دانلود کتاب Microbial Cell Factories Engineering for Production of Biomolecules

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Front Matter
Copyright
Dedication
Contributors
About the editor
Foreword
Preface
Acknowledgments
An introduction to microbial cell factories for production of biomolecules
Introduction
Microbial hosts as microbial cell factories
Escherichia coli as a cell factory
Corynebacterium glutamicum as a cell factory
Lactococcus lactis as a cell factory
Bacillus subtilis as a cell factory
Pseudomonas putida as a cell factory
Saccharomyces cerevisiae as a cell factory
Pichia pastoris as a cell factory
Hansenula polymorpha as a cell factory
Yarrowia lipolytica as a cell factory
Cyanobacteria as a cell factory
Design and optimization of microbial cell factories
Conclusion and future remarks
References
Advances in long DNA synthesis
Introduction, history, and evolution of gene synthesis
Technological developments
Oligo synthesis
Column-based oligo synthesis
Array-based oligo synthesis
Gene synthesis
Array-based gene synthesis
Larger DNA assemblies
Whole-genome synthesis
Assembly of genetic parts for biosynthetic pathway building and its limitation
Applications of synthetic genes
Biosensing
Therapeutics
Blood glucose homeostasis
Cancer
Disease mechanisms and prevention
Novel treatments for bacterial infections
Biofuels and biomaterials
Current challenges in DNA synthesis
Biosynthetic pathway for the development of microfactories
Future developments
References
Discovery of enzymes responsible for cyclization and postmodification in triterpenoid biosynthesis
Introduction
Enzymes responsible for cyclization and postmodification of triterpenoid are crucial for triterpenoid biosynthesis
Approaches for discovery of enzymes in cyclization and postmodification of triterpenoid
Traditional approaches
Gene deletion
Gene silencing
Enzymatic activity guided protein purification
Mutation-based approaches
Synthetic biology approaches
Genomic-guided heterologous expression
Transcriptomic-guided heterologous expression
Combinatorial approaches
Concluding remarks and future perspectives
References
Synthetic biology approaches for secondary metabolism engineering
Introduction
Secondary metabolism
Biosynthetic clusters for secondary metabolites
Top-down strategies: The known biology
Characterization of the biological modules in secondary metabolism
Functional assembly of modules
Functional testing of the customized biosynthetic clusters
Bottom-up strategies: De novo systems
Conclusions and further perspectives
References
Synthetic biology design tools for metabolic engineering
Introduction
Tools for metabolic modeling
Computer models of metabolism
Trade-off between growth and production, and consideration of productivity
Addressing the interaction between synthetic gene circuits and host
Tools for metabolic pathway design
Metabolic pathway selection
Enzyme sequence selection
Tools for metabolic pathway experimental design
Bottom-up synthetic biology design of experiments
Optimal design of experiments in metabolic engineering
Tools for metabolic pathway dynamic regulation
Biosensors design for metabolic engineering
Metabolic pathway dynamic regulation
Machine learning tools for metabolic pathway design
Automated design workflows and standardization
Standardized information representation in synthetic biology
Workflow development for metabolic engineering
Integration with lab management software
Conclusions and future perspectives
References
Metabolic engineering for microbial cell factories
Introduction
Metabolic engineering approaches
Emergence of systems metabolic engineering
Systems metabolic engineering strategies
Design of systems metabolic engineering project
Selection of appropriate host platform
Construction of synthetic metabolic pathways
Optimization of metabolic fluxes
The principles and tools for pathway prediction and design
The pathways constructed using rational and computational strategies
De novo pathway design
In silico pathway prediction
Enzyme engineering and creation for synthetic pathways
Metabolic flux analysis
Enhancing tolerance against products and inhibitors
Scale up and industrial production
Conclusion and future perspectives
References
CRISPR-based tools for microbial cell factories
Introduction
CRISPR-Cas editing at the single gene level
Gene editing with CRISPR-Cas
CRISPR-Cas editing of single genes in bacteria
