دانلود کتاب Current Developments in Biotechnology and Bioengineering: Designer Microbial Cell Factories: Metabolic Engineering and Applications

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Front Cover Current Developments in Biotechnology and Bioengineering Copyright Page Contents List of contributors Preface I. Metabolic Engineering of Cells: General and Basics 1 Metabolic engineering: tools for pathway rewiring and value creation 1.1 Introduction 1.2 Tools for metabolic engineering 1.2.1 Microbial strain selection and improvement 1.2.2 Synthetic biology tools 1.2.3 Protein engineering tools 1.2.4 Omics tools 1.2.4.1 Genomics and transcriptomics tools 1.2.4.2 Proteomics and metabolomics tools 1.2.4.3 Fluxomics tools 1.2.4.4 Meta-omics tools 1.2.5 Genome engineering tools 1.3 Value generation by metabolic engineering 1.4 Conclusions and perspectives References 2 Membrane transport as a target for metabolic engineering 2.1 Introduction 2.2 Membrane transport proteins 2.3 Substrate uptake 2.4 Transport from and into organelles 2.5 Product export 2.6 Cellular robustness 2.7 Substrate channeling and membrane transport 2.8 Undesired transport processes 2.9 Conclusions and perspectives References 3 Analysis and modeling tools of metabolic flux 3.1 Introduction 3.2 13C-metabolic flux analysis 3.2.1 13C-metabolic flux analysis in steady-state systems 3.2.2 13C-metabolic flux analysis in nonstandard systems 3.2.2.1 13C-metabolic flux analysis of autotrophic metabolism 3.2.2.2 13C-metabolic flux analysis in the nongrowth stage 3.2.2.3 13C dynamic metabolic flux analysis 3.3 Constraint-based stoichiometric metabolic flux analysis 3.3.1 Genome-scale metabolic network model tools 3.3.1.1 Method of genome-scale metabolic network model construction 3.3.1.1.1 Manual model reconstruction method 3.3.1.1.2 Automatic model reconstruction method 3.3.1.2 Database and software required for model construction 3.3.1.3 Model analyzing algorithm 3.3.1.3.1 Flux balance analyzing algorithm 3.3.1.3.2 Genetic disturbance algorithm 3.3.2 Research progress of genome-scale metabolic network model 3.3.2.1 Model reconstruction 3.3.2.2 Model application 3.3.2.2.1 Predict and analyze the growing phenotype of microorganisms 3.3.2.2.2 Analysis of network properties 3.3.2.2.3 Guide metabolic engineering 3.4 Conclusions and perspectives References 4 Equipped C1 chemical assimilation pathway in engineering Escherichia coli 4.1 Introduction 4.2 Approaches for the assessment of CO2 assimilation capability 4.3 Physiological effect of RuBisCo system 4.4 Strategies to enhance the RuBisCo system 4.5 Transforming the heterotrophs to autotrophs 4.6 Prospective of RuBisCo-based chemical production 4.7 Conclusions and perspectives References 5 Microbial tolerance in metabolic engineering 5.1 Introduction 5.2 Microbial stresses and responses 5.2.1 Physiological stress factors 5.2.1.1 Chemical stresses 5.2.1.2 Physical stresses 5.2.2 Microbial responses to stress factors 5.2.2.1 Regulatory responses to stress factors 5.2.2.2 Removal of the toxic chemicals or metabolic intermediates by enzymatic conversion 5.2.2.3 Alteration of membrane structure and/or transport 5.2.2.4 Protein homeostasis 5.2.2.5 Cross tolerance 5.3 Strategies to improve microbial tolerance 5.3.1 Rational approaches 5.3.1.1 Expression of efflux pump 5.3.1.2 Overexpression of chaperones 5.3.1.3 Engineering of cell envelope 5.3.1.4 Engineering of transcriptional regulatory systems 5.3.2 Adaptive laboratory evolution 5.3.2.1 Adaptive