fermentation biotechnology

Fermentation Biotechnology Fermentation Biotechnology Badal C Saha, Editor Agricultural Research Service US.Department of Agriculture Sponsored by tbe ACS Division of Biochemical Technology American Chemical Society, Washington, DC e Fermentation biotechnology Library of Congress Cataloging-in-Pubiication Data Fermentation biotechnology / Badal C Saha, editor p cm. (ACS symposium series ;862) "Sponsored by the ACS Division of Biochemical Technology." Includes bibliographical references and index ISBN 0-841 2-3845-6 Fermentation-Congresses I Saha, Badal C., 1949- 11 American Chemical Society (224th : 2002 ; Boston, Mass.) 111 Series The paper used in this publication meets the minimum requirements of ~ m e r i i a n National Standard for Information Sciences-Permanence of Paper for Printed Library Materials, ANSI 239.48-1 984 Copyright Q 2003 American Chemical Society Distributed by Oxford University Press All Rights Resewed Reprographic copying beyond that permitted by Sections 107 or 108 of the U.S Copyright Act is allowed for internal use only, provided that a perchapter fee of $24.75 plus $0.75 per page is paid to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA Republication or reproduction for sale of pages in this book is permitted only under license from ACS Direct these and other permission requests to ACS Copyright Office, Publications Division, 1155 16th St., N.W., Washington, DC 20036 The citation of trade names andlor names of manufacturers in this publication is not to be construed as an endorsement or as approval by ACS of the commercial products or services referenced herein; nor should the mere reference herein to any drawing, specification, chemical process, or other data be regarded as a license or as a conveyance of any right or permission to the holder, reader, or any other person or corporation, to manufacture, reproduce, use, or sell any patented invention or copyrighted work that may in any way be related thereto Registered names, trademarks, etc., used in this publication, even without specific indication thereof, are not to be considered unprotected by law PRINTED IN THE UNITED STATES OF AMERICA American Chemical Society Library Foreword The ACS Symposium Series was first published in 1974 to provide a mechanism for publishing symposia quickly in book form The purpose of the series is to publish timely, comprehensive books developed fkom ACS sponsored symposia based on current scientific research Occasionally, books are developed fiom symposia sponsored by other organizations when the topic is of keen interest to the chemistry audience Before agreeing to publish a book, the proposed table of contents is reviewed for appropriate and comprehensive coverage and for interest to the audience Some papers may be excluded to better focus the book; others may be added to provide comprehensiveness When appropriate, overview or introductory chapters are added Drafts of chapters are peer-reviewed prior to final acceptance or rejection, and manuscripts are prepared in camera-ready format As a rule, only original research papers and original review papers are included in the volumes Verbatim reproductions of previously published papers are not accepted ACS Books Department Preface Tremendous advances have been made in fermentation biotechnology for the production of a wide variety of commodity chemicals and pharmaceuticals It is timely to provide a book that can assist practicing scientists, engineers, and graduate students with effective tools for tackling the future challenges in fermentation biotechnology This book was developed fiom a symposium titled Advances in Fermentation Process Development, presented at the 224th National Meeting of the American Chemical Society (ACS) in Boston, Massachusetts, August 18-22, 2002 and sponsored by the ACS Division of Biochemical Technology It presents a compilation of seven symposium manuscripts and eight solicited manuscripts representing recent advances in fermentation biotechnology research The chapters in the book have been organized in five sections: Production of Specialty Chemicals, Production of Pharmaceuticals, Environmental Bioremediation, Metabolic Engineering, and Process Validation An overview chapter on commodity chemicals production by fermentation has been included I am fortunate to have contributions fiom world-class researchers in the field of fermentation biotechnology I am taking this opportunity to express my sincere appreciation to the contributing authors, the reviewers who provided excellent comments to the editor, the ACS Division of Biochemical Technology, and the ACS Books Department for making possible the publication of this book I hope that this book will actively serve as a valuable