CRISPR-Cas editing of single genes in yeast
CRISPR-Cas editing at the genome level
CRISPR-optimized MAGE recombineering
CRISPR-EnAbled Trackable genome Engineering (CREATE)
Curing strategies for editing (gRNA) plasmids facilitate iterative CRISPR editing
CRISPR-Cas9 genome engineering tools in yeast
Gene regulation tools
CRISPR interference
CRISPR activation
Conclusions
References
Escherichia coli, the workhorse cell factory for the production of chemicals
Introduction: Escherichia coli, a model microorganism for basic and applied research
Precursor biotransformation
Whole-cell biocatalysis via single-step ``pathways´´: Harnessing enzymatic promiscuity
Protein engineering: Modification of enzymes by directed evolution
Cofactors pools and regeneration
Multistep biosynthesis pathways: One-pot multicatalysis
De novo biotransformations and metabolic engineering
Metabolites of industrial interest
d-Lactate
Dicarboxylic acids (succinate and malate)
Pyruvate
Amino acids
Biofuels
Biohydrogen
Bioethanol
Coproduction of biohydrogen and bioethanol
1-Butanol, 1-propanol, isopropanol and isobutanol
Biopolymers
Diols: 1,3-PDO, 1,2-PDO, and 1,4-BDO
PHA
Concluding remarks
References
Bacillus subtilis-based microbial cell factories
Introduction
Bacillus as a workhorse for high-value compound biosynthesis
Pathways involved in enzymes and primary metabolites biosynthesis
Gene clusters involved in secondary metabolites biosynthesis
Engineered Bacillus subtilis
Metabolic modeling for strains optimization of B. subtilis
Genome editing
Homologous recombination-based modification
CRISPR/Cas9-mediated genome editing
Transcriptional engineering to overproduce biomolecules or proteins of interest by B. subtilis
Promoter exchange in B. subtilis
Promoter engineering in B. subtilis
Expression of cryptic biosynthetic gene clusters
Engineered Bacillus on the translational level
Factors affecting translation rate
Regulation
Stability-enhancing sequences
Ribosome-binding site (RBS)
Other factors
Engineered Bacillus on transport level
Use of coproducts for the synthesis of high-value chemicals
Use of original substrates for B. subtilis culture media
Use of renewable resources for the production of secondary metabolites by Bacillus
Use of organic waste agroresidue and wastewater for the production of enzyme by Bacillus
Use of organic waste agroresidue for the production of biomolecule during solid-state fermentation of Bacillus
Minibacillus
Conclusion and future remarks
References
Pseudomonas putida-based cell factories
Introduction
Pseudomonas putida as a host for the production of natural products
Polyhydroxyalkanoates
Surfactants
Terpenoids
Prodigiosin
Concluding remarks
References
Further reading
Streptomyces-based cell factories for production of biomolecules and bioactive metabolites
Introduction
Streptomyces habitats
General characteristics of the genus Streptomyces
Growth requirements of Streptomyces species
Production of secondary metabolites
Streptomyces species as cell factories for production of antibiotics
Definition of antibiotics
The antibiotics derived from Streptomyces strains
Anticancer, immunostimulatory, immunosuppressive, and antioxidative agents produced by Streptomyces species
Streptomyces species as cell factories for production of active metabolites applied against causative agents of a numb ...
Kasugamycin
Polyoxin
Azalomycin
Validamycin
Geldanamycin and nigericin
Streptomyces species as cell factories for production of insecticides and antiparasitic agents
Tetranactin
Ivermectin
Streptomyces species as cell factories for production of a variety of enzymes
L-asparaginase
Cholesterol oxidase
Uricase (gout treatment enzyme)
Antidiabetic produced by Streptomyces species
Cholesterol synthesis inhibitors produced by Streptomyces species
Lytic enzymes
Cellulases
Amylase
Proteases and keratinases
Chitinolytic enzymes (chitinases)
Chitosanase
Streptomyces species as cell factories for production of lipases
Streptomyces species as cell factories for production of bioemulsifiers and biosurfactants
Streptomyces species as cell factories for production of pigments
Streptomyces species as cell factories for synthesis of nanoparticles
Production of vitamins
Production of odors
Conclusion and future perspective
References
Further reading
Corynebacterium glutamicum as a robust microbial factory for production of value-added proteins and small mol ...
