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E-raamat: Current Developments in Biotechnology and Bioengineering: Synthetic Biology, Cell Engineering and Bioprocessing Technologies

Edited by (Center of Innovative and Applied Bioprocessing, Mohali, India), Edited by (Center), Edited by (Dean of the School of Biotechnology, Jiangnan University, China), Edited by (Executive Director, Centre for Energy and Environmental Sustainability-India, Lucknow, India)
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  • Ilmumisaeg: 20-Nov-2018
  • Kirjastus: Elsevier Science Ltd
  • Keel: eng
  • ISBN-13: 9780444640864
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  • Formaat: EPUB+DRM
  • Ilmumisaeg: 20-Nov-2018
  • Kirjastus: Elsevier Science Ltd
  • Keel: eng
  • ISBN-13: 9780444640864
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Current Developments in Biotechnology & Bioengineering: Synthetic Biology, Cell Engineering & Bioprocessing Technologies covers the current perspectives and outlook of synthetic biology in agriculture, food, and health sectors. This book begins with the basics about synthetic biology and cell engineering. and then moves on to exploring in more detail covering topics like applications of synthetic biology, industrial bioprocesses and future perspectives. Information on cell engineering is also presented with state-of-art information about manipulation in endogenous metabolic network, fine tuning of metabolic pathways, de novo biosynthetic pathway design, enzyme engineering targeted to improved kinetics and stability, and potential applications of the novel biological systems in bioprocess technology to achieve production of value-added compounds with specific biological activities.

  • Provides a conceptual understanding of synthetic biology, and cellular and metabolic engineering
  • Includes comprehensive information on new developments and advancements
  • Lists applications of synthetic biology in agriculture, food and health
List of Contributors
xiii
Preface xvii
SECTION 1 Synthetic Biological Systems; Concepts and Molecular Toolkits
7(68)
Chapter 1 Basics and Roots of Synthetic Biology
3(20)
Sudhir P. Singh
Shilpi Bansal
Ashok Pandey
1 Introduction
3(1)
2 Basic Tools and Techniques Applied in Synthetic Biology
4(6)
2.1 DNA Synthesis and DNA Sequencing
4(1)
2.2 Chassis
5(1)
2.3 Transcriptional Engineering
6(2)
2.4 Genome Modification Tools
8(2)
2.5 Computer-Aided Tools
10(1)
3 Root Systems in Synthetic Biology
10(3)
3.1 Escherichia coli
10(1)
3.2 Yeast
11(1)
3.3 In Vitro Culture System
12(1)
4 Selected Examples of the Application of Synthetic Biology for Biomolecule Production
13(2)
4.1 Oil
13(1)
4.2 Taxol
13(1)
4.3 Semisynthetic Artemisinin
14(1)
4.4 Genome Engineering for Isopropanol Production
15(1)
4.5 Designer Microbe for 1,4-Butanediol Biosynthesis
15(1)
5 Conclusions and Perspectives
15(8)
Acknowledgments
16(1)
References
16(6)
Further Reading
22(1)
Chapter 2 Advances in Cell-Free Biosynthetic Technology
23(24)
Yuan Lu
1 Introduction
23(3)
2 Cell-Free Systems
26(7)
2.1 Systems and Advantages
26(3)
2.2 Testing
29(2)
2.3 Biomanufacturing
31(2)
3 Emerging and Practical Applications
33(6)
3.1 Difficult-to-Express Proteins
33(1)
3.2 Nonstandard Amino Acids
34(4)
3.3 Paper-Based Biosensor System
38(1)
4 Conclusions and Perspectives
39(8)
References
40(7)
Chapter 3 Genome Engineering Tools in Plant Synthetic Biology
47(28)
Krishan Mohan Rai
Kaushik Ghose
Anshulika Rai
Harpal Singh
Rakesh Srivastava
Venugopal Mendu
1 Introduction
47(1)
2 Plant Synthetic Biology
48(1)
3 Major Phases and Tools Involved in the Design and Implementation of the Synthetic Biology Concepts
49(3)
3.1 Designing or Conceptualization Phase
50(1)
3.2 DNA Construction Phase
50(2)
3.3 Preliminary Testing and Practical Application Phase
52(1)
4 Major Genome Engineering Tools Used in Plant Synthetic Biology
52(12)
4.1 Engineering Genomes with Sequence-Specific Nuclease Design
54(4)
4.2 Genome Engineering at Transcription Level
58(4)
4.3 Engineering at the Translational Level
62(2)
5 Conclusions and Perspectives
64(11)
References
65(10)
SECTION 2 Genome Engineering and Biosynthetic Repertoires
75(688)
Chapter 4 Constructing Synthetic Pathways in Plants: Strategies and Tools
77(38)
Anuj Dwivedi
Kamal Kumar
Praveen Kumar Verma
1 Introduction
77(1)
2 Prephase of Modern Synthetic Biology
78(2)
2.1 Synthetic Biology: Redesign of Biology Through Engineering
79(1)
