Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy

Preface     xivAcknowledgments     xvContributors     xviOur Challenge Is to Acquire Deeper Understanding of Biomass Recalcitrance and Conversion   Michael E. Himmel   Stephen K. Picataggio     1The modern lignocellulose biorefinery     1Biomass recalcitrance to deconstruction     1Plants evolved to resist microbial and enzymatic assault!     2Are biomass-degrading enzymes working maximally?     2Chemical pretreatments are still required to reveal cell wall cellulose     3Fermenting cell wall sugars: the stage is set for systems/synthetic biology     4References     5The Biorefinery   Thomas D. Foust   Kelly N. Ibsen   David C. Dayton   J. Richard Hess   Kevin E. Kenney     7Introduction     7Phase III - lignocellulosic biorefineries     10Feedstocks     12Biochemical conversion     17Thermochemical biorefinery     23Introduction     23R&D needs to achieve economic viability     26Advanced biorefinery     28Advanced, large-tonnage feedstock supply systems     28Systems biology to improvebiochemical processing     30Selective thermal transformation to improve thermochemical processing     32Technology integration, economies of scale, and evolutionary process optimization     34References     35Anatomy and Ultrastructure of Maize Cell Walls: An Example of Energy Plants   Shi-You Ding   Michael E. Himmel     38Introduction     38Cell wall anatomy     38Plant tissues     39Cell wall biosynthesis and molecular structure     41Biosynthesis     42Cell wall lamellae     45The macrofibril and elementary fibril     46The microfibril     47Cellulose     48Matrix polymers     49Advanced approaches for characterizing cell wall structure     49Atomic force microscopy     49Biophotonics and nonlinear microscopy     50Single molecule methods     50Computer simulations     51Summary     53Acknowledgment     55References     55Chemistry and Molecular Organization of Plant Cell Walls   Philip J. Harris   Bruce A. Stone     61Introduction      61Chemistry of cell wall polymers     62Chemistry of cell wall polysaccharides     62Chemistry of cell wall proteins     70Molecular associations between wall polymers     70Non-covalent interactions between wall polymers     70Covalent interactions between wall polymers     71Covalent cross-linking between wall polymers prevents polysaccharide utilization     78Molecular architecture of plant cell walls     79Primary cell walls     79Lignified secondary walls     81Degradabilities of the walls of different cell types by enzymes     83References     85Cell Wall Polysaccharide Synthesis   Debra Mohnen   Maor Bar-Peled   Chris Somerville     94Introduction     94Cellulose     96Enzymology     98Cellulose deposition     100Regulation of cellulose synthesis     101Hemicellulose     104Mannan     104Xyloglucan     105Xylan     108Mixed linkage glucans     110Pectins     110Location of pectin synthesis     114Pectin biosynthetic glycosyltransferases     115Methyltransferases     119Acetyltransferases     119Other pectin modifying enzymes     119Homogalacturonan synthesis     120Xylogalacturonan synthesis     127Apiogalacturonan synthesis     127Synthesis of rhamnogalacturonan II (RG-II)     128Rhamnogalacturonan I (RG-I) synthesis     130The cell biology and compartmentalization of cell wall synthesis     136Nucleotide sugars     137Fermentation and nucleotide-sugars: a long history     140Fermentation and nucleotide-sugars: a long history     140Sugar kinase - pyrophosphorylase pathway to synthesize NDP-sugars     140Direct production of NDP-sugars     140NDP-sugar Interconversion Pathway     140SLOPPY, a general UDP-sugar pyrophosphorylase     142UDP-[alpha]-D-glucose (UDP-Glc)     143ADP-[alpha]-D-glucose (ADP-Glc)     145UDP-[alpha]-D-galactose (UDP-Gal)     146UDP-L-rhamnose (UDP-Rha)     147UDP-[alpha]-D-glucuronic acid (UDP-GlcA)     147UDP-[alpha]-D-galacturonic acid (UDP-GalA)     150UDP-[alpha]-D-xylose (UDP-Xyl)      151UDP-D-apiose (UDP-Api)     151UDP-L-arabinose pyranose (UDP-Ara)     152UDP-arabinose furanose (UDP-Araf)     153GDP-[alpha]-D-mannose (GDP-Man)     153GDP-[beta]-L-fucose (GDP-Fuc)     154GDP-[beta]-L-galactose (GDP-Gal), GDP-[beta]-L-gluclose gulose (GDP-Gul)     154CMP-[beta]-KDO (CMP-KDO)     154Other enzymes involved in NDP-sugar