Chemistry | Biochemistry » Biochemistry and Biosynthesis of Wood Components

Source: http://www.doksinet Biochemistry and Biosynthesis of Wood Components Dr. David S-Y Wang Professor Department of Forestry, NCHU Course Topics • General introduction of wood • Chemical composition of wood • Biosynthesis of cell wall polysaccharides • Phenylpropane derivatives • Lipids synthesis • Isoprenoids synthesis • Formation and development of wood tissues • Formation of earlywood, latewood, and heartwood Source: http://www.doksinet Some familiar uses of woodTrees: as a Amaterial andBiochemical as a Remarkable Bounty 1175 source of other cellulose-derived products Selected miscellaneous uses of woods for artistic and/or functional applications, reflecting various material (wood (a) (b) (c) biopolymer) properties 1176 Trees: A Remarkable Biochemical Bounty (d) (g) (a) (b) (c) (d) (e) (f) (g) (h) (i) (j) (k) (l) (m) (n) (o) (p) (f) (e) (i) (h) (j) (m) (l) (k) (o) (n) (q) (r) (s) (p) Figure 2 Selected miscellaneous uses of

woods for artistic and/or functional applications, reflecting various material (wood biopolymer) properties: Mandolin (a); many musical instruments employ wood from specific species in order to produce particular sounds/tones. Hokkaido bear carving (b) (provenance: near Lake Toya, Japan); Wood-carved fruit assortment (c); An elephant carving of red cedar (Toona ciliata) wood, with a king and carriage (Visakhapatnam, Andhra Pradesh, India) (d); Decorative carvings on choir stall seating in the Mosteiro dos Jeronimos (Lisbon, Portugal) (e and f); Lion carving in the same monastery (g); Close-up of an oak choir stall (fifteenth century) by Jörg Syrlin the Elder, in the Ulm Cathedral, Germany (h); Totem pole in the Canadian Museum of Civilization (Gatineau, Québec, Canada) (i); Wood sculpture in the Chateau de Some familiar uses of wood as a material and as a source of other cellulose-derived products: Wood Vizille for lumber garden (Vizille, France) (j); Artificial flowers made from

wood shavings (k); and a wooden ox-cart drawing logs (l) (Pucón, Chile). Black-faced ibis carvings (m) (Vilları́ca, Chile); Wooden bananas decoration (n) (Brotas, Brazil); Fine furniture examples, composites such as waferboard (b); Wood pallets (c); Aerial photograph of pulp and paper mill (Tembec, such as a Louis XIV commode (o) and a Louis XVI bureau (p). Images from L B Davin, Washington State University (a, c, e–n); ng, Québec, Canada), with the light-colored wood chip piles in the center of the image used as raw material H. Moore, Washington State University (b and d); LG Antique Restoration, Los Angeles, CA, USA (http://ifixantiquescom with permission) (o); and French Accents Antiques (http://www.faccentscom, with permission) (p) s wound into large rolls (which can weigh up to !25 tons), with this resulting from processing wood chips to make pressing the same to remove water and drying pulp (e); Selected pulp and paper products (toiletries/paper towels, ues, packaging

(e.g, egg and cardboard boxes, paper tissues) (f); books (i); newsprint (not shown), and so on xamples of wood products in building construction, such as a typical ‘chalet’ in the Alps, France (g); the Golden Kyoto, Japan (j); and the main gate of the Kanda Shrine in Tokyo, Japan (n); Pencils (m); toys (o, p); boats (q); utility nd cooking/eating utensils (s); A forested hillside in British Columbia, Canada (h); and in the Lake District of Chile rvested timber temporarily piled (l); Images from L. B Davin, Washington State University (a, c, f–s); http:// oodnews.com (b); M G Paice, Pulp and Paper Institute of Canada, Pointe Claire, Québec, Canada (d); and ks, North Melbourne, Victoria, Australia (http://www.forestworkscomau), with permission (e) Trees: A Remarkable Biochemical Bounty Rubber trees (Hevea brasiliensis) 1177 tapped for latex (a) (c) (b) (d) (e) (f) (g) Figure 3 Rubber trees (Hevea brasiliensis) (a) are tapped for latex (b) that is used for rubber

