Bioprocessing of renewable resources to commodity bioproducts

BIOPROCESSING OF RENEWABLE RESOURCES TO COMMODITY BIOPRODUCTS Tai Lieu Chat Luong BIOPROCESSING OF RENEWABLE RESOURCES TO COMMODITY BIOPRODUCTS Edited by Virendra S Bisaria Akihiko Kondo About the Cover: The pyramid represents successive and increasingly selective processing stages in bioconversion of plant biomass to industrial chemicals The chemicals in white bubbles are the industrial commodity bioproducts pertaining to the realm of “white biotechnology” Cover illustration/design by Ruchi Uppal Rights of Cover Design are owned by Prof Virendra S Bisaria Copyright © 2014 by John Wiley & Sons, Inc All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, 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Microbial biotechnology Biomass energy I Bisaria, Virendra S., editor of compilation II Kondo, Akihiko, 1959- editor of compilation TP248.27.M53B5626 2014 662′ 88–dc23 2013046035 Printed in the United States of America 10 CONTENTS PREFACE xv CONTRIBUTORS xix PART I ENABLING PROCESSING TECHNOLOGIES Biorefineries—Concepts for Sustainability Michael Sauer, Matthias Steiger, Diethard Mattanovich, and Hans Marx 1.1 1.2 1.3 Introduction Three Levels for Biomass Use The Sustainable Removal of Biomass from the Field is Crucial for a Successful Biorefinery 1.4 Making Order: Classification of Biorefineries 1.5 Quantities of Sustainably Available Biomass 1.6 Quantification of Sustainability 1.7 Starch- and Sugar-Based Biorefinery 1.7.1 Sugar Crop Raffination 1.7.2 Starch Crop Raffination 1.8 Oilseed Crops 1.9 Lignocellulosic Feedstock 1.9.1 Biochemical Biorefinery (Fractionation Biorefinery) 1.9.2 Syngas Biorefinery (Gasification Biorefinery) 1.10 Green Biorefinery 1.11 Microalgae 1.12 Future Prospects—Aiming for Higher Value from Biomass References 10 11 12 14 14 14 16 16 18 19 20 21 24 Biomass Logistics 29 Kevin L Kenney, J Richard Hess, Nathan A Stevens, William A Smith, Ian J Bonner, and David J Muth 2.1 2.2 Introduction Method of Assessing Uncertainty, Sensitivity, and Influence of Feedstock Logistic System Parameters 30 31 v vi CONTENTS 2.2.1 2.2.2 2.3 2.4 2.5 Analysis Step 1—Defining the Model System Analysis Step 2—Defining Input Parameter Probability Distributions 2.2.3 Analysis Step 3—Perform Deterministic Computations 2.2.4 Analysis Step 4—Deciphering the Results Understanding Uncertainty in the Context of Feedstock Logistics 2.3.1 Increasing Biomass Collection Efficiency by Responding to In-Field Variability 2.3.2 Minimizing Storage Losses by Addressing Moisture Variability Future Prospects Financial Disclosure/Acknowledgments References Pretreatment of Lignocellulosic Materials 31 31 32 34 36 36 38 40 40 41 43 Karthik Rajendran and Mohammad J Taherzadeh 3.1 3.2 3.3 3.4 3.5 3.6 Introduction Complexity of Lignocelluloses 3.2.1 Anatomy of Lignocellulosic Biomass 3.2.2 Proteins Present in the Plant Cell Wall 3.2.3 Presence of Lignin in the Cell Wall of Plants 3.2.4 Polymeric Interaction in the Plant Cell Wall 3.2.5 Lignocellulosic Biomass Recalcitrance Challenges in Pretreatment of Lignocelluloses Pretreatment Methods and Mechanisms 3.4.1 Physical Pretreatment Methods 3.4.2 Chemical and Physicochemical Methods 3.4.3 Biological Methods Economic Outlook Future Prospects References Enzymatic Hydrolysis of Lignocellulosic Biomass 44 45 45 46 47 48 49 52 53 53 56 61 64 67 68 77 Jonathan J Stickel, Roman Brunecky, Richard T Elander, and James D McMillan 4.1 4.2 Introduction Cellulase, Hemicellulase, and Accessory Enzyme Systems and Their Synergistic Action on Lignocellulosic Biomass 4.2.1 Biomass Recalcitrance 4.2.2 Cellulases 4.2.3 Hemicellulases 4.2.4 Accessory Enzymes 4.2.5 Synergy with Xylan Removal and Cellulases 78 79 79 80 81 81 82 CONTENTS 4.3 4.4 4.5 4.6 4.7 Enzymatic Hydrolysis at High Concentrations of Biomass Solids 4.3.1 Conversion Yield Calculations 4.3.2 Product Inhibition of Enzymes 4.3.3 Slurry Transport and Mixing 4.3.4 Heat and Mass Transport Mechanistic Process Modeling and Simulation Considerations for Process Integration and Economic Viability 4.5.1 Feedstock 4.5.2 Pretreatment 4.5.3 Downstream Conversion Economic Outlook Future Prospects Acknowledgments References Production of Cellulolytic Enzymes vii 83 84 85 86 87 88 91 91 92 94 95 96 97 97 105 Ranjita Biswas, Abhishek Persad, and Virendra S Bisaria 5.1 5.2 5.3 5.4 5.5 5.6 Introduction Hydrolytic Enzymes for Digestion of Lignocelluloses 5.2.1 Cellulases 5.2.2 Xylanases Desirable Attributes of Cellulase for Hydrolysis of Cellulose Strategies Used for Enhanced Enzyme Production 5.4.1 Genetic Methods 5.4.2 Process Methods Economic Outlook Future Prospects References Bioprocessing Technologies 106 107 107 108 109 110 110 114 123 123 124 133 Gopal Chotani, Caroline Peres, Alexandra Schuler, and Peyman Moslemy 6.1 6.2 6.3 6.4 Introduction Cell Factory Platform 6.2.1 Properties of a Biocatalyst 6.2.2 Recent Trends in Cell Factory