Functional Genetics of Industrial Yeasts

cover.jpg......Page 1
front-matter.pdf......Page 2
Functional Genetics of Industrial Yeasts......Page 4
Table of contents......Page 6
List of contributors......Page 12
1.1.1 History......Page 16
1.1.2 Yeast diversity......Page 17
1.1.3 Yeast biotechnology and yeast genetics......Page 18
1.1.4 Setup of this book......Page 19
1.2 From classical genetics to modern genomics......Page 20
1.3.1 Baker's yeast......Page 21
1.3.2 Wine yeast......Page 22
1.4 Of apples pears: new food yeast......Page 23
1.5 Yeast as model system......Page 24
1.5.2 Kluyveromyces lactis......Page 25
1.6.2 Metabolic pathway engineering......Page 26
1.7 Perstectives, rules and regulations......Page 28
2.1 Introduction......Page 32
2.2.1 An overview of the genome and functional genetic analysis of laboratory S. cerevisiae strains: a basis for comparison with industrial yeasts......Page 34
2.2.2 Genomes of industrial Saccharomyces and non-Saccharomyces yeasts......Page 39
2.2.3 Funktional analyses of industrially relevant yeasts......Page 41
2.2.4 Classical genetic features of laboratory and industrial yeasts......Page 43
2.3.1 Issues affecting the choise of genetic strategy......Page 45
2.3.2 Mating......Page 46
2.3.3 Mutagenesis......Page 50
2.3.4 Protoplast / spheroplast fusion......Page 52
2.3.6 Screeming strains for improvements......Page 53
2.4 Improvements to strains via classical genetics......Page 54
2.4.1.1 Genomic localization of MAL loci......Page 55
2.4.1.3 The MAL regulator......Page 56
2.4.1.5 Genetic variation of MalR control......Page 58
2.4.1.6 Improvement of maltose utilization - a complex issue......Page 59
2.5 Conclusions and prospects......Page 61
3.1 Introduction......Page 71
3.2.1.1 DNA content......Page 73
3.2.1.2 Chromosomal reorganizations......Page 74
3.2.1.3 Homology with the DNA of laboratory strains......Page 75
3.3.1 Fermentative characteristics......Page 76
3.3.1.1 Sugar metabolism, transport and control......Page 77
3.3.1.2 The protein kinase A (PKA) pathway......Page 78
3.3.1.3 Strategies to enhance fermentative performance......Page 79
3.3.2 Osmotolerance and Na+ toxicity resistance......Page 81
3.3.2.1 Sources of osmotic stress......Page 82
3.3.2.3 Osmotic shock: primary responses......Page 83
3.3.2.4 Transcriptional activation and main secondary responses......Page 84
3.3.2.5 Strategies and targets for the improvement of osmotolerance......Page 87
3.3.3 Cryoresistance......Page 89
3.3.3.2 Cellular factors involved in cryoresistance......Page 90
3.3.3.3 The cold and freeze response......Page 93
3.3.3.4 Strategies and targets for improvement of cryoresistance......Page 95
3.4.2 Baking applications......Page 97
3.4.3 T. delbrueckii as a model system......Page 98
3.5 Conclusions......Page 99
4.1 Introduction......Page 112
4.2.1 The advantages and disadvantages of spontaneous and inoculated fermentations......Page 113
4.2.2 The development of active dried wine yeast Starter culture strains......Page 114
4.3.1 The morphology, reproduction and genetic constitution of wine yeasts......Page 115
4.3.2 The genetic methods for the analysis and modification of wine yeasts......Page 117
4.4 Strategies and targets for the improvement of wine yeasts......Page 122
4.4.1 Improvement of fermentation Performance......Page 124
4.4.1.2 Improved efficiency of sugar and nitrogen utilisation......Page 125
4.4.1.3 Increased tolerance to antimicrobial compounds......Page 127
4.4.2.1 Improved protein and polysaccharide clarification......Page 129
4.4.2.2 Controlled cell flocculation and flotation......Page 131
4.4.3.1 Increased production of resveratrol......Page 133
4.4.3.2 Reduced formation of ethyl carbamate......Page 134
4.4.3.3 Reduced formation of biogenic amines......Page 135
4.4.3.4 Increased production of biopreservative compounds and enzymes......Page 136
4.4.4 Improvement of wine flavour and other sensory qualities......Page 138
4.4.4.1 Enhanced liberation of grape terpenoids......Page 139
4.4.4.3 Optimised production of glycerol and higher alcohols......Page 140
4.4.4.4 Bio-adjustment of wine acidity......Page 141
4.4.4.6 Reduced sulphite and sulphide production......Page 142
4.5 Conclusions and future perspectives......Page 143
5.1 The role of yeast in beer production......Page 156
5.2 Brewer’s yeast: a chimera in Service......Page 158
5.3 How to breed brewer’s yeast......Page 162
5.4.1. Feeding the beast: carbohydrate fermentation......Page 164
5.4.2 Flavour components: too little and too much......Page 166
5.4.3. Flavour stability: a way to increased shelf life......Page 169
5.4.4 Diacetyl and maturation: how to Speed things up......Page 170
5.4.5 Sedimentation and filtration......Page 172
5.6 Concluding remarks......Page 173
6.1 Introduction......Page 184
6.2.1 Taxonomy of Kluyveromyces ssp. and phylogenetic relationship to S. cerevisiae......Page 185
6.2.2.1 Centromeres and telomeres on the six K. lactis chromosomes......Page 186
6.2.2.2 Linear cytoplasmic DNA plasmids conferring the Killer phenotype......Page 187
