Richard Egel (Ed.)

The Molecular Biology of Schizosaccharomyces pombe

Springer-Verlag Berlin Heidelberg GmbH

Richard Egel (Ed.)

The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond

With 68 Figures, 2 in Color, and 15 Tables

" Springer

Professor Dr. Richard Egel Department of Genetics Institute of Molecular Biology University of Copenhagen 0ster Farimagsgade 2A 1353 Copenhagen K Denmark

Cover: Meiotic nuclear divisions before sporulation in fission yeast (see Fig. 20.2 for details)

ISBN 978-3-642-05631-4 ISBN 978-3-662-10360-9 (eBook) DOI 10.1007/978-3-662-10360-9

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Preface

This book on the molecular gearings of fission yeast is cordially dedicated to Carsten Bresch, Michi Egel-Mitani, Herbert Gutz, Paul Nurse, Amar Klar, and Urs Leupold. With these candid personalities - all influential to the casting of my pro­fessional and private career - I had the good fortune of sharing coauthorship at very significant steps towards developing a sensible touch for the subtle charm of this wonderful model organism (Bresch et al. 1968; Egel and Egel-Mitani 1974; Egel and Gutz 1981; Beach et al. 1982; Egel et al. 1984; Leupold et al. 1989).

As to the timing of the book, repeated queries from participants at our Copenha­gen EMBO courses on Molecular Genetics with the Fission Yeast Schizosaccharo­myces pombe have indicated that a collective treatise on this subject would be highly welcome. This initial impression was overwhelmingly confirmed by the en­thusiastic consent I met among the prospective authors when I first approached them on specific contributions to present their field of expertise - as well as by the encouraging support expressed by the Springer-Verlag crew. A notable prede­cessor of this treatise, "The first attempt to assemble the lore of fission yeast" (Nasim et al. 1989), roughly coincided with the pioneering breakthrough of link­ing the major cyclin-dependent kinase of fission yeast to cell cycle timing in gen­eral - later awarded by the Nobel Prize to Paul Nurse. The present volume shortly follows the completion of the genome sequence, another timely milestone for ex­perimental research on S. pombe.

In conceiving this monograph, largely devoted to a single species, I was eager to combine the major areas of current molecular research in this yeast for conve­nient presentation in a single volume. This, of course, put severe limitations on all contributors alike, who easily could have doubled their page numbers and cor­responding references. Therefore, I take this opportunity to apologize to the nu­merous researchers at the bench whose additional articles could not be cited for space reasons alone, or only appeared in one of several relevant chapters. Also, comprehensive coverage of comparative discussions of other organisms was not the prime objective of this book. In this age of online search engines, however, supplementary material on any particular topic should not be too difficult to ob­tain.

The various chapters represent expert contributions from outstanding re­searchers in their respective fields. I gratefully acknowledge the elaborate efforts invested in this collective project by the individual authors - often on top of hea­vy academic burdens. In editing this formidable collection, I deeply appreciated the constructive cooperation of the communicating authors in aiming at a chain

VI Preface

of integrated chapters in a book, rather than a loose collection of separate re­views. May real impact indeed be measured by how many users hang on and read it all from front to back. I learned a lot myself throughout the process and thoroughly enjoyed the privilege of being the first to read this book.

May specialists not only glance at the sections closest to their expertise, but also widen their perspectives to adjacent topics and beyond; and may newcomers to the field, in particular, embrace the riches of knowledge accrued on ever so many interactive aspects of molecular fission yeast genetics and cell biology. This organism of little, inconspicuous cells has managed to survive in virtual obscurity for just as long as humankind's own ancestors - and any other form of extant life, for that matter. Now it has entered the limelight of learned curiosity and, in­deed, big science.

The holistic approach of unravelling all the details in a single, so-called model organism is necessarily repetitive in many ways when already established princi­ples need to be verified for the given case again. More often than not, the general paradigm holds and is thereby corroborated further; yet, when the particular or­ganism occasionally appears to play by different rules, new light is shed on how functional unity is maintained in this special form of life. All the more revealing are those salient instances of discovery when novel aspects are recognized in the model organism first and subsequently prove to be of general significance to other species, humankind included. The lore of fission yeast abounds with exam­ples for each of these categories at various levels of cell organization.

Such illustrious examples are spread throughout the individual chapters of this book. A guided tour and some highlights are incorporated in the introductory parts of Chapter 1. New progress and significant additions appear almost every week in Medline updates. Thus, last but not least, this book is also dedicated to all the untold workers at the bench already now preparing for the next compen­dium on the molecular organization of cells in fission yeast.

Beach D, Nurse P, Egel R (1982) Molecular rearrangement of mating-type genes in fission yeast. Nature 296:682-683

Bresch C, Miiller G, Egel R (1968) Genes involved in meiosis and sporulation of a yeast. Mol Gen Genet lO2:301-306

Egel R, Egel-Mitani M (1974) Premeiotic DNA synthesis in fission yeast. Exp Cell Res 88:127-134

Egel R, Gutz H (1981) Gene activation by copy transposition in mating-type switching of homothallic fission yeast. Curr Genet 3:5-12

Egel R, Beach DH, Klar AJS (1984) Genes required for initiation and resolution steps of mating-type switching in fission yeast. Proc Nat! Acad Sci USA 81:3481-3485

Leupold U, Nielsen 0, Egel R (1989) Pheromone-induced meiosis in P-specific mutants of fission yeast. Curr Genet 15:403-405

Nasim A, Young P, Johnson BF (1989) Molecular biology of the fission yeast. Academic Press, San Diego

Copenhagen, February 2003 RICHARD EGEL

I IE

Contents

Chapter 1 Fission Yeast in General Genetics R. EGEL

1.1 Historical Preface ................................. . 1.2 Cell and Life Cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2.1 The Vegetative Cell Division Cycle . . . . . . . . . . . . . . . . . . . . . . . 2 1.2.2 Mating Types and Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.3 Recombination and Genetic Mapping .................... 5 1.3.1 Meiotic Recombination .............................. 5 1.3.2 The Genetic Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.4 A Yeast on Its Own ................................. 8 1.5 Supplementary Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 References ............................................. 10

Chapter 2 The Genome and Beyond J. BAHLER, V. WOOD

13

2.1 The Fission Yeast Genome Sequence ..................... 13 2.1.1 Genome Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.1.2 Genome Comparisons ............................... 16 2.2 Post-Genomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.2.1 Genome-Wide Approaches ............................ 19 2.2.2 DNA Microarrays .................................. 19 2.2.3 Dealing with Large Datasets ........................... 21 2.3 Concluding Remarks ................................ 23 References ............................................. 23

Chapter 3 Protein Kinases Driving the Cell Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . 27 K.L. GOULD

3.1 3.2 3.3 3.4

Introduction ..................................... . Cdc2p/Cdk1 p Discovery ............................. . Cyclin Partners ................................... . Rum1 p Inhibitor .................................. .

