Whole Cell Biocatalysis
Fundamentals and Applications
- 1st Edition - July 16, 2025
- Editors: Sergio Huerta-Ochoa, Lilia Arely Prado-Barragán, Cristobal Noe Aguilar
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 2 3 9 9 8 - 4
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 2 3 9 9 9 - 1
Whole Cell Biocatalysis, a volume in the Foundations and Frontiers of Enzymology series, offers a detailed overview of the process of biocatalysis using whole cells as an alte… Read more
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Whole Cell Biocatalysis, a volume in the Foundations and Frontiers of Enzymology series, offers a detailed overview of the process of biocatalysis using whole cells as an alternative to enzyme biocatalysis. The book examines the potential applications and advantages of whole cell biocatalysis, including its use in the production of fine chemicals, renewable energy, and drug discovery and development. Whole cell biocatalysis for large scale production and non-conventional media are also covered. In addition, the latest methods and techniques are investigated, including cell immobilization, permeabilization, synthetic biology, computational metabolic engineering, and molecular genetics.
This book provides a comprehensive summary on whole cell biocatalysis and the latest developments in this emerging field. It is an invaluable reference for researchers working across biochemistry, enzymology, biotechnology, and related fields.
- Considers the advantages and challenges of whole cell biocatalysis to enhance production processes in various industries
- Includes a range of techniques to investigate and facilitate whole cell biocatalysis
- Covers whole cell biocatalysis in non-conventional media
- Studies biocatalytic cascade reactions
Researchers and students in biochemistry, enzymology, biotechnology, and related areas Researchers, students and experts in biochemical engineering, chemical and pharmaceutical industries
Contributors
About the editors
Preface
CHAPTER 1 Advantages and new potential applications of whole-cell biocatalysis
Sergio Huerta-Ochoa
1 Introduction
1.1 History of whole-cell biocatalysis development
1.2 Technical advances and economic advantages of whole-cell biocatalysis
1.3 Reaction media in whole-cell biocatalysis
1.4 Main microorganisms used as whole-cell factories
2 Key advances and potential applications
2.1 Cell permeabilization
2.2 Cell immobilization
2.3 Metabolic engineering
2.4 Cascade reactions
2.5 Chemoenzymatic synthesis
2.6 Sustainable manufacturing
2.7 Pharmaceutical production
2.8 Biodegradation and bioremediation
2.9 Renewable energy production
3 Trends and perspectives
References
CHAPTER 2 Reprogramming microbial cells to improve the production of biopharmaceuticals and fine chemicals
Alvaro R. Lara, Marcos López-Perez, and Francisco J. Fernández
1 Introduction to molecular genetics in the production of chemical and pharmaceutical substances
1.1 Significance of chemical and pharmaceutical substance production in the industry and their impact on the global economy
1.2 Use of microorganisms in the production of chemical and pharmaceutical substances, with emphasis on fungi
1.3 Improving fungal strains through classical genetic techniques with emphasis on antibiotics
1.4 Reasons for the use of molecular genetic techniques
2 Classic molecular cloning techniques
2.1 Molecular cloning: A clear definition
2.2 Cloning of genes and DNA fragments
2.3 DNA and complementary DNA (cDNA) libraries
2.4 Featured examples of molecular cloning in antibiotic production
3 Gene dosage optimization
3.1 Gene dosage and modulation of gene dosage
3.2 Gene dosage optimization in industrial production: Importance and examples
3.3 Other alternatives: E.g., increasing precursor availability and/or improving precursor and penicillin transport
4 Advanced genetic engineering tools
4.1 Advances in genetic engineering
4.2 High-throughput sequencing (NGS) techniques
4.3 Promoters and RBS (bio-bricks) libraries
4.4 Synthetic biology
4.5 CRISPR-Cas9 technology
5 Cell factories for whole-cell biocatalysis
5.1 Minimal cell factories
5.2 Robust cell factories
5.3 Schemes for autonomous control of the metabolic fluxes and induction of product synthesis
6 The future of molecular genetics in the production of chemical and pharmaceutical substances
References
CHAPTER 3 Mitigation of greenhouse gas emissions from biogas-producing facilities: A novel whole-cell technology platform based on anaerobic oxidation of methane
Guillermo Quijano and Ivonne Figueroa-González
1 Introduction
2 GHG emissions from biogas-producing facilities