production. Selected rubber products include tires (c), pencil erasers (d), boots (e), latex gloves (f), and rubber bands (g). Images from D Nandris; H. Chrestin, Institut de Recherche pour le Development (IRD), Mahidol University, Bangkok, Thailand (a and b), and L B Source: http://www.doksinet 1178 Trees: A Remarkable Biochemical Bounty Lacquer tree (Rhus vernicifera) (a) (b) (c) Urushi (d) (f) (e) (g) (h) Figure 4 Lacquer tree, objects of art and Russian lacquer boxes. The lacquer tree (Rhus vernicifera) (a and b) is the source of urushi (c), used to make objects of art such as in d, e, and g. The most sought after Russian lacquer boxes (f and h) originate from four villages – Palekh, Fedoskino, Kholui, and Mstera. Items in (f) are from Fedoskino, whereas that in (h) is from Palekh They are made of ‘papier mâché’ painted with several coats of black lacquer on the outside and red lacquer on the inside. Extremely fine brushes are used to create the fine lines

and details in each painting. Finally, when the painting is finished a layer of transparent lacquer is applied. Altogether, this can take several months to complete Images from S Ross, Urushi Artist, Japan (a–c, e, and g), and L. B Davin, Washington State University (d, f, and h) 3.272 Evolution of the Woody Growth Habit: Land Colonization and Adaptation Trees: A Remarkable Biochemical Bounty (a) (c) 1179 Present-day trees or tree forms are classified under ferns, gymnosperms, and angiosperms, although only the latter two groups produce wood from a cambium. The total number of extant arborescent species is currently (b) difficult to precisely establish because of variations in definitions used.3 Nevertheless, !100 000 are thought to 3,5 Of the 100 000 or be in existence globally, this representing up to 25% of all plant species. Acacia senegal (a,sob)tree is species, the source however, there are less than 1000 that are gymnosperms; the bulk are the angiosperms.6 (Named from the

ancient Greek, gymnosperm, meaning naked seed, refers to plants with of seeds thatarabic are borne(c). externally, on a gum Some asselected scale or similar structure, whereas angiosperm refers to those with vessel seed, indicating the carpel in which the seed develops.7) The enormous breadth of the topic of tree resources alone limits any substantial discussion uses of gum Arabic: as an of shrubs, bushes, and lianas (woody vines), even though they can have a woody growth habit. Plants apparently first emerged on land from their forerunner algal ancestors during the mid-Ordovician ingredient in soft drinks, candies, period, some 460 Mya.8,9 Over this lengthy evolutionary period, numerous truly remarkable innovations and adaptations occurred that eventually led to our familiar tree forms. This ultimately afforded the 350 000 or so lossshapes, compositions distinct plant species in existence today, and thus the fantastic diversity in weight terms of plant sizes, habitats,(e.g, and

associated phytochemical constituents. In achieving this colonization of land, some of the remarkable evolutionary (d) Slim Fast), and so Gum arabic changes manifested over the passage of time included, among others: generation of specialized cellon. types, such as lignified (reinforced) secondary cell walls and vascular tissues; formation of protective wood and bark tissues, and other specialized cell types within; the ability to continuously orient/reorient massive canopies; is also usedphotosynthetic as a binder (e) for watercolor paint (f) as it dissolves (e) (f) (g) (h) readily in water. It is also used in shoe polish (g), and as a wettable adhesive, such as in postage stamps (h). mages from D. Lesueur, CIRAD, Tropical Soil Biology and Fertility Institute of CIAT, World Agroforestry Centre, Nairobi, Source: http://www.doksinet a (a–c), L. B Davin (d and h), and H Moore (e–g) Washington State University (a) (b) (d) (c) (f) (e) re 6 Maple trees (Acer saccharum) and

maple syrup. Trees are tapped annually for their sap in early spring before buds ge (a), Maple with saptrees collection (b and c) and largeand amounts of sap then Trees processed to produce syrup of (Acer saccharum) maple syrup. are(d) tapped annually fordifferent their grades (e, f). trees are tapped once annually (some twice), with each tap yielding !80 l of sap which is then concentrated to !1.5 l Images sap in earlyFamily spring before buds emerge collection (bWashington and c) andState large B. Putnam, Putnam Farm, Cambridge, Vermont,(a), USAwith (a–d,sap f), and L. B Davin, University (e). amounts of sap then processed (d) to produce syrup of different grades (e, f). Most A Remarkable Biochemical Bounty trees are tapped once annually (some twice), with each tap yielding around 80 L of sap which is then concentrated to around 1.5 L (b) (c) 1180 Trees: A Remarkable Biochemical Bounty (a) 1180 (b) (c) Trees: A Remarkable Biochemical Bounty -derived amber (fossilized resin)

