Progress in Nucleic Acid Research and Molecular Biology 49 PDF
Preview Progress in Nucleic Acid Research and Molecular Biology 49
PROGRESS IN Nucleic Acid Research and Molecular Biology Volume 49 PROGRESS IN Nucleic Acid Research and Molecular Biology Volume 49 This Page Intentionally Left Blank PROGRESS IN Acid Nucleic Research and Molecular Biology edited by WALDO E. COHN KlVlE MOLDAVE Biology Dioision Departnicnt of Molecular Biology Oak Ridge Notiond I~ilioratcir~~ and Biocheinistry Oak Ridge, Tcnneusce Uniocrsity of Californiu, lroine Iminc, California Volume 49 ACADEMIC PRESS Son Diego New York Boston London Sydney Tokyo Toronto This book is printed on acid-free paper. @ Copyright 0 1994 by ACADEMIC PRESS, INC. All Rights Reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Academic Press, Inc. A Division of Harcourt Brace & Company 525 B Street, Suite 1900, San Diego, California 92101-4495 United Kingdom Edition published by Academic Ress Limited 24-28 Oval Road, London NWl 7DX International Standard Serial Number: 0079-6603 International Standard Book Number: 0-12-540049-7 PRINTED IN THE UNITED STATES OF AMERICA 9 4 9 5 % 9 7 9 8 9 9 B B 9 8 7 6 5 4 3 2 1 Contents ABBREVIATIONASN D SYMBOLS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix SOME ARTICLESP LANNED FOR FUTURE VOLUMES . . . . . . . . . . . . . . . xi The Prosomes (Multicatalytic Proteinases; Proteasomes) and Their Relationship to the Untranslated Messenger Ribonucleoproteins, . . . . . . . . the Cytoskeleton, and Cell Differentiation , , 1 Klaus Schemer and Faycal Bey I. The Biological and Cytological Bases of the Prosome System . . . . . . . 3 11. The Prosoines . . . . . . ... . . . . . . . .. . . .. . . .. .. . .. .. .. . . . .. . . . . . . .. 12 111. The Multicatalytic Proteinase Activity of the Prosoines and the 26-S Proteasoine . . . . . . . . . . . . . . . . . . . . , . . . , . . . . . . . . . . . . . , . , . . , . 23 IV. Prosoines, the Cytoskeleton, and the Hypothesis of inRNA Cytodistrihtion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 V. Prosoines Vary in Their Subunit Composition in Relation to Differentiation and Embryonic Development . . . . . . . . . . . . . . . . . . 44 VI. Variations of Prosome Patterns in Pathology . . . . . . . . . . . . . . . . . . . . . . 47 VII. Attempts at Comprehension . . . . . . . , . , . . . . , . . . . . . . . . . . . . . . . . . . . 51 VIII. Glossary . . . . . .. .. . , . . . . . . . . . . . . , . , . , . . . .. . . . * .. . * .. . . . . . . . . . 57 Hcferences . . . . . . . . , . . . , . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 Biological Implications of the Mechanism of Action of Human DNA (Cytosine-5)methyltransferase . . . . . . 65 Steven S. Smith I. Mechanism of Action of the Huinan DNA (Cytosine-5)inethyltransfera.s~. ................................. 66 11. Selectivity of Huinan DNA Methyltransferases . . . . . . . . . . . . . . . . . . . 73 111. Biological Iinplications of the Mechanism . . . . . . . . . . . . . . . . . . . . . . . . 84 IV. Conclusions . . . .. .. . . . . . . . . .. . . ... , ... . . . . . . . .. . . .. .. .. .. , . ,. 105 References . . . . . . . . . . . , . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 V vi CONTENTS Molecular Properties and Regulation of ..................... G-Protein-Coupled Receptors 113 Claire M . Fraser. Norman H . Lee. Susan M . Pellegrino and Anthony R . Kerlavage I . G-Protein-Mediated Signal Transduction ......................... 114 I1. G-Protein-Coupled Receptors Are a Large Gene Fainily ........... 115 111. Mokcular Basis of Receptor-Ligand Interactions ................. 121 IV . Molecular Basis of Receptor/G-Protein Interactions ............... 130 V. Identification of Functional Domains Involved in Receptor Desensitization and Down-regulation ............................ 136 VI . Genetic Eleineiits Controlling G-Protein-Coupled Receptor .................................................. Expression 143 VII . Identification of Novel G-Protein-Coupled Receptors by Partial cDNA Sequencing ............................................ 147 VIII . Conclusions ................................................. 149 References .................................................. 149 The Human Immunodeficiency Virus Type-1 Long Terminal Repeat and Its Role ............................... in Gene Expression 157 Joseph A . Garcia and Richard B . Gaynor I . Gene Expression Studies ...................................... 158 I1 . Activation Signals ............................................ 160 I11 . Transcriptional Control Elenients ............................... 162 IV . Processing of HIV-1 inRNA .................................... 173 V. Transhtional Control .......................................... 174 VI . tat Studies .................................................. 177 VII . Interventional Strategies ...................................... 182 VIII . Ghsary .................................................... 185 References .................................................. 185 Processing of Eukaryotic Ribosomal RNA .......... 