ADVANCES IN APPLIED MICROBIOLOGY
I Metabolic Engineering of Cells: General and Basics 1 Metabolic engineering: tools for pathway rewiring and value creation 3 11 Introduction 3 12 Tools for metabolic engineering 4 121 Microbial strain selection and improvement 4 122 Synthetic biology tools 6 123 Protein engineering tools 6 124 Omics tools 7 125 Genome engineering tools 10 13 Value generation by metabolic engineering 11 14 Conclusions and perspectives 19 References 20 2 Membrane transport as a target for metabolic engineering 27 21 Introduction 27 22 Membrane transport proteins 28 23 Substrate uptake 29 24 Transport from and into organelles 33 25 Product export 34 26 Cellular robustness 36 27 Substrate channeling and membrane transport 37 28 Undesired transport processes 38 29 Conclusions and perspectives 39 References 39 3 Analysis and modeling tools of metabolic flux 45 31 Introduction 45 32 13C-metabolic flux analysis 46 321 13C-metabolic flux analysis in steady-state systems 46 322 13C-metabolic flux analysis in nonstandard systems 49 33 Constraint-based stoichiometric metabolic flux analysis 50 331 Genome-scale metabolic network model tools 50 332 Research progress of genome-scale metabolic network model 58 34 Conclusions and perspectives 63 References 63 4 Equipped C1 chemical assimilation pathway in engineering Escherichia coli 69 41 Introduction 69 42 Approaches for the assessment of CO2 assimilation capability 70 43 Physiological effect of RuBisCo system 72 44 Strategies to enhance the RuBisCo system 75 45 Transforming the heterotrophs to autotrophs 78 46 Prospective of RuBisCo-based chemical production 80 47 Conclusions and perspectives 82 References 82 5 Microbial tolerance in metabolic engineering 85 51 Introduction 85 52 Microbial stresses and responses 86 521 Physiological stress factors 86 522 Microbial responses to stress factors 89 53 Strategies to improve microbial tolerance 92 531 Rational approaches 93 532 Adaptive laboratory evolution 95 54 Challenges in developing and using tolerant strains 97 55 Conclusions and perspectives 98 References 99 6 Application of proteomics and metabolomics in microbiology research 107 61 Introduction 107 62 Proteomics in microbiology 108 621 Proteomic methodology 108 622 Proteomic application in microbiology 112 63 Metabolomics in microbiology 115 631 Metabolomic methodology 115 632 Metabolomic applications in microbiology 119 64 Conclusions and perspectives 121 References 122 7 Approaches and tools of protein tailoring for metabolic engineering 131 71 Introduction 131 72 Approaches for the engineering of protein 133 721 Directed evolution 134 722 Rational design 137 723 Semirational design or combined methods 139 73 Applications of protein engineering 139 731 Enzyme engineering for improving the catalytic activity 140 732 Engineering the enzymes for cofactor utilization 140 733 Regulatory protein engineering for the enhancement of the metabolic pathway 141 734 Altering substrate and product specificity 142 735 Engineering the regulatory elements of the enzymes 143 736 Assimilation of unnatural amino acid into a protein 144 737 Enzymes scaffold engineering to control metabolite flux 144 738 De novo engineering of enzymes 146 739 Formation of enzyme complex through colocalization for the advancement in the metabolic pathway 147 74 Conclusions and perspectives 148 References 149 8 Microbial metabolism of aromatic pollutants: High-throughput OMICS and metabolic engineering for efficient bioremediation 151 81 Introduction 151 82 Aromatic compounds: impact and toxicity 153 83 Microbial metabolism of aromatic compounds/pollutants 155 831 Microbes involved 155 832 Metabolic pathways 156 833 Enzymes involved in the metabolism 156 84 High-throughput OMICS: insights into aromatics metabolism 159 841 Metagenomics 160 842 Metatranscriptomics 167 843 Metaproteomics 171 844 Meta-metabolomics 175 85 Metabolic engineering for efficient aromatics biodegradation 177 851 Designing the metabolic pathway 177 852 Building the desired strain 182 853 Testing and analyzing the engineered strain 185 86 Conclusions and perspectives 186 Acknowledgment 187 References 187 9 Microbial