metabolism     155Future questions and directions     156Perspectives     159Acknowledgments     159References     159Structures of Plant Cell Wall Celluloses   Rajai H. Atalla   John W. Brady   James F. Matthews   Shi-You Ding   Michael E. Himmel     188Introduction     188Background     189Cellulose microfibrils     190Molecular modeling     194Raman spectra     200Alternative patterns of aggregation     203Alternative approaches to the problem of crystallinity     210References     210Lignins: A Twenty-First Century Challenge   Laurence B. Davin   Ann M. Patten   Michael Jourdes   Norman G. Lewis      213Lignin: molecular basis and role in plant adaptation to land     213Lignin pathway evolution, deposition, and function in vascular anatomical development     218Vascular plant diversification and lignification     218Heartwood and reaction (compression/tension) wood tissues     223Pioneers of monolignol biosynthesis, recent progress, and metabolic flux analyses     225Phenylalanine formation     226Metabolic flux analyses and transcriptional profiling in the monolignol pathway     227Phenylalanine and tyrosine ammonia lyases     227Cytochrome P-450s and hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferases     2284-Coumarate CoA ligases     229Cinnamoyl CoA reductases and cinnamyl alcohol dehydrogenases     230COMTs and CCOMTs     230Proteins of unknown physiological/biochemical functions in monolignol metabolism, "CAD1" and "sinapyl alcohol dehydrogenase, SAD"     232Recent developments: metabolic networks in the monolignol/lignin forming pathway (Arabidopsis) and (current) database annotations/limitations - opportunities and challenges     234Inherent shortcomings in lignin analyses: a critical juncture and the urgent need     235Lignin isolation procedures     236Lignin subunit and lignin structural analyses by NMR spectroscopy     237Quantification of lignin amounts, lignin degradation protocols, and synthetic dehydropolymerizates     239Modulation of monolignol pathway and peroxidase enzymatic steps: predictable effects on the vascular apparatus and on limited substrate degeneracy during proposed lignin template polymerization     242PAL, C4H, pC3H, HCT, and 4CL downregulation/mutation     243CCR, CAD, F5H, and COMT downregulation/mutation, and the enigma of monolignol radical generation     254Transcriptional control over secondary wall fiber formation: ramifications for lignification and vascular integrity     268Native lignin macromolecular configuration     268Early beginnings: the Freudenberg (random coupling) and the Forss (regular repeating unit) models for lignins     269Further refinement of structural depictions of lignins (1970s to the present date): a reassessment     272A new beginning: the need to fully define native lignin macromolecular configuration proper     274Future outlook: remaining questions in lignin macromolecular assembly/configuration, proposed lignin template replication, and overall cell wall formation     285Acknowledgments     287References     287Computational Approaches to Study Cellulose Hydrolysis   Michael F. Crowley   Ross C. Walker      306Introduction     306Molecular mechanics     307The force field equation     307Interatomic potentials     308Non-bonded cutoffs and long range electrostatics     311Molecular model types     312Force fields     313Carbohydrate force fields     314Solvent models     314Molecular dynamics     315Dynamics methods     316Finite difference methods     316System size limitations     316Quantum mechanics/molecular dynamics     317Analysis methods     317Enhanced sampling and free energy methods     319Free energy methods     320Studying cellulose hydrolysis     322Work to date     322Approaches to current questions about structure and hydrolysis     323Performance and future of cellulose modeling     324Current performance     324Future possibilities     325Acknowledgments     326References     326Mechanisms of Xylose and Xylo-oligomer Degradation During Acid Pretreatment   Xianghong Qian   Mark R. Nimlos     331Background      331Computational techniques     333Molecular dynamics simulations     333Static electronic structure theory     334Xylose degradation reactions in vacuum     335Effects of solvent water molecules     339Xylobiose calculations     