Preface p. xiv
Acknowledgments p. xv
Contributors p. xvi
Our Challenge Is to Acquire Deeper Understanding of Biomass Recalcitrance and Conversion
p. 1
The modern lignocellulose biorefinery p. 1
Biomass recalcitrance to deconstruction p. 1
Plants evolved to resist microbial and enzymatic assault! p. 2
Are biomass-degrading enzymes working maximally? p. 2
Chemical pretreatments are still required to reveal cell wall cellulose p. 3 Fermenting cell wall sugars: the stage is set for systems/synthetic biology p. 4
References p. 5
The Biorefinery p. 7
Introduction p. 7
Phase III - lignocellulosic biorefineries p. 10
Feedstocks p. 12
Biochemical conversion p. 17
Thermochemical biorefinery p. 23
Introduction p. 23
R&D; needs to achieve economic viability p. 26
Advanced biorefinery p. 28
Advanced, large-tonnage feedstock supply systems p. 28
Systems biology to improve biochemical processing p. 30
Selective thermal transformation to improve thermochemical processing p. 32 Technology integration, economies of scale, and evolutionary process optimization p. 34
References p. 35
Anatomy and Ultrastructure of Maize Cell Walls: An Example of Energy Plants p. 38
Introduction p. 38
Cell wall anatomy p. 38
Plant tissues p. 39
Cell wall biosynthesis and molecular structure p. 41
Biosynthesis p. 42
Cell wall lamellae p. 45
The macrofibril and elementary fibril p. 46
The microfibril p. 47
Cellulose p. 48
Matrix polymers p. 49
Advanced approaches for characterizing cell wall structure p. 49
Atomic force microscopy p. 49
Biophotonics and nonlinear microscopy p. 50
Computer simulations p. 51
Summary p. 53
Acknowledgment p. 55
References p. 55
Chemistry and Molecular Organization of Plant Cell Walls p. 61
Introduction p. 61
Chemistry of cell wall polymers p. 62
Chemistry of cell wall polysaccharides p. 62
Chemistry of cell wall proteins p. 70
Molecular associations between wall polymers p. 70
Non-covalent interactions between wall polymers p. 70
Covalent interactions between wall polymers p. 71
Covalent cross-linking between wall polymers prevents polysaccharide utilization p. 78
Molecular architecture of plant cell walls p. 79
Primary cell walls p. 79
Lignified secondary walls p. 81
Degradabilities of the walls of different cell types by enzymes p. 83
References p. 85
Cell Wall Polysaccharide Synthesis p. 94
Introduction p. 94
Cellulose p. 96
Enzymology p. 98
Cellulose deposition p. 100
Regulation of cellulose synthesis p. 101
Hemicellulose p. 104
Mannan p. 104
Xyloglucan p. 105
Xylan p. 108
Mixed linkage glucans p. 110
Pectins p. 110
Location of pectin synthesis p. 114
Pectin biosynthetic glycosyltransferases p. 115
Methyltransferases p. 119
Acetyltransferases p. 119
Other pectin modifying enzymes p. 119
Homogalacturonan synthesis p. 120
Xylogalacturonan synthesis p. 127
Apiogalacturonan synthesis p. 127
Synthesis of rhamnogalacturonan II (RG-II) p. 128
Rhamnogalacturonan I (RG-I) synthesis p. 130
Nucleotide sugars p. 137
Fermentation and nucleotide-sugars: a long history p. 140
Fermentation and nucleotide-sugars: a long history p. 140
Sugar kinase - pyrophosphorylase pathway to synthesize NDP-sugars p. 140
Direct production of NDP-sugars p. 140
NDP-sugar Interconversion Pathway p. 140
SLOPPY, a general UDP-sugar pyrophosphorylase p. 142
UDP-[alpha]-D-glucose (UDP-Glc) p. 143
ADP-[alpha]-D-glucose (ADP-Glc) p. 145
UDP-[alpha]-D-galactose (UDP-Gal) p. 146
UDP-L-rhamnose (UDP-Rha) p. 147
UDP-[alpha]-D-glucuronic acid (UDP-GlcA) p. 147
UDP-[alpha]-D-galacturonic acid (UDP-GalA) p. 150
UDP-[alpha]-D-xylose (UDP-Xyl) p. 151
UDP-D-apiose (UDP-Api) p. 151
UDP-L-arabinose pyranose (UDP-Ara) p. 152
UDP-arabinose furanose (UDP-Araf) p. 153
GDP-[alpha]-D-mannose (GDP-Man) p. 153
GDP-[beta]-L-fucose (GDP-Fuc) p. 154
GDP-[beta]-L-galactose (GDP-Gal), GDP-[beta]-L-gluclose gulose (GDP-Gul) p. 154
CMP-[beta]-KDO (CMP-KDO) p. 154