Construction for Bioprocessing Fermentation Process Recovery Process 6.4.1 Active Dry Yeast 6.4.2 Unclarified Enzyme Product 6.4.3 Clarified Enzyme Product 6.4.4 BioisopreneTM 134 136 137 140 142 147 148 149 150 151 viii CONTENTS 6.5 6.6 6.7 PART II Formulation Process 6.5.1 Solid Forms 6.5.2 Slurry or Paste Forms 6.5.3 Liquid Forms Final Product Blends Economic Outlook and Future Prospects Acknowledgment Nomenclature References 153 154 159 160 161 162 163 163 163 SPECIFIC COMMODITY BIOPRODUCTS Ethanol from Bacteria 169 Hideshi Yanase 7.1 7.2 7.3 7.4 7.5 Introduction Heteroethanologenic Bacteria 7.2.1 Escherichia coli 7.2.2 Klebsiella oxytoca 7.2.3 Erwinia spp and Enterobacter asburiae 7.2.4 Corynebacterium glutamicum 7.2.5 Thermophilic Bacteria Homoethanologenic Bacteria 7.3.1 Zymomonas mobilis 7.3.2 Zymobacter palmae Economic Outlook Future Prospects References Ethanol Production from Yeasts 170 172 173 177 178 179 180 183 184 189 191 192 193 201 Tomohisa Hasunuma, Ryosuke Yamada, and Akihiko Kondo 8.1 8.2 8.3 Introduction Ethanol Production from Starchy Biomass 8.2.1 Starch Utilization Process 8.2.2 Yeast Cell–Surface Engineering System for Biomass Utilization 8.2.3 Ethanol Production from Starchy Biomass Using Amylase-Expressing Yeast Ethanol Production from Lignocellulosic Biomass 8.3.1 Lignocellulose Utilization Process 8.3.2 Fermentation of Cellulosic Materials 202 205 205 205 206 208 208 209 CONTENTS 8.3.3 8.3.4 8.4 8.5 Fermentation of Hemicellulosic Materials Ethanol Production in the Presence of Fermentation Inhibitors Economic Outlook Future Prospects References Fermentative Biobutanol Production: An Old Topic with Remarkable Recent Advances ix 215 217 218 220 220 227 Yi Wang, Holger Janssen and Hans P Blaschek 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 10 Introduction Butanol as a Fuel and Chemical Feedstock History of ABE Fermentation Physiology of Clostridial ABE Fermentation 9.4.1 The Clostridial Cell Cycle 9.4.2 Physiology and Enzymes of the Central Metabolic Pathway Abe Fermentation Processes, Butanol Toxicity, and Product Recovery 9.5.1 ABE Fermentation Processes 9.5.2 Butanol Toxicity and Butanol-Tolerant Strains 9.5.3 Fermentation Products Recovery Metabolic Engineering and “Omics”—Analyses of Solventogenic Clostridia 9.6.1 Development and Application of Metabolic Engineering Techniques 9.6.2 Butanol Production by Engineered Microbes 9.6.3 Global Insights into Solventogenic Metabolism Based on “Transcriptomics” and “Proteomics” Economic Outlook Current Status and Future Prospects References Bio-based Butanediols Production: The Contributions of Catalysis, Metabolic Engineering, and Synthetic Biology 228 229 230 232 232 233 236 236 237 238 239 239 242 245 246 247 251 261 Xiao-Jun Ji and He Huang 10.1 10.2 Introduction Bio-Based 2,3-Butanediol 10.2.1 Via Catalytic Hydrogenolysis 10.2.2 Via Sugar Fermentation 262 264 264 265 x CONTENTS 10.3 10.4 10.5 11 Bio-Based 1,4-Butanediol 10.3.1 Via Catalytic Hydrogenation 10.3.2 Via Sugar Fermentation Economic Outlook Future Prospects Acknowledgments References 1,3-Propanediol 276 276 277 279 280 280 280 289 Yaqin Sun, Chengwei Ma, Hongxin Fu, Ying Mu, and Zhilong Xiu 11.1 11.2 11.3 11.4 11.5 11.6 11.7 11.8 12 Introduction Bioconversion of Glucose into 1,3-Propanediol Bioconversion of Glycerol into 1,3-Propanediol 11.3.1 Strains 11.3.2 Fermentation 11.3.3 Bioprocess Optimization and Control Metabolic Engineering 11.4.1 Stoichiometric Analysis/MFA 11.4.2 Pathway Engineering Down-Processing of 1,3-Propanediol Integrated Processes 11.6.1 Biodiesel and 1,3-Propanediol 11.6.2 Glycerol and 1,3-Propanediol 11.6.3 1,3-Propanediol and Biogas Economic Outlook Future Prospects Acknowledgments A List of Abbreviations References Isobutanol 290 291 292 292 293 301 302 302 304 308 311 311 313 314 314 315 316 316 317 327 Bernhard J Eikmanns and Bastian Blombach 12.1 12.2 12.3 Introduction The Access Code for the Microbial Production of Branched-Chain Alcohols: 2-Ketoacid Decarboxylase and an Alcohol Dehydrogenase Metabolic Engineering Strategies for Directed Production of Isobutanol 12.3.1 Isobutanol Production with Escherichia coli 12.3.2 Isobutanol Production with Corynebacterium glutamicum 328 329 331 331 335 CONTENTS 12.4 12.5 12.6 12.7 13 12.3.3 Isobutanol Production with Bacillus subtilis 12.3.4 Isobutanol Production with Clostridium cellulolyticum 12.3.5 Isobutanol Production with Ralstonia eutropha 12.3.6 Isobutanol Production with Synechococcus elongatus 12.3.7 Isobutanol Production with Saccharomyces cerevisiae Overcoming Isobutanol Cytotoxicity Process Development for the Production of Isobutanol Economic Outlook Future Prospects Abbreviations Nomenclature References Lactic Acid xi 337 339 339 340 341 341 343 345 346 347 347 349 353 Kenji Okano, Tsutomu Tanaka, and Akihiko Kondo 13.1 13.2 13.3 13.4 13.5 13.6 13.7 14 History of Lactic Acid Applications of Lactic Acid Poly Lactic Acid Conventional