6.2.2.3 Circular nuclear plasmids......Page 188
6.2.4 Mating types......Page 189
6.3.1.1 Introduction......Page 190
6.3.1.2 Glucose uptake......Page 192
6.3.1.3 Upper part of glycolysis......Page 193
6.3.1.4 Pyruvate metabolism......Page 194
6.3.1.5 Crabtree effect and fermentation......Page 195
6.3.1.6 Acetate and ethanol consumption......Page 197
6.3.1.7 Regulator genes......Page 198
6.3.2 Lactose utilization......Page 201
6.3.3 The petite-negative phenotype......Page 203
6.3.4 Killer Strains......Page 204
6.4. Industrial applications......Page 205
7.1 Introduction......Page 219
7.2.2 Expression cloning strategies......Page 221
7.2.3 Promoter Systems for Protein production......Page 222
7.3 Sorting of heterologous Proteins to specific subcellular locations......Page 224
7.3.1.1 Genes involved in peroxisome biogenesis and degradation......Page 225
7.3.1.2 Sorting of heterologous proteins to the peroxisomal matrix......Page 226
7.3.1.3 Sorting of heterologous membrane proteins to the peroxisomal membrane......Page 228
7.3.2 Protein secretion......Page 230
7.4 Concluding remarks......Page 231
8.1 Introduction......Page 238
8.2.1.1 Breeding programs......Page 239
8.2.2.1 Transformation and vectors......Page 240
8.2.2.3 Insertional mutagenesis......Page 241
8.3 Yarrowia lipolytica as a model for Protein secretion......Page 242
8.3.2 Slsl p, prototype of a new ADP/ATP exchange factor family for eukaryotic Hsp70p......Page 243
8.3.3 Other new components affecting secretion......Page 245
8.3.4 Function of the S. cerevisiae homologues of SEC genes......Page 246
8.4.3 Identification and characterization of Y. lipolytica morphogenetic genes......Page 247
8.4.4 Pathway conservation in Y. lipolytica, S. cerevisiae, and C. albicans......Page 250
8.5.1 Mitochondrial metabolism......Page 251
8.5.2 Mitochondrial respiratoty chain......Page 253
8.5.3 Mitochondrial genome......Page 254
8.5.4 Respiratoty chain complex I......Page 255
8.5.5 The hydrogenase model for the catalytic core of complex I......Page 257
8.6.1.2 Utilisation of other carbohydrates......Page 258
8.6.3 Utilisation of monocarboxylic acids......Page 259
8.6.5 Utilization of hydrocarbons as carbon Source......Page 260
8.6.6 Hydrolysis of fats......Page 261
8.7 Peroxisome assembly in the yeast Yarrowia lipolytica......Page 262
8.7.1 Metabolic functions and biogenesis of peroxisomes......Page 263
8.7.3 A revision of the peroxisome biogenesis paradigm: peroxisomes assemble by a multistep pathway......Page 264
8.7.4 Peroxisome fusion......Page 265
8.7.5 The endoplasmic reticulum plays an essential role in peroxisome assem bly......Page 267
8.7.6 Folded, oligomeric Proteins are imported into peroxisomes......Page 268
8.8 Future prospects......Page 269
9.1 Introduction to microbial and yeast food spoilage......Page 283
9.2.2 Growth characteristics......Page 285
9.2.4 Preservation strategies......Page 286
9.3 The yeast envelope, antifungal targets, and (preservation) stress resistance......Page 287
9.3.1 Gell wall sugars and their Synthesis......Page 289
9.3.2 Membrane localised transporters of low molecular weight compounds......Page 290
9.3.3 Gell wall Proteins and stress response......Page 292
9.3.4 Sensing the extracellular environment and signalling stress.......Page 294
9.4. A new method for the analysis of gene expression profiles......Page 295
9.5 Concluding remarks and future prospects......Page 297
10.1 Introduction......Page 306
10.2.1 Phyllosphere yeasts......Page 308
10.2.2 Biocontrol of postharvest diseases......Page 309
10.2.3 Non-conventional killer yeasts in biocontrol......Page 314
10.3.1.1 Basidiomycetous yeasts and related imperfect species......Page 315
10.3.1.4 Pichia guilliermondii and Candida guilliermondii......Page 317
10.3.2 Genetics of the killer Character in non-conventional biocontrol yeasts......Page 318
10.4 Available genetic methods for biocontrol yeasts......Page 319
10.4.1 Molecular methods for identification and phylogenetic analysis of biocontrol yeasts......Page 320
10.4.2 Methods for the manipulation of biocontrol yeasts......Page 323
10.5.1 Application of mutants in biocontrol Systems......Page 325
10.5.2 Application of genetically engineered strains in biocontrol Systems......Page 326
10.6 Conclusions and outlook......Page 327
11.1 Introduction......Page 339
11.2 Examples of metabolic engineering......Page 341
11.2.2 Heterologous Protein production......Page 343
11.2.3 Improvement of fluxes......Page 344
11.3 Challenges in metabolic engineering......Page 346
11.4 Functional genomics......Page 348
11.4.1 Comparative sequence analysis......Page 349
11.4.2 Transtriptome analysis......Page 350
11.4.3 Global mutant analysis......Page 351
11.4.4 Proteome analysis......Page 352
11.4.5 Interactome analysis......Page 353
11.4.7 Fluxome analysis......Page 354
11.5 Functional genomics in metabolic engineering......Page 355
11.5.1 Need for integrated approach......Page 358
11.6 Future prospects......Page 359
Index......Page 369