laboratory evolution for tolerance against organic acids and alcohols 5.3.2.2 Adaptive laboratory evolution for tolerance against salts and dissolved oxygen 5.3.2.3 Adaptive laboratory evolution and system-level analyses 5.4 Challenges in developing and using tolerant strains 5.5 Conclusions and perspectives References 6 Application of proteomics and metabolomics in microbiology research 6.1 Introduction 6.2 Proteomics in microbiology 6.2.1 Proteomic methodology 6.2.1.1 Bottom-up proteomics Discovery and targeted proteomics Label and label-free quantification 6.2.1.2 Top-down proteomics 6.2.2 Proteomic application in microbiology 6.2.2.1 Identification of pathogenic bacteria 6.2.2.2 Host-pathogen interactions 6.2.2.3 Characterization of biological membrane 6.2.2.4 Antibiotics resistance 6.2.2.5 Advanced growth rate of bacteria 6.2.2.6 Energy conversion 6.3 Metabolomics in microbiology 6.3.1 Metabolomic methodology 6.3.1.1 Nuclear magnetic resonance spectroscopy 6.3.1.2 Mass spectrometer Gas chromatography-MS Liquid-chromatography-MS 6.3.1.3 Metabolites identification 6.3.2 Metabolomic applications in microbiology 6.3.2.1 Improvement of the production of various bioproduction targets 6.3.2.2 Exploration of the effect of unknown gene 6.3.2.3 Development of synthetic methylotrophic strains 6.4 Conclusions and perspectives References 7 Approaches and tools of protein tailoring for metabolic engineering 7.1 Introduction 7.2 Approaches for the engineering of protein 7.2.1 Directed evolution 7.2.2 Rational design 7.2.3 Semirational design or combined methods 7.3 Applications of protein engineering 7.3.1 Enzyme engineering for improving the catalytic activity 7.3.2 Engineering the enzymes for cofactor utilization 7.3.3 Regulatory protein engineering for the enhancement of the metabolic pathway 7.3.4 Altering substrate and product specificity 7.3.5 Engineering the regulatory elements of the enzymes 7.3.6 Assimilation of unnatural amino acid into a protein 7.3.7 Enzymes scaffold engineering to control metabolite flux 7.3.8 De novo engineering of enzymes 7.3.9 Formation of enzyme complex through colocalization for the advancement in the metabolic pathway 7.4 Conclusions and perspectives References 8 Microbial metabolism of aromatic pollutants: High-throughput OMICS and metabolic engineering for efficient bioremediation 8.1 Introduction 8.2 Aromatic compounds: impact and toxicity 8.3 Microbial metabolism of aromatic compounds/pollutants 8.3.1 Microbes involved 8.3.2 Metabolic pathways 8.3.3 Enzymes involved in the metabolism 8.4 High-throughput OMICS: insights into aromatics metabolism 8.4.1 Metagenomics 8.4.2 Metatranscriptomics 8.4.3 Metaproteomics 8.4.4 Meta-metabolomics 8.5 Metabolic engineering for efficient aromatics biodegradation 8.5.1 Designing the metabolic pathway 8.5.1.1 Pathway prediction tools 8.5.1.2 Toxicity prediction databases 8.5.1.3 Molecular biology module databases 8.5.1.4 Metabolic modeling 8.5.1.5 Choosing the ideal chassis (host) 8.5.2 Building the desired strain 8.5.2.1 Plasmid-based expression 8.5.2.2 Genome engineering strategies Homologous recombination Recombineering Transposon-based tools 8.5.3 Testing and analyzing the engineered strain 8.6 Conclusions and perspectives References 9 Microbial consortium engineering for the improvement of biochemicals production 9.1 Introduction 9.2 Classification of microbial consortia 9.2.1 Modes of construction 9.2.1.1 Natural microbial consortium 9.2.1.2 Artificial microbial consortium 9.2.1.3 