Molecular biology of bacteriophage T4:
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| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Washington, DC
ASM Press
1994
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVIII, 615 S. Ill., graph. Darst. |
| ISBN: | 1555810640 |
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MARC
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| 245 | 1 | 0 | |a Molecular biology of bacteriophage T4 |c ed.-in-chief: Jim D. Karam |
| 246 | 1 | 3 | |a Bacteriophage T4 |
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| adam_text | |MOLECULARBIOLOGYOF
Bacteriophage T4
EDITOR-IN-CHIEF:JimDKaram
Department of Biochemistry, Tulane University Medical Center, New Orleans, Louisiana
EDITORS: John W Drake
Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
Kenneth N Kreuzer
Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina
Gisela Mosig
Department of Molecular Biology, Learned Laboratory, Vanderbilt University, Nashville, Tennessee
Dwight H Hall
School of Biology, Georgia Institute of Technology, Atlanta, Georgia
Frederick A Eiserling
Department of Microbiology, University of California-Los Angeles, Los Angeles, California
Lindsay W Black
Department of Biological Chemistry University of Maryland School of Medicine, Baltimore, Maryland
Eleanor K Spicer
Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
Elizabeth Kutter
The Evergreen State College, Olympia, Washington
Karin Carlson
Department of Microbiology, Faculty of Sciences, University of Uppsala Biomedical Center, Uppsala, Sweden
Eric S Miller
Department of Microbiology, North Carolina State University, Raleigh, North Carolina
AmericanSocietyforMicrobiology Washington,DC
CONTENTS
Section Editors x
Contributors xi
Foreword xvii
1 An Overview of the T4 Developmental Program CHRISTOPHER K MATHEWS 1
Structure of the Virion and Early Steps in Infection Early Metabolic Events • DNA Replication
Control of Gene Expression • Morphogenesis and DNA Packaging • Lysis
I DNA METABOLISM
Editors: John W Drake and Kenneth N Kreuzer
2 DNA Transactions in T4-Infected Escherichia coli JOHN W DRAKE and KENNETH N
KREUZER 11
Nucleotide Metabolism • Initiating DNA Replication • The Replication Fork • Recombination •
Intron Mobility • DNA Repair • Mutation • T4 DNA Metabolism
3 Deoxyribonucleoside Triphosphate Synthesis and T4 DNA Replication G ROBERT GREEN- 14
BERG, PING HE, JOHN HILFINGER, and MIN-JEN TSENG
dNTP Synthesis in Relation to DNA Replication • dNMPs from Host DNA Degradation • Studies
In Situ • Interaction of T4 DNA Replication with dNTP Synthesis • Isolation and Properties of the
DSC • Pools • dNTP Ratios and Fidelity of Replication • Other T4 Pathways That May Require
the DSC • Enzymes in the Pathway from rNDPs to dNTPs • Some Conclusions
4 Initiation of DNA Replication KENNETH N KREUZER and SCOTT W MORRICAL 28
Nomenclature of T4 Replication Modes • Introduction to Protein Requirements • The Switch
from Early to Late • Localization of T4 Replication Origins • Mechanism of Origin-Dependent
Replication • Recombination-Dependent DNA Replication In Vivo • Recombination-Dependent
DNA Replication In Vitro- _ J
5 The Bacteriophage T4 DNA Replication Fork NANCY G NOSSAL 43
Overview of the T4 Replication Fork • T4 DNA Polymerase, Accessory Proteins, and Gene 32 Pro
tein • Primase-Helicase Complex • Coupling of Leading-and Lagging-Strand Synthesis • Sim
ilarities of the T4 and Other Replication Systems • Concluding Remarks
6 Homologous Recombination GISELA MOSIG 54
Recombination Models and Pathways • Analyzing T4 Recombination • Properties of the DNA
That Alter T4 Recombination • T4 Recombination Genes • Gene and Protein Interactions in
Recombination Pathways • Conclusions and Outlook
7 Mobile Introns in the T-Even Phages JONATHAN CLYMAN, SUSAN QUIRK, and MARLENE 83
BELFORT
Mobility of the Phage Introns • Intron Endonucleases and Their Targets • Double-Strand-Break
Repair Model for Mobility • Accessory Factors in Intron Homing • How Did It All Happen?
