Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy Book

Preface     xiv
Acknowledgments     xv
Contributors     xvi
Our Challenge Is to Acquire Deeper Understanding of Biomass Recalcitrance and Conversion   Michael E. Himmel   Stephen K. Picataggio     1
The modern lignocellulose biorefinery     1
Biomass recalcitrance to deconstruction     1
Plants evolved to resist microbial and enzymatic assault!     2
Are biomass-degrading enzymes working maximally?     2
Chemical pretreatments are still required to reveal cell wall cellulose     3
Fermenting cell wall sugars: the stage is set for systems/synthetic biology     4
References     5
The Biorefinery   Thomas D. Foust   Kelly N. Ibsen   David C. Dayton   J. Richard Hess   Kevin E. Kenney     7
Introduction     7
Phase III - lignocellulosic biorefineries     10
Feedstocks     12
Biochemical conversion     17
Thermochemical biorefinery     23
Introduction     23
R&D needs to achieve economic viability     26
Advanced biorefinery     28
Advanced, large-tonnage feedstock supply systems     28
Systems biology to improvebiochemical processing     30
Selective thermal transformation to improve thermochemical processing     32
Technology integration, economies of scale, and evolutionary process optimization     34
References     35
Anatomy and Ultrastructure of Maize Cell Walls: An Example of Energy Plants   Shi-You Ding   Michael E. Himmel     38
Introduction     38
Cell wall anatomy     38
Plant tissues     39
Cell wall biosynthesis and molecular structure     41
Biosynthesis     42
Cell wall lamellae     45
The macrofibril and elementary fibril     46
The microfibril     47
Cellulose     48
Matrix polymers     49
Advanced approaches for characterizing cell wall structure     49
Atomic force microscopy     49
Biophotonics and nonlinear microscopy     50
Single molecule methods     50
Computer simulations     51
Summary     53
Acknowledgment     55
References     55
Chemistry and Molecular Organization of Plant Cell Walls   Philip J. Harris   Bruce A. Stone     61
Introduction      61
Chemistry of cell wall polymers     62
Chemistry of cell wall polysaccharides     62
Chemistry of cell wall proteins     70
Molecular associations between wall polymers     70
Non-covalent interactions between wall polymers     70
Covalent interactions between wall polymers     71
Covalent cross-linking between wall polymers prevents polysaccharide utilization     78
Molecular architecture of plant cell walls     79
Primary cell walls     79
Lignified secondary walls     81
Degradabilities of the walls of different cell types by enzymes     83
References     85
Cell Wall Polysaccharide Synthesis   Debra Mohnen   Maor Bar-Peled   Chris Somerville     94
Introduction     94
Cellulose     96
Enzymology     98
Cellulose deposition     100
Regulation of cellulose synthesis     101
Hemicellulose     104
Mannan     104
Xyloglucan     105
Xylan     108
Mixed linkage glucans     110
Pectins     110
Location of pectin synthesis     114
Pectin biosynthetic glycosyltransferases     115
Methyltransferases     119
Acetyltransferases     119
Other pectin modifying enzymes     119
Homogalacturonan synthesis     120
Xylogalacturonan synthesis     127
Apiogalacturonan synthesis     127
Synthesis of rhamnogalacturonan II (RG-II)     128
Rhamnogalacturonan I (RG-I) synthesis     130
The cell biology and compartmentalization of cell wall synthesis     136
Nucleotide sugars     137
Fermentation and nucleotide-sugars: a long history     140
Fermentation and nucleotide-sugars: a long history     140
Sugar kinase - pyrophosphorylase pathway to synthesize NDP-sugars     140
Direct production of NDP-sugars     140
NDP-sugar Interconversion Pathway     140
SLOPPY, a general UDP-sugar pyrophosphorylase     142
UDP-[alpha]-D-glucose (UDP-Glc)     143
ADP-[alpha]-D-glucose (ADP-Glc)     145
UDP-[alpha]-D-galactose (UDP-Gal)     146
UDP-L-rhamnose (UDP-Rha)     147
UDP-[alpha]-D-glucuronic acid (UDP-GlcA)     147
UDP-[alpha]-D-galacturonic acid (UDP-GalA)     150
UDP-[alpha]-D-xylose (UDP-Xyl)      151
UDP-D-apiose (UDP-Api)     151
UDP-L-arabinose pyranose (UDP-Ara)     152
UDP-arabinose furanose (UDP-Araf)     153
GDP-[alpha]-D-mannose (GDP-Man)     153
GDP-[beta]-L-fucose (GDP-Fuc)     154
