Progress in Nucleic Acid Research and Molecular Biology 49

409 Pages·1994·13.22 MB·English

by  Waldo E. Cohn and Kivie Moldave (Eds.)

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
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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).