KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Nature’s hierarchical materials

Lignins are complex natural polymers resulting from oxidative coupling of, primarily, 4-hydroxyphenylpropanoids. An understanding of their nature is evolving as a result of detailed structural studies, recently aided by the availability of lignin-biosynthetic-pathway mutants and transgenics. The currently accepted theory is that the lignin polymer is formed by combinatorial-like phenolic coupling reactions, via radicals generated by peroxidase-H2O2, under simple chemical control where monolignols react endwise with the growing polymer. As a result, the actual structure of the lignin macromolecule is not absolutely defined or determined. The ``randomness'' of linkage generation (which is not truly statistically random but governed, as is any chemical reaction, by the supply of reactants, the matrix, etc.) and the astronomical number of possible isomers of even a simple polymer structure, suggest a low probability of two lignin macromolecules being identical. A recent challenge to the currently accepted theory of chemically controlled lignification, attempting to bring lignin into line with more organized biopolymers such as proteins, is logically inconsistent with the most basic details of lignin structure. Lignins may derive in part from monomers and conjugates other than the three primary monolignols (p-coumaryl, coniferyl, and sinapyl alcohols). The plasticity of the combinatorial polymerization reactions allows monomer substitution and significant variations in final structure which, in many cases, the plant appears to tolerate. As such, lignification is seen as a marvelously evolved process allowing plants considerable flexibility in dealing with various environmental stresses, and conferring on them a striking ability to remain viable even when humans or nature alter ``required'' lignin-biosynthetic-pathway genes/enzymes. The malleability offers significant opportunities to engineer the structures of lignins beyond the limits explored to date.

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Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids

L-tryptophan, L-phenylalanine, and L-tyrosine are aromatic amino acids (AAAs) that are used for the synthesis of proteins and that in plants also serve as precursors of numerous natural products, such as pigments, alkaloids, hormones, and cell wall components. All three AAAs are derived from the shikimate pathway, to which ≥30% of photosynthetically fixed carbon is directed in vascular plants. Because their biosynthetic pathways have been lost in animal lineages, the AAAs are essential components of the diets of humans, and the enzymes required for their synthesis have been targeted for the development of herbicides. This review highlights recent molecular identification of enzymes of the pathway and summarizes the pathway organization and the transcriptional/posttranscriptional regulation of the AAA biosynthetic network. It also identifies the current limited knowledge of the subcellular compartmentalization and the metabolite transport involved in the plant AAA pathways and discusses metabolic engineering efforts aimed at improving production of the AAA-derived plant natural products.

The shikimate pathway and aromatic amino acid biosynthesis in plants.

SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) is a master transcriptional switch activating the developmental program of secondary wall biosynthesis. Here, we demonstrate that a battery of SND1-regulated transcription factors is required for normal secondary wall biosynthesis in Arabidopsis thaliana. The expression of 11 SND1-regulated transcription factors, namely, SND2, SND3, MYB103, MYB85, MYB52, MYB54, MYB69, MYB42, MYB43, MYB20, and KNAT7 (a Knotted1-like homeodomain protein), was developmentally associated with cells undergoing secondary wall thickening. Of these, dominant repression of SND2, SND3, MYB103, MYB85, MYB52, MYB54, and KNAT7 significantly reduced secondary wall thickening in fiber cells. Overexpression of SND2, SND3, and MYB103 increased secondary wall thickening in fibers, and overexpression of MYB85 led to ectopic deposition of lignin in epidermal and cortical cells in stems. Furthermore, SND2, SND3, MYB103, MYB85, MYB52, and MYB54 were able to induce secondary wall biosynthetic genes. Direct target analysis using the estrogen-inducible system revealed that MYB46, SND3, MYB103, and KNAT7 were direct targets of SND1 and also of its close homologs, NST1, NST2, and vessel-specific VND6 and VND7. Together, these results demonstrate that a transcriptional network consisting of SND1 and its downstream targets is involved in regulating secondary wall biosynthesis in fibers and that NST1, NST2, VND6, and VND7 are functional homologs of SND1 that regulate the same downstream targets in different cell types.

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A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.