multidisciplinary (biochemistry, microbiology, molecular biology, and biochemical engineering) contribution to the continually expanding field of fermentation biotechnology Badal C Saha Fermentation Biotechnology Research Unit National Center for Agricultural Utilization Research Agricultural Research Service U.S Department of Agriculture 1815 North University Street Peoria, IL 61604 (309) 68 1-6276 (telephone) (309) 681-6427 (fax) sahabc@ncaur.usda.gov (email) Fermentation Biotechnology Chapter Commodity Chemicals Production by Fermentation: An Overview Badal C Saha Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S Department of Agriculture, Peoria, IL 61604 Various commodity chemicals such as alcohols, polyols, organic acids, amino acids, polysaccharides, biodegradable plastic components, and industrial enzymes can be produced by fermentation This overview focuses on recent research progress in the production of a few chemicals: ethanol, 13-propanediol, lactic acid, polyhydroxyakanoates, exopolysaccharides and vanillin The problems and prospects of cost-effective commodity chemical production by fermentation and future directions of research are presented During the last two decades, tremendous improvements have been made in fermentation technology for the production of commodity chemicals and high value pharmaceuticals In addition to classical mutation, selection, media design, and process optimization, metabolic engineering plays a significant role in the improvement of microbial strains and fermentation processes Classical mutation includesrandom screeningand rationalized selection.Rationalized selection can be based on developing auxotropic strains, deregulated mutants, mutants resistant to feedback inhibition and mutants resistant to repression (1) In addition to the O 2004 American Chemical Society classical approach to media design and statistical experimentaldesign, evolutionary computational methods and d f i c i a l neural networks have been employed for media design and process optimization ( I ) Important regulatory mechanisms involved in the biithesis of fennentation pmducts by a microorganism include substrate induction, feedback regulation, and nutritional regulation by sources of carbon, nitrogen, and phosphorus (2) Various metabolic engineering approaches have been taken to produce or improve the production of a metabolite by fermentation (3) These are: (i) heterologous protein production, (ii) extension of o substrate range, (iii) pathway leading t new products, (iv) pathways for degradation of xenobiotics, (v) engineering of cellular physiology for process improvement, (vi) elimination or reduction of by-product formation, and (vii) improvement of yield or productivity As the demand for bio-based products is increasing, attempts have been made to replace more and more traditional chemical processes with faster, cheaper, and better enzymatic or fennentation methods Significant progress has been made for fermentative production of numerous compounds such as ethanol, organic acids, calcium magnesium acetate (CMA), butanol, amino acids, exopolysaccharides, surfactants, biodegradable polymers, antibiotics, vitamins, carotenoids, industrial enzymes, biopesticideq and biopharmaceuticals Fermentation biotechnology contributes a lot to the pollution control and w managemen This chaptergives an overview ofthe recent research and developmentsin fermentationbiotechnology for production of certain common commodity chemicals by fermentation Ethanol Ethanol has widespread application as an industrial chemical, gasoline additive, or straight liquid motor fuel In 2002, over billion gallons of ethanol were produced in the USA The demand for ethanol is expected to rise very sharply as a safer alternative to methyl tertiary bury1 ether (MTBE),the most common additive to gasoline used to provide cleaner combustion MTBE has been found to contaminateground water Also, there is increased interest to replace foreign fossil fuel with a much cleaner domestic alternative fuel derived from renewable resources Currently, more than 95% of fie1 ethanol is produced in the USA by fermenting glucose derived from corn starch In the USA, ethanol is made from corn by using both wet milling and dry milling In corn wet milling, protein, oil, and fiber components are separated before starch is liquefied and saccharified to glucose which is then fermented to ethanol by the conventional yeast Sacchmomyces cerevisiae In dry milling, ethanol is made from steam cooked whole ground corn by using simultaneoussaccharification and fermentation (SSF) process Ethanol is generally recovered from fermentation broth by distillation range dissolved oxygen setpoint also covers high shear (and faster mixing times) and low