3 Conventional aerobic biotechnologies for treating residual dissolved methane
3.1 Aerobic methanotrophic metabolism
3.2 Packed bed reactors and two-phase partitioning systems
3.3 Aerobic membrane bioreactors
4 Whole-cell technology platform for anaerobic methane oxidation
4.1 Fundamentals and process microbiology of the N-AOM process
4.2 Bioreactors and operating conditions reported for N-AOM implementation
5 Perspectives
References
CHAPTER 4 Computational metabolic engineering using genome-scale metabolic models and constraint-based methods
Carlos Coello-Castillo, Freddy Castillo-Alfonso, and Roberto Olivares-Hernández
1 Defining metabolic engineering
2 Microbial cell factory
3 Strategies for designing microbial cell factories
4 The engineering cycle
5 The principles for the calculation of metabolic fluxes
6 Linear programming for metabolic network modeling
7 Genome-scale mathematical modeling
8 Reconstruction of the metabolic model
9 Metabolic engineering and systems biology
10 Data integration
11 Metabolic engineering and systems biology strategies
References
CHAPTER 5 Whole-cell biocatalysis in nonconventional media
Dulce María Palmerín-Carreno
1 Introduction
2 Nonconventional media used for biocatalysis
2.1 Whole-cell function in nonconventional media
3 Reaction and transport mechanisms in nonconventional media
3.1 Partitioning bioreactors
3.2 Solid-gas bioreactors
4 Applications of reaction in nonconventional media
5 Conclusions
References
CHAPTER 6 Nanostructured magnetic systems in whole-cell biocatalysis
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
1 Introduction
2 Coated magnetic nanoparticles and their properties for catalysis
3 Mechanisms of interactions between cells and magnetic nanoparticles
4 Toxicity of magnetic nanoparticles on microbial cells
5 Application of magnetic nanoparticles in catalysis with bacteria and yeast
6 Surface adhesion fermentation using magnetic nanoparticles: Advantages and disadvantages
7 Scale-up considerations
8 Hyperthermia with magnetic nanoparticles and its possible application
9 Future perspectives
Author contributions
Acknowledgments
Conflict of interest
References
CHAPTER 7 Filamentous fungi as biopharmaceutical protein factories
Ulises Carrasco Navarro and María Fernanda Cerón-Moreno
1 Protein secretion in filamentous fungi
2 Co- or posttranslational transport from ribosome to ER
3 Folding and polypeptide modifications
4 Golgi complex and O-glycosylation
5 Spitzenkörper
6 Biopharmaceutical protein production in filamentous fungi
7 Genetic tools for recombinant protein production in filamentous fungi
8 Concluding remarks
References
CHAPTER 8 Proteomic analysis: Application to the study of signal transduction pathways in Penicillium chrysogenum and Acremonium chrysogenum
Ulises Carrasco Navarro, María Fernanda Cerón-Moreno and Francisco J. Fernández
1 About Penicillium chrysogenum and Acremonium chrysogenum
2 Cell signaling
3 Proteomics
3.1 Techniques employed in proteomic analysis
3.2 Proteomic analysis of cell signaling pathways in P. chrysogenum
4 Conclusions
References
CHAPTER 9 Fungal lipase obtained by surface adhesion fermentation using magnetic chitosan-coated nanoparticles
Anna Ilina, Rodolfo Ramos-González, Elva Arechiga-Carvajal, Patricia Segura-Ceniceros, José L. Martínez-Hernández, and Cynthia Barrera
1 Introduction
2 Materials and methods
2.1 Microorganisms and crop development
2.2 Support preparation
2.3 Characterization of the immobilization process of A. niger spores on NPM-Q
2.4 Surface adhesion fermentation (SAF)
2.5 Assay for the determination of lipase activity
3 Results and discussion
3.1 Interaction characterization of A. niger spores and NPM-Q
3.2 Comparison of lipase production by submerged fermentation and surface-attachment fermentation
4 Conclusion
References
CHAPTER 10 In vitro plant cultures as a viable biotechnological tool for the biosynthesis of steroidal hormones of clinical interest
Gabriel Alfonso Gutierrez-Rebolledo, Mariana Zuleima Perez-González, Mariana Sánchez-Ramos, and Francisco Cruz-Sosa
1 Introduction
1.1 Global prospects in the clinical use and industrial production of hormones
1.2 Biosynthesis pathways of steroid structures in plant cells
2 Aim of the chapter
3 Methodology
4 Results
4.1 In vitro plant cell cultures by biotechnological techniques
4.2 Analytical methods applied to secondary metabolites produced by plant cell cultures
5 Discussion
6 Conclusions
Disclaimer
Acknowledgments
References
CHAPTER 11 Whole-cell biocatalysis for large-scale production
Zhi-Qiang Liu, Xue Cai, Xiao-Jian Zhang, Ji-Dong Shen, Fang-Ying Zhu, and Yu-Guo Zheng
