Table of Contents
Cover image
Title page
Copyright
List of contributors
Preface
Section I: Metabolic Engineering of Cells: General and Basics
Chapter 1. Metabolic engineering: tools for pathway rewiring and value creation
Abstract
1.1 Introduction
1 2 Tools for metabolic engineering
1.3 Value generation by metabolic engineering
1.4 Conclusions and perspectives
References
Chapter 2. Membrane transport as a target for metabolic engineering
Abstract
2.1 Introduction
2.2 Membrane transport proteins
2.3 Substrate uptake
2.4 Transport from and into organelles
2.5 Product export
2.6 Cellular robustness
2.7 Substrate channeling and membrane transport
2.8 Undesired transport processes
2.9 Conclusions and perspectives
References
Chapter 3. Analysis and modeling tools of metabolic flux
Abstract
3.1 Introduction
3.2 13C-metabolic flux analysis
3.3 Constraint-based stoichiometric metabolic flux analysis
3.4 Conclusions and perspectives
References
Chapter 4. Equipped C1 chemical assimilation pathway in engineering Escherichia coli
Abstract
4.1 Introduction
4.2 Approaches for the assessment of CO2 assimilation capability
4.3 Physiological effect of RuBisCo system
4.4 Strategies to enhance the RuBisCo system
4.5 Transforming the heterotrophs to autotrophs
4.6 Prospective of RuBisCo-based chemical production
4.7 Conclusions and perspectives
References
Chapter 5. Microbial tolerance in metabolic engineering
Abstract
5.1 Introduction
5.2 Microbial stresses and responses
5.3 Strategies to improve microbial tolerance
5.4 Challenges in developing and using tolerant strains
5.5 Conclusions and perspectives
References
Chapter 6. Application of proteomics and metabolomics in microbiology research
Abstract
6.1 Introduction
6.2 Proteomics in microbiology
6.3 Metabolomics in microbiology
6.4 Conclusions and perspectives
References
Chapter 7. Approaches and tools of protein tailoring for metabolic engineering
Abstract
7.1 Introduction
7.2 Approaches for the engineering of protein
7.3 Applications of protein engineering
7.4 Conclusions and perspectives
References
Chapter 8. Microbial metabolism of aromatic pollutants: Highthroughput OMICS and metabolic engineering for efficient bioremediation
Abstract
8.1 Introduction
8.2 Aromatic compounds: impact and toxicity
8.3 Microbial metabolism of aromatic compounds/pollutants
8.4 High-throughput OMICS: insights into aromatics metabolism
8.5 Metabolic engineering for efficient aromatics biodegradation
8.6 Conclusions and perspectives
Acknowledgment
References
Chapter 9. Microbial consortium engineering for the improvement of biochemicals production
Abstract
9.1 Introduction
9.2 Classification of microbial consortia
9.3 Construction of a microbial consortium
9.4 Applications of microbial consortium engineering
9.5 Recent synthetic microbial consortia and their applications
9.6 Challenges in microbial consortium engineering
9.7 Conclusions and perspectives
Acknowledgment
References
Further reading
Section II: Metabolic Engineering of Cells:
Applications
Chapter 10. Metabolic engineering strategies for effective utilization of cellulosic sugars to produce value-added products
Abstract
10.1 Introduction
10.2 Sustainable carbon sources for biorefineries
10.3 Microbial cell factories for carbon source coutilization and production of value-added chemicals
10.4 Conclusions and perspectives
Acknowledgments
References
Chapter 11. Production of fine chemicals from renewable feedstocks through the engineering of artificial enzyme cascades
Abstract
11.1 Introduction
11.2 Advantages of enzyme cascades
11.3 Artificial enzyme cascades versus natural enzyme cascades
11.4 Importance of fine chemicals production from renewable feedstocks through artificial enzyme cascades
11.5 General principle of engineering of enzyme cascades
11.6 Examples of production of fine chemicals from bio-based Lphenylalanine using artificial enzyme cascades
11.7 Examples of production of fine chemicals from renewable feedstocks glucose and glycerol using artificial enzyme cascades
11.8 Conclusions and perspectives
References
Chapter 12. Metabolic engineering of microorganisms for the production of carotenoids, flavonoids, and functional polysaccharides
Abstracts
12.1 Introduction
12 2 Metabolic engineering of plant natural products
12.3 Metabolic engineering of functional polysaccharides
12.4 Conclusions and perspectives
References
Chapter 13. Bioengineering in microbial production of biobutanol from renewable resources
Abstract
13.1 Introduction
13.2 Applications and production of butanol
13.3 Biological production of butanol
13.4 Metabolic pathways of biobutanol production
13.5 Enhancement of biobutanol production
13.6 Conclusions and perspectives
Acknowledgments
References
