Tai Lieu Chat Luong Edited by Horst Feldmann Yeast Related Titles Bolsover, S R., Shephard, E A., White, H A., Hyams, J S Cell Biology A Short Course 2011 ISBN: 978-0-470-52699-6 Karp, G Cell Biology International Student Version 2010 ISBN: 978-0-470-50576-2 Merz, W G., Hay, R J (eds.) Topley and Wilson’s Microbiology and Microbial Infections, Medical Mycology 2009 ISBN: 978-0-470-66029-4 Edited by Horst Feldmann Yeast Molecular and Cell Biology 2nd, Completely Revised and Greatly Enlarged Edition With contributions from Paola Branduardi, Bernard Dujon, Claude Gaillardin, and Danilo Porro The Editor Prof Dr Horst Feldmann Adolf Butenandt Institute Molecular Biology Ludwig-Maximilians-Universität München Schillerstr 44 80336 München Germany Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose No warranty can be created or extended by sales representatives or written sales materials The Advice and strategies contained herein may not be suitable for your situation You should consult with a professional where appropriate Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages Library of Congress Card No.: applied for Correspondence address Prof Dr Horst Feldmann Ludwig-Thoma-Strasse 22B 85232 Bergkirchen Germany Cover Budding yeast marked with GFP British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http://dnb.d-nb.de # Wiley-VCH Verlag & Co KGaA, Boschstr 12, 69469 Weinheim, Germany Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical, and Medical business with Blackwell Publishing All rights reserved (including those of translation into other languages) No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers Registered names, trademarks, etc used in this book, even when not specifically marked as such, are not to be considered unprotected by law Print ISBN: ePDF ISBN: ePub ISBN: mobi ISBN: oBook ISBN: 978-3-527-33252-6 978-3-527-65921-0 978-3-527-65919-7 978-3-527-65920-3 978-3-527-65918-0 Cover Adam-Design, Weinheim, Germany Typesetting Thomson Digital, Noida, India Printing and Binding Markono Print Media Pte Ltd, Singapore Printed on acid-free paper jV Contents Preface XVII Authors XIX Introduction 1.1 Historical Aspects 1.2 Yeast as a Eukaryotic Model System Further Reading Yeast Cell Architecture and Functions 2.1 General Morphology 2.2 Cell Envelope 2.2.1 Cell Wall 2.2.2 Plasma Membrane 2.3 Cytoplasm and Cytoskeleton 2.3.1 Yeast Cytoplasm 2.3.2 Yeast Cytoskeleton 2.3.2.1 Microtubules 2.3.2.2 Actin Structures 2.3.2.3 Motor Proteins 11 2.3.2.3.1 Myosins 12 2.3.2.3.2 Kinesins 13 2.3.2.3.3 Dynein 12 2.3.2.4 Other Cytoskeletal Factors 13 2.3.2.4.1 Proteins Interacting with the Cytoskeleton 2.3.2.4.2 Transport of Organellar Components 13 2.4 Yeast Nucleus 14 2.4.1 Overview 14 2.4.2 Nuclear Pore 14 2.4.2.1 Historical Developments 14 2.4.2.2 Current View of the Nuclear Pore 15 2.4.2.3 Yeast Nucleolus 17 2.4.3 Yeast Chromosomes 17 2.5 Organellar Compartments 17 2.5.1 ER and the Golgi Apparatus 18 2.5.2 Transport Vesicles 18 2.5.3 Vacuolar System 20 2.5.3.1 Yeast Vacuole 20 2.5.3.2 Vacuolar Degradation 21 2.5.4 Endocytosis and Exocytosis 21 2.5.5 Mitochondria 21 2.5.5.1 Mitochondrial Structure 21 2.5.6 Peroxisomes 22 Further Reading 23 13 j Contents VI Yeast Metabolism 25 3.1 Metabolic Pathways and Energy 25 3.2 Catabolism of Hexose Carbon Sources 25 3.2.1 Principal Pathways 25 3.2.2 Respiration Versus Fermentation 26 3.2.3 Catabolism of Other Sugars – Galactose 27 3.2.4 Metabolism of Non-Hexose Carbon Sources 28 3.3 Gluconeogenesis and Carbohydrate Biosynthesis 30 3.3.1 Gluconeogenesis 30 3.3.2 Storage Carbohydrates 30 3.3.2.1 Glycogen 30 3.3.2.2 Trehalose 31 3.3.3 Unusual Carbohydrates 31 3.3.3.1 Unusual Hexoses and Amino Sugars 31 3.3.3.2 Inositol and its Derivatives 32 3.3.3.3 N- and O-Linked Glycosylation 33 3.3.4 Structural Carbohydrates 34 3.4 Fatty Acid and Lipid Metabolism 35 3.4.1 Fatty Acids 35 3.4.2 Lipids 35 3.4.3 Glycolipids 36 3.4.3.1 Phosphatidylinositol and Derivatives 36 3.4.3.2 Sphingolipids 38 3.4.3.3 Glycosylphosphatidylinositol (GPI) 39 3.4.4 Isoprenoid Biosynthesis 40 3.5 Nitrogen Metabolism 42 3.5.1 Catabolic Pathways 42 3.5.2 Amino Acid Biosynthesis Pathways 44 3.5.2.1 Glutamate Family 44 3.5.2.2 Aspartate Family 44 3.5.2.3 Branched Amino Acids 45 3.5.2.4 Lysine 46 3.5.2.5 Serine, Cysteine, and Glycine 46 3.5.2.6 Alanine 46 3.5.2.7 Aromatic Amino Acids 46 3.5.2.8 Histidine 47 3.5.2.9 Amino Acid Methylation 47 3.6 Nucleotide Metabolism 48 3.6.1 Pyrimidine Derivatives 48 3.6.2 Purine Derivatives 48 3.6.3 Deoxyribonucleotides 50 3.6.4 Nucleotide Modification 50 3.7 Phosphorus and Sulfur Metabolism 51 3.7.1 Phosphate 51 3.7.2 Sulfur 52 3.7.2.1 Fixation and Reduction of Sulfate 52 3.7.2.2 Cycle of Activated Methyl Groups 53 3.8 Vitamins and Cofactors 53 3.8.1 Biotin 53 3.8.2 Thiamine 53 3.8.3 Pyridoxine 54 3.8.4 NAD 54 3.8.5 Riboflavin Derivatives 54 3.8.6 Pantothenic Acid and Coenzyme A 55 3.8.7 Folate 55 j Contents VII 3.8.8 Tetrapyrroles 55 3.8.9 Ubiquinone (Coenzyme Q) 56 3.9 Transition Metals 57 Further Reading 58 Yeast Molecular Techniques 59 4.1 Handling of Yeast Cells 59 4.1.1 Growth of Yeast Cells 59 4.1.2 Isolation of Particular Cell Types and Components 59 4.2 Genetic Engineering and Reverse Genetics 59 4.2.1 Molecular Revolution 59 4.2.2 Transformation of Yeast Cells 61 4.2.2.1 Yeast Shuttle Vectors 61 4.2.2.2 Yeast Expression Vectors 62 4.2.2.3 Secretion of Heterologous Proteins from Yeast 63 4.2.2.4 Fluorescent Proteins Fused to Yeast Proteins 63 4.2.3 Yeast Cosmid Vectors 64 4.2.4 Yeast Artificial Chromosomes 65 4.3 More Genetic Tools from Yeast Cells 65 4.3.1 Yeast Two-Hybrid System 65 4.3.2 Yeast Three-Hybrid System 66 4.3.3 Yeast One-Hybrid (Matchmaker) System 67 4.4 Techniques in Yeast Genome Analyses 67 4.4.1 Microarrays 67 4.4.1.1 DNA-Based Approaches 67 4.4.1.2 Proteome Analyses 68 4.4.2 Affinity Purification 70 4.4.3 Mass Spectrometry 70 Further Reading 72 Yeast Genetic Structures and Functions 73 5.1 Yeast Chromosome Structure and Function 73 5.1.1 Yeast Chromatin 73 5.1.1.1 Organization of Chromatin Structure 73 5.1.1.2 Modification of Chromatin Structure 73 5.1.1.2.1 Modification of Histones 73 5.1.1.2.2 Remodeling Chromatin Structure Overview 5.1.2 Centromeres 85 5.1.3 Replication Origins and Replication 85 5.1.3.1 Initiation of Replication 85 5.1.3.2 Replication Machinery 88 5.1.3.2.1 DNA Polymerases 88 5.1.3.2.2 Replication and Replication Factors 89 5.1.3.2.3 Postreplication Repair and DNA Damage Tolerance 89 5.1.3.3 Replication and Chromatin 90 5.1.3.3.1 Chromatin Reorganization 90 5.1.3.3.2 Silencing and Boundaries 91 5.1.3.4 DNA Damage Checkpoints 93 5.1.3.4.1 Checkpoints During Replication 93 5.1.3.4.2 DSB Repair 94 5.1.4 Telomeres 96 5.1.5 Transposons in Yeast 98 5.1.5.1 Classes of Transposable Elements 98 5.1.5.2 Retrotransposons in S cerevisiae 98 5.1.5.2.1 Ty Elements and their Genomes 98 81 j Contents VIII 5.2 5.3 5.4 5.5 5.6 5.1.5.2.2 Behavior of Ty Elements 99 5.1.5.2.3 Expression of Ty Elements 100 5.1.5.3 Ty Replication 101 5.1.5.4 Interactions between Ty Elements and their Host 102 Yeast tRNAs, Genes, and Processing 103 5.2.1 Yeast tRNAs 103 5.2.1.1 Yeast Led the Way to tRNA Structure 103 5.2.1.2 Yeast tRNA Precursors and Processing 105 5.2.2 Current Status of Yeast tRNA Research 106 5.2.2.1 Yeast tRNAs and their Genes 106 5.2.2.2 tRNA Processing and Maturation 106 5.2.2.3 Participation of tRNAs in an Interaction Network 109 5.2.2.3.1 Aminoacylation of tRNAs 109 5.2.2.3.2 Rules, Codon Recognition, and Specific tRNA Modification 111 5.2.2.3.3 Recognition of tRNAs in the Protein Biosynthetic Network 111 Yeast Ribosomes: Components, Genes, and Maturation 113 5.3.1 Historical Overview 113 5.3.2 Ribosomal Components 113 5.3.2.1 Ribosomal RNAs 113 5.3.2.2 Ribosomal Proteins 114 5.3.3 Components and Pathways of Yeast Ribosome Maturation 114 Messenger RNAs 116 5.4.1 First Approaches to the Structure of Yeast mRNAs 116 5.4.2 Introns and Processing of pre-mRNA 117 5.4.3 Provenance of Introns 121 Extrachromosomal Elements 121 5.5.1 Two Micron DNA 121 5.5.2 Killer Plasmids 121 5.5.3 Yeast Prions 121 Yeast Mitochondrial Genome 123 Further Reading 125 Gene Families Involved in Cellular Dynamics 127 6.1 ATP- and GTP-Binding Proteins 127 6.1.1 ATPases 127 6.1.1.1 P-Type ATPases 127 6.1.1.2 V-Type ATPases 127 6.1.1.3 Chaperones, Cochaperones, and Heat-Shock Proteins 6.1.1.3.1 HSP70 Family 128 6.1.1.3.2 HSP40 Family 129 6.1.1.3.3 HSP90 Family 129 6.1.1.3.4 HSP60 Family 132 6.1.1.3.5 HSP104 132 6.1.1.3.6 HSP26 and HSP42 132 6.1.1.3.7 HSP150 133 6.1.1.3.8 HSP31/32/33 133 6.1.1.3.9 HSP30 133 6.1.1.3.10 HSP10 133 6.1.1.3.11 Others 133 6.1.1.4 Other ATP-Binding Factors 133 6.1.2 Small GTPases and Their Associates 133 6.1.2.1 RAS Family 134 6.1.2.2 RAB Family 134 6.1.2.3 RHO/RAC Family 134 6.1.2.4 ARF Family 134 6.1.2.5 Ran GTPAse 136 6.1.3 G-Proteins 136 128 j Contents IX 6.2 6.3 6.4 6.5 6.1.3.1 Mating Pheromone G-Protein 136 6.1.3.2 Gpr1-Associated G-Protein 137 6.1.3.3 RGS Family 137 