Abstract
Cloning and identification of genes from the cambium of woody plants are important steps in the investigation of wood formation. In order to clone and identify the genes involved in wood formation, a cDNA library was constructed from the cambial tissue of Betula platyphylla Suk (birch). From the cDNA library, 2,878 high-quality ESTs were generated, representing 1,540 tentative unique genes (TUGs). Approximately 70% of the ESTs were matched to proteins in the NR database in GenBank and were grouped into 12 functional categories according to their functional annotation. Fifty TUGs potentially involved in wood formation, including the process of lignin biosynthesis, cell wall structure, cell wall polysaccharides synthesis or development regulation, were identified from the EST collection. The time course expression analysis of 13 wood formation related genes was further studied using RNA gel blot and semi-quantitative RT-PCR. The results showed that these genes were primarily expressed in tissue that was collected during two time periods, spring (26 April to 11 June) and later summer (30 July to 18 Sept). The bimodal expression curve of the genes indicates that both of these time periods are critical in wood formation in birch, and may be associated with cell wall expansion earlier in the year, and cell wall strengthening later in the year.
Similar content being viewed by others
References
Allona I, Quinn M, Shoop E, Swope K, St Cyr S, Carlis J, Riedl J, Retzel E, Campbell MM, Sederoff R, Whetten RW (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci USA 95:9693–9698. doi:10.1073/pnas.95.16.9693
Bao W, O'Malley DM, Sederoff RR (1992) Wood contains a cell-wall structural protein. Proc Natl Acad Sci USA 89:6604–6608. doi:10.1073/pnas.89.14.6604
Baucher M, Halpin C, Petit-Conil M, Boerjan W (2003) Lignin: genetic engineering and impact on pulping. Crit Rev Biochem Mol Biol 38:305–350. doi:10.1080/10409230391036757
Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546. doi:10.1146/annurev.arplant.54.031902.134938
Bohnert HJ, Ayoubi P, Borchert C, Bressan RA, Burnap RL, Cushman JC, Cushman MA, Deyholos M, Fischer R, Galbraith DW, Hasegawa PM, Jenks M, Kawasaki S, Koiwa H, Kore-eda S, Lee BH, Michalowski CB, Misawa E, Nomura M, Ozturk N, Postier B, Prade R, Song CP, Tanaka Y, Wang H, Zhu JK (2001) A genomics approach towards salt stress tolerance. Plant Physiol Biochem 39:295–311. doi:10.1016/S0981-9428(00)01237-7
Darley CP, Forrester AM, McQueen-Mason SJ (2001) The molecular basis of plant cell wall extension. Plant Mol Biol 47:179–195. doi:10.1023/A:1010687600670
Demura T, Fukuda H (2007) Transcriptional regulation in wood formation. Trends Plant Sci 12:64–70. doi:10.1016/j.tplants.2006.12.006
Djerbi S, Lindskog M, Arvestad L, Sterky F, Teeri TT (2005) The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes. Planta 221:739–746. doi:10.1007/s00425-005-1498-4
Goldberg R, Liberman M, Mathieu C, Pierron M, Catesson AM (1987) Development of epidermal cell wall peroxidases along the mung bean hypocotyl: possible involvement in the cell wall stiffening process. J Exp Bot 38:1378–1390
Grabber JH, Hatfield RD, Lu F, Ralph J (2008) Coniferyl ferulate incorporation into lignin enhances the alkaline delignification and enzymatic degradation of cell walls. Biomacromolecules 9:2510–2516. doi:10.1021/bm800528f
Gray-Mitsumune M, Blomquist K, McQueen-Mason S, Teeri TT, Sundberg B, Mellerowicz EJ (2008) Ectopic expression of a wood-abundant expansin PttEXPA1 promotes cell expansion in primary and secondary tissues in aspen. Plant Biotechnol J 6:62–72. doi:10.1111/j.1467-7652.2007.00295.x
Gueguen Y, Cadoret JP, Flament D, Barreau-Roumiguière C, Girardot AL, Garnier J, Hoareau A, Bachère E, Escoubas JM (2003) Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster. Gene 303:139–145. doi:10.1016/S0378-1119(02)01149-6
Hatfield R, Vermerris W (2001) Lignin formation in plants. The dilemma of linkage specificity. Plant Physiol 126:1351–1357
Hellgren JM, Olofsson K, Sundberg B (2004) Patterns of auxin distribution during gravitational induction of reaction wood in poplar and pine. Plant Physiol 135(1):212–220. doi:10.1104/pp.104.038927
Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlén M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P, Sandberg G (2001) A transcriptional roadmap to wood formation. Proc Natl Acad Sci USA 98:14732–14737. doi:10.1073/pnas.261293398
Hu WJ, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Tsai CJ, Chiang VL (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat Biotechnol 17:808–812. doi:10.1038/11758
Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877. doi:10.1101/gr.9.9.868
Humphreys JM, Chapple C (2002) Rewriting the lignin roadmap. Curr Opin Plant Biol 5:224–229. doi:10.1016/S1369-5266(02)00257-1
Kim H, Ralph J, Yahiaoui N, Pean M, Boudet AM (2000) Cross-coupling of hydroxycinnamyl aldehydes into lignins. Org Lett 2:2197–2200. doi:10.1021/ol005906o
Koutaniemi S, Warinowski T, Kärkönen A, Alatalo E, Fossdal CG, Saranpää P, Laakso T, Fagerstedt KV, Simola LK, Paulin L, Rudd S, Teeri TH (2007) Expression profiling of the lignin biosynthetic pathway in Norway spruce using EST sequencing and real-time RT-PCR. Plant Mol Biol 65:311–328. doi:10.1007/s00425-005-1498-4
Lapierre C, Pilate G, Pollet B, Mila I, Leplé JC, Jouanin L, Kim H, Ralph J (2004) Signatures of cinnamyl alcohol dehydrogenase deficiency in poplar lignins. Phytochemistry 65:313–321. doi:10.1016/j.phytochem.2003.11.007
Li X, Weng JK, Chapple C (2008) Improvement of biomass through lignin modification. Plant J 54:569–581. doi:10.1111/j.1365-313X.2008.03457.x
Ma QH (2007) Characterization of a cinnamoyl-CoA reductase that is associated with stem development in wheat. J Exp Bot 58:2011–2021. doi:10.1093/jxb/erm064
Marjamaa K, Kukkola E, Lundell T, Karhunen P, Saranpää P, Fagerstedt KV (2006) Monolignol oxidation by xylem peroxidase isoforms of Norway spruce (Picea abies) and silver birch (Betula pendula). Tree Physiol 26:605–611. doi:10.1093/treephys/26.5.605
Martz F, Maury S, Pinçon G, Legrand M (1998) cDNA cloning, substrate specificity and expression study of tobacco caffeoyl-CoA 3-O-methyltransferase, a lignin biosynthetic enzyme. Plant Mol Biol 36:427–437. doi:10.1023/A:1005969825070
McQueen-Mason S, Durachko DM, Cosgrove DJ (1992) Two endogenous proteins that induce cell wall extension in plants. Plant Cell 4:1425–1433
Mellerowicz EJ, Sundberg B (2008) Wood cell walls: biosynthesis, developmental dynamics and their implications for wood properties. Curr Opin Plant Biol 11:293–300. doi:10.1016/j.pbi.2008.03.003
O'Connell A, Holt K, Piquemal J, Grima-Pettenati J, Boudet A, Pollet B, Lapierre C, Petit-Conil M, Schuch W, Halpin C (2002) Improved paper pulp from plants with suppressed cinnamoyl-CoA reductase or cinnamyl alcohol dehydrogenase. Transgenic Res 11:495–503. doi:10.1023/A:1020362705497
Park S, Han KH (2003) An auxin-repressed gene (RpARP) from black locust (Robinia pseudoacacia) is posttranscriptionally regulated and negatively associated with shoot elongation. Tree Physiol 23:815–823. doi:10.1093/treephys/23.12.815
Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J (2004) Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 55:263–280. doi:10.1007/s11103-004-0621-4
Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J (2005) Generation, annotation, analysis and database integration of 16, 500 white spruce EST clusters. BMC Genomics 6:144. doi:10.1186/1471-2164-6-144
Reddy AS, Poovaiah BW (1990) Molecular cloning and sequencing of a cDNA for an auxin-repressed mRNA: correlation between fruit growth and repression of the auxin-regulated gene. Plant Mol Biol 14:127–136
Rouse D, Mackay P, Stirnberg P, Estelle M, Leyser O (1998) Changes in auxin response from mutations in an AUX/IAA gene. Science 279:1371–1373. doi:10.1126/science.279.5355.1371
Samuga A, Joshi CP (2002) A new cellulose synthase gene (PtrCesA2) from aspen xylem is orthologous to Arabidopsis AtCesA7 (irx3) gene associated with secondary cell wall synthesis. Gene 296:37–44. doi:10.1016/S0378-1119(02)00864-8
Shani Z, Dekel M, Tsabary G, Goren R, Shoseyov O (2004) Growth enhancement of transgenic poplar plants by overexpression of Arabidopsis thaliana endo-1, 4-β-glucanase (cel1). Mol Breed 14:321–330. doi:10.1023/B:MOLB.0000049213.15952.8a
