The yeast nucleus:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Oxford [u.a.]
Oxford Univ. Pr.
2000
|
| Edition: | 1. publ. |
| Series: | Frontiers in molecular biology
33 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIX, 316 S. Ill., graph. Darst. |
| ISBN: | 0199637733 0199637725 |
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Record in the Search Index
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| adam_text | Contents
The colour plate is between pages 44 and 45
List of contributors xv
Abbreviations %vii
1 Functional genomics with yeast i
DANIELA DELNERI AND STEPHEN G. OLIVER
1. Introduction 1
2. Organization of the yeast genome and the problem of redundancy 1
3. Informatic analysis 4
4. Large scale functional analysis 5
5. Quantitative phenotypic analysis 7
6. The transcriptome 8
7. The proteome 10
8. Conclusion and prospects 12
Acknowledgements 13
References 13
2 Chromosomal DNA replication in yeast: enzymes and
mechanisms 19
STUART A. MACNEILL AND PETER M. J. BURGERS
1. Introduction 19
2. Biogenesis of the replication fork: an overview 20
3. Replication origin structure, recognition, and activation 22
3.1 Overview 22
3.2 Origins of chromosomal replication 22
3.3 Origin recognition complex 25
3.4 Cdc6p 27
3.5 MCM protein complex 28
3.6 Cdc7p Dbf4p protein kinase 29
viii j CONTENTS
3.7 Cdc45p 30
3.8 Dynamic protein complexes at the replication fork 31
4. Initiation of replication: from origin unwinding to primer
synthesis 31
4.1 Overview 31
4.2 Replication protein A (RP A) 31
4.3 Pol a primase complex 33
5. Polymerase switching: enzymes and mechanisms 34
5.1 Overview 34
5.2 Replication factor C (RF C): the eukaryotic clamp loader 34
5.3 PCNA, the eukaryotic sliding clamp 37
5.4 DNA polymerase 8 38
5.5 DNA polymerase e 40
5.6 PCNA binding via a conserved protein sequence motif 41
6. Okazaki fragment processing 42
6.1 Overview 42
6.2 FEN 1 nuclease 42
6.3 Dna2 43
6.4 DNA ligase I 43
6.5 A model for the processing of Okazaki fragments in yeast 44
7. Conclusions 45
Acknowledgements 46
References 46
3 The cell cycle 58
MIKE TYERS AND PAUL JORGENSEN
1. Overview 58
2. Background 58
2.1 Life cycles of budding yeast and fission yeast 58
2.2 Foundations of the CDK paradigm 59
3. CDK regulation 60
3.1 CDK families 60
3.2 Cyclins that activate Cdc2/Cdc28p 61
3.2.1 Fission yeast cyclins 61
3.2.2 Budding yeast cyclins 64
3.2.3 Cdc2/Cdc28p substrates 65
CONTENTS | ix
3.3 Control of CDK activity by phosphorylation 66
3.3.1 Inhibition by tyrosine phosphorylation 66
3.3.2 Activation by CAK 70
3.4 CDK inhibitors 71
3.4.1 Skip and Ruml 71
3.4.2 Farlp 71
3.4.3 Other CKIs 72
3.5 Other factors required for CDK activity 72
3.5.1 Sucl/Ckslp 72
3.5.2 Cdc37p 73
3.6 CDK structure 73
4. Transcriptional control in the cell cycle 74
4.1 Cell cycle regulated transcription in budding yeast 74
4.1.1 The Gl S programme 74
4.1.2 The G2 M programme 77
4.1.3 The M Gl programme 78
4.1.4 Insights from genome wide analysis 78
4.2 Cell cycle regulated transcription in fission yeast 79
4.3 Environmental inputs into transcriptional programmes 79
5. Programmed proteolysis 80
5.1 The ubiquitin system 80
5.2 SCF ubiquitin ligases and phosphorylation dependent proteolysis 81
5.3 The anaphase promoting complex 85
5.4 The mitotic exit/septation pathway 87
5.5 Mitotic order and checkpoints 90
6. The cell cycle as a bistable oscillator 90
6.1 The CDK cycle and the replication segregation cycle 91