and jewelry. Amber is found in extensive deposits in different parts of the y Chironomidae) in amber (a). Amber is used in the making of jewelry, for example, necklace (b) and earrings (a) (b) (c) Figure 7 H. Tree-derived amber (fossilized resin) and jewelry. Amber is found in extensive deposits in different parts of the men from Professor R. S Zack, Washington State University Images from Moore, Washington State world: Fly (family Chironomidae) in amber (a). Amber is used in the making of jewelry, for example, necklace (b) and earrings d Amber Goods – Amber Jewelry (http://www.ambergoodsie), with permission (b, c) (c). Amber specimen from Professor R S Zack, Washington State University Images from H Moore, Washington State University (a) and Amber Goods – Amber Jewelry (http://www.ambergoodsie), with permission (b, c) Cinnamon (Cinnamomum verum) 0 Trees: A Remarkable Biochemical Bounty Tree-derived amber (fossilized resin) and jewelry (a) (b) (a) (b) (a) (c) (b) Figure

7 Tree-derived amber (fossilized resin) and jewelry. Amber is found in extensive deposits in different parts of the world: Fly (family Chironomidae) in amber (a). Amber is used in the making of jewelry, for example, necklace (b) and earrings (c). Amber specimen from Professor R S Zack, Washington State University Images from H Moore, Washington State University (a) and Amber Goods – Amber Jewelry (http://www.ambergoodsie), with permission (b, c) (c) (d) Cloves (b) (Syzygium aromaticum) ure 7 Tree-derived (c) amber (fossilized resin) and jewelry. (d) Amber is found in extensive deposits in different parts of the (a) d: Fly (family Chironomidae) in amber (a). Amber is used in the making of jewelry, for example, necklace (b) and earrings Amber specimen from Professor R. S Zack, Washington State University Images from H Moore, Washington State versity (a) and Amber Goods – Amber Jewelry (http://www.ambergoodsie), with permission (b, c) (a) (b) Cocoa beans (Theobroma cacao) (e)

(f) (c) (e) Nutmeg (Myristica (f) fragrans) (c) (g) (d) (g) (d) Figure 8 Selected examples of common spices from tree species: Cinnamon (Cinnamomum verum; a), cloves (Syzygium (e) aromaticum; b), nutmeg (Myristica fragrans;(f)c), and bay leaves (Laurus nobilis; d). Cocoa (g) beans (Theobroma cacao; e–f) can be processed into chocolate (g) and other products. Images from H Moore, Washington State University (a–d), Consulat de Bay leaves São Tomé & Principe, Marseille, France (e, f) and L. B Davin, Washington State University (g). (Laurus nobilis) elaboration of verum; a plethora often species-specific cted examples(e) of common spices from tree species: Cinnamon (Cinnamomum a),ofcloves (Syzygium distinct biochemical pathways leading to, for example, chemical (f) (g) defensebeans systems; evolution ofcacao; distincte–f) plant pollination/reproductive strategies and adaptations, and a myriad of nutmeg (Myristica fragrans; c), and bay leaves (Laurus nobilis; d).

Cocoa (Theobroma can relatedState regulatory processes at the genomic/proteomic and metabolic levels. to chocolate (g) and other products. Images from H Moore, Washington University (a–d), Consulat de ncipe, Marseille, France (e, f) and L. B Davin, Washington State University (g) Trees: A Remarkable Biochemical Bounty Source: http://www.doksinet Edward M. Rubin1,2 (a) 1181 (b) The development of alternatives to fossil fuels as an energy source is an urgent global priority. Cellulosic bi Phytochemical treasures: T. brevifolia (a) potential to contribute to meeting the demand for liquid fuel, but land-use requirements and process inefficien C. acuminata (b) accumulate the Camptotheca hurdles for large-scale deployment of biomass-to-biofueland technologies. Genomic information gathered from acuminata Taxus brevifolia biosphere, including potential energy crops and microorganisms able to break down biomass, will be vital for (1) Taxol (2) Camptothecin cancer chemotherapeutics,

taxol (1) and prospects of significant cellulosic biofuel production. O Me O NH O O O OH O O O OH H HO O O O N O O OH O (c) T H C N Me camptothecin (2), respectively. Cinchona (d) spp. (eg, Cinchona calisaya) (c) and S CH he capture of solar energy through photosynthesis is a proexpensive. However, the recent and pressing desire alba (d) natives are sources of the medicinals cess that enables the storage of energy in the form of cell wall to fossil fuels has made the rapid improve polymers (that is, cellulose, hemicellulose and lignin). The production a high acid priority, (4) Acetylsalicylic acid quinine (3) and acetylsalicylic (4). Thein which biologically Cinchona officinalis Salix alba in these polymers can be accessed in a variety (‘bioenergy’)-relevant genomic insights and resour (3) Quinineenergy stored bark medicinal compound,role camphor (5),1). used of ways, ranging from simple burning to complex bioconversion important (Table (f) (e)

