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Acknowledgments vii
Contributors xvii
Preface xix
1 Monolignol Biosynthesis and its Genetic Manipulation: The Good, the Bad, and the Ugly 1Richard A. Dixon, M.S. Srinivasa Reddy, and Lina Gallego-Giraldo
1.1 Introduction 2
1.2 Function and distribution of lignin in plants 2
1.3 Targets for modification of lignin biosynthesis 5
1.3.1 Gene targets 1. Biosynthetic enzymes 5
1.3.1.1 L-phenylalanine ammonia-lyase (PAL) 6
1.3.1.2 Cinnamate 4-hydroxylase (C4H) 6
1.3.1.3 4-coumarate: coenzyme-A ligase (4CL) 6
1.3.1.4 Enzymes of the coumaroyl shikimate shunt 7
1.3.1.5 Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) 7
1.3.1.6 Ferulate 5-hydroxylase (F5H) 8
1.3.1.7 Caffeic acid 3-O-methyltransferase (COMT) 8
1.3.1.8 Cinnamoyl-CoA reductase 8
1.3.1.9 Cinnamyl alcohol dehydrogenase (CAD) 9
1.3.2 Gene targets 2. Transcription factors 9
1.4 Impacts of lignin modification through targeting of the monolignol biosynthetic pathway 9
1.4.1 L-phenylalanine ammonia-lyase (PAL) 10
1.4.2 Cinnamate 4-hydroxylase (C4H) 10
1.4.3 4-coumarate: coenzyme-A ligase (4CL) 11
1.4.4 Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) 13
1.4.5 4-coumaroyl shikimate 3'-hydroxylase (C3'H) 14
1.4.6 Caffeoyl CoA 3-O-methyltransferase (CCoAOMT) 15
1.4.7 Ferulate 5-hydroxylase (F5H) 17
1.4.8 Caffeic acid O-methyltransferase (COMT) 18
1.4.9 Cinnamoyl-CoA reductase (CCR) 20
1.4.10 Cinnamyl alcohol dehydrogenase (CAD) 22
1.5 Impacts of lignin modification through targeting of TFs 23
1.5.1 NAC master switches 24
1.5.2 MYB repressors of monolignol biosynthesis 24
1.5.3 WRKY repressors of lignification in pith 24
1.6 Monolignol pathway modification and plant growth 25
1.7 Conclusions: it isn't all that bad! 26
References 27
2 Perturbing Lignin Biosynthesis: Metabolic Changes in Response to Manipulation of the Phenylpropanoid Pathway 39Nickolas A. Anderson and Clint Chapple
2.1 Introduction 40
2.1.1 Cell wall-bound phenylpropanoids 40
2.1.2 Soluble phenylpropanoids 43
2.2 Changes in metabolism associated with phenylpropanoid-pathway disruptions 44
2.2.1 Phenylalanine ammonia-lyase (PAL) 44
2.2.2 Cinnamate 4-hydroxylase (C4H) 45
2.2.3 4-coumarate: CoA ligase (4CL) 46
2.2.4 Hydroxycinnamoyl-coenzyme A: shikimate/quinate hydroxycinnamoyltransferase (HCT)/p-coumaroyl shikimate 3'-hydroxylase (C3'H) 46
2.2.5 Cinnamoyl CoA reductase (CCR) 47
2.2.6 Ferulate 5-hydroxylase (F5H) 48
2.2.7 Caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT)/caffeoyl CoA 3-O-methyltransferase (CCoAOMT) 49
2.2.8 Cinnamyl alcohol dehydrogenases (CAD) 50
2.3 Atypical lignins 50
2.4 Dwarfism 51
2.5 Conclusions 52
References 52
3 Function, Structure, and Evolution of Flavonoid Glycosyltransferases in Plants 61Keiko Yonekura-Sakakibara and Kazuki Saito
3.1 Introduction 61
3.2 UDP-dependent glycosyltransferases 63
3.2.1 Functional identification of flavonoid UGTs 63
3.2.1.1 Flavonoid 3-O-glycosyltransferases 63
3.2.1.2 Flavonoid 7-O-glycosyltransferases 63
3.2.1.3 Flavonoid glycosyltransferases that glycosylate the sugar moiety attached to a flavonoid aglycone 67
3.2.1.4 Flavonoid 3'-O-glycosyltransferase 69
3.2.1.5 Flavonoid C-glycosyltransferase 69
3.2.2 3D structures of flavonoid UGTs 70
3.2.3 Functional evolution in UGTs 72
3.2.3.1 Functional evolution in flavonoid UGTs 74
3.3 Glycoside hydrolase-type glycosyltransferases 75
3.3.1 Functional identification of flavonoid GH1-type glycosyltransferases 75
3.3.1.1 Anthocyanin 5/7-O-glycosyltransferases 75