6.1.1 The switch at Gl S 91
6.1.2 Entry into mitosis 91
6.1.3 The switch at M Gl 92
6.1.4 Throwing the switches 92
6.2 Genome stability and the cell cycle 93
6.2.1 CDK activity and DNA replication 93
6.2.2 Defective switches and genome instability 93
6.2.3 Ploidy control and developmental alternatives 94
6.2.4 Dependency relationships 94
6.3 Fundamental issues 95
Acknowledgements 95
References 95
x I CONTENTS
4 Cell cycle checkpoints 106
KRISTI CHRISPELL FORBES AND TAMAR ENOCH
1. Introduction 106
1.1 Cell cycle checkpoints 106
1.2 Overview of checkpoint pathways 109
2. The checkpoint response to damaged and unreplicated DNA 109
2.1 Genes required for the checkpoint response to DNA damage 110
2.2 Possible checkpoint signals 112
2.2.1 Single stranded DNA as a potential checkpoint signal 113
2.2.2 Repair/replication complexes as checkpoint signals 114
2.2.3 Replication factor C and the checkpoint response 114
2.2.4 XRCCl related yeast proteins and the checkpoint response 115
2.2.5 Polymerase e and the checkpoint response 116
2.2.6 Checkpoint signals: conclusions 117
2.3 Transducers of the checkpoint response 117
2.4 Targets of the checkpoint pathway 119
2.4.1 G2 M arrest in fission yeast 119
2.4.2 G2 M arrest in budding yeast 120
2.5 Gl arrest 121
3. S phase delay 122
3.1 Possible targets of the intra S checkpoint 123
4. Other targets of the damaged and unreplicated DNA checkpoint
pathways 124
4.1 Transcription 124
4.2 Recovery and tolerance 125
4.3 Essential function of MECl(Sc) and RAD53(Sc) 125
5. Checkpoint response to damaged and unreplicated DNA: summary
and perspectives 126
6. The spindle checkpoint 126
6.1 Sensors and transducers of the spindle checkpoint signal 127
6.2 Does the spindle checkpoint target the APC? 130
7. Checkpoint control and human disease 131
8. Future prospects 132
Acknowledgments 133
References 133
CONTENTS ! xi
5 Mechanisms of nuclear division 143
HIROHISA MASUDA AND YASUSHI HIRAOKA
1. Introduction 143
2. Mitosis 143
2.1 Overview of mitotic nuclear division 143
2.2 Microtubule organization and nuclear behaviour during the mitotic
cell cycle 145
2.3 Structure and duplication of the SPB 146
2.4 Mechanism of microtubule nucleation at the SPB 149
2.5 Roles of cytoplasmic microtubules and motor proteins in nuclear
positioning 150
2.6 Roles of motor proteins in spindle assembly 152
2.7 Chromosome condensation and sister chromatid cohesion 153
2.8 Interaction between kinetochores and microtubules 155
2.9 Molecular mechanism responsible for the onset of anaphase 156
2.10 Dynamics of chromosome separation 157
3. Meiosis 158
3.1 Overview of meiotic nuclear division 158
3.2 Behaviour of chromosomes and microtubules in meiosis 160
3.3 Nuclear positioning of telomeres and centromeres in meiosis 162
3.4 Homologous chromosome pairing in meiotic prophase 163
3.5 Homologous chromosome synapsis in meiotic prophase 165
3.6 Sister chromatid cohesion during meiotic divisions 166
4. Conclusion 167
Acknowledgements 168
References 168
6 RNA polymerase II transcriptional machinery 176
MICHAEL HAMPSEY
1. Introduction 176
2. Promoter elements I77
3. RNA polymerase II 178
3.1 RNAPII structure 179
3.2 The C terminal repeat domain 179
3.3 RNAP II holoenzyme complexes 180
xii I CONTENTS
4. General transcription factors 181
4.1 TBP 182
4.2 TFIIB 184
4.3 TFIIF 184
4.4 TFIIE 185
4.5 TFIIH 185
5. Chromatin 186
5.1 Chromatin structure 186
5.2 Chromatin and transcription 187
