Research Article | Volume: 6, Issue: 2, March-April, 2018
Isolation and in silico characterization of full-length cinnamyl alcohol dehydrogenase gene involved in lignin biosynthesis in Neolamarckia cadamba
Cinnamyl alcohol dehydrogenase (CAD) catalyzes the reduction of cinnamaldehyde to ρ-coumaryl, coniferyl, and sinapyl alcohols during the last stage of lignin biosynthesis pathway. The CAD gene expression is believed to be important toward the phenotypic characteristics of plants. In the present study, a full-length CAD gene was successfully inferred from EST database (NcdbESTs) of Neolamarckia cadamba through a contig mapping approach. Reverse transcription polymerase chain reaction was conducted to validate the identity of the isolated CAD gene. The full-length CAD gene, designated as NcCAD, is 1,240 bp long with a 1,086 bp open reading frame encoding a protein of 361 amino acids, a 68 bp 5’-UTR, and a 86 bp 3’-UTR. Phylogenetic analysis showed that NcCAD was grouped in the cluster containing both CAD and sinapyl alcohol dehydrogenase (SAD) genes, in which both genes are involved in lignin biosynthesis. This result also demonstrated that the NcCAD gene may pose intermediate characteristics of both CAD and SAD genes. This NcCAD gene can serve as a good candidate gene for further insight into the wood properties of N. cadamba through association genetics study.
Tchin BL, Ho WS, Pang SL. Isolation and in silico characterization of full-length cinnamyl alcohol dehydrogenase gene involved in lignin biosynthesis in Neolamarckia cadamba. J App Biol Biotech. 2018;6(2):1-5. DOI: 10.7324/JABB.2018.60201
1. Lewis NG. A 20th century roller coaster ride: A short account of lignifications. Curr. Opin. Plant Biol. 1999; 2(2): 153-162. https://doi.org/10.1016/S1369-5266(99)80030-2 | |
2. Brett C, Waldron K. Physiology and Biochemistry of Plant Cell Walls. London: Unwin Hyman; 1990. https://doi.org/10.1007/978-94-010-9641-6 | |
3. Higuchi T. Biochemistry and molecular biology of wood. New York: Springer; 1997. https://doi.org/10.1007/978-3-642-60469-0 | |
4. Kutsuki H, Shimada M, Higuchi T. Regulatory role of cinnamyl alcohol dehydrogenase in the formation of guaiacyl and syringyl lignins. Phytochemistry. 1982; 21 (1): 19-23. https://doi.org/10.1016/0031-9422(82)80006-X | |
5. Ma QH. Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J. Exp. Bot. 2010; 61 (10): 2735-2744. https://doi.org/10.1093/jxb/erq107 | |
6. O'Malley DM, Porter S, Sederoff RR. Purification, characterization and cloning of cinnamyl alcohol dehydrogenase in loblolly pine (Pinus taeda L.). Plant Physiol. 1991; 98: 1364-1371. https://doi.org/10.1104/pp.98.4.1364 | |
7. Galliano H, Cabane M, Eckerskorn C, Lottspeich F, Sandermann H Jr, Ernst D. 1993. Molecular cloning, sequence analysis and elicitor-/ozone-induced accumulation of cinnamyl alcohol dehydrogenase from Norway spruce (Picea abies L.). Plant Mol. Biol. 1993; 23: 145-156. https://doi.org/10.1007/BF00021427 | |
8. Goffner D, Joffroy I, Grima-Pettenati J, Halpin C, Knight ME, Schuch W, Boudet AM. Purification and characterization of isoforms of cinnamyl alcohol dehydrogenase from Eucalyptus xylem. Planta. 1992; 188: 48-53. https://doi.org/10.1007/BF01160711 | |
9. Kim S, Kim M, Bedgar DL, Moinuddin SGA, Cardenas CL, Davin LB, Kang C, Lewis NG. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. P. Natl. A. Sci. 2004; 101 (6): 1455-1460. https://doi.org/10.1073/pnas.0307987100 | |
10. Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, Diloreto DS, Yellanki P, Carlson JE. The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization and expression. BMC Plant Biol. 2009; 9(1): 26. https://doi.org/10.1186/1471-2229-9-26 | |
11. Baucher M, Halpin C, Petit-Conil M, Boerjan W. Lignin: Genetic engineering and impact on pulping. Crit. Rev. Biochem. Mol. Biol. 2003; 38: 305-350. https://doi.org/10.1080/10409230391036757 | |
12. Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytol. 2010; 188: 515-532. https://doi.org/10.1111/j.1469-8137.2010.03415.x | |
13. Yu Q, Li B, Nelson CD, McKeand SE, Batista VB, Mullin TJ. Association of the cad-n1 allele with increased stem growth and wood density in full-sib families of loblolly pine. Tree Genetics and Genomes. 2006; 2: 98-108. https://doi.org/10.1007/s11295-005-0032-y | |
14. Tchin BL, Ho WS, Pang SL, Ismail J. Gene-associated single nucleotide polymorphism (SNP) in cinnamate 4-hydroxylase (C4H) and cinnamyl alcohol dehydrogenase (CAD) genes from Acacia mangium superbulk trees. Biotechnology. 2011; 10(4): 303-315. https://doi.org/10.3923/biotech.2011.303.315 | |
15. Tchin BL, Ho WS, Pang SL, Ismail J. Association genetics of the cinnamyl alcohol dehydrogenase (CAD) and cinnamate 4-hydroxylase (C4H) genes with basic wood density in Neolamarckia cadamba. Biotechnology. 2012; 11(6): 307-317. https://doi.org/10.3923/biotech.2012.307.317 | |
16. Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB. Association genetics in Pinus taeda L. I. wood property traits. Genetics. 2007; 175: 399-409. https://doi.org/10.1534/genetics.106.061127 | |
17. Ho WS, Pang SL, Julaihi, A. Identification and analysis of expressed sequence tags present in xylem tissues of kelampayan (Neolamarckia cadamba (Roxb.) Bosser). Physiology and Molecular Biology of Plants. 2014; 20(3): 393-397. https://doi.org/10.1007/s12298-014-0230-x | |
18. Pang SL, Ho WS, Mat-Isa MN, Julaihi, A. Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (Kelampayan). Tree Genetics and Genomes. 2015; 11:47 https://doi.org/10.1007/s11295-015-0873-y | |
19. Tiong SY, Chew SF, Ho WS, Pang SL. Genetic diversity of Neolamarckia cadamba using dominant DNA markers based on inter-simple sequence repeats (ISSRs) in Sarawak. Advances in Applied Science Research. 2014; 5(3): 458-463 | |
20. Phui SL, Ho WS, Pang SL, Julaihi, A. Development and polymorphism of simple sequence repeats (SSRs) in Kelampayan (Neolamarckia cadamba – Rubiaceae) using ISSR suppression method. Archives of Applied Science Research. 2014; 6(4): 209-218. | |
21. Zaky ZM, Zaki MA, Fasihuddin BA, Ho WS, Pang SL. Comparison of mimosine content and nutritive values of Neolamarckia cadamba and Leucaena leucocephala with Medicago sativa as forage quality index. International Journal of Scientific and Technology Research. 2014; 3(8): 146-150. | |
22. Joker D. 2000. Seed Leaflet Neolamarckia cadamba (Roxb.) Bosser (Anthocephalus chinensis (Lam.) A. Rich. ex Walp.). Danida Forest Seed Centre. 2000; 17. Available from: http://www.dfsc.dk. | |
23. Patel D, Kumar V. 2008. Pharmacognostical studies of Neolamarckia cadamba (roxb.) Bosser leaf. Int. J. Green Pharm. 2008; 2(1): 26-27. https://doi.org/10.4103/0973-8258.39159 | |
24. Zaky ZM, Fasihuddin BA, Ho WS, Pang SL. GC-MS analysis of phytochemical constituents in leaf extracts of Neolamarckia cadamba (Rubiaceae) from Malaysia. International Journal of Pharmacy and Pharmaceutical Sciences. 2014; 6(9): 123-127. | |
25. Tiong SY, Ho WS, Pang SL, Ismail J. In silico analysis of cellulose synthase gene (NcCesA1) in developing xylem tissues of Neolamarckia cadamba. American Journal of Bioinformatics. 2014, 3(2): 30-44. | |
26. Tiong SY, Ho WS, Pang SL, Ismail J. Bioinformatics analysis of xyloglucan endotransglycosylase/hydrolase (XTH) gene from developing xylem of a tropical timber tree Neolamarckia cadamba. American Journal of Bioinformatics. 2014, 3(1): 1-16. | |
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 1990; 215(3): 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2 | |
28. Sigrist CJA, Cerutti L, Castro ED, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. 2010. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2010; 38(1): D161-D166. https://doi.org/10.1093/nar/gkp885 | |
29. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Research. 2011; 39: D225-D229. https://doi.org/10.1093/nar/gkq1189 | |
30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol. Biol. Evol. 2011, 28: 2731-9. https://doi.org/10.1093/molbev/msr121 | |
31. Kelley LA, Sternberg MJE. 2009. Protein structure prediction on the web: a case study using the Phyre server. Nat. Protoc. 2009; 4(3): 363-371. https://doi.org/10.1038/nprot.2009.2 | |
32. Holm L, Rosenstrom P. 2010. Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38: W545-W549. https://doi.org/10.1093/nar/gkq366 | |
33. Li L, Cheng XF, Leshkevich J, Umezawa T, Harding SA, Chiang VL. The last step of syringyl monolignol biosynthesis in angiosperm is regulated by a novel gene encoding sinapyl alcohol dehydrogenase. The Plant Cell. 2001; 13: 1567-1585. https://doi.org/10.1105/tpc.13.7.1567 | |
34. Bomati EK, Noel, JP. Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase. The Plant Cell. 2005; 17: 1598-1611. https://doi.org/10.1105/tpc.104.029983 | |
35. Raes J, Rohde A, Christensen JH, Peer YVD, Boerjan W. (2003). Genome-wide characterization of the lignifications toolbox in Arabidopsis. Plant Physiology. 2003; 133: 1051-1071. https://doi.org/10.1104/pp.103.026484 | |
36. Tobias CM, Chow EK. Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification. Planta. 2005; 220 (5): 678-688. https://doi.org/10.1007/s00425-004-1385-4 | |
37. Ho WS, Pang SL, Lau P, Ismail J. Sequence variation in the cellulose synthase (SpCesA1) gene from Shorea parvifolia ssp. parvifolia mother trees. Journal of Tropical Agricultural Science. 2011; 34(2): 323-329. | |
38. Tiong SY, Ho WS, Pang SL, Ismail J. Nucleotide diversity and association genetics of xyloglucan endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba. Journal of Biological Sciences. 2014; 14(4): 267-275. https://doi.org/10.3923/jbs.2014.267.275 | |
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