Muutke küpsiste eelistusi

E-raamat: Industrial Biotechnology: Microorganisms

Series edited by (KAIST,Daejon,Republik Korea), Series edited by (Massachusetts Institute of Technologie, USA), Edited by (University of California, Los Angeles, USA), Series edited by (Chalmers University,Göteborg, S), Edited by (TU Braunschweig, Braunschweig, Germany)
  • Formaat: EPUB+DRM
  • Sari: Advanced Biotechnology
  • Ilmumisaeg: 15-Mar-2017
  • Kirjastus: Blackwell Verlag GmbH
  • Keel: eng
  • ISBN-13: 9783527807802
Teised raamatud teemal:
  • Formaat - EPUB+DRM
  • Hind: 346,97 €*
  • * hind on lõplik, st. muud allahindlused enam ei rakendu
  • Lisa ostukorvi
  • Lisa soovinimekirja
  • See e-raamat on mõeldud ainult isiklikuks kasutamiseks. E-raamatuid ei saa tagastada.
  • Raamatukogudele
  • Formaat: EPUB+DRM
  • Sari: Advanced Biotechnology
  • Ilmumisaeg: 15-Mar-2017
  • Kirjastus: Blackwell Verlag GmbH
  • Keel: eng
  • ISBN-13: 9783527807802
Teised raamatud teemal:

DRM piirangud

  • Kopeerimine (copy/paste):

    ei ole lubatud

  • Printimine:

    ei ole lubatud

  • Kasutamine:

    Digitaalõiguste kaitse (DRM)
    Kirjastus on väljastanud selle e-raamatu krüpteeritud kujul, mis tähendab, et selle lugemiseks peate installeerima spetsiaalse tarkvara. Samuti peate looma endale  Adobe ID Rohkem infot siin. E-raamatut saab lugeda 1 kasutaja ning alla laadida kuni 6'de seadmesse (kõik autoriseeritud sama Adobe ID-ga).

    Vajalik tarkvara
    Mobiilsetes seadmetes (telefon või tahvelarvuti) lugemiseks peate installeerima selle tasuta rakenduse: PocketBook Reader (iOS / Android)

    PC või Mac seadmes lugemiseks peate installima Adobe Digital Editionsi (Seeon tasuta rakendus spetsiaalselt e-raamatute lugemiseks. Seda ei tohi segamini ajada Adober Reader'iga, mis tõenäoliselt on juba teie arvutisse installeeritud )

    Seda e-raamatut ei saa lugeda Amazon Kindle's. 

An overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside genetic and metabolic engineering tools, the text covers computational tools, safety aspects and industrial-scale production.

The latest volume in the Advanced Biotechnology series provides an overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside describing tools for genetic and metabolic engineering for strain improvement, the authors also impart topical information on computational tools, safety aspects and industrial-scale production.

Following an introduction to general concepts, historical developments and future technologies, the text goes on to cover multi-purpose bacterial cell factories, including those organisms that exploit anaerobic biosynthetic power. Further chapters deal with microbes used for the production of high-value natural compounds and those obtained from alternative raw material sources, concluding with eukaryotic workhorses.