3.3.1.2 Anthocyanin 3-O-6''-O-coumaroylglucoside: glucosyltransferase 76
3.3.2 The reaction mechanism of GH1-type glycosyltransferases 78
3.4 Conclusions 78
References 78
4 The Chemistry and Chemical Ecology of Ellagitannins in Plant-Insect Interactions: From Underestimated Molecules to Bioactive Plant Constituents 83Juha-Pekka Salminen
4.1 Introduction 84
4.2 Definitions and chemical structures of hydrolyzable tannins 85
4.3 Biosynthetic pathways of hydrolyzable tannins in plants 87
4.3.1 Tannin biosynthetic pathways have many branching points that affect the flux of biosynthetic energy towards different tannins 90
4.3.2 Biosynthesis of gallic acid, galloylglucoses, and gallotannins 91
4.3.3 Biosynthesis of ellagitannins 92
4.4 Distributions of different types of tannin in plants 94
4.5 Tannins in plant-herbivore interactions 98
4.5.1 General aspects of tannins and plant-herbivore interactions 98
4.5.2 The tannin oxidation hypothesis and its verification in plant-herbivore interactions 102
4.5.3 The ease of oxidation of individual ellagitannins can be predicted by their chemical structures and chromatographic properties 104
4.5.4 Other factors that may affect ellagitannin activities against insect herbivores 107
4.6 Conclusions 108
Acknowledgments 109
References 109
5 Diverse Ecological Roles of Plant Tannins: Plant Defense and Beyond 115C. Peter Constabel, Kazuko Yoshida, and Vincent Walker
5.1 Introduction 115
5.2 Overview of tannin structure and function in defense 116
5.2.1 Structural diversity and distribution 116
5.2.2 In vitro biochemical activities 119
5.2.3 Old and new views on tannins in defense 120
5.2.4 The antimicrobial nature of tannins 122
5.3 Tissue localization and ecological function 124
5.3.1 Distribution of tannins in vegetative tissues 125
5.3.2 Tannins in seeds and fruit 126
5.3.3 Ecology of fruit tannins 127
5.4 Tannins in plant-soil-environment interactions 129
5.4.1 Tannin distribution and stability in soil 129
5.4.2 Impact of tannins on soil nitrogen cycling and microbial activity 130
5.4.3 Interaction with community and ecosystem processes 131
5.4.4 Tannins and other plant stress adaptations 133
5.5 Conclusions 134
Acknowledgments 134
References 134
6 Epigenetics, Plant (Poly)phenolics, and Cancer Prevention 143Clarissa Gerhauser
6.1 Introduction 143
6.2 Influence of polyphenols on DNA methylation 145
6.2.1 DNA methylation in normal and tumor cells 145
6.2.2 Inhibition of DNMTs in vitro 145
6.2.3 Inhibition of DNA methylation in cellular systems and in vivo 147
6.2.3.1 Quercetin 147
6.2.3.2 Nordihydroguaiaretic acid (NDGA) 147
6.2.3.3 Resveratrol 158
6.2.3.4 Apple polyphenols 159
6.2.3.5 Black raspberry polyphenols 159
6.3 Influence of polyphenols on histone-modifying enzymes 160
6.3.1 Acetylation of histones and non-histone proteins 161
6.3.1.1 Anacardic acid 161
6.3.1.2 Curcumin 165
6.3.1.3 Garcinol 166
6.3.1.4 Gallic acid 167
6.3.1.5 Delphinidin 167
6.3.2 Deacetylation by HDACs and sirtuins 168
6.3.2.1 Inhibition of HDAC activity 168
6.3.2.2 Modulation of sirtuin activity 168
6.3.3 Histone methylation marks 171
6.3.3.1 Histone lysine methylation 171
6.3.3.2 Histone lysine demethylation 171
6.4 Influence of noncoding miRNAs on gene expression 172
6.5 Chemopreventive polyphenols affecting the epigenome via multiple mechanisms 173
6.5.1 (-)-epigallocatechin 3-gallate (EGCG) and green-tea polyphenols (GTPs) 173
6.5.1.1 DNA methylation 174