Other enzymes involved in NDP-sugar metabolism p. 155
Future questions and directions p. 156
Perspectives p. 159
Acknowledgments p. 159
References p. 159
Structures of Plant Cell Wall Celluloses p. 188
Introduction p. 188
Background p. 189
Cellulose microfibrils p. 190
Molecular modeling p. 194
Raman spectra p. 200
Alternative patterns of aggregation p. 203
Alternative approaches to the problem of crystallinity p. 210
References p. 210
Lignins: A Twenty-First Century Challenge p. 213
Lignin: molecular basis and role in plant adaptation to land p. 213 Lignin pathway evolution, deposition, and function in vascular anatomical
development
p. 218
Vascular plant diversification and lignification p. 218
Pioneers of monolignol biosynthesis, recent progress, and metabolic flux analyses p. 225
Phenylalanine formation p. 226
Metabolic flux analyses and transcriptional profiling in the monolignol pathway p. 227
Phenylalanine and tyrosine ammonia lyases p. 227
Cytochrome P-450s and hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferases
p. 228
4-Coumarate CoA ligases p. 229
Cinnamoyl CoA reductases and cinnamyl alcohol dehydrogenases p. 230
COMTs and CCOMTs p. 230
Proteins of unknown physiological/biochemical functions in monolignol metabolism, "CAD1" and "sinapyl alcohol dehydrogenase, SAD"
p. 232
Recent developments: metabolic networks in the monolignol/lignin forming pathway (Arabidopsis) and (current) database annotations/limitations - opportunities and challenges
p. 234
Inherent shortcomings in lignin analyses: a critical juncture and the urgent need p. 235
Lignin isolation procedures p. 236
Lignin subunit and lignin structural analyses by NMR spectroscopy p. 237 Quantification of lignin amounts, lignin degradation protocols, and synthetic
dehydropolymerizates
p. 239
Modulation of monolignol pathway and peroxidase enzymatic steps: predictable
effects on the vascular apparatus and on limited substrate degeneracy during proposed lignin template polymerization
p. 242
PAL, C4H, pC3H, HCT, and 4CL downregulation/mutation p. 243
CCR, CAD, F5H, and COMT downregulation/mutation, and the enigma of monolignol radical generation
p. 254
Transcriptional control over secondary wall fiber formation: ramifications for lignification and vascular integrity
p. 268
Native lignin macromolecular configuration p. 268
Early beginnings: the Freudenberg (random coupling) and the Forss (regular repeating unit) models for lignins
p. 269
Further refinement of structural depictions of lignins (1970s to the present date): a reassessment
p. 272
A new beginning: the need to fully define native lignin macromolecular configuration proper
p. 274
Future outlook: remaining questions in lignin macromolecular
assembly/configuration, proposed lignin template replication, and overall cell wall formation p. 285
Acknowledgments p. 287
References p. 287
Computational Approaches to Study Cellulose Hydrolysis p. 306
Introduction p. 306
Molecular mechanics p. 307
The force field equation p. 307
Interatomic potentials p. 308
Molecular model types p. 312
Force fields p. 313
Carbohydrate force fields p. 314
Solvent models p. 314
Molecular dynamics p. 315
Dynamics methods p. 316
Finite difference methods p. 316
System size limitations p. 316
Quantum mechanics/molecular dynamics p. 317
Analysis methods p. 317
Enhanced sampling and free energy methods p. 319
Free energy methods p. 320
Studying cellulose hydrolysis p. 322
Work to date p. 322
Approaches to current questions about structure and hydrolysis p. 323
Performance and future of cellulose modeling p. 324
Current performance p. 324
Future possibilities p. 325
Acknowledgments p. 326
References p. 326
Mechanisms of Xylose and Xylo-oligomer Degradation During Acid Pretreatment p. 331
Background p. 331
Computational techniques p. 333
Molecular dynamics simulations p. 333