27 27 28 30

VIII Contents

3.5 3.5.1 3.5.2 3.5.2.1 3.5.2.2 3.6.3 3.6 3.7 3.7.1 3.7.2

Regulatory Phosphorylation .......................... . T -Loop Phosphorylation ............................. . Tyrosine Phosphorylation ............................ . Wee1p and Mik1p - Inhibitory Kinases .................. . Cdc25p Phosphatase ............................... . PIo1p and Autoamplification .......................... . Suclp Adaptor ................................... . Some Future Directions ............................. . Localization Studies ................................ . Substrates ....................................... .

References

Chapter 4 Checkpoint Controls Halting the Cell Cycle A. M. CARR, T. CASPAR!

4.1 4.1.1 4.1.2 4.1.3 4.1.4 4.1.4.1 4.1.4.2 4.1.4.3 4.2 4.2.l

DNA Integrity Checkpoints ........................... . The G j Checkpoint ................................ . The SdNTP-M Checkpoint ............................ . The Intra-S Checkpoint ............................. . The Gz-M Checkpoint .............................. . DNA Damage Recognition ........................... . Signal Propagation ................................. . Signal Delivery ................................... . Checkpoint Proteins ................................ . Rad3 and Rad26 .................................. .

30 30 31 32 32 33 34 34 34 35 36

41

41 41 42 42 43 44 44 45 45 45

4.2.2 The RFC and PCNA-Related Checkpoint Proteins ............ 46 4.2.3 Rad4/Cut5, Crb2 and Chk1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 4.2.4 Mrcl and Cds1 .................................... 48 4.2.5 Other Proteins Implicated in the Checkpoints . . . . . . . . . . . . . . . 49 4.2.5.1 Rad18 - Does It Define an Additional Checkpoint Response? . . . . 49 4.2.5.2 Rad24 and Rad25 .................................. 50 4.2.5.3 Cell Cycle Regulators Cdc25, Wee1, Mik1 and Cdc2 . . . . . . . . . . . 50 4.2.6 DNA Repair and Checkpoint Proteins .................... 52 4.3 Concluding Remarks ................................ 53 References ............................................. 53

Chapter 5 Stress Responses in S. pombe W. M. TOONE, N. JONES

5.1 5.2 5.3 5.4 5.5 5.6 5.7

Introduction ..................................... . Key Stress Response Regulators ........................ . Heat Stress ...................................... . ER Stress ....................................... . Oxidative Stress ................................... . Osmotic and Salt Stress ............................. . General Stress Response ............................. .

57

57 58 60 64 65 67 68

Contents IX

5.8 Perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 References ............................................. 69

Chapter 6 DNA Replication in S. pombe ................................ 73 H. MASUKATA, J.A. HUBERMAN, M.G. FRATTINI, T.J. KELLY

6.1 The Logic of DNA Replication ......................... 73 6.2 Replication Origins ................................. 75 6.2.1 Why Are Replication Origins Interesting? . . . . . . . . . . . . . . . . . . 75 6.2.2 How Are Replication Origins Identified and Characterized? .. . . . 76 6.2.3 Biological Characteristics of S. pombe Replication Origins . . . . . . 77 6.2.4 Nucleotide Sequence Elements Important for Origin Function ... 78 6.2.5 Individual ARS Elements ............................. 79 6.2.5.1 arsl ............................................ 81 6.2.5.2 ars2004.......................................... 82 6.2.5.3 ars3001.......................................... 82 6.2.5.4 ars3002.......................................... 82 6.2.5.5 Two Less Well Characterized ARS Elements ................ 82 6.2.6 Timing of Origin Firing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 6.2.7 Relationship to Replication Origins in Animal Cells .......... 83 6.2.8 Origins, Replication Timing and Heterochromatin ........... 84 6.3 Recognition of Fission Yeast Origins by ORC .. . . . . . . . . . . . . . 84 6.4 Assembly of the Pre-Replication Complex (pre-RC) . . . . . . . . . . . 86 6.5 Activation of S Phase-Promoting Protein Kinases ............ 88 6.6 Establishment of the Replication Fork .................... 89 6.7 Prevention of Re-Replication by CDK .................... 90 6.8 Checkpoints and Origin Firing ......................... 92 6.9 DNA Replication - Future Directions . . . . . . . . . . . . . . . . . . . . . 93 References ............................................. 94

Chapter 7 DNA Repair Pathways O. FLECK

7.1 7.2 7.2.1 7.2.2 7.2.3 7.2.3.1 7.2.3.2 7.3 7.3.1 7.3.2 7.3.2.1 7.3.2.2 7.4

Introduction ..................................... . The Long-Patch Mismatch Repair Pathway ................ . The Methyl-Directed Mismatch Repair Pathway in E. coli ...... . The MutS/MutL-Related Mismatch Repair System in Eukaryotes .. The MutS/MutL-Related Repair System in S. pombe .......... . Repair of Replication Errors .......................... . Correction of Mismatches in Meiotic Recombination ......... . Nucleotide Excision Repair ........................... . Human Nucleotide Excision Repair ..................... . Nucleotide Excision Repair in S. pombe .................. . Repair of DNA Damage ............................. . Mismatch Correction and Mutation Avoidance ............. . Uve1-Dependent Repair ............................. .

