Article Figures & Data
Figures
- Figure 1.
CAZyme-encoding genes involved in carbon flow to the cell wall. General scheme of carbon flow from photosynthesis (green chloroplast in source cell) or mobilization of starch reserves (yellow amyloplast in sink cell) to the production of cell wall carbohydrates (blue). Major CAZyme families are identified, including GTs, GHs, PLs, and CEs. Note that some functions only involve a subset of family members (e.g. GT4, GT2). 1, SUS and CesA complexes are known to associate at the plasma membrane for direct conversion of Suc to UDP-Glc for cellulose biosynthesis.
- Figure 2.
Comparison of the genetic diversity of CAZymes and expansins in poplar (Populus) and Arabidopsis. In the P. trichocarpa sequenced genome, genes were identified by similarity to known CAZymes and compared to the genes found in the Arabidopsis genome. A total of 1,647 poplar genes and 969 Arabidopsis genes were identified. Pie charts show proportional size of each gene family, GT, GH, and other CAZyme families (PL and CE), and expansins (EXPs).
- Figure 3.
Differential expression of CAZyme families and expansins in poplar. Families significantly overexpressed (Fisher's exact test, P ≤ 5%) in at least one tissue and with more than 20 ESTs for GHs, 15 ESTs for GTs, and eight ESTs for other CAZymes and expansins are shown.
- Figure 4.
Tissue-specific expression patterns of most expressed CAZyme-encoding genes. EST clones representing all genes with significant expression pattern (Fisher's exact test, P ≤ 5%) are presented. The clones were grouped according to clustering obtained with Genespring version 6.1, using standard correlation. Shading intensity corresponds to the EST frequency in each cDNA library for easy visualization of most highly expressed genes. Red shading indicates clone frequency ≥8 × 10−3 and yellow shading the frequency ≥0.10 × 10−3.
- Figure 5.
Comparison of CAZyme-encoding gene expression in poplar SAM and young leaf by EST frequency profiling and cDNA microarrays. Genes were grouped by functions, and their combined expression was presented as either the total number of ESTs (left pies) or the combined signal strength on a cDNA microarray (right pies). While some specific differences were observed, the general pattern of expression of CAZyme-encoding genes grouped by functions was similar by two methods. Shown here are data for dissected SAM and leaf, but comparisons of root and bark tissues showed similar results (data not shown).
- Figure 6.
Differential regulation of SUS and β-amylase genes. The three most abundantly expressed SUS and β-amylase genes show strong tissue-specific expression patterns. These patterns are not observable in cDNA microarray data due to the high degree of cross-hybridization of these highly homologous sequences (data not shown). SUS1 and SUS2 are predominantly expressed during wood formation, while SUS3 has a broad expression and is excluded from wood-forming cells. BAMY1 is expressed in dormant tissues, such as seasonally dormant cambium and seeds, and also in roots. Other β-amylases are found in mature leaves and induced strongly upon cold stress.
- Figure 7.
Differential expression of the highly expressed cell wall-related CAZyme-encoding genes. A, Differential expression of secondary wall-related CesA-encoding genes (PttCesA1, PttCesA3-1, PttCesA3-2, and PttCesA9-1) and other CesA-encoding genes. Note that PttCel9A1-1 and PttGH19A follow the expression of secondary wall CesAs, whereas the other related chitinase, PttGH19_15, follows the expression of other CesA-encoding genes. B, Differential expression of XTH genes. Specific XTH genes are expressed in the cambium, cambial region, TW, dormant cambium, seeds, bark, and petioles. PttXTH34 has been previously published as PttXET16A (Bourquin et al., 2002). C, Wood, leaves, and bark and petiole-specific expansins, PttEXPA1 and PttEXPA3, were previously published as PttEXP1 and PttEXP3, respectively (Gray-Mitsumune et al., 2004).
- Figure 8.
Global expression analysis of CAZyme-encoding genes involved in synthesis/metabolism of major carbohydrates in poplar and Arabidopsis. CAZyme-encoding genes were grouped by metabolic function for the major carbohydrates found in plants. Pies represent relative transcript abundance (poplar) or total signal intensity (Arabidopsis) for all genes of each group from each tissue and treatment in the poplar EST library and Arabidopsis microarrays (see “Materials and Methods”). Note that some poplar tissues have two pies for seasonally active (spring/summer) and dormant (fall/winter) tissues. Plants were subjected to 5°C for 3 to 4 d (poplar) or 4°C for 24 h (Arabidopsis) for cold leaf pie charts. Arabidopsis hypocotyls were collected after 7 d (from AtGenExpress) or after 3 months when a large amount of wood with fibers was produced (courtesy of Dr. Malcolm Bennett).
Tables
- Table I.
Comparison of coding sequences from different poplar species with coding sequences of P. trichocarpa
Other Poplar Species Used for EST Libraries Populus trichocarpa Nucleotide Sequence Divergencea % P. alba (Pal) 2.37 ± 0.9 P. alba × P. tremula (Pat) 2.51 ± 1.59 P. tremuloides (Ptl) 1.81 ± 0.47 P. tremula × P. tremuloides (Ptt) 2.11 ± 1.0 ↵a Full-length EST nucleotide sequences aligned and average percent difference calculated. N = 4, 2, 9, and 26, respectively, by row.
- Table II.
The EST library distribution and number of expressed genes in CAZyme and expansin families in different poplar tissuesa
EXP, Expansins; Tot, total; Cam, cambial region; Dor Cam, dormant cambium; Act Cam, active cambium; Dor Bud, dormant bud; Flw, male and female mature flowers.