range with low shear and poor mixing In processes without oxygen control impeller agitation speed becomes the validation parameter with dissolved oxygen as a secondary (dependent) variable Biomass accumulation and time are frequently utilized process control parameters This is encountered as an instruction to transfer culture from one stage of the process to another at a particular biomass or a particular time This being on the premise that growth rate and culture physiology are effectively synonymous The experiments reported by Herbert (6)show that this premise is reasonable where the culture growth rate is defined by rate of supply of a particular nutrient (i.e in fed-batch or semicontinuous growth) It is also reasonable to assume that, all other parameters being consistent, the microorganism will grow at a particular rate and have a particular physiology The important caveat may be the case of temperature or pH where growth rate may be lower or higher but the organism will have essentially the same physiological status since it is growing at the maximum rate possible under the circumstances and neither would be expected to impose a particular metabolic condition However, this relates to interpretation of validation and not validation per se Both biomass and time would have ranges associated with them to allow for normal (acceptable) process variability (see figure for example) The rationale is that a process is "normal" if the organism displays a particular growth profile and anything outside of this is aberrant and should be rejected These ranges must therefore be validated The problem is that growth rate is not a factor which can be tightly controlled by the operators It is generally not possible to run a process to a specified value of either time or biomass independently of the other Process development involves evaluation of optimum biomass to achieve a particular outcome for product recovery and purification This is generally within a timeframe convenient to the operator's schedule The issue with biomass determination is that of precision of the method used Optical density is less precise because it often involves significant sample dilution to remain within the linear response range of the spectrophotometer, because time taken between sampling and analysis is variable and conditions are uncontrolled; and it is sample handling dependent (for example cells can settle, introducing non-homogeneity of sample) Online, real time methods such as biomass-specific sensors or metabolite production (especially COz) are preferred, but may not be universally applied for example in the shake flask stages of a process Shake Flask Tdals Target OD llm; Wndow 18-22 Hours Time (h) Figure Growth projles for 10 200 mL shake flask cultures of Streptomyces lividans grown in 1.0 L Erlenmeyerflash with bafles in glucose-casein peptone-salts medium at 32 97 and 240 rpm in a New Brunswick Series 25 Incubator shaker Validation of the biomasdtime process control parameters is probably only possible concurrently with process development During this phase, a database of information can be obtained on what is the range of values for time to achieve a specified biomass when the process is conducted normally Time, by itself, is sometimes used to define when, during a process, to something for example start a feed, or induce expression The preferred option in this case is to substitute a biomass-related parameter for time In the absence of an appropriate indicator other than time, it is essential to validate a range to demonstrate proper process control This is in the context of normal growth profile variability and hence biomass at the defined time of process Conclusion In conclusion, validation of a fermentation process involves consideration of many inter-related parameters Some of these are operator-specified and some concern the response of the organism to the imposed conditions The preferred basis for design of a validation protocol is a sound understanding of the physiology of the organism This understanding is acquired during the development phase and can be applied with good scientific rationale to address the real potential for process failure References A guide to Good Validation Practice.; Kanarek A.D.; D&MD Publications, Weestborough, USA, 200 Shillenn, J.K Ed "Validation Practices for Biotechnology Products." ASTM Publication STP 1260, USA, 1996 Cossar, J.D Current Opinion in Drug Discovery and Development 2001,4(6), 756-759 Prokop, A Adv Appl Microbial 1995,40, 155-236 Schaechter, M.; Maaloe, 0.; Kjeldgard, N.O J Gen Microbial 1958, 19,592-606 Herbert, D Symp Soc Gen Microbiol 1961, 11, 391-416 Author Index Alves, Paula M., 124 Ataai, M M., 207 Carrondo, Manuel J T., 124 Chang, Jo-Shu, 159 Cossar, D., 257 