6.1.3.4 G-Like Proteins 137 Regulatory ATPases: AAA and AAAỵ Proteins 138 6.2.1 ATP-Dependent Proteases 138 6.2.2 Membrane Fusion Proteins 139 6.2.3 Cdc48 139 6.2.4 Peroxisomal AAA Proteins 139 6.2.5 Katanin and Vps4p 139 6.2.6 Dynein 139 6.2.7 DNA Replication Proteins 140 6.2.8 RuvB-Like Proteins 140 6.2.9 Other AAAỵ Yeast Proteins 140 Protein Modication by Proteins and Programmed Protein Degradation 141 6.3.1 Ubiquitin–Proteasome System (UPS) 141 6.3.1.1 Initial Discoveries 141 6.3.1.2 Ubiquitin and Factors in the Ubiquitin-Mediated Pathway 6.3.1.3 E3 Ubiquitin Ligases 142 6.3.1.3.1 HECT-Type Ligases 142 6.3.1.3.2 RING Finger-Type Ligases 143 6.3.1.3.3 Functions of Selected E3 Ligases 144 6.3.1.4 Ubiquitin-Specific Proteases 147 6.3.2 Yeast Proteasomes 147 6.3.2.1 Initial Discoveries 147 6.3.2.2 Structure of the Proteasome 148 6.3.2.3 Regulation of Yeast Proteasome Activity 148 6.3.3 More Functions for Ubiquitin 150 6.3.4 Ubiquitin-Like Proteins (ULPs) and Cognate Factors 151 6.3.4.1 SUMO 151 6.3.4.2 Rub1 152 6.3.4.3 Ubiquitin Domain Proteins 152 6.3.4.4 Substrate Delivery to the Proteasome 153 Yeast Protein Kinases and Phosphatases 153 6.4.1 Protein Kinases in Yeast 153 6.4.1.1 PKA as a Prototype Kinase 153 6.4.1.2 Yeast Possesses a Multitude of Kinases 153 6.4.2 Protein Phosphatases in Yeast 158 Yeast Helicase Families 159 6.5.1 RNA Helicases in Yeast 166 6.5.1.1 Structures and Motifs 166 6.5.1.2 Functions of RNA Helicases in Yeast 167 6.5.2 DNA Helicases in Yeast 168 6.5.2.1 Structures and Motifs 168 6.5.2.2 Functions of DNA Helicases 168 6.5.2.2.1 ASTRA Complex 170 6.5.2.2.2 RAD Epistasis Group 170 6.5.2.2.3 Monomeric DNA Helicases 170 Further Reading 173 Yeast Growth and the Yeast Cell Cycle 175 7.1 Modes of Propagation 175 7.1.1 Vegetative Reproduction 175 7.1.1.1 Budding 175 7.1.1.2 Septins and Bud Neck Filaments 178 7.1.1.3 Spindle Pole Bodies and their Dynamics 179 141 j Appendix D: Selected Abbreviations 430 Table D.1 ETS FACS FACT FAD FAPP2 FDA FEAR FGM FHA FITC FOX FRE FSM FYVE GABA gag GCN GDP GFP GHG GINS GPI GRAS GSE GTF GTP HAST HAT HDAC HEAT HECT HEH HJ HMG HMT HOG HOPS HSF HSE HSP HSS int IMP IMS IRES ITS LCB LIM LLO LTR MADS MAP MBF MCB MCE MCM MEK MEKK MELAS MEN MERRF (Continued) external transcribed spacer fluorescence-activated cell sorting facilitates chromatin transactions flavin adenine dinucleotide four phosphate adapter protein Food and Drug Administration (US) Cdc14 early anaphase release fermentable-growth-medium-induced forkhead-associated fluorescein isothiocyanate winged-helix/forkhead filamentous response element forespore membrane domain in Fab1, yotb, Vac1p, and EEA1) g-aminobutyric acid group-specific antigen general nitrogen control guanosine diphosphate Green Fluorescent Protein greenhouse gas(es) Go, Ichi, Nii, San glycosylphosphatidylinositol generally regarded as safe gap sorting in the endosomes complex general transcription factor guanosine triphosphate Hda1p-affected subtelomeric histone acetyltransferase histone deacetylase domain in Huntingtin, elongation factor-3, protein phosphatase 2A, TOR1 homologous to the E6-AP C-terminus helix–extension–helix Holliday junction high mobility group histone methyltransferase high osmolarity growth homotypic vacuolar fusion and protein sorting heat-shock factor heat-shock element heat-shock protein hydrophobic sorting signal integrase inosine monophosphate intramembrane space iron-responsive elements internal transcribed spacer long-chain base homeodomain in Lin-11, Isl-1, Mec-3 lipid-linked oligosaccharide long terminal repeat transcription factor family (Mcm1, Amagous, Deficiens, SRF) mitogen-activated protein multiprotein bridging factor Mlu1 cell cycle box Mcm1 cell cycle element minichromosome maintenance mitogen-activated protein kinase kinase (MAPKK) mitogen-activated protein kinase kinase kinase (MAPKKK) mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes mitotic exit network myoclonus epilepsy, ragged red fibers (continued) j Appendix D: Selected Abbreviations 431 Table D.1 MIM MOM MTOC MVB NAC NAD NBD NCR NER NES NHEJ NLS NMD NOR NPC NTC NTS NSF NUP NXF ORC ORF OSCP OSBP OST PAK PAM PAPS PAS PCNA PCR PD PDI PDH PDR PFGE PIKK PH PHS PI PKA PKC PL PLA PRC PPP PRD PRR PVC PVE PTS PTT QPS RAC RAP REF RENT RFC RGS RNA RNA (Continued) mitochondrial inner membrane mitochondrial outer membrane microtubule organizing center multivesicular body nascent-polypeptide associated complex nicotinamide adenine dinucleotide nucleotide-binding domain nitrogen catabolite repression nucleotide excision repair nuclear export sequence nonhomologous end-joining nuclear localization signal nonsense-mediated mRNA decay nucleolar organizing region nuclear pore complex nieteen complex nontranscribed spacer N-ethylmaleimide-sensitive fusion nucleoporin nuclear export factor origin recognition complex open reading frame oligomycin sensitivity-conferring protein oxysterol-binding protein oligosaccharyl transferase p21-activated protein kinase processing activity of mitochondria phosphoadenylylsulfate phagophore assembly site proliferating cell nuclear antigen polymerase chain reaction propanediol protein disulfide isomerase pyruvate dehydrogenase pleiotropic drug resistance pulsed-field gel electrophoresis phosphoinositide-3 kinase-related kinase pleckstrin homology phytosphingosin Ptdins; phosphatidylinositol protein kinase A protein kinase C Phospholipid polylactic acid preinitiation complex phosphoprotein phosphatase proline-rich domain postreplication repair prevacuolar compartment prevacuolar endosome peroxisomal targeting signals polytrimethylene terephthalate qualified presumption of safety ribosome-associated complex repressor-activator protein RNA export factor-binding protein regulator of nucleolar silencing and telophase exit replication factor C regulators of G-protein signaling ribonucleic acid ribonucleic acid (continued) j Appendix D: Selected Abbreviations 432 Table D.1 RNP ROS RP RPA RRM rRNA RSC SAC SAM SBF SCB SCF SCP SFF SIR SIT SNARE snoRNA snRNA SPB SOD SPB SPC SRP STRE STY SUMO TAF TBP TCR TGN THF THO TIM TLS TOM TOR TM Tn TPR TRAPP TREX TRITC tRNA TTP Ty UAS UBA UBP UDP UIM ULP UMP UPR UPS UTP VLP WGD WHO YAC YGSC YFP (Continued) ribonucleoprotein reactive oxygen species ribosomal protein replication protein A RNA recognition motif ribosomal ribonucleic acid remodels structure of chromatin spindle assembly checkpoint S-adenosylmethionine SCB-binding factor Swi4/6-dependent cell cycle box scaffold–cullin–F-box single cell production Swi factor silent information regulator siderophore-iron transporters soluble NSF attachment protein receptor small nucleolar RNA small nuclear RNA spindle pole body superoxide dismutase spindle pole body signal peptidase complex signal recognition particle stress-responsive element space-time yield small ubiquitin-like modifier transcription activating factor TATA-box binding factor transcription-coupled repair trans-Golgi network tetrahydrofolate THO/TREX complex translocase of the inner mitochondrial membrane translesion synthesis pathway translocase of the outer mitochondrial membrane target of rapamycin trans-membrane transposon tetratricopeptide repeat transport protein particles transcription export complex tetramethylrhodamine isothiocyanate transfer ribonucleic acid thymidine triphosphate yeast transposon upstream activating sequence ubiquitin associated domain ubiquitin-specific protease uridine diphosphate ubiquitin interacting motif ubiquitin-like protein uridine monophosphate unfolded protein response ubiquitin-proteasome system uridine triphosphate virus-like particle whole-genome duplication World Health Organization yeast artificial chromosome Yeast Genetic Stock Center Yellow Fluorescent Protein j433 Index a a-synuclein 363 AAA protease 308 AAA protein 138f AAAỵ protein 133ff ABC protein 133, 295 ABC transporter 296f., 401 N-acetyl-galactosamine (GalNAc) 32 N-acetyl-glucosamine (GlcNAc) 32 N-acetyl-mannosamine (ManNAc) 32 acidic domain 11, 28, 291 actin – actin cable 9f – actin cortical patch 12 – actin cytoskeleton polarization 286 – actin filament 10 – – assembly 10 – – bundle 10 – – disassembly 11 – actin patch 10f – actin ring 12 – actin skeleton – actin structure – actomyosin 12 – cortical actin 11 – transport actin-related protein 84 active transport 8, 226f adaptation to anoxic condition 401 adaptor hypothesis 103 S-adenosylmethionine (SAM, AdoMet, activated methionine) 53 adenylate cyclase 273 ADP ribosylation factor (ARF) 134 affinity purification 70 affinity tag 70 agglutination – a-agglutinin 365 age-related disease 183, 344 aging 183, 286, 344 alanine 46 allantoate 30, 49, 234 allantoin 49 Alzheimer’s disease 343, 363 AmiGO 330 amino acid – amino acid biosynthesis 43f – amino acid control 290 – amino acid methylation 47 – amino acid transport 234 – aminoacyl-tRNA 109 – aminoacyl-tRNA synthetase 109 – aminoacylation 109 – aminoacylation test 104 – aromatic amino acid 46 – branched amino acid 