340Experimental investigation of hydrolysis     344The hydrolysis of xylobiose     345The hydrolysis of xylan     346Corn stover     347Conclusions     348Future studies     349Acknowledgment     349References     349Enzymatic Depolymerization of Plant Cell Wall Hemicelluloses   Stephen R. Decker   Matti Siika-aho   Liisa Viikari     352Introduction     352Hemicellulase types, activities, and specificities     355Depolymerases     359Xylanases     359Mannanases     360[beta]-glucanases     361Xyloglucanases     362Debranching enzymes (accessory enzymes)     362[alpha]-glucuronidase     363[alpha]-arabinofuranosidase     363[alpha]-D-galactosidase     363Acetyl xylan esterase     363Ferulic acid esterase     364Hemicellulase activities for biomass feedstocks     364Xylan     365Galactoglucomannan and glucomannan     366Arabinogalactan, xyloglucan, and [beta]-glucan     367Hydrolysis of solubilized hemicellulose     367Acknowledgment     368References     368Aerobic Microbial Cellulase Systems   David B. Wilson     374Introduction     374Understanding cellulases     375Diversity of cellulases     376Cellulose-binding domains     379Cellulase synergism     380Cellulases from Trichoderma reesei     380Other fungal cellulases     381Cellulolytic aerobic bacteria     382Outlook     386References     386Cellulase Systems of Anaerobic Microorganisms from the Rumen and Large Intestine   Harry J. Flint     393Introduction     393Cellulolytic and hemicellulolytic bacteria from the rumen     394Ruminococcus flavefaciens     394Other Clostridium-related anaerobic bacteria     396Plant cell wall breakdown by eukaryotic microorganisms     398Rumen fungi     398Rumen protozoa     398Information from metagenomics     399The large intestine     400Conclusions     400Acknowledgment     401References     401The Cellulosome: A Natural Bacterial Strategy to Combat Biomass Recalcitrance   Edward A. Bayer   Bernard Henrissat   Raphael Lamed     407Introduction     407The cellulosome concept     408Cellulosomal carbohydrate-active enzymes     410The cellulosome-cellulose interaction     415Cell-surface disposition of cellulosomes     417Cellulosome assault on recalcitrant cellulose substrates     418Degradation of cellulose by the C. thermocellum cellulosome     420The cellulosome rationale     423Acknowledgments     426References     426Pretreatments for Enhanced Digestibility of Feedstocks   David K. Johnson   Richard T. Elander     436Introduction     436Enzyme usage and enzyme-type considerations for pretreated biomass     437Desired properties of pretreatment processes     437Physicochemical properties of pretreated biomass believed to affect cellulose digestibility     438Pretreatment approaches     439Physical pretreatments     440Rapid decompression pretreatments     440Autohydrolysis pretreatments     442Acidic pretreatments     443Alkaline pretreatments     444Solvent pretreatments     445Supercritical fluid pretreatments     446Oxidative pretreatments     446Biological pretreatment     447Future prospects     447Acknowledgment     449References     449Understanding the Biomass Decay Community   William S. Adney   Daniel van der Lelie   Alison M. Berry   Michael E. Himmel     454Introduction     454Defining biomass decay communities     456Fungi identified with plant biomass     457Bacteria identified with plant biomass     459Interactions between saprophytic fungi and bacteria     463Characterization of microbial communities that degrade biomass     464Biochemical approaches to define biomass degrading communities     465Molecular approaches for defining biomass-degrading communities      466Microarray methods suitable for biomass sampling     470Conclusions     472Acknowledgment     472References     473New Generation Biomass Conversion: Consolidated Bioprocessing   Y.-H. Percival Zhang   Lee R. Lynd     480Introduction     480Consolidated bioprocessing     481CBP advances     483Native cellulolytic microorganisms     483Recombinant cellulolytic strategy     488Future directions     489Acknowledgment     490References     490Index     495

\ From the Publisher"Biomass Recalcitrance is a must-have.... The compilation covers fundamentals as well as hot topics that will provide new insights and knowledge to many readers." (ChemSusChem, June 2009)\ \ \