Synthetic microbial consortium 9.2.2 Modes of interaction 9.2.2.1 Synergistic 9.2.2.2 Mutualistic 9.2.2.3 Commensalism 9.2.2.4 Competition 9.2.2.5 Parasitism 9.2.3 Functional modes 9.2.3.1 Environment maintenance consortium 9.2.3.2 Nutrient exchange consortium 9.2.3.3 Substrate facilitator consortium 9.2.3.4 Signal exchange consortium 9.3 Construction of a microbial consortium 9.3.1 Source of carbon 9.3.2 Inoculum ratio 9.3.3 Spatial organization 9.3.4 Physiological parameters 9.3.5 Availability of nutrients 9.4 Applications of microbial consortium engineering 9.4.1 Production of bioactive molecules 9.4.2 Production of biopolymers 9.4.2.1 Polyhydroxyalkonates 9.4.2.2 Exopolysaccharides 9.4.3 Production of fermented food products 9.4.4 Bioenergy 9.4.4.1 Biodiesel 9.4.4.2 Bioalcohol 9.4.4.3 Biohydrogen 9.4.5 Production of biochemicals 9.4.5.1 Production of acetic acid 9.4.5.2 Production of butyric acid 9.4.5.3 Production of carotenoids 9.4.5.4 Production of single-cell protein 9.4.6 Bioremediation 9.4.6.1 Degradation of heavy metals 9.4.6.2 Degradation and decolorization of textile effluent 9.4.6.3 Degradation of petroleum waste 9.4.6.4 Water eutrophication 9.5 Recent synthetic microbial consortia and their applications 9.5.1 Coculturing 9.5.2 Metabolic engineering 9.5.3 Enzyme engineering 9.5.4 Fermentation systems 9.6 Challenges in microbial consortium engineering 9.7 Conclusions and perspectives References Further reading II. Metabolic Engineering of Cells: Applications 10 Metabolic engineering strategies for effective utilization of cellulosic sugars to produce value-added products 10.1 Introduction 10.2 Sustainable carbon sources for biorefineries 10.2.1 Carbohydrates from lignocellulosic biomass 10.2.1.1 Cellulose and glucose 10.2.1.2 Hemicellulose and xylose 10.2.1.3 Cellobiose and other cellodextrins 10.2.2 Levulinic acid from cellulose 10.3 Microbial cell factories for carbon source coutilization and production of value-added chemicals 10.3.1 Escherichia coli 10.3.2 Corynebacterium glutamicum 10.3.3 Pseudomonas putida 10.3.4 Saccharomyces cerevisiae 10.4 Conclusions and perspectives References 11 Production of fine chemicals from renewable feedstocks through the engineering of artificial enzyme cascades 11.1 Introduction 11.2 Advantages of enzyme cascades 11.3 Artificial enzyme cascades versus natural enzyme cascades 11.4 Importance of fine chemicals production from renewable feedstocks through artificial enzyme cascades 11.5 General principle of engineering of enzyme cascades 11.5.1 Basic designs of cascade 11.5.1.1 Linear cascades 11.5.1.2 Orthogonal cascades 11.5.1.3 Cyclic cascades 11.5.1.4 Coupled cascades 11.5.1.5 Divergent cascades 11.5.2 Operation of enzyme cascade reactions 11.5.2.1 In vitro cascade reaction 11.5.2.2 In vivo cascade reaction 11.5.3 The development of enzyme cascades for the conversion of renewable feedstocks to high-value fine chemicals 11.5.3.1 Pathway design 11.5.3.2 Enzyme selection 11.5.3.3 Engineering strains for expressing all enzymes required in cascade 11.6 Examples of production of fine chemicals from bio-based l-phenylalanine using artificial enzyme cascades 11.6.1 Artificial enzyme cascades for the production of alcohols 11.6.2 Artificial enzyme cascades for the production of carboxylic acids 11.6.3 Artificial enzyme cascades for production of amines 11.7 Examples of production of fine chemicals from renewable feedstocks glucose and glycerol using artificial enzyme cascades 11.7.1 Single strain approach 11.7.2 