processes. The high energy content and portability of biologically as a cough suppressant, is derived from Azadirachtin A derived fuels, and their significant compatibility (6)with existing petBiomass Cinnamomum camphora (e). The neem roleum-based transportation infrastructure, helps to explain their From the perspective of transportation fuels, plants attractiveness as a fuel source. Despite the increasing use of biofuels tree (A. solar indica;energy f) harbors the insecticide, collectors and thermochemical energy s such as biodiesel and sugar- or starch-based ethanol, evidence sug(5) Camphor is the storage of energy Azadirachta gests that transportation fuels based on lignocellulosic biomass repazadirachtin A (6). Poisons, such as in a form that can later indica 1 thermochemical or enzymatic conversion that distin resent the most scalable alternative fuel source . Lignocellulosic strychnine (7) other and cyanogenic compounds, from renewable energy sources. Cellulosic bio (g) (h)

biomass in the form of plant materials (for example, grasses, wood referred to as lignocellulosic biomass, is an abun and crop residues) offers the possibility of a renewable, geograph(8)R-Amygdalin (R)-amygdalin (8), (R)-prunasin (9), are resource that can be used for the production of a ically distributed and relatively greenhouse-gas-favourable source of Strychnos 3 the almond tree Nux-vomica from S. Nuxvomica (f) and portation fuels . The three main components of l sugars that can be converted to ethanol and other liquid fuels. cellulose, hemicellulose and lignin (Fig. 2), with the Prunus (7) Strychnine Calculations of the productivity of lignocellulosic feedstocks, in part P. dulcis (g), respectively dulcis tions of the three dependent on the material sourc based on their ability to grow on marginal agricultural land, indicates (9) R-Prunasin main structural component of plant cell walls, is that they can probably have a large impact on transportation needs Figure 9 Phytochemical

treasures: T. brevifolia (a) and C acuminata (b) accumulate the cancer chemotherapeutics, taxol (1) glucose molecules, linked to one another primar without significantly compromising the land needed for food crop and camptothecin (2), respectively. Cinchona spp (eg, Cinchona calisaya) (c) and S alba (d) are sources of the medicinals quinineproduction (3) and acetylsalicylic2.acid (4) The medicinal compound, camphor (5), used as a cough suppressant, is derived from bonds5. Hemicellulose, the second most abundan Cinnamomum camphora (e). The neem tree (A indica; f) harbors the insecticide, azadirachtin A (6) Poisons, such as strychnine lignocellulosic biomass, is not a chemically well de (7) and cyanogenic compounds, (R)-amygdalin (8), (R)-prunasin (9), are from S.involves Nux-vomica (f) and the almond treeof P. dulcis (g), Lignocellulosic biofuel production collection biomass, respectively. Images from R E B Ketchum, Washington State University (a), J Manhart, Department of Biology,

Texas A&M but rather a family of polysaccharides, composed of University, College Station, TX (b), The Plants, Kyoto Pharmaceutical University, Kyoto, Japan (c), A. M(predeconstruction ofGarden cellof Medicinal wall polymers into component sugars Patten, Washington State University (d), L. B Davin, Washington State University (e), Cal Lemke, University of Oklahoma, 6-carbon monosaccharide units, that links cellu treatment and Pflanzen, saccharification), and conversion of the sugars to Norman, OK (f), Köhler’s Medizinal 1887 (g), R. Sanchez-Perez; F. Dicenta, CSIC-CEBAS, Murcia, Spain (h). microfibrils and cross-links with lignin, creating a c biofuels (fermentation) (Fig. 1) Partially because of the historically of bonds that provide structural strength5. Finally low demand for biologically based transportation fuels, each step in dimensional polymer of phenylpropanoid units, ca this process is in the early stages of optimization for efficiency and as the cellular glue

providing the plant tissue and the throughput. The crops from which biomass is currently derived have Biology of Bioconversion of Solar into Biofuels with compressive strength and the cell wall with stiff not been domesticated for this particular purpose and theEnergy present to providing resistance to insects and pathogens. methods for saccharification and fermentation are inefficient and H O OH O H N HO O H MeO N HO O H O O O OM e H HO OH O H O O O H O M eO O O O OH O HO N HO OH H N O H H O OH HO HO O HO HO O O OH O O OH N N Physical pre-treatment, chemicals and enzymes Fuel-producing microorganisms Solar energy Biofuels Feedstock Figure 1 | Biology of solar energy in energy is collecte photosynthesis an lignocellulose. De the cellulosic mat and 6-carbon sug physical and chem treatment, follow enzymes from bio organisms. The s be subsequently c fuels by microorg Sugars 1 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut

Creek, California 94598, USA. 2Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, C Solar energy is collected by plants via photosynthesis and stored as lignocellulose. Limited. All rights reserved Decomposition of the cellulosic material2008 into Macmillan simple 5-Publishers and 6-carbon sugars is achieved by physical and chemical pretreatment, followed by exposure to enzymes from biomassdegrading organisms. The simple sugars can be subsequently converted into fuels by microorganisms. Source: http://www.doksinet NATUREjVol 454j14 August 2008 REVIEWS Structure of lignocellulose OH OH OH O O O OH OH OH p-Coumaryl alcohol Coniferyl alcohol H Sinapyl alcohol G S Macrofibril Plant Plant cell Macrofibril Lignin Cell wall Lignin 10–20 nm Hemicellulose Pentose Hexose n-3 Crystalline cellulose n-3 n-3 n-3 Glucose Cellodextrin n-3 Hydrogen bond Figure 2 | Structure of lignocellulose. The main component of lignocellulose is cellulose, a

b(1–4)-linked chain of glucose molecules. Hydrogen bonds between different layers of the polysaccharides contribute to the resistance of crystalline cellulose to degradation. Hemicellulose, the second most abundant component of lignocellulose, is composed of various 5- and 6-carbon sugars such as arabinose, galactose, glucose, mannose and xylose. Lignin is composed of three major phenolic components, namely p-coumaryl alcohol (H), coniferyl alcohol (G) and sinapyl alcohol (S). Lignin is synthesized by polymerization of these components and their ratio within the polymer varies between different plants, wood tissues and cell wall layers. Cellulose, hemicellulose and lignin form structures called microfibrils, which are organized into macrofibrils that mediate structural stability in the plant cell wall. compared to that of teosinte. Some of the most rapid increases have occurred in the past 40 years, both from advances in agronomic practices and, importantly, from the application of

modern genetics. The optimization of bioenergy crops as feedstocks for transportation fuels is in its infancy, but already genomic information and resources are being developed that will be essential for accelerating their domestication. Many of the traits targeted for optimization in potential cellulosic energy crops are those that would improve growth on poor agricultural lands, to minimize competition with food crops over land use. Populus trichocarpa (poplar), the first tree and potential bioenergy crop to have its genome sequenced (Table 1)9, illustrates some of the issues and potential of applying genomics to the challenge of optimizing energy crops. The traits for which the genetic underpinnings will be sought in the genomes of bioenergy-relevant plants, such as poplar, include those affecting growth rates, response to competition for light, branching habit, stem thickness and cell wall chemistry. Significant effort will go into maximizing biomass yield per unit land area,

because this more than any other factor will minimize the impact on overall land use. One can imagine trees optimized to have short stature to increase light access and enable dense growth, large stem diameter, and reduced branch count to maximize energy density for transport and processing. Trees have evolved with highly rigid and stable cell walls due to heavy selective pressure for long life and an upright habit. Plants domesticated for energy production, with a crop cycle time of only a few years, would have less need for a rigid cell wall than wild plants with lifetimes of a hundred years or more. Alterations in the ratios and structures of the various macromolecules forming the cell wall are a major target in energy crop domestication to facilitate post-harvest deconstruction at the cost of a less rigid plant. Already, by comparing several of the presently available plant genomes (poplar9, rice10,11, Arabidopsis12; see Table 1) coupled with largescale plant gene function and

expression studies, a number of candidate genes for domestication traits have been identified13,14. These include many genes involved in cellulose and hemicellulose synthesis as well as those believed to influence various morphological growth characteristics such as height, branch number and stem thickness15. In addition to homology-based strategies, other genome-enabled strategies for identifying domestication candidate genes are being used. These include quantitative trait analysis of natural variation and genome-wide mutagenesis coupled with phenotypic screens for traits such as recalcitrance to sugar release, acid digestibility and general cell wall composition. The availability of high-throughput transgenesis in several plant systems16 will facilitate functional studies to determine the in vivo activities of the large number of domestication candidate genes. Using these strategies, genes affecting features such as plant height, stem elongation and trunk radial growth, drought

tolerance, and cell wall stability are but a few of the features that are likely to be identified as targets for domestication n How do trees (plants) synthesis ”Natural Products”? n Why do plants synthesis them? 843 2008 Macmillan Publishers Limited. All rights reserved Source: http://www.doksinet Our Understanding of How Wood Develops Is Not Complete n With a few exceptions, very little is known about the cellular, molecular, and developmental processes that underlie wood formation. n Xylogenesis represents an example of cell differentiation in an exceptionally complex form. Xylogenesis n The formation of wood. n Controlled by a wide variety of factors both exogenous (photoperiod and temperature) and endogenous (phytohormones) and by interaction between them. f Woody Plants Major groups of endogenous plant hormones Indole-3-acetic acid (IAA) Gibberellin Cytokinins trans-Zeatin FIGURE 3.16 Seasonal changes in cambial activity of pear trees