45 amino sugar 31 g-aminobutyric acid (GABA) 43 d-aminolevulinate 234 ammonium 42 – ammonium transport 233f amylolytic enzyme 365 anabolic pathway 25 anaphase 198 – anaphase promoting complex (APC) 196 aneuploid 409 anion transport 232f antibody – display 365 – fragment 362 anticodon-sparing principle 111 antioxidant 133, 185, 231, 294, 349ff antiport 226 antisense transcription 201 antistress chaperone 132 AP-1 transcription factor 295 apo-cytochrome 56, 123, 236ff., 302, 395 apoptosis 184ff., 344 – apoptotic chromatin condensation 255 aquaporin 226 arbutin 376 archaea 44, 94, 108ff., 162ff., 265ff Arf family 134 arginine 43, 293 – arginine boxes 293f – arginine metabolism 293 arming yeast 364ff Arp complex – Arp2/3 complex 10 ARS-binding factor 86 artemisinin 354 artificial chromosome 65 Arxula adeninivorans 349, 373ff ascus 2, 181 – ascospore 35, 175ff., 202, 409f Ashbya gossypii 377 aspartate 44 – aspartate family 44 Aspergillus 8, 182, 356, 365 assembly of Tel, Rvb and Atm-like kinase complex (ASTRA) 169f astaxanthin 353f ATG, see auto – Atg1 complex 217 Yeast: Molecular and Cell Biology, Second Edition Edited by Horst Feldmann # 2012 Wiley-VCH Verlag GmbH & Co KGaA Published 2012 by Wiley-VCH Verlag GmbH & Co KGaA ATP – ATP synthase 239 – – F0F1-ATP synthase complex 309 – – F1F0-ATP synthase 239 – ATP-dependent permease 226 – ATP-dependent serine protease 308 – ATPase 127ff., 226 – – ATP-dependent Hỵ-ATPase 127 F-ATPase 239 Hỵ-ATPase 127ff., 226ff – – P-type ATPase 127, 226 – – regulatory ATPase 138 – – V-ATPase 227 – – V-type ATPase 127 – ATPase activity 83ff., 129ff., 195, 210, 220 – ATPase domain 128ff – ATP-binding protein 127 – F1F0-ATP synthase 239 Aurora kinase complex 196 auto – autolysed yeast 352 – autonomous replication origin (ARS) 85 – autophagy 216ff., 286 – autophagy-related genes (ATG) 218, 286 – autophosphorylation 94, 280ff – autoubiquitination 146 axial budding 175 b b-barrel pathway 308 B-type cyclin (CLB) 190 baker’s yeast 349 BAR (Bin/Amphiphysin/Rvs domain)protein 218 base excision repair (BER) 261 basic leucine zipper (bZIP) domain 295 bio– biobutanol 357 – biodiversity 347ff – bioeconomy 348 – bioethanol 357f – biofuel 357 – bioinformatics 348 – biological diversity 388 – bioluminescence 62 – biomass 29, 327ff., 352ff – biomedical research 362 – biopharmaceuticals 359, 421 – biorefinery 352 – biotechnology 313, 347ff – biotin 53, 355 j Index 434 bi– biparental 301 – bipolar 175 – bipolar budding 137, 175 – bipolar spindle 196 Blastobotrys (Arxula) adeninivorans 381 blue biotechnology 347 borealin 196 boundary 91f box C/D snoRNA 114 box H/ACA snoRNA 115 branch point 117 branching enzyme 30 brewer’s yeast 349 bromodomain 78ff bud 177 – bud neck 10ff., 134, 152, 177ff – bud neck filament 178 – bud scar 6, 128, 175ff – bud site selection 176f – budding 18, 175, 218 – budding vesicle 209 bZIP domain, see basic leucine zipper domain c C-terminal domain (CTD) 77, 246 C-terminal repeat domain (CTD) 192, 261 calcium 227f – calcineurin 160, 227f – calmodulin 12, 227f – calnexin 134 – calponin 11 – transport 227 cAMP (cyclic AMP) 193, 273ff cAMP-dependent protein kinase A (PKA) 273 Candida – albicans 281, 371ff., 384ff., 395ff – boidinii 349, 380f – dubliniensis 372, 384, 396 – glabrata 372ff., 384ff., 395ff – tropicalis 371ff., 389, 396ff cap-binding complex 270 carbamoylphosphate 293 carbohydrate 31ff – biosynthesis 30 – transporter 233 carbon source 28, 280 – nonconventional 29 cargo 209, 311 – cargo receptor 40, 311f – cargo recruitment 219 b-carotene 353f carotenoid 353 caspase 217 catabolism – catabolic pathway 25, 42 – catabolite inactivation 27 – catabolite repression 27, 43, 293, 380, 400 – hexose carbon sources 25 catalase – catalase A 310 – catalase T 310 cation transport 223 CBF3 (subcomplex) 196 CCR4–NOT complex 252 Cct ring complex 129 Cdc fourteen early anaphase release, see FEAR Cdc (cell division cycle) protein 188 Cdc-associated protein 189 CDK, see cyclic, cyclocell – cell aggregation – cell cortex 11, 180 – cell cycle 175ff – cell cycle arrest 93ff., 132, 168, 193, 249, 278ff – cell cycle checkpoint 187ff – cell cycle element 192 – cell cycle phase 59, 190ff., 324 – cell cycle progression 5, 84ff., 136, 152, 188ff., 286 – cell cycle regulation 281 – cell cycle-specific degradation 193 – cell cycle-specific transcription 191 – cell death 183, 228 – – programmed 184 – cell division 9ff., 61, 73, 128ff., 175ff., 186ff – cell envelope – cell growth 175, 286 – cell identity 399 – cell integrity control 279 – cell integrity pathway 7, 34, 275ff – cell morphology 5, 176 – cell motility 179 – cell polarity 134, 175 – cell separation 14, 175, 193 – cell skeleton – cell structure – cell surface 21, 39, 229ff., 362ff – cell surface display 364 – cell transformation 62 – cell wall 7f – cell wall chitin 35 – cell wall glucan 34 – cell wall mannan 34 – cell-cell adhesion cellobiose 28, 376ff cellular dynamics 127ff cellulolytic enzyme 365 central, centro– central plaque 179 – central stalk 120, 239 – centromere (CEN) 85, 257, 385 – centromeric plasmid (YCp) 62 – centrosome 139, 188 ceramide 38 ceramide-specific transfer protein (CERT) 216 channel 226 – nuclear pore as a gated channel 15 chaperone 128ff – chaperonin 132 – chaperonin ring complex (CCT) – chaperoning function 128 chiasmata 200ff chimera 410 chip – ChIP assay 323 – ChIP-chip (chromatin immunoprecipitation followed by DNA microarray analysis) 323f – ChIPOTle (chromatin immunoprecipitation on tiled arrays) 323 – proteome chip 325 chitin 35 chorismate 46 chromatin 73ff., 90, 282 – apoptotic chromatin condensation 255 – chromatin assembly factor (CAF) 90 – chromatin configuration 103 – chromatin immunoprecipitation 323 – chromatin modification 73, 254 – chromatin modifying complex 73 – chromatin remodelling 91, 133, 255 – chromatin remodeling complex 73ff chromosome 17, 73, 200, 317f., 383 – chromosomal passenger complex (CPC) 196 – chromosome end replication 96 – chromosome segregation 198 CIA, see cytocis-Golgi network (CGN) 18 cis-regulatory element 402 citric acid cycle 21, 25ff CKI, see cyclic, cycloclade 371ff clamp-loader 86ff class C core vacuole/endosome tethering complex (CORVET) 213 clathrin-coated vesicle 20, 210ff CLB, see B-type cyclin clone, cloning – clonal reproduction 409 – cloning vehicle 60 cluster homology region (CHR) 318 co-chaperone 128 – cochaperonin 132f coated beads 70, 326, 361 coated vesicle 19, 134, 209f – clathrin-coated vesicle 20, 210 – COPI-coated vesicle 20, 210 – COPII-coated vesicle 19, 210 cobalt 57 cobalamin 56 coding region 192, 253ff., 317ff codon 319 – codon adaptation index (CAI) 320ff – codon recognition 111 – codon usage 322 – codon-anticodon interaction 320 coenzyme – coenzyme A (CoA) 55 – coenzyme Q (ubiquinone) 56 cofactor 53 – transport 234 cofilin 11 cohesin 194 cohesion 193 coiled-coil 10ff., 194, 210f – - coiled-coil domain 10, 120, 198 cold-shock 132 colony hybridization 59f COMPASS complex 79, 255 condensin 195 j Index 435 conformation – conformational change 128ff., 190, 238f., 247f., 275, 289, 342ff conjugation 181 contractile ring 10 COPI-coated vesicle 20 COPII-coated vesicle 19 COP9 signalosome 146 copia group 99 copper 57, 230 core particle (20 S), see proteasome cortex 177 – cortical actin 11 – cortical patch 10 cosmid, see vector cotranslational translocation, see translocation countercurrent distribution 104 Crabtree effect 27 cross-over 200 Cryptococcus neoformans 393 CTD, see C-terminal repeat domain CTG clade 372 cullin 143ff., 184 cyclic, cyclo– cyclic AMP (cAMP) 193, 273ff – cyclin 189f – cyclin-dependent kinase (CDK) 86, 187ff – CDK inhibitor (CKI) 190 – cyclophilin 129 cysteine 46 cyto– cytochrome 21, 56, 236, 241, 302 – cytochrome b 237 – cytochrome bc1 complex 237 – cytochrome c 236 – cytochrome c1 237 – cytochrome c oxidase (COX) 238, 302 – cytokinesis 175 – cytoplasm – cytoplasm-to-vacuole targeting (Cvt) pathway 37 – cytoplasm-to-vacuole transport (Cvt) pathway 216 – cytoplasmic filament 223 – cytoplasmic heredity 123 – cytoplasmic inheritance 123 – cytoskeleton 8f – cytosol 6ff., 43ff., 114, 127ff., 148, 186ff., 227ff., 271, 311, 357, 398 – cytosolic iron–sulfur protein assembly (CIA) machinery 304 Cvt pathway, see cytod D-loop (displacement loop) 95, 112 DAPI staining data analysis platform 329 daughter cell 10ff., 61, 175ff., 228, 258, 276, 286, 302ff., 335 deacetylation 255 DEAD-box protein 164ff deadenylation 253ff Debaromyces hansenii 378 deletion mutant 68 delta 99ff deoxyribonucleotide 50 destruction box 190ff., 273 desumoylation 151 detoxification 303 deubiquitination – deubiquitination module 77 – deubiquitinating protease 147 DExD/H-box family 164 DEXH-box protein 163 diauxie 27 differentiation 200f., 273, 391, 409 dihydrosphingosin (DHS) 38 dimethyl-allyl-pyrophosphate 40 dimorphic switch 278 diploid, diploidy 2, 175ff., 201, 225, 278, 327ff., 407ff disaccharide 28f disease gene 335ff distiller’s yeast 349 DNA – 2m (2 micron) DNA 121 – DNA binding domain 28, 46ff., 