consortium engineering for the improvement of biochemicals production 201 91 Introduction 201 92 Classification of microbial consortia 202 921 Modes of construction 202 922 Modes of interaction 203 923 Functional modes 204 93 Construction of a microbial consortium 206 931 Source of carbon 206 932 Inoculum ratio 207 933 Spatial organization 207 934 Physiological parameters 208 935 Availability of nutrients 209 94 Applications of microbial consortium engineering 209 941 Production of bioactive molecules 209 942 Production of biopolymers 210 943 Production of fermented food products 217 944 Bioenergy 218 945 Production of biochemicals 220 946 Bioremediation 221 95 Recent synthetic microbial consortia and their applications 224 951 Coculturing 224 952 Metabolic engineering 225 953 Enzyme engineering 225 954 Fermentation systems 226 96 Challenges in microbial consortium engineering 226 97 Conclusions and perspectives 227 Acknowledgment 227 References 228 Further reading 232 II Metabolic Engineering of Cells: Applications 10 Metabolic engineering strategies for effective utilization of cellulosic sugars to produce value-added products 237 101 Introduction 237 102 Sustainable carbon sources for biorefineries 238 1021 Carbohydrates from lignocellulosic biomass 238 1022 Levulinic acid from cellulose 244 103 Microbial cell factories for carbon source coutilization and production of value-added chemicals 245 1031 Escherichia coli 245 1032 Corynebacterium glutamicum 248 1033 Pseudomonas putida 249 1034 Saccharomyces cerevisiae 250 104 Conclusions and perspectives 252 Acknowledgments 253 References 253 11 Production of fine chemicals from renewable feedstocks through the engineering of artificial enzyme cascades 261 111 Introduction 261 112 Advantages of enzyme cascades 261 113 Artificial enzyme cascades versus natural enzyme cascades 263 114 Importance of fine chemicals production from renewable feedstocks through artificial enzyme cascades 264 115 General principle of engineering of enzyme cascades 264 1151 Basic designs of cascade 264 1152 Operation of enzyme cascade reactions 266 1153 The development of enzyme cascades for the conversion of renewable feedstocks to high-value fine chemicals 267 116 Examples of production of fine chemicals from bio-based L-phenylalanine using artificial enzyme cascades 269 1161 Artificial enzyme cascades for the production of alcohols 269 1162 Artificial enzyme cascades for the production of carboxylic acids 271 1163 Artificial enzyme cascades for production of amines 272 117 Examples of production of fine chemicals from renewable feedstocks glucose and glycerol using artificial enzyme cascades 273 1171 Single strain approach 273 1172 Coupled strains approach 274 118 Conclusions and perspectives 276 References 277 12 Metabolic engineering of microorganisms for the production of carotenoids, flavonoids, and functional polysaccharides 281 121 Introduction 281 122 Metabolic engineering of plant natural products 282 1221 Flavanones 283 1222 Flavones 287 1223 Flavonols 288 1224 Flavanols 289 1225 Anthocyanins 290 1226 Isoflavones 291 1227 Resveratrol 292 1228 Limonene 293 1229 Lycopene 294 12210 Carotene 295 12211 Astaxanthin 295 12212 ?-Ionone 295 12213 Emodin 296 12214 Cannabinoids 296 123 Metabolic engineering of functional polysaccharides 296 1231 Levan 297 1232 Hyaluronic acid 297 1233 Heparosan and chondroitin 298 124 Conclusions and perspectives 298 References 300 13 Bioengineering in microbial production of biobutanol from renewable resources 307 131 Introduction 307 132 Applications and production of butanol 308 133 Biological production of butanol 308 134 Metabolic pathways of biobutanol production 310 1341 Acetonebutanolethanol pathway 311 1342 Keto-acid pathways 313 135 Enhancement of biobutanol production 315 1351 Optimization of fermentation conditions 315 1352 Bioengineering for biobutanol production 316 136 Conclusions and perspectives 328 Acknowledgments 330 References 330 14 Engineered microorganisms for bioremediation 335 141 Introduction 335 142 Types of bioremediation 336 1421 Limitations associated with bioremediation 338 143 Genetically engineered organisms