3 Why Synthetic Biology in Plants?
80(1)
4 Advanced Synthetic Biology Approaches for Pathways Construction
81(11)
4.1 Assembly and Transformation of Large DNA Constructs
81(1)
4.2 Ligation-Dependent Assembly Method
82(2)
4.3 Overlap-Dependent Methods
84(3)
4.4 Genomes Engineering/Surgery With Sequence-Specific Nucleases
87(3)
4.5 Gene Regulation by Custom DNA-Binding Domains
90(1)
4.6 Artificial Promoters and Transcription Factors
91(1)
4.7 Epigenetic Editing Through Programmable DNA-Binding Domains
91(1)
5 Genetic Transformation of Crops
92(4)
5.1 Plant Organellar Genome Transformation
92(1)
5.2 Plastids (Chloroplasts) Transformation
93(1)
5.3 Mitochondria Transformation
93(1)
5.4 Plant Nuclear Genome Transformation
94(1)
5.5 Plant Artificial Chromosomes
95(1)
6 Synthetic Biology: A Reprogrammed Language to Understand the Complexity of Plant Genome
96(4)
6.1 Metabolic Engineering ft
97(1)
6.2 Artificial Genetic Circuit in Crop Plants
98(1)
6.3 Optogenetics in Pathways Engineering
99(1)
6.4 Receptor Engineering
99(1)
6.5 Signals Engineering
100(1)
7 Synthetic Biology in Agriculture Crops
100(4)
8 Conclusion and Perspectives
104(11)
Acknowledgments
104(1)
References
104(11)
Chapter 5 Synthetic Regulatory Tools to Engineer Microbial Cell Factories for Chemical Production
115(28)
Sungho Jang
Hyun Gyu Lim
Jina Yang
Sang Woo Seo
Gyoo Yeol Jung
1 Introduction
115(2)
2 Synthetic Static Regulators
117(8)
2.1 Synthetic Static Regulators for Transcriptional Regulation
117(3)
2.2 Synthetic Static Regulators for Translational Regulation
120(2)
2.3 Synthetic Static Regulators for Posttranslational Regulation
122(3)
3 Synthetic Dynamic Regulators
125(9)
3.1 Protein-Based Synthetic Dynamic Regulators
126(4)
3.2 RNA-Based Synthetic Dynamic Regulators
130(4)
4 Conclusions and Perspectives
134(9)
References
134(9)
Chapter 6 A CRISPR Technology and Bio molecule Production by Synthetic Biology Approach
143(620)
Jitesh Kumar
Lokesh Kumar Narnoliya
Anshu Alok
1 Introduction
143(2)
2 Synthetic Biology Tools for Biomolecule Production
145(6)
2.1 Conventional Genome Engineering for Biomolecule Production
146(1)
2.2 Genome Engineering Based on CRISPR/Cas System
147(2)
2.3 Emerging Tools of Genome Editing Based on CRISPR/Cas
149(1)
2.4 CRISPR/Cas-Based Genetic Circuits
149(1)
2.5 Synthetic Transcription Factors for Synthetic Biology
150(1)
2.6 Synthetic Genomics
150(1)
3 Genome Manipulations Using CRISPR/Cas System for the Production of High-Value Biomolecules in Microbes
151(5)
3.1 Genome Manipulations for the Production of High-Value Biomolecules in Bacteria
151(2)
3.2 Genome Manipulations for the Production of High-Value Biomolecules in Yeast
153(2)
3.3 Genome Manipulations for the Production of High-Value Biomolecules in Fungi
155(1)
4 Conclusion and Perspective
156(607)
Acknowledgments
157(1)
References
157(6)
SECTION 3 Biocatalyst Engineering and Industrial Bioprocesses
163(2)
Chapter 7 Enzyme Engineering and Industrial Bioprocess
165(1)
Chen Deng
Tingting Huang
Zhu Jiang
Xueqin Lv
Long Liu
Jian Chen
Guocheng Du
1 Enzyme Gene Cloning and Expression
165(8)
1.1 Prokaryotic Expression System
166(4)
1.2 Yeast Expression System
170(3)
2 Molecular Modification of Enzymes
173(7)
2.1 Irrational Design
173(3)
2.2 Rational Design of Enzymes
176(3)
2.3 Semirational Design
179(1)
3 Industrial Enzyme Applications
180(5)
3.1 Introduction
180(2)
3.2 The Application of Enzymes in Different Industrial Fields
182(3)
4 Conclusions and Perspectives
185(4)
References
186(3)
Chapter 8 Synthetic Biology for Production of Commercially Important Natural Product Small Molecules
189(18)
Sumit G. Gandhi
1 Introduction
189(2)
2 Unraveling Secondary Metabolite Pathways
191(3)
3 Selection of Host Organism: The "Chassis"
194(3)
4 Assembly of Synthetic Biology Modules
197(1)
5 Challenges in Building Synthetic Gene Circuits
197(1)
6 Artemisinin-A Case Study
198(2)
7 Conclusion and Perspectives
200(7)
References
201(6)
