Rethinking the Tools of the RNA World an Artificially Evolved Ribozyme Can Catalyse the Synthesis of RNA by Using Trinucleotide Triphosphates As Building Blocks
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Building Blocks That Fall from the Sky
Building blocks that fall from the sky How did life on Earth begin? Scientists from the “Heidelberg Initiative for the Origin of Life” have set about answering this truly existential question. Indeed, they are going one step further and examining the conditions under which life can emerge. The initiative was founded by Thomas Henning, Director at the Max Planck Institute for Astronomy in Heidelberg, and brings together researchers from chemistry, physics and the geological and biological sciences. 18 MaxPlanckResearch 3 | 18 FOCUS_The Origin of Life TEXT THOMAS BUEHRKE he great questions of our exis- However, recent developments are The initiative was triggered by the dis- tence are the ones that fasci- forcing researchers to break down this covery of an ever greater number of nate us the most: how did the specialization and combine different rocky planets orbiting around stars oth- universe evolve, and how did disciplines. “That’s what we’re trying er than the Sun. “We now know that Earth form and life begin? to do with the Heidelberg Initiative terrestrial planets of this kind are more DoesT life exist anywhere else, or are we for the Origins of Life, which was commonplace than the Jupiter-like gas alone in the vastness of space? By ap- founded three years ago,” says Thom- giants we identified initially,” says Hen- proaching these puzzles from various as Henning. HIFOL, as the initiative’s ning. Accordingly, our Milky Way alone angles, scientists can answer different as- name is abbreviated, not only incor- is home to billions of rocky planets, pects of this question. -
Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
The Place of RNA in the Origin and Early Evolution of the Genetic Machinery
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: The Place of RNA in the Origin and Early Evolution of the Genetic Machinery Günter Wächtershäuser Life 2014, 4, 1050-1091, doi:10.3390/4041050 Reviewer 1: Anonymous Reviewer 2: Wolfgang Buckel Editor: Niles Lehman (Guest editor of Special Issue “The Origins and Early Evolution of RNA”) Received: 24 October 2014 First Revision Received: 2 December 2014 Accepted: 9 December 2014 Published: 19 December 2014 First Round of Evaluation Round 1: Reviewer 1 Report and Author Response In this massive and dense manuscript, Günter Wächtershäuser furthers his views and opinions on the origin and evolution of life. He reviews some of his previous work and presents an alternative to the dominant ‘Ancient RNA world’ hypothesis. The alternative views he previously generated are much expanded in this manuscript. In light of recent research developments and argumentation (some of it reviewed), his views should be considered a welcome addition to the many ideas that populate the “origin of life” field of inquiry that counter the dominant paradigm. I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript. I must note that a careful evaluation of all facets requires expertise in a multitude of disciplines (from prebiotic chemistry and structural biology to evolutionary bioinformatics and biochemistry) and considerable time, none of which I possess. Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary Section 1. The place of RNA in LUCA (page 2): In search of features that are more conserved (carrying deep phylogenetic memory) than the sequence of genes, Wächtershäuser focuses on a paper of his in Systematic and Applied Microbiology (1998) that uses gene content and order of microbial genomes to make inferences about the last universal common ancestor (LUCA) of cellular life. -
How Might a Pre-Biotic Ribozyme Catalyze RNA Assembly in an RNA World?