Lactic Acid Production Lactic Acid Production From Renewable Resources 13.5.1 Lactic Acid Bacteria 13.5.2 Escherichia coli 13.5.3 Corynebacterium glutamicum 13.5.4 Yeasts Economic Outlook Future Prospects Nomenclature References Microbial Production of 3-Hydroxypropionic Acid From Renewable Sources: A Green Approach as an Alternative to Conventional Chemistry 354 354 354 356 357 359 364 368 370 373 374 374 375 381 Vinod Kumar, Somasundar Ashok, and Sunghoon Park 14.1 14.2 14.3 14.4 Introduction Natural Microbial Production of 3-HP Production of 3-HP from Glucose by Recombinant Microorganisms Production of 3-HP from Glycerol by Recombinant Microorganisms 14.4.1 Glycerol Metabolism for the Production of 3-HP and Cell Growth 382 383 385 388 389 INDEX FRD, see Fumarate reductase Fructokinase gene, 190 Fructose, 13 FTS, see Fischer-Tropsch synthesis Fumarase, 410–429 Fumarate and nitrate reductase regulator, 331 Fumarate reductase, 175, 331 Fumaric acid accumulation in Rhizopus, 417–422 biochemical mechanism for biosynthesis of cytosolic fumarase, 419–422 molar yield, 417–418 reductive reactions of TCA cycle, 418–419 economic outlook, 424–427 biorefinery, 427 platform microorganism, 427–429 edible product preparation l-Aspartic acid, 410 l-Malic acid, 410 microbial synthesis of carbon sources, 414 fumaric acid transport, 416 producer organisms, 412–414 production processes, 416–417 solid-state fermentations, 414–415 submerged fermentation conditions, 415–416 uses, 410–411 Fungus morphology, submerged fermentation, 415–416 Fusarium oxysporum, 119 Fusarium sp, 123 GABA, see γ-Aminobutyric acid GAD, see Glutamate decarboxylase Gasification biorefinery, see Syngas biorefinery Gasoline, 229, 328–329, 329t Gas stripping, 239 GAX, see Glucuronoarabinoxylan GBL, see -Butyrolactone GDH, see Glutamate dehydrogenase GDHt, see Glycerol dehydratase Gene encoding α-acetolactate decarboxylase, 306 Gene encoding aldehyde dehydrogenase, 305 Generally regarded as safe (GRAS), 147, 184 Geobacillus stearothermophilus NCA1503, 182 Geobacillus thermoglucosidasius, 182 Geotrichum sp., 383 GFL, see Glucose facilitator protein GH, see Glycoside hydrolase Gloeophyllum trabeum GtCel2A, 110 GlpK, see Glycerol kinase β-Glucan, 210 Glucaric acid, 521, 525, 528, 533 547 Glucoamylase, 109 Glucomannans, 81 Gluconate, 13 Gluconic acid, 135 Glucose facilitator protein, 176 Glucose-6-phosphate dehydrogenase, 510 β-Glucosidase, 85, 107, 112, 209, 361 Glucuronidases, 82, 83 Glucuronoarabinoxylan, 52 Glutamate decarboxylase, 481 Glutamate dehydrogenase, 475–477, 484 Glutamate:succinic semialdehyde transaminase, 484 Glutamic acid as building block production of chemicals, 481–487 production by Corynebacterium glutamicum, 475–478 metabolic engineering, 478–481 molecular mechanism, 475, 476–478 Glycerol, 15, 135, 313, 480 Glycerol dehydratase, 292, 392 Glycerol dehydrogenase, 292 Glycerol kinase, 394 Glycerol metabolism, 292 and cell growth, 389–390 for production of 3-HP, 389–390 Glycoproteins, 46 Glycoside hydrolase, 80 Glycosylphosphatidylinositol, 206 G6PDH, see Glucose-6-phosphate dehydrogenase GPI, see Glycosylphosphatidylinositol GPI anchor, 206 Granulation, 158–159 Granulobacter butylicus, 230 Granulobacter saccharobutyricus, 230 GRAS, see Generally regarded as safe Green biorefinery, 19–20 Greenhouse gas, see Carbon dioxide Gymnosperms, 47 Haemophilus influenzae, 448 Hansenula polymorpha, 214 3HB, see 3-hydroxybutyrate 4HB, see 4-hydroxybutyrate HemA gene, 487 HemA protein, 487 Hemicellulases, 17, 45, 78, 81, 208, 275 and cellulases, 82–83 Hemicellulosic materials fermentation to ethanol, 216–217 utilization, 215 xylose fermentation, 215–216 548 INDEX Herschel–Bulkley model, 90 Heteroethanologenic bacteria Corynebacterium glutamicum ethanologenesis, 179–180 pentose and cellobiose fermentation, 180 Enterobacter asburiae, 178–179 Erwinia spp., 178–179 Escherichia coli cellobiose, 176–177 cellulose fermentation, 176–177 ethanologenesis, 173–175 pentose fermentation, 175–176 Klebsiella oxytoca cellobiose, 178 cellulose fermentation, 178 ethanologenesis, 177 pentose and hemicellulose fermentation, 177–178 metabolic engineering of, 173f thermophilic bacteria ethanologenesis, 180–181 pentose and cellulosic fermentation, 181–183 Heteropolysaccharides, 48 HFCS, see High fructose corn syrups High fructose corn syrups, 135 High-pressure steam, 55 HMF, see Hydroxymethylfurfural; 5-hydroxymethylfurfural Homoethanologenic bacteria Zymobacter palmae cellobiose, 189–191 cellulose fermentation, 189–191 ethanologenesis, 189 pentose fermentation, 189–190 Zymomonas mobilis cellobiose, 188 cellulose fermentation, 188 ethanologenesis, 184–185 pentose fermentation, 185–188 3-HP, see 3-hydroxypropionic acid 3-HPA, see 3-hydroxypropionaldehyde Humicola insolens, 219 Hydrolytic enzymes adsorption, 109 catalytic efficiency, 109 end-product inhibition resistance, 109 shear inactivation, 109 thermal stability, 109 Hydrolytic