Of interest to biotechnologists and microbiologists, as well as those working in the biotechnological, chemical, food and pharmaceutical industries.The latest volume in the Advanced Biotechnology series provides an overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside describing tools for genetic and metabolic engineering for strain improvement, the authors also impart topical information on computational tools, safety aspects and industrial-scale production.
Following an introduction to general concepts, historical developments and future technologies, the text goes on to cover multi-purpose bacterial cell factories, including those organisms that exploit anaerobic biosynthetic power. Further chapters deal with microbes used for the production of high-value natural compounds and those obtained from alternative raw material sources, concluding with eukaryotic workhorses. 
Of interest to biotechnologists and microbiologists, as well as those working in the biotechnological, chemical, food and pharmaceutical industries.
Volume 1
List of Contributors
xvii
About the Series Editors
xxix
Preface
xxxi
Part I Industrial Biotechnology: From Pioneers to Visionary
1(148)
1 History of Industrial Biotechnology
3(82)
Arnold L. Demain
Erick J. Vandamme
John Collins
Klaus Buchholz
1.1 The Beginning of Industrial Microbiology
3(4)
1.2 Primary Metabolites and Enzymes
7(1)
1.2.1 Birth, Rise, and Decline of the Term "Biotechnology" in the Period 1900 - 1940
7(1)
1.2.2 Influential Scholars Boosting Industrial Fermentation from 1900 to 1940
8(1)
1.2.3 Milestone Achievements in Industrial Fermentation Technology
10(1)
1.2.3.1 The Acetone- Butanol-Ethanol (ABE) Fermentation Process
10(1)
1.2.3.2 A Novel Vitamin C Fermentation Process
11(1)
1.2.3.3 The Lactic Acid Fermentation Process
11(1)
1.2.3.4 Fermentative Production of Glycerol
12(1)
1.2.3.5 L-(-)-Ephedrine by Fermentation
12(1)
1.2.3.6 Steroid Transformations
13(1)
1.2.3.7 The Citric Acid Fermentation Process
13(1)
1.2.3.8 Gluconic Acid Process
13(1)
1.2.3.9 Other Important Fermentation Processes and Products
14(1)
1.2.3.10 Applied Biocatalysis and Industrial Enzymes
14(2)
1.3 The Antibiotic Era
16(1)
1.3.1 Penicillin
16(1)
1.3.2 The Cephalosporins
20(1)
1.3.3 The Waksman Era
23(1)
1.3.4 Mutagenesis and Strain Improvement
24(1)
1.3.5 Semisynthetic Antibiotics to Combat Resistant Microbes
26(1)
1.4 The Biotechnology Era Between 1970 and 2015
27(1)
1.4.1 Biotechnology in the 1960s and 1970s; Governmental and Political Initiatives
27(1)
1.4.2 The Development of New Biotechnology Companies
29(1)
1.4.3 New Bioengineering Tools
35(1)
1.4.4 Products
39(1)
1.4.4.1 Food, Feed, Industrial Commodities, and Specialties
39(1)
1.4.4.2 Biopharmaceuticals
43(1)
1.4.4.3 Plant Products, Seeds
46(1)
1.4.5 Further Aspects
47(1)
1.4.5.1 Scientific Status
47(1)
1.4.5.2 Political, Institutional, and Socioeconomic Conditions
47(1)
1.4.5.3 Economic Studies
47(1)
1.4.5.4 Science Studies
48(1)
1.5 How Pioneering Developments Led to Genetic Engineering
48(1)
1.5.1 Preamble: People and Principles in Developing Enabling Technologies
48(1)
1.5.2 Academic Freedom and Patenting: Hindrance to Science or Lever for Innovation?
49(1)
1.5.3 Conceptual Leaps and Jumps
50(1)
1.5.4 Surprise Discoveries Initiate Novel Areas/Methods of Research
51(1)
1.5.5 Methodology Without Which Gene Technology Would Not Have Been Possible
52(1)
1.5.5.1 Centrifugation: Preparation of Molecules of Different Sizes, Shapes, and/or Densities: Velocity Gradient Centrifugation
53(1)
1.5.5.2 X-ray Crystallography: Understanding Molecular Structure at the Atomic Level
54(1)
1.5.5.3 Chromatography with Solvent Motion or Electric Charge: Detection of Mutant Gene Products
55(1)
1.5.5.4 Protein Sequencing
55(1)
1.5.5.5 Nucleic Acid Sequencing - the Prelude: Phage + Bacterial Genetics and Biochemistry, the Gene Concept
56(3)
1.5.6 DNA: Its Transfer to and Selection in Living Cells
59(1)
1.5.7 Gene Cloning (1971-1982) the Era of Modern Biotechnology Based on Molecular Biology Begins
60(1)
1.5.7.1 A Prerequisite for Cloning: Nucleic Acid, Biochemistry, and Enzymology
60(1)
1.5.7.2 Applying Known Methods or a Conceptual Jump: the Details
61(3)
1.5.8 Genome Mapping: Clone Libraries, Restriction Maps, and RFLPs
64(1)
1.5.8.1 Prelude: Human Genetics before Genome Sequencing
64(1)
1.5.8.2 Important Ideas on Gene Mapping in the DNA Age
64(1)
1.5.8.3 DNA Hybridization Chip Sequencing and More
69(1)
1.5.8.4 Mega Sequencing: Impact on Biotechnology
69(2)
1.5.9 Expressing Genes in Other Organisms: Transgenic Animals Carrying rDNA
71(1)
1.5.10 Future Trends
72(1)
References
73(12)
2 Synthetic Biology: An Emerging Approach for Strain Engineering
85(26)
Jie Sun
Hal Alper
2.1 Introduction
85(1)
2.2 Basic Elements
86(1)
2.2.1 Gene Synthesis
87(1)
2.2.2 Transcriptional Control
89(1)
2.2.2.1 Promoter Engineering
89(1)
2.2.2.2 Optimization of Gene Expression Vectors
94(2)
2.3 Functional and Robust Modules
96(1)
2.3.1 Synthetic Pathway Modules
96(1)
2.3.1.1 Pathway Assembly Tools
97(1)
2.3.1.2 Pathway Metabolic Flux Optimization Approaches
97(2)
2.3.2 Synthetic Circuit Modules
99(1)
2.3.2.1 Examples of Synthetic Circuits
99(1)
2.3.2.2 Synthetic Circuit Design
100(1)
2.3.2.3 Next-Generation Synthetic Circuits
102(1)
2.4 Microbial Communities
102(2)
2.5 Conclusions and Future Prospects
