1
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Sweeney KJ, Le T, Jorge MZ, Schellinger JG, Leman LJ, Müller UF. Peptide conjugates with polyaromatic hydrocarbons can benefit the activity of catalytic RNAs. Chem Sci 2023; 14:10318-10328. [PMID: 37772096 PMCID: PMC10529712 DOI: 10.1039/d3sc03540a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Early stages of life likely employed catalytic RNAs (ribozymes) in many functions that are today filled by proteins. However, the earliest life forms must have emerged from heterogenous chemical mixtures, which included amino acids, short peptides, and many other compounds. Here we explored whether the presence of short peptides can help the emergence of catalytic RNAs. To do this, we conducted an in vitro selection for catalytic RNAs from randomized sequence in the presence of ten different peptides with a prebiotically plausible length of eight amino acids. This in vitro selection generated dozens of ribozymes, one of them with ∼900-fold higher activity in the presence of one specific peptide. Unexpectedly, the beneficial peptide had retained its N-terminal Fmoc protection group, and this group was required to benefit ribozyme activity. The same, or higher benefit resulted from peptide conjugates with prebiotically plausible polyaromatic hydrocarbons (PAHs) such as fluorene and naphthalene. This shows that PAH-peptide conjugates can act as potent cofactors to enhance ribozyme activity. The results are discussed in the context of the origin of life.
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Affiliation(s)
- Kevin J Sweeney
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Tommy Le
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Micaella Z Jorge
- Department of Chemistry & Biochemistry, University of San Diego San Diego CA 92110 USA
| | - Joan G Schellinger
- Department of Chemistry & Biochemistry, University of San Diego San Diego CA 92110 USA
| | - Luke J Leman
- Department of Chemistry, The Scripps Research Institute La Jolla CA 92037 USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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3
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DasGupta S, Nykiel K, Piccirilli JA. The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA (NEW YORK, N.Y.) 2021; 27:1017-1024. [PMID: 34131025 PMCID: PMC8370743 DOI: 10.1261/rna.078813.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kamila Nykiel
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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4
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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5
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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6
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Catalytic RNA, ribozyme, and its applications in synthetic biology. Biotechnol Adv 2019; 37:107452. [DOI: 10.1016/j.biotechadv.2019.107452] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
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7
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Moon WJ, Liu J. Replacing Mg2+by Fe2+for RNA‐Cleaving DNAzymes. Chembiochem 2019; 21:401-407. [DOI: 10.1002/cbic.201900344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Woohyun J. Moon
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
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8
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Abstract
The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.
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9
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Pressman AD, Liu Z, Janzen E, Blanco C, Müller UF, Joyce GF, Pascal R, Chen IA. Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA. J Am Chem Soc 2019; 141:6213-6223. [PMID: 30912655 PMCID: PMC6548421 DOI: 10.1021/jacs.8b13298] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Molecular
evolution can be conceptualized as a walk over a “fitness
landscape”, or the function of fitness (e.g., catalytic activity)
over the space of all possible sequences. Understanding evolution
requires knowing the structure of the fitness landscape and identifying
the viable evolutionary pathways through the landscape. However, the
fitness landscape for any catalytic biomolecule is largely unknown.
The evolution of catalytic RNA is of special interest because RNA
is believed to have been foundational to early life. In particular,
an essential activity leading to the genetic code would be the reaction
of ribozymes with activated amino acids, such as 5(4H)-oxazolones, to form aminoacyl-RNA. Here we combine in vitro selection
with a massively parallel kinetic assay to map a fitness landscape
for self-aminoacylating RNA, with nearly complete coverage of sequence
space in a central 21-nucleotide region. The method (SCAPE: sequencing
to measure catalytic activity paired with in vitro evolution) shows
that the landscape contains three major ribozyme families (landscape
peaks). An analysis of evolutionary pathways shows that, while local
optimization within a ribozyme family would be possible, optimization
of activity over the entire landscape would be frustrated by large
valleys of low activity. The sequence motifs associated with each
peak represent different solutions to the problem of catalysis, so
the inability to traverse the landscape globally corresponds to an
inability to restructure the ribozyme without losing activity. The
frustrated nature of the evolutionary network suggests that chance
emergence of a ribozyme motif would be more important than optimization
by natural selection.
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Affiliation(s)
- Abe D Pressman
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Chemical Engineering , University of California , Santa Barbara , California 93106 , United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K.,IBMM, CNRS, University of Montpellier, ENSCM , 34090 Montpellier , France
| | - Evan Janzen
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Biomolecular Sciences and Engineering , University of California , Santa Barbara , California 93106 , United States
| | - Celia Blanco
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry , University of California , San Diego , California 92093 , United States
| | - Gerald F Joyce
- Salk Institute for Biological Studies , La Jolla , California 92037 , United States
| | - Robert Pascal
- IBMM, CNRS, University of Montpellier, ENSCM , 34090 Montpellier , France
| | - Irene A Chen
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Biomolecular Sciences and Engineering , University of California , Santa Barbara , California 93106 , United States
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10
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Autour A, Bouhedda F, Cubi R, Ryckelynck M. Optimization of fluorogenic RNA-based biosensors using droplet-based microfluidic ultrahigh-throughput screening. Methods 2019; 161:46-53. [PMID: 30902664 DOI: 10.1016/j.ymeth.2019.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 12/19/2022] Open
Abstract
Biosensors are biological molecules able to detect and report the presence of a target molecule by the emission of a signal. Nucleic acids are particularly appealing for the design of such molecule since their great structural plasticity makes them able to specifically interact with a wide range of ligands and their structure can rearrange upon recognition to trigger a reporting event. A biosensor is typically made of three main domains: a sensing domain that is connected to a reporting domain via a communication module in charge of transmitting the sensing event through the molecule. The communication module is therefore an instrumental element of the sensor. This module is usually empirically developed through a trial-and-error strategy with the testing of only a few combinations judged relevant by the experimenter. In this work, we introduce a novel method combining the use of droplet-based microfluidics and next generation sequencing. This method allows to functionally characterize up to a million of different sequences in a single set of experiments and, by doing so, to exhaustively test every possible sequence permutations of the communication module. Here, we demonstrate the efficiency of the approach by isolating a set of optimized RNA biosensors able to sense theophylline and to convert this recognition into fluorescence emission.