Domach, M M., 207 Fang, Qing-Hua, 108 Huang, E., 142 Inui, Masayuki, 175 Ishizaki, Ayaaki, 21 Jeong, K J., 193 Jongserijit, Boonsri, 221 Kanamnuay, Nitjakarn, 22 Kiatpapan, Pornpimon, 22 Koepsel, R., 207 Kos, Peter B., 175 Lee, S Y., 193 Lodes, E., 142 Marcelino, Isabel, 124 Miranda, Pedro M., 124 Moreira, Jose L., 124 Murooka, Yoshikatsu, 22 Nakata, Kaori, 175 Piao, Yong Zhe, 22 Richter, B., 142 Saha, Badal C., 3,67 Shah, A., 142 Shimizu, Kazuyuki, 233 Shu, Chin-Hang, 89 Swartz, J R., 142 Tang, Ya-Jie, 108 Thongchul, Nuttha, 36 Vertbs, Alain A., 175 Yamashita, Mitsuo, 221 Yang, Shang-Tian, 36,52 Yukawa, Hideaki, 175 Zawada, J., 142 Zhong, Jian-Jiang, 108 Zhu, T., 207 Zhu, Ying, 52 Subject Index Acarbose, carbohydrate-based therapeutic, 91t, 99 Acetate production and growth in cell extracts production, Escherichia coli, 148-152f Acetate production disruption by gene inactivation in Clostridium tyrobutyricum, 57-58 Acetate production in butyric acid formation, 54 Aeration rate, effect on fermentation in rotating fibrous bed bioreactor, 47-49 Agitation rate effects, stirred tank cultures using microcarriers, 135136f Air flow rate, main process validation parameter, 268-269 Alginate, production, overview, 11 Amino acids, production by fermentation, 187f 5-Aminolevulinic acid and vitamin B12 production in genetically engineered Propionibacteriumfieudenreichii, 221-232 5-Aminolevulinic acid biosynthesis, pathways, 222,224f-225f Amphotericin B, carbohydrate-based therapeutic, 91t, 98, 103 Anaerobic fermentation, kinetic model, 22-25 Anaerobic microorganisms, continuous fermentation system, 1-35 Analytical methods butyric acid production, 57 L(+)-lactic acid production, 41 Aspergillus candidus, filmentous fungus, mannitol production, 7 Aureobasidium pullulans, yeast-like fungus, mannitol production, 76 Azo dyes bioprocess development for bacterial decolorization, 163-170 industrial uses, 163 Bacterial decolorization, azo dyes, 163-170 Bacterial mercury resistance, 160162 Biofilm systems, fmed-bed bioreactor with immobilized cells, bacterial decolorization, azo dyes, 168169f Biomass determination, method precision in process Validation, 269 Biomass from carbon dioxide photosynthesis, sago palm, 32 Biomass/time, main process validation parameter, 269-270 Bovine serum, contamination with viruses, 97 2,3-Butanediol, production by fermentation, 12t Butyrate tolerance, Clostridium tyrobutyricum mutants, 62-64 Butyrate tolerance study, 57 Butyric acid applications, 53 production enhancement by Clostridium tyrobutyricum, 52-66 synthesis Erom petrochemicals, 53 Calicheamicin, carbohydrate-based therapeutic, 1t Candida, mannitol production by yeasts, 76 Caprine jugular endothelium cells, culture methods studies, 126-140 Carbohydrate-based therapeutics fermentation process development, 89-107 production methods, overview, 93f summary, 90-9 1t See also Glycoproteins Carbohydrate recognition systems, fundamentals, 95-96 Carbohydrate uses, progress in glycobiology, 90 I3carbonNMR spectrometry use in metabolic flux analysis, 237-240 Catabolic pathway for lactic acid, h r a t e , and ethanol production, Rhizopus oiyzae, 37-38f Catalytic hydrogenation, fructose, 69f Calvin cycle, 245, 247 Cell extract preparation, Clostridium tyrobutyricum, Cell extracts production, Escherichia coli, high density media culture, 142-156 Cell free protein synthesis in cell extracts production, Escherichia coli, 151 Cells and growth media, folic acid production in Escherichia coli, 21 Center for Biologics Evaluation and Research See FDA Center for Biologics Evaluation and Research Cerezyme, carbohydrate-based therapeutic, 1t Chemical route, disaccharide synthesis, 92,94f Chemical synthesis, carbohydratebased therapeutics production, advantages, 95t Chinese traditional medicine, medicinal mushroom See Medicinal mushroom, Ganoderma lucidurn, Chinese traditional medicine Citric acid production by fermentation, 12t Clostridium acetobutylicum, butyrate operon source, 57-58 Clostridium tyrobutyricum butyric acid production, 52-66 butyrate-producing mutant development, 54-57 Codon usage difference, effect minimization, 197 Cofactor regeneration in enzymatic production, mannitol, 77-78 Cornbinatorialbiosynthesis, role in new or hybrid natural products production, 103 Commercial production, Vitamin B 12, 222,226,228 Commodity chemicals, production by fermentation, overview, 3-1 Computational results, genetic engineering strategies for enhanced folic acid production in Escherichia coli, 212-214,216t Contaminationproof system, nisin Z concentration, 30 Continuous bacterial decolorization, azo dyes aerobiclanaerobic sequences,165167f cultures combined with microfiltration membrane, 166167 Continuous bioreactor development, L-lactic acid fermentation, 