Chapter 14. Engineered microorganisms for bioremediation
Abstract
14.1 Introduction
14.2 Types of bioremediation
14.3 Genetically engineered organisms in bioremediation
14.4 Genetic engineering techniques
14.5 Bioremediation using GEMs
14.6 Field applications of GEMs
14.7 Risk assessment of GEMs
14.8 Conclusions and perspectives
References
Chapter 15. Agricultural applications of engineered microbes
Abstract
15.1 Introduction
15.2 Agricultural applications of genetically modified microbes
15.3 Conclusions and perspectives
Acknowledgments
References
Chapter 16. Rhizosphere microbiome engineering
Abstract
16.1 Introduction
16.2 Plant-associated microbes/microbiome
16.3 Rhizosphere microbiome engineering
16.4 Emerging areas of research
16.5 Conclusions and perspectives
Acknowledgments
References
Chapter 17. Genetically engineered microbes in micro-remediation of metals from contaminated sites
Abstract
17.1 Introduction
17.2 Classification of bioremediation
17.3 Metal-contaminated sites: a problem
17.4 Genetically modified micro-organisms
17.5 Conclusions and perspectives
Acknowledgment
References
Chapter 18. Biofuel production from renewable feedstocks: Progress through metabolic engineering
Abstract
18.1 Introduction
18.2 Heterologous genetic expression in plants to improve feedstock properties
18.3 System metabolic engineering for biofuels production
18 4 Microbial production of biofuels from renewable feedstock
18.5 Challenges and techno-economic analysis of emerging biofuels
18.6 Conclusions and perspectives
Acknowledgments
References
Chapter 19. Synthetic biology and the regulatory roadmap for the commercialization of designer microbes
Abstract
19.1 Introduction
19.2 Synthetic biology
19.3 Framework of synthetic biology
19.4 Tools in synthetic biology
19.5 Applications of synthetic biology
19.6 Legal aspect of designer microbes
19.7 Regulatory challenges for the commercialization of designer microbes
19.8 Conclusions and perspectives
References
Index
Copyright
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List of contributors
Nagvanti Atoliya, Department of Microbiology, Barkatullah University, Bhopal, Madhya Pradesh, India
Apekcha Bajpai, Department of Microbiology, Barkatullah University, Bhopal, Madhya Pradesh, India
Neha Basotra, Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
Arvind Kumar Bha , Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
Bhupinder Singh Chadha, Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
Dhrubajyoti Cha opadhyay, Sister Nivedita University, Kolkata, West Bengal, India
Han-Ju Chien, Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
Aditi P. Dahake, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, U ar Pradesh, India
Manali Das, School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
Tushar Dhamale, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
Abhishek S. Dhoble, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, U ar Pradesh, India
Guocheng Du
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, P.R. China
Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, P.R. China
Abhrajyoti Ghosh, Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
Amit Ghosh
School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
Anupama Ghosh, Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
Mengyue Gong, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, P.R. China
Swadha Gupta, School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, Gujarat, India
Shyamalina Haldar, Department of Biochemistry, Asutosh College, University of Calcu a, Kolkata, West Bengal, India
Philip Johnsen, Department of Biology, University of Waterloo, Waterloo, ON, Canada
Swati Joshi, ICMR-National Institute of Occupational Health, Ahmedabad, Gujarat, India
Amandeep Kaur, Department of Botany, Panjab University, Chandigarh, Panjab, India
Alka Kumari, Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
Cheng-Yu Kuo, Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
Chien-Chen Lai
Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
Graduate institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
Sung Kuk Lee, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Hongbiao Li, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P.R. China
Si-Yu Li, Department of Chemical Engineering, National Chung Hsing University, Taichung, Taiwan
Zhi Li, Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
Long Liu
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, P.R.
China
Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, P.R. China
Yanfeng Liu
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, P.R.
China
Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, P.R. China
Xueqin Lv
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, P.R.
