Microbial Cell Factories Engineering for Production of Biomolecules

Description

Microbial Cell Factories Engineering for Production of Biomolecules presents a compilation of chapters written by eminent scientists worldwide. Sections cover major tools and technologies for DNA synthesis, design of biosynthetic pathways, synthetic biology tools, biosensors, cell-free systems, computer-aided design, OMICS tools, CRISPR/Cas systems, and many more. Although it is not easy to find relevant information collated in a single volume, the book covers the production of a wide range of biomolecules from several MCFs, including Escherichia coli, Bacillus subtilis, Pseudomonas putida, Streptomyces, Corynebacterium, Cyanobacteria, Saccharomyces cerevisiae, Pichia pastoris and Yarrowia lipolytica, and algae, among many others. This will be an excellent platform from which scientific knowledge can grow and widen in MCF engineering research for the production of biomolecules. Needless to say, the book is a valuable source of information not only for researchers designing cell factories, but also for students, metabolic engineers, synthetic biologists, genome engineers, industrialists, stakeholders and policymakers interested in harnessing the potential of MCFs in several fields. 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 A B C D E F G H I K L M N O P Q R S T U V W X Y Z