8 Repair of Lethal DNA Damage KENNETH N KREUZER and JOHN W DRAKE 89
Introduction • The denVSystem • Replication Repair • Recombinational Repair • Host
Systems Operant on T4
9 Mutagenesis JOHN W DRAKE and LYNN S RIPLEY 98
Methods of Analysis • Gene Structure and Mutational Spectra • The Cornerstone of Mutation
Analysis • Transition Mutagens • Transversion Mutagens • Chromosome Mutations • Frame-
shift Mutagenesis • Complex Mutations • Curious Mutations • Mutators and Antimutators •
Error-Prone Repair • More Mutagens • Even More Mutagens
v
vi CONTENTS
II REGULATION OF GENE EXPRESSION
Editors: Gisela Mosig and Dwight H Hall
10 Gene Expression: A Paradigm of Integrated Circuits GISELA MOSIG and DWIGHT H HALL 127
Transcription • RNA Processing and Degradation • Translational Controls
11 Transcription from Early Promoters KAIWILKENS and WOLFGANG RUGER 132
Structure and Regulation of RNA Polymerase • Structure of T-Even DNA • Prokaryotic Promoters
and Transcription Initiation • T4 Early Promoters • Summary
12 Regulation of Middle-Mode Transcription BARBARA STITT and DEBORAH HINTON 142
Introduction • Middle RNA from MotA-Dependent Middle Promoters • Production of Middle RNA
by Elongation of IE RNA • Conclusions
13 Regulation of Late-Gene Expression KELLY P WILLIAMS, GEORGE A KASSAVETIS, DANIEL R
HERENDEEN, and E PETER GEIDUSCHEK 161
Early Discoveries • T4 Late Promoters • Transcription Machinery of the Phage T4-Infected Cell •
Regulation of Expression of the Late Genes • Mechanism of Transcriptional Initiation at Late Pro
moters • Role of Concurrent DNA Replication • Concluding Comments • Appendix
14 mRNA Processing and Degradation A J CARPOUSIS and H M KRISCH 176
Identification of RNase E Cleavages in T4 Transcripts • Effect of the RNase E Mutation on the
Decay of T4 mRNAs • Role of E coli RNase III and the T4 regB Endoribonuclease in Phage mRNA
Decay • Reexamination of the Role of RNase E in E coli mRNA Decay • Specificity of RNase E •
Degradation of the Gene 32 mRNA by RNase E • RNase E Processing In Vitro • Conclusion
15 Synthesis and Maturation of T4-Encoded tRNAs GISELA MOSIG 182
History and Dedication • Functions • Transcription • Maturation • An RNA Processing
Complex? • Conclusions
16 The Self-Splicing Introns of Bacteriophage T4 DAVID A SHUB, TIMOTHY COETZEE, DWIGHT
H HALL, and MARLENE BELFORT 186
Three Self-Splicing Group I Introns in Bacteriophage T4 • The Intron Core Secondary Structures •
Genetic Studies • Hybrid Introns • The Intron Core Tertiary Structure • Functional Analysis of
Splicing • The Intron ORFs • Regulatory Implications • Where Did the T4 Introns Come From?
