Whole Cell Biocatalysis

Contributors<br>About the editors<br>Preface<br><br>CHAPTER 1 Advantages and new potential applications of whole-cell biocatalysis<br>Sergio Huerta-Ochoa<br><br>1 Introduction<br>1.1 History of whole-cell biocatalysis development<br>1.2 Technical advances and economic advantages of whole-cell biocatalysis<br>1.3 Reaction media in whole-cell biocatalysis<br>1.4 Main microorganisms used as whole-cell factories<br>2 Key advances and potential applications<br>2.1 Cell permeabilization<br>2.2 Cell immobilization<br>2.3 Metabolic engineering<br>2.4 Cascade reactions<br>2.5 Chemoenzymatic synthesis<br>2.6 Sustainable manufacturing<br>2.7 Pharmaceutical production<br>2.8 Biodegradation and bioremediation<br>2.9 Renewable energy production<br>3 Trends and perspectives<br>References<br><br>CHAPTER 2 Reprogramming microbial cells to improve the production of biopharmaceuticals and fine chemicals<br>Alvaro R. Lara, Marcos López-Perez, and Francisco J. Fernández<br><br>1 Introduction to molecular genetics in the production of chemical and pharmaceutical substances<br>1.1 Significance of chemical and pharmaceutical substance production in the industry and their impact on the global economy<br>1.2 Use of microorganisms in the production of chemical and pharmaceutical substances, with emphasis on fungi<br>1.3 Improving fungal strains through classical genetic techniques with emphasis on antibiotics<br>1.4 Reasons for the use of molecular genetic techniques<br>2 Classic molecular cloning techniques<br>2.1 Molecular cloning: A clear definition<br>2.2 Cloning of genes and DNA fragments<br>2.3 DNA and complementary DNA (cDNA) libraries<br>2.4 Featured examples of molecular cloning in antibiotic production<br>3 Gene dosage optimization<br>3.1 Gene dosage and modulation of gene dosage<br>3.2 Gene dosage optimization in industrial production: Importance and examples<br>3.3 Other alternatives: E.g., increasing precursor availability and/or improving precursor and penicillin transport<br>4 Advanced genetic engineering tools<br>4.1 Advances in genetic engineering<br>4.2 High-throughput sequencing (NGS) techniques<br>4.3 Promoters and RBS (bio-bricks) libraries<br>4.4 Synthetic biology<br>4.5 CRISPR-Cas9 technology<br>5 Cell factories for whole-cell biocatalysis<br>5.1 Minimal cell factories<br>5.2 Robust cell factories<br>5.3 Schemes for autonomous control of the metabolic fluxes and induction of product synthesis<br>6 The future of molecular genetics in the production of chemical and pharmaceutical substances<br>References<br><br>CHAPTER 3 Mitigation of greenhouse gas emissions from biogas-producing facilities: A novel whole-cell technology platform based on anaerobic oxidation of methane<br>Guillermo Quijano and Ivonne Figueroa-González<br><br>1 Introduction<br>2 GHG emissions from biogas-producing facilities<br>3 Conventional aerobic biotechnologies for treating residual dissolved methane<br>3.1 Aerobic methanotrophic metabolism<br>3.2 Packed bed reactors and two-phase partitioning systems<br>3.3 Aerobic membrane bioreactors<br>4 Whole-cell technology platform for anaerobic methane oxidation<br>4.1 Fundamentals and process microbiology of the N-AOM process<br>4.2 Bioreactors and operating conditions reported for N-AOM implementation<br>5 Perspectives<br>References<br><br>CHAPTER 4 Computational metabolic engineering using genome-scale metabolic models and constraint-based methods<br>Carlos Coello-Castillo, Freddy Castillo-Alfonso, and Roberto Olivares-Hernández<br><br>1 Defining metabolic engineering<br>2 Microbial cell factory<br>3 Strategies for designing microbial cell factories<br>4 The engineering cycle<br>5 The principles for the calculation of metabolic fluxes<br>6 Linear programming for metabolic network modeling<br>7 Genome-scale mathematical modeling<br>8 Reconstruction of the metabolic model<br>9 Metabolic engineering and systems biology<br>10 Data integration<br>11 Metabolic engineering and systems biology strategies<br>References<br><br>CHAPTER 5 Whole-cell biocatalysis in nonconventional media<br>Dulce María Palmerín-Carreno<br><br>1 Introduction<br>2 Nonconventional media used for biocatalysis<br>2.1 Whole-cell function in nonconventional media<br>3 Reaction and transport mechanisms in nonconventional media<br>3.1 Partitioning bioreactors<br>3.2 Solid-gas