104(1)
Acknowledgments
104(1)
References
104(7)
3 Toward Genome-Scale Metabolic Pathway Analysis
111(14)
Jurgen Zanghellini
Matthias P. Gerstl
Michael Hanscho
Govind Nair
Georg Regensburger
Stefan Muller
Christian Jungreuthmayer
3.1 Introduction
111(3)
3.2 DD Method
114(2)
3.3 Calculating Short EFMs in Genome-Scale Metabolic Networks
116(4)
3.4 Conclusions
120(1)
Acknowledgments
121(1)
References
121(4)
4 Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping
125(24)
Ashty S. Karim
Quentin M. Dudley
Michael C. Jewett
4.1 Introduction
125(2)
4.2 Background
127(1)
4.2.1 Purified Enzyme Systems
128(1)
4.2.2 Crude Cell Lysate Systems
128(1)
4.3 The Benefits of Cell-Free Systems
129(1)
4.3.1 Purified Enzyme Systems
130(1)
4.3.2 Crude Cell Lysate Systems
133(1)
4.3.3 Variations of Cell-Free Systems
134(1)
4.4 Challenges and Opportunities in Cell-Free Systems
135(1)
4.4.1 Purification
136(1)
4.4.2 Spatial Organization
137(1)
4.4.3 Cell-Free System Stability
138(1)
4.4.4 Modeling
139(1)
4.5 Recent Advances
140(1)
4.6 Summary
141(1)
Acknowledgments
141(1)
References
142(7)
Part II Multipurpose Bacterial Cell Factories
149(178)
5 Industrial Biotechnology: Escherichia coil as a Host
151(32)
Matthew Theisen
James C. Liao
5.1 Introduction
151(1)
5.1.1 Background
151(1)
5.1.2 Historical Context
152(1)
5.2 E. coli Products
152(1)
5.2.1 Amino Acids
152(1)
5.2.2 Organic Acids
156(1)
5.2.3 Alcohols
157(1)
5.2.4 Diols
159(1)
5.2.5 Hydrogen and Alkanes
160(1)
5.2.6 Fatty Acids
160(1)
5.2.7 Sugar Alcohols
161(1)
5.2.8 Isoprenoids
161(1)
5.2.9 Polymers
162(1)
5.2.10 Natural Products
163(1)
5.2.11 Protein as Product
164(1)
5.3 Rewiring Central Metabolism
165(1)
5.3.1 NOG and Carbon Efficiency
165(1)
5.3.2 Methanol and CO2 Utilization
165(1)
5.3.3 Advancing Analytical Techniques
166(1)
5.4 Alternative Carbon Sources
167(1)
5.4.1 Complex Carbohydrates
167(1)
5.4.2 Glycerol
168(1)
5.4.3 Protein to Fuel
169(1)
5.5 E. coli Techniques and Concerns
169(1)
5.5.1 Genetic Manipulation
169(1)
5.5.2 Phage Contamination
169(1)
5.6 Conclusions
170(1)
References
171(12)
6 Industrial Microorganisms: Corynebacterium glutamicum
183(38)
Judith Becker
Christoph Wittmann
6.1 Introduction
183(2)
6.2 Physiology and Metabolism
185(1)
6.2.1 Substrate Assimilation, Catabolic Pathways, and Gluconeogenesis
186(1)
6.2.2 Tricarboxylic Acid Cycle and Glyoxylate Shunt
187(1)
6.2.3 Reactions of the Pyruvate Node
189(1)
6.2.4 Anabolism
192(1)
6.3 Genetic Manipulation of Corynebacterium glutamicum
192(1)
6.3.1 Plasmids
192(1)
6.3.2 Transformation Methods
194(1)
6.3.3 Engineering Gene Expression
195(1)
6.4 Systems Biology of Corynebacterium glutamicum
196(1)
6.4.1 Genome Analysis
196(1)
6.4.2 Transcriptome Analysis
197(1)
6.4.3 Proteome Analysis
198(1)
6.4.4 Metabolome Analysis
198(1)
6.4.5 Fluxome Analysis
199(1)
6.5 Application in Biotechnology
200(1)
6.5.1 Wild-Type Producers and Classical Mutants
200(1)
6.5.2 Top-Selling Amino Acids
200(1)
6.5.2.1 Glutamate Biosynthesis
201(1)
6.5.2.2 L-Lysine Biosynthesis
201(1)
6.5.2.3 Biosynthesis of Aromatic Amino Acids
202(1)
6.5.3 Tailoied Strains by Recombinant DNA Technology
202(1)
6.6 Conclusions and Perspectives
202(1)
References
203(18)
7 Host Organisms: Bacillus subtilis
221(78)
Hans-Peter Hohmann
Jan M. van Dijl
Laxmi Krishnappa
Zoltan Progai
7.1 Introduction and Scope
221(1)
7.2 Identification of Genetic Traits Pertinent to Enhanced Biosynthesis of a Value Product
222(3)
7.3 Traits to Be Engineered for Enhanced Synthesis and Secretion of Proteinaceous Products
225(1)
7.3.1 Signal Peptides and Signal Peptidases
225(1)
7.3.2 Protein Transport Pathways
226(1)
7.3.2.1 The Sec Pathway
226(1)
7.3.2.2 The Tat Pathway
228(1)
7.3.2.3 Extracellular and Membrane-Bound Proteases of B. subtilis
229(2)
7.4 Engineering of Genetic Traits in Bacillus subtilis
231(1)
7.4.1 Natural Competence and Double Crossover Integration
232(1)
7.4.2 Tools to Modify Protein Expression Levels in B. subtilis Production Strains
233(1)
7.4.2.1 Promoters of Various Strength for Customized mRNA Synthesis
233(1)
7.4.2.2 Gene Amplification and Plasmid Vectors
234(1)
7.4.2.3 mRNA-Stabilizing Elements and Transcriptional Terminators
234(1)
7.4.2.4 RBS Elements
235(1)
7.4.2.5 Signal Peptides
236(1)
7.4.3 Modification of the Amino Acid Sequence of an Enzyme
237(1)
7.4.4 Transforming DNA Constructs Obtained by Template-Free Synthesis or by PCR
237(1)
7.4.5 Production Strains Devoid of Antibiotic Resistance Markers
238(1)
7.4.5.1 Chromosomal Modification with Transiently Employed Selection Markers
238(1)
7.4.5.2 Counterselection Strategies to Force the Deletion of Dominant Markers
239(1)
7.4.5.3 Removal of the Selection Marker by Cre/loxP Site-Specific Recombination
240(1)
7.4.5.4 Recombineering
241(1)
7.4.6 Introduction of Exogenous DNA into Bacillus Strains Incapable of Developing Natural Competence
242(1)
7.4.6.1 Phage Transduction
242(1)
7.4.6.2 Protoplast Transformation and Protoplast Fusion
243(1)
7.4.6.3 Electrotransformation
243(1)
7.4.7 Lysed Protoplast Transformation
244(1)
7.5 Genome Reduction
245(2)
7.6 Significance of Classical Strain Improvement in Times of Synthetic Biology
247(1)
7.6.1 Generation of Genetic Diversity in Random Fashion
248(1)
7.6.2 Screening Platforms
249(1)
7.6.3 High-Throughput, Low-Intensity Fed-Batch Cultivation
250(1)