27-29 Continuous fermentation system for anaerobic microorganisms, 1-35 See also Fermentation Continuous proof system, L-lactic acid production, 30-32 Control variables in industrial fermentation process, 263-270 Corynebacteria, vectors for genetic engineering, 175-1 Cowdria ruminatium, heartwater infection agent, 125 Cost estimate comparisons, culture methods for caprine jugular endothelium cells, 138-1 39 Critical process parameters in process validation, identification, 260-261 Cultivation and measurement, folic acid production in Escherichia coli, 21 1-212 Culture adaptation in fed-batch fermentation, Clostridium tyrobutyricum, 58 Culture medium, excretory production, recombinant proteins, Escherichia coli, 202 Culture methods, mass production, ruminant endothelial cells, 124141 Cytoplasm, Escherichia coli targeted protein production, 198-199 Decolorization, azo dyes See Bacterial decolorization, azo dyes Defined medium in cell extracts production, Escherichia coli, 144145 Deoxysugar biosynthesis pathways, modification, 103-1 04 Disaccharide synthesis, chemical route, 92, 94f DNA isolation and manipulation, butyrate-producing mutant development, 55 DNA microarray technology, 234 DNA techniques, Corynebacterium glutamicum manipulation, 177- 178 Downstream processing, mannitol from fermentation, 79 Doxorubicin, carbohydrate-based therapeutic, 91t, 98, 103 Drugs See Therapeutics, carbohydrate-based, summary Dulbecco's Modified Eagle's Medium for caprine jugular endothelium cells, 126 Embden-Meyerhof-Parnas pathway, 109 End product inhibition, kinetic model, anaerobic fermentation, 22-25 Endothelial cells, veterinary studies, 125 Environmental factors, effects on biosynthesis, carbohydrate-based therapeutics, 98-99 Enzymatic production, mannitol, 7779 Enzymatic synthesis, carbohydratebased therapeutics production, advantages, 95t Enzyme reactions, mannitol production by bacteria, 73-75 Enzymes leading to extracellular f polysaccharide formation, 109-1 1O Erythritol, production by fermentation, 12t Erythromycin, carbohydrate-based therapeutic, 91t, 98, 103 Erthyrose-4-phosphate, folic acid precursor, 208-209f Escherichia coli cell extracts production, high density media culture, 142-1 56 enhanced protein production by fermentation, 193-206 metabolic network, 208-209f protein targeting into different compartments, 198-202 recombinant strain in mercury detoxification, 161-1 63 Escherichia coli-Corynebacterium glutamicum, shuttle vectors, 179186 Ethanol production catabolic pathways, Rhizopus olyzae, 37-38f fermentation, overview, 4-6 Zymomonas mobilis, 1-32 Excretory production into culture medium, recombinant proteins, Escherichia coli, 202 Exopolysaccharides, production by fermentation, overview, 1 Expression vector development in propionibacteria, 223,226-227t Extracellular polysaccharides, biosynthesis by Ganodenna lucidum production, 14,116,118-1 19f proposed pathway, 109-1 O f Extract preparation and protein synthesis in cell extracts production, Escherichia coli, 147-1 48 FDA Center for Biologics Evaluation and Research, 258 FDA Code of Federal Regulations, Good Manufacturing Practices, 257 Fed-batch fermentation, butyric acid production by Clostridium tyrobutyricum, 58-63 Fed-batch processes with high cell density fermentation, bacterial decolorization, azo dyes, 165 Fed-batch strategies in mercury detoxification operations, 162, 170 Fermentation carbohydrate-based therapeutics production, advantages, 95t cellular engineering for enhanced protein production, 193-206 commodity chemicals production, overview, 3-17 comparison between bacterial and fungal lactic acid methods, 37t improvement by metabolic engineering, 235 See also Continuous fermentation system for anaerobic microorganisms Fermentation conditions in cell extracts production, Escherichia coli, 145-146 Fermentation kinetic study, butyrateproducing mutant development, 56 Fermentation kinetics butyric acid production by Clostridium tyrobutyricum, 59-63 L(+)-lactic acid production by Rhizopus oryzae, 42-49 Fermentation process development, carbohydrate-based therapeutics, 89-107 Fermentation process validation, 262- 263 Fibrous bed bioreactor butyric acid production, 52-66 construction and fermentation, 56 Filamentous fungal morphology control, immobilization, 36-51 Filamentous fungi, microbial production, mannitol, 76-77 Fixed-bed bioreactor containing immobilized cells, bacterial decolorization, azo dyes, 168-1 69f Flux vector calculation, metabolic flux distribution, 23 5-236 Foldases for soluble protein production in periplasm, Escherichia coli, 201 t Folic acid in American diets, 208 Folic acid production chemical synthesis, 208 metabolic engineering, 207-2 19 stoichiometric model and methods, 210-212 Food and Drug Administration