17 Control of Translation Initiation: mRNA Structure and Protein Repressors ERIC S MILLER, JIM
D KARAM, and ELEANOR SPICER 193
T4 Translation Initiation Regions • RNA Structures • Other Translational Controls • T4 Transla
tional Repressor Proteins • Conclusions
III PHAGE MORPHOGENESIS
Editors: Frederick A Eiserling and Lindsay W Black
18 Pathways in T4 Morphogenesis FREDERICK A EISERLING and LINDSAY W BLACK 209
19 Molecular Chaperones in T4 Assembly COSTA P GEORGOPOULOS and CLAfiS H LINDER 213
The Problem of Protein Folding • Molecular Chaperones • The groE Operon • Regulation of
groE Expression • The GroEL Protein • Chaperonin Action of GroEL • Suppression of T4
Growth Defects by Overexpression of GroEL • Role of Gp31 during T4 Development • Model for
the Role of the GroEL Chaperone during T4 Development
20 Morphogenesis of the T4 Head LINDSAY W BLACK, MICHAEL K SHOWE, and ALASDAIR C
STEVEN 218
The T4 Head Assembly Pathway • Structure of the T4 Capsid and Polymorphic Variants • Host
and Phage Molecular Chaperones Activate the Major Capsid Protein, Gp23, for Assembly • Initia
tion of Prohead Assembly • Prohead Elongation and Termination • Prohead Proteolysis and Mat
uration • Shell Transformation: Capsid Expansion and Binding of Accessory Proteins • DNA
Packaging • Structure of Packaged DNA • Head Maturation • Appendix: Early Observations and
Definition of the Morphogenetic Problems
21 T4 Tail Structure and Function DAVID H COOMBS and FUMIOARISAKA 259
Introduction • Tail Genetics • Transcription of Tail Genes • Tail Proteins • Tail Assembly • Tail
Structure • Tail Function during Infection
CONTENTS vii
22 Long Tail Fibers: Genes, Proteins, Structure, and Assembly W B WOOD, FREDERICK A EISER-
LING, and R A CROWTHER 282
Genetic Control of Tail Fiber Structure, Assembly, and Attachment • Assembly of the Tail Fiber •
Attachment of Tail Fibers to the Phage Baseplate • Structure of Assembled Distal Half Fibers •
Sequence Analysis • Conclusion
23 Receptor Recognition by T-Even-Type Coliphages ULF HENNING and SAID HASHEMOL-
HOSSEINI 291
The T4 and T2 Families • Receptor Recognition by Phages of the T4 Family • Receptor Recogni
tion by Phages of the T2 Family • Variability of Receptor Recognition by Phages: A Prokaryotic
Analogy to the Immune Systems
IV STRUCTURE-FUNCTION RELATIONSHIPS OF SELECTED T4-INDUCED PROTEINS
Editor: Eleanor K Spicer, with Kenneth R Williams and William H Konigsberg
24 Correlating Structure to Function in Proteins: T4 Gp32 as a Prototype KENNETH R WILLIAMS,
YOUSIF SHAMOO, ELEANOR K SPICER, JOSEPH E COLEMAN, and WILLIAM H
KONIGSBERG 301
Limited Proteolysis • Chemical Modification and Mutagenesis • NMR Spectroscopy • Photo
chemical Cross-Linking to Nucleic Acids • Conclusion
25 The Function of Zinc(II) in Gene 32 Protein (Gp32) Y SHAMOO, K R WILLIAMS, and W H
KONIGSBERG 305
26 Genetic Dissection of T4 DNA Polymerase Structure-Function Relationships LINDA J REHA-
KRANTZ 307
27 Protein-Protein and Protein-DNA Interactions in the T4 DNA Polymerase Accessory Protein Com
plex MARK C YOUNG, MICHAEL K REDDY, THALE C JARVIS, EDWARD P GOGOL, MARY K
DOLEJSI, and PETER H von HIPPEL 313
Biophysical and Biochemical Studies of the Accessory Protein Complex • Structure-Function
Studies of the Accessory Protein Complex by UVLaser Cross-Linking and Cryo-EM • Biochemical
Identification of the Sliding Clamp • Concluding Remarks
28 Structure-Function Analysis of T4 Endonuclease VML DODSON and R STEPHEN LLOYD 318
Amino Acid Residues Involved in Nontarget DNA Binding • Identification of a Metal-Binding Site
by Site-Directed Mutagenesis • Mutations That Enhance Catalytic Activities • Amino Acid Alter
ations That Affect Enzyme Structure • Pyrimidine Dimer-Specific Binding • Chemical Modifica
tion Analyses • Proof that the N-Terminal a-Amino Group Is the Catalytically Important
Nucleophile in the Endonuclease V Reaction
29 Functional Domains in T4-Thymidylate Synthase as Probed by Site-Directed Mutagenesis FRANK
MALEY, LAURA LaPAT-POLASKO, VERNA FRASCA, and GLADYS F MALEY 322
Elevated Expression and Isolation of T4 TS • Effect of Modifying Amino Acids in Specific
Domains of T4 TS • Nucleotide-Binding Site • The Folate-Binding Domain • The Phosphate-
Binding Domain • Significance
30 Structure and Function of T4 Glutaredoxin (Thioredoxin) HANS EKLUND 326
Three-Dimensional Structure • The Active Site • A Putative Glutathione-Binding Site • Active-
Site Mutations • Thioredoxin Reductase Activity • A Second Glutaredoxinlike T4 Protein?