Coupled strains approach 11.8 Conclusions and perspectives References 12 Metabolic engineering of microorganisms for the production of carotenoids, flavonoids, and functional polysaccharides 12.1 Introduction 12.2 Metabolic engineering of plant natural products 12.2.1 Flavanones 12.2.2 Flavones 12.2.3 Flavonols 12.2.4 Flavanols 12.2.5 Anthocyanins 12.2.6 Isoflavones 12.2.7 Resveratrol 12.2.8 Limonene 12.2.9 Lycopene 12.2.10 Carotene 12.2.11 Astaxanthin 12.2.12 β-Ionone 12.2.13 Emodin 12.2.14 Cannabinoids 12.3 Metabolic engineering of functional polysaccharides 12.3.1 Levan 12.3.2 Hyaluronic acid 12.3.3 Heparosan and chondroitin 12.4 Conclusions and perspectives References 13 Bioengineering in microbial production of biobutanol from renewable resources 13.1 Introduction 13.2 Applications and production of butanol 13.3 Biological production of butanol 13.4 Metabolic pathways of biobutanol production 13.4.1 Acetone–butanol–ethanol pathway 13.4.2 Keto-acid pathways 13.5 Enhancement of biobutanol production 13.5.1 Optimization of fermentation conditions 13.5.2 Bioengineering for biobutanol production 13.5.2.1 Spectrum of fermentation substrates 13.5.2.2 Modified pathways 13.5.2.3 Increased solvent tolerance 13.6 Conclusions and perspectives References 14 Engineered microorganisms for bioremediation 14.1 Introduction 14.2 Types of bioremediation 14.2.1 Limitations associated with bioremediation 14.3 Genetically engineered organisms in bioremediation 14.3.1 Genetically modified bacteria in bioremediation 14.3.2 Genetically modified fungi in mycoremediation 14.3.3 Algae in phycoremediation 14.3.4 Genetically modified plants in phytoremediation as an alternative 14.4 Genetic engineering techniques 14.4.1 Protein engineering 14.4.2 Pathway modification 14.4.3 Advanced genome engineering 14.4.4 Quorum sensing: an emerging area for bioremediation 14.5 Bioremediation using GEMs 14.5.1 Heavy metals 14.5.2 Pesticides and herbicides 14.5.3 Dyestuff 14.5.4 Oils and petroleum products 14.6 Field applications of GEMs 14.6.1 Bioremediation potential 14.6.2 Survival in harsh habitats 14.6.3 Bioprocess controlled monitoring 14.7 Risk assessment of GEMs 14.8 Conclusions and perspectives References 15 Agricultural applications of engineered microbes 15.1 Introduction 15.2 Agricultural applications of genetically modified microbes 15.2.1 Applications of genetically modified microbes in plant growth and nutrition 15.2.1.1 Symbiotic nitrogen fixers Genetically modified Rhizobium Genetically modified Alcaligenes faecalis Genetically modified Xanthobacter autotrophicus 15.2.1.2 Nonsymbiotic nitrogen fixers Genetically modified Azospirillum 15.2.1.3 Genetically modified phosphate-solubilizing microbes 15.2.2 Applications of genetically modified microbes in plant stress tolerance 15.2.2.1 Role of genetically modified microbes to control insect pests 15.2.2.2 Role of genetically modified microbes to control plant diseases 15.2.2.3 Application of genetically modified microbes in plant protection from ice-nucleation 15.3 Conclusions and perspectives References 16 Rhizosphere microbiome engineering 16.1 Introduction 16.2 Plant-associated microbes/microbiome 16.2.1 Holobiome 16.2.2 Plant growth-promoting rhizobacteria and their contribution in plant growth and development 16.2.2.1 Enhancement of plant nutrient acquisition 16.2.2.2 Dealing with abiotic stress 16.2.2.3 Phytohormone production 16.2.2.4 Antagonism against phytopathogens 16.2.3 Need for rhizosphere engineering 16.3 Rhizosphere