101

101 102 102 102 103 103 104 106 106 107 107 108 110

x Contents

7.5 Base Excision Repair ................................ III 7.6 Recombinational Repair Activities . . . . . . . . . . . . . . . . . . . . . . . 112 7.6.1 Homologous DSB Repair ............................. ll2 7.6.2 Nonhomologous End Joining .......................... 112 References ............................................. 113

Chapter 8 The Retrotransposons of S. pombe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 H.L. LEVIN

8.1 Introduction .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ll7 8.2 The Structure of the Tf Elements and Their Function . . . . . . . . . 118 8.3 The Transposition Sites of T£1 ......................... 120 8.4 A Unique Mechanism of Self-Priming in Tf1 ............... 122 8.5 Specialized Mechanism for Transport of T£1 into the Nucleus . . . . 125 8.6 Concluding Remarks ................................ 126 References ............................................. 127

Chapter 9 Mating-Type Cassettes: Structure, Switching and Silencing. . . . . . . . . . . . 129 B. ARCANGIOLI, G. THON

9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 9.2 Mating-Type Switching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 9.2.1 Biological Aspects .................................. 129 9.2.2 Mating-Type Loci .................................. l30 9.2.3 Mating-Type Switching Pattern ......................... l30 9.2.4 cis- and trans-Acting Elements Controlling the Switching Potential 133 9.2.5 Single-Strand DNA Modification and Gene Conversion at mati .. 134 9.2.6 Asymmetric Developmental Potential and Replication Polarity . . . l35 9.3 Silencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . l38 9.3.1 Silenced Region. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . l38 9.3.2 Silencing Assays ................................... 139 9.3.3 cis-Acting Elements - Epigenetic States ................... l39 9.3.4 trans-Acting Factors - Heterochromatin Formation. . . . . . . . . . . 140 9.3.5 Redundancy of Silencing ............................. 141 9.3.6 Boundaries of the Silenced Region ...................... 142 9.4 Interplay Between Mating-Type Switching and Silencing ....... 142 References ............................................. 144

Chapter 10 Centromere and Kinetochore Structure and Function R. ALLSHIRE

10.1 10.2 10.3 10.3.1

Introduction Centromere Localization and Dynamics .................. . Centromere DNA .................................. . Organization ..................................... .

149

149 150 151 151

Contents

10.3.2 10.3.3 10.3.4 10.4 10.4.1 10.4.2 10.4.3 10.4.4 10.4.5 10.5 10.5.1 10.5.2 10.5.3 10.5.4 10.5.5 10.6 10.6.1

Functional Elements - Mitosis Functional Elements - Meiosis Suppression of Recombination Within Centromeres ......... . Centromere Chromatin and Silencing ................... . Chromatin Structure ............................... . Histone Modifications .............................. . Transcriptional Silencing ............................ . Connections with Other Silent Chromatin ................ . Factors Contributing to Silent Centromeric Chromatin ....... . Centromere and Kinetochore-Associated Proteins ........... . Outer-Repeat Proteins .............................. . A Link with the RNAi Machinery ...................... . CENP-B-Like Proteins .............................. . Inner-Repeat and Central-Core Proteins .................. . Microtubule-Interacting Proteins at Centromeres ........... . Cohesion and Segregation Defects ...................... . Mitotic Centromere Cohesion ......................... .

XI

151 154 155 155 155 155 156 156 157 158 158 159 160 160 162 163 163

10.6.2 Centromeric Cohesion During Meiosis I, the Reductional Division 164 10.6.3 Aurora Kinase - A Passenger at Centromeres . . . . . . . . . . . . . . . 165 10.7 Concluding Remarks ................................ 165 References ............................................. 166

Chapter 11 Chromosome Cohesion and Segregation K. TAKAHASHI, M. YANAGIDA

171

11.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 11.2 Anaphase-Promoting Complex and Related Factors . . . . . . . . . . . 172 11.2.1 The APC/C Proteasome Connection. . . . . . . . . . . . . . . . . . . . . . 172 11.2.2 The Spindle Assembly Checkpoint . . . . . . . . . . . . . . . . . . . . . . . 175 11.3 Separase and Securin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 11.4 Cohesin and Related Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 11.4.1 The Cohesin Complex ............................... 178 11.4.2 Meiosis-Specific Cohesin Subunits . . . . . . . . . . . . . . . . . . . . . . . 180 11.4.3 Cohesin Loading by Adherin .......................... 181 11.4.4 Establishment of Cohesion ............................ 181 11.5 Condensin and Related Factors ....... . . . . . . . . . . . . . . . . . . 182 11.5.1 The Condensin Complex ............................. 182 11.5.2 Chromosomal Passenger Proteins ....................... 183 11.5.3 Other Factors Involved in Condensation. . . . . . . . . . . . . . . . . . . 184 11.6 Concluding Remarks ................................ 185 References ............................................. 186

XII Contents

Chapter 12 Telomere Organization and Nuclear Movements Y. HIRAOKA, Y. CHIKASHIGE

12.1 12.2 12.2.1 12.2.2 12.2.3 12.3 12.3.1 12.3.2 12.3.3

Introduction ..................................... . Telomere Organization .............................. . Molecular Organization of the Telomere .................. . Telomeric Heterochromatin and Nuclear Positioning ......... . Telomere Integrity and Chromosome Circularization ......... . Nuclear Movements ................................ . Meiotic Telomere Clustering and Nuclear Movements ........ . Microtubule Dynamics During Nuclear Movements .......... . The Role for Telomeres in Meiosis ...................... .