China
Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, P.R. China
Kesen Ma, Department of Biology, University of Waterloo, Waterloo, ON, Canada
Madhu, Department of Botany, Panjab University, Chandigarh, Panjab, India
Harshit Malhotra, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
Balaram Mohapatra, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
Sangita Mondal, Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
I-Son Ng, Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
Thuan Phu Nguyen-Vo, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Ashok Pandey, Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, U ar Pradesh, India
Anju Pappachan, School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, Gujarat, India
Sung Hoon Park, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Pradipta Patra, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
Prashant S. Phale, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
Anil Prakash, Department of Microbiology, Barkatullah University, Bhopal, Madhya Pradesh, India
Yashika Raheja, Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
Ranju Kumari Rathour, Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
Braja Kishor Saha, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
Aditya Sarnaik, Chemical Engineering, School for Engineering of Ma er, Transport, and Energy, Arizona State University, Tempe, AZ, United States
Chandran Sathesh-Prabu, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Michael Sauer, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
Weilan Shao, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, P.R. China
Deepak Sharma, Department of Biotechnology and Bioinformatics, Jaypee University of Information and Technology, Waknaghat, Solan, Himachal Pradesh, India
Gaurav Sharma, Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
Nitish Sharma, Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
Sudhir P. Singh, Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
Balaji Sundara Sekar, Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
Shih-I Tan, Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
g y
Rameshwar Tiwari, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Santosh Kumar Upadhyay, Department of Botany, Panjab University, Chandigarh, Panjab, India
Arul M. Varman, Chemical Engineering, School for Engineering of Ma er, Transport, and Energy, Arizona State University, Tempe, AZ, United States
Wei-Chen Wang, Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
Zilong Wang, Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
Junjun Wu
School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, P.R. China
College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P.R. China
Chenyang Zhang
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, P.R. China
Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, P.R. China
Yi-Feng Zheng, Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
Jingwen Zhou, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P.R. China
Preface
Swati Joshi, Ashok Pandey, Ranjna Sirohi and Sung Hoon Park
The book titled Current Developments in Biotechnology and Bioengineering, Designer Microbial Cell Factories: Metabolic Engineering and Applications. The book is dedicated to the basic and applied aspects of metabolic engineering for the creation of microbial cell factories to generate value-added chemicals and solutions to combat global challenges including the generation of green and clean fuel, value out of waste, and a spectrum of chemicals for sustainable development.
Metabolic engineering is a fast evolving interdisciplinary field, witnessing rapid changes through the advancements in molecular biology, microbial physiology, mathematical modeling, synthetic biology, systems biology, metabolomics, interactomics, fluxomics, proteomics, genomics, etc. Using insights from diverse fields, metabolic engineering experiments intend to optimize cellular metabolism to achieve sustainable and cost-effective manufacturing of desired molecules. With the power of programming biological cells, metabolic engineers are advancing toward establishing biofoundries producing both specialty and high-volume chemicals at green and sustainable industrial scale. A gamut of biomolecules having pharmaceutical, nutraceutical, material, food and feed additive, agricultural, and environmental applications are being produced through metabolic engineering. We are witnessing the translation of this technology for the benefit of society as spin-off biotech companies such as Photanol, Amyris, Conagen, Gingko Bioworks, and Biopatrolia are se ing up in this area. To reach its potential, research in metabolic engineering is yet to traverse several
unexplored areas. In pursuit of presenting different facets of this technology, this book has been edited for authors offering insights on multiple topics.
Topics covered in this book include various omics platforms in the area of engineering microbial cell factories; recent trends and technological advancements in the field for generation of designer microbes; membrane transport as an emerging target of metabolic engineering; 13C-labeled and genome-scale metabolic model for metabolic flux analysis; C1 chemical assimilation pathway in the engineering Escherichia coli; different approaches of RuBisCo system toward a low-carbon society; microbial tolerance and its improvement in metabolic engineering; proteomics and protein engineering tools for metabolic engineering; application of high throughput omics tools and metabolic engineering for the metabolism of pollutant aromatics; microbial consortium engineering and its industrial applications; metabolic engineering strategies for efficient coutilization of various sugars for the production of value-added chemicals; engineering of artificial enzyme cascades and production of fine chemicals; metabolic engineering of microbes for the production of plant secondary metabolites and oleo-chemicals; value-added consumable organic acids through metabolic engineering; bioengineering for industrially viable production of bio-butanol; engineered microbes in bioremediation; engineering rhizospheric microbes composition and constituents for improvement of plant growth promotion activity; engineered microbes in metal micro-remediation; and the worldwide scenario of biofuel production through metabolic engineering and regulatory aspects of commercialization of designer microbes.
The book covers the current trends and technological advances related to metabolic engineering of microbes. It also provides a comprehensive coverage of omics and next-gen platforms employed, metabolic flux analysis, modeling tools for pathway modulation, and engineering along with regulatory aspects during the commercialization of engineered microbes. This book also illustrates the biotechnological applications of these microbes in different fields
ranging from the generation of biofuels to production of specific chemicals. All the chapters of this book provide state-of-the-art information on the subject ma er. We strongly believe this book will be valuable to students, researchers, academicians, industry personnel, and stakeholders across the globe and satiate their interest in metabolic engineering.
We deeply appreciate the remarkable work done by the authors in compiling the relevant information on different aspects of designer microbial factories through metabolic engineering as well as their applications, which we believe will be very useful to the scientific fraternity. We gratefully acknowledge the reviewers for their valuable comments, which helped in improving the scientific content of various chapters. We sincerely thank the Elsevier team comprising Dr. Kostas Marinakis, Former Senior Book Acquisition Editor, Dr. Katie Hammon, Senior Book Acquisition Editor, and the entire Elsevier production team for their support in publishing this book.