7.6.4 Medium-Throughput, High-Intensity Fed-Batch Cultivation
251(1)
7.7 Resource-Efficient B. subtilis Fermentation Processes
252(2)
7.8 Safety of Bacillus subtilis
254(1)
7.8.1 Absence of Acquired Added Antimicrobial Resistance Genes
255(1)
7.8.2 Safety of Surfactin
256(1)
7.8.3 Absence of Toxin Production
257(1)
7.8.4 Absence of Sporulation
258(1)
7.9 Bacillus Production Strains on the Factory Floor: Some Examples
258(1)
7.9.1 Nucleotides
258(1)
7.9.2 Riboflavin
263(1)
7.9.3 (R)-Pantothenic Acid
267(1)
7.9.4 Production Strains for Metabolites with Unusual Biochemistry
271(1)
7.9.4.1 Biotin (Vitamin B7)
271(1)
7.9.4.2 Thiamine (Vitamin B1)
273(1)
7.9.4.3 Pyridoxine (Vitamin B6)
275(3)
7.9.5 Enzymes
278(2)
Acknowledgments
280(1)
References
280(19)
8 Host Organism: Pseudomonas putida
299(28)
Ignacio Poblete-Castro
Jose M. Borrero-de Acuria
Pablo I. Nikel
Michael Kohlstedt
Christoph Wittmann
8.1 Introduction
299(1)
8.2 Physiology and Metabolism
300(1)
8.2.1 Substrate Uptake
300(1)
8.2.2 Major Catabolic Pathways
300(1)
8.2.3 Degradation of Xenobiotics
302(1)
8.2.4 Regulation of Core Carbon and Energy Metabolism
303(1)
8.3 Genetic Manipulation
304(1)
8.3.1 Transformation
304(1)
8.3.2 Engineering Gene Expression
304(3)
8.4 Systems Biology
307(1)
8.4.1 Genomics and Genome Scale-Modeling
308(1)
8.4.2 Transcriptomics
308(1)
8.4.3 Proteomics
309(1)
8.4.4 Metabolomics and Fluxomics
310(1)
8.4.5 Multiomics Studies
311(1)
8.5 Application in Biotechnology
311(1)
8.5.1 Biopolymers and Advanced Materials
312(1)
8.5.2 High-Value Chemicals
314(1)
8.6 Future Outlook
315(1)
References
315(12)
Part III Exploiting Anaerobic Biosynthetic Power
327(126)
9 Host Organisms: Clostridium acetobutylicum/Clostridium beijerinckii and Related Organisms
329(36)
Frank R. Bengelsdorf
Anja Poehthin
Stefanie K. Flitsch
Sonja Linder
Bettina Schiel-Bengelsdorf
Benjamin A. Stegmann
Preben Krabben
Edward Green
Ying Zhang
Nigel Minton
Peter Durre
9.1 Introduction
329(1)
9.2 Microorganisms
330(1)
9.2.1 C. acetobutylicum
330(1)
9.2.2 C. beijerinckii
331(1)
9.2.3 C. saccharobutylicum
331(1)
9.2.4 C. saccharoperbutylacetonicum
332(1)
9.3 Bacteriophages
332(1)
9.3.1 History of Bacteriophages Infecting Solventogenic Clostridia
332(1)
9.3.2 Phage Specificity
335(1)
9.3.3 Phage Effect
335(1)
9.4 ABE Fermentation of Solvent-Producing Clostridium Strains
336(6)
9.5 Genome-Based Comparison of Solvent-Producing Clostridium Strains
342(3)
9.6 Regulation of Solvent Formation in C. acetobutylicum
345(1)
9.7 Genetic Tools for Clostridial Species
346(7)
9.8 Industrial Application of ABE Fermentation
353(2)
Acknowledgments
355(1)
References
355(10)
10 Advances in Consolidated Bioprocessing Using Clostridium thermocellum and Thermoanaerobacter saccharolyticum
365(30)
Lee R. Lynd
Adam M. Guss
Michael E. Himmel
Dhananjay Beni
Chris Herring
Evert K. Holwerda
Sean J. Murphy
Daniel G. Olson
Julie Paye
Thomas Rydzak
Xiongjun Shao
Liang Tian
Robert Worthen
10.1 Introduction
365(1)
10.2 CBP Organism Development Strategies
366(1)
10.3 Plant Cell Wall Solubilization by C. thermocellum
367(1)
10.3.1 Understanding and Describing Solubilization
367(1)
10.3.2 Comparative Solubilization Effectiveness
368(4)
10.4 Bioenergetics of C. thermocellum Cellulose Fermentation
372(1)
10.4.1 Membrane Energetics
372(1)
10.4.2 Sugar Conversion to Pyruvate
374(1)
10.4.3 End-Product Formation
376(2)
10.5 Metabolic Engineering
378(1)
10.5.1 Transformation and Genetic Tool Development
378(1)
10.5.2 Ethanol Tolerance and Titer
378(1)
10.5.3 Metabolic Engineering for High Ethanol Yield
380(1)
10.5.3.1 Metabolic Engineering of T saccharolyticum
381(1)
10.5.3.2 Hydrogenases
382(1)
10.5.3.3 The Pyruvate to Ethanol Pathway in T saccharolyticum
382(1)
10.5.3.4 Engineering C. thermocellum and Comparison with T saccharolyticum
383(1)
10.5.3.5 Current State of Strain Development
386(1)
10.6 Summary and Future Directions
386(2)
Acknowledgments
388(1)
References
388(7)
11 Lactic Acid Bacteria
395(58)
Luciana Ruiz-Rodriguez
Juliana Bleckwedel
Maria Eugenia Ortiz
Micaela Pescuma
Fernanda Mozzi
11.1 Introduction
395(3)
11.2 Fermented Foods
398(1)
11.2.1 Fermented Milks
400(1)
11.2.2 Cheeses
403(1)
11.2.3 Fermented Meats
403(1)
11.2.4 Nondairy Drinks and Foods
404(1)
11.2.4.1 Roots (Yacon)
404(1)
11.2.4.2 Fruits and Legumes
405(1)
11.2.4.3 Gluten-Free Foods
406(1)
11.3 Industrially Relevant Compounds
406(1)
11.3.1 Food Ingredients
406(1)
11.3.1.1 Antimicrobial Compounds
406(1)
11.3.1.2 Aroma Compounds
414(1)
11.3.1.3 Enzymes
416(4)
11.3.2 Nutraceutics
420(1)
11.3.2.1 Low-Calorie Sugars
420(1)
11.3.2.2 Vitamins
423(1)
11.3.2.3 Conjugated Linoleic Acids
426(1)
11.3.2.4 gamma-Aminobutyric Acid
427(1)
11.3.2.5 Seleno-Proteins
428(1)
11.3.2.6 Exopolysaccharides
429(1)
11.3.3 Bulk Compounds
430(1)
11.3.3.1 Lactic Acid
430(1)
11.3.3.2 Biofuels
433(1)
11.4 Conclusions
434(1)
Conflict of Interest
435(1)
References
435(18)
Volume 2
List of Contributors
xv
About the Series Editors
xxvii
Preface
xxix
Part IV Microbial Treasure Chests for High-Value Natural Compounds
453(52)
12 Host Organisms: Myxobacterium
455(32)
Silke C. Wenzel
Rolf Muller
12.1 Introduction into the Myxobacteria
455(2)
12.2 Phylogeny and Classification
457(2)
12.3 Physiology
459(1)
12.4 Growth and Nutritional Requirements
460(2)
12.5 Genetics and Genomics
462(2)
12.6 Secondary Metabolism
464(4)