Science Highlight – April 2007 How Might a Pre-biotic Ribozyme Catalyze RNA Assembly in an RNA World? Which came first, nucleic acids or proteins? This question is molecular biology's version of the "chicken-or-the-egg" riddle. Genes made of nucleic acids (DNA or RNA) contain the instructions for making proteins, but enzymes made of proteins are needed to replicate genes. For those who try to understand how life origi- nated, this once seemed an intractable paradox. The discovery 25 years ago that RNA can be enzymatic permits us to speculate that pre-biotic self-replicating molecules may have been RNAs (1,2). This is known as the "RNA World" hypothesis, and with the discovery of RNA catalysis, it is now possible to imagine a prebiotic The L1 Ligase ribozyme at the moment 'RNA World' (or even one populated by early life forms) of bond creation. in which self-replicating ribozymes (RNA-based enzymes that possess the catalytic ability to copy themselves) accomplished both tasks, thus avoiding the potential “chicken-or-the-egg” conundrum (3). But there's a catch. In order to copy RNA, fragments or monomers that have 5'-triphosphates must be ligated together. This is true for modern polymerases, and is also the most likely mechanism by which a ribozyme self-replicase in an RNA World might function. Yet no one has found a modern natural ribozyme that catalyze this The RNA nucleotide triphosphate ligation reaction required reaction (pictured right). for RNA polymerization and self-replication. RNA in vitro evolution and selection has however enabled several research groups to discover RNA sequences that can in fact cata- lyze the required chemical reaction (shown above) for 5'-triphos- phate RNA fragment ligation, and one group has even produced a primitive but functional RNA-based RNA polymerase ribozyme (4). -
A Tetracycline-Dependent Ribozyme Switch Allows Conditional Induction of Gene Expression in Caenorhabditis Elegans
ARTICLE https://doi.org/10.1038/s41467-019-08412-w OPEN A tetracycline-dependent ribozyme switch allows conditional induction of gene expression in Caenorhabditis elegans Lena A. Wurmthaler1,2, Monika Sack1,2, Karina Gense2,3, Jörg S. Hartig1,2 & Martin Gamerdinger2,3 The nematode Caenorhabditis elegans represents an important research model. Convenient methods for conditional induction of gene expression in this organism are not available. Here 1234567890():,; we describe tetracycline-dependent ribozymes as versatile RNA-based genetic switches in C. elegans. Ribozyme insertion into the 3’-UTR converts any gene of interest into a tetracycline- inducible gene allowing temporal and, by using tissue-selective promoters, spatial control of expression in all developmental stages of the worm. Using the ribozyme switches we established inducible C. elegans polyglutamine Huntington’s disease models exhibiting ligand- controlled polyQ-huntingtin expression, inclusion body formation, and toxicity. Our approach circumvents the complicated expression of regulatory proteins. Moreover, only little coding space is necessary and natural promoters can be utilized. With these advantages tetracycline-dependent ribozymes significantly expand the genetic toolbox for C. elegans. 1 Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany. 2 Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany. 3 Department of Biology, University of Konstanz, 78457 Konstanz, Germany. Correspondence and requests for materials should be addressed to J.S.H. (email: [email protected]) or to M.G. (email: [email protected]) NATURE COMMUNICATIONS | (2019) 10:491 | https://doi.org/10.1038/s41467-019-08412-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-08412-w nducible regulatory systems are very powerful research tools to single A-to-G point mutation in the catalytic core of the HHR9 Iinvestigate the cellular function of individual genes. -
The Difficult Case of an RNA-Only Origin of Life
Emerging Topics in Life Sciences (2019) 3 469–475 https://doi.org/10.1042/ETLS20190024 Perspective The difficult case of an RNA-only origin of life Kristian Le Vay and Hannes Mutschler Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Downloaded from https://portlandpress.com/emergtoplifesci/article-pdf/3/5/469/859756/etls-2019-0024c.pdf by Max-Planck-Institut fur Biochemie user on 28 November 2019 Correspondence: Hannes Mutschler ([email protected]) The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of- equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems. The conjecture that life on Earth evolved from an ‘RNA World’ remains one of the most popular hypotheses for abiogenesis, even 60 years after Alex Rich first put the idea forward [1]. For some, evi- dence based upon ubiquitous molecular fossils and the elegance of the idea that RNA once had a dual role as information carrier and prebiotic catalyst provide overwhelming support for the theory. Nevertheless, doubts remain surrounding the chemical evolution of an RNA world, whose classical scenario is based on a temporal sequence of nucleotide formation, enzyme-free polymerisation/replica- tion, recombination, encapsulation in lipid vesicles (or other compartments), evolution of ribozymes and finally the innovation of the genetic code and its translation (Figure 1)[2,3]. -