Total Cam Dor Camb Act Camb TW WCD Bark Root Leaf Young Leaf Cold Leaf Old Petiole Apical Bud SAMb Dor Bud Flw Male Flw Fem Seed ESTs Total 2,449 269 98 190 394 157 121 112 143 168 156 138 140 138 119 78 170 115 GH 1,115 78 52 67 125 73 59 53 74 65 59 52 77 37 51 32 80 81 GT 970 94 32 64 189 70 34 28 55 58 63 34 37 63 53 23 47 26 PL 66 21 2 1 20 1 1 1 0 5 0 6 0 4 0 1 3 0 CE 117 6 3 10 12 2 8 5 8 15 4 16 3 2 0 10 12 1 EXP 181 50 0 17 19 4 11 4 1 15 26 11 5 7 0 3 6 2 Expressed genes Total 597 133 53 137 139 79 82 68 66 101 71 91 84 93 53 59 101 52 GH 222 46 20 42 47 34 36 25 25 35 25 33 36 33 28 26 45 27 GT 304 58 25 55 63 37 30 25 30 44 39 30 28 43 21 21 38 18 PL 14 7 2 1 8 1 1 1 0 3 0 2 0 3 0 1 1 0 CE 36 6 3 7 7 1 6 5 6 10 3 10 3 2 0 4 4 1 EXP 21 9 0 10 6 3 4 4 1 5 1 6 4 4 0 1 4 2 ↵a Numbers of EST clones corresponding to CAZyme-encoding genes and expansins (top half) or the number of genes with at least one corresponding EST (bottom half) in the collection of similar-sized cDNA libraries representing different tissues/developmental stages.
↵b Libraries constructed from amplified cDNA, not directly comparable to other libraries but comparable to each other and internally.
- Table III.
EST tissue distributiona of CAZyme-encoding genes involved in major pathways of carbohydrate synthesis/metabolism
Cam Reg, Cambial region; Dor Cam, dormant cambium; Act Cam, active cambium; Dor Bud, dormant bud; Flw, male and female mature flowers.
Genes Dor Camb Act Camb Cam Reg TW WCD Bark Root Young Leaf Mature Leaf Leaf Cold Petiole SAMb Act Bud Dor Bud Male Flw Fem Flw Seed SUS, GT4 3 9 21 84 14 2 3 1 2 0 2 6 2 4 1 5 7 SPS, GT4 2 2 0 2 1 0 1 1 3 1 0 1 0 1 0 0 0 Invertase, GH32 and GH100 1 2 0 4 1 3 4 3 3 1 0 1 1 5 7 3 1 Starch synthesis 17 2 0 3 0 1 0 6 0 4 3 6 2 10 0 5 0 Amylases 4 0 1 1 3 6 5 3 15 39 6 2 6 22 2 3 13 Callose synthases, CAS, GT48 3 2 3 0 5 1 2 1 1 0 2 2 0 0 0 1 0 Secondary wall CesAs, GT2 0 0 9 24 17 0 0 1 0 0 0 0 0 0 0 0 0 Other CesAs, GT2 1 2 3 4 0 2 0 1 2 2 0 3 0 1 2 2 0 KOR-like cellulases, GH9 0 1 3 22 8 1 0 1 0 0 3 1 1 0 0 1 1 ELP1-like, GH19 0 1 16 20 2 0 0 3 0 1 1 0 2 1 0 0 0 CSLD, GT2 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 1 Other cellulases, GH9 0 4 2 5 0 0 1 2 0 0 1 2 3 0 2 2 0 CSLA, GT2 0 1 1 1 2 1 0 1 0 0 1 2 1 0 0 0 2 Galactomannan α-1,6-galactosyl transferases, GAT, GT34 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Xylanase PttXyn10A, GH10 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Xylan glucuronate transferase, Fra8-like, GT47 0 0 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 Mannanases, GH5 0 0 3 0 1 0 0 0 0 0 2 0 0 0 2 1 0 Xyloglucan α-1,6-xylosyltrasnferases XT, GT34 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 RGP1, GT75 1 1 0 0 0 3 0 0 1 2 1 0 1 1 2 1 0 Xyloglucan galactosyltransferase, GAT, subfamily A, GT47 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 XTH subfamily 3, GH16 0 0 0 4 1 1 0 2 1 0 2 0 0 2 2 1 0 XTH subfamilies 1 and 2, GH16 6 13 8 8 0 10 9 3 1 17 15 6 9 0 3 7 33 EXPA 0 15 48 18 1 10 2 11 0 0 6 6 3 0 3 6 2 EXPB 0 1 1 1 3 1 1 0 0 0 4 0 0 0 0 0 0 QUA1-like, GT8 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 β-Glucuronyltransferase, GUT, GT47 0 0 4 14 4 0 1 0 0 1 1 0 1 0 0 4 0 RG II xylosyltransferase, XT, GT77 0 2 1 1 1 1 1 0 2 0 0 2 0 0 0 0 1 Pectate lyases, PL1 2 1 20 15 0 1 1 5 0 0 5 4 0 0 1 3 0 RG II lyases, PL4 0 0 1 5 1 0 0 0 0 0 1 0 0 0 0 0 0 Polygalacturonases, GH28 2 13 8 6 1 5 1 2 1 1 3 1 1 1 1 1 0 Pectin acetylesterases, CE13 1 3 2 7 0 2 2 5 3 2 8 1 0 0 3 1 0 Pectin methylesterase, CE8 2 8 4 5 2 5 3 10 1 6 8 1 3 0 7 10 1
Supplemental Data
Supplemental Figure and Tables
Files in this Data Supplement:
- Supplemental Data - Supplemental Data Legends
- Supplemental Data - Supplemental Figure
- Supplemental Data - Supplemental Table I
- Supplemental Data - Supplemental Table II