enzymes (for digestion of lignocelluloses) cellulases, 107–108 xylanases, 108–109 2-Hydroxy acids, 367 3-Hydroxybutyrate, 367 4-Hydroxybutyrate, 277 4-Hydroxybutyrate dehydrogenase, 484 β-Hydroxybutyryl-CoA dehydrogenase (Hbd), 235, 240 3-Hydroxyhexanoate, 367 Hydroxymethylfurfural, 176 5-Hydroxymethylfurfural, 53 3-Hydroxypropionaldehyde, 290, 383 2-Hydroxypropionic acid, 354 3-Hydroxypropionic acid biochemical pathways for, 385, 386f biosynthetic pathways for, 389 from glucose by recombinant microorganisms ATP yield, 385, 387t thermodynamic feasibility, 387t from glycerol by recombinant microorganisms CoA-dependent pathway, 390–392 CoA-independent pathway, 392–394 coproduction of 3-HP and PDO, 394–396 glycerol metabolism, 389–390 microbial production by-products formation, 399–400 redox balance, 399–400 toxicity and tolerance, 396–399 vitamin B12 supply, 400 metabolic pathway for, 391f natural microbial production of, 383–384 3-Hydroxyvalerate, 367 Hypocrea jecorina, 107 See also Trichoderma reesei IBE, see Isopropanol–butanol–ethanol ICDH, see Isocitrate dehydrogenase IEA, see International Energy Association Indole, 290 Insulin, 148 Integrated processes, 148, 414 biodiesel and 1,3-propanediol, 311–313 elements, 135–136 glycerol and 1,3-propanediol, 313–314 1,3-propanediol and biogas, 314 International Energy Association, Ionic liquids pretreatment (lignocelluloses), 61–62 IPTG, see Isopropyl β-d-1-thiogalactopyranoside; Isopropyl β-d-1-thiogalactopyranoside Irradiation, 55 ISA, see Isotopomer spectral analysis Isobutanol chemical properties, 329t economic outlook, 345–346 INDEX metabolic engineering strategies for production of with Bacillus subtilis, 337–339 with Clostridium cellulolyticum, 339 with Corynebacterium glutamicum, 335–337 with Escherichia coli, 331–335 with Ralstonia eutropha, 339–340 with Saccharomyces cerevisiae, 341 with Synechococcus elongatus, 340 process development, 343–345 Isobutene, 329 Isocitrate dehydrogenase, 478 Isoetes, 47 Isoprene, 137, 151–152 Isopropanol–butanol–ethanol, 240 Isopropyl β-d-1-thiogalactopyranoside, 140, 393 Isotopomer spectral analysis, 304 KDC, see 2-ketoacid decarboxylases 2-Ketoacid decarboxylases, 330–331, 336 β-Ketoadipate pathway, 528 α-Ketoglutaric semialdehyde dehydrogenase, 393 KGSADH, see α-ketoglutaric semialdehyde dehydrogenase Kinases, 477 Klebsiella oxytoca, 176, 177–178, 265, 268, 292 cellobiose, 178 cellulose fermentation, 178 ethanologenesis, 177 pentose and hemicellulose fermentation, 177–178 Klebsiella pneumoniae, 265, 291, 292, 303–307, 313, 390, 392, 525 DSM 2026, 393 Kluyveromyces lactis, 372 Kluyveromyces marxianus, 214 LAB, see Lactic acid bacteria Lactate dehydrogenase, 235, 305, 331, 361 Lactic acid applications chemical, 354 cosmetic, 354 food, 354 pharmaceutical, 354 conventional production, 356–357, 358t economic outlook, 373 history, 354 poly lactic acid, 354–356 production from renewable resources Corynebacterium glutamicum, 368–369 Escherichia coli, 364–368 549 lactic acid bacteria, 359–364 yeasts, 370–373 Lactic acid bacteria, 481 heterofermentative, 356 homofermentative, 356 Lactobacilli brevis, 292 Lactobacilli buchneri, 292 Lactobacilli diolivorans, 292 Lactobacillus brevis, 242, 269, 361, 393, 483, 514 Lactobacillus casei, 111, 370 Lactobacillus collinoides, 383 Lactobacillus delbrueckii subsp lactis JCM 1148, 357 Lactobacillus helveticus, 356 Lactobacillus manihotivorans LMG 18010, 359 Lactobacillus paracasei, 483 Lactobacillus pentosus, 361 Lactobacillus plantarum, 111, 361, 483 Lactobacillus plantarum NCIMB 8826, 356 Lactobacillus reuteri, 304, 383 Lactobacillus rhamnosus CASL, 357 Lactococcus lactis, 330, 331, 449, 514 Lactococcus lactis gadB gene, 483 Lactococcus lactis subsp lactis ATCC 19435, 357 Lactose, 354 Lactose dehydrogenase gene, 179 α-L-arabinofuranosidase, 108, 113 Latin Hypercube sampling method, 32 Lb delbrueckii, 368 Lb pentosus NRIC 1069, 364 Lb plantarum NCIMB 8826, 361 Lc lactis IL 1403, 361, 362 Lc lactis IO-1, 362 LCA, see Life-cycle analysis; Life cycle assessment LDH, see Lactate dehydrogenase Leuconostoc (Leuc.) lactis, 361 Leudeking–Piret equation, 145 Levansucrase gene, 190 Life-cycle analysis, 11–12 Life cycle assessment, 530–534 Lignin, 9, 17, 45, 78, 208 polymerization, 47 and polysaccharides interactions, 48–49 Lignocelluloses biomass recalcitrance in, 44, 49–52 complexity anatomy of lignocellulosic biomass, 45–46 lignin presence in cell wall of plants, 47–48 polymeric interaction in plant cell wall, 48–49 proteins present in plant cell wall, 46 550 INDEX Lignocelluloses (Continued ) components, 275 compositions, 44, 45t economic outlook duration of pretreatment, 66 efficiency of pretreatment, 66 energy consumption of pretreatment, 66 materials recovery, 66 risks and environmental aspects of pretreatment, 66 in nature, 44 pretreatment challenges, 52–53 pretreatment methods and mechanisms advantages and disadvantages of, 65t biological