12.7 Myxococcus
468(1)
12.7.1 Introduction
468(1)
12.7.2 Secondary Metabolism of Myxococcus xanthus
469(1)
12.7.3 Myxococcus xanthus as Expression Host
470(1)
12.7.4 Heterologous Expression of the Epothilone Gene Cluster from Sorangium cellulosum in Myxococcus xanthus
471(1)
12.7.5 Production of Myxovirescin by Fermentation of Myxococcus virescens
472(1)
12.8 Sorangium
472(1)
12.8.1 Introduction
472(1)
12.8.2 Sorangium cellulosum So ce56
472(1)
12.8.3 The Anticancer Drug Ixabepilone is a Derivative of Epothilone from Sorangium cellulosum So ce90
474(1)
12.8.4 Other Sorangium Secondary Metabolites Holding Promise for Future Application
475(1)
12.9 Outlook
476(1)
References
476(11)
13 Host Organism: Streptomyces
487(18)
Oksana Bilyk
Andriy Luzhetskyy
13.1 Introduction
487(2)
13.2 Streptomyces Genome Manipulation Toolkits
489(1)
13.2.1 Site-Specific Recombinases
490(1)
13.2.2 Transposons
491(1)
13.2.3 I-Scel Endonuclease and CRISPR/Cas9
492(1)
13.2.4 Reporter Genes for Streptomycetes
492(1)
13.2.5 Genetic Controlling Elements for Streptomycetes
493(2)
13.3 Hots for Heterologous Production of Natural Products
495(1)
13.3.1 S. coelicolor
496(1)
13.3.2 S. avermitillis
497(1)
13.3.3 S. albus
497(2)
Acknowledgments
499(1)
References
499(6)
Part V Extending the Raw Material Basis for Bioproduction
505(138)
14 Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective
507(74)
Andrew J. Loder
Benjamin M. Zeldes
Jonathan M. Conway
James A. Counts
Christopher T Straub
Piyum A. Khatibi
Laura L. Lee
Nicholas P. Vitko
Matthew W. Keller
Amanda M. Rhaesa
Gabe M. Rubinstein
Israel M. Scott
Gina L. Lipscomb
Michael W.W. Adams
Robert M. Kelly
14.1 Introduction
507(2)
14.2 Bioprocessing Advantages for Extremely Thermophilic Hosts
509(1)
14.3 Biobased Chemicals and Fuels: Targets and Opportunities
510(2)
14.4 Considerations for Selecting an Extremely Thermophilic Host
512(1)
14.5 General Strategies for Genetic Manipulation of Extreme Thermophiles
513(8)
14.6 Limitations and Barriers to Genetic Modification of Extreme Thermophiles
521(2)
14.7 Current Status of Metabolic Engineering Efforts and Prospects in Extreme Thermophiles
523(1)
14.7.1 Pyrococcus furiosus
523(1)
14.7.1.1 Genetic Tools - R furiosus
523(1)
14.7.1.2 Metabolic Engineering - P. furiosus
528(9)
14.7.2 Thermococcus Species
537(1)
14.7.2.1 Genetic Tools - Thermococcus Species
537(1)
14.7.2.2 Metabolic Engineering - Thermococcus Species
538(1)
14.7.3 Sulfolobus Species
538(1)
14.7.3.1 Genetics Tools - Sulfolobus Species
539(1)
14.7.3.2 Metabolic Engineering - Sulfolobus Species
541(1)
14.7.4 Thermotoga maritima
541(1)
14.7.4.1 Genetic Tools - Thermotoga Species
542(1)
14.7.4.2 Metabolic Engineering - Thermotoga Species
544(1)
14.7.5 Thermus Species
544(1)
14.7.5.1 Genetic Tools - Thermus Species
545(1)
14.7.5.2 Metabolic Engineering - Thermus Species
547(1)
14.7.6 Caldicellulosiruptor bescii
548(1)
14.7.6.1 Genetics Tools - Caldicellulosiruptor bescii
548(1)
14.7.6.2 Metabolic Engineering - Caldicellulosiruptor bescii
550(2)
14.7.7 Thermoanaerobacter Species
552(1)
14.7.7.1 Genetic Tools - Thermoanaerobacter Species
552(1)
14.7.7.2 Metabolic Engineering - Thermoanaerobacter Species
553(2)
14.7.8 Caldanaerobacter subterraneus subsp. tengcongensis
555(1)
14.7.8.1 Genetics Tools - Caldanaerobacter subterraneus subsp. tengcongensis
555(1)
14.7.8.2 Metabolic Engineering - Caldanaerobacter subterraneus subsp. tengcongensis
556(1)
14.8 Metabolic Engineering of Extreme Thermophiles - Tool Kit Needs
556(1)
14.8.1 Promoters
556(1)
14.8.2 Ribosomal Binding Sites
557(1)
14.8.3 Reporter Genes
558(1)
14.9 Conclusions and Future Perspectives
558(2)
Acknowledgments
560(1)
References
560(21)
15 Cyanobacteria as a Host Organism
581(24)
Fabienne Duchoud
Derrick S.W. Chuang
James C. Liao
15.1 Introduction and Relevance: Cyanobacteria as a Host Organism
581(1)
15.2 General Description of Cyanobacteria
582(1)
15.2.1 A Diverse Bacterial Group and Its Metabolisms
582(1)
15.2.2 Nitrogen Fixation
583(1)
15.2.3 Circadian Clock
584(1)
15.2.4 Light/Dark Regulation
584(1)
15.3 Genetic Tools
585(1)
15.3.1 Transformation
585(1)
15.3.2 Promoters
586(1)
15.3.3 Terminators
587(1)
15.3.4 Ribosome Binding Sites
588(1)
15.4 Improving Photosynthetic Efficiency
588(1)
15.4.1 Improving Light Harvesting
588(1)
15.4.2 Improving Carbon Fixation
589(1)
15.5 Direct Conversion of CO2 into Biofuels and Chemicals
590(1)
15.5.1 Fuels and Chemicals from Acetyl-CoA
590(1)
15.5.2 Fuels and Chemicals from Keto Acids
594(1)
15.5.3 Chemicals from TCA Cycle Intermediates
596(1)
15.5.4 Hydrogen
596(1)
15.6 Conclusions
597(1)
References
597(8)
16 Host Organisms: Algae
605(38)
Elizabeth A. Specht
Prema S. Karunanithi
Javier A. Gimpel
William S. Ansari
Stephen P. Mayfield
16.1 Introduction to Algae as an Industrial Organism
605(1)
16.1.1 Algal Diversity
605(1)
16.1.2 Scalability and Growth Rate
606(1)
16.1.3 Genetic Malleability
606(1)
16.2 Algal Genetic Engineering
606(1)
16.2.1 Nuclear Genetic Engineering
607(1)
16.2.1.1 Nuclear Transformation Methods
607(1)
16.2.1.2 Regulation of Nuclear Transgene Expression
607(1)
16.2.1.3 Tools for Increased Nuclear Gene Expression
608(1)
16.2.1.4 Selection and Screening Methods
608(1)
16.2.1.5 Gene Targeting and Genome Editing
609(1)
16.2.2 Chloroplast Genetic Engineering
610(1)
16.2.2.1 Chloroplast Transformation Methods
