Whole Cell Biocatalysis

Sergio Huerta-Ochoa (PhD, 1993, Reading University, UK) has been part of the Staff of the Biotechnology Department during 35 years at “Autónoma Metropolitana” University in Mexico City. He spent a sabbatical year (2007-2008) as an Honorary Research Associate at the Department of Biochemical Engineering, University College London, UK. His expertise is mainly focused on engineering of bioconversion processes using whole-cells in partitioning bioreactors. He is Co-author of 48 papers in indexed international journals (h index 14, Scopus-Elsevier, May 2017) and supervised up to 13 MSc and 5 PhD theses. One of these PhD theses titled “Study of mass transfer, kinetic and deactivation of a three phase partitioning bioreactor using whole cells” won the Alfredo Sánchez Marroquín 2015 award by the Mexican Society of Biotechnology and Bioengineering (SMBB). He is awarded with the “Level II” membership of the National Researchers System of Mexico (SNI), and Member of the Mexican Academy of Science since 2014. Dr. Lilia Arely Prado Barragán (PhD, 1997, University of Nottingham) has been part of the staff of the Biotechnology Department for 35 years at the Universidad Autónoma Metropolitana in Mexico City. She has published 51 articles in indexed international journals, 18 book chapters and co-edited 3 books. She has supervised 9 Masters theses and 12 Doctoral theses. She belongs to the National System of Researchers (SNI) in "Level I”, and has been a member of the Mexican Academy of Sciences since 2016. Prof. Dr. Cristobal N. Aguilar, Chemist, PhD, was the Director of the Research and Postgraduate Programs at Autonomous University of Coahuila (2018–2024, Mexico, where from 2014 to 2018, he was the Dean of the School of Chemistry. He is a Level III member of S.N.I. (Mexican System of Researchers). He has received several prizes and awards, among which the most important are the National Prize of Research 2010 of the Mexican Academy of Sciences, the Prize “Carlos Casas Campillo 2008” of the Mexican Society of Biotechnology and Bioengineering, the National Prize AgroBio–2005, the Mexican Prize in Food Science and Technology from CONACYT-Coca Cola México 2003, the 2018 Outstanding Researcher Award by the International Association of Bioprocessing, and the 2019 Coahuila State Innovation Science and Technology Award. He's developed more than 30 research projects, including seven international exchange projects. He is a member of the Mexican Academy of Science (since 2014).

• ContributorsAbout the editorsPrefaceCHAPTER 1 Advantages and new potential applications of whole-cell biocatalysisSergio Huerta-Ochoa1 Introduction1.1 History of whole-cell biocatalysis development1.2 Technical advances and economic advantages of whole-cell biocatalysis1.3 Reaction media in whole-cell biocatalysis1.4 Main microorganisms used as whole-cell factories2 Key advances and potential applications2.1 Cell permeabilization2.2 Cell immobilization2.3 Metabolic engineering2.4 Cascade reactions2.5 Chemoenzymatic synthesis2.6 Sustainable manufacturing2.7 Pharmaceutical production2.8 Biodegradation and bioremediation2.9 Renewable energy production3 Trends and perspectivesReferencesCHAPTER 2 Reprogramming microbial cells to improve the production of biopharmaceuticals and fine chemicalsAlvaro R. Lara, Marcos López-Perez, and Francisco J. Fernández1 Introduction to molecular genetics in the production of chemical and pharmaceutical substances1.1 Significance of chemical and pharmaceutical substance production in the industry and their impact on the global economy1.2 Use of microorganisms in the production of chemical and pharmaceutical substances, with emphasis on fungi1.3 Improving fungal strains through classical genetic techniques with emphasis on antibiotics1.4 Reasons for the use of molecular genetic techniques2 Classic molecular cloning techniques2.1 Molecular cloning: A clear definition2.2 Cloning of genes and DNA fragments2.3 DNA and complementary DNA (cDNA) libraries2.4 Featured examples of molecular cloning in antibiotic production3 Gene dosage optimization3.1 Gene dosage and modulation of gene dosage3.2 Gene dosage optimization in industrial production: Importance and examples3.3 Other alternatives: E.g., increasing precursor availability and/or improving precursor and penicillin transport4 Advanced genetic engineering tools4.1 Advances in genetic engineering4.2 High-throughput sequencing (NGS) techniques4.3 Promoters and RBS (bio-bricks) libraries4.4 Synthetic biology4.5 CRISPR-Cas9 technology5 Cell factories for whole-cell biocatalysis5.1 Minimal cell factories5.2 Robust cell factories5.3 Schemes for autonomous control of the metabolic fluxes and induction of product synthesis6 The future of molecular genetics in the production of chemical and pharmaceutical substancesReferencesCHAPTER 3 Mitigation of greenhouse gas emissions from biogas-producing facilities: A novel whole-cell technology platform based on anaerobic oxidation of methaneGuillermo Quijano and Ivonne Figueroa-González1 Introduction2 GHG emissions from biogas-producing facilities3 Conventional aerobic