31 Use of Chemical Modification and Limited Proteolysis To Study Structural Changes in the Tail
Sheath Protein Gp 18 FUMIO ARISAKA 329
Differential Chemical Modification of Tyrosine Residues • Modification of the Cysteine Residues
by ABD-F • Limited Proteolysis of MonomericGp 18
32 Structural and Genetic Analysis of the Stability and Function of T4 Lysozyme J A WOZNIAK,
X -J ZHANG, L H WEAVER, and B W MATTHEWS 332
Locations of Destabilizing Substitutions • Analysis of the Hydrophobic Effect • Cavity-Filling
Mutants • Protein Stabilization via Entropic Effects • Protein Stabilization via Electrostatic
Interactions • Stabilization via Disulfide Bridges • An S-S Bridge Activity Switch • a-Helix
Propensity and the Protein-Folding Problem • Protein Flexibility
viii CONTENTS
V HOST-PHAGE INTERACTIONS
Editors: Elizabeth Kutter and Karin Carlson, with Burt on Guttman
33 The Transition from Host to Phage Metabolism after T4 Infection ELIZABETH KUTTER,
BURTON GUTTMAN, and KARIN CARLSON 343
34 Recognition, Attachment, and Injection EDWARD GOLDBERG, LEONAS GRINIUS, and
LUCIENNE LETELLIER 347
Reversible Attachment • Irreversible Attachment • DNA Injection
35 Effects on Host Genome Structure and Expression E KUTTER, T WHITE, M KASHLEV, M
UZAN, J McKINNEY, and B GUTTMAN 357
Host Nucleoid Structure • Hm-Cyt in T4 DNA and the Inhibition of Host Transcription • Mecha
nism of Ale Action • Nuclear Disruption and the Blocking of Host Replication • Inhibitionof
Translation of Host mRNA • Other Potential Shutoff Functions and Mechanisms
36 Restriction and Modification KARIN CARLSON, ELISABETH A RALEIGH, and STANLEY
HATTMAN 369
Modification and Protection of T4 DNA • Phage Adenosine Methylation (dam) • Host Restriction:
Rgl(Mcr) • Antirestriction Effects • Restriction by T4 • Outlook: Biological Roles of Restriction-
Modification Systems
37 T4-Induced Inhibition of Proteolysis in Escherichia coli LEE D SIMON 382
38 Effects of T4 Infection on Membrane Lipid Synthesis DION HARPER, VLADIMIR ERYOMIN,
TERRY WHITE, and ELIZABETH KUTTER 385
Lipid Changes after T4 Infection • Efforts To Establish the Enzymatic Basis for Lipid Changes •
Effects of T4 Mutations on the Stimulation of PG Synthesis • Membrane Protein Synthesis after T4
Infection • Outlook
39 T4 Phage Exclusion Mechanisms LARRY SNYDER and GABRIEL KAUFMANN 391
rex Exclusion • prr Exclusion • The Exclusion of T4 by the Lit Protein of e 14 • Significance of
Phage Exclusion Systems
40 Lysis and the Interaction between Free Phages and Infected Cells STEPHEN T ABEDON 397
Definitions • Genes • Mechanisms of Action • Conclusion
41 Effects of Bacterial Growth Conditions and Physiology on T4 Infection ELIZABETH KUTTER,
EDUARD KELLENBERGER, KARIN CARLSON, SEAN EDDY, JAMES NEITZEL, LYNN
MESSINGER, JANINE NORTH, and BURTON GUTTMAN 406
Normal Habitat of T4-Like Phages • Normal Intracellular Ionic Conditions and Effects of Phage
Infection • Infection at Increased or Greatly Decreased Oxygen Tension • Infection of Cells Using
Energy Sources That Result in Slow Growth • Infection of Stationary-Phase Cells • Infection at