Siedlecka A, Wiklund S, Péronne MA, Micheli F, Lesniewska J, Sethson I, Edlund U, Richard L, Sundberg B, Mellerowicz EJ (2008) Pectin methyl esterase inhibits intrusive and symplastic cell growth in developing wood cells of Populus. Plant Physiol 146:554–565. doi:10.1104/pp.107.111963
Stafstrom JP, Ripley BD, Devitt ML, Drake B (1998) Dormancy-associated gene expression in pea axillary buds. Cloning and expression of PsDRM1 and PsDRM2. Planta 205:547–552. doi:10.1007/s004250050354
Sterky F, Regan S, Karlsson J, Hertzberg M, Rohde A, Holmberg A, Amini B, Bhalerao R, Larsson M, Villarroel R, Van Montagu M, Sandberg G, Olsson O, Teeri TT, Boerjan W, Gustafsson P, Uhlén M, Sundberg B, Lundeberg J (1998) Gene discovery in the wood-forming tissues of poplar: analysis of 5, 692 expressed sequence tags. Proc Natl Acad Sci USA 95:13330–13335
Tan K-S, Hoson T, Masuda Y, Kamisaka S (1992) Involvement of cell wall-bound diferulic acid in light-induced decrease in growth rate and cell wall extensibility of Oryza coleoptiles. Plant Cell Physiol 33:103–108
Ujino-Ihara T, Yoshimura K, Ugawa Y, Yoshimaru H, Nagasaka K, Tsumura Y (2000) Expression analysis of ESts derived from the inner bark of Cryptomeria japonica. Plant Mol Biol 43:451–457. doi:10.1023/A:1006492103063
Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–1868. doi:10.1126/science.276.5320.1865
van der Rest B, Danoun S, Boudet AM, Rochange SF (2006) Down-regulation of cinnamoyl-CoA reductase in tomato (Solanum lycopersicum L.) induces dramatic changes in soluble phenolic pools. J Exp Bot 57:1399–1411. doi:10.1093/jxb/erj120
Vanholme R, Morreel K, Ralph J, Boerjan W (2008) Lignin engineering. Curr Opin Plant Biol 11:278–285. doi:10.1016/j.pbi.2008.03.005
Weng JK, Li X, Stout J, Chapple C (2008) Independent origins of syringyl lignin in vascular plants. Proc Natl Acad Sci USA 105:7887–7892. doi:10.1073/pnas.0801696105
Williamson RE, Burn JE, Hocart CH (2002) Towards the mechanism of cellulose synthesis. Trends Plant Sci 7:461–467. doi:10.1016/S1360-1385(02)02335-X
Yang J, Park S, Kamdem DP, Keathley DE, Retzel E, Paule C, Kapur V, Han KH (2003) Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia. Plant Mol Biol 52:935–956. doi:10.1023/A:1025445427284
Yang SH, van Zyl L, No EG, Loopstra CA (2004) Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda). Plant Sci 166:1185–1195. doi:10.1016/j.plantsci.2003.12.030
Yokoyama R, Nishitani K (2006) Identification and characterization of Arabidopsis thaliana genes involved in xylem secondary cell walls. J Plant Res 119:189–194. doi:10.1007/s10265-006-0261-7
Zhao HY, Lu J, Lu SY, Zhou YH, Wei JH, Song YR, Wang T (2005) Isolation and functional characterization of a cinnamate 4-hydroxylase promoter from Populus tomentosa. Plant Sci 168:1157–1162. doi:10.1016/j.plantsci.2004.12.022
Zhong R, Morrison WH 3rd, Freshour GD, Hahn MG, Ye ZH (2003) Expression of a mutant form of cellulose synthase AtCesA7 causes dominant negative effect on cellulose biosynthesis. Plant Physiol 132:786–795. doi:10.1104/pp.102.019331
Zhou GK, Zhong R, Richardson EA, Morrison WH 3rd, Nairn CJ, Wood-Jones A, Ye ZH (2006) The poplar glycosyltransferase GT47C is functionally conserved with Arabidopsis Fragile fiber8. Plant Cell Physiol 47:1229–1240. doi:10.1093/pcp/pcj093
Zhou GK, Zhong R, Himmelsbach DS, McPhail BT, Ye ZH (2007) Molecular characterization of PoGT8D and PoGT43B, two secondary wall-associated glycosyltransferases in poplar. Plant Cell Physiol 48:689–699. doi:10.1093/pcp/pcm037
Acknowledgements
This work has been supported by the Foundation of Heilongjiang Province (No. C200803), Heilongjiang Province International Scientific and Technological Cooperation Project (WB07N02), and National Key Technology R&D Project (2006BAD01A1603, 2006BAD24B05).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wang, C., Wang, Y., Diao, G. et al. Isolation and Characterization of Expressed Sequence Tags (ESTs) from Cambium Tissue of Birch (Betula platyphylla Suk). Plant Mol Biol Rep 28, 438–449 (2010). https://doi.org/10.1007/s11105-009-0172-6
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11105-009-0172-6