Chapter 9 Biosynthetic Technology and Bioprocess Engineering
207(26)
Fengxue Xin
Weiliang Dong
Zhongxue Dai
Yujia Jiang
Wei Yan
Ziyao Lv
Yan Fang
Min Jiang
1 Biosynthetic Technology
207(14)
1.1 Synthetic Biology
207(1)
1.2 Genetic Engineering
208(6)
1.3 Cell Engineering
214(1)
1.4 Enzyme Engineering
215(6)
2 Bioprocess Engineering
221(5)
2.1 Fermentation Mode
221(5)
3 Conclusions and Perspectives
226(7)
References?
227(6)
SECTION 4 Applications of Synthetic Biology
233(130)
Chapter 10 Regulated Gene Expression by Synthetic Modulation of the Promoter Architecture in Plants
235(22)
Bindu Pandey
Pravin Prakash
Praveen Chandra Verma
Rakesh Srivastava
1 Introduction
235(1)
2 Plant Promoter: An Overview of Its Architecture and Classification
236(8)
2.1 Plant Promoter Elements: The Importance of Regulated Gene Expression
236(1)
2.2 Promoter Classification
237(5)
2.3 The Transcriptional Complexes and the Transcription Factors at the Plant Promoters
242(2)
3 Plant Promoter Engineering: Concept and Mechanism
244(1)
4 Applications of Modulated and Synthetic Plant Promoters for the Regulated Gene Expression
245(2)
5 Conclusion
247(10)
References
248(9)
Chapter 11 Biosynthesis of High-Value Amino Acids by Synthetic Biology
257(38)
Samer Singh
Budhi Sagar Tiwari
1 Introduction
257(4)
1.1 Amino Acids Market and Use
258(3)
2 Synthetic Biology (Synbio) in Amino Acids Production
261(14)
2.1 Synthetic Biology as Game Changer
261(1)
2.2 Synthetic Biology Approaches and Levels of Precision and Control
262(2)
2.3 Biosynthesis Pathways of Amino Acids and Synthetic Biology Targets
264(1)
2.4 Synthetic Biology Approaches in Production of Major Proteinogenic Amino Acids
264(8)
2.5 Recent Advances Made in the Production of Branched-Chain Amino Acids
272(1)
2.6 Production of Aromatic Amino Acids
273(1)
2.7 Synthetic Biology Approaches for Production of Nonproteinogenic Amino Acids and Derivatives
274(1)
3 Future Perspective of Synthetic Biology--Underutilized or Developing Approaches for Improving the Yield
275(9)
3.1 Abstracted Modular Circuits for Better Pathway Engineering
275(1)
3.2 Scaffolds and Compartments for Channeling of Substrates and Intermediates or Decrease Their Toxic Effects
275(2)
3.3 Coculture and Coproduction Strategies for Complementing Activities: For Efficient Energy or Source Utilization/Mobilization
277(2)
3.4 Metagenomic Landscape for Synbio Applications--Identification and Use of Novel Enzymes and Pathways
279(1)
3.5 Optimized or Synthetic Chassis Organisms
280(1)
3.6 Future of Synthetic Biology Production Units
281(3)
4 Conclusions and Perspectives
284(11)
Acknowledgments
284(1)
References
285(10)
Chapter 12 Synthetic Biology Approaches for the Production of 2-Butanol
295(16)
Ye Zhang
Dehua Liu
Zhen Chen
1 Introduction
295(3)
2 Metabolic Pathways for the Synthesis of 2-Butanol
298(2)
3 Key Enzymes for the Biosynthesis of 2-Butanol
300(3)
3.1 Diol Dehydrogenase
300(2)
3.2 Alcohol Dehydrogenase
302(1)
4 Potential Industrial Strains for the Production of 2-Butanol
303(2)
5 Key Challenges for the Bioproduction of 2-Butanol
305(1)
5.1 Engineering of Pathways Enzymes and Cellular Metabolism to Increase the Titer of 2-Butanol
305(1)
5.2 Engineering of Strains' Tolerance to 2-Butanol
305(1)
5.3 Engineering of Strain's Substrate Spectrum
306(1)
6 Conclusions and Perspectives
306(5)
Acknowledgments
307(1)
References
307(4)
Chapter 13 Synthetic Biology Approaches for the Production of Isoprenoids in Escherichia coli
311(20)
Hongwei Tian
Bakht Zada
Birla H. Singh
Chonglong Wang
Seon-Won Kim
1 Diversity of Isoprenoids and Synthesis Routes
311(4)
1.1 Synthesis Routes of Isoprenoid Building Blocks
311(3)
1.2 Prenyltransferase and Terpene Synthase Contribute to the Diverse of Isoprenoid Skeletons
314(1)
1.3 Tailoring Enzymes Create the Diverse Functions of Isoprenoids
314(1)
2 Development of Enabling Technology in Synthetic Biology
315(4)
2.1 Technologies of Controlled Expression of Genes Relieving Production Bottlenecks