GDP-[beta]-L-galactose (GDP-Gal), GDP-[beta]-L-gluclose gulose (GDP-Gul)     154
CMP-[beta]-KDO (CMP-KDO)     154
Other enzymes involved in NDP-sugar metabolism     155
Future questions and directions     156
Perspectives     159
Acknowledgments     159
References     159
Structures of Plant Cell Wall Celluloses   Rajai H. Atalla   John W. Brady   James F. Matthews   Shi-You Ding   Michael E. Himmel     188
Introduction     188
Background     189
Cellulose microfibrils     190
Molecular modeling     194
Raman spectra     200
Alternative patterns of aggregation     203
Alternative approaches to the problem of crystallinity     210
References     210
Lignins: A Twenty-First Century Challenge   Laurence B. Davin   Ann M. Patten   Michael Jourdes   Norman G. Lewis      213
Lignin: molecular basis and role in plant adaptation to land     213
Lignin pathway evolution, deposition, and function in vascular anatomical development     218
Vascular plant diversification and lignification     218
Heartwood and reaction (compression/tension) wood tissues     223
Pioneers of monolignol biosynthesis, recent progress, and metabolic flux analyses     225
Phenylalanine formation     226
Metabolic flux analyses and transcriptional profiling in the monolignol pathway     227
Phenylalanine and tyrosine ammonia lyases     227
Cytochrome P-450s and hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferases     228
4-Coumarate CoA ligases     229
Cinnamoyl CoA reductases and cinnamyl alcohol dehydrogenases     230
COMTs and CCOMTs     230
Proteins of unknown physiological/biochemical functions in monolignol metabolism, "CAD1" and "sinapyl alcohol dehydrogenase, SAD"     232
Recent developments: metabolic networks in the monolignol/lignin forming pathway (Arabidopsis) and (current) database annotations/limitations - opportunities and challenges     234
Inherent shortcomings in lignin analyses: a critical juncture and the urgent need     235
Lignin isolation procedures     236
Lignin subunit and lignin structural analyses by NMR spectroscopy     237
Quantification of lignin amounts, lignin degradation protocols, and synthetic dehydropolymerizates     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     242
PAL, C4H, pC3H, HCT, and 4CL downregulation/mutation     243
CCR, CAD, F5H, and COMT downregulation/mutation, and the enigma of monolignol radical generation     254
Transcriptional control over secondary wall fiber formation: ramifications for lignification and vascular integrity     268
Native lignin macromolecular configuration     268
Early beginnings: the Freudenberg (random coupling) and the Forss (regular repeating unit) models for lignins     269
Further refinement of structural depictions of lignins (1970s to the present date): a reassessment     272
A new beginning: the need to fully define native lignin macromolecular configuration proper     274
Future outlook: remaining questions in lignin macromolecular assembly/configuration, proposed lignin template replication, and overall cell wall formation     285
Acknowledgments     287
References     287
Computational Approaches to Study Cellulose Hydrolysis   Michael F. Crowley   Ross C. Walker      306
Introduction     306
Molecular mechanics     307
The force field equation     307
Interatomic potentials     308
Non-bonded cutoffs and long range electrostatics     311
Molecular model types     312
Force fields     313
Carbohydrate force fields     314
Solvent models     314
Molecular dynamics     315
Dynamics methods     316
Finite difference methods     316
System size limitations     316
Quantum mechanics/molecular dynamics     317
Analysis methods     317
Enhanced sampling and free energy methods     319
Free energy methods     320
Studying cellulose hydrolysis     322
Work to date     322
Approaches to current questions about structure and hydrolysis     323
Performance and future of cellulose modeling     324
Current performance     324
Future possibilities     325
Acknowledgments     326
References     326
Mechanisms of Xylose and Xylo-oligomer Degradation During Acid Pretreatment   Xianghong Qian   Mark R. Nimlos     331
Background      331
Computational techniques     333
Molecular dynamics simulations     333
Static electronic structure theory     334
Xylose degradation reactions in vacuum     335