6.5.1.2 Histone-modifying enzymes (HATs, HDACs, HMTs) 178
6.5.1.3 miRNAs 181
6.5.2 Genistein and soy isoflavones 183
6.5.2.1 DNA methylation 183
6.5.2.2 Influence on histone acetylation and methylation 189
6.5.2.3 miRNAs affected by isoflavones 192
6.6 Conclusions 195
6.6.1 DNA methylation 195
6.6.2 Histone-modifying enzymes 195
6.6.3 miRNAs 196
6.6.4 Summary 196
References 196
7 Discovery of Polyphenol-Based Drugs for Cancer Prevention and Treatment: The Tumor Proteasome as a Novel Target 209Fathima R. Kona, Min Shen, Di Chen, Tak Hang Chan, and Q. Ping Dou
7.1 Introduction 209
7.2 Secondary metabolites of plants 210
7.3 Plant polyphenols and their analogs 211
7.3.1 Classification and bioavailability of plant polyphenols 211
7.3.2 Tea and tea polyphenols 212
7.3.3 Targeting of the tumor proteasome by tea polyphenols 216
7.3.4 EGCG analogs as proteasome inhibitors 217
7.3.4.1 Peracetate and other prodrugs of EGCG 219
7.3.4.2 Fluoro-substituted EGCG analogs 222
7.3.4.3 Para-amino substituent on the D ring 222
7.3.4.4 Bis-galloyl derivatives of EGCG 223
7.3.4.5 Methylation-resistant (-)-EGCG analogs 223
7.3.5 Other molecular targets of tea polyphenols 224
7.3.5.1 AMPK activation 224
7.3.6 Proteasome inhibitory action of other plant polyphenols 225
7.4 Natural polyphenols in reversal of drug resistance 226
7.4.1 Mechanisms of tumor drug resistance 226
7.4.2 The ubiquitin-proteasome pathway in drug resistance 226
7.4.3 EGCG and overcoming drug resistance 227
7.4.4 Genistein and overcoming drug resistance 228
7.4.5 Curcumin and overcoming drug resistance 228
7.4.6 Clinical trials using polyphenols and chemotherapy 229
7.5 Conclusions 231
Acknowledgments 231
References 231
8 Flavonoid Occurrence, Bioavailability, Metabolism, and Protective Effects in Humans: Focus on Flavan-3-ols and Flavonols 239Luca Calani, Margherita Dall'Asta, Renato Bruni, and Daniele Del Rio
8.1 Introduction 240
8.2 Focus on flavan-3-ols and flavonols: chemical structures and dietary sources 240
8.2.1 Flavan-3-ols 240
8.2.2 Flavonols 243
8.3 Metabolism and bioavailability of flavonoids in humans 244
8.3.1 Flavan-3-ols 245
8.3.2 Flavonols 251
8.4 In vitro studies 255
8.4.1 Flavan-3-ols 256
8.4.1.1 Phase II metabolites 256
8.4.1.2 Microbe-derived metabolites 259
8.4.2 Flavonols 260
8.4.2.1 Phase II metabolites 260
8.4.2.2 Microbe-derived metabolites 265
8.5 In vivo studies 266
8.5.1 Cardiovascular and endothelial protection 267
8.5.1.1 Flavan-3-ols 267
8.5.1.2 Flavonols 268
8.5.2 Neuroprotection 269
8.5.2.1 Flavan-3-ols 269
8.5.3 Cancer prevention 269
8.5.3.1 Flavan-3-ols 269
8.5.3.2 Flavonols 270
8.6 Conclusions 271
References 272
9 Inhibition of VEGF Signaling by Polyphenols in Relation to Atherosclerosis and Cardiovascular Disease 281Rebecca L. Edwards and Paul A. Kroon
9.1 Introduction 282
9.2 VEGF and VEGF signaling 282
9.3 VEGF signaling and angiogenesis 286
9.4 Angiogenesis and atherosclerosis 286
9.5 Polyphenols in foods and diets, and their absorption and metabolism 289
9.6 Effects of polyphenols on VEGF signaling, angiogenesis, and atherosclerosis 290
9.6.1 VEGF signaling 314
9.6.2 Angiogenesis 315
9.6.3 Atherosclerosis 315
9.7 Relationships between polyphenol consumption and CVD risk 316
9.7.1 Epidemiological studies 316
9.7.2 Intervention studies 318
9.8 Conclusions 319
Acknowledgments 320
References 320
10 Phenolic Compounds from a Sex-Gender Perspective 327Ilaria Campesi, Annalisa Romani, Maria Marino, and Flavia Franconi
10.1 Introduction 328