methods, 61–64 chemical and physicochemical methods, 56–61 physical methods, 53–55 structure, 44 Lignocellulose utilization process, 208–209 Lignocellulosic biomass, 16–17 biomass recalcitrance, 49–52 biorefineries, enzymatic hydrolysis of, 78–96 feedstock, 9, 16 Lignocellulosic biomass recalcitrance cellulose morphologies, 50–51 twisting cellulose microfibrils, 51–52 Lignocellulosic feedstock, biochemical biorefinery, 16–18 syngas biorefinery, 18–19 Lime pretreatment (lignocelluloses), 58 Liquid–liquid extraction technique, 238–239, 310 Lycopodium, 47 Machinery performance, 34 Malonic acid, 382 Malonyl-CoA, 383, 388 Mannheimia haemolytica, 448 Mannheimia succiniciproducens, 446–447 Mannitol, 354 2-MD, see 2-methyl-1,3-dioxane Mdh, see Encoding malate dehydrogenase Mechanistic models, 88–91 MEK, see Methyl ethyl ketone Melanconium betulinum, 383 Melanocarpus albomyces, 117–121 Membrane reactors, 86 MEP, see Methylerythritol MEP pathway, 137 Mesophiles, 107 Metabolic engineering 2,3-butanediols production heterologous host, 269–272 homologous hosts, 268–269 of glutamic acid production by Corynebacterium glutamicum anaplerotic reactions importance, 478–479 improvement approaches, 480 metabolic flux redistribution, 478 from renewable resources, 480–481 pathway engineering elimination of by-products formation, 305–306 1,3-propanediol formation pathway construction, 306–307 utilization of cofactor I/II, 304–305 stoichiometric analysis/MFA, 302–304 Metabolic engineering strategies isobutanol production with Bacillus subtilis, 337–339 Clostridium cellulolyticum, 339 Corynebacterium glutamicum, 335–337 Escherichia coli, 331–335 Ralstonia eutropha, 339–340 Saccharomyces cerevisiae, 341 Synechococcus elongatus, 340 Metabolic flux analysis, 303 Metallosphaera sedula, 383 Methanosarcina mazei, 314 Methyl acrylate, 382 2-Methyl-1-butanol, 331 3-Methyl-1-butanol, 330–342 2-Methyl-1,3-dioxane, 310 Methylerythritol, 137 Methyl ethyl ketone, 263 Methylglyoxal synthase gene, 176 Mevalonate pathway, 137 MFA, see Metabolic flux analysis MIC, see Minimum inhibitory concentration Michaelis–Menten concepts, 88 Microalgae advantages, 20 problem, 21 Microfibrils, 45 Microsoft Excel, 31 Milling, 53–55 Minimum inhibitory concentration, 399 Molecular mechanism of glutamic acid production by Corynebacterium glutamicum metabolic change, 476–478 overproduction, 475–476 Molecular sieves techniques, 309 INDEX Monilophytes, 47 Monoclinic Iβ , 50, 51 Monosodium glutamic acid, 474 Monte Carlo analysis, 30 MSG, see Monosodium glutamic acid MVA, see Mevalonate pathway Mycobacterium tuberculosis, 477 Mycobacterium vaccae, 452 Myo-inositol oxygenase, 525 Myo-inositol-1-phosphate synthase, 525 Myriant Technologies LLC, 459–462 Net primary production, 10 Neurospora crassa, 210, 513 Neutralizing agents, submerged fermentation, 416 N-glycan, 111 Nitrogen fertilizers, 13 N-methylmorpholine-N-oxide, 59 NMMO, see N-methylmorpholine-N-oxide Nonrenewable carbon sources, NPP, see Net primary production Nylon 4, 483 ODHC, see 2-oxoglutarate dehydrogenase complex OECD, see Organization for Economic Cooperation and Development Oil crop biorefinery, 15 Oilseed crops coconut, 14–15 oil palm, 14–15 peanut, 14–15 rapeseed, 14–15 soybean, 14–15 sunflower, 14–15 4-O-Methyl glucuronic acid, 108 Onion-type morphology, 154 Organization for Economic Cooperation and Development, 162 Orpinomyces, 112, 215 OTR, see Oxygen transfer rate OUR, see Oxygen uptake rate β-Oxidation pathway, 524–525 Oxidation pretreatment (lignocelluloses), 59 Oxidizing agents pretreatment (lignocelluloses), 58–59 2-Oxogluratrate, 475 2-Oxoglutarate dehydrogenase complex, 476–477 Oxygen transfer rate, 137 Oxygen uptake rate, 137, 146 Ozonolysis pretreatment (lignocelluloses), 58–59 551 P aeruginosa, 525 P putida KT2440, 525 PAA, see Peracetic acid Paenibacillus barcinonensis, 113 Paenibacillus curdlanolyticus B-6, 112 Paenibacillus macerans, 123 Paenibacillus polymyxa, 265 Partial/complete cell recycle, 142 PASC, see Phosphoric acid swollen cellulose Pasteur, Louis, 230 Pasteurellaceae family Actinobacillus succinogenes, 444–446 Basfia succiniciproducens, 447–448 Mannheimia succiniciproducens, 446–447 Pasteurella multocida, 448 Pathway engineering elimination of by-products formation, 305–306 1,3-propanediol formation pathway construction, 306–307 utilization of cofactor I/II, 304–305 PBS, see Polybutylene succinate PBT, see Polybutylene terephthalate PC, see Pyruvate carboxylase P-coumaryl alcohol, 47 PDC, see Pyruvate decarboxylase PDH, see Pyruvate dehydrogenase PDHC, see Pyruvate dehydrogenase complex PDO, see 1,3-propanediol Pdu, see Propanediol utilization PduL, see Phosphotransacylase PduP, see Propionaldehyde dehydrogenase PduQ, see Propanol dehydrogenase PduW, see Propionate kinase Pectin, 45 Pediococcus acidilactici, 367 PEG, see Polyethylene glycol Penicillin G, 148 Penicillium funiculosum, 111 Penicillium oxalicum, 123 Pentose phosphate