Manual of Industrial Microbiology and Biotechnology

786 Pages·2010·44.78 MB·English

by  Richard H. Baltz

MIMB3 title pages final 2/16/10 2:22 PM Page i
M A N U A L O F
Industrial Microbiology
and Biotechnology
THIRD EDITION
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MIMB3 title pages final 2/16/10 2:22 PM Page iii
M A N U A L O F
Industrial Microbiology
and Biotechnology
T H I R D E D I T I O N
EDITORS IN CHIEF
Richard H. Baltz
CognoGen Biotechnology Consulting, Indianapolis, Indiana
Julian E. Davies
University of British Columbia, Vancouver, British Columbia, Canada
Arnold L. Demain
Charles A. Dana Research Institute (R.I.S.E.), Drew University, Madison, New Jersey
E D I T O R S
Alan T. Bull Prakash Masurekar
School of Biosciences, University of Kent, Canterbury, Department of Plant Biology & Plant Pathology,
Kent, United Kingdom School of Environmental and Biological Sciences,
Rutgers University, New Brunswick, New Jersey
Beth Junker
Bioprocess Research and Development, Merck Research
Christopher D. Reeves
Laboratories, Rahway, New Jersey
Amyris Biotechnologies, Emeryville, California
Leonard Katz
SynBERC - Synthetic Biology Engineering Research
Huimin Zhao
Center, University of California-Berkeley,
Departments of Chemical and Biomolecular Engineering,
Emeryville, California
Chemistry, and Bioengineering, Institute for Genomic
Lee R. Lynd Biology, Center for Biophysics and Computational
Thayer School of Engineering, Dartmouth College, Biology, University of Illinois at Urbana-Champaign,
Hanover, New Hampshire Urbana, Illinois
Washington, DC
Copyright © 2010 ASM Press
American Society for Microbiology
1752 N Street, N.W.
Washington, DC 20036-2904
Library of Congress Cataloging-in-Publication Data
Manual of industrial microbiology and biotechnology / editors in chief, Richard H. Baltz, Julian E.
Davies, and Arnold L. Demain ; editors, Alan T. Bull ... [et al.]. -- 3rd ed.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-55581-512-7 (alk. paper)
1. Industrial microbiology--Handbooks, manuals, etc. 2. Industrial microbiology--Handbooks,
manuals, etc. 3. Biotechnology--Handbooks, manuals, etc. I. Baltz, Richard H. II. Davies, Julian E.
III. Demain, A. L. (Arnold L.), 1927- IV. American Society for Microbiology.
[DNLM: 1. Biotechnology. 2. Industrial Microbiology. QW 75 M294 2010]
QR53.M33 2010
660.6'2--dc22
2010001077
ISBN 978-1-55581-512-7
All Rights Reserved
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington,
DC 20036-2904, U.S.A.
Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, U.S.A.
Phone: [phone]
Fax: [phone]
Email: [email protected]
Online: estore.asm.org
Contents
Contributors / xi 6. Metabolomics for the Discoery of Noel
Editors / ix Compounds / 73
Preface / xvii JENS C. FRISVAD
7. Methods To Access Silent Biosynthetic
SECTION I
Pathways / 78
ISOLATION AND SCREENING FOR ROBERT H. CICHEWICz, JON C. HENRIKSON,
SECONDARY METABOLITES AND XIAORU WANG, AND KATIE M. BRANSCUM
ENZYMES / 1
VOLUME EDITOR: J. E. DAVIES
SECTION II
SECTION EDITOR: A. T. BULL
FERMENTATION AND CELL CULTURE / 97
Isolation VOLUME EDITOR: A. L. DEMAIN
1. New Approaches to Microbial SECTION EDITOR: P. MASUREKAR
Isolation / 3
8. Miniaturization of Fermentations / 99
SLAVA S. EPSTEIN, KIM LEWIS, DOMINICA NICHOLS,
WOUTER A. DUETz, MATTHEW CHASE,
AND EKATERINA GAVRISH
AND GERALD BILLS
2. Selectie Isolation of Actinobacteria / 13
9. Solid-Phase Fermentation: Aerobic and
MICHAEL GOODFELLOW
Anaerobic / 117
RAMUNAS BIGELIS
Identity / Dereplication