Different Temperatures • Conclusions
VI EXPERIMENTS IN T4 GENETICS
Editors: Karin Carlson and Eric S Miller
42 Working with T4 KARIN CARLSON and ERIC S MILLER 421
Introduction • Working with Bacteriophage T4
43 General Procedures KARIN CARLSON and ERIC S MILLER, Editors 427
43 1 Enumerating Phage: The Plaque Assay 427
General Procedures and Materials • Procedures To Enumerate Phage • Killing Titer
43 2 Preparing and Purifying Phage Stocks 430
Obtaining Phage from Plaques • Primary Lysates • Secondary Lysates • Purification of T4
Phage
43 3 Preparing Phage with Unmodified DNA 433
43 4 Single-Step Growth KARIN CARLSON 434
Appendix: The Poisson Distribution
44 T4 Genetics KARIN CARLSON and ERIC S MILLER, Editors 438
44 1 General Considerations for Strain Construction 438
Standard Cross • Enhanced Recombination • Selective Conditions • Testing Recombinants
from Phage Crosses • Assaying Recombinants
CONTENTS ix
44 2 Rapid Screening of Phage Progeny from Multiple-Factor Crosses HELEN ENGMAN
KREUZER and ERIC S MILLER 442
44 3 Mapping Mutations by Phage Crosses JOHN W DRAKE 444
A Standard Cross
44 4 Complementation and Recombination JOHN S WIBERG 446
44 5 Induced Mutagenesis and Isolation of T4 Mutants JOHN W DRAKE and LYNN S RIPLEY 447
Mutagenesis Protocols • Recovery and Analysis of Mutants • Appendix: UV Irradiation of T4
44 6 Directed Insertion/Substitution Mutagenesis KENNETH N KREUZER and HAROLD E
SELICK 452
The Integration/Segregation Cycle • Designing Mutations
45 Characterization and Analysis of T4 DNA ERIC S MILLER and KARIN CARLSON, Editors 455
45 1 Isolation of T4 Phage DNA MAJA KRICKER and KARIN CARLSON 455
Rapid Isolation of DNA Using CTAB • Isolation of Highly Pure, Intact DNA Using Phenol
45 2 Radiolabeling and Isolation of Intracellular T4 DNA: Analysis of In Vivo Restriction KARIN
CARLSON 456
Density Gradient Purification of T4 DNA
45 3 Quantitation of T4 DNA Synthesis by Radiolabeling ERIC S MILLER 459
45 4 Correlation of Deoxyribonucleotide Synthesis and DNA Replication Measured by Tritium
Release JOHN M HILFINGER 461
45 5 Sequencing of Genomic T4 DNA MAJA KRICKER 463
45 6 Polymerase Chain Reaction Amplification of DNA from T4 Plaques CATHERINE E
JOZWIK and ERIC S MILLER 464
45 7 Analysis of Escherichia coli Restriction Systems Using T4 ELISABETH A RALEIGH 466
46 Characterization and Analysis of T4 RNA and Proteins ERIC S MILLER and KARIN CARLSON,
Editors 468
46 1 Large-Scale Isolation of mRNA from T4-Infected Cells JIM D KARAM, TIEN HSU, and
ERIC S MILLER 468
Growth Conditions and RNA Yields
46 2 Rapid Bacteriophage T4 mRNA Preparations and the Primer Extension Assay DAVID S
McPHEETERS 470
Isolation of mRNA from T4-Infected Cells • Primer Extension Sequencing of RNA from T4-
Infected Cells
46 3 In Vitro Labeling of T4 Introns JONATHAGOTT 472
46 4 Radiolabeling of T4 Proteins and Their Analysis by Gel Electrophoresis ERIC S MILLER 473
46 5 Detection of Plasmid-Encoded T4 Proteins: Radiolabeling and Biological Activity ERIC S
MILLER and JIM D KARAM 474