See FDA Fraxinus ornus bark, mannitol source, 68 Fructose/glucose mixtures, high pressure hydrogenation in mannitol production, 68-70 Fuel ethanol See Ethanol production Fumarate production, catabolic pathways, Rhizopus oryzae, 37-38f Fungal morphology, immobilization effect, 4 P-Galactosidase activity measurement, 112-1 13 Ganoderma lucidum, submerged fermentation, 109-123 See also Medicinal mushroom, Ganodenna lucidum, Chinese traditional medicine Gas chromatography-mass spectrometry See GC-MS Gel entrapment systems, fixed-bed bioreactor containing immobilized cells, bacterial decolorization, azo dyes, 168 Gene and protein expressions metabolic flux analysis, 24 1,244f248 regulation mechanism, 245-248 Genetic engineering strategies for enhanced folic acid production in Escherichia coli, 212-216t Genomic technologies, overview, 234-235 Gluconic acid production by fermentation, 12t Glucose and acetate chromatography in cell extracts production, Escherichia coli, 147 Glucose feeding algorithm in cell extracts production, results, Escherichia coli, 155 Glucose feeding in cell extracts production, Escherichia coli, 146147,151,1535 155 Glutamate/glutamine, folic acid precursor, 208-209f Glycerol, production by fermentation, 12t Glycobiology progress, uses of carbohydrates, 90 Glycoconjugate fermentation, engineering perspectives, Glycoproteins glycosylation pattern modified by metabolic engineering techniques, 103 homogeneous glycoform maintenance, techniques, 99-103 See also Carbohydrate-based therapeutics Goats, caprine jugular endothelium cells isolation, 126 Good Manufacturing Practice Guidance for Active Pharmaceutical Ingredients, industry guidelines, 257 Good Manufacturing Practices, FDA Code of Federal Regulations, 257 "Good scientific argument" use in process validation, 261 Growth and acetate production in cell extracts production, Escherichia coli, 148-152f GS-MS use in metabolic flux analysis, 240-242f Haemophilus b conjugate, carbohydrate-based therapeutic, It-92 Heartwater infection agent, Cowdria ruminatium, 125 Heparin, carbohydrate-based therapeutic, t-92 Heterofermentative lactic acid bacteria, microbial production, mannitol, 70-75 Heterogeneous glycoforrns incomplete synthesis, N-linked carbohydrate structures, 99 microheterogeneity, 101, 103 See also Homogeneous glycoforms; Homogeneous glycoprotein High cell density culture techniques, primary goal, 194 High cell density defined media culture, production, Escherichia coli cell extracts, 142-1 56 High performance liquid chromatography See HPLC Homogeneous glycoforms, glycoprotein maintenance, techniques, 99-1 03 See also Heterogeneous glycoforms Homogeneous glycoprotein, Ribonuclease B, synthesis, 101102f See also Heterogeneous glycoforms Hosts and media in glycoconjugate fermentation, choices, 96-97 HPLC fermentation broth samples, 1, 57 glucose and acetate quantitation, 147 I Hydrogen NMR spectrometry use in metabolic flux analysis, 237 2-Hydroxypropionic acid See Lactic acid Irniglucerase See Cerezyme, carbohydrate-based therapeutic Immobilization effect on fungal morphology, 42-43 Impeller agitation speed, &in process validation parameter, 268-269 In-process control testing in process validation for fermentation, 260261 Inclusion body formation minimization, 198-1 99 Inoculum concentration effects, stirred tank cultures, 135-137 Inoculum preparation in cell extracts production, Escherichia coli, 145 Inorganic phosphate assay in cell extracts production, Escherichia coli, 147 Integrational mutagenesis in Clostridium tyrobutyricum, 57-58 Integrational plasmids construction, butyrate-producing mutant development, 55 Intracellular polysaccharides, biosynthesis by Ganodenna lucidum, 112-1 16,118 Isotope distributions use in metabolic flux analysis, 236-24 1,242f-243f Isotopomer distribution in metabolic flux analysis, 235,237-243f Itaconic acid, production by fermentation, 12t Kinetic model, anaerobic fermentation, 22-25 Kinetic study, butyrate-producing mutant development, 56 Kinetics, fermentation butyric acid production by Clostridium tyrobutyricum, 59-63 L(+)-lactic acid production by Rhizopus oryzae, 4 Kinetics, mercury detoxification, 161163 Kinetics, PGI activity and lactate concentration, Ganodenna lucidum, 118, 120f Lactic acid process yield from sago palm starch, 33 Lactic acid production chemical synthesis, 37 fermentation, 7-9,22 32,37t Rhizopus oryzae, 36-5 rotating fibrous bed bioreactor, 3940f; 45-48 Lactobacillus bacteria, effective mannitol producers, 70-74 Lactococcus lactis, continuous fermentation system development, 21-35 Lactose feeding effect on cell growth and Pgalactosidase activity, 116-1 18 enhanced a-PGM activity and EPS production, 118-1 19f Lectins as receptors in biological processes, 95-96 