pathway, 215, 303 PEP, see Phosphoenolpyruvate PEP-dependent DHAK II, 292 Peracetic acid, 59–60 PERT distribution function, 31 Pervaporation, 308 PET, see Production of ethanol PFL, see Pyruvate formate lyase; Pyruvic acid (PA)–FA lyase PFOR, see Pyruvate ferredoxin oxidoreductase PGA, see Poly(γ-glutamic acid) PHA, see Polyhydroxyalkanoates Phanerochaete chrysosporium, 62, 209 Phase I biorefineries, 552 INDEX Phase II biorefineries, Phase III biorefineries, 8, 17 PHB, see Polyhydroxybutyrate Phiahophora sp, 123 Phomopsis phaseoli, 383 Phosphatase, 477 Phosphoenolpyruvate, 362, 385, 443 Phosphoenol pyruvate carboxylase, 365, 424, 478–479 Phosphoketolase pathway, 356 Phosphoric acid swollen cellulose, 209 Phosphotransacetylase, 331, 365 Phosphotransacylase, 389 Phosphotransbutyrylase, 235 Phosphotransferase system, 176, 307 Photosynthetic organisms, 4–5 Photovoltaic system, 6–7 Pichia farinosa, 291 Pichia kudriavzevii, 214 Pichia pastoris, 110 Pichia stipitis, 513 Piromyces, 112, 215 PLA, see Poly lactic acid; Polylactic acid Platform microorganism, 427–429 Pleurotus ostreatus, 62 PntAB gene, 388 Podospora anserine, 525 Polybutylene succinate, 437 Polybutylene terephthalate, 437 Polyethers, 290 Polyethylene glycol, 159, 161 Poly(γ-glutamic acid), 481 production by microorganisms, 484–485 Polyhydroxyalkanoates, 484 Polyhydroxybutyrate, 339 Poly(3-hydroxypropionate), 382 Poly(3-hydroxypropionate-co-3hydroxybutyrate), 382 Poly lactic acid, 12, 354–356 Polymer biosynthesis enzymes ß-ketothiolase (PhaA), 339 Polyporus brumalis, 63 Polypropylene, 437 Polytrimethylene terephthalate, 290 Polyurethanes, 290 Polyvinylchloride, 437 Populus tomentiglandulosa, 118 PPC, see Phosphoenolpyruvate carboxylase PPP, see Pentose phosphate pathway PQO, see Pyruvate:quinone oxidoreductase Pretreatment techniques biological, 17 chemical acid, 17 alkaline, 17 green solvents, 17 physical extrusion, 17 irradiation, 17 milling, 17 physicochemical ammonia fiber explosion, 17 ammonia recycle percolation, 17 liquid hot-water pretreatment, 17 microwave chemical, 17 steam explosion, 17 Primary cell walls, 45 Product-driven biorefineries, Production of ethanol, 175–176 Products recovery, ABE fermentation adsorption, 238 gas stripping, 239 liquid–liquid extraction technique, 238–239 perstraction, 238 pervaporation, 238 reverse osmosis, 238 1,2-Propanediol, 389 1,3-Propanediol bioconversion of glucose single-step fermentation, 291 two-step fermentation, 291–292 bioconversion of glycerol bioprocess optimization and control, 301–302 fermentation, 293–301 strains, 292–293 down-processing of, 308–311 economic outlook, 314–315 integrated processes biodiesel and 1,3-propanediol, 311–313 glycerol and 1,3-propanediol, 313–314 1,3-propanediol and biogas, 314 metabolic engineering pathway engineering, 304–307 stoichiometric analysis/MFA, 302–304 oxydoreductase, 292, 305 Propanediol utilization, 389 Propanol dehydrogenase, 389 Propiolactone, 382 Propionaldehyde dehydrogenase, 389, 392 Propionate kinase, 389 γ-Proteobacterium, 443 Proteomics, 246 Pseudoalteromonas haloplanktis, 107 Pseudomonas alcaligenes sp., 411 Pseudomonas fluorescens, 188 Pseudomonas putida, 242, 342, 528 Pseudomonas syringae, 525 INDEX Psychrophiles, 107 PTA, see Phosphotransacetylase PTS, see Phosphotransferase system PTT, see Polytrimethylene terephthalate PuuC, see Aldehyde dehydrogenase Pycnoporus cinnabarinus, 62 Pyrococcus furiosus, 111 Pyrolysis, 55 Pyrolysis oils, Pyrrolidones, 437 Pyruvate carboxylase, 424, 478 Pyruvate decarboxylase, 174, 370 Pyruvate dehydrogenase complex, 181, 336, 477 Pyruvate ferredoxin oxidoreductase, 181 Pyruvate formate lyase, 173, 181, 331 Pyruvate:quinone oxidoreductase, 336 Pyruvic acid (PA)–FA lyase, 365 Quinolines, 290 Ralstonia eutropha, 339–340 Reactive extraction process, 310 Rennovia process, 521 Reverdia, 462 RFBB, see Rotating fibrous-bed bioreactor Rhizopus, 357 Rhizopus delemar, 413 Rhizopus nigricans, 412 Rhizopus oryzae, 357, 413–424 advantages and disadvantages, 428t transformation systems for, 422 Rhizopus oryzae glucoamylase, 207 Rhyniophytes, 47 RNA-sequencing technology, 245 Rodococcus erythropolis, 528 Rodococcus sp., 524 Rotary vacuum drum filtration, 151 Rotating fibrous-bed bioreactor, 117 Ruminococcus albus, 188 Ruminococcus flavefaciens, 209, 211 RVDF, see Rotary vacuum drum filtration SA, see Succinic acid Saccharification and fermentation, 182 Saccharomyces carlsbergensis, 184 Saccharomyces cerevisiae, 137, 174, 202, 203, 206, 209, 242, 291, 330, 331, 341, 393, 420, 454, 499, 501, 508–512, 525 cerevisiae W303-1A, 307 Saccharomycopsis fibuligera, 209, 210 Salmonella arizona, 487 Salmonella enterica, 389 Salting-out extraction, 308, 311, 312 Scheffersomyces stipitis, 215 553 SDH, see Succinate dehydrogenase Secondary cell wall, 45 Second generation bio-adipic acid, 528–530 Second-generation bioethanol, 170–172, 184, 191, 192–193, 208 Second-generation biorefineries, 10 Second