3. Taxonomic Characterization of
10. Bacterial Cultiation for Production of
Prokaryotic Microorganisms / 28
Proteins and Other Biological Products / 132
GIOVANNA E. FELIS, SANDRA TORRIANI,
JOSEPH SHILOACH AND URSULA RINAS
JOHAN E. T. VAN HyLCKAMA VLIEG, AND
AHARON OREN
11. Heterologous Protein Expression in Yeasts
Screening and Filamentous Fungi / 145
4. Enzymes from Extreme Enironments / 43 NINGyAN zHANG AND zHIQIANG AN
DON A. COWAN, BRONWyN M. KIRBy,
TRACy L. MEIRING, MANUEL FERRER, 12. Mammalian Cell Culture for
MARIA-EUGENIA GUAzzARONI, Biopharmaceutical Production / 157
OLGA V. GOLySHINA, AND PETER N. GOLySHIN JINyOU zHANG
5. Cell-Based Screening Methods for 13. Manufacture of Mammalian Cell
Anti-Infectie Compounds / 62 Biopharmaceuticals / 179
STEFANO DONADIO AND MARGHERITA SOSIO JINyOU zHANG

■
i CONTENTS
14. Plant Cell Culture / 196 SECTION IV
NANCy L. PAIVA GENETIC ENGINEERING OF SECONDARY
METABOLITE SYNTHESIS / 345
15. Insect Cell Culture / 212
VOLUME EDITOR: R. H. BALTZ
SPIROS N. AGATHOS
SECTION EDITOR: L. KATZ
SECTION III 24. Glycosylation of Secondary Metabolites
GENETICS, STRAIN IMPROVEMENT, AND To Produce Noel Compounds / 347
RECOMBINANT PROTEINS / 223 ANDREAS BECHTHOLD AND KATHARINA PROBST
VOLUME EDITOR: R. H. BALTZ
SECTION EDITOR: C. D. REEVES 25. Metabolic Engineering of
Escherichia coli for the Production of a
16. Genetic Engineering of Precursor to Artemisinin, an Antimalarial
Corynebacteria / 225 Drug / 364
MASATO IKEDA AND SEIKI TAKENO CHRISTOPHER J. PETzOLD AND JAy D. KEASLING
17. Genetic Manipulation of 26. Heterologous Production of
Clostridium / 238 Polyketides in Streptomyces coelicolor and
MARITE BRADSHAW AND ERIC A. JOHNSON Escherichia coli / 380
JAMES T. KEALEy
18. Genetic Manipulation of
Myxobacteria / 262 27. Genetic Engineering of Acidic
WESLEy P. BLACK, BRyAN JULIEN, Lipopeptide Antibiotics / 391
EDUARDO RODRIGUEz, AND zHAOMIN yANG RICHARD H. BALTz, KIEN T. NGUyEN,
AND DyLAN C. ALEXANDER
19. Strain Improement of Escherichia coli To
Enhance Recombinant Protein Production / 273 28. Genetic Engineering To Regulate
MICHAEL E. PyNE, KARAN S. SUKHIJA, Production of Secondary Metabolites in
AND C. PERRy CHOU Streptomyces / 411
SUSAN E. JENSEN
20. Genetic Engineering Tools for
Saccharomyces cerevisiae / 287 29. Genetic Engineering of Myxobacterial
VERENA SIEWERS, UFFE H. MORTENSEN, Natural Product Biosynthetic Genes / 426
AND JENS NIELSEN BRyAN JULIEN AND EDUARDO RODRIGUEz
21. Protein Expression in Nonconentional
SECTION V
Yeasts / 302
INDUSTRIAL ENZYMES, BIOCATALYSIS, AND
THOMAS W. JEFFRIES AND JAMES M. CREGG
ENZYME EVOLUTION / 439
22. Genetics, Genetic Manipulation, and VOLUME EDITOR: J. E. DAVIES
Approaches to Strain Improement of SECTION EDITOR: H. ZHAO
Filamentous Fungi / 318
30. Tools for Enzyme Discoery / 441
VERA MEyER, ARTHUR F. J. RAM,
AND PETER J. PUNT yASUHISA ASANO
23. Genetic Manipulations of Mammalian 31. Enzyme Engineering: Combining
Cells for Protein Expression / 330 Computational Approaches with Directed
ANNE KANTARDJIEFF, WEI-SHOU HU, GARGI SETH, Eolution / 453
AND R. SCOTT McIVOR LOUIS A. CLARK
32. Enzyme Engineering by Directed
Eolution / 466
MANFRED T. REETz
■
CONTENTS ii
33. Industrial Applications of Enzymes as 43. Bioethanol Production from
Catalysts / 480 Lignocellulosics: Some Process Considerations
NIKHIL U. NAIR, WENG LIN TANG, and Procedures / 621
DAWN T. ERIKSEN, AND HUIMIN zHAO CHARLES A. ABBAS, WU LI BAO, KyLE E. BEERy,
PAMELA CORRINGTON, CONSUELO CRUz, LUCAS