in bioremediation 338 1431 Genetically modified bacteria in bioremediation 340 1432 Genetically modified fungi in mycoremediation 341 1433 Algae in phycoremediation 341 1434 Genetically modified plants in phytoremediation as an alternative 342 144 Genetic engineering techniques 343 1441 Protein engineering 343 1442 Pathway modification 343 1443 Advanced genome engineering 344 1444 Quorum sensing: an emerging area for bioremediation 344 145 Bioremediation using GEMs 345 1451 Heavy metals 345 1452 Pesticides and herbicides 348 1453 Dyestuff 349 1454 Oils and petroleum products 350 146 Field applications of GEMs 350 1461 Bioremediation potential 350 1462 Survival in harsh habitats 351 1463 Bioprocess controlled monitoring 351 147 Risk assessment of GEMs 352 148 Conclusions and perspectives 353 References 353 15 Agricultural applications of engineered microbes 363 151 Introduction 363 152 Agricultural applications of genetically modified microbes 364 1521 Applications of genetically modified microbes in plant growth and nutrition 364 1522 Applications of genetically modified microbes in plant stress tolerance 369 153 Conclusions and perspectives 371 Acknowledgments 372 References 372 16 Rhizosphere microbiome engineering 377 161 Introduction 377 162 Plant-associated microbes/microbiome 378 1621 Holobiome 378 1622 Plant growth-promoting rhizobacteria and their contribution in plant growth and development 379 1623 Need for rhizosphere engineering 382 163 Rhizosphere microbiome engineering 383 1631 Soil amendment 383 1632 Targeted plant-microbe engineering 386 164 Emerging areas of research 387 1641 Organic amendments/root exudates: biochemical approach 387 1642 Artificial microbial consortia 389 1643 Microbial-based plant breeding 390 1644 Host mediated microbiome engineering: molecular strategies 391 165 Conclusions and perspectives 391 Acknowledgments 392 References 392 17 Genetically engineered microbes in micro-remediation of metals from contaminated sites 397 171 Introduction 397 172 Classification of bioremediation 398 1721 In situ bioremediation 399 1722 Intrinsic bioremediation 401 1723 Engineered in situ bioremediation 401 1724 Ex situ bioremediation 401 1725 Microbes assisted bioremediation (microremediation) 401 173 Metal-contaminated sites: a problem 402 1731 Heavy metal remediation 403 1732 Heavy metals and toxicity 404 1733 Microbial biorecovery of heavy metals 405 174 Genetically modified micro-organisms 406 1741 Wild type microbes 408 1742 Engineered microbes 410 175 Conclusions and perspectives 412 Acknowledgment 413 References 413 18 Biofuel production from renewable feedstocks: Progress through metabolic engineering 417 181 Introduction 417 182 Heterologous genetic expression in plants to improve feedstock properties 420 183 System metabolic engineering for biofuels production 423 1831 In silico approaches in metabolic engineering 423 1832 Metabolic engineering strategies 427 184 Microbial production of biofuels from renewable feedstock 430 1841 Bioethanol 430 1842 Biodiesel 433 1843 Drop-in biofuels 436 185 Challenges and techno-economic analysis of emerging biofuels 437 186 Conclusions and perspectives 438 Acknowledgments 440 References 440 19 Synthetic biology and the regulatory roadmap for the commercialization of designer microbes 449 191 Introduction 449 192 Synthetic biology 451 193 Framework of synthetic biology 451 194 Tools in synthetic biology 453 1941 Design of gene circuit 453 1942 Synthetic transcription factors 455 1943 Genome engineering 456 1944 Computer-aided tools in synthetic biology 457 195 Applications of synthetic biology 458 1951 Production of advance biofuels 458 1952 Applications in drug development 459 1953 Bioremediation of pollutants with integrated synthetic biology 460 196 Legal aspect of designer microbes 461 1961 Mentioned below are the federal laws, regulations and policies 461 1962 Other regulations 465 197 Regulatory challenges for the commercialization of designer microbes 465 1971 Social and economic issues 466 1972 Biosafety issues 466 1973 Other issues 467 1974 Risk assessment and management 467 198 Conclusions and perspectives 469 References 469