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

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
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