10.2 Phenolic compound classification and molecular mechanisms 329
10.3 Sex-gender and the xenokinetics of phenolic compounds 330
10.4 Sex-gender differences in xenodynamics 333
10.5 Conclusions 334
References 334
11 Thermodynamic and Kinetic Processes of Anthocyanins and Related Compounds and their Bio-Inspired Applications 341Fernando Pina
11.1 Introduction 342
11.2 Anthocyanins in aqueous solution 342
11.2.1 Step-by-step procedure for calculating rate and equilibrium constants 349
11.2.1.1 Step 1: determination of the equilibrium constant K'a 349
11.2.1.2 Step 2: determination of the equilibrium constant Ka 349
11.2.1.3 Step 3: determination of the equilibrium constant Kt and the respective rate constants 350
11.2.1.4 Step 4: determination of the hydration rate and equilibrium constants 350
11.2.1.5 Step 5: determination of the isomerization rate and equilibrium constants 350
11.2.1.6 Step 6: verification of the self-consistency of all the data 351
11.3 Influence of anthocyanin self-aggregation on the determination of rate and equilibrium constants 351
11.4 Photochromism: applications bio-inspired in anthocyanins 357
11.4.1 Systems lacking the cis-trans isomerization barrier 357
11.4.2 Systems exhibiting high cis-trans isomerization barriers 361
11.4.2.1 The concept of right-lock-read-unlock-erase optical memories 361
11.4.3 Styryl-1-benzopyrylium (styryl flavylium) and naphthoflavylium 362
11.4.4 Dye-sensitized solar cells based on anthocyanins 362
11.5 How to construct an energy-level diagram 364
11.6 How to calculate the mole-fraction distribution of a network species 367
References 368
12 Synthetic Strategies and Tactics for Catechin and Related Polyphenols 371Ken Ohmori and Keisuke Suzuki
12.1 Introduction 371
12.2 Early synthetic work 375
12.3 Stereoselective approaches to flavan-3-ols 380
12.3.1 Synthesis of catechin-series (= 2,3-trans) derivatives 380
12.3.2 Synthesis of epi-series (= 2,3-cis) catechins 393
12.4 Conclusions 407
Abbreviations 407
Acknowledgments 408
References 408
Index 411
Richard A. Dixon1, M.S. Srinivasa Reddy2, and Lina Gallego-Giraldo1
1Department of Biological Sciences, University of North Texas, Denton, TX, USA
2Forage Genetics International, West Salem, WI, USA
Abstract: Economic and environmental factors favor the adoption of lignocellulosic bioenergy crops for production of liquid transportation fuels. However, lignocellulosic biomass is recalcitrant to saccharification (sugar release from cell walls), and this is, at least in part, due to the presence of the phenylpropanoid-derived cell-wall polymer lignin. A large body of evidence exists documenting the impacts of lignin modification in plants. This technology can lead to improved forage quality and enhanced processing properties for trees (paper pulping) and lignocellulosic energy crops. We here provide a comprehensive review of the literature on lignin modification in plants. The pathway has been targeted through down-regulation of the expression of the enzymes of the monolignol pathway and down-regulation or over-expression of the transcription factors that control lignin biosynthesis and/or programs of secondary cell-wall development. Targeting lignin modification at some steps in the monolignol pathway can result in impairment of plant growth and development, often associated with the triggering of endogenous host-defense mechanisms. Recent studies suggest that it may be possible to decouple negative growth impacts from lignin reduction.