6. Transcriptional coactivators 188
6.1 The SRB MED complex 188
6.2 TFIID 190
6.3 Histone acetyltransferases 192
6.4 The SWI SNF chromatin remodelling complex 194
7. General repressors 195
7.1 Ydrlp Bur6p 195
7.2 Motlp 196
7.3 Histone deacetylases 196
8. Mechanisms of transcriptional activation 197
9. Summary and perspectives 198
Acknowledgements 199
References 200
7 The structure of yeast centromeres and telomeres and
the role of silent heterochromatin 212
ALISON L. PIDOUX AND ROBIN C. ALLSHIRE
1. Introduction 212
2. DNA structure of S. potnbe centromeres 214
3. Proteins associated with S. potnbe centromeres or implicated in
kinetochore function 218
4. S. cerevisiae centromeres 221
5. Kinetochore proteins in S. cerevisiae 223
6. Comparison of S. potnbe and S. cerevisiae centromeres and
kinetochores 228
7. S. pombe telomeres and associated proteins 229
8. S. cerevisiae telomeres and associated proteins 233
9. Comparison of S. pombe and S. cerevisiae telomeres 235
CONTENTS | xiii
10. Conclusions and perspectives 236
Acknowledgements 237
References 237
8 Splicing pre mRNA introns 246
ANDREW E. MAYES, JUDITH A. POTASHKIN AND JEAN D. BEGGS
1. The occurrence of introns in yeast 246
2. The spliceosomal machinery 249
2.1 snRNAs: structure, conservation, and interactions 249
2.2 Proteins 251
2.2.1 Identification of proteins involved in splicing 251
2.2.2 Sm and Sm like core snRNP proteins 252
2.2.3 snRNP particle specific proteins 254
2.2.4 Non snRNP proteins 256
2.2.5 Conservation of splicing factors between yeasts and humans 256
3. An overview of spliceosome assembly 258
4. Who does what 259
5. DEAD/DExH box proteins 265
6. The regulation of splicing 266
6.1 Regulated splicing of specific introns 266
6.2 Phosphorylation 266
7. Links between splicing and other processes 267
7.1 Splicing, capping, and polyadenylation 267
7.2 Transcription and splicing 267
7.3 Splicing and mRNA stability 267
7.4 Splicing and the cell cycle 268
8. What remains to be done? 269
Acknowledgements 269
References 270
9 Yeast nuclear transport 276
CHARLES N. COLE
1. Introduction 276
2. Nuclear pore complexes 276
2.1 Organization and structure of NPCs 277
2.2 Nucleoporins 277
xiv | CONTENTS
2.2.1 Essential and non essential nucleoporins 280
2.2.2 Nucleoporin localization and NPC clustering 280
2.2.3 Structural and functional roles of nucleoporins 283
2.2.4 Nucleoporin subcomplexes 284
2.2.5 Assembly of NPCs 285
3. Protein import 285
3.1 Early studies on protein import 285
3.2 Defining the signals for protein import 285
3.3 Identification of the NLS receptor 286
3.4 The Gsplp/Ran GTPase system 286
3.4.1 Gsplp/Ran 286
3.4.2 Rnalp, the GTPase activating protein for Gsplp 288
3.4.3 Prp20p, the guanine nucleotide exchange factor for Gsplp 288
3.4.4 Are components of the Ran/Gsplp system involved in processes
other than nuclear transport? 289
3.4.5 Gsplp/Ran binding proteins 289
3.5 Other receptors for protein import 290
3.6 Mechanism of protein import 291
4. Protein shuttling and protein export 291
4.1 Assays for studying protein export and shuttling 292
4.2 Nuclear export signals (NESs) 292
4.3 Receptors for protein export 292
4.4 Other protein export factors 293
4.5 Recycling of transport receptors 293
5. RNA export 294
5.1 mRNA export 295
5.1.1 Nucleoporins required for mRNA export 296
5.1.2 Additional mRNA export factors 296
5.1.3 Receptors for mRNA export 297
5.2 tRNA export 298
5.3 Export of rRNA and ribosomal subunits 299