166, 183, 294, 333 – DNA damage 202 – DNA damage checkpoint 93, 203 – DNA damage sensor 94 – DNA damage tolerance 89 – DNA helicase 89, 133, 168ff – DNA plasmid 397 – DNA polymerase 86ff – DNA repair, see also nucleotide excision repair, base excision repair and mismatch repair 259 – DNA repeat 122, 342, 385 – DNA replication 202 – DNA sequencing 60 – DNA synthesis 200 – DNA transaction 168 – DNA-protein interaction 323 – DnaJ-like 129 – mitochondrial DNA 302 – recombinant DNA 60 dolichol 42 – dolichol phosphate mannose synthase 337 dolichyl phosphate (Dol-P) 33 domain – acidic domain 11, 28, 291 – bromo domain 78ff – C-terminal repeat domain 192, 261 – bZIP domain 295 – DNA binding domain 28, 46ff., 166, 183, 294, 333 – FYVE domain 214 – HEAT domain 283 – HECT domain 142 – LIM domain 134 double strand – double-strand break (DSB) 90, 376, 409 – double-strand break repair (DSBR) 76, 94, 172, 194 downstream processing (DSP) 369 drug resistance 401 dye dynactin 13 dynactin complex 13 dynamic transcriptome analysis (DTA) 332 dynamin 20, 218 dynein 13, 139 e E1 ubiquitin activating enzyme 141 E2 ubiquitin conjugating enzyme 141 E3 ubiquitin ligase 142ff early cell cycle box (ECB) 192 EF-hand 135, 228 EGO complex 136f Egypt 1, 349 electron transport chain 236 electroporation 2, 62, 350 elongation 270 – elongation complex 251 elongator complex 77 elongin-cullin-socs (ECS) ligase complex 146 elutriator 59 endo – endocytosis 11, 21, 218 – endonuclease 89ff., 106ff., 123, 127, 223ff., 260ff., 302, 360 – endoplasmic reticulum (ER) 14ff., 33ff., 207ff., 226ff., 298 – – targeting 39 – endosomal sorting complexes required for transport (ESCRT) 219 – – ESCRT-I complex 219 – – ESCRT-II complex 219 – – ESCRT-III complex 220 – endosome 21 – – early endosome 219ff – – late endosome 216ff energy 25, 301 enzyme 365 – enzyme modifying nucleotides in RNA 51 – enzyme production 361 epigenetic information 81, 91, 258 epistasis 332 – epistasis group 93, 145, 170ff ER, see endo ER-associated degradation (ERAD) 214 – pathway 214f Eremothecium (Ashbya) gossypii 377 ergosterol 42 ERK (extracellular signal-regulated kinase), see MAP kinase ESCRT complex, see endo ethanol 29f N-ethylmaleimide-sensitive fusion protein (NSF) 139 euchromatin 92 exo – exocyst complex 221 – exocytosed material 21 – exocytosis 21, 221 – exon 121 – exonuclease 89ff., 170, 223, 261ff., 345 – exosome 223, 266f – exosome-mediated pathway 265 – export complex 223 exportin 221 expression profile 322 j Index 436 external transcribed spacer (ETS) 114 extracellular 63, 227ff., 258, 275, 289, 310, 343, 366ff., 382 extrachromosomal element 121 f F-box protein 144 facilitates chromatin transactions (FACT) 85 FAIRE (formaldehyde-assisted isolation of regulatory elements) 324 farnesene 354 farnesyl-5-pyrophosphate 40 FAT (FRAP, ATM, TTRAP) domain 283 fatty acid 35 – biosynthesis 35 – unsaturated 35 FEAR pathway 17 FEAR (Cdc fourteen early anaphase release) 199 – FEAR network 199 fecosterol 42 feed yeast 351 fermentation 25, 369 – alcoholic 25 ferroxidase 229f Fe/S cluster 236, 304 Fe/S protein 304 filament – filamentation/invasion pathway 278 – filamentous fungi 358, 377ff., 391ff., 411 – filamentous growth 181 – filamentous response element (FRE) 279 fimbrin 11 firing 87ff., 190, 251 fission 186, 301ff – fission yeast 52, 86ff., 187 flavonoid 354 flippase 127, 226 flocculation 7, 182f., 281, 316, 353, 369, 387, 398 – flocculin 365 flow cytometry fluorescence – fluorescence-activated cell-sorting (FACS) flux balance analysis (FBA) 327 fluxome 353, 421 folate 55 food yeast 349 forespore membrane (FSM) 178, 202 formin 10 – actin assembly 10 four phosphate adapter protein (FAPP2) 216 frame – frameshifting 100f – open reading frame (ORF) 100f., 264, 314ff frataxin 305 French press 59 fructose 31 fucose 31 function – functional analysis 69, 322 – functional genomics 322 – molecular evolution of functions 397 fusion – fusion of mitochondria 309, 345 – fusion product 361 – fusion protein 5, 63ff., 100, 114, 139, 218, 251, 324ff., 360ff – membrane fusion 31, 131, 138f., 160, 210f FYVE domain 214 g G-like protein 137 G-protein 136 – G-protein complex 278 – heterotrimeric G-protein 136 – small G-protein 211 G1 cyclin 190 G1 phase 192 G2/M phase 191 GABA, see g-aminobutyric acid gain of function 398 GAL gene 289 – GAL4 system 256 – regulator 28 GAL regulon 400 galactose 27 – catabolism 27 – ‘galactose’ genes 289f – galactose induction 290 – galactose metabolism 289 – galactose transport 290 – galactose utilization 400 – -galactosidase 29, 61ff., 376 gated synchrony system 328 Gateway1 vector 343 GCD (general control derepressed) gene 291 GCN (general control nonderepressible) gene 291 GDI displacement factor (GDF) 212 GDP dissociation inhibitor (GDI) 212 GEF, see guanine nucleotide exchange factor gel – 2D-gel separation 325 – pulsed field gel electrophoresis (PFGE) 17f., 314 gene 103, 315ff., 388ff – diversification of the gene repertoire 389 – gene activation 77ff., 251, 281f., 403 – gene array 386 – gene cluster 412 – gene conversion 99, 121, 170, 271, 302, 399, 409 – gene disruption 2, 156, 241, 314ff – gene duplication 317f., 412 – gene expression 241ff., 322 – gene formation 415ff – Gene Ontology Database 330 – gene organization 315 – gene regulation 273ff – gene replacement 2, 68, 314 – gene repression 281f – gene silencing 399 – generation time – genetic element 385 – genetic engineering 59ff – genetic interaction network 329 – genetic map 315 – genetic redundancy 317 – protein-encoding gene 315 general amino acid control (GAAC) 45ff., 290 general transcription factor (GTF) 246 Genolevures 371ff genome, genomic 73, 313ff., 364, 383 – evolutionary genomics 407ff – genome duplication 318, 372, 413 – genome instability 185, 335, 341ff – genome-wide deletion mutants 68 – genome-wide oscillations 328 – genomic profiling 322 – genomics 313ff – genotype, genotypic 302, 332 – synthetic genome 333 geranyl-5-pyrophosphate 40 geranylgeranyltransferase (GGTase I) 134 GFP, see green fluorescent protein GGA protein 215 GINS complex (named for Go, Ichi, Nii, and San for five, one, two, and three in Japanese) 87 glucose – biosynthesis 30 – glucan 34 – glucan synthase 34 – gluconeogenesis 30 – glucose effect 401 – glucose induction 288 – glucose metabolism 287 – glucose oxidation 25 – glucose regulation 287ff – glucose repression 27 – glucose transport 289 – glucose-regulated gene 257 – yeast b-glucan 352 glutamate 42ff – degradation 42f – glutamate family 44 glutamine 42 glutaredoxin 305 glutathione (GSH) 44, 185, 228ff., 305, 351 glycerol 29 glycerophospholipid 36 glycine 46 glyco – glycogen 30 – glycogen biosynthesis 30 – glycogen metabolism 30 – glycogen mobilization 31 – glycogen synthase 30 – glycogen synthase complex (GS) 30 – glycolipid 36 – glycolysis 25ff., 401ff – glycoprotein 6f., 21, 29ff., 133, 229 – glycosyl-phosphatidyl-inositol (GPI) anchor 39 – – attachment 39 – – biosynthesis 39 – – glycan 40 – – metabolism 40 j Index 437 – – remodeling 40 – – signal sequence 39 – – structure 39 – glycosylation – – N-linked glycosylation 33 – – O-linked glycosylation 33 50 -GMP 351f GNAT (general control nonderepressible 5related acetyltransferase) family 74ff gold biotechnology 348 Golgi apparatus (Golgi complex) 18 Golgi network 215 – cis-Golgi network (CGN) 18 – trans-Golgi network (TGN) 215 GPI (glycosyl-phosphatidyl inositol) 7f., 32ff GPI-inositol deacylase 40 green biotechnology 347 green fluorescent protein (GFP) 5, 62 grey biotechnology 348 group I introns 302 group II introns 302, 396 group-specific antigen (gag) 98ff GTF, see general transcription factor GTP – GTPase – – Rho-type GTPase 177 – – small GTPase 133, 177, 211 – GTPase-activating protein (GAP) 9, 134ff – GTPase-binding protein 127 guanine nucleotide exchange factor (GEF) 270 guide RNA 114 gypsy group 99 h Hỵ-ATPase, see ATP Hỵ-transporting ATPase 127 hairpin structure 265, 342 half-bridge 179 Hansenula polymorpha 349, 371f haploid, haploidy 2, 137, 175ff., 200ff., 275ff., 301f., 348 HAST (Hda1p-affected subtelomeric) domain 92 heat – heat-shock condition 332 – heat-shock element (HSE) 294 – heat-shock factor (HSF) 294 – heat-shock gene promoter 257 – heat-shock protein (HSP) 128ff., 294 – HSP10 133 – HSP26 132 – HSP30 133 – HSP31/32/33 133 – Hsp40 129 – – HSP42 132 – HSP60 family 132 – – Hsp60p 132 – HSP70 family 128ff – HSP90 family 129 – HSP104 132 – HSP150 133 HEAT (huntingtin, elongation factor 3, regulatory subunit A of PP2A, TOR1) domain 283 heavy metal 44f., 127, 226ff HECT domain 142 HECT ubiquitin ligase 145 HECT-type ligase 142 helicase 159ff – DNA helicase 89, 133, 168ff – helicase A 89 – helicase motifs 159, 171 – helicase superfamily 83 – RNA helicase 118, 133, 166 helix-extension-helix motif (HEH) 137 helix-loop-helix protein 85, 182, 257 helix-turn-helix domain 294 helix–turn–helix transcription factor 189 heme 55f Hemiascomycetes, hemiascomycetous 371ff hetereo– heterochromatin 399 – heterothallic 2, 374ff – heterotrimeric G-protein 