Once thought to be just a messenger that allows genetic information encoded in DNA to direct the formation of proteins, RNA (ribonucleic acid) is now known to be a highly versatile molecule that has multiple roles in cells. It can function as an enzyme, scaffold various subcellular structures, and regulate gene expression through a variety of mechanisms, as well as act as a key component of the protein synthesis and splicing machinery. Perhaps most interestingly, increasing evidence indicates that RNA preceded DNA as the hereditary material and played a crucial role in the early evolution of life on Earth.
This volume reviews our understanding of two RNA worlds: the primordial RNA world before DNA, in which RNA was both information store and biocatalyst; and the contemporary RNA world, in which mRNA, tRNA, rRNA, siRNA, miRNA, and a host of other RNAs operate.
The early chapters of the book analyze the role of RNA in the first life forms and the appearance of cells. Subsequent chapters examine riboswitches and ribozymes, establishing what the RNA molecule is capable of alone. The book goes on to discuss the evolution of ribosomes and the functions of RNPs, before reviewing the recent work that has revolutionized our understanding of gene regulation by non-coding RNAs, including miRNAs and siRNAs. Also covered are viral RNAs, telomerase RNA, and tools for scientists who work on RNA. The book is thus essential reading for all molecular biologists and biochemists, as well as chemists interested in RNA technology, information storage, or enzyme catalysis.
Contents
Preface
Foreword to the First Edition of The RNA World
Francis Crick
Prologue to the First Edition of The RNA World
James D. Watson
The RNA Worlds in Context
Thomas R. Cech
THE EARLY RNA WORLD
Setting the Stage: The History, Chemistry, and Geobiology behind RNA
Steven A. Benner, Hyo-Joong Kim, and Zunyi Yang
The Origins of the RNA World
Michael P. Robertson and Gerald F. Joyce
Getting Past the RNA World: The Initial Darwinian Ancestor
Michael Yarus
The Origins of Cellular Life
Jason P. Schrum, Ting F. Zhu, and Jack W. Szostak
WHAT RNA CAN DO BY ITSELF
Riboswitches and the RNA World
Ronald R. Breaker
Riboswitches: Structures and Mechanisms
Andrew D. Garst, Andrea L. Edwards, and Robert T. Batey
Small Self-cleaving Ribozymes
Adrian R. Ferré-D’Amaré and William G. Scott
Group II Introns: Mobile Ribozymes that Invade DNA
Alan M. Lambowitz and Steven Zimmerly
EXIT THE RNA WORLD: PROTEIN SYNTHESIS ON RIBOSOMES
The Roles of RNA in the Synthesis of Protein
Peter B. Moore and Thomas A. Steitz
Evolution of Protein Synthesis from an RNA World
Harry F. Noller
The Ribosome: Some Hard Facts about Its Structure and Hot Air about Its Evolution
V. Ramakrishnan
RNP-ZYMES: WHAT RNA CAN DO IN COLLABORATION WITH PROTEIN
Noncoding RNPs of Viral Origin
Joan Steitz, Sumit Borah, Demian Cazalla, Victor Fok, Robin Lytle, Rachel Mitton-Fry, Kasandra Riley, and Tasleem Samji
Spliceosome Structure and Function
Cindy L. Will and Reinhard Lührmann
Telomerase: An RNP Enzyme Synthesizes DNA
Elizabeth H. Blackburn and Kathleen Collins
RNA REGULATED GENE EXPRESSION
Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations
Susan Gottesman and Gisela Storz
RNA in Defense: CRISPRs Protect Prokaryotes against Mobile Genetic Elements
Matthijs M. Jore, Stan J.J. Brouns, and John van der Oost
Ancestral Roles of Small RNAs: An Ago-Centric Perspective
Leemor Joshua-Tor and Gregory J. Hannon
RNA Interference and Heterochromatin Assembly
Tom Volpe and Robert A. Martienssen
The X as Model for RNA’s Niche in Epigenomic Regulation
Jeannie T. Lee
The Long Arm of Long Noncoding RNAs: Roles as Sensors Regulating Gene Transcriptional Programs
Xiangting Wang, Xiaoyuan Song, Christopher K. Glass, and Michael G. Rosenfeld
TOOLS FOR RNA SCIENCE
Folding and Finding RNA Secondary Structure
David H. Mathews, Walter N. Moss, and Douglas H. Turner
Predicting and Modeling RNA Architecture
Eric Westhof, Benoît Masquida, and Fabrice Jossinet
RNA Reactions One Molecule at a Time
Ignacio Tinoco, Gang Chen, and Xiaohui Qu
Aptamers and the RNA World, Past and Present
Larry Gold, Nebojsa Janjic, Thale Jarvis, Dan Schneider, Jeffrey J.Walker, Sheri K. Wilcox, and Dom Zichi
In Vivo RNAi: Today and Tomorrow
Norbert Perrimon, Jian-Quan Ni, and Lizabeth Perkins
Index