generation feedstocks, 328 Selaginella, 47 SEM analysis, 56 Sensitivity, 32, 33f ranking of, 34f Separate hydrolysis and fermentation, 17, 170, 191, 205, 273 Sequential hydrolysis and fermentation, 96 Serratia marcescens, 265, 268 SHF, see Separate hydrolysis and fermentation Simultaneous saccharification and co-fermentation, 17, 170, 203, 209, 273, 276, 414 Sinapyl alcohol, 47 Single-step fermentation, 291 SLH, see Surface layer homology SOE, see Salting-out extraction Solid-state fermentation systems, 115, 120–122, 414–415 Solventogenesis, 233 onset of, 246 Solventogenic clostridia, metabolic engineering of butanol production by engineered microbes, 242–245 development and application, 239–242 proteomics, 245–246 transcriptomics, 245–246 Solventogenic metabolism, 245–246 Sorghum, 13 Sorghum vulgare, 449 Sporotrichum pulverulentum, 63 Sporotrichum thermophile StCel5A, 110 Spray drying, 155–156 SSCF, see Simultaneous saccharification and co-fermentation SSF, see Solid-state fermentation systems Staphylococcus aureus, 211 Starch and sugar biorefineries, 12–14 characteristics, 12 process structure steps bioconversion of sugars to ethanol, 13 ethanol separation and purification, 13 obtainment of a solution of fermentable sugars, 13 products bioethanol, 13 fructose, 13 554 INDEX Starch and sugar biorefineries (Continued ) gluconate, 13 glucose, 13 Starch-containing plants cassava, 12 maize, 12 potatoes, 12 rice, 12 wheat, 12 Starch crop raffination, 14 Starch utilization process, 205 Starchy biomass cassava, 205 rice, 205 sweet potato, 205 sweet sorghum, 205 Stationary phase, clostridial ABE fermentation, 232 Steam explosion pretreatment (lignocelluloses), 56 Stereum hirsutum, 63 Stirred tank bioreactor, 115–116 Stoichiometric analysis, 302–304 Stoichiometry, 143 STR, see Stirred tank bioreactor Streptococcus bovis, 207, 481 Streptococcus thermophilus, 483 Streptomyces thermovulgaris, 123 Streptomyces viridochromogenes, 113 Succinate biotechnological production of, 437 microorganisms for Anaerobiospirillum succiniciproducens, 443–444 Corynebacterium glutamicum, 451–454 Escherichia coli, 448–451 family Pasteurellaceae, 444–448 yeast-based producers, 454–455 Succinate dehydrogenase, 450 Succinate esters, 437 Succinic acid, 8, 364 for bio-based chemistry, 436–437 downstream processing, 456–458 economic outlook, 462–463 manufacturing companies, 458–462 BioAmber Inc., 459 Myriant Technologies LLC, 459–462 Reverdia, 462 Succinity GmbH, 462 microorganisms for bio-succinate production, 437–455 neutral versus acidic conditions, 455–456 Succinity GmbH, 462 Sugar-containing crops sugar beet, 12 sugar cane, 12 Sugar crop raffination, 14 Sugar fermentation, 265–276 Sulfolobus metallicus, 383 Sulfolobus sp strain VE6, 383 Sulfosuccinamates, 437 Surface layer homology, 113 Sustainability, of biomass, 7–8 quantification of, 11–12 Synechococcus elongatus, 242, 340 Syngas, microbial conversion, 19 Syngas biorefinery, 18–20 System variables, 34 Tableting, 154, 159 TCA, see Tricarboxylic acid TCA cycle, 303, 437–438, 449, 454–455 reductive reactions of, 418–419 Tetrahydrofuran, 436–437 Thermoanaerobacter, 172 Thermoanaerobacterium saccharolyticum, 113, 181 Thermoanaerobacter mathranii, 181 Thermoanaerobacter sp, 107 Thermoanaerobium, 172 Thermoascus aurantiacus, 120 Thermobacillus xylanolyticus, 120 Thermobifida fusca, 112 Thermochemical processing, Thermomyces lanuginosus, 111 Thermophilic bacteria, 180–183 ethanologenesis, 180–181 pentose and cellulosic fermentation, 181–183 Thermotoga maritima, 107 Thermotolerant yeast, 214 THF, see Tetrahydrofuran Thiolase (Thl), 235 Third-generation biorefineries, 10 Tracheophytes, 47 Trametes versicolor G20, 63 Transcriptomics, 245 Transesterification, 14–15, 311–313 Transhydrogenase, 512 Transketolase gene (tkt), 362 Trehalose, 148 Tricarboxylic acid, 303 Trichoderma harzianum, 276 Trichoderma koningii, 111 INDEX Trichoderma reesei, 63, 82, 106, 110, 111, 209 EGII, 214 exoglucanases, 107 Cel6A, 107 Cel7A, 107 Trichoderma sp., 383 Trichoderma viride, 117 Triclinic Iα , 50, 51 Two-step fermentation, 291–292, 300 UASB, see Upflow anaerobic sludge bed Ubiquinone, 137 Uncertainty, 32, 33f in feedstock logistics, 36–40 collection efficiency, 36–38 storage dry matter losses, 38–40 normalized ranking of, 35f Unclarified enzyme product, 149–150 Upflow anaerobic sludge bed, 182 Uracil catabolism, 383 URC, see Uracil catabolism URC pathway, 383 Uronate dehydrogenase, 525 Uronic acid, 108 US oil consumption, 11f Vapor–liquid equilibrium, 308 Verdezyne process, 522 VHb, see Vitreoscilla hemoglobin Vibrion butyrique, 230 Vide supra, 12 Vitamin B12 , 400 Vitreoscilla, 268 Vitreoscilla hemoglobin, 269 VLE, see Vapor–liquid equilibrium Weizmann, Chaim, 230 Wood–Ljungdahl Pathway, 242 World Economic Forum, 162 Xanthomonas albilineans, 188 XDH, see Xylitol dehydrogenase XI, see Xylose isomerase XK, see Xylulokinase X5P, see Xylulose-5-phosphate XR, see Xylose