Keywords: monolignol biosynthesis, genetic modification, transcription factor, gene silencing, saccharification
Lignin is a major component of plant secondary cell walls, and the second most abundant plant polymer on the planet. It constitutes about 15–35% of the dry mass of vascular plants (Adler, 1977). Considerable attention has been given over the past several years to the reduction of lignin content in model plant species, forages, trees, and dedicated bioenergy feedstocks. This is because forage digestibility, paper pulping, and liquid fuel production from biomass through fermentation are all affected by recalcitrance of lignocellulose, primarily due to the presence of lignin, which blocks access to the sugar-rich cell-wall polysaccharides cellulose and hemicellulose for enzymes and microorganisms (Pilate et al., 2002; Reddy et al., 2005; Chen & Dixon, 2007).
Much is now known of the biosynthesis of lignin and its control at the transcriptional level. This informs the targets that have been selected for genetic modification of lignin content and composition in transgenic plants. Which gene is down- or up-regulated has a considerable effect on lignin content and composition. Equally, lignin modification can have profound impacts on plant growth and development, ranging from good through bad to “downright ugly,” but these impacts are again strongly target-dependent. Understanding the mechanisms that can impact plant growth—which equate to agronomic performance—in crop species “improved” through lignin modification is critical for economic advancement of the forage and biofuels industries. Although still poorly understood, these mechanisms may also throw light on basic plant developmental and defense processes.
Lignin is an aromatic heteropolymer derived primarily from three hydroxycinnamyl alcohols: 4-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, which give rise, respectively, to the 4-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) subunits of lignin (Freudenberg & Neish, 1968; Ralph et al., 2004). G units are mono-methoxylated, S units are di-methoxylated, and H units are not methoxylated (Fig. 1.1). These monomers are linked through oxidative coupling catalyzed by both peroxidases and laccases (Boudet et al., 1995). Unlike cellulose and other polymers that have labile linkages (e.g. glycosidic or peptide) between their building blocks, the units of lignin are linked by strong ether and carbon–carbon bonds (Sarkanen, 1971). Lignin is present in the secondarily thickened cell walls of plants, where it is critical to cell-wall structural integrity and gives strength to stems (Chabannes et al., 2001b; Jones et al., 2001). Lignin also imparts hydrophobicity to vascular elements for water transport. The lignin content of the mature internodes of stems of alfalfa (Medicago sativa), the world's major forage legume and a target of much of the work to be described in this article, is about 17% of the dry weight (Guo et al., 2001a).
Fig. 1.1 Scheme for monolignol biosynthesis in dicotyledonous angiosperms, including revisions encompassing the different biochemical activities of cinnamoyl-CoA reductase (CCR) forms in Medicago truncatula (Zhou et al., 2010). See text for enzyme abbreviations.