191

191 192 192 194 195 196 196 198 199

12.3.4 Genetic Control for Telomere Clustering .................. 202 12.4 Concluding Remarks ................................ 202 References ............................................. 203

Chapter 13 The Mitotic Spindle and Genome Segregation . . . . . . . . . . . . . . . . . . . . . 207 LM. HAGAN

13.1 13.2 13.2.1 13.2.2 13.3 13.3.1 13.3.2 13.4 13.4.1 13.4.2 13.4.3

Introduction ..................................... . S. pombe Microtubules .............................. . The Microtubule Cytoskeleton ......................... . Structure of the Mitotic Spindle ....................... . Spindle Pole Body ................................. . SPB Structure and Duplication ........................ . Composition of the SPB ............................. . Microtubule-Associated Proteins ....................... . Motors Versus Non-motor MAPs ....................... . Microtubule Motor Proteins .......................... . The BimC-Related Kinesin Cut7 ....................... .

207 207 207 209 210 210

212 213 213 214 214

13.4.4 C-Terminal Kinesins Pkl1 and Kpl2 . . . . . . . . . . . . . . . . . . . . . . 215 13.4.5 The Kip3-Related KLPs: Klp5 and Klp6 ................... 215 13.4.6 Non-motor MAPs: Disl, MtcllAlp14 and Mal3 .............. 216 13.5 Regulatory Aspects ................................. 217 13.5.1 Regulation of Spindle Formation. . . . . . . . . . . . . . . . . . . . . . . . 217 13.5.2 Coordinating Cell Cycle Progression from the SPB ........... 218 13.5.3 Control of Mitotic Progression ......................... 220 13.6 Perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 References ............................................. 221

Chapter 14 The Fission Yeast Actomyosin Cytoskeleton Y. GACHET, D. P. MULVIHILL, J. S. HYAMS

14.1 14.2

Introduction ..................................... . Various Roles of Actin Function ....................... .

225

225 225

Contents XIII

14.2.1 Actin Is Involved in Cell Growth and Division 225 14.2.2 Actin Is Also Important for Sex ........................ 227 14.2.3 Actin and Actin-Binding Proteins ....................... 228 14.2.4 Anti-Actin Drugs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230 14.2.5 Actin Is Involved in Spindle Orientation .................. 231 14.2.6 Actin-Microtubule Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 231 14.3 Fission Yeast Myosins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232 14.3.1 Myosins Are Motor Proteins ............. . . . . . . . . . . . . . . 232 14.3.2 Myosin II ........................................ 232 14.3.3 Myosin V ........................................ 236 14.3.4 Myosin I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 14.4 Concluding Remarks ................................ 237 References ............................................. 238

Chapter 15 Regulation of Cytokinesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 M. K. BALASUBRAMANIAN, D. MCCOLLUM

15.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 15.2 Positioning of the Actomyosin Ring and the Division Septum ... 244 15.3 Actomyosin Ring Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . 246 15.4 Coordination of Mitotic Exit with Division Septum Assembly

- the SIN ........................................ 247 15.5 The SIN and the Cytokinesis Checkpoint . . . . . . . . . . . . . . . . . . 248 15.6 Assembly of the Division Septum ....................... 249 15.7 Concluding Remarks ................................ 250 References ............................................. 251

Chapter 16 Control of Cell Polarity and Morphogenesis in Fission Yeast F. CHANG, F. VERDE

255

16.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255 16.2 Signal Transduction and the Control of Cell Morphology. . . . . . . 256 16.3 Cytoskeleton Organization ............................ 259 16.3.1 The Interphase Actin Cytoskeleton ...................... 259 16.3.2 The Interphase Microtubule Cytoskeleton. . . . . . . . . . . . . . . . . . 260 16.4 The Teal System: Linking Microtubules to Cell Polarity. . . . . . . . 261 16.5 Nuclear Positioning - Setting the Cell Division Site .......... 263 16.6 Concluding Remarks ................................ 264 References ............................................. 265

Chapter 17 Cell Wall Synthesis A. DURAN, P. PEREZ

269

17.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269 17.2 Cell Wall Composition and Structure. . . . . . . . . . . . . . . . . . . . . 270

XIV Contents

17.3 Biosynthesis and Modification of the Cell Wall Components .... 27l 17.3.1 p-D-Glucan....................................... 271 17.3.2 a-D-Glucan....................................... 272 17.3.3 Chitin........................................... 273 17.3.4 Other Polymers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273 17.4 Regulation of Cell Wall Biosynthesis ..................... 274 17.5 Concluding Remarks ................................ 275 References ............................................. 276

Chapter 18 Mating-Type Control and Differentiation O. NIELSEN

281

18.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281 18.2 Cell-Type Identity .................................. 284 18.2.1 Control of Mating Type .............................. 284 18.2.2 Pheromone Production. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285 18.3 Pheromone Response. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285 18.3.1 Pheromone Response Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . 285 18.3.2 Activation of Byr2 ........... . . . . . . . . . . . . . . . . . . . . . . . 286 18.3.3 Pheromone-Induced Transcription. . . . . . . . . . . . . . . . . . . . . . . 287 18.3.4 The Ras1 Pathway ............. . . . . . . . . . . . . . . . . . . . . . 288 18.4 Morphological Response to Pheromone ................... 288 18.4.1 Reorganization of Cell Polarity . . . . . . . . . . . . . . . . . . . . . . . . . 288 18.4.2 Agglutination, Cell Fusion and Karyogamy. . . . . . . . . . . . . . . . . 289 18.5 Nutritional Sensing ................................. 290 18.6 Mating and the Cell Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292 References ............................................. 293

Chapter 19 Initiation of Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297 M. YAMAMOTO

19.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297 19.2 Molecular Events at the Onset of Meiosis . . . . . . . . . . . . . . . . . . 298 19.3 Repressors and Activators of Meiosis . . . . . . . . . . . . . . . . . . . . . 299 19.3.1 Regulation of the stell Gene. . . . . . . . . . . . . . . . . . . . . . . . . . . 299 19.3.2 Pat! Kinase and Its Pseudosubstrate Mei3p ................ 300 19.4 Mei2p, an RNA-Binding Protein Pivotal in Meiosis ........... 302 19.4.1 Mei2p Localization - A Nucleocytoplasmic Shuttle ........... 302 19.4.2 Mei2p Control - Downregulation by Phosphorylation ........ . 303 19.5 Transcriptome for Meiosis ............................ 304 19.6 Meiosis-Specific Cohesin and Chromosome Segregation ....... 305 19.7 Other Factors Relevant to Meiosis ........... . . . . . . . . . . . . 306 19.8 Concluding Remarks ................................ 307 References ............................................. 307