From Evert (1960). Originally published by the University of Seasonal changes of pear trees California Press; reprintedin bycambial permissionactivity of the Regents of the University of California. Benzylaminopurine CH2=CH2 Abscisic acid (ABA) Source: http://www.doksinet Xylogenesis n tion, a new amplification technique was developed, allowing RNA to be isolated from submilligram amounts of tissues to generate probes for microarray analysis [6!]. Since then, a further generation of microarray slides has been produced with over 13 500 features representing 33 000 ESTs; a further generation is planned to accommodate over 20 000 features derived from 100 000 sequenced ESTs. ever, without further advances in sequencing and bioinformatics, it seems unlikely that we will obtain genomic information from any gymnosperm in the near future. This is because gymnosperms have a massive genome with haploid DNA contents of, on average, 15 500 Mbp [7], as compared with 125 Mbp for

Arabidopsis [8] and 550 Mbp for poplar [9]. Genomic sequencing Genetic maps of varying quality have been generated for several forest tree species, using a variety of approaches. QTLs have been identified for a range of traits, such as wood density, fibre length and resistance [10–13,14!!,15]. However, the gains from QTL mapping for breeding purposes have been severely restricted by the great difficulties in identifying the gene (or genes) located at the QTL. There are two reasons for these difficulties Firstly, the long time to flowering hampers repeated It is driven by the coordinated expression of numerous structural genes Genetic mapping involved in cell origination, differentiation, programmed cell death, and Although EST sequencing is a cheap and quick way to identify expressed genes, we also need to know the complete genomic sequence of one or more tree species. The genomic sequence is necessary for several reasons. Firstly, it is highly unlikely that all the genes of any

tree will be identified by EST sequencing alone. Secondly, even if there are several hundred genes unique to trees, it would be extremely useful to identify their individual heartwood (HW) formation and by virtually unknown regulatory genes orchestrating this ordered developmental sequence. Figure 1 Review TRENDS in Plant Science Vol.12 No2 65 Current Opinion in Biotechnology Conifers (left-hand side) exhibit many aspects of unique biology, but genomics. By contrast, Conifers (left-hand side) exhibit many aspects of unique biology, but unfortunately are not practical as models in functional Arabidopsis (right-hand side)unfortunately and poplar (centre) are not two model systems in combination, providegenomics. an excellent platform for functional are practical as that, models in functional By genomics studies of ‘tree’-related biology. These systems can also be used for research to follow up observations made in conifer systems, as both contrast, Arabidopsis (right-hand

side) and poplar (centre) are two poplar and Arabidopsis have secondary growth as exemplified by the cross-sections. model systems that, in combination, provide an excellent platform for functional genomics studies of ʻtreeʼ-related biology. These systems Current Opinion in Biotechnology 2003, 14:206–213 can also be used for research to follow up observations made in conifer systems, as both poplar and Arabidopsis have secondary Wood formation from procambium and vascular cambium. (a) Schematic model of xylem (wood) formation Procambial cells and daughter cells produced by nitials differentiate into phloem cells and xylem (wood) cells. Xylem (wood) cells include tracheary elements and fibres Tracheids and vessels are constituents of growth as exemplified by the cross-sections. Wood formation from procambium and vascular cambium www.current-opinioncom y elements. Two types of vessels are observed in angiosperms: protoxylem vessels that commonly have annular and spiral secondary

wall thickenings and m vessels that usually have reticulate and pitted thickenings. (b) Cross-section of a poplar stem (c) Cross-section of an Arabidopsis hypocotyl (d) Tracheary s induced in the Arabidopsis xylogenic culture. (e) Vessel elements transdifferentiated from the cortex cells of Arabidopsis roots overexpressing the VND7 protein abidopsis undergoes secondary growth in roots, otyls and stems. Routine removal of inflorescence induces secondary xylem at the root–hypocotyl junc18,19], which is used for generating ESTs [20]. Arasis plants grown under a combination of short- and ay conditions can also produce extensive secondary in hypocotyls and inflorescence stems [21–23]. The dary xylem tissues induced artificially in Arabidopsis otyls and stems are remarkably similar to those of oplar tree [18,19,21,23] (Figure 1b,c). In addition, dopsis inflorescence stems develop interfascicular ells with thick secondary walls when internodes of ems cease to elongate. Recently, a new in