6. Regulation of nucleocytoplasmic transport 300
6.1 Regulated protein transport 300
6.2 Regulation of mRNA export 301
7. Coupling nucleocytoplasmic transport to other biological processes 302
8. Questions for future research 303
Acknowledgements 303
References 303
Index 312
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV013540492 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:47:38Z |
| institution | BVB |
| isbn | 0199637733 0199637725 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-009244831 |
| oclc_num | 44573286 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-703 DE-634 DE-11 |
| owner_facet | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-703 DE-634 DE-11 |
| physical | XIX, 316 S. Ill., graph. Darst. |
| publishDate | 2000 |
| publishDateSearch | 2000 |
| publishDateSort | 2000 |
| publisher | Oxford Univ. Pr. |
| record_format | marc |
| series | Frontiers in molecular biology |
| series2 | Frontiers in molecular biology |
| spelling | The yeast nucleus ed. by Peter Fantes ... 1. publ. Oxford [u.a.] Oxford Univ. Pr. 2000 XIX, 316 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Frontiers in molecular biology 33 Cell nuclei Fungal molecular biology Saccharomyces cerevisiae Cytology Schizosaccharomyces pombe Cytology Zellkern (DE-588)4067544-0 gnd rswk-swf Saccharomyces cerevisiae (DE-588)4178812-6 gnd rswk-swf Chromosom (DE-588)4010162-9 gnd rswk-swf Schizosaccharomyces pombe (DE-588)4179645-7 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Saccharomyces cerevisiae (DE-588)4178812-6 s Zellkern (DE-588)4067544-0 s DE-604 Schizosaccharomyces pombe (DE-588)4179645-7 s Chromosom (DE-588)4010162-9 s Genanalyse (DE-588)4200230-8 s Fantes, Peter Sonstige oth Frontiers in molecular biology 33 (DE-604)BV010329078 33 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009244831&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The yeast nucleus Frontiers in molecular biology Cell nuclei Fungal molecular biology Saccharomyces cerevisiae Cytology Schizosaccharomyces pombe Cytology Zellkern (DE-588)4067544-0 gnd Saccharomyces cerevisiae (DE-588)4178812-6 gnd Chromosom (DE-588)4010162-9 gnd Schizosaccharomyces pombe (DE-588)4179645-7 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4067544-0 (DE-588)4178812-6 (DE-588)4010162-9 (DE-588)4179645-7 (DE-588)4200230-8 (DE-588)4143413-4 |
| title | The yeast nucleus |
| title_auth | The yeast nucleus |
| title_exact_search | The yeast nucleus |
| title_full | The yeast nucleus ed. by Peter Fantes ... |
| title_fullStr | The yeast nucleus ed. by Peter Fantes ... |
| title_full_unstemmed | The yeast nucleus ed. by Peter Fantes ... |
| title_short | The yeast nucleus |
| title_sort | the yeast nucleus |
| topic | Cell nuclei Fungal molecular biology Saccharomyces cerevisiae Cytology Schizosaccharomyces pombe Cytology Zellkern (DE-588)4067544-0 gnd Saccharomyces cerevisiae (DE-588)4178812-6 gnd Chromosom (DE-588)4010162-9 gnd Schizosaccharomyces pombe (DE-588)4179645-7 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Cell nuclei Fungal molecular biology Saccharomyces cerevisiae Cytology Schizosaccharomyces pombe Cytology Zellkern Saccharomyces cerevisiae Chromosom Schizosaccharomyces pombe Genanalyse Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009244831&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV010329078 |
| work_keys_str_mv | AT fantespeter theyeastnucleus |