizable replicative and functional characteristics of molecular alphabets and their concatenates. A primary replicative alphabet based on the simplest possible molecular complementarity can potentially enable evolutionary processes to occur, including the encoding of secondarily functional alphabets. Very large uniquely specified ('non-alphabetic') molecules cannot feasibly underlie systems capable of the replicative and evolutionary properties which characterize complex biosystems. Transitions in the molecular evolution of alphabets can be related to progressive bridging of barriers which enable higher levels of biosystem organization. It is thus highly probable that molecular alphabets are an obligatory requirement for complex chemically-based life anywhere in the universe. In turn, reference to molecular alphabets should be usefully applied in current definitions of life.
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Affiliation(s)
- Ian S Dunn
- CytoCure LLC, Suite 430C, 100 Cummings Center, Beverly, MA, 01915, USA,
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