Introduction
Protein secretion system in C. glutamicum
The Sec-dependent pathway
The Tat-dependent pathway
C. glutamicum protein expression system
Expression plasmid vectors of C. glutamicum
Promoters for optimized gene expression in C. glutamicum
Classification of promoters in C. glutamicum expression system
Sources of engineered promoters in C. glutamicum expression system
Sequence optimization of ribosome binding sites (RBS) for gene expression in C. glutamicum
Signal peptide applied in C. glutamicum expression vectors
Other expression elements
Replicons
Resistance markers
Gene editing tools applied in C. glutamicum
pKl8mobsacB and pKl9mobsacB based on homologous recombination technology
Gene knockout system based on Cre/loxP site-specific recombination technology
C. glutamicum as a major workhorse for production of small molecules
Rational metabolic engineering
2OG-derived chemicals
OAA-derived chemicals
Various more chemicals derived from central metabolism of C. glutamicum
Directed evolution
Adaptive laboratory evolution
Biosensors and high-throughput engineering
Conclusions
References
Production of high value-added chemicals by engineering methylotrophic cell factories
Introduction
New progress in genetic manipulation tools for engineering of MeCFs
Advances in engineering of the metabolic pathway in/from methylotrophs
Improvement of methylotrophic phenotypes via evolution
Producing high value-added chemicals by engineering MeCFs
Metabolic potential of native methylotrophs for synthesizing secondary metabolites
Conclusions and perspectives
References
Cyanobacteria-based microbial cell factories for production of industrial products
Introduction
Bioremediation
Biodiesel
Biohydrogen
Bioplastic
Microbial fuel cell
Nanoparticle synthesis by cyanobacteria
Exopolysaccharides producing cyanobacteria
Pigments producing cyanobacteria as microbial fuel cell
Carotenoids
3-Phycobiliproteins
Phycocyanin
Phycoerythrin
Antiviral, antibacterial, antifungal, and anticancer compounds obtain by cyanobacteria
Conclusion and future perspectives
References
Integrated omics perspective to understand the production of high-value added biomolecules (HVABs) in microal ...
Introduction
Unraveling biosynthetic pathways for the production of HVABs
Genomic and phylogenomic analysis
Transcriptomics and proteomics
Metabolomics
Metabolic flux analysis
Integrated omics for the redesigning/remapping metabolic pathways for enhanced HVAB production
Top-down approach (gene to metabolite)
Genome-scale mEtabolic models (GEMs)
Microalgal cell factories: An overview
Conclusions and future remarks
References
Saccharomyces cerevisiae as a microbial cell factory
Introduction
Methods and applications for yeast transformation
Transformation methods
DNA vectors for expressing genes
Promoters
Engineering of S. cerevisiae
CRISPR system-mediated engineering
Surface-display engineering
Metabolic engineering of S. cerevisiae
Cellulose degradation
Xylose utilization
LA production
Production of fine chemicals
Production of recombinant protein
Conclusion
References
Pichia pastoris-based microbial cell factories
Introduction
Genetic engineering tools for P. pastoris
Integrative expression of genes
Episomal expression of genes
Promoter engineering
Genome editing by CRISPR
Protein production by P. pastoris
Useful proteins produced by P. pastoris
Strategies for enhancing protein production
Fermentative chemical production by P. pastoris
Fermentative chemicals produced by P. pastoris
Strategies for enhancing fermentative chemical production
Chemical production by P. pastoris whole-cell biocatalyst
Oxidation reaction
Reduction reaction
ATP-dependent reaction
Cell surface-displayed enzyme reaction
Conclusions
References
Yarrowia lipolytica engineering as a source of microbial cell factories
Introduction
Main characteristics of Yarrowia lipolytica
A short history of Yarrowia lipolytica use
Overview of basic tools for Yarrowia lipolytica engineering
Expression/secretion vectors and transcription unit components
Choosing a replicative or an integrative vector
Vectors carrying multiple transcription units
Regulatory components of transcription units
Promoters
Terminators
Targeting components of transcription units
Cellular organelles targeting and compartmentalization
Signal sequences for secretion
Signal sequences for surface display
Strains and selection markers
Most commonly used recipient strains
Recipient strains with increased homologous recombination efficiency
Glycoengineered strains and their interest for therapeutic applications
Selection marker genes
A post-2010 era of new engineering technologies
New DNA assembly methods
In vivo assembly of metabolic pathways
Design of artificial chromosomes
In vitro DNA assembly methods
Genome editing technologies
CRISPR tools for gene editing
CRISPR tools for repression or activation of transcription
CRISPR tools for base editing
CRISPR tools for whole genome analysis
Other gene editing and transposomics tools
Sexual hybridization through mating-type switching
Yarrowia lipolytica developing applications and future prospects
High-throughput expression platforms for protein engineering and more
Obese Yarrowia lipolytica strains
Whole-cell Yarrowia lipolytica factories for single-cell oil production
Use of waste or renewable resources for production of biofuels and more
Whole-cell factories producing carotenoids, other terpenoids, and polyketides
Whole-cell factories for organic acid production
Bioengineered hybrid materials for environmental applications
What future prospects?