136 – heterozygous, heterozygosity 2, 345, 410f – – loss of heterozygosity (LOH) 410 hexose 31 hexose carbon sources 25 – catabolism 25 high– high osmolarity 161 – high osmolarity growth (HOG) 280 – high osmolarity pathway (HOG pathway) 275ff – high-throughput analysis 347, 398 histidine 47 histidine kinase domain 280 histone 6, 73 – histone 2A (H2A) 6, 73ff., 241, 317 – histone 2A.Z (H2A.Z) 73ff., 84ff – histone 2B (H2B) 144, 317 – histone (H3) 144, 317 – histone (H4) 6, 73ff., 243, 317 – histone acetylation 74 – histone acetyltransferase (HAT) 74ff – histone code 81 – histone deacetylase (HDAC) 78f – histone deacetylation 255 – histone demethylation 79 – histone genes 83, 241, 318 – histone interacting protein 78 – histone methylation 79 – histone methyltransferase (HMT) 79f – histone modification 73ff – histone phosphorylation 81 – histone sumoylation 80 – histone ubiquitinylation 79 – histone variant 73ff., 84ff HOG, see high holliday junction (HJ) 95, 140, 165, 200 homeostasis 283 homing 127, 271 – homing endonuclease 276, 302, 399, 410 homo – homogenizer 59 – – glass bead homogenization 59 – homolog 319, 335 – homologous recombination (HR) 95 – homothallic 275f., 375ff – homozygous, homozygosity 178, 409ff HOPS complex 213f horizontal gene transfer 416 horizontal transfer 398 HSP, see heat humanized yeast system 344, 362f Huntington’s disease 342, 363 hybridization experiment 68 hydrocortisone 355 hydrogen peroxide 22, 132, 184f., 229, 255, 295f., 303ff hydrophilicity 219, 295 hydrophobic sorting signal (HSS) 308 hydrophobicity 134 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) 40 hypertension 137, 336ff hyperosmotic 38, 162, 280f., 296, 378 hyphae 5, 181, 377 i ICAT (isotope-coded affinity tags) 70 ICPL (isotope-coded protein labels) 70 imitation switch (ISWI) 83ff – ISW1 83, 258 – ISW2 84 – ISWI-type ATPase 84 immunosuppressant 158, 283 50 -IMP 352 importin 221 importomer 311 inbreeding 409 initiation – initiation of replication 85 – initiation of transcription 244ff – initiation of translation 269f – translational initiation factor (eIF) 269 inner mitochondrial membrane (MIM), see mitochondrium, mitochondrial inner plaque 179 INO80 84 inositol 32 – inositol-phosphates 32ff – inositolphosphoceramide (IPC) 32ff insulin 359 integrase (int) 98 intein 271 inter– interaction – – DNA-protein interaction 323 – – interaction network 109 – – host-retroelement interaction 102 – – protein-protein interaction 65, 325 – – receptor interaction 65 – – RNA-protein interaction 66, 97, 109, 167 – intermembrane AAA protease (iAAA) 309 – internal A and B promoter boxes 98 – internal transcribed spacer (ITS) 114 – interphase 14, 136, 175, 187 – interspecies 331, 407ff – intervening sequence 106 intra– intracellular 5, 150, 193, 226f – intracellular circuit 141 j Index 438 – intracellular protein sorting 207 – intracellular target 151 – intracellular traffic(king) 134, 208 – intracellular transport 13ff., 97 – intramembrane space (IMS) 306 – intraspecies 407 introgression 415 intron 117ff., 316, 393 – intron excision 108 – intron-exon boundary 167 – protein intron 271 invagination 8, 21, 218ff invasive growth 182f – invasive growth pathway 183, 278 invertase 6ff., 26ff., 63, 182, 215, 317 ion transporter 226ff iron 57, 229 – iron homeostasis 304, 345 – iron transport 227ff., 323 – iron-responsive elements (IRES) 265 – iron-sulfur cluster 304 – iron-sulfur protein 304 ISC (iron–sulfur cluster) assembly machinery 304 ISC (iron–sulfur cluster) export machinery 304 isoacceptor 319 isogamous 409 isoleucine 45 isopentenyl-pyrophosphate 40 isopeptidase 147ff isoprenoid 40, 353 – isoprenoid biosynthesis 40 isoprenyl side chain 134 ISWI, see imitation switch iTRAQ (amine-reactive isobaric tagging reagents) 71 k kanamycin 61ff karyo – electrophoretic karyotypeing 314 – karyogamy 181 – karyopherin 37, 137, 221ff., 340 – karyotyping 17, 65 katanin 139 killer plasmid 121 kinase 2, 10, 44ff., 154ff., 335ff – Aurora kinase complex 196 – cAMP-dependent protein kinase A (PKA) 273 – Casein kinase I family 156 – Casein kinase II family 156 – cyclin-dependent kinase (CDK) 86, 187ff – dolichol kinase 33 – kinase domain 158, 280ff., 291 – MAP (mitogen-activated protein) kinase (MAPK) 275 – MAP kinase kinase (MAPKK or MEK) 275 – MAP kinase kinase kinase (MAPKKK or MEKK) 275 – p21-activated protein kinase (PAK) 276 – phosphatidyl inositol (PI) kinase 37 – phosphatidyl inositol-4-kinase 13 – phosphoinositide-3 kinase related kinase (PIKK) 170 – polo-like kinase 200ff – protein kinase 153ff – protein kinase A (PKA) 153, 273 – protein kinase C (PKC) 34, 134f., 154, 177 – tyrosine kinase 198, 280 kinesin 13 kinesin-related protein 13 kinetochore 196f kleisin 194 Kluyveromyces 349 – lactis 349, 371ff., 383ff., 393ff – marxianus 374ff., 385, 396f – thermotolerans 372ff., 384ff., 396ff – waltii 375ff., 396f Komagataella (Pichia) pastoris 380 l Lachancea (Saccharomyces) kluyveri 375 lactic acid 356 lactic yeast 349 lactose utilization 400 lagging strand 89 lanosterol 41 lariat 117ff leading strand 89 lectin leucine 45 licensing 76, 86, 140 life cycle lifespan 93, 183f., 286 – chronological 183 – replicative 183 light microscopy LIM domain 134 lineage 372, 383ff., 389ff., 411ff lipase 365 lipid 35 – biosynthesis 35 – lipid rafts 21 – lipid-linked oligosaccharide (LLO) 33 – lipid-related disease 364 – metabolism 35 liquid culture 59 loading factor 86 long-chain base (LCB) 39 longevity 184 loss of function 398 loss of heterozygosity (LOH) 410 luciferase 61 lumen, luminal 18, 33ff., 202, 215ff., 228 – ER lumen 33ff., 129ff., 157, 208ff – lumenal side 311 – peroxisomal lumen 311 lycopene 354 lysine 46 lysosome 18ff., 207ff., 381 m Mad complex 198 MADS box 192 MADS-box family 293 MALDI-mass fingerprinting maltase 26ff manganese 57, 232 325 mannan 35 mannan oligosaccharide (MOS) 352 mannoprotein 6f., 318 mannose 31f MAP (microtubule-associated protein), see microMAP (mitogen-activated protein) kinase (MAPK) 275 MAP kinase kinase (MAPKK or MEK) 275 MAP kinase kinase kinase (MAPKKK or MEKK) 275 MAP kinase pathway 281 MAP kinase phosphatase (MKP) 161, 279 mapping – genetic 315 MARS (multiaminoacyl-tRNAsynthetase), see tRNA mass spectrometric analysis (MS) 68ff., 325 mating 175 – mating pheromone 21, 34, 59, 136, 147ff., 181ff., 227, 277 – mating pheromone G-protein 136 – mating type 399 – mating type cassette 276ff – mating-type pathway 275 – mating-type switch 13, 81ff., 166ff., 182, 276f., 376, 395, 409 matrix – matrix AAA protease (m-AAA) 308 – matrix processing peptidase (MPP) 307 maturase 123, 302 maturation promoting factor (MPF) 187 MCB (MluI cell cycle box) 192, 253 – motif 190 MCB-binding factor (MBF) 190ff MCE (Mcm1 cell cycle element) 192 MCM, see minichromosome maintenance complex media formulation 368 mediator 249f – Mediator complex 28, 75f., 246ff., 290 megasatellite 386 meiosis 200f – checkpoint 202 – meiosis I 200 – meiosis II 200 – regulation 201 MEK (MAP/ERK kinase), see MAP kinase kinase MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) 345 membrane – membrane curvature 218 – membrane fusion 210 – membrane fusion protein 139 – membrane potential 228, 238, 307 – membrane sorting pathway 307 – membrane transporter 226 – – endosomal membrane 37, 127, 219ff – – mitochondrial membrane 21, 235ff., 306ff – – nuclear membrane 14ff., 102, 131, 179f – – peroxisomal membrane 309ff – – plasma membrane 6ff j Index 439 – – transmembrane domain 21, 28, 39ff., 208ff., 229f – membrane vesicle 202 – membrane-bound 34ff., 134ff., 212ff., 273ff., 297 MEN, see mitosis, mitotic MERFF (myoclonus epilepsy, ragged red fibers) 346 messenger RNA, see mRNA metabolism – metabolic cycle 328 – metabolic engineering 352 – metabolic flux 327 – metabolic pathway 25 – metabolite transporter 235 – metabolome 330, 353, 421 metallo– metalloenzyme 32, 226, 269 – metallopeptidase 308 – metalloreductase 229 – metallothionein 231 metaphase 146, 161, 175ff., 187ff., 198ff methanol-utilizing yeast 380 methionine 44f – activated, see S-Adenosylmethionine – methionine biosynthetic pathway 44 – methionine salvage pathway 45 – methionine-specific tRNA 112 methyl group – activated 53 mevalonate-5-pyrophosphate 40 MIA pathway 306f micro– micro-array 67, 322 – microautophagy 136, 217, 381 – microfilament – microorganisms in biotechnology 348 – microtubule – microtubule attachment 85 – microtubule organization 179 – microtubule organizing center (MTOC) 9, 179 – microtubule-associated protein (MAP) 180, 344 middle sporulation gene 202 minichromosome maintenance (MCM) complex 86 mismatch repair (MMR) 261 mitochondrium, mitochondrial 21f., 301ff – mitochondrial aminoacyl-tRNA ligase 110f – mitochondrial disease 344f., 363 – mitochondrial DNA 302, 395 – mitochondrial fission 309 – mitochondrial fusion 309 – mitochondrial genetics 123 – mitochondrial genome 123, 395 – mitochondrial matrix 21, 25, 132f., 235ff., 304ff – mitochondrial membrane 21, 235ff., 306ff – – inner (MIM) 21, 235ff., 306 – – outer (MOM) 21, 306f – mitochondrial polymerase (polymerase g) 345 – mitochondrial protein 21, 45ff., 235, 301ff – mitochondrial quality control 308f – mitochondrial remodeling 309 – mitochondrial structure 21 – mitochondrial transport 235 – mitochondrial tRNA gene 346 – nuclear mitochondrial DNA sequence (NUMT) 418 mitogen-activated protein (MAP) kinase, see MAP kinase mitosis, mitotic 191ff – mitotic apparatus 94 – mitotic exit network (MEN) 199 – mitotic spindle 13, 180 MMR, see mismatch repair MluI cell cycle box, see MCB mobile element 302, 395f modified nucleoside 105 molecular signaling cascade 273ff molecular technique 59ff monitoring technique – non invasive 366 monopolin 202 monoterpenoid 354 monoubiquitination 311 morphogenesis 34, 139, 178f., 273ff mother cell 2, 13, 93, 121, 140, 175ff., 202, 276, 286, 311, 378, 409ff motor protein 11 mRNA 116f., 263 – cap-binding complex 270 – mRNA decay 265 – – nonsense-mediated mRNA decay (NMD) 265ff – mRNA localization machinery 13 – mRNA precursor 117 – mRNA processing 117 – mRNA splicing 17, 188, 298 – mRNA retention 223 – nuclear export 225 – nuclear mRNA quality control 223 – transport 77 MRP snoRNA 115 MRX complex 94, 170 mucin 278ff multicopy plasmid 62 multivesicular body (MVB) 218 – sorting pathway 218 mutagenesis 90, 117, 352, 374 mycose myosin 12 – type I 12 – type II 12 – type V 12 MYST (MOZ, YBF2/SAS3, SAS2, and TIP60) family 76 n N-acetyl-galactosamine (GalNAc) 32 N-acetyl-glucosamine (GlcNAc) 32 N-acetyl-mannosamine (ManNAc) 32 N-end rule pathway 147 N-ethylmaleimide-sensitive fusion protein (NSF) 139 N-glycosylation 33 NAC (nascent-polypeptide associated complex) 129 NAD, see nicotinamide adenine dinucleotide NEDDylation 146 NER, see nucleotide neuro– neurodegenerative disorder 341f., 363 – neurological disorder 342 NHEJ, see non-homologous end joining nicotinamide adenine dinucleotide (NAD) 54 nicotinic acid 54, 375, 398 nine-teen complex (NTC) 119 nitrate 44 nitrogen – inorganic and organic sources 42 – nitrogen catabolite repression (NCR) 43ff., 293 – nitrogen metabolism 42 – nitrogen starvation 30, 132ff., 178, 201, 274 NMD, see mRNA non-crossover 95, 166ff non-hexose carbon source 28 non-homologous end joining (NHEJ) 94 noncoding RNA 392 nonessential gene 341 nonsense – nonsense codon 268 – nonsense mutation 122 – nonsense suppression 122 nontranscribed spacer (NTS) 114 NSF, see N-ethylmaleimide-sensitive fusion protein nuclear, nucleus – nuclear division 200 – nuclear envelope 14ff., 38ff., 179ff – nuclear export 14, 221ff – nuclear export factor (NXF) 224 – nuclear export sequence (NES) 223, 286 – nuclear fusion 9ff., 181, 278 – nuclear import 14, 221 – nuclear localization signal (NLS) 221 – nuclear membrane 14ff., 102, 131, 179f – nuclear mitochondrial DNA sequence (NUMT) 418 – nuclear mRNA quality control 223 – nuclear pore 14f – – biogenesis 16 – nuclear pore complex (NPC) 14 – – outer core complex 16 – nuclear structure 14 – nuclear traffic 221 – nuclear transport 221 – nucleolar organizing region (NOR) 17 – nucleolus 14 – nucleoporin (Nup) 16 nucleation center 10 nucleoside – modified 105 nucleosome, nucleosomal 73, 90 – nucleosomal organization 259 – nucleosome occupancy 258 – nucleosome positioning 259, 403 – nucleosome remodelling 83f., 258 – nucleosome structure 73, 81 j Index 440 – nucleosome-free region (NFR) 403 – nucleosome-remodeling complex (RSC) 195 nucleotide – nucleotide excision repair (NER) 259f – nucleotide metabolism 48 – nucleotide modification 50 – nucleotide-binding domain (NBD) 297 – transport of nucleotide constituent/ nucleotide sugar 234 nucleus, see nuclear, nucleus NURF (nucleosome remodeling factor) 84 nutrients 30, 283 – gene regulation 283 – nutritional condition 203 – transporter for nutrient molecules 233 o O-glycosylation 33 OBO-Edit 330 ohnolog(ue) 413 Okazaki fragment 89 oligomeric Golgi complex (COG) 210 oligomycin sensitivity-conferring protein (OSCP) 239 oligosaccharide – extension 34 – trimming 34 oligosaccharyltransferase (OST) complex 34 one-hybrid system 67 open reading frame (ORF) 100f., 264, 314ff ORC, see origin of replication organelle, organellar 207 – cylindrical organelle 179 – marker enzyme – organellar biogenesis 301ff – organellar compartment 17 – organellar transport 13 organic acid 356 origin of replication (ORC) 85f., 385 origin recognition complex (ORC) 86 ornithine 43ff., 293 osmo– osmoregulation 21, 29, 226 – osmosensor 278ff – osmotic gradient 280 – osmotic shock 153, 162, 332 – osmotolerant yeast 378 OST complex, see oligosaccharyltransferase (OST) complex outer mitochondrial membrane (MOM), see mitochondrium, mitochondrial outer plaque 179 overlay test 67 oxidative stress 295 oxygen 22, 25ff., 43, 56, 184f., 229ff., 273ff., 303f., 357 oxysterol-binding protein (OSBP) 216 p p21-activated protein kinase (PAK) 276 p97/VCP (valosin-containing protein) 139 pachytene 200ff – pachytene checkpoint 203 PAF complex 252 PAM complex 307 pantothenic acid 55 paralog(ue) 398, 414 paraplegin 309 Parkinson’s disease 343, 363 PAS, see phagophore assembly site or prePAS domain 157 Pasteur 1, 27, 348 Pasteur effect 27 pathway – loss and relocalization 398 paxillin 134 PCNA, see proliferating cell nuclear antigen PCNA-like clamp 93 PCR technique 68 PDR 296 PDRE element 150 pentose phosphate cycle 25 pentose sugar 29 perinuclear 151, 224 periplasm 7, 52, 221, 354 periplasmic space 6ff permeability transition pore (PTP) 185 permease 28, 49ff., 136, 182, 226ff., 284 – ATP-dependent permease 226 peroxin 310 peroxisome 22, 309ff – peroxisomal disease 381 – peroxisomal targeting signal (PTS) 311 petite colonies 301, 345 Pex protein 310 PFGE, see pulsed field gel electrophoresis PH domain, see pleckstrin homology domain phagophore assembly site (PAS) 216 phenotype, phenotypic 332 phenylalanine 46 pheromone signalling 136 PHO System 256 phosph– phosphatase 153ff – phosphate metabolism 51 – phosphate transport 232 – phosphatidyl inositol (PI or PtdIns) 36 – phosphatidyl inositol (PI) kinase 37 – phosphatidyl inositol phosphate (PIP) 36f – phosphatidyl inositol phosphate (PIP) phosphatase 38 – phosphatidyl inositol-3,5-bisphosphate (PI(3,5)P2) 37 – phosphatidyl inositol-4,5-biphosphate (PI(4,5)P2) 37 – phosphatidyl inositol-4-kinase 13 – phosphatidyl inositol-3-phosphate (PI(3)P) 37 – phosphatidyl inositol-4-phosphate (PI(4)P) 37 – 3-phosphoadenylylsulfate (PAPS) 53 – phosphoinositide phosphatase 159ff – phosphoinositide-3 kinase related kinase (PIKK) 170 – phospholipid 8, 39, 51, 127, 214ff., 228, 275ff., 311 – phosphoprotein phosphatase (PPP) 168ff phylogeny, phylogenetic 408 – phylogenetic relationship 407 – phylogenetic tree 138, 229, 382, 401 phytosphingosin (PHS) 39, 184 Pichia – guilliermondi 372 – methanolica 349, 381 – pastoris 309, 372ff., 383f., 391ff – sorbitophila 372ff., 387ff – stipitis 349, 372ff., 384ff., 396ff PIN domain 115, 223f plasma membrane plasma membrane Ca2ỵ-ATPase (PMCA) 228 plasmid 397 – autonomously replicating plasmid (YRp) 62 – centromeric plasmid (YCp) 62 – episomal plasmid (YEp) 62 – integrative plasmid (YIp) 62 – killer plasmid 121 pleckstrin homology (PH) domain 37 pleiotropic drug resistance (PDR) 130, 296, 401 polarisome 177 polarized cell growth 176 polarized growth 10ff., 134, 202, 228, 274 polo-like kinase 200ff poly– poly(A) RNA-binding protein 224 – polyadenylation 117, 261f – polyketides 355 – polymerase, see DNA and RNA – – mitochondrial DNA polymerase (polymerase g) 345 – polymorphism 122, 137, 315, 330f., 347, 382, 392 – polypeptide synthesis 270 – polyphosphate 6, 21, 52 – polyubiquitination 311 population 407 – asymmetrical growth of clonal population 411 porphobilinogen 56, 234 post-replication repair (PRR) 89 post-translational processing 63 post-transcriptional regulation 404 post-translational translocation 208 PP1- type phosphatase 158ff PP2A-type phosphatase 160 PP2B-type phosphatase 158ff PP2C (PPM family type 2C protein phosphatase) 161 pre– 90 S preribosome complex 115, 167 – pre-40S 115 – pre-60S ribosomal particle 116 – pre-initiation complex (PRC) 86 – pre-mRNA – – mRNA splicing 17, 188, 298 – – processing 117, 261ff – – retention 223 – pre-vacuolar compartment (PVC) 21, 150, 216ff – pre-vacuolar endosome (PVE) 21, 221 – preautophagosomal structure (PAS) 216 – preprotein 131, 271, 306ff – preprotein sorting 307 j Index 441 – prereplication (prereplicative) complex (pre-RC or PRC) 86, 140, 404 – prespore 202 prefoldin 129 prenylation 134f presequence pathway 306f primer 89 primordial exons 121 prion 121f probiotic – probiotic yeast 351 – probiotics 351 process design 366 process development 367 processome complex 115, 167 production process 368 profiling 10 prohibitin 132 proliferating cell nuclear antigen (PCNA) 87ff proline 43f proline-rich domain (PRD) 221 promoter 28ff., 43ff., 62ff., 76ff., 91ff., 150, 190ff., 231, 241ff., 250ff., 294ff., 315, 402ff – heat-shock gene promoter 257 propanediol (1,3-propanediol) 357 prophase 175, 187, 201ff prosome 147 prospore 202 protease – ATP-dependent 