Effects of solvent water molecules     339
Xylobiose calculations     340
Experimental investigation of hydrolysis     344
The hydrolysis of xylobiose     345
The hydrolysis of xylan     346
Corn stover     347
Conclusions     348
Future studies     349
Acknowledgment     349
References     349
Enzymatic Depolymerization of Plant Cell Wall Hemicelluloses   Stephen R. Decker   Matti Siika-aho   Liisa Viikari     352
Introduction     352
Hemicellulase types, activities, and specificities     355
Depolymerases     359
Xylanases     359
Mannanases     360
[beta]-glucanases     361
Xyloglucanases     362
Debranching enzymes (accessory enzymes)     362
[alpha]-glucuronidase     363
[alpha]-arabinofuranosidase     363
[alpha]-D-galactosidase     363
Acetyl xylan esterase     363
Ferulic acid esterase     364
Hemicellulase activities for biomass feedstocks     364
Xylan     365
Galactoglucomannan and glucomannan     366
Arabinogalactan, xyloglucan, and [beta]-glucan     367
Hydrolysis of solubilized hemicellulose     367
Acknowledgment     368
References     368
Aerobic Microbial Cellulase Systems   David B. Wilson     374
Introduction     374
Understanding cellulases     375
Diversity of cellulases     376
Cellulose-binding domains     379
Cellulase synergism     380
Cellulases from Trichoderma reesei     380
Other fungal cellulases     381
Cellulolytic aerobic bacteria     382
Outlook     386
References     386
Cellulase Systems of Anaerobic Microorganisms from the Rumen and Large Intestine   Harry J. Flint     393
Introduction     393
Cellulolytic and hemicellulolytic bacteria from the rumen     394
Ruminococcus flavefaciens     394
Other Clostridium-related anaerobic bacteria     396
Plant cell wall breakdown by eukaryotic microorganisms     398
Rumen fungi     398
Rumen protozoa     398
Information from metagenomics     399
The large intestine     400
Conclusions     400
Acknowledgment     401
References     401
The Cellulosome: A Natural Bacterial Strategy to Combat Biomass Recalcitrance   Edward A. Bayer   Bernard Henrissat   Raphael Lamed     407
Introduction     407
The cellulosome concept     408
Cellulosomal carbohydrate-active enzymes     410
The cellulosome-cellulose interaction     415
Cell-surface disposition of cellulosomes     417
Cellulosome assault on recalcitrant cellulose substrates     418
Degradation of cellulose by the C. thermocellum cellulosome     420
The cellulosome rationale     423
Acknowledgments     426
References     426
Pretreatments for Enhanced Digestibility of Feedstocks   David K. Johnson   Richard T. Elander     436
Introduction     436
Enzyme usage and enzyme-type considerations for pretreated biomass     437
Desired properties of pretreatment processes     437
Physicochemical properties of pretreated biomass believed to affect cellulose digestibility     438
Pretreatment approaches     439
Physical pretreatments     440
Rapid decompression pretreatments     440
Autohydrolysis pretreatments     442
Acidic pretreatments     443
Alkaline pretreatments     444
Solvent pretreatments     445
Supercritical fluid pretreatments     446
Oxidative pretreatments     446
Biological pretreatment     447
Future prospects     447
Acknowledgment     449
References     449
Understanding the Biomass Decay Community   William S. Adney   Daniel van der Lelie   Alison M. Berry   Michael E. Himmel     454
Introduction     454
Defining biomass decay communities     456
Fungi identified with plant biomass     457
Bacteria identified with plant biomass     459
Interactions between saprophytic fungi and bacteria     463
Characterization of microbial communities that degrade biomass     464
Biochemical approaches to define biomass degrading communities     465
Molecular approaches for defining biomass-degrading communities      466
Microarray methods suitable for biomass sampling     470
Conclusions     472
Acknowledgment     472
References     473
New Generation Biomass Conversion: Consolidated Bioprocessing   Y.-H. Percival Zhang   Lee R. Lynd     480
Introduction     480
Consolidated bioprocessing     481
CBP advances     483
Native cellulolytic microorganisms     483
Recombinant cellulolytic strategy     488
Future directions     489
Acknowledgment     490
References     490
Index     495