197 Duane C . Eichler and Nessly Craig I . Processing Sites and Processing Pathways ........................ 199 . I1 The Relationship between Ribosomal-RNA Processing and Post-transcriptional Modifications ........................... 231 111. Suininary .................................................... 233 References .................................................. 234 CONTENTS vii Adenylyl Cyclases: A Heterogeneous Class .......................... of ATP-Utilizing Enzymes 241 Octavian B2rzu and Antoine Danchin I . Adenylyl Cyclases of Gram-Negative Facultative Anaerobes ........ 242 I1 . The Calmodulin-Activated Bacterial Toxic Adenylyl Cyclases ....... 2-51 I11 . Class 111 Adenylyl Cyclases .................................... 261 IV. Similarity of Adenylyl and Guanylyl Cyclases ..................... 267 V. Evolution of Adenylyl Cyclases ................................. 271 VI . Are Adenylyl Cyclases Pulse-Generating Enzymes? ............... 275 VII . Glossary .................................................... 276 References .................................................. 277 ......... Mutational Spectrometry: Means and Ends 285 K . Khrapko. P. Andre. R . Cha. G . Hu and W. G . Thilly I . Goals and Problems .......................................... 285 I1 . Allele-specific PCR (ASP) ...................................... 289 I11 . High-efficiency Restriction Assay (HERA) ........................ 295 IV. Methods Using Differential DNA Melting to Separate Mutants ..... 302 References .................................................. 311 Polynucleotide Recognition and Degradation .................................... by Bleomycin 31 3 Stefanie A . Kane and Sidney M . Hecht I . Bleomycin: Structure and Domains ............................. 314 I1 . Metal Complexes of Bleomycin ................................. 314 111. Chemistry of Fe(1I). B leoinycin ................................. 316 IV. Chemistry of DNA Degradation ................................ 322 V. Gther Metallobleomycins ...................................... 327 VI . Interaction of Bleomycin with DNA ............................. 329 VII . Cleavage of RNA Mediated by Fe(I1)-B leomycin ................. 338 VIII . Strand-Scission of Altered DNA Structures Mediated by Fe(I1)-Bleomycin .......................................... 344 IX . Concluding Remarks .......................................... 348 References .................................................. 349 viii CONTENTS Interaction of Epidermal Growth Factor ................................. with Its Receptor 353 . . Stephen R Campion and Salil K Niyogi I . Sequence and Structure of EGF and EGF Receptor .............. 355 I1 . Generation and Characterization of Mutant Human EGF Analogues ................................................... 359 111. Effects of Single-site Mutations on Receptor-Ligand Association .... 365 IV. Cumulative Effect of Multiple Mutations on Receptor Binding ...... 377 V. Conclusions ................................................. 379 References .................................................. 380 ..................................................... INDEX 3% Abbreviations and Symbols All cuntril)utors to this Series are asked to use the terminology (a1)I)revhtions and symhols) rewinmended by the IUPAC-IUB Commission on Biochemical Nomenclature (CBN) and appnwed by IUPAC and IUB, and the Editors endeavor to assure conformity. These ham- mendations have lwen puldished in many journals (1.2) and compndk (3); they are therefore wnsidered to 1w generully kaown. Those used in nucleic wid work, originally set out in section 5 of the first kwrnmendutions (I)a nd subsequently revised and expunded (2,3), are given in amdensed Form in the frnntmatter of Volumes 9-33 ofthis series. A recent expansion of the one- letter system (5) follcnvs. SINGLE-LL"ITERC ODER ECOMMENDATIONS(5" ) Symlnl Meaning Origin of symhd C Gaanosine A Adenosine T(U) (rilw$I%ymidine(U ridine) C Cytidine C or A puRiiie T(U) or C pyrimidine A or C aMino C or T(U ) Keto C or C Strong inter&ion (3 H-lxmls) A or T(U) Weak interx~on(2 H-lxmds) A or C or T(U) not C; H follows C in the alphabet C or T( U) or C not A; B follows A C or C or A not T (not U); V follows U G or A or T(U) not C; 1) follows C C or A or T(U) or C aNy nuclcnmide (i.e., unspecified) Q Queuosine (nucleoside of queuine) .Modified from Proc. Nut/. A d . S ci. U.S.A. 83, 4 (1986). W has Iwen used for wyosine, the nuclwside of "ImY " (wye). VDh as ken usd for dihydrnuridine (hU or H, Ud). Enzymes In naming enzymes. the 19fM mommendations of the IUI Commission on Biwhemid Nomenclature (4) are folltnved as far as pssihle. At first mention. each enzyme is desrribed either by its systeinitic name or by the ecluution for the reru.tit,na tdy7ed or by the reammended trivial name. followed by its EC numlwr in parentheses. Thereafter. a trivial name may he used. Enzyme rimes ure not to I= dhwiated except when the sulMmte has an 4qmved tlhl,revMon (e.g., A m . h ut not LDH, is IwreptalJe).
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