Chemical Evolution Theory of Life's Origins the Lattimer, AST 248, Lecture 13 – P.2/20 Organics
Chemical Evolution Theory of Life's Origins 1. the synthesis and accumulation of small organic molecules, or monomers, such as amino acids and nucleotides. • Production of glycine (an amino acid) energy 3HCN+2H2O −→ C2H5O2N+CN2H2. • Production of adenine (a base): 5 HCN → C5H5N5, • Production of ribose (a sugar): 5H2CO → C5H10O5. 2. the joining of these monomers into polymers, including proteins and nucleic acids. Bernal showed that clay-like materials could serve as sites for polymerization. 3. the concentration of these molecules into droplets, called protobionts, that had chemical characteristics different from their surroundings. This relies heavily on the formation of a semi-permeable membrane, one that allows only certain materials to flow one way or the other through it. Droplet formation requires a liquid with a large surface tension, such as water. Membrane formation naturally occurs if phospholipids are present. 4. The origin of heredity, or a means of relatively error-free reproduction. It is widely, but not universally, believed that RNA-like molecules were the first self-replicators — the RNA world hypothesis. They may have been preceded by inorganic self-replicators. Lattimer, AST 248, Lecture 13 – p.1/20 Acquisition of Organic Material and Water • In the standard model of the formatio of the solar system, volatile materials are concentrated in the outer solar system. Although there is as much carbon as nearly all other heavy elements combined in the Sun and the bulk of the solar nebula, the high temperatures in the inner solar system have lead to fractional amounts of C of 10−3 of the average. -
Hammerhead Ribozymes Against Virus and Viroid Rnas
Hammerhead Ribozymes Against Virus and Viroid RNAs Alberto Carbonell, Ricardo Flores, and Selma Gago Contents 1 A Historical Overview: Hammerhead Ribozymes in Their Natural Context ................................................................... 412 2 Manipulating Cis-Acting Hammerheads to Act in Trans ................................. 414 3 A Critical Issue: Colocalization of Ribozyme and Substrate . .. .. ... .. .. .. .. .. ... .. .. .. .. 416 4 An Unanticipated Participant: Interactions Between Peripheral Loops of Natural Hammerheads Greatly Increase Their Self-Cleavage Activity ........................... 417 5 A New Generation of Trans-Acting Hammerheads Operating In Vitro and In Vivo at Physiological Concentrations of Magnesium . ...... 419 6 Trans-Cleavage In Vitro of Short RNA Substrates by Discontinuous and Extended Hammerheads ........................................... 420 7 Trans-Cleavage In Vitro of a Highly Structured RNA by Discontinuous and Extended Hammerheads ........................................... 421 8 Trans-Cleavage In Vivo of a Viroid RNA by an Extended PLMVd-Derived Hammerhead ........................................... 422 9 Concluding Remarks and Outlooks ........................................................ 424 References ....................................................................................... 425 Abstract The hammerhead ribozyme, a small catalytic motif that promotes self- cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically -
Structural Simplicity and Mechanistic Complexity in the Hammerhead Ribozyme
CHAPTER SEVEN Structural Simplicity and Mechanistic Complexity in the Hammerhead Ribozyme Sara M. O’Rourke, William G. Scott1 The Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA, United States 1Corresponding author: e-mail address: [email protected] Contents 1. Background and Structural Overview 178 2. Fast Minimal Hammerhead Ribozymes 181 3. Acid-Base Catalysis and the Hammerhead Ribozyme 182 4. Is the Hammerhead Ligation Reaction the Reverse of the Cleavage Reaction? 191 5. Do Cooperative Interactions in the Hammerhead Ribozyme Facilitate General Base Catalysis in the Cleavage Reaction? 