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Affiliation(s)
- Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Farah Bouhedda
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Roger Cubi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France.
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11
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Bray MS, Lenz TK, Haynes JW, Bowman JC, Petrov AS, Reddi AR, Hud NV, Williams LD, Glass JB. Multiple prebiotic metals mediate translation. Proc Natl Acad Sci U S A 2018; 115:12164-12169. [PMID: 30413624 PMCID: PMC6275528 DOI: 10.1073/pnas.1803636115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life's oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution.
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Affiliation(s)
- Marcus S Bray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Timothy K Lenz
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jay William Haynes
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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12
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Okafor CD, Lanier KA, Petrov AS, Athavale SS, Bowman JC, Hud NV, Williams LD. Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event. Nucleic Acids Res 2017; 45:3634-3642. [PMID: 28334877 PMCID: PMC5397171 DOI: 10.1093/nar/gkx171] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/08/2017] [Indexed: 12/19/2022] Open
Abstract
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.
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Affiliation(s)
- C Denise Okafor
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Kathryn A Lanier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Shreyas S Athavale
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
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13
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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14
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Stephenson JD, Popović M, Bristow TF, Ditzler MA. Evolution of ribozymes in the presence of a mineral surface. RNA (NEW YORK, N.Y.) 2016; 22:1893-1901. [PMID: 27793980 PMCID: PMC5113209 DOI: 10.1261/rna.057703.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Mineral surfaces are often proposed as the sites of critical processes in the emergence of life. Clay minerals in particular are thought to play significant roles in the origin of life including polymerizing, concentrating, organizing, and protecting biopolymers. In these scenarios, the impact of minerals on biopolymer folding is expected to influence evolutionary processes. These processes include both the initial emergence of functional structures in the presence of the mineral and the subsequent transition away from the mineral-associated niche. The initial evolution of function depends upon the number and distribution of sequences capable of functioning in the presence of the mineral, and the transition to new environments depends upon the overlap between sequences that evolve on the mineral surface and sequences that can perform the same functions in the mineral's absence. To examine these processes, we evolved self-cleaving ribozymes in vitro in the presence or absence of Na-saturated montmorillonite clay mineral particles. Starting from a shared population of random sequences, RNA populations were evolved in parallel, along separate evolutionary trajectories. Comparative sequence analysis and activity assays show that the impact of this clay mineral on functional structure selection was minimal; it neither prevented common structures from emerging, nor did it promote the emergence of new structures. This suggests that montmorillonite does not improve RNA's ability to evolve functional structures; however, it also suggests that RNAs that do evolve in contact with montmorillonite retain the same structures in mineral-free environments, potentially facilitating an evolutionary transition away from a mineral-associated niche.
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Affiliation(s)
- James D Stephenson
- NASA Postdoctoral Program, NASA Ames Research Center, Moffett Field, California 94035, USA
- Space Science and Astrobiology Division, Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Milena Popović
- Space Science and Astrobiology Division, Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
- Blue Marble Space Institute of Science, Seattle, Washington 98145, USA
| | - Thomas F Bristow
- Space Science and Astrobiology Division, Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Mark A Ditzler
- Space Science and Astrobiology Division, Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
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15
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Saunders AM, DeRose VJ. Beyond Mg 2+: functional interactions between RNA and transition metals. Curr Opin Chem Biol 2016; 34:152-158. [PMID: 27616014 DOI: 10.1016/j.cbpa.2016.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg2+ to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni2+, Co2+, and Mn2+ have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA function. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.
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Affiliation(s)
- Adam M Saunders
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States
| | - Victoria J DeRose
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States.
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16
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Saunders AM, DeRose VJ. Beyond Mg(2+): functional interactions between RNA and transition metals. Curr Opin Chem Biol 2016; 31:153-9. [PMID: 27031926 DOI: 10.1016/j.cbpa.2016.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/25/2016] [Indexed: 12/19/2022]
Abstract
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg(2+) to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni(2+), Co(2+), and Mn(2+) have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.
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Affiliation(s)
- Adam M Saunders
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States
| | - Victoria J DeRose
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States.
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17
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Janković S, Ćirković MM. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection. ORIGINS LIFE EVOL B 2016; 46:67-79. [PMID: 26419865 DOI: 10.1007/s11084-015-9464-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/11/2015] [Indexed: 01/21/2023]
Abstract
Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.
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Affiliation(s)
- Srdja Janković
- University Children's Hospital, Tiršova 10, 11000, Belgrade, Serbia.
| | - Milan M Ćirković
- Astronomical Observatory of Belgrade, Volgina 7, 11000, Belgrade, Serbia.
- Future of Humanity Institute, Faculty of Philosophy, University of Oxford, Suite 8, Littlegate House, 16/17 St Ebbe's Street, Oxford, OX1 1PT, UK.
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Crucial steps to life: From chemical reactions to code using agents. Biosystems 2016; 140:49-57. [DOI: 10.1016/j.biosystems.2015.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 01/21/2023]
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