Contents

Chapter 20 Control of Late Meiosis and Ascospore Formation C.SHIMODA,~NAKAMURA

20.1 Introduction .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20.2 The Expression of Genes Responsible for Late Meiosis

xv

311

311

and Sporulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312 20.2.1 Isolation and Molecular Analysis of Sporulation-Specific Genes .. 312 20.2.2 Transcriptional Control of spo Genes. . . . . . . . . . . . . . . . . . . . . 315 20.2.3 Post-Transcriptional Regulation of mesl Gene Expression ...... 316 20.3 Dissecting the Sporulation Process ...................... 316 20.3.1 Overview........................................ 316 20.3.2 A Link Between Meiosis II and Sporulation ................ 317 20.3.2.1 A Novel Cdc7 Protein Kinase Complex Involved

in Meiosis II and Sporulation ............ . . . . . . . . . . . . . . 317 20.3.2.2 Other Meiosis II Regulators ........................... 318 20.3.3 Morphological Alteration of the SPB Needed for Sporulation . . . . 318 20.3.3.1 Electron-Microscopic Observations ...................... 318 20.3.3.2 Components of the SPB Responsible for Its Structural Alteration. 319 20.3.4 Formation of Forespore Membranes ..................... 319 20.3.4.1 Forespore Membrane Assembly Leading to Spore Formation .... 319 20.3.4.2 Origin of Vesicles Needed for Forespore Membrane Formation. . . 321 20.3.4.3 A Link Between Meiosis and Forespore Membrane Assembly . . . . 322 20.3.5 Construction of Spore Walls . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 20.4 Spore Germination ................................. 323 20.5 Concluding Remarks ................................ 324 References ............................................. 325

Chapter 21 RNA Polymerases and Accessory Factors ............... . . . . . . . . . 329 M. KIMURA, H. MITSUZAWA, A. ISHIHAMA

21.1 21.2 21.2.1 21.2.2 21.2.3 21.2.4 21.2.5 21.2.6 21.2.7 21.3 21.3.1 21.3.2 21.4 21.5 21.5.1 21.5.2

Introduction ..... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . RNA Polymerase II (Pol II) ........................... . Synthesis of Rpb Subunits ........................... . Transcription of the rpb Genes ........................ . Assembly of Rpb Subunits ........................... . Structure of Pol II ................................. . Subunit Functions ................................. . Phosphorylation of Rpb Subunits ...................... . CTD Kinases and CTD Phosphatase .................... . Pol II-Specific Transcription Factors .................... . General Transcription Factor TFIID ..................... . Mediators ....................................... . RNA Polymerase I (Pol I) ............................ . RNA Polymerase III (Pol III) ......................... . Pol III -Transcribed Genes and Promoters . . . . . . . . . . . . . . . . . . Pol III Subunits ................................... .

330 330 330 332 333 334 334 334 335 336 336 337 338 338 338 339

XVI Contents

21.5.3 Pol III Transcription Apparatus. . . . . . . . . . . . . . . . . . . . . . . . . 339 21.6 Concluding Remarks ................................ 340 References ............................................. 340

Chapter 22 Core Promoters in S. pombe: TATA and HomolD Boxes I. WITT, K. KIVINEN, N.F. KXUFER

22.1 22.2 22.2.1 22.2.2 22.3

Introduction ..................................... . The TATA Core Promoter ............................ . TATA, Transcription Initiation Site and Initiator Element ...... . TATA Elements in Core Promoters of RNA Polymerases I and III . The HomolD Core Promoter .......................... .

22.3.1 HomolD and Transcription Initiation .................... . 22.3.2 HomolD-Binding Proteins and Basal-Transcription Machinery .. . 22.3.3 HomolE, a Proximal VAS in a HomolD Core Promoter ....... . 22.4 Regulation of Genes Containing the HomolD Core Promoter . . . . 22.5 Prospects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References ............................................ .

Chapter 23 Mechanism and Control of Pre-mRNA Splicing ................... . A.N. KUHN, N.F. KXUFER

23.1 Introduction ..................................... . 23.2 The Spliceosomal RNA Machinery ...................... . 23.3 Intron Structure .................................. . 23.4 Assembly of the Spliceosome ......................... . 23.4.1 In Vitro Analysis of Spliceosome Assembly ............... . 23.4.2 How Are Spliceosomes Assembled in vivo? ................ . 23.5 Proteins in Pre-mRNA Splicing ........................ . 23.5.1 RNA-Rearranging Proteins ........................... . 23.5.2 The Central Organizer .............................. . 23.5.3 Prp4p, a Kinase Involved in Pre-mRNA Splicing ............ . 23.5.3.1 Interactions of Prp4p Kinase with Spliceosomal Proteins ...... . 23.5.3.2 Prplp, a Physiological Substrate of Prp4p Kinase ........... . 23.5.3.3 Control of Pre-mRNA Splicing by Prp4p Kinase - Two Models .. . 23.5.4 SR Proteins ...................................... . 23.6 Is There Alternative Splicing in S. pombe? ................ . 23.7 SMN and snRNP Maturation/Recycling .................. . 23.8 Pre-mRNA Splicing and the Link to the Cell Cycle .......... . 23.9 Outlook ........................................ . References ............................................ .