316(1)
2.2 Technologies of Synthetic Pathway Engineering
317(1)
2.3 Technologies for Metabolic Network Engineering
318(1)
3 Synthetic Biology for the Production of Isoprenoids
319(5)
3.1 Synthetic Biology Approaches for Production of Bulk Isoprenoids in Escherichia coli
320(2)
3.2 Synthetic Biology Approaches for Production of Value-Added Isoprenoids
322(1)
3.3 Protein Engineering and Systems Biology Promote Production of Isoprenoids
323(1)
4 Conclusions
324(7)
Acknowledgments
325(1)
References
326(5)
Chapter 14 System Metabolic Engineering Applications in Corynebacterium crenatum for L-Arginine Production
331(32)
Zhiming Rao
Meijuan Xu
Zhenghong Xu
1 Introduction
331(1)
2 L-Arginine Biosynthesis by Microorganisms
331(3)
2.1 Strains Producing L-Arginine
333(1)
2.2 L-Arginine Biosynthetic Pathway and Its Regulation in Corynebacterium sp
333(1)
3 Fermentative Production of L-Arginine by Corynebacterium sp
334(20)
3.1 Wild-Type Corynebacterium crenatum for L-Arginine Production
334(1)
3.2 Fermentation Strategies of L-Arginine
335(2)
3.3 Genetic Engineering for L-Arginine Production
337(1)
3.4 Metabolic Engineering of Corynebacterium crenatum for L-Arginine Production
338(9)
3.5 System and Synthetic Metabolic Engineering for L-Arginine Production
347(6)
3.6 Industrial Production of L-Arginine
353(1)
4 Extraction and Purification of L-Arginine
354(2)
5 Conclusions and Perspectives
356(7)
Acknowledgments
356(1)
References
356(7)
SECTION 5 Future Perspectives of Synthetic Metabolism
363(50)
Chapter 15 Synthetic Metabolism and Its Significance in Agriculture
365(28)
Ruchika
Jogindra Naik
Ashutosh Pandey
1 Plant Metabolism
365(2)
2 Secondary Metabolism
367(1)
3 Classification of Secondary Metabolites
367(2)
3.1 Terpenoids
368(1)
3.2 Flavonoids
368(1)
3.3 Alkaloids
369(1)
3.4 Carotenoids
369(1)
4 Synthetic Biology
369(2)
5 Strategies to Engineer Plant Metabolism
371(1)
6 General Strategies to Engineer Metabolic Pathways
372(2)
7 Strategies to Engineer Primary Metabolism
374(1)
8 Strategies to Engineer Secondary Metabolism
375(1)
9 Regulation of Plant Primary Metabolism
376(2)
10 Regulation of Secondary Metabolism
378(1)
11 Application of Synthetic Biology in Agriculture
379(1)
12 Modulation of Plant Secondary Metabolic Pathways
380(2)
13 Microorganisms and Plants
382(1)
14 Photosynthesis
382(1)
15 Insect Resistance
383(1)
16 Disease Resistance
383(1)
17 Conclusions and Perspectives
384(9)
Acknowledgments
385(1)
References
386(7)
Chapter 16 Applications and Future Perspectives of Synthetic Biology Systems
393(20)
Manisha Chownk
Karnika Thakur
Anjali Purohit
Alokika Vashisht
Sudesh Kumar
1 Introduction
393(2)
2 Genetic Manipulations in Synthetic Biology for Value-Added Products
395(3)
3 Applications of Synthetic Biology in Pharmaceuticals
398(3)
4 Applications of Synthetic Biology in Biofuels Production
401(3)
5 Cell-Free Protein Synthesis in Synthetic Biology
404(3)
6 Conclusions and Perspectives
407(6)
Acknowledgments
407(1)
References
407(6)
Index 413
Dr. Sudhir P. Singh obtained his Ph.D. in the year 2011 from University of Lucknow, India. Subsequently, he worked as research associate and then as Project Scientist at National Agri-Food Biotechnology Institute, Mohali, India. He joined Center of Innovative and Applied Bioprocessing, Mohali, India in 2015, as Scientist-C. He has been working in the area of molecular biology, and synthetic biology. In the area of plant molecular biology his some of the significant contribution are: development stringently regulated expression systems for inducing male sterility and male sterility-fertility restoration system in plants, investigation of tissue and cell-type specific distribution pattern of mineral nutrients in wheat grains and its possible impacts on bioavailability, the first transcriptome analysis and molecular insights into seed development biology in the fruit crops, Custard apple and Litchi, and secondary metabolite