1 Introduction
2 Design of whole-cell biocatalysts
2.1 The optimization and design of biosynthetic pathways
2.2 Improvement of pathway flux
2.3 Dynamic regulation of enzyme concentrations
2.4 Enhanced urban transportation
3 Biocatalysis of whole cells in biphase media
3.1 Biphasic media-catalyzed lipase
3.2 Reactions facilitated by reductase in aqueous-organic media
3.3 Conclusions
4 Immobilization of whole-cell catalyst
4.1 Strategy for entrapment and encapsulation
4.2 Adhesion technique
4.3 The covalent coupling method
4.4 Utilizing a combined methodologies approach
5 One-pot multicell catalysis
6 Conclusions
References
Author Index
Subject Index
About the editors
Preface
CHAPTER 1 Advantages and new potential applications of whole-cell biocatalysis
Sergio Huerta-Ochoa
1 Introduction
1.1 History of whole-cell biocatalysis development
1.2 Technical advances and economic advantages of whole-cell biocatalysis
1.3 Reaction media in whole-cell biocatalysis
1.4 Main microorganisms used as whole-cell factories
2 Key advances and potential applications
2.1 Cell permeabilization
2.2 Cell immobilization
2.3 Metabolic engineering
2.4 Cascade reactions
2.5 Chemoenzymatic synthesis
2.6 Sustainable manufacturing
2.7 Pharmaceutical production
2.8 Biodegradation and bioremediation
2.9 Renewable energy production
3 Trends and perspectives
References
CHAPTER 2 Reprogramming microbial cells to improve the production of biopharmaceuticals and fine chemicals
Alvaro R. Lara, Marcos López-Perez, and Francisco J. Fernández
1 Introduction to molecular genetics in the production of chemical and pharmaceutical substances
1.1 Significance of chemical and pharmaceutical substance production in the industry and their impact on the global economy
1.2 Use of microorganisms in the production of chemical and pharmaceutical substances, with emphasis on fungi
1.3 Improving fungal strains through classical genetic techniques with emphasis on antibiotics
1.4 Reasons for the use of molecular genetic techniques
2 Classic molecular cloning techniques
2.1 Molecular cloning: A clear definition
2.2 Cloning of genes and DNA fragments
2.3 DNA and complementary DNA (cDNA) libraries
2.4 Featured examples of molecular cloning in antibiotic production
3 Gene dosage optimization
3.1 Gene dosage and modulation of gene dosage
3.2 Gene dosage optimization in industrial production: Importance and examples
3.3 Other alternatives: E.g., increasing precursor availability and/or improving precursor and penicillin transport
4 Advanced genetic engineering tools
4.1 Advances in genetic engineering
4.2 High-throughput sequencing (NGS) techniques
4.3 Promoters and RBS (bio-bricks) libraries
4.4 Synthetic biology
4.5 CRISPR-Cas9 technology
5 Cell factories for whole-cell biocatalysis
5.1 Minimal cell factories
5.2 Robust cell factories
5.3 Schemes for autonomous control of the metabolic fluxes and induction of product synthesis
6 The future of molecular genetics in the production of chemical and pharmaceutical substances
References
CHAPTER 3 Mitigation of greenhouse gas emissions from biogas-producing facilities: A novel whole-cell technology platform based on anaerobic oxidation of methane
Guillermo Quijano and Ivonne Figueroa-González
1 Introduction
2 GHG emissions from biogas-producing facilities
3 Conventional aerobic biotechnologies for treating residual dissolved methane
3.1 Aerobic methanotrophic metabolism
3.2 Packed bed reactors and two-phase partitioning systems
3.3 Aerobic membrane bioreactors
4 Whole-cell technology platform for anaerobic methane oxidation
4.1 Fundamentals and process microbiology of the N-AOM process
4.2 Bioreactors and operating conditions reported for N-AOM implementation
5 Perspectives
References
CHAPTER 4 Computational metabolic engineering using genome-scale metabolic models and constraint-based methods
Carlos Coello-Castillo, Freddy Castillo-Alfonso, and Roberto Olivares-Hernández
1 Defining metabolic engineering
2 Microbial cell factory
3 Strategies for designing microbial cell factories
4 The engineering cycle
5 The principles for the calculation of metabolic fluxes
6 Linear programming for metabolic network modeling
7 Genome-scale mathematical modeling
8 Reconstruction of the metabolic model
9 Metabolic engineering and systems biology
10 Data integration
11 Metabolic engineering and systems biology strategies
References
CHAPTER 5 Whole-cell biocatalysis in nonconventional media
Dulce María Palmerín-Carreno
1 Introduction
2 Nonconventional media used for biocatalysis
2.1 Whole-cell function in nonconventional media