Lentinan, carbohydrate-based therapeutic, 1t-92 Leucocyte adhension to endothelial cells, 95-96f Leuconostoc bacteria, effective mannitol producers, 70-73,75 Linear programming metabolic network analysis, 208,209 Living Cell Reaction process, 186188 Long-term lactic acid production in rotating fibrous bed bioreactor, 4548 Mannitol, general properties and use, 68 Mannitol hexanitrate, use as vasodilator, 68 Mannitol production chemical processes, 68-70,8 1t fermentation, 67-85, 1t Mass production, ruminant endothelial cells, culture methods, 124-141 Media and hosts in glycoconjugate fermentation, choices, 96-97 Medicinal mushroom, Ganoderma lucidurn, Chinese traditional medicine, 109 See also Ganoderma lucidurn, submerged fermentation Medium culture caprine jugular endothelium cells, 126,128-129 high density for Escherichia coli cell extracts production, 142-1 56 Medium optimization in glycoconjugate fermentation, 97-98 Mercury See Microbial mercury detoxification; Mercury resistance Mercury resistance, genetic basis, 160-162f Metabolic engineering for production 5-aminolevulinic acid and vitamin B 12 in Propionibacteriurn fieudenreichii, 22 1-232 folic acid in Escherichia coli, 207219 Metabolic engineering techniques, carbohydrate-based therapeutics, 103-104 Metabolic flux analysis based on isotope distributions, 236241,242f-243f quantification, 235-236 with gene and protein expressions, 24 1,244f-248 Metabolic flux distribution, flux vector calculation, 235-236 Metabolic network, Escherichia coli, 208-209f Metabolic network analysis tool, MetaboLogic, 208,210 MetaboLogic, metabolic network analysis tool, 208,210 3-Methoxy-4-hydroxybenzaldehyde See Vanillin Methyl tertiarybutyl ether in gasoline, Microbial mercury detoxification, bioprocess development, 160-1 62, 169-1 70 Microbial production, mannitol, 70-77 Microcarriers in stirred tank cultures, caprine jugular endothelium cells, 132-137 Miglitol, carbohydrate-based therapeutic, 1t Model and analysis methods, folic acid production in Escherichia coli, 210-212 MTBE See Methyl tertiary butyl ether in gasoline Mutant development for butyric acid production, Clostridium tyrobutyricum, 54-55 Mycelial morphology control, importance in fungal fermentation, 38-39 N-linked carbohydrate structures, incomplete synthesis, 99 Of N-linked glycan, synthesis, l O Natural rubber plantation for fermentation, 33 Nisin Z concentration, contamination proof system, 30 NMR See I3carbon NMR spectrometry use in metabolic flux analysis; ' ~ ~ d r o N M R ~en spectrometry use in metabolic flux analysis Oenococcus sp bacteria, mannitol producers, 70,75 Optimization, microcarrier and inoculum concentration effects, stirred tank cultures, 135-1 37 Oxygen effects on fermentation in rotating fibrous bed bioreactor, 47, 49 Oxygen supply experiments, 111, 113-1 16 Oxygen transfer experiments in I+ -) (lactic acid production, 40-4 f Oxygen uptake rate in L(+)-lactic acid production, 40-4 f PCR amplification, butyrateproducing mutant development, 55 Penicillum scabrosum, filmentous fungus, mannitol production, 77 Periplasm, secretion into, Escherichia coli, protein targeting, 20G201 pH dependence substrate feed, continuous fermentation system, schematic, 28f pH value effect on azo dye bacterial decolorization, 164 main process validation parameter, 264-266 2-Phenylethanol, production by fermentation, 12t Phosphoenol pyruvate, folic acid precursor, 208-209f a-Phosphoglucomutase in biosynthesis by Ganodenna lucidum, 109-1 10f, 112-113,118-119f Phosphoglucose isomerase in biosynthesis by Ganoderma lucidum, 109-1 10f, 112-113,118, l20f Pircularia oryzae, filamentous fungus, mannitol production, 76 Plasmid copy number, factor in optimal recombinant production, 197-1 98 Plasrnid transformation, butyrateproducing mutant development, 5556 Poly (hydroxyalkanoates), production by fermentation, overview, 9-10 Poly (3-hydroxybutyrate-co-3hydroxyhexanoate), fermentation strategy, 9-1 Poly (3-hydroxybutyric acid), production by fermentation, overview, Positional representation in metabolid flux analysis, 237, 240 Process development entry point, fermentation, 260 Process optimization, glycoconjugate fermentation, 98-99 Process validation, definition, 258259 Promoters for high-level recombinant protein production, 194-196 1,3-Propanediol, production by fermentation, overview, 6-7 Propionibacteria, expression vector development, 223,226-227t Propionibacteriumfreudenreichii, genetically engineered, vitamin B12 and 5-aminolewlinic acid production, 22 1-232 Propionibacterium spp in vitamin B12 production bioprocess, 228-230 Propionic acid, production by fermentation, 12t Prospective validation in manufacturing processes, 258 Protein and gene expressions, regulation mechanism, 245-248 Protein