194 6. Summary and Concluding Remarks 195 6.1 The Structure of the Hammerhead Ribozyme May Be Much Simpler Than We Have Thought 196 6.2 The Mechanism of the Hammerhead Ribozyme May Be Much More Complicated Than We Have Thought 196 6.3 Concluding Remarks 200 References 201 Abstract Natural or full-length hammerhead ribozymes are up to 1000-fold more active than their minimal counterparts that lack a complex tertiary interaction that pre-organizes and stabilizes the ribozyme active site, positioning RNA functional groups to facilitate acid-base catalysis. The recent discovery that a single tertiary contact (an AU Hoogsteen pair) between Stems I and II confers essentially all of the enhanced activity greatly simplifies our understanding of the structural requirements for hammerhead ribozyme activity. In contrast, the simplest mechanistic interpretations are challenged with the presentation of more complex alternatives. These alternatives are elucidated and criti- cally analyzed in the context of several of the active hammerhead ribozyme structures now available. # Progress in Molecular Biology and Translational Science, Volume 159 2018 Elsevier Inc. -
Ribozymes Targeted to the Mitochondria Using the 5S Ribosomal Rna
RIBOZYMES TARGETED TO THE MITOCHONDRIA USING THE 5S RIBOSOMAL RNA By JENNIFER ANN BONGORNO A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2005 Copyright 2005 by Jennifer Bongorno To my grandmother, Hazel Traster Miller, whose interest in genealogy sparked my interest in genetics, and without whose mitochondria I would not be here ACKNOWLEDGMENTS I would like to thank all the members of the Lewin lab; especially my mentor, Al Lewin. Al was always there for me with suggestions and keeping me motivated. He and the other members of the lab were like my second family; I would not have had an enjoyable experience without them. Diana Levinson and Elizabeth Bongorno worked with me on the fourth and third mouse transfections respectively. Joe Hartwich and Al Lewin tested some of the ribozymes in vitro and cloned some of the constructs I used. James Thomas also helped with cloning and was an invaluable lab manager. Verline Justilien worked on a related project and was a productive person with whom to bounce ideas back and forth. Lourdes Andino taught me how to use the new phosphorimager for my SYBR Green-stained gels. Alan White was there through it all, like the older brother I never had. Mary Ann Checkley was with me even longer than Alan, since we both came to Florida from Ohio Wesleyan, although she did manage to graduate before me. Jia Liu and Frederic Manfredsson were there when I needed a beer. -
The Origins of the RNA World
The Origins of the RNA World Michael P. Robertson and Gerald F. Joyce Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 Correspondence: [email protected] SUMMARY The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the compo- nents of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macro- molecules. A thorough consideration of this “RNA-first” view of the origin of life must recon- cile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving mole- cule, just as DNA and proteins were preceded by RNA. Outline 1 Introduction 4 Concluding remarks 2 An “RNA-first” view of the origin of life References 3 An “RNA-later” view of the origin of life Editors: John F. -
One Sequence, Two Ribozymes: Could Access by Neutral Drift Every Sequence on Both Networks
R EPORTS minus the background levels observed in the HSP in X-100 for 15 min at 4¡C with intermittent mixing, 62. M. R. Peterson, C. G. Burd, S. D. Emr, Curr. Biol. 9, 159 the control (Sar1-GDPÐcontaining) incubation that and elutes were pooled. Proteins were precipitated by (1999). prevents COPII vesicle formation. In the microsome MeOH/CH3Cl and separated by SDSÐpolyacrylamide 63. M. G. Waters, D. O. Clary, J. E. Rothman, J. Cell Biol. control, the level of p115-SNARE associations was gel electrophoresis (PAGE) followed by immunoblot- 118, 1015 (1992). less than 0.1%. ting using p115 mAb 13F12. 64. D. M. Walter, K. S. Paul, M. G. Waters, J. Biol. Chem. 46. C. M. Carr, E. Grote, M. Munson, F. M. Hughson, P. J. 51. V. Rybin et al., Nature 383, 266 (1996). 273, 29565 (1998). Novick, J. Cell Biol. 146, 333 (1999). 52. K. G. Hardwick and H. R. Pelham, J. Cell Biol. 119, 513 65. N. Hui et al., Mol. Biol. Cell 8, 1777 (1997). 47. C. Ungermann, B. J. Nichols, H. R. Pelham, W. Wick- (1992). 66. T. E. Kreis, EMBO J. 5, 931 (1986). ner, J. Cell Biol. 140, 61 (1998). 53. A. P. Newman, M. E. Groesch, S. Ferro-Novick, EMBO 67. H. Plutner, H. W. Davidson, J. Saraste, W. E. Balch, 48. E. Grote and P. J. Novick, Mol. Biol. Cell 10, 4149 J. 11, 3609 (1992). J. Cell Biol. 119, 1097 (1992). (1999). 54. A. Spang and R. Schekman, J. Cell Biol. 143, 589 (1998). 68. D. S.