Research abstract for Jack W. Szostak, Ph.D. We are interested in the chemical and physical processes that facilitated the transition from chemical evolution to biological evolution on the early earth. As a way of exploring these processes, our laboratory is trying to build a synthetic cellular system that undergoes Darwinian evolution.
Our view of what such a chemical system would look like centers on a model of a primitive cell, or protocell, that consists of two main components: a self-replicating genetic polymer and a self-replicating membrane boundary (Figure 1). The job of the genetic polymer is to carry information in a way that allows for both replication and variation, so that new sequences that encode useful functions can be inherited and can further evolve. The role of the protocell membrane is to keep these informational polymers localized, so that the functions they encode lead to an advantage in terms of their own replication or survival. Figure 1: Protocell model. Conceptual model of a heterotrophic protocell.
RNA World. From Wikipedia, the free encyclopedia RNA with its nitrogenous bases to the left and DNA to the right. The RNA world hypothesis proposes that a world filled with life based on ribonucleic acid (RNA) predates the current world of life based on deoxyribonucleic acid (DNA) and protein. RNA, which can both store information like DNA and act as an enzyme like proteins, may have supported cellular or pre-cellular life. Some hypotheses as to the origin of life present RNA-based catalysis and information storage as the first step in the evolution of cellular life. The RNA world is proposed to have evolved into the DNA and protein world of today. DNA, through its greater chemical stability, took over the role of data storage while protein, which is more flexible in catalysis through the great variety of amino acids, became the specialized catalytic molecules.
History Properties of RNA RNA as an enzyme RNA enzymes, or ribozymes, are possible although not common in today's DNA-based life. BBC Radio 4 Programmes - Frontiers, Acts of Creation. Artificial life and the RNA world. By Matthew Cobb Two things come together from earlier this year. First, there was a lot of argument here, in the Times Literary Supplement and elsewhere over Stephen C. Meyer’s Signature in the Cell. One of the many issues in question was the ancient “RNA world”, which Meyer has argued is implausible. Now there’s an excellent 30-minute BBC Radio 4 programme “Acts of Creation” which puts the two stories together, and looks at attempts round the world to push the field of “artificial biology” even further.
One of the problems with this idea is that precisely because RNA is so fragile, it is very difficult to imagine molecules of it sloshing around in Darwin’s “warm little pond” without simply degrading. You should be able to listen to the programme from anywhere in the world by going here. Like this: Like Loading... The RNA world lives on the TLS letter page. Chemical Bonding Center: RNA World. Welcome to the Chemical Bonding Center. Exploring Life's Origins: Understanding the RNA World. Talk:RNA world hypothesis. RNA World. Figure 1. Key polymerase activities of the RNA World and known organisms. Plants, fungi, protozoa, and certain animals use a cell-encoded RNA-dependent RNA polymerase (cRdRP) to amplify RNAs used for RNA Silencing. Welcome to the RNA World Learning Project. This learning project allows Wikiversity participants to explore the so-called "RNA world hypothesis". The phrase RNA World is used in biology when exploring the idea that RNA molecules may have served as genetic molecules and enzymes before DNA and proteins.
The first specific genetic role discovered for RNA in cells was as mRNA intermediates between DNA genes and the proteins specified by genes. RNA Silencing[edit] Figure 2. RNA silencing is a cellular phenomenon in which short, double-stranded RNA "triggers" can prevent the expression of specific genes[2]. Paula Salgado and her colleagues have studied the structure of one such polymerase, called QDE-1. What they found was a remarkable similarity (Figure 3, below). Figure 3. RNA World/Project description/en – Rechenkraft. RNA World project description RNA World is a distributed supercomputer that uses Internet-connected computers to advance RNA research. This system is dedicated to identify, analyze, structurally predict and design RNA molecules on the basis of established bioinformatics software in a high-performance, high-throughput fashion.
In contrast to classical bioinformatic approaches, RNA World does not rely on individual desktop computers, web servers or supercomputers. Instead, it represents a continuously evolving cluster of world-wide distributed machines of any type. In its present form, RNA World runs a fully automated high-throughput analysis software version of Infernal1, a program suite originally developed in Sean Eddys laboratory for the systematic identification of non-coding RNAs. Why RNA? Every protein in a cell is produced from a transiently synthesized messenger molecule, termed mRNA.
References (1) Infernal 1.0: inference of RNA alignments. The RNA World and the Origins of Life - Molecular Biology of the Cell - NCBI Bookshelf. The RNA Worlds in Context. Thomas R. Cech + Author Affiliations Correspondence: thomas.cech@colorado.edu There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today's biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection.
Copyright © 2011 Cold Spring Harbor Laboratory Press; all rights reserved. Riboswitches and the RNA World. Ronald R. Breaker + Author Affiliations Correspondence: ronald.breaker@yale.edu Riboswitches are structured noncoding RNA domains that selectively bind metabolites and control gene expression (Mandal and Breaker 2004a; Coppins et al. 2007; Roth and Breaker 2009). Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation. Newfound classes of riboswitches are being reported at a rate of about three per year (Ames and Breaker 2009), and these have been shown to selectively respond to fundamental metabolites including coenzymes, nucleobases or their derivatives, amino acids, and other small molecule ligands. The characteristics of some riboswitches suggest they could be modern descendents of an ancient sensory and regulatory system that likely functioned before the emergence of enzymes and genetic factors made of protein (Nahvi et al. 2002; Vitreschak et al. 2004; Breaker 2006).