610(1)
16.2.2.2 Gene Regulation in the Chloroplast
611(1)
16.2.2.3 Chloroplast Selection and Reporters
611(1)
16.2.3 Other Transformable Species
612(1)
16.2.3.1 Parameters for Transformation Optimization
612(1)
16.2.3.2 Species Successfully Transformed
613(1)
16.3 Therapeutic and Nutraceutical Applications
613(1)
16.3.1 Protein Therapeutics
614(1)
16.3.1.1 Human Antibodies and Antibody-Drug Conjugates
614(1)
16.3.1.2 Other Chloroplast-Produced Protein Therapeutics
615(1)
16.3.1.3 Nuclear-Expressed Protein Therapeutics
615(1)
16.3.2 Nutraceuticals and Nutritional Supplements
616(1)
16.3.2.1 Omega-3 Fatty Acids
616(1)
16.3.2.2 Source of Organic Selenium
616(1)
16.3.2.3 Carotenoids from Wild-Type and Engineered Algae
616(1)
16.3.3 Recombinant Vaccines
617(1)
16.3.3.1 Vaccine Antigens Produced in Algae
617(1)
16.3.3.2 Animal Efficacy Studies
618(1)
16.3.3.3 Recombinant Oral Vaccines
619(1)
16.4 Bioenergy Applications
619(1)
16.4.1 Altering Lipid Metabolism
620(1)
16.4.1.1 Changes in Nutrient Availability
620(1)
16.4.1.2 Changes in Temperature
621(1)
16.4.1.3 Changes in Light Intensity
621(1)
16.4.1.4 Genetic Manipulation of Lipid C9ntent
621(1)
16.4.2 Increasing Photosynthetic Efficiency
622(1)
16.4.2.1 Improving Light Utilization
622(1)
16.4.2.2 Improving Photosynthetic Efficiency
622(1)
16.4.2.3 Expanding the Photosynthetically Active Spectrum
623(1)
16.4.3 Modifying Carbon Assimilation
623(1)
16.4.3.1 Engineering RuBisCO
624(1)
16.5 Other Industrial Applications
624(1)
16.5.1 Animal Feedstocks
625(1)
16.5.1.1 Algal Protein Extracts as Animal Feedstocks
625(1)
16.5.1.2 Engineered Algae to Enhance Immune Function
625(1)
16.5.2 Industrial Enzymes
626(1)
16.5.2.1 Enzymes for Processing Cellulosic Biofuels
626(1)
16.5.2.2 Enzymes for Food Processing
626(1)
16.6 Industrial-Scale Algal Production
627(1)
16.6.1 Enclosed Photobioreactors and Fermenters
627(1)
16.6.1.1 Optimizing Photobioreactor Design
628(1)
16.6.1.2 Modifying Trophic Conversion Pathways for Heterotrophic Growth
628(1)
16.6.2 Open Pond Growth
629(1)
16.6.2.1 Media and Water Optimization
629(1)
16.6.2.2 Efficient Harvesting Methods
629(1)
16.7 Conclusions and Potential of Algal Platforms
630(1)
References
630(13)
Part VI Eukaryotic Workhorses: Complex Cells Enable Complex Products
643(72)
17 Host Organisms: Mammalian Cells
645(28)
Jennifer Pfizenmaier
Ralf Takors
17.1 Introduction
645(1)
17.2 Basics of Cellular Structure and Metabolism
646(1)
17.2.1 Cellular Structure
646(1)
17.2.2 Metabolism
650(1)
17.3 The Genome of CHO Cells
651(1)
17.4 Molecular Biology Tools
652(2)
17.5 Kinetics of Growth and Product Formation
654(2)
17.6 Intracellular Metabolome Analysis
656(5)
17.7 Proteome and Gene Expression Analysis
661(1)
17.8 Improving Cellular Performance by Genetic and Metabolic Engineering
662(2)
17.9 Outlook
664(1)
References
664(9)
18 Industrial Microorganisms: Saccharomyces cerevisiae and other Yeasts
673(14)
Diethard Mattanovich
Brigitte Gasser
Michael Egermeier
Hans Marx
Michael Sauer
18.1 Industrial Application of Yeasts
673(2)
18.2 Baker's Yeast as Versatile Host for Metabolic Engineering
675(2)
18.3 Protein Production in Yeasts
677(1)
18.4 Lipid Production in Yeasts
678(2)
18.5 Pentose-Utilizing Yeasts
680(1)
18.5.1 Engineered S. cerevisiae
680(1)
18.5.2 Yeasts that Naturally Utilize Xylose and Other Pentoses
681(1)
18.6 Conclusions
681(1)
Conflict of Interest
682(1)
References
682(5)
19 Industrial Microorganisms: Pichia pastoris
687(28)
Diethard Mattanovich
Michael Sauer
Brigitte Gasser
19.1 Physiology and Genetics of Pichia pastoris
687(1)
19.1.1 Methylotrophic Yeasts
687(1)
19.1.2 Taxonomy and Natural Isolates
688(1)
19.1.3 Genomics
689(1)
19.1.4 Physiology
689(2)
19.2 Methylotrophic Metabolism
691(1)
19.2.1 Dissimilation of Methanol to Generate Energy
692(1)
19.2.2 Assimilation of Methanol to Form Biomass
692(1)
19.2.3 Implications for Production Processes
693(1)
19.3 Application for the Production of Recombinant Proteins
693(1)
19.3.1 Promoters
693(1)
19.3.2 Protein Secretion
695(1)
19.3.3 Vectors and Selection Markers
696(1)
19.3.4 Integration of Multiple Gene Copies
698(1)
19.3.5 Metabolic Engineering to Enhance Productivity of Recombinant Proteins
700(1)
19.3.6 Engineering Protein Folding and Secretion Pathways to Enhance Productivity
701(1)
19.3.7 Protein Glycosylation and Glycoengineering
703(1)
19.3.8 Recombinant Proteins on the Market
703(1)
19.4 Application of P pastoris for Metabolite Production
703(2)
19.5 Conclusion
705(1)
References
705(10)
Index 715
Christoph Wittmann is Director of the Institute of Systems Biotechnology at Saarland University, Saarbrücken, Germany. Having obtained his academic degrees from Braunschweig Technical University, Germany, he was postdoc at Helsinki University, Finland, held chairs for Biotechnology at Münster University, Germany, and for Biochemical Engineering at Braunschweig Technical University and was invited guest professor at Université Rangueil de Toulouse, France, before taking up his present position. He has authored more than 150 scientific publications, more than 20 books and book chapters, holds more than 20 patents and has received several scientific awards, including the Young Scientist Award of the European Federation of Biotechnology, and is board member of various scientific journals.