343

343 343 343 345 345 345 346 347 348 349 350

353

353 354 356 356 356 357 357 358 358 358 359 360 361 362 362 363 364 365 365

Contents XVII

Chapter 24 Transcription Termination .................................. 369 A. P. HADCROFT, N. J. PROUDFOOT

24.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369 24.2 Pol II Transcription Termination. . . . . . . . . . . . . . . . . . . . . . .. 370 24.2.1 Polyadenylation Signals .............................. 370 24.2.1.1 Mammals ........................................ 370 24.2.1.2 Budding Yeast .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 371 24.2.1.3 Fission Yeast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 371 24.2.2 Transcript Processing and Transcription Termination ......... 372 24.3 Pol I Transcription Termination ........................ 375 24.4 Pol III Transcription Termination ....................... 377 24.5 Concluding Remarks ................................ 378 References ............................................. 378

Chapter 25 Ubiquitin-Dependent Proteolysis by the Proteasome M. STONE, C. GORDON

381

25.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381 25.2 Structure of the Proteasome ......... . . . . . . . . . . . . . . . . . . 382 25.2.1 20S Core. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382 25.2.2 19S Regulator ..................................... 383 25.3 Genes Encoding 26S Proteasome Subunits in S. pombe ........ 384 25.4 Recognition and Delivery of Substrates ................... 385 25.5 Localization of the Proteasome ......... . . . . . . . . . . . . . . . . 387 25.6 Chaperone Activity of the 26S Proteasome . . . . . . . . . . . . . . . . . 388 25.7 Deubiquitinating Activity and the Proteasome .............. 389 25.8 The Proteasome and the Cell Cycle ...................... 390 25.9 Concluding Remarks ................................ 390 References ............................................. 391

Chapter 26 Processing Proteases in S. pombe . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 395 G. LADDS, J. DAVEY

26.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395 26.2 Processing of the P-Factor Mating Pheromone .............. 395 26.2.1 Signal Peptidase ................................... 397 26.2.2 The Dibasic Endopeptidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397 26.2.2.1 Proteases with Shared Functions to Krpl ..... . . . . . . . . . . . .. 398 26.2.3 Trimming by Carboxypeptidase and Aminopeptidase ......... 400 26.3 Processing of the M-Factor Mating Pheromone. . . . . . . . . . . . .. 401 26.3.1 C-Terminal Proteolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401 26.3.2 N-Terminal Proteolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403 26.4 Concluding Remarks ................................ 403 References ............................................. 404

XVIII Contents

Chapter 27 Protein Glycosylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405 T. R. GEMMILL, R. B. TRIMBLE

27.1 Introduction ..................................... . 405 27.2 The Galactosyltransferases ............................ 405 27.3 O-Glycosylation - Overview ........................... 406 27.4 N-Glycosylation - Overview ........................... 407 27.5 GPI Anchor Biosynthesis ............................. 411 27.6 Concluding Remarks ................................ 411 References ............................................. 412

Chapter 28 Mitochondrial Genetics in a Petite-Negative Yeast B. SCHAFER, K. WOLF

28.1 28.2 28.3 28.4 28.4.1 28.4.2 28.4.3

28.5 28.5.1 28.5.2 28.6 28.6.1 28.6.2 28.7 28.7.1 28.7.2 28.8 28.8.1 28.8.2 28.8.3 28.8.4 28.8.5 28.8.6

Introduction to Fission Yeast Mitochondria ............... . Replication, Repair, Integrity and Segregation of mt DNA ..... . Petite Negativity .................................. . Mitochondrial Mutants .............................. . Segregational Petites ............................... . Mitochondrial Drug Resistance Mutations ................ . Mitochondrial Mutants Conferring Respiratory Deficiency (rhoo, rho-, mit-) .................................. . Formal Mitochondrial Genetics ........................ . Mitotic Segregation in Diploids ........................ . Random-Spore and Tetrad Analysis ..................... . Organization of the mt Genome ....................... . Transcription .................................... . Genes of the Translational Apparatus .................... . The Bifunctional Gene rps3 .......................... . The Structure of the rps3 Gene ........................ . Functional Analysis of the rps3 Gene .................... . Mosaic Genes and Introns ........................... . Construction of an Intronless mt Genome ................ . Group I Introns ................................... . Functions of Group I Intron-Encoded Proteins ............. . Group II Introns .................................. . Group II Intron-Encoded Proteins ...................... . Horizontal Intron Transfer? ........................... .

415

415 415 417 418 418 418

418 420 420 420 421 421 421 422 422 422 423 423 423 424 425 426 426

References ............................................. 427

Contents

Chapter 29 Fission Yeast Phylogenesis and Evolution M. SIPICZKI

29.1 Introduction

XIX

431

431 29.2 Taxonomy and Systematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431 29.3 Phylogenetic Position of the Genus ........ . . . . . . . . . . . . . . 433 29.3.1 Phylogenetic Roots from Comparative Sequence Analyses ...... 433 29.3.2 Fungi and Animals, Sister Clades in Most Phylogenies ........ 434 29.3.3 Schizosaccharomyces, a Basal Branch of Ascomycota .......... 435 29.3.4 "Close" Relationship to a Diverse Group? . . . . . . . . . . . . . . . . . . 436 29.3.5 Phylogenesis Within the Genus . . . . . . . . . . . . . . . . . . . . . . . . . 436 29.3.6 Horizontal Gene Transfer? ............................ 437 29.3.7 Time Scaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437 29.4 Descent from Multicellular Filamentous Ancestors ........... 438 29.5 Is Schizosaccharomyces Close to the Roots of Fungi and Animals? . 439 29.6 Different Rates of Evolution in Different Lineages of Yeast? ..... 440 29.7 Concluding Remarks ................................ 440 References ............................................. 441

Subject Index .......................................... 445

List of Contributors

ALLSHIRE, R. Well come Trust Centre for Cell Biology Institute of Cell and Molecular Biology The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK

ARCANGIOLI, B.

Departement de Biologie Moleculaire Institut Pasteur, 25 rue du Dr. Roux 75724 Paris cedex 15, France

BAHLER, J. The Wellcome Trust Sanger Institute Hinxton, Cambridge CBIO 1SA, UK

BALASUBRAMANIAN, M.K.

The Institute of Molecular Agrobiology The National University of Singapore 1 Research Link, Singapore 117604

CARR, A.M.

Genome Damage and Stability Centre University of Sussex Science Park Road Falmer, Brighton, BN1 9RQ, UK

CASPARI, T. Pieris ProteoLab AG Lise-Meitner-StraEe 30 85354 Freising, Germany

CHANG,F.