Footnotes Editors: John F. The Roles of RNA in the Synthesis of Protein. + Author Affiliations Correspondence: peter.moore@yale.edu The crystal structures of ribosomes that have been obtained since 2000 have transformed our understanding of protein synthesis. In addition to proving that RNA is responsible for catalyzing peptide bond formation, these structures have provided important insights into the mechanistic details of how the ribosome functions. This review emphasizes what has been learned about the mechanism of peptide bond formation, the antibiotics that inhibit ribosome function, and the fidelity of decoding. Footnotes Editors: John F. Copyright © 2010 Cold Spring Harbor Laboratory Press; all rights reserved. Setting the Stage: The History, Chemistry, and Geobiology behind RNA. No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth.
Further, a definition-theory for life is needed to develop hypotheses relating to the “RNA First” model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; (c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.
Copyright © 2010 Cold Spring Harbor Laboratory Press; all rights reserved. Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations. + Author Affiliations Correspondence: susang@helix.nih.gov and storz@helix.nih.gov Small RNA regulators (sRNAs) have been identified in a wide range of bacteria and found to play critical regulatory roles in many processes. The major families of sRNAs include true antisense RNAs, synthesized from the strand complementary to the mRNA they regulate, sRNAs that also act by pairing but have limited complementarity with their targets, and sRNAs that regulate proteins by binding to and affecting protein activity. The sRNAs with limited complementarity are akin to eukaryotic microRNAs in their ability to modulate the activity and stability of multiple mRNAs. In many bacterial species, the RNA chaperone Hfq is required to promote pairing between these sRNAs and their target mRNAs. Understanding the evolution of regulatory sRNAs remains a challenge; sRNA genes show evidence of duplication and horizontal transfer but also could be evolved from tRNAs, mRNAs or random transcription.
Footnotes. RNA Granules in Germ Cells. + Author Affiliations Correspondence: evoronina@jhmi.edu (E.V.); gseydoux@jhmi.edu (G.S.); psc@uci.edu (P.S. -C.); inagamor@uci.edu (I.N.) “Germ granules” are cytoplasmic, nonmembrane-bound organelles unique to germline. Germ granules share components with the P bodies and stress granules of somatic cells, but also contain proteins and RNAs uniquely required for germ cell development. In this review, we focus on recent advances in our understanding of germ granule assembly, dynamics, and function. One hypothesis is that germ granules operate as hubs for the posttranscriptional control of gene expression, a function at the core of the germ cell differentiation program.
Copyright © 2011 Cold Spring Harbor Laboratory Press; all rights reserved. Evolution of Protein Synthesis from an RNA World. Harry F. Noller + Author Affiliations Correspondence: harry@nuvolari.ucsc.edu Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World. Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Footnotes Editors: John F.
Copyright © 2010 Cold Spring Harbor Laboratory Press; all rights reserved. Aptamers and the RNA World, Past and Present. + Author Affiliations Correspondence: lgold@somalogic.com Aptamers and the SELEX process were discovered over two decades ago. These discoveries have spawned a productive academic and commercial industry. The collective results provide insights into biology, past and present, through an in vitro evolutionary exploration of the nature of nucleic acids and their potential roles in ancient life. Aptamers have helped usher in an RNA renaissance. Here we explore some of the evolution of the aptamer field and the insights it has provided for conceptualizing an RNA world, from its nascence to our current endeavor employing aptamers in human proteomics to discover biomarkers of health and disease.
Footnotes Editors: John F. Copyright © 2010 Cold Spring Harbor Laboratory Press; all rights reserved. RNA in Defense: CRISPRs Protect Prokaryotes against Mobile Genetic Elements. Gerald Joyce, Scripps Research Institute, Recreating the RNA Wor. Thomas R. Cech: Exploring the New RNA World. By Thomas R. Cech 1989 Nobel Laureate in Chemistry Not too long ago, most people considered RNA to be just a disposable copy of the really important nucleic acid, DNA. It is the double helix of DNA, after all, that shows up on magazine covers and television; DNA is the material of our genes and chromosomes, the stuff that determines our genetic inheritance. RNA – ribonucleic acid – is a copy of the DNA instructions that serves as a messenger to direct protein synthesis, which is then destroyed after it has fulfilled its function. My research group in Colorado played a role in discovering novel activities of RNA in the early 1980s. An Explosion of Breakthroughs Within the past few years, RNA research has reached new heights.
An RNA Machine Makes Proteins One of the most important molecular "machines" in living cells is the ribosome. The ribosome is an unusual catalyst, composed of three RNA molecules (four in some species) as well as dozens of proteins. Riboswitches RNA Interference 1. 2. 3. RNA world hypothesis. From Citizendium, the Citizens' Compendium Schematic showing the fold of the QDE-1 RNA interference polymerase. The dimeric molecule is shown with the polypeptide chains colored from blue at the N termini to red at the C termini.
From: RNA Silencing Sheds Light on the RNA World Jones R PLoS Biology Vol. 4, No. 12, e448 doi:10.1371/journal.pbio.0040448 The RNA world hypothesis proposes that RNA was the first life-form on earth, later developing a cell membrane around it and becoming the first prokaryotic cell. Support The RNA World hypothesis is supported by the RNA's ability to store, transmit, and duplicate genetic information, just like DNA does. RNA can also act as a ribozyme (an enzyme made of ribonucleic acid). The phrase "RNA World" was first used by Walter Gilbert in 1986. Base pairing RNA and DNA are made of long stretches of specific nucleotides, often called "bases", attached to a sugar-phosphate backbone. These chains are proposed as the first, primitive forms of life. A.G.