James Liao is currently President of Academia Sinica in Taiwan. Having obtained his PhD degree from University of Wisconsin, Madison, USA, he started his career at Eastman Kodak Company, before moving to Texas A&M, USA, and then to the University of California in Los Angeles (UCLA), USA, for his academic career. Professor Liao has received numerous scientific awards, including the US Presidential Green Chemistry Challenge Award and the Italian ENI award in renewable energy. He is also a member of the US National Academy of Sciences, National Academy of Engineering, and Academia Sinica in Taiwan.

Sang Yup Lee is Distinguished Professor at the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST). He is currently the Director of the Center for Systems and Synthetic Biotechnology, Director of the BioProcess Engineering Research Center, and Director of the Bioinformatics Research Center. He has published more than 500 journal papers, 64 books and book chapters, and more than 580 patents (either registered or applied). He received numerous awards, including the National Order of Merit, the Merck Metabolic Engineering Award, the ACS Marvin Johnson Award, Charles Thom Award, Amgen Biochemical Engineering Award, Elmer Gaden Award, POSCO TJ Park Prize, and HoAm Prize. He currently is Fellow of American Association for the Advancement of Science, the American Academy of Microbiology, American Institute of Chemical Engineers, Society for Industrial Microbiology and Biotechnology, American Institute of Medical and Biological Engineering, the World Academy of Science, the Korean Academy of Science and Technology, and the National Academy of Engineering of Korea. He is also Foreign Member of National Academy of Engineering USA. He is currently honorary professor of the University of Queensland (Australia), honorary professor of the Chinese Academy of Sciences, honorary professor of Wuhan University (China), honorary professor of Hubei University of Technology (China), honorary professor of Beijing University of Chemical Technology (China), and advisory professor of the Shanghai Jiaotong University (China). Lee is the Editor-in-Chief of the Biotechnology Journal and Associate Editor and board member of numerous other journals. Lee is currently serving as a member of Presidential Advisory Committee on Science and Technology (Korea).