Columbia University College of Physicians and Surgeons, Department of Microbiology 701 W. 168th St., New York New York 10032, USA

CHIKASHIGE, Y. Kansai Advanced Research Center Commmunications Research Laboratory, 588-2 Iwaoka, Iwaoka-cho Nishi-ku, Kobe 651-2492, Japan

DAVEY, J. Department of Biological Sciences University of Warwick Coventry CV 4 7 AL, UK

DURAN, A. Instituto de Microbiologia Bioquimica & Departamento de Microbiologia y Genetica CSIC/Universidad de Salamanca 37007 Salamanca, Spain

EGEL, R. Department of Genetics University of Copenhagen Oster Farimagsgade 2A 1353 Copenhagen K, Denmark

FLECK, O. Institute of Cell Biology University of Bern BaltzerstraEe 4 3012 Bern, Switzerland

FRATTINI, M.

Program in Molecular Biology Memorial Sloan-Kettering Cancer Center 1275 York Ave., New York New York 10021, USA

GACHET, Y. Department of Biology University College London Gower Street London WC1E 6BT, UK

XXII

GEMMILL, T. R. Wadsworth Center, Empire State Plaza P.o. Box 509, Albany New York 12201-0509, USA

GORDON, C. MRC Human Genetics Unit Western General Hospital Crewe Road Edinburgh EH4 2XU, UK

GOULD, K.L.

HHMI and Department of Cell and Developmental Biology Vanderbilt University School of Medicine Nashville, Tennessee 37232, USA

HADCROFT, A. P. Sir William Dunn School of Pathology University of Oxford South Parks Road Oxford OXI 3RE, UK

HAGAN,I.M.

Paterson Institute for Cancer Research Wilmslow Road Manchester M20 4BX, UK

HIRAOKA, Y. Kansai Advanced Research Center Communications Research Laboratory 588-2 Iwaoka, Iwaoka-cho Nishi-ku, Kobe 651-2492, Japan

HUBERMAN, J. A. Department of Cancer Genetics Roswell Park Cancer Institute Elm & Carlton Street, Buffalo, New York 14263, USA

HYAMS, J.S.

Department of Biology University College London Gower Street London WClE 6BT, UK

ISHIHAMA, A. Nippon Institute for Biological Science Division of Molecular Biology Shimachi 9-2221, Orne Tokyo 198-0024, Japan

List of Contributors

JONES, N. Paterson Institute for Cancer Research Wilmslow Road Manchester M20 4BX, UK

KAUFER, N. F. Institut fUr Genetik-Biozentrum Technische Universitat Braunschweig Spielmannstr. 7 38106 Braunschweig, Germany

KELLY, T. Program in Molecular Biology Memorial Sloan-Kettering Cancer Center 1275 York Ave., New York New York 10021, USA

KIMURA, M.

National Institute of Genetics Department of Molecular Genetics Mishima, Shizuoka 411-8540, Japan

KIVINEN, K.

European Bioinformatics Institute Well come Trust Genome Campus Hinxton Cambridge CBlO lSD, UK

KUHN, A.N. Institut fUr Genetik-Biozentrum Technische Universitat Braunschweig Spielmannstr. 7 38106 Braunschweig, Germany

LADDS, G.

Department of Biological Sciences University of Warwick Coventry CV 4 7 AL, UK

LEVIN, H.L.

Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development NIH, Bethesda Maryland 20892, USA

MASUKATA, H.

Department of Biology Graduate School of Science Osaka University 1-1, Machikaneyama-cho, Toyonaka Osaka 560-0043, Japan

List of Contributors

MCCOLLUM, D. Department of Microbiology and Molecular Genetics, The University of Massachusetts Medical School, Worcester Massachusetts 01605, USA

MITSUZAWA, H. National Institute of Genetics Department of Molecular Genetics Mishima, Shizuoka 411-8540, Japan

MULVIHILL, D. P.

Department of Biology University College London Gower Street London WC1E 6BT, UK

NAKAMURA, T.

Department of Biology Graduate School of Science Osaka City University Sumiyoshi-ku Osaka 558-8585, Japan

NIELSEN, O. Department of Genetics University of Copenhagen Oster Farimagsgade 2A 1353 Copenhagen K, Denmark

PEREZ, P.

Instituto de Microbiologia Bioquimica & Departamento de Microbiologia y Gem!tica CSIC/Universidad de Salamanca 37007 Salamanca, Spain

PROUDFOOT, N. J. Sir William Dunn School of Pathology University of Oxford South Parks Road Oxford OX1 3RE, UK

SCHAFER, B. Institut fUr Biologie IV (Mikrobiologie) RWTH Aachen Worringer Weg 52056 Aachen, Germany

SHIMODA, C.

Department of Biology Graduate School of Science Osaka City University Sumiyoshi-ku Osaka 558-8585, Japan

SIPICZKI, M. Department of Genetics University of Debrecen P.O. Box 56 4010 Debrecen, Hungary

STONE, M.

MRC Human Genetics Unit Western General Hospital Crewe Road Edinburgh EH4 2XU, UK

TAKAHASHI, K. Division of Cell Biology Institute of Life Science Kurume University 2432-3 Aikawa-machi, Kurume, Fukuoka, 839-0861, Japan

THON, G. Department of Genetics University of Copenhagen Oster Farimagsgade 2A 1353 Copenhagen K, Denmark

TOONE, W.M.

Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave. Toronto, Ontario M5G1X5, Canada

TRIMBLE, R. B. Wadsworth Center, Empire State Plaza PO Box 509, Albany New York 12201-0509, USA

VERDE,F.