reductase Xylanases, 81–83, 108–123, 177, 245, 276 555 Xylan backbones, 81 Xylanosome, 114 Xylitol biological production, general principles for, 498–501 economic outlook, 514 microbial production aeration, 501–503 carbon sources, 501 fermentation strategies, optimization of, 503–508 production by genetically engineered microorganisms cofactor engineering, 510–512 xylitol-producing recombinant construction, 508–510 production from xylose, 499 use, 497 Xylitol dehydrogenase, 215, 508, 512 Xylobiose, 108 Xyloglucans, 52, 81 1,4-β-d-xylohydrolase, 108 Xylooligosaccharides, 108 Xylose, 81, 108, 359, 498–505 Xylose fermentation, 215–216 Xylose isomerase, 215, 384 Xylose isomerase gene (xylA), 364 Xylose reductase, 215, 508 Xylosidase gene, 177 β-Xylosidases, 81, 108 Xylulokinase, 215 Xylulose-5-phosphate, 215, 362 XYR1 activator, 111 Yarrowia lipolitica, 111 Yeast cell–surface engineering, 205–206 Zosterophylls, 47 Zymobacter palmae, 172 cellobiose, 189–191 cellulose fermentation, 189–191 ethanologenesis, 189 pentose fermentation, 189–190 Zymomonas mobilis, 170, 172, 183 cellobiose, 188 cellulose fermentation, 188 ethanologenesis, 184–185 pentose fermentation, 185–188 70 20 60 10 50 FIGURE 2.10 Isopleth moisture distribution of an end view of a stack of × × 8-ft large square bales (stacked 1-bale wide × bales high) showing the influence of Northern exposure on bale moisture Cotton linter Control Degree of polymerization Relative amount of polymer Relative amount of polymer BMCC Control Degree of polymerization FIGURE 4.3 Qualitative comparison of mechanistic model predictions (top row, from Griggs et al (2012b)) with experimental results (bottom row, from Srisodsuk et al (1998)) for the changing DP distribution of cellulose during enzymatic hydrolysis by EGI and CBHI The left column compares results for bacterial microcrystalline cellulose (BMCC) with a relatively low initial DP, and the right column compares results for cotton linter with a relatively high initial DP Bioprocessing of Renewable Resources to Commodity Bioproducts, First Edition Edited by Virendra S Bisaria and Akihiko Kondo © 2014 John Wiley & Sons, Inc Published 2014 by John Wiley & Sons, Inc FIGURE 8.2 yeast cells Starch Pyruvate Glycolytic Pathway Glucose (a) Glucose Acetoaldehyde CBH Cellulose EG ETHANOL BGL Cellooligosaccharide Yeast cell Glucoamylase α-Amylase Starch Pyruvate Glycolytic Pathway Glucose (b) BGL EG ETHANOL CBH Cellulose Cellooligosaccharide Acetoaldehyde Glucose Direct conversion of starchy and lignocellulosic biomass to ethanol using enzyme-secreting (a) or enzyme surface–displaying (b) Yeast cell α-Amylase Glucoamylase Glucan 11% Yeast cell 11% Xylan 3% Others 19% Yeast cell 13% Glucan 2% Xylan 4% Others 20% Lignin and ash 61% Lignin and ash 56% (a) (b) FIGURE 8.3 Composition of residual matter obtained after the fermentation of 200 g-dryweight/L rice straw, hydrothermally pretreated (Matano et al., 2012), in the presence of 10 FPU/g-biomass cellulase with wild-type (a) and cellulase-displaying Saccharomyces cerevisiae strain, NBRC1440/B-EC3 (b) Xylan Xylooligosaccharide β-Xylosidase Xylanase Xylose XR Xylitol Xylose XDH Xylulose XK Xylulose-5P Yeast cell Pentose Phosphate Pathway Glycolytic Pathway ETHANOL FIGURE 8.5 A recombinant yeast strain displaying hemicellulolytic enzymes such as xylanase and β-xylosidase on the cell surface and expressing xylose-assimilating enzymes such as XR, XDH, and XK FIGURE 16.2 Metabolic pathways relevant in the context of succinate production from glucose with focus on the type of reaction or reaction sequence—oxidative reactions are indicated by red arrows, reductive reactions by green arrows The cofactors involved are also shown The pathways are grouped according to their major purpose in three boxes: grey box—initial substrate degradation pathways, yellow box—succinate-producing pathways, blue box—pyruvate dissimilation pathways The reactions or reaction sequences are numbered as follows: 1, glucose uptake and glycolysis; 2, oxidative pentose phosphate pathway (PPP) branching with the Entner-Doudoroff pathway; 3, pyruvate kinase; 4, PEP carboxylase; 5, PEP carboxykinase (note that some enzymes used GDP/GTP rather than ADP/ATP); 6, pyruvate carboxylase; 7, reductive TCA cycle including malate dehydrogenase, fumarase, and fumarate reductase or succinate:quinone oxidoreductase; 8, glyoxylate shunt including isocitrate lyase and malate synthase; 9, oxidative TCA cycle including citrate synthase, aconitase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase complex, and succinyl-CoA synthetase; 10, pyruvate dehydrogenase complex, pyruvate decarboxylase; 11, pyruvate formate lyase; 12, lactate dehydrogenase; 13, formate dehydrogenase (NAD+ dependent) or formate hydrogen lyase; 14, alcohol dehydrogenase; 15, phosphotransacetylase and acetate kinase FIGURE 19.3 acid Biorefinery concepts that integrate the first and second generation bio-adipic