138 proteasome 147ff – 19 S (regulatory particle) 148 – 20 S (core particle) proteasome 148 – 26 S proteasome 148 – regulation of yeast proteasome activity 148 protein, proteo– diversification of the protein repertoire 388 – DNA-protein interaction 323 – protein acetylation 55, 63ff., 324 – protein analysis 324 – protein complex 325 – protein degradation 141 – – programmed 141 – protein disulfide isomerase (PDI) 129 – protein folding 18, 128ff., 298 – protein import 311 – protein intron 271 – protein kinase 153ff – protein kinase A (PKA) 153, 273 – protein kinase C (PKC) 34, 134f., 154, 177 – protein methylation 47ff., 63, 79ff – protein modification 62, 141 – – post-translational 62 – protein N-glycosylation 33 – protein O-glycosylation 34 – protein precursor 100, 208 – protein quality control 20 – protein secretion 62 – protein serine/threonine phosphatase 160 – protein sorting 207f – protein splicing 271 – protein trafficking 208 – protein transport 305 – protein ubiquitination 69, 77ff., 142ff., 193, 251 – protein-conducting channel 207, 307 – protein–protein interaction 65, 325 – proteinopathies 342ff – proteoglycan 18ff – proteolysis 193 – proteome 324, 398 – proteome chip 325 – proteomics 68 proton – ATP-dependent proton pump 226 – proton gradient 238 – proton gradient ATPase 227 – proton pumping 226f – proton-motive force 239 protoplast 7, 381 pseudogene 316, 387 pseudohyphae 278 – pseudohyphal growth 182f., 278 pseudoknot 115, 302 P-type ATPase, see ATPase PTP (protein phosphotyrosine phosphatase) family 159ff pulsed field gel electrophoresis (PFGE) 17f., 314 purine 48 – degradation 49 – purine ring 48 pyridoxine 54 pyrimidine 48 – pyrimidine ring 49ff PVC, see prePVE, see preq quality control – mitochondrial quality control 308f – nuclear mRNA quality control 223 – protein 20 r Rab family 134, 212 RAC (ribosome-associated complex) 129 RAD (radiation sensitive) protein 97 – RAD epistasis group 170 – Rad51 filament 95 Rap, see repressor rapamycin 158ff., 279ff Ras – RAS superfamily 133f – Ras-cAMP signaling pathway 273 – ras-related nuclear protein (Ran) 136 – Ran GTPAse 136 reactive oxygen species (ROS) 185, 295 – detoxification 303 recombination 203 – Rec8p (recombination) 202 – recombinant antibody 362 – recombinant DNA 60 – recombinant DNA technology 8, 29, 59ff., 348ff – recombinant production 358 – recombinase 95 – whole recombinant yeast cell 362 red biotechnology 347 red fluorescent protein (RFP) 64 reducing equivalent 50 regulat– regulation 251 – regulator of nucleolar silencing and telophase exit (RENT) 93 – regulatory network 400 – regulatory particle (19 S) 148f remodels structure of chromatin (RSC) complex 81ff RENT, see regulatrepair – DNA repair 259ff – postreplication 89 repetitive DNA 98, 342, 385 replica plating 64 replication, replicative 85ff., 202 – checkpoint 93 – chromosome end 96 – DNA replication protein 140 – replication factor 89 – replication factor C (RFC) 86f – – RFC1 89 – replication fork 88 – replication factories (machinery) 86ff – replication origin (ORC) 85f., 385 – replication protein A (RPA) 89 – replicative DNA helicase complex 140, 169 – replicative lifespan 183 repressor 253, 281 – repressor protein 192 – repressor-activator protein (RAP) 283 respiration, respiratory 25f – respiratory (electron transport) chain 26, 236 – respiratory competence 2, 308f – respiratory complex 237, 396 – respiratory complex II 236 – respiratory complex III 236 – respiratory complex IV 236 – respiratory deficiency 123, 301ff – respiratory quotient 238 restriction 59 – restriction enzyme 60 resveratrol 355 retention 12, 223, 234, 279, 342, 379 reticulum-associated degradation, see ERassociated degradation retrieval 210, 221 retro– class I retroposon 414 – class II retroposon 98 – retroelement 98ff – retrogene 414 – retrograde transport 18f., 145ff., 210, 221ff – retromer coat 221 – retrotransposon 98 reverse genetics 59 reverse transcription 101 rhesus factor 237 RGS (regulators of G-protein signaling) family 137 Rho/Rac family 134 riboflavin 54 j Index 442 ribonucleotide diphosphate reductase (RNR) 50 ribosome, ribosomal 113 – 35S rRNA precursor 392 – ribosomal protein (RP) 114 – ribosomal protein gene 113 – ribosomal RNA (rRNA) 392 – ribosomal RNA gene 93, 113 – ribosomal RNA processing 114f – ribosome assembly 113f – ribosome biosynthesis 286 – ribosome maturation 114 – ribosome-associated complex (RAC) 129 ribozyme 302 Rieske iron-sulfur protein 237 RING finger protein 142ff., 166, 215 RING-type ubiquitin ligase 143ff RNA – 5S RNA 392 – 5S RNA gene 392 – enzymes modifying nucleotides 51 – guide RNA 114 – noncoding RNA 392 – RNA export factor-binding protein (REF) 224 – RNA helicase 118, 133, 166 – RNA interference 399 – RNA polymerase 241 ff – – DNA-dependent RNA polymerase 242 – – RNA polymerase I (Pol I) 242 – – RNA polymerase II (Pol II) 245ff – – RNA polymerase III (Pol III) 243 – RNA recognition motif (RRM) 193 – RNA-protein complex 118, 166 rRNA, see ribosome rRNA gene, see ribosome ROS, see reactive oxygen species RSC, see remodels structure of chromatin complex rubylation 146 RuvB-like protein 140 s S phase 200 S-adenosylmethionine (SAM, AdoMet, activated methionine) 53 SAC, see spindle Sac1p (suppressor of actin) 38 Saccharomyces – bayanus 374, 389, 400 – carlsbergensis 349 – castellii 386, 400 – cerevisiae 1, 6, 348, 371ff., 383ff., 391ff – – retrotransposon 98 – exiguus 374, 389ff – kluyveri 372ff – kudriacevii 396 – mikatae 403 – paradoxus 101, 376, 403 – servazii 389 Saccharomycetaceae 372ff., 383ff., 397ff Saccharomycotina 372ff SAGA (Spt–Ada–Gcn5 acetyltransferase) 76, 251 SAM complex 308 scaffold 15ff., 152ff., 178 SCB-binding factor (SBF) 192 SCF protein 143 Scheffersomyces (Pichia) stipitis 379 schizophrenia 137, 339 Schizosaccharomyces pombe 348, 371ff., 385ff., 395ff Schwanniomyces (Debaryomyces) occidentalis 349 secretion – secretory pathway 207 – secretory vesicles 12ff., 134, 207ff., 221 securin 94, 198 segmental duplication 414 segregation 202 – chromosome segregation 198 self-splicing 302 senescence 93ff sensing technique – non invasive 366 separase 194ff separin 194 septin 178 – septin ring 176 – septin–protein interaction 179 septum 7, 35, 160, 175ff sequence – genome sequencing 313 – sequencing 313, 331 – sequencing DNA 60 – – Maxam-Gilbert technique 60 – – Sanger technique 60 – sequencing projects 313, 371ff – sequencing RNA 60, 323 serine 43ff serine/threonine specific phosphatase 158 sexual reproduction 181 SGD 330 shmoo formation 181 shugoshin 202 shuttle vector, see vector siderophore–iron transporter (SIT) 228, 375 sigma 100 signal 150 – glucose-sensing signal transduction pathway 287 – signal hypothesis 207 – signal peptidase complex (SPC) 208 – signal receptor 208 – signal recognition particle (SRP) 207, 243 – signal transduction 2ff., 81, 93f., 136, 152ff., 198, 232, 244, 275ff., 303, 330 – signaling cascade 273ff – signaling network 403 SILAC (stable isotope labeling by amino acids in cell culture) 70 silent information regulator (SIR) 91 SIR complex 91 siroheme 56 sister chromatid 193 SKI complex 265 small ribonuclear-protein complex (snRNP) 118 small ubiquitin-related modifier (SUMO) 151 – SUMO E3 ligase 151 – SUMO-specific E1 activity 151 SMC complex 194 SNAP (synaptosomal-associated protein) 139, 210 SNARE (soluble NSF attachment protein receptor) 210 – SNARE motif 210 – SNAREpin 210 – t-SNARE 210 – v-SNARE 210 snoRNA (small nucleolar RNA) 114f., 392 SOD, see superoxide dismutase soluble NSF attachment protein receptor, see SNARE SPB, see spindle SPC, see signal species – species specific 374ff., 388ff., 403 spheroplast sphingolipid 38 spindle – bipolar spindle 196 – movement 13 – spindle assembly checkpoint (SAC) 196ff – spindle attachment 196 – spindle checkpoint (SCP) 94, 157, 180, 196ff – spindle morphogenesis 180 – spindle pole body (SPB) 14, 179, 280 – spindle pole body duplication 180f – spindle translocation 180 splicing 117 – protein splicing 271 – splice cycle 117ff – spliceosome 118f – – alternative splicing 118, 382, 393ff – – assembly 118 – – cycle 118 – – mRNA splicing 17, 188, 298 – – pre-mRNA splicing 117f., 131, 164ff., 323 – – protein splicing 127, 264ff – – tRNA splicing 106ff spore – spore wall 202 – spore wall assembly pathway 280 – sporulation 202, 280 squalene 40 SRB (suppressors of RNA polymerase B)/ mediator 249 Src-homology-3 (SH3) 273 Ssn6–Tup1 complex 282 – repression 281 stator stalk 239 sterile receptor (Ste2/Ste3) 278 sterol – biosynthesis 40 stilbenoid 354 stop-transfer sequence 307 storage carbohydrate 30 strand – double strand 81, 101, 245 – lagging strand 89 – leading strand 89 – single strand 89ff., 168, 260f – strand exchange 94f., 166ff., 339 – strand segregation 195ff j Index 443 – strand transfer 101 – strand unwinding 87 stress 283, 294 – chemical stress 295 – cold stress 295 – heat stress, see also heat 294 – oxidative stress 295 – stress factor 150 – stress protein 294 – stress response 294, 401 – stress tolerance 43, 294 – stress-responsive element (STRE) 294ff subtelomeric element 96 subtelomeric region 317, 386 succinic acid 357 sugar 29 sulfate – fixation 52 – reduction 52 sulfate assimilation 45ff sulfite reductase 56 sulfur metabolism 52 SUMO, see small ubiquitin-related modifier SUMOylation 151 – histone 80 superoxide dismutase (SOD) 303 superoxide radical 294, 303f suppress– suppression 27, 122, 153, 170, 249, 341 – suppressor 37, 152, 177, 225, 249ff., 275, 342 – suppressor tRNA 65, 320 – tumor suppressor 81ff surviving 413 Swi five factor (SFF) 192 SWI/SNF 81ff Swi4/6-dependent cell cycle box (SCB) 253 SWR1 84 symport 226 synaptojanin-like protein 162 synaptonemal complex 201ff synchronization of growth 59 synteny 383 synthetic biology 332 synthetic genetic array analysis 329 a-synuclein 363 synucleinopathies 343 systems biology 330 systems biotechnology 348 t TAF, see transcription – Taf14p 84, 249 tandem affinity purification (TAP) 325 tandem gene array 387 target of rapamycin, see TOR target site 18f., 46, 81, 101f., 153, 258, 293, 324 target site selection 102 TATA box 241 TATA-box binding protein (TBP) 74, 242ff., 340ff tau 103 tau protein 343 taxol 354 taxonomy 408 TBP (TATA-binding protein), see TATA-box binding protein TCR, see transcription telo– telomerase 96ff – telomere 96f., 257, 385f – telomere length 97f – telomere replication 97 – telomeric repeat 386 – telophase 14, 79, 93, 175, 187, 192ff termination – transcriptional 100, 252 – translational 270 terminator 103, 113, 162, 247, 315f terpene 353 terpenoid 353 tethering complex 210ff tetrad analysis 2, 71 tetrapyrrol derivative 55 tetratricopeptide repeat (TPR) 129, 282 – tetratricopeptide repeat protein 265 TGN, see trans-Golgi network thermoprotection 294 thermotolerant, thermotolerance 132, 153, 376 – thermotolerant yeast 381 thiamine 53 thiol oxidase 133 thioredoxin peroxidase 133 THO complex 224 three-hybrid system 66 threonine 43f TIM (translocase of the inner mitochondrial membrane) 307 – TIM22 307 – TIM23 complex 307 TLC1 (telomerase Component) RNA 97 TOM (translocase of the outer mitochondrial membrane) 306f topogenic signal 207 topoisomerase 95, 151, 194 TOR (target of rapamycin) 283ff – TOR complex 283 – TORC1 complex 284ff – TORC2 complex 284ff toruidal-shaped complex 162 toxin 121, 295ff., 376ff., 397 TRAMP complex 266 trans-Golgi network (TGN) 215 trans-regulating factor 241 trans-regulatory element 402 transamidation 40 transcription 241ff., 261 – general transcription factor (GTF) 246 – regulation 251 – transcription activating factor (TAF) 247ff – transcription elongation 77 – transcription export (TREX) complex 224 – transcription factor 241, 295, 401 – transcription factor TFIIA 247 – transcription factor TFIIB 247 – transcription factor TFIID 247 – transcription factor TFIIE 247 – transcription factor TFIIF 247 – transcription factor TFIIH 247 – – – – – transcription factor TFIIS 247 transcription-coupled repair (TCR) 224 transcriptional activator 248 transcriptional elongation 254 transcriptional initiation 80, 103, 246, 258, 282, 316ff – transcriptional regulation 400 – transcriptional repressor 28, 49, 183ff., 241, 253, 288 transcriptome 322 transfer ribonucleic acid, see tRNA transferring 361 transformation methods 61f transition element 228 transition metal 57 – transport 228 translation 268 – cotranslation 208 – cotranslational translocation 208 – post-translational translocation 208 – translation factor 122, 225, 264 – translation initiation 269 – translation profile 323 – translation termination 267ff – translational control 291 – translational elongation 270 – translational frameshift 100f – translational regulation 238, 290 – translational release 122 – translational start site 270 translesion synthesis pathway (TLS) 90 translocation – cotranslational 208 – translocase of the inner mitochondrial membrane (TIM) 307 – translocase of the outer mitochondrial membrane (TOM) 306f – translocation channel 208 – translocation pathway 208 – – cotranslational 208 – – post-translational 208 translocon 208 transmembrane protein – GPI-anchored 41 transmembrane-spanning (TM) domain 297 transport 207ff – ABC transporter 296f., 401 – actin-based transport – ammonium transport 233f – anion transport 232f – cation transport 226f – ion transporter 226ff – membrane transporter 226 – metabolite transporter 235 – mitochondrial transporter 235 – organellar component 13 – protein transport 305 – retrograde transport 18 – transport of carbohydrate 233 – transport protein particle 211 – transport vesicle 18, 40, 210ff., 228 – transporter for nutrient molecule 233 transposon 98, 395 TRAPP complex 211ff – TRAPP I 211ff – TRAPP II 211ff j Index 444 trehalose 31 TREX (transcription export) complex 224 TRF1 complex 97 TRiC (chaperonin-containing Tcomplex) 129 trigger loop 245 trinucleotide repeats 341 tRNA 103ff., 391 – aminoacylation 109 – isolation 104 – methionine-specific tRNA 112 – mitochondrial tRNA gene 346 – multiaminoacyl-tRNAsynthetase (MARS) 109 – nuclear export of tRNA 225 – tRNA biosynthesis 105 – tRNA gene 106, 257, 319f., 391 – tRNA gene expression 106 – tRNA identity 105 – tRNA maturation 106 – tRNA modification 109ff – tRNA precursor 105f – tRNA processing 105f – tRNA sequence 104 – tRNA slippage 100 – tRNA 3D structure 105 – tRNA transport – – aminoacyl tRNA 109 – – aminoacyl tRNA synthetase 109 tropomyosin 13 tryptophan 46 tubulin – a-tubulin – b-tubulin – g-tubulin twinfilin 158 two– two micron DNA 121 – two-component signal 158 – two-component system 280 – two-gate model 16 – two-hybrid analysis 65, 325 Ty element 98ff – codon usage in Ty ORF 100 – expression 100 – genome 98 – Ty integrase 98 – Ty protease 98 – Ty replication 101 – Ty retrovirus-like particles (VLP) 98 – Ty1 element 99 – Ty2 element 99ff – Ty3 element 100 – Ty4 element 101 – Ty5 element 99ff tyrosine 46 tyrosine kinase 198, 280 u U3 snoRNA 115 UBA domain 153 UBD (ubiquitin domain) 153 ubiquinone (coenzyme Q) 42, 56 ubiquitin 79, 141ff – ubiquitin activating enzyme (E1) 141 – ubiquitin associated domain (UBA) 153 – ubiquitin conjugates 142 – – – – – ubiquitin conjugating enzyme (E2) 141 ubiquitin domain protein 152 ubiquitin interacting motif (UIM) 152 ubiquitin ligase (E3) 142ff ubiquitin-binding zinc finger (UBZ) 90 – ubiquitin-like protein (ULP) 151 – ubiquitin-like protein modifier 151 – ubiquitin-proteasome system (UPS) 141 – ubiquitin-specific protease (UBP) 147 ubiquitinylation 311 – histone 79 UBL domain 153 UBX domain 153 Ubr1p 144 ULP, see ubiquitin unfolded protein response (UPR) 298 – UPR element (UPRE) 298 uniparental 301 uniport 226ff., 319 untranslated open reading frame (uORF) 268, 291 upstream activating sequence (UAS) 28, 65, 77, 192, 254 upstream activation site (UAS) 43 upstream repression site (URS) 43 ureidosuccinate 48f., 234 uroporphyrinogen III 56 v V-type ATPase, see ATPase vacuole, vacuolar 6ff., 18ff – vacuolar ATPase 227 – vacuolar degradation 21 – vacuolar network 216 – vacuolar system 20 – vacuolar transport 234 valine 45 vector – cosmid vector 64 – episomal vector 62 – expression vector 62 – plasmid vector 61 – shuttle vector 61f vegetative growth 175 verprolin 11f vesicle 209 – budding vesicle 209 – coated vesicle 19f., 134, 209ff – vesicle transport 18 vesicle docking 211 virus-like particle (VLP) 98 vitamin 53ff – transport 234 – vitamin B1 53 – vitamin B2 54 – vitamin B6 54 – vitamin B12 55 – vitamin C 354 VPS mutants 216ff w Walker A and B motif 138, 163 WD40 domain 19, 78, 143, 197f white biotechnology 347 whole genome duplication (WGD) 372, 413 318, winged-helix/forkhead (FOX) 189ff wobble rules 320 WW domain 143 x xylose 379 – xylose-utilizing yeast 379 y Y0 element 96 YAC, see yeast Yarrowia lipolytica 228ff., 309, 349, 371ff., 382ff., 393ff yeast – yeast artificial chromosome (YAC) 65 – yeast carbon metabolism 49ff., 153, 379ff – yeast cell 5f – – aggregation – – disruption 59 – – growth 59, 175 – – handling 59 – – isolation of particular cell types and components 59 – – transformation 61 – – whole recombinant yeast cell 362 – yeast cell wall 7, 352 – yeast chromatin 73 – yeast chromosome 17, 73 – yeast cytoplasm – yeast cytoskeleton – yeast genetic structure 73ff – yeast energy production 26 – yeast envelope – yeast extract 351 – yeast interactome 325 – yeast metabolic cycle (YMC) 328 – yeast metabolic network 327 – yeast metabolism 25ff – yeast molecular technique 59ff – yeast nitrogen metabolism 42ff – yeast nucleolus 17 – yeast nucleus 14 – yeast one-hybrid system 67 – yeast organelle – yeast ribosome 113 – yeast synthetic biology 332 – yeast systems biology 330 – yeast three-hybrid system 66 – yeast two-hybrid system 65, 325 – yeast vacuole 20 – yeast vector 61 yeast triple A protein, see AAA protein yellow biotechnology 348 z zinc 57, 231 zinc-finger 45ff., 80, 90, 118, 129, 149, 166, 177, 195, 220ff., 231, 244ff., 275, 288, 295ff Zygosaccharomyces – – bailii 349 – – rouxii 349, 372ff., 385ff., 395ff zygote 181, 195ff., 301, 409 zymosan 352 zymosterol 42