Wood is formed by the successive addition of secondary xylem, which consists of cells with a conspicuously thickened secondary wall composed mainly of lignin and cellulose. Several genes involved in lignin and cellulose biosynthesis have been characterized, but the factors that regulate the formation of secondary walls in woody tissues remain to be identified. In this study, we show that plant-specific transcription factors, designated NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis thaliana. In nst1-1 nst3-1 double knockout plants, the secondary wall thickenings in interfascicular fibers and secondary xylem, except for vascular vessels, were completely suppressed without affecting formation of cells destined to be woody tissues. Conversely, as shown previously for NST1, overexpression of NST3 induced ectopic secondary wall thickenings in various aboveground tissues. Furthermore, the expression of chimeric repressors derived from NST1 and NST3 suppressed secondary wall thickenings in the presumptive interfascicular fibers. Because putative orthologs of NST1 and NST3 are present in the genome of poplar, our results suggest that they are also key regulators of the formation of secondary walls in woody plants and could be used as a tool for the genetic engineering of wood and its derivatives.

NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis

Afin de clarifier le role joue par les microfibrilles dans la genese des contraintes de croissance dans l'arbre, une analyse experimentale a ete realisee sur 7 essences feuillues des Appalaches produisant ou non des fibres gelatineuses dans la partie superieure des tiges inclinees. Dans le cas des essences produisant des fibres gelatineuses, des contraintes elevees sont observees au niveau des zones a forte proportion surfacique de couches gelatineuses en section transverse. Pour les essences ne produisant pas de fibres gelatineuses, la contrainte longitudinale de tension est d'autant plus grande que l'angle des microfibrilles est petit [...]

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Growth stresses in tension wood: role of microfibrils and lignification

Physical, chemical, and biological properties of wood depend largely on the properties of cellulose, noncellulosic polysaccharides, and lignin, and their assembly mode in the cell wall. Information on the assembly mode in the main part of the ginkgo tracheid wall (middle layer of secondary wall, S2) was drawn from the combined results obtained by physical and chemical analyses of the mechanically isolated S2 and by observation under scanning electron microscopy. A schematic model was tentatively proposed as a basic assembly mode of cell wall polymers in the softwood tracheid as follows: a bundle of cellulose microfibrils (CMFs) consisting of about 430 cellulose chains is surrounded by bead-like tubular hemicellulose-lignin modules (HLM), which keep the CMF bundles equidistant from each other. The length of one tubular module along the CMF bundle is about 16 ± 2 nm, and the thickness at its side is about 3–4 nm. In S2, hemicelluloses are distributed in a longitudinal direction along the CMF bundle and in tangential and radial directions perpendicular to the CMF bundle so that they are aligned in the lamellae of tangential and radial directions with regard to the cell wall. One HLM contains about 7000 C6-C3 units of lignin, and 4000 hexose and 2000 pentose units of hemicellulose.

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Nanostructural assembly of cellulose, hemicellulose, and lignin in the middle layer of secondary wall of ginkgo tracheid

The purpose of this study is to investigate the effect of repeated moisture change on the crystallinity and crystal size of cellulose microfibrils (CMF) in sugi (Cryptomeria japonica D.Don) and karamatsu (Larix kaempferi Gord.) wood cell wall. Based on obtained results, we discussed the qualitative change in the fine structure of CMF caused by repeated dry-and-wet (RDW) treatments. Green quarter-sawn specimens (5 × 16 × 15 mm in thickness × length × width) and microcrystalline cellulose powder (Avicel) were prepared, and these specimens were subjected to 7 times at most of heated or unheated RDW treatments. After giving RDW treatments, specimens were seasoned to the fiber saturated point and absolutely dried. Wide angle X-ray diffraction measurements were adopted to determine the crystallinity and the crystal size in each condition. Results indicate that crystallinity and crystal size in wood specimens gradually increased with the progress of heated or unheated RDW treatments, while no such increases were observed in Avicel powder. Those results suggest that RDW treatments promote the crystallization of CMF in wood cell wall, regardless of heating. We presume that noncrystalline cellulose forms hydrogen bonding with the cellulose at the surface of crystalline region with the progress of RDW treatments, thus enlarging the crystal size. Avicel powder did not show features that were observed in wood specimens by RDW treatments, because it contained few noncrystalline cellulose.

Masato Yoshida

Papers

NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis

Growth stresses in tension wood: role of microfibrils and lignification

Nanostructural assembly of cellulose, hemicellulose, and lignin in the middle layer of secondary wall of ginkgo tracheid

Crystallization of cellulose microfibrils in wood cell wall by repeated dry-and-wet treatment, using X-ray diffraction technique

Method of determining the mean microfibril angle of wood over a wide range by the improved Cave's method