46 6 In Vitro Selection and Amplification of Protein-Bound RNA Ligands CRAIG TUERK 475
General Considerations
47 Morphogenesis and Structural Biology ERIC S MILLER and KARIN CARLSON, Editors 480
47 1 Role of a Host Chaperonin in T4 Growth JOHN S WIBERG 480
47 2 In Vitro Packaging of DNA and Assembly of Infectious T4 Particles LINDSAY W BLACK 481
47 3 Visualization of T4 Phage by Electron Microscopy KARIN CARLSON 482
EPILOGUE: Unsolved Mysteries and the T4 Paradigm BRUCE M ALBERTS 485
APPENDIXES
Editors: Elizabeth Kutter and Gisela Mosig
A Genomic Map of Bacteriophage T4 ELIZABETH KUTTER, TOM STIDHAM, BURTON GUTTMAN,
ERIC KUTTER, DAVID BATTS, SHANE PETERSON, TSOTNE DJAVAKHISHVILI, FUMIO
ARISAKA, VADIM MESYANZHINOV, WOLFGANG ROGER, and GISELA MOSIG 491
The Sequence-Based Map
B Gel Analysis of T4 Prereplicative Proteins JOHN COWAN, KATHY d ACCI, BURTON GUTTMAN,
and ELIZABETH KUTTER 520
REFERENCES 529
INDEX 603
|
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| id | DE-604.BV010038974 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T17:45:24Z |
| institution | BVB |
| isbn | 1555810640 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-006657967 |
| oclc_num | 246899854 |
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| owner_facet | DE-703 DE-355 DE-BY-UBR DE-29T DE-11 DE-M49 DE-BY-TUM |
| physical | XVIII, 615 S. Ill., graph. Darst. |
| publishDate | 1994 |
| publishDateSearch | 1994 |
| publishDateSort | 1994 |
| publisher | ASM Press |
| record_format | marc |
| spelling | Molecular biology of bacteriophage T4 ed.-in-chief: Jim D. Karam Bacteriophage T4 Washington, DC ASM Press 1994 XVIII, 615 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bakteriophage T4 (DE-588)4330449-7 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Bakteriophage T4 (DE-588)4330449-7 s DE-604 Molekularbiologie (DE-588)4039983-7 s Karam, Jim D. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006657967&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Molecular biology of bacteriophage T4 Bakteriophage T4 (DE-588)4330449-7 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| subject_GND | (DE-588)4330449-7 (DE-588)4039983-7 |
| title | Molecular biology of bacteriophage T4 |
| title_alt | Bacteriophage T4 |
| title_auth | Molecular biology of bacteriophage T4 |
| title_exact_search | Molecular biology of bacteriophage T4 |
| title_full | Molecular biology of bacteriophage T4 ed.-in-chief: Jim D. Karam |
| title_fullStr | Molecular biology of bacteriophage T4 ed.-in-chief: Jim D. Karam |
| title_full_unstemmed | Molecular biology of bacteriophage T4 ed.-in-chief: Jim D. Karam |
| title_short | Molecular biology of bacteriophage T4 |
| title_sort | molecular biology of bacteriophage t4 |
| topic | Bakteriophage T4 (DE-588)4330449-7 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| topic_facet | Bakteriophage T4 Molekularbiologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006657967&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT karamjimd molecularbiologyofbacteriophaget4 AT karamjimd bacteriophaget4 |