vitro nic system was established in which Arabidopsis nsion cells were induced to differentiate into ary elements by culturing in the presence of brassi[24,25] (Figure 1d). e cDNA clones that were sequenced for EST analysis used for comprehensive transcriptional profiling by microarrays (or macroarrays) in loblolly pine [3,26], locust [9,27], Eucalyptus [10,28], poplar [29–31] and [15,17]. In addition to the cDNA microarray analysis, methods such as serial analysis of gene expression cDNA-amplified fragment length polymorphism ,34] and differential display [35], have been successdopted for transcriptional profiling during wood forn. Genome-wide expression profiling using Affymetrix Chip array ATH1, which represents !23 750 Arabigenes [36], was carried out with wood-forming Arais tissues and organs [22,23,37,38], as well as with ntiating tracheary elements in the in vitro xylogenic culture [24]. Moreover, laser microdissection [39,40] and fluorescence-activated cell sorting analysis

have proven, in combination with microarray analysis, to be useful tools for global gene expression profiling in specific cell types [41]. These analyses have uncovered several genes whose expression was changed significantly during wood formation (Table 1), including genes encoding cell wall structural proteins and various enzymes associated with the biosynthesis of secondary cell wall polysaccharides (e.g cellulose), the degradation and modification of primary cell walls, the biosynthesis of lignin precursors, the polymerization of lignin in secondary walls, and programmed cell death [14,42]. Because the expression of these genes is highly coordinated, it is expected that specific transcription factors might regulate their expression in a coordinated fashion. Indeed, transcriptional profiling indicates that many genes encoding transcription factors are expressed preferentially during wood formation in various plant species (Table 1). WOOD BIOSYNTHESIS Transcription factors

regulating wood formation The characterization of Arabidopsis mutants with defects in vascular development, and reverse genetic analysis of vascular tissue-related genes revealed by transcriptional profiling has furthered our knowledge of transcriptional regulation during wood formation [14,43–45]. As a result, several classes of transcription factors involved in wood formation have come under the spotlight. n Cell division n Cell expansion (elongation and radial enlargement) n Cell wall thickening (involving cellulose, hemicellulose, cell AUX/IAAs and auxin response factors Mutation of the MONOPTEROS/AUXIN RESPONSE FACTOR 5 (MP/ARF5) gene, which encodes a transcription ncedirect.com wall proteins, and lignin biosynthesis and deposition) n Programmed cell death n HW formation. Source: http://www.doksinet Wood Cells Originate from Vascular Cambium Activity n The vascular cambium is a secondary meristem derived from the procambium, which in turn

develops from the apical meristem. n The cambium plays a major role in the diametral growth of gymnosperm and angiosperm shoots and roots and is of great significance, particularly in respect to the wood that is produced. n Cambial activity ensures the perennial life of trees through the regular renewing of functional xylem and phloem. Drawing of a transverse section of the cambial zone of maritime pine (Pinus pinaster) showing the fusiform (F) and ray (R) initial cells in the cambial zone (CZ). X, Centripetal xylem differentiation with radially enlarging, maturing, and mature xylem. P, Centrifugal phloem differentiation with radially enlarging, maturing, and mature phloem. Empty arrowhead indicates a newly deposited radial wall. Full arrowhead indicates a newly deposited tangential wall. Source: http://www.doksinet Three-dimensional scheme of maritime pine wood showing the relatively homogeneous structure of conifer xylem. Ninety percent of the wood is made of tracheids,

and the remainder is composed of ray parenchyma and longitudinal parenchyma cells, as well as resin ducts in certain species. Sap water ascends via the xylem and nutritive sap descends via the phloem. Sap can also be transported radially via the ray cells and tangentially by bordered pits. It is important to note the different direction and faces which are needed to describe wood structure: transverse, radial, and tangential sections. The Differentiation of Xylem Cells Involves Four Major Steps n Cell expansion n Deposition of a thick multilayered secondary cell wall n Lignification n Cell death Source: http://www.doksinet n Derivative cells expand longitudinally and radically to reach their final size during the formation of the primary wall. Xyloglucan endotransglycosylases, endoglucanases, expansins, pectin methyl esterases, and pectinases are among the primary determinants of this process. n Once expansion is completed, the formation of the