microbiome engineering 16.3.1 Soil amendment 16.3.1.1 Inorganic/organic soil amendment 16.3.1.2 Microbial inoculants as biofertilizer/biopesticide 16.3.2 Targeted plant-microbe engineering 16.4 Emerging areas of research 16.4.1 Organic amendments/root exudates: biochemical approach 16.4.1.1 Movement toward rhizosphere 16.4.1.2 Survival within the rhizosphere 16.4.1.3 Adhesion and colonization on root surfaces 16.4.2 Artificial microbial consortia 16.4.3 Microbial-based plant breeding 16.4.4 Host mediated microbiome engineering: molecular strategies 16.5 Conclusions and perspectives References 17 Genetically engineered microbes in micro-remediation of metals from contaminated sites 17.1 Introduction 17.2 Classification of bioremediation 17.2.1 In situ bioremediation 17.2.1.1 Bioventing 17.2.1.2 Bioslurping 17.2.1.3 Bioaugmentation 17.2.1.4 Biosorption 17.2.1.5 Bioaccumulation 17.2.2 Intrinsic bioremediation 17.2.3 Engineered in situ bioremediation 17.2.4 Ex situ bioremediation 17.2.5 Microbes assisted bioremediation (microremediation) 17.3 Metal-contaminated sites: a problem 17.3.1 Heavy metal remediation 17.3.2 Heavy metals and toxicity 17.3.3 Microbial biorecovery of heavy metals 17.4 Genetically modified micro-organisms 17.4.1 Wild type microbes 17.4.2 Engineered microbes 17.4.2.1 Mercury 17.4.2.2 Arsenic 17.4.2.3 Lead and cadmium 17.5 Conclusions and perspectives References 18 Biofuel production from renewable feedstocks: Progress through metabolic engineering 18.1 Introduction 18.2 Heterologous genetic expression in plants to improve feedstock properties 18.3 System metabolic engineering for biofuels production 18.3.1 In silico approaches in metabolic engineering 18.3.1.1 “Omics-”approach in system biology 18.3.1.2 Genome-scale metabolic models 18.3.1.3 In silico optimization methods 18.3.2 Metabolic engineering strategies 18.3.2.1 Overexpression of genes 18.3.2.2 Engineering of the regulatory regions 18.3.2.3 Knock-down/-out of competing pathways 18.3.2.4 Directed evolution/mutations toward improving rate-limiting step 18.4 Microbial production of biofuels from renewable feedstock 18.4.1 Bioethanol 18.4.2 Biodiesel 18.4.2.1 Biodiesel from microbes 18.4.2.2 Algal biodiesel 18.4.3 Drop-in biofuels 18.5 Challenges and techno-economic analysis of emerging biofuels 18.6 Conclusions and perspectives References 19 Synthetic biology and the regulatory roadmap for the commercialization of designer microbes 19.1 Introduction 19.2 Synthetic biology 19.3 Framework of synthetic biology 19.4 Tools in synthetic biology 19.4.1 Design of gene circuit 19.4.2 Synthetic transcription factors 19.4.3 Genome engineering 19.4.4 Computer-aided tools in synthetic biology 19.5 Applications of synthetic biology 19.5.1 Production of advance biofuels 19.5.2 Applications in drug development 19.5.3 Bioremediation of pollutants with integrated synthetic biology 19.6 Legal aspect of designer microbes 19.6.1 Mentioned below are the federal laws, regulations and policies 19.6.1.1 Europe 19.6.1.2 United States of America (USA) 19.6.1.3 India 19.6.1.4 China 19.6.1.5 Japan 19.6.2 Other regulations 19.6.2.1 The cartagena protocol on biosafety to the convention on biological diversity 19.6.2.2 The codex alimentarius commission (Codex) 19.7 Regulatory challenges for the commercialization of designer microbes 19.7.1 Social and economic issues 19.7.2 Biosafety issues 19.7.3 Other issues 19.7.4 Risk assessment and management 19.8 Conclusions and perspectives References Index Back Cover