pathways in Rose-scented geranium, development of approaches based on Rootstock-scion or modified viral genome based long distance signalling as possible strategies for inducing trait modification such as seedlessness. His current research focus is towards development of synthetic biocatalysts for biotransformation of agro-industrial by-products and residues into value added biomolecules. In the area of biosynthetic technology his some of the significant contribution are: development of novel approaches for transformation of agro-industrial residues and bioresources into functional and prebiotic biomolecules, development of a novel strategy for the improvement of operational stability of D-psiose 3-epimerase enzyme. He has been interested in employing the basic knowledge for translational research. He has published 33 research papers in peer reviewed journals, 4 review articles/book chapters, and 4 patents to his credit. Prof. Ashok Pandey is currently Executive Director, Centre for Energy and Environmental Sustainability-India, Lucknow. His major research and technological development interests are industrial and environmental biotechnology and energy biosciences, focusing on biomass to biofuels and chemicals, waste to wealth and energy, etc.

Professor Guocheng Du is the Dean of School of Biotechnology, Jiangnan University, China. He is the distinguished professor of Changjiang Scholars, Ministry of Education, China. His current main research focus is on bioprocess engineering and metabolic engineering. He has about 200 publications/communications, which include 52 patents, 8 books, 160 original and review papers, etc. He won two Second Prizes of State Science and Technology Award in 2006 and 2012, respectively. He has been conferred Honorary Doctorate degree from Jiangnan University, China. Professor Guocheng Du is deputy director in the committee of biochemical engineering modelling and control, Chinese Society for Microbiology, and deputy director of Beer Branch, China Alcoholic Drinks Industry Association. He is the associate editor of Journal of the Science of Food and Agriculture and the editorial board member of Bioresource Technology. Dr Sudesh Kumar obtained his PhD in 2002 from the Department of Biochemistry, CCS Haryana Agricultural University, Hisar. Subsequently, he worked as post-doctoral fellow at ICGEB, New Delhi (2002-2004). He joined CSIR-Institute of Himalayan Bioresource Technology, Palampur in 2004 as Scientist. In April, 2016, he joined as Scientist-F at Center of Innovative and Applied Bioprocessing (CIAB). He has been working in the area of plant metabolic engineering and nanobiology and current research focus is towards improving the efficacy of hydrolytic enzymes through synthetic biology and nanobiology approaches for developing the efficient transformation process for biomass into value added products. Dr Kumar has published 110 research articles in peer reviewed journals, one book and 12 book chapters. His work has been cited 5000 times and has an h-index of 35. For his outstanding research contributions in the area of plant sciences, he has been honoured with many prestigious awards such as Indian National Science Academy (INSA)-Young Scientist Award- 2008, The National Academy of Science, India (NASI)-Platinum Jubilee Young Scientist Award-2009, Council of Scientific and Industrial Research (CSIR)-Young Scientist Award-2010. He has been awarded BOYSCAST Fellowship during 2008 by DST, GOI for conducting advanced research at UCR, Riverside, USA for one year. He has been also selected NAAS-Associate” by the National Academy of Agricultural Sciences from 2013 and conferred Prof. Hira Lal Chakravarty Memorial Award” of Indian Science Congress Association (ISCA) for the year 2012-2013. He has been honoured with Haryana Yuva Vigyan Ratna Award” 2011-12 for his excellent research contributions.
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