XXIII

Department of Biochemistry and Molecular Biology University of Miami School of Medicine P.O. Box 016129 Miami, Florida 33136-1015, USA

WITT, I. Max Planck Institut Molecular Plant Physiology Am Muhlenberg 1, 14476 Golm, Germany

WOLF, K. Institut fUr Biologie IV (Mikrobiologie) RWTH Aachen Worringer Weg 52056 Aachen, Germany

XXIV

WOOD, V. The Wellcome Trust Sanger Institute Him:ton, Cambridge CBIO ISA, UK

YAMAMOTO, M. Department of Biophysics & Biochemistry Graduate School of Science University of Tokyo, Hongo Tokyo 113-0033, Japan

List of Contributors

YANAGIDA, M. Department of Gene Mechanisms Graduate School of Biostudies Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto, 606-8502, Japan

List of Abbreviations

AAA ABC ACS AFM AP APC/C ARS ATM BDM BER bZIP pGS CAK cAMP CAR ChIP cCRD CDK CER CESR CF CLC eM CPD CRE CS cs CSC CTD DAPI DDK dNTP DSB DSE DTT DUB EE ELC EM ER ESE ESR

ATP-binding ATPase (domain) ATP-binding cassette (transporter) ARS consensus sequence atomic force microscopy apyrimidinic/apurinic (sites) anaphase promoting complex or cyclosome autonomously replicating sequence ataxia telangiectasia mutated (kinase) 2,3 butanedione-2-monoxime base excision repair (pathway) basic leucine zipper (proteins) (1,3)P-D-glucan synthase CDK-activating kinase cyclic AMP cytokinetic actomyosin ring chromatin immunoprecipitation carboxyl-terminal cysteine-rich domain cyclin-dependent kinase common environmental response core environmental stress response core factor checkpoint loading complex centi-Morgan = % recombinants cyclo-pyrimidine dimer cAMP response element chitin synthase cold-sensitive checkpoint sliding clamp C-terminal domain 4" ,6-diamino-2-phenylindole Dbf4-dependent kinase deoxy-nucleoside triphosphate double-stranded DNA break downstream sequence element (termination) 1 ,4-dithio-DL-threitol deubiquitinating enzyme efficiency element (termination) essential light chain (myosin) electron microscopy endoplasmic reticulum exon sequence element environmental stress response

XXVI List of Abbreviations

FACS fluorescence-assisted cell sorting F -actin fibre actin FISH fluorescent in situ hybridisation FLEX FREAC (forkhead)-like consensus element of spa six FOA 5-fluoro-orotic acil - -G-actin globular actin GAP GTPase-activating protein GEF guanine-nucleotide exchange factor GFP green fluorescent protein GGR global genome repair (pathway) GPI glycosylphosphatidylinositol (anchor) G-protein GTP-binding protein GST glutathione S-transferase GTF general (or basal) transcription factor HMG high-mobility group (non-histone proteins) HMTase histone methyl transferase HR homologous recombination(al) HSF heat shock factor HU hydroxyurea Inr initiator element (transcription) IR ionising radiation JNK cJun-N-terminal kinase kb kilo base pairs K; kDa kilo Dalton KLPs kinesin-like proteins kMT kinetochore microtubule LTR long terminal repeat MADS-box MCMI, AGAMOUS, DEFICIENS and SRF (serum response factor) family MAPs microtubule-associated proteins MAPK mitogen-activated protein kinase MBC methylbenzylcarbamylate MBF Mlul-binding factor (cell cycle) MCM minichromosome maintenance (complex) MI/II meiosis I/II MLCK myosin light chain kinase MMR mismatch repair (pathway) MMS methyl methane sulfonate MPF maturation-promoting factor (-CDK) MT microtubule mt mitochondria(l) MTOC microtubule-organising centre nCRD amino-terminal cysteine-rich domain NER nucleotide excision repair (pathway) NES nuclear-export signal NETO new-end take-off NHEJ non-homologous end joining NLS nuclear-localization signal NMR nuclear magnetic resonance nt nucleotides NTP nucleoside triphosphate ORC origin recognition complex ORF open reading frame PAGE polyacrylamide gel electrophoresis PAK p2I-activated kinase PAN proteasome-activating nucleotidase PBS primer-binding site

List of Abbreviations

PCNA PCR P-Dol PERK PIC PKA;C PMS PMT Pol I - III pre-IC pre-RC PTGS PTRF RBD rDNA RFC RISC RLC RNAi RNP ROS RPT RPN RR RRM RT S SAGA SAPK SBF S-CDK SCF SDE SDS SIN siRNA snRNA SMC SMN SPB SSB STREP TAF TBP TBZ TCR TF 7TM TOG TPR ts TSA UAF UAS UBA UBL

proliferating-cell nuclear antigen polymerase chain reaction phosphodolichol pancreatic ER kinase preinitiation complex (transcription) protein kinase A/C postmeiotic segregation protein mannosyltransferase RNA polymerase I-III pre-initiation complex pre-replicative complex post-transcriptional gene silencing Pol I and transcript release factor RNA-binding domain ribosomal RNA genes replication factor C RNA-induced silencing complex regulatory light chain (myosin) RNA interference ribonucleoprotein reactive-oxygen species regulatory-particle ATPase regulatory-particle non-ATPase recombinational repair (pathway) RNA recognition motif reverse transcriptase Svedberg; sedimentation constant Spt-Ada-GcnS acetyltransferase (complex) stress-activated MAP kinase Swi4-binding factor S-phase cyclin-dependent kinase Skpl-Cullin-F-box (protein complex) site-determining element sodium dodecyl sulphate septation initiation network small interfering RNA small nuclear RNA structural maintenance of chromosomes (proteins) survival motor neuron (protein complex) spindle pole body single-stranded DNA break stress response element; s. pombe TBP-associated factor TATA-binding protein thiabendazole transcription-coupled repair (pathway) transcription factor 7x trans membrane-spanning (receptors) tumor overexpressed gene (family; human) tetratricopeptide (motif) temperature-sensitive trichostatin upstream activating factor upstream activation sequence ubiquitin-associated domain ubiquitin-like domain

XXVII

XXVIII

UBP UCH UIM UPR URS UTR UV UVER VCP WCC WGA XP

ubiquitin-specific processing proteases ubiquitin C-terminal hydrolases ubiquitin-interacting motif unfolded-protein response upstream repressing sequence untranslated region ultra-violet light UV-damaged DNA endonuclease-dependent excision repair valosin-containing protein whole-chromatid conversion wheat-germ agglutinin Xeroderma pigmentosum

List of Abbreviations