secondary cell wall begins, driven by the coordinated expression of numerous genes specifically involved in the biosynthesis and assembly of four major compounds: polysaccharides (cellulose, hemicelluloses), lignins, cell wall proteins and other minor soluble (stilbenes, flavonoids, tannins, and terpenoids), and insoluble (pectins and cell wall proteins) compounds in a neutral solvent. n Between 40% and 50% of wood consists of cellulose. The fundamental structure units are the microfibrils (MFs), which are the result of a strong association of inter- and intrachain hydrogen bonds between the different chains of β-linked Glc residuesin a manner so precise that microfibrillar cellulose is largely crystalline. n A first breakthrough had been the identification of genes encoding the catalytic subunit of the cellulose synthase (Ces) complex. In Arabidopsis, at least six genes encode putative catalytic subunits of Ces. In addition, a large gene family of over 20 more distantly

related genes, so-called Ces-like (Csl) genes, exists, whose gene products most likely are involved in the synthesis of other polysaccharides. Source: http://www.doksinet n In higher plants, the substrate for Ces (UDP-d-Glc) is provided by Suc synthase. The complex Ces/Suc synthase is thought to have a cytoplasmic localization and the growing cellulose chain may be secreted through the membrane via a pore. n Cortical microtubules (mainly composed of α- and β - tubulin) may determine the wall pattern by defining the position and orientation of cellulose MFs during the differentiation of conducting elements, probably by guiding the movement of the cellulose-synthesizing complex in the plasma membrane. n However, although in many cases co-orientation of microtubules and MFs were observed, mathematical models relying on the geometry of the cell, have been proposed to challenge this dogma. n The water-insoluble cellulose MFs are associated with mixtures of soluble

noncellulosic polysaccharides, the hemicelluloses, which account for about 25% of the dry weight of wood. n They generally occur as heteropolymer such as glucomannan, galactoglucomannan, arabinogalactan, and glucuronoxylan, or as a homopolymer like galactan, arabinan, and β-1,3- glucan. n The biosynthesis of these polysaccharides occurs in the Golgi apparatus by a process that can be divided into two main steps: the synthesis of the backbone by polysaccharide synthases, and the addition of side chain residues in reactions catalyzed by a variety of glycosyltransferases. Source: http://www.doksinet n The third major component of wood (25%–35%) is lignin, a phenolic polymer derived from three hydroxycinnamyl alcohols (monolignols): pcoumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, giving rise to H, G, and S units, which differ from each other only by their degree of methoxylation. n Lignin embeds the polysaccharide matrix giving rigidity and cohesiveness

to the wood tissue as a whole, and providing the hydrophobic surface needed for the transport of water. Lignin content and monomeric composition vary widely among different taxa, individuals, tissues, cell types, and cell wall layers. n Lignin biosynthesis has been the most studied pathway, resulting in the cloning of several structural genes. n However, it is somewhat surprising that recent attempts at engineering lignin biosynthesis have demonstrated that our current models of the pathway are incomplete. Source: http://www.doksinet n Cell wall proteins and pectins are among the other minor compounds of the cell wall. Although different proteins are present in the cell wall at different times during development, the amount of protein remaining in the wood is small. n Nevertheless, such proteins could play important roles determining the composition and morphology of xylem cell walls. Abundant cell wall associated proteins have been found in many plants and have

traditionally been classified into four main groups: Gly-rich proteins, Prorich proteins, arabinogalactan proteins, and Hyp-rich glycoproteins (or extensins). These proteins are cross-linked into the cell wall and probably have structural functions. n Pectins are thought to play a fundamental role in the regulation of cell wall extensibility. They are also thought to be exported from the Golgi apparatus as highly esterified galacturonan and then de-esterified by cell wall bound pectin methylesterases, thus allowing the formation of intermolecular bonds through calcium ions. Source: http://www.doksinet n Pectin ¨ A mixture of polymers from sugar acids, such as D-galacturonic acid, which are connected by (α1,4) glycosidic links. ¨ Some ¨ The of the carboxyl groups are esterified by methyl groups. free carbonyl groups of adjacent chains are linked by Ca and Mg ion. ¨ Preparing n jellies and jams. When lignification is completed, conducting xylem

elements undergo programmed cell death, involving cell-autonomous, active, and ordered suicide, in which specific hydrolases (Cys and Ser proteases, nucleases, and RNase) are recruited. n Several factors (auxins, cytokinins, and Suc) prepare the cell to die by determining the profile of hydrolases synthesized by the cell. These hydrolases are inactive in the vacuole. By a signal that remains unknown, a calcium flux provokes the vacuoles to collapse with the release of hydrolases that degrade all of the cellular content but not the secondary cell wall