34. Biomass-Conerting Enzymes and LOVELESS, MARTIN SPARKS, AND KELLI TREI
Their Bioenergy Applications / 495
44. Surface Microbiology of Cellulolytic
FENG XU
Bacteria / 634
ALEXANDRU DUMITRACHE, GIDEON M. WOLFAARDT,
35. The Use of Enzymes for Non-Aqueous
AND LEE R. LyND
Organic Transformations / 509
ELTON P. HUDSON, MICHAEL J. LISzKA, AND
45. Physiological and Methodological Aspects
DOUGLAS S. CLARK
of Cellulolytic Microbial Cultures / 644
NICOLAI S. PANIKOV AND LEE R. LyND
36. Enzyme Promiscuity and Eolution of
New Protein Functions / 524
SECTION VII
BERT VAN LOO AND FLORIAN HOLLFELDER
BIOLOGICAL ENGINEERING AND SCALE-UP
37. Enzyme Production in Escherichia OF INDUSTRIAL PROCESSES / 657
coli / 539 VOLUME EDITOR: A. L. DEMAIN
DANIEL J. SAyUT, PAVAN K. R. KAMBAM, SECTION EDITOR: B. JUNKER
WILLIAM G. HERRICK, AND LIANHONG SUN
46. Raw Materials Selection and Medium
Deelopment for Industrial Fermentation
38. Bioprocess Deelopment / 549
Processes / 659
LUTz HILTERHAUS AND ANDREAS LIESE
SAMUN K. DAHOD, RANDOLPH GREASHAM,
AND MAX KENNEDy
SECTION VI
MICROBIAL FUELS (BIOFUELS) AND FINE 47. Scale-Up of Microbial Fermentation
CHEMICALS / 563 Process / 669
VOLUME EDITOR: A. L. DEMAIN XIAOMING yANG
SECTION EDITOR: L. R. LYND
48. Cell Culture Bioreactors: Controls,
39. Accessing Microbial Communities for Measurements, and Scale-Down Model / 676
WAN-SEOP KIM
Solutions to Biofuels Production / 565
CARL B. ABULENCIA, STEVEN M. WELLS,
49. Continuous Culture / 685
KEVIN A. GRAy, MARTIN KELLER, AND
AN-PING zENG AND JIBIN SUN
JOEL A. KREPS
50. Adances in Sensor and Sampling
40. Micro-Algal Culture as a Feedstock for
Technologies in Fermentation and Mammalian
Bioenergy, Chemicals, and Nutrition / 577
Cell Culture / 700
SUSAN T. L. HARRISON, MELINDA J. GRIFFITHS,
ADEyMA y. ARROyO
NICHOLAS LANGLEy, CARyN VENGADAJELLUM,
AND ROBERT P. VAN HILLE 51. Bioreactor Automation / 719
DAVID HOPKINS, MELISSA ST. AMAND,
41. Metabolic Engineering Strategies for AND JACK PRIOR
Production of Commodity and Fine Chemicals:
Escherichia coli as a Platform Organism / 591 52. Purification and Characterization of
PATRICK C. CIRINO Proteins / 731
ULRICH STRyCH AND RICHARD C. WILLSON
42. Improing Microbial Robustness Using
Systems Biology / 605 Author Index / 743
JONATHAN R. MIELENz AND DAVID A. HOGSETT
Subject Index / 745
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Editors in Chief
Richard H. Baltz Arnold L. Demain
CognoGen Biotechnology Consulting, Indianapolis, Charles A. Dana Research Institute (R.I.S.E.),
IN 46220 Drew University, Madison, NJ 07940
Julian E. Daies
University of British Columbia, Vancouver,
British Columbia, V6R 1z3 Canada
Editors
Alan T. Bull Prakash Masurekar
School of Biosciences, University of Kent, Canterbury, Department of Plant Biology & Plant Pathology,
Kent CT2 7NJ, United Kingdom School of Environmental and Biological Sciences,
Rutgers University, New Brunswick, NJ 08901-8520
Beth Junker
Bioprocess Research and Development, Christopher D. Reees
Merck Research Laboratories, Rahway, NJ 07065 Amyris Biotechnologies, Emeryville, CA 94608
Leonard Katz Huimin Zhao
SynBERC - Synthetic Biology Engineering Research Center, Departments of Chemical and Biomolecular Engineering,
University of California-Berkeley, Emeryville, CA 94608 Chemistry, and Bioengineering, Institute for
Genomic Biology, Center for Biophysics and Computational
Lee R. Lynd Biology, University of Illinois at Urbana-Champaign,
Thayer School of Engineering, Dartmouth College, Urbana, IL 61801
Hanover, NH 03755
ix