biotechnologies for treating residual dissolved methane3.1 Aerobic methanotrophic metabolism3.2 Packed bed reactors and two-phase partitioning systems3.3 Aerobic membrane bioreactors4 Whole-cell technology platform for anaerobic methane oxidation4.1 Fundamentals and process microbiology of the N-AOM process4.2 Bioreactors and operating conditions reported for N-AOM implementation5 PerspectivesReferencesCHAPTER 4 Computational metabolic engineering using genome-scale metabolic models and constraint-based methodsCarlos Coello-Castillo, Freddy Castillo-Alfonso, and Roberto Olivares-Hernández1 Defining metabolic engineering2 Microbial cell factory3 Strategies for designing microbial cell factories4 The engineering cycle5 The principles for the calculation of metabolic fluxes6 Linear programming for metabolic network modeling7 Genome-scale mathematical modeling8 Reconstruction of the metabolic model9 Metabolic engineering and systems biology10 Data integration11 Metabolic engineering and systems biology strategiesReferencesCHAPTER 5 Whole-cell biocatalysis in nonconventional mediaDulce María Palmerín-Carreno1 Introduction2 Nonconventional media used for biocatalysis2.1 Whole-cell function in nonconventional media3 Reaction and transport mechanisms in nonconventional media3.1 Partitioning bioreactors3.2 Solid-gas bioreactors4 Applications of reaction in nonconventional media5 ConclusionsReferencesCHAPTER 6 Nanostructured magnetic systems in whole-cell biocatalysisNayra 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 Ilina1 Introduction2 Coated magnetic nanoparticles and their properties for catalysis3 Mechanisms of interactions between cells and magnetic nanoparticles4 Toxicity of magnetic nanoparticles on microbial cells5 Application of magnetic nanoparticles in catalysis with bacteria and yeast6 Surface adhesion fermentation using magnetic nanoparticles: Advantages and disadvantages7 Scale-up considerations8 Hyperthermia with magnetic nanoparticles and its possible application9 Future perspectivesAuthor contributionsAcknowledgmentsConflict of interestReferencesCHAPTER 7 Filamentous fungi as biopharmaceutical protein factoriesUlises Carrasco Navarro and María Fernanda Cerón-Moreno1 Protein secretion in filamentous fungi2 Co- or posttranslational transport from ribosome to ER3 Folding and polypeptide modifications4 Golgi complex and O-glycosylation5 Spitzenkörper6 Biopharmaceutical protein production in filamentous fungi7 Genetic tools for recombinant protein production in filamentous fungi8 Concluding remarksReferencesCHAPTER 8 Proteomic analysis: Application to the study of signal transduction pathways in Penicillium chrysogenum and Acremonium chrysogenumUlises Carrasco Navarro, María Fernanda Cerón-Moreno and Francisco J. Fernández1 About Penicillium chrysogenum and Acremonium chrysogenum2 Cell signaling3 Proteomics3.1 Techniques employed in proteomic analysis3.2 Proteomic analysis of cell signaling pathways in P. chrysogenum4 ConclusionsReferencesCHAPTER 9 Fungal lipase obtained by surface adhesion fermentation using magnetic chitosan-coated nanoparticlesAnna Ilina, Rodolfo Ramos-González, Elva Arechiga-Carvajal, Patricia Segura-Ceniceros, José L. Martínez-Hernández, and Cynthia Barrera1 Introduction2 Materials and methods2.1 Microorganisms and crop development2.2 Support preparation2.3 Characterization of the immobilization process of A. niger spores on NPM-Q2.4 Surface adhesion fermentation (SAF)2.5 Assay for the determination of lipase activity3 Results and discussion3.1 Interaction characterization of A. niger spores and NPM-Q3.2 Comparison of lipase production by submerged fermentation and surface-attachment fermentation4 ConclusionReferencesCHAPTER 10 In vitro plant cultures as a viable biotechnological tool for the biosynthesis of steroidal hormones of clinical interestGabriel Alfonso Gutierrez-Rebolledo, Mariana Zuleima Perez-González, Mariana Sánchez-Ramos, and Francisco Cruz-Sosa1 Introduction1.1 Global prospects in the clinical use and industrial production of hormones1.2 Biosynthesis pathways of steroid structures in plant cells2 Aim of the chapter3 Methodology4 Results4.1 In vitro plant cell cultures by biotechnological techniques4.2 Analytical methods applied to secondary metabolites produced by plant cell cultures5 Discussion6 ConclusionsDisclaimerAcknowledgmentsReferencesCHAPTER 11 Whole-cell biocatalysis for large-scale productionZhi-Qiang Liu, Xue Cai, Xiao-Jian Zhang, Ji-Dong Shen, Fang-Ying Zhu, and Yu-Guo Zheng1 Introduction2 Design of whole-cell biocatalysts2.1 The optimization and design of biosynthetic pathways2.2 Improvement of pathway flux2.3 Dynamic regulation of enzyme concentrations2.4 Enhanced urban transportation3 Biocatalysis of whole cells in biphase media3.1 Biphasic media-catalyzed lipase3.2 Reactions facilitated by reductase in aqueous-organic media3.3 Conclusions4 Immobilization of whole-cell catalyst4.1 Strategy for entrapment and encapsulation4.2 Adhesion technique4.3 The covalent coupling method4.4 Utilizing a combined methodologies approach5 One-pot multicell catalysis6 ConclusionsReferencesAuthor IndexSubject Index