Lignin composition varies among major phyla of vascular plants (Boerjan et al., 2003). Dicotyledonous and monocotyledonous angiosperm lignins contain G and S units as the two major monomer species, with low levels of H units. Monocotyledonous lignins have more H units than dicotyledonous lignins (Baucher et al., 1998), but care must be taken not to attribute other components to H units, as often happens (Boerjan et al., 2003). Fern and gymnosperm lignins have primarily G units and low levels of H units, but S units have been found in cuplet fern, yew plum pine, sandarac-cypress, and a few genera in the Gnetophyta (Weng et al., 2008b). Some lower plants, like Selaginella moellendorfii (Weng et al., 2008a,b) and Marchantia polymorpha, have both G and S units in their lignins (Espineira et al., 2011), despite predating hardwoods/dicots and even softwoods. The apparent presence of H, G, and S units in the lignin from the seaweed Calliarthron cheilosporioides (Martone et al., 2009) may indicate convergent evolution of lignin.
The presence of each methoxyl group on a monolignol unit results in one less reactive site, and therefore fewer available potential coupling combinations during polymerization. Thus, S lignin is more linear and less crosslinked than G/S lignin, and provides a strong yet flexible polymer that is especially advantageous to herbaceous angiosperms (Bonavitz & Chapple, 2010). A correlation has been shown between the degradability of the cell walls in forages and the amount of G lignin, as lignin rich in G units is more highly condensed, making it less amenable to degradation (Jung & Deetz, 1993). Thus, transgenic poplar plants with lignin rich in G units are, like softwoods, more difficult to pulp because of their more condensed lignin (Lapierre et al., 1999).
Lignin content increases with progressive maturity of stems; this relationship has been studied in detail in alfalfa (Jung et al., 1997; Chen et al., 2006), ryegrass (Tu et al., 2010), tall fescue (Buxton & Redfearn, 1997; Chen et al., 2002), and switchgrass (Mann et al., 2009; Shen et al., 2009). Decreasing the lignin content increases the digestibility of alfalfa for ruminant animals (Baucher et al., 1999; Guo et al., 2001a,b; Reddy et al., 2005) and improves processing efficiency for the production of liquid biofuels through saccharification and fermentation (Chen & Dixon, 2007). Lignin composition has also been linked with reduced cell-wall digestibility (Jung & Deetz, 1993). However, the importance of lignin composition for digestibility has been questioned based on the results of studies with synthetic lignins, which show lignin composition per se to have no effect (Grabber et al., 1997).
Plants have primary and secondary cell walls, which differ in both function and composition. Primary walls allow cells to expand and divide, while providing mechanical strength. Once cell growth stops, a much thicker secondary cell wall is deposited in some specialized cell types. These include vessels and fibers in the stem, sclereid cells, endodermal tissue of roots, some cells of anthers and pods important for dehiscence (Zhong & Ye, 2009), and seed coats (Marles et al., 2008; Chen et al., 2012). Generally, secondary cell walls consist of three layers, named S1 (outer), S2 (middle), and S3 (inner). Lignin deposition starts at the cell corners in the region of the middle lamella and the primary wall when S1 formation has started. Most of the lignin is deposited in the S2 layer and impregnates the cellulose and hemicelluloses there (Donaldson, 2001; Boerjan et al., 2003). Based on UV microscopy, the density of lignin is higher in the middle lamella and primary walls than in the secondary walls of secondarily thickened cells, but the secondary walls have more lignin content as they constitute the largest proportion of the total cell wall (Fergus et al., 1969). Usually H units are deposited first during cell-wall formation, followed by G units and then S units (Terashima et al., 1993, 1998; Donaldson, 2001). However, S units have been identified in lignin from corn coleoptiles, indicating that S lignin deposition may also start early in development (Musel et al., 1997). H lignin is believed to determine the shape of the cells by acting as a matrix for deposition of G and S units (Terashima et al., 1998). Vascular cells without H units may be free to expand and assume a round shape. In general, a higher...
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