Jens Nielsen is Professor and Director to Chalmers University of Technology (Sweden) since 2008. He obtained an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Technical University of Denmark (DTU) and after that established his independent research group and was appointed full Professor there in 1998. He was Fulbright visiting professor at MIT in 1995-1996. At DTU, he founded and directed the Center for Microbial Biotechnology. Jens Nielsen has published more than 350 research papers, co-authored more than 40 books and he is inventor of more than 50 patents. He has founded several companies that have raised more than 20 million in venture capital. He has received numerous Danish and international awards and is member of the Academy of Technical Sciences (Denmark), the National Academy of Engineering (USA), the Royal Danish Academy of Science and Letters, the American Institute for Medical and Biological Engineering and the Royal Swedish Academy of Engineering Sciences.

Professor Gregory Stephanopoulos is the W. H. Dow Professor of Chemical Engineering at the Massachusetts Institute of Technology (MIT, USA) and Director of the MIT Metabolic Engineering Laboratory. He is also Instructor of Bioengineering at Harvard Medical School (since 1997). He received his BS degree from the National Technical University of Athens and his PhD from the University of Minnesota (USA). He has co-authored approximately 400 research papers and 50 patents, along with the first textbook on Metabolic Engineering. He has been recognized by numerous awards from the American Institute of Chemical Engineers (AIChE) (Wilhelm, Walker and Founders awards), American Chemical Society (ACS), Society of industrial Microbiology (SIM), BIO (Washington Carver Award), the John Fritz Medal of the American Association of Engineering Societies, and others. In 2003 he was elected member of the National Academy of Engineering (USA) and in 2014 President of AIChE.