production, cellular engineering, Escherichia coli, 193206 Protein targeting into three compartments of Escherichia coli, 198-202 Pseudomonas sp in vitamin BIZ production bioprocess, 226,227,230 Raw materials, main process validation parameter, 263-265f Recombinant DNA protein product, representative validation scheme, 262-27 Relenza, carbohydrate-based therapeutic, It, 96 Repeated batch fermentation in rotating fibrous bed bioreactor, 4548f Replicative plasmids construction, butyrate-producing mutant development, 55 Resistance markers, shuttle vector series, E Coli-Corynebacterium glutamicum, 185-186 Response variables in industrial fermentation process, 263 Rhizopus oryzae catabolic pathways, 37-38f L(+)-lactic acid production, 36-5 Rhodotorula minuta, yeast, mannitol production from pentose sugars, 76 Ribosome pool, decrease as cause of inefficient translation, 197 mRNA levels, gene prk, 246t-247 mRNA stability, factor in achieving high-level gene expression, 196 Rotating fibrous bed bioreactor fermentation kinetics, 42-49 long-term lactic acid production, 4548 oxygen effects on fermentation, 47, 49 schematic, 39-40f Rotating fibrous matrix, role in filamentous fimgal morphology control, 36-5 Ruminant endothelial cells, culture methods for mass production, 124141 Sago palm industry, 32-34 Sago palm plantation in industry model, 33f Sago starch, L-lactic acid process yield, 33 Sampling in cell extracts production, Escherichia coli, 147 Scale up, static culture studies, caprine jugular endothelium cells, 131-1 32 Schizophyllan See Sonifilan, carbohydrate-based therapeutic Secretion into Escherichia coli periplasm, protein targeting, 200201 Shear forces on system components, effects on process, 268-269 Shuttle vector construction, Escherichia coli-Corynebacterium glutamicum, 179-1 Shuttle vector series, Escherichia coli-Corynebacterium glutamicum, 182-183, 185-186 Sonifilan, carbohydrate-based therapeutic, 11-92 Sorbitol, production by fermentation, 12t Static culture studies, caprine jugular endothelium cells, 126-1 27, 129132 Sterile cell formation, kinetic model, anaerobic fermentation, 23-25 Stirred tank fermentor, fermentation kinetics, 4 Stirred tank studies, caprinejugular endothelium cells, 127, 132-137 Stoichiometric model and methods, folic acid production in Escherichia coli, 210-212 Submerged fermentation, Ganoderma lucidum, polysaccharide and ganoderic acid production, 108-1 23 Substrate feeding strategy, anaerobic fermentation, 25-27f Succinic acid, production by fermentation, 12t Sugar alcohol See Mannit01 Synechocystis, culture environment effect on regulation mechanisms, 245-248 Temperature, main process validation parameter, 266-268 Therapeutics, carbohydrate-based, summary, 90-9 1t Tirnelbiornass, main process validation parameter, 269-270 Topiramate, carbohydrate-based therapeutic, 1t Tomlopsis yeasts, mannitol production from glycerol, 75-76 Transcription and translation control See Translation and transcription control, recombinant protein production Translation and transcription control, recombinant protein production, 194-198 Transposon trap vector, 182,184 Validation, main process parameters, 263-270 Validation protocol development, 260-262 Validation scheme, classical recombinant DNA protein product, 262-27 Vancocin, carbohydrate-based therapeutic, 1t, 98 Vancomycin See Vancocin, carbohydrate-based therapeutic Vanillin, production by fermentation, overview, 11,13 Vectors for genetic engineering, Colynebacteria, 175-1 91 Vitamin B I2and 5-aminolevulinic acid production in genetically engineered Propionibacteriumfieudenreichii, 221-232 Vitamin B12 production, 12t, 22 1-232 Voglibose, carbohydrate-based therapeutic, 1t Xylitol, production by fermentation, 12t Waste treatment azo dyes, bacterial decolorization, 163-170 limitations of biotechnology methods, 160 mircrobial mercury detoxification processes, 160-1 63,169-170 "Worst case" conditions, use in process validation, 26 Xanthan gum production, overview, 11 Yeasts, microbial production, mannitol, 75-76 Zanamivir See Relenza, carbohydratebased therapeutic Zymomonas mobilis, ethanol production in continuous fermentation system, 1-32 ... (fax) sahabc@ncaur.usda.gov (email) Fermentation Biotechnology Chapter Commodity Chemicals Production by Fermentation: An Overview Badal C Saha Fermentation Biotechnology Research Unit, National... biochemical engineering) contribution to the continually expanding field of fermentation biotechnology Badal C Saha Fermentation Biotechnology Research Unit National Center for Agricultural Utilization... Technology American Chemical Society, Washington, DC e Fermentation biotechnology Library of Congress Cataloging-in-Pubiication Data Fermentation biotechnology / Badal C Saha, editor p cm. (ACS symposium