References
Engineering of microbial cell factories for production of plant-based natural products
Introduction
Host microorganisms
Metabolic engineering strategies in microorganisms for production of PNPs
Increasing precursor availability
Biosynthetic pathway engineering
Enzymatic engineering
Terpenoids
Lycopene
Taxol
Alkaloids
Benzylisoquinoline alkaloids
Polyphenols
Resveratrol
Naringenin
Conclusion and future challenges
Funding
References
Engineering of microbial cell factories for omics-guided production of medically important biomolecules
Introduction
Omics-driven microbial chassis development
Design, build, test, and learn of natural product synthesis in engineered microbes
Parts discovery for natural and new-to-nature natural products using systems biology platform
Omics-driven bioproduction of medically important biomolecules and natural products
Terpene synthase for plug-and-play terpene production
Strictosidine biosynthetic genes for refactoring of monoterpene indole alkaloid biosynthesis
Transcriptome-enabled discovery and microbial expression flavonoid biosynthetic genes
Conclusions and perspectives
References
Advances and applications of cell-free systems for metabolic production
Introduction
In vitro transcription-translation (TX-TL) systems
E. coli lysate-based TX-TL system
Other prokaryotic and eukaryotic lysate-based cell-free systems
PURE cell-free system
In vitro systems using purified enzymes
Glycolysis
Terpene production
Hydrogen production
n-Butanol production
CO2 fixation
Photobiocatalysis
Enzymatic electrocatalysis
Applications of TX-TL systems for bioproduction
Bioproduction and rapid prototyping
Engineering and evolution of enzymes
Bottom-up development of synthetic cells with cell-free systems
Conclusions and perspectives
References
Microbial biosensors for discovery and engineering of enzymes and metabolism
Introduction
Types and construction of microbial biosensors
Allosteric transcription factor-based biosensors
Riboswitch-based biosensors
Application of biosensors for the engineering of enzymes and metabolic pathways
Screening and selection
Dynamic regulation
Application of biosensors for the discovery of novel enzymes and metabolic pathways
The necessity of high-throughput screening approaches for discovery of novel gene and operon functions
Functional screening for novel enzymes with desired activities
Altering transcription factor expression to study gene and operon function
Methods to characterize transcription factor-DNA interactions
Toward high-throughput systems to characterize transcription factor-effector interactions
Conclusions and perspectives
References
Manipulation of global regulators in Escherichia coli for the synthesis of biotechnologically relevant products
Introduction of Escherichia coli metabolism
Global regulation of metabolism
Signal transduction
Control of the central carbon metabolism by global regulation
Global regulation in response to the carbon source: Crp and Cra
Crp
Cra
Regulation of intermediary metabolism: CreBC and Rob
CreBC
Rob
Regulation of central carbon metabolism in response to oxygen availability: ArcAB and FNR
ArcAB
FNR
Manipulation of global regulators: Its effect on the synthesis of biotechnological compounds
Biofuels
Ethanol
Butanol and higher alcohols
Polyhydroxyalkanoates
1,3-propanediol
Succinic acid
Concluding remarks
References
Index
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