Static electronic structure theory p. 334
Xylose degradation reactions in vacuum p. 335
Effects of solvent water molecules p. 339
Xylobiose calculations p. 340
Experimental investigation of hydrolysis p. 344
The hydrolysis of xylobiose p. 345
The hydrolysis of xylan p. 346
Corn stover p. 347
Conclusions p. 348
Future studies p. 349
Acknowledgment p. 349
References p. 349
Enzymatic Depolymerization of Plant Cell Wall Hemicelluloses p. 352
Introduction p. 352
Hemicellulase types, activities, and specificities p. 355
Depolymerases p. 359
Mannanases p. 360
[beta]-glucanases p. 361
Xyloglucanases p. 362
Debranching enzymes (accessory enzymes) p. 362
[alpha]-glucuronidase p. 363
[alpha]-arabinofuranosidase p. 363
[alpha]-D-galactosidase p. 363
Acetyl xylan esterase p. 363
Ferulic acid esterase p. 364
Hemicellulase activities for biomass feedstocks p. 364
Xylan p. 365
Galactoglucomannan and glucomannan p. 366
Arabinogalactan, xyloglucan, and [beta]-glucan p. 367
Hydrolysis of solubilized hemicellulose p. 367
Acknowledgment p. 368
References p. 368
Aerobic Microbial Cellulase Systems p. 374
Introduction p. 374
Understanding cellulases p. 375
Diversity of cellulases p. 376
Cellulose-binding domains p. 379
Cellulase synergism p. 380
Cellulases from Trichoderma reesei p. 380
Other fungal cellulases p. 381
Cellulolytic aerobic bacteria p. 382
Outlook p. 386
References p. 386
Cellulase Systems of Anaerobic Microorganisms from the Rumen and Large Intestine p. 393
Introduction p. 393
Cellulolytic and hemicellulolytic bacteria from the rumen p. 394
Ruminococcus flavefaciens p. 394
Other Clostridium-related anaerobic bacteria p. 396
Plant cell wall breakdown by eukaryotic microorganisms p. 398
Rumen fungi p. 398
Rumen protozoa p. 398
Information from metagenomics p. 399
The large intestine p. 400
Conclusions p. 400
Acknowledgment p. 401
References p. 401
Introduction p. 407
The cellulosome concept p. 408
Cellulosomal carbohydrate-active enzymes p. 410
The cellulosome-cellulose interaction p. 415
Cell-surface disposition of cellulosomes p. 417
Cellulosome assault on recalcitrant cellulose substrates p. 418 Degradation of cellulose by the C. thermocellum cellulosome p. 420
The cellulosome rationale p. 423
Acknowledgments p. 426
References p. 426
Pretreatments for Enhanced Digestibility of Feedstocks p. 436
Introduction p. 436
Enzyme usage and enzyme-type considerations for pretreated biomass p. 437
Desired properties of pretreatment processes p. 437
Physicochemical properties of pretreated biomass believed to affect cellulose digestibility
p. 438
Pretreatment approaches p. 439
Physical pretreatments p. 440
Rapid decompression pretreatments p. 440
Autohydrolysis pretreatments p. 442
Acidic pretreatments p. 443
Alkaline pretreatments p. 444
Solvent pretreatments p. 445
Supercritical fluid pretreatments p. 446
Oxidative pretreatments p. 446
Biological pretreatment p. 447
Future prospects p. 447
Acknowledgment p. 449
References p. 449
Understanding the Biomass Decay Community p. 454
Introduction p. 454
Defining biomass decay communities p. 456
Fungi identified with plant biomass p. 457
Bacteria identified with plant biomass p. 459
Interactions between saprophytic fungi and bacteria p. 463
Characterization of microbial communities that degrade biomass p. 464 Biochemical approaches to define biomass degrading communities p. 465 Molecular approaches for defining biomass-degrading communities p. 466
Microarray methods suitable for biomass sampling p. 470
Conclusions p. 472
Acknowledgment p. 472
New Generation Biomass Conversion: Consolidated Bioprocessing p. 480
Introduction p. 480
Consolidated bioprocessing p. 481
CBP advances p. 483
Native cellulolytic microorganisms p. 483
Recombinant cellulolytic strategy p. 488
Future directions p. 489
Acknowledgment p. 490
References p. 490
Index p. 495