bioreactors<br>4 Applications of reaction in nonconventional media<br>5 Conclusions<br>References<br><br>CHAPTER 6 Nanostructured magnetic systems in whole-cell biocatalysis<br>Nayra Ochoa-Viñals, Rodolfo Ramos-González, Dania Alonso-Estrada, Mayela Govea-Salas, Ariel García-Cruz, Roberto Arredondo-Valdes, José L. Martínez-Hernández, Arturo S. Palacios-Ponce, and Anna Ilina<br><br>1 Introduction<br>2 Coated magnetic nanoparticles and their properties for catalysis<br>3 Mechanisms of interactions between cells and magnetic nanoparticles<br>4 Toxicity of magnetic nanoparticles on microbial cells<br>5 Application of magnetic nanoparticles in catalysis with bacteria and yeast<br>6 Surface adhesion fermentation using magnetic nanoparticles: Advantages and disadvantages<br>7 Scale-up considerations<br>8 Hyperthermia with magnetic nanoparticles and its possible application<br>9 Future perspectives<br>Author contributions<br>Acknowledgments<br>Conflict of interest<br>References<br><br>CHAPTER 7 Filamentous fungi as biopharmaceutical protein factories<br>Ulises Carrasco Navarro and María Fernanda Cerón-Moreno<br><br>1 Protein secretion in filamentous fungi<br>2 Co- or posttranslational transport from ribosome to ER<br>3 Folding and polypeptide modifications<br>4 Golgi complex and O-glycosylation<br>5 Spitzenkörper<br>6 Biopharmaceutical protein production in filamentous fungi<br>7 Genetic tools for recombinant protein production in filamentous fungi<br>8 Concluding remarks<br>References<br><br>CHAPTER 8 Proteomic analysis: Application to the study of signal transduction pathways in Penicillium chrysogenum and Acremonium chrysogenum<br>Ulises Carrasco Navarro, María Fernanda Cerón-Moreno and Francisco J. Fernández<br><br>1 About Penicillium chrysogenum and Acremonium chrysogenum<br>2 Cell signaling<br>3 Proteomics<br>3.1 Techniques employed in proteomic analysis<br>3.2 Proteomic analysis of cell signaling pathways in P. chrysogenum<br>4 Conclusions<br>References<br><br>CHAPTER 9 Fungal lipase obtained by surface adhesion fermentation using magnetic chitosan-coated nanoparticles<br>Anna Ilina, Rodolfo Ramos-González, Elva Arechiga-Carvajal, Patricia Segura-Ceniceros, José L. Martínez-Hernández, and Cynthia Barrera<br><br>1 Introduction<br>2 Materials and methods<br>2.1 Microorganisms and crop development<br>2.2 Support preparation<br>2.3 Characterization of the immobilization process of A. niger spores on NPM-Q<br>2.4 Surface adhesion fermentation (SAF)<br>2.5 Assay for the determination of lipase activity<br>3 Results and discussion<br>3.1 Interaction characterization of A. niger spores and NPM-Q<br>3.2 Comparison of lipase production by submerged fermentation and surface-attachment fermentation<br>4 Conclusion<br>References<br><br>CHAPTER 10 In vitro plant cultures as a viable biotechnological tool for the biosynthesis of steroidal hormones of clinical interest<br>Gabriel Alfonso Gutierrez-Rebolledo, Mariana Zuleima Perez-González, Mariana Sánchez-Ramos, and Francisco Cruz-Sosa<br><br>1 Introduction<br>1.1 Global prospects in the clinical use and industrial production of hormones<br>1.2 Biosynthesis pathways of steroid structures in plant cells<br>2 Aim of the chapter<br>3 Methodology<br>4 Results<br>4.1 In vitro plant cell cultures by biotechnological techniques<br>4.2 Analytical methods applied to secondary metabolites produced by plant cell cultures<br>5 Discussion<br>6 Conclusions<br>Disclaimer<br>Acknowledgments<br>References<br><br>CHAPTER 11 Whole-cell biocatalysis for large-scale production<br>Zhi-Qiang Liu, Xue Cai, Xiao-Jian Zhang, Ji-Dong Shen, Fang-Ying Zhu, and Yu-Guo Zheng<br><br>1 Introduction<br>2 Design of whole-cell biocatalysts<br>2.1 The optimization and design of biosynthetic pathways<br>2.2 Improvement of pathway flux<br>2.3 Dynamic regulation of enzyme concentrations<br>2.4 Enhanced urban transportation<br>3 Biocatalysis of whole cells in biphase media<br>3.1 Biphasic media-catalyzed lipase<br>3.2 Reactions facilitated by reductase in aqueous-organic media<br>3.3 Conclusions<br>4 Immobilization of whole-cell catalyst<br>4.1 Strategy for entrapment and encapsulation<br>4.2 Adhesion technique<br>4.3 The covalent coupling method<br>4.4 Utilizing a combined methodologies approach<br>5 One-pot multicell catalysis<br>6 Conclusions<br>References<br><br>Author Index<br>Subject Index