3 Reaction and transport mechanisms in nonconventional media
3.1 Partitioning bioreactors
3.2 Solid-gas bioreactors
4 Applications of reaction in nonconventional media
5 Conclusions
References
CHAPTER 6 Nanostructured magnetic systems in whole-cell biocatalysis
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
1 Introduction
2 Coated magnetic nanoparticles and their properties for catalysis
3 Mechanisms of interactions between cells and magnetic nanoparticles
4 Toxicity of magnetic nanoparticles on microbial cells
5 Application of magnetic nanoparticles in catalysis with bacteria and yeast
6 Surface adhesion fermentation using magnetic nanoparticles: Advantages and disadvantages
7 Scale-up considerations
8 Hyperthermia with magnetic nanoparticles and its possible application
9 Future perspectives
Author contributions
Acknowledgments
Conflict of interest
References
CHAPTER 7 Filamentous fungi as biopharmaceutical protein factories
Ulises Carrasco Navarro and María Fernanda Cerón-Moreno
1 Protein secretion in filamentous fungi
2 Co- or posttranslational transport from ribosome to ER
3 Folding and polypeptide modifications
4 Golgi complex and O-glycosylation
5 Spitzenkörper
6 Biopharmaceutical protein production in filamentous fungi
7 Genetic tools for recombinant protein production in filamentous fungi
8 Concluding remarks
References
CHAPTER 8 Proteomic analysis: Application to the study of signal transduction pathways in Penicillium chrysogenum and Acremonium chrysogenum
Ulises Carrasco Navarro, María Fernanda Cerón-Moreno and Francisco J. Fernández
1 About Penicillium chrysogenum and Acremonium chrysogenum
2 Cell signaling
3 Proteomics
3.1 Techniques employed in proteomic analysis
3.2 Proteomic analysis of cell signaling pathways in P. chrysogenum
4 Conclusions
References
CHAPTER 9 Fungal lipase obtained by surface adhesion fermentation using magnetic chitosan-coated nanoparticles
Anna Ilina, Rodolfo Ramos-González, Elva Arechiga-Carvajal, Patricia Segura-Ceniceros, José L. Martínez-Hernández, and Cynthia Barrera
1 Introduction
2 Materials and methods
2.1 Microorganisms and crop development
2.2 Support preparation
2.3 Characterization of the immobilization process of A. niger spores on NPM-Q
2.4 Surface adhesion fermentation (SAF)
2.5 Assay for the determination of lipase activity
3 Results and discussion
3.1 Interaction characterization of A. niger spores and NPM-Q
3.2 Comparison of lipase production by submerged fermentation and surface-attachment fermentation
4 Conclusion
References
CHAPTER 10 In vitro plant cultures as a viable biotechnological tool for the biosynthesis of steroidal hormones of clinical interest
Gabriel Alfonso Gutierrez-Rebolledo, Mariana Zuleima Perez-González, Mariana Sánchez-Ramos, and Francisco Cruz-Sosa
1 Introduction
1.1 Global prospects in the clinical use and industrial production of hormones
1.2 Biosynthesis pathways of steroid structures in plant cells
2 Aim of the chapter
3 Methodology
4 Results
4.1 In vitro plant cell cultures by biotechnological techniques
4.2 Analytical methods applied to secondary metabolites produced by plant cell cultures
5 Discussion
6 Conclusions
Disclaimer
Acknowledgments
References
CHAPTER 11 Whole-cell biocatalysis for large-scale production
Zhi-Qiang Liu, Xue Cai, Xiao-Jian Zhang, Ji-Dong Shen, Fang-Ying Zhu, and Yu-Guo Zheng
1 Introduction
2 Design of whole-cell biocatalysts
2.1 The optimization and design of biosynthetic pathways
2.2 Improvement of pathway flux
2.3 Dynamic regulation of enzyme concentrations
2.4 Enhanced urban transportation
3 Biocatalysis of whole cells in biphase media
3.1 Biphasic media-catalyzed lipase
3.2 Reactions facilitated by reductase in aqueous-organic media
3.3 Conclusions
4 Immobilization of whole-cell catalyst
4.1 Strategy for entrapment and encapsulation
4.2 Adhesion technique
4.3 The covalent coupling method
4.4 Utilizing a combined methodologies approach
5 One-pot multicell catalysis
6 Conclusions
References
Author Index
Subject Index
- Edition: 1
- Published: July 16, 2025
- Language: English
SH
Sergio Huerta-Ochoa
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.
Affiliations and expertise
Department of Biotechnology, Universidad Autonoma Metropolitana, MexicoLP
Lilia Arely Prado-Barragán
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.
Affiliations and expertise
Department of Biotechnology, Universidad Autónoma Metropolitana, MexicoCA
Cristobal Noe Aguilar
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).
Affiliations and expertise
Autonomous University of Coahuil, Saltillo, MexicoRead Whole Cell Biocatalysis on ScienceDirect