Cloning and in silico analysis of a cinnamyl alcohol dehydrogenase gene in Pennisetum purpureum

Journal of Genetics

Volumn 93, Issue 1, 2014, Pages 145-158

  Tang, Ran ^a   Zhang, Xiang Qian ^a   Li, You Han ^a   Xie, Xin Ming ^a  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

cinnamyl alcohol dehydrogenase; clone; in silico analysis; lignin biosynthesis; Pennisetum purpureum

Indexed keywords

ALCOHOL DEHYDROGENASE; CINNAMYL ALCOHOL DEHYDROGENASE;

AMINO ACID SEQUENCE; BIOLOGY; CHEMICAL STRUCTURE; ENZYME ACTIVE SITE; EXON; GENE ORDER; GENETICS; INTRON; MOLECULAR CLONING; MOLECULAR GENETICS; MULTIGENE FAMILY; PENNISETUM; PHYLOGENY; PLANT GENE; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ALCOHOL OXIDOREDUCTASES; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; EXONS; GENE ORDER; GENES, PLANT; INTRONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PENNISETUM; PHYLOGENY; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84902990527     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-014-0355-2     Document Type: Article

References (62)

1. Arnold K., Bordoli L., Kopp J. and Schwede T. 2006 The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics22, 195-201.
2. Barakat A., Bangniewska-Zadworna A., Choi A., Plakkat U., Diloreto D. S., Yellanki P. et al. 2009 The cinnamyl alcohol dehydrogenase gene family in Populus, phylogeny, organization, and expression. BMC Plant Bio. 9: 26.
3. Baucher M., Chabbert B., Pilate G., van Doorsselaere J., Tollier M. T., Petit-Conil M. et al. 1996 Red xylem and higher lignin extractability by down-regulating a cinnamyl alcohol dehydrogenase in poplar. Plant Physiol. 112, 1479-1490.
4. Baucher M., Bernard-Vailhe M. A., Chabbert B., Besle J. M., Opsomer C., van Montagu M. and Botterman J. 1999 Down-regulation of cinnamyl alcohol dehydrogenase in transgenic alfalfa (Medicago sativa L.) and the effect on lignin composition and digestibility. Plant Mol. Biol. 39, 437-447.
5. Boerjan W., Ralph J. and Baucher M. 2003 Lignin biosynthesis. Annu. Rev. Plant Biol. 54, 519-546.
6. Brill E. M., Abrahams S., Hayes C. M., Jenkins C. L. D. and Watson J. M. 1999 Molecular characterization and expression of a wound-inducible cDNA encoding a novel cinnamyl-alcohol dehydrogenase enzyme in lucerne. Plant Mol. Biol. 41, 279-291.
7. Bukh C., Nord-Larsen P. H. and Rasmussen S. K. 2012 Phylogeny and structure of the cinnamyl alcohol dehydrogenase gene family in Brachypodium distachyon. J. Exp. Bot. 63, 6223-6236.
8. Chen L., Auh C. K., Dowling P., Bell J., Chen F., Hopkins A. et al. 2003 Improved forage digestibility of tall fescue (Festuca arundinacea) by transgenic down regulation of cinnamyl alcohol dehydrogenase. Plant Biotechnol. J. 1, 437-449.
9. Deng W. W., Zhang M., Wu J. Q., Jiang Z. Z, Tang L., Li Y. Y. et al. 2011 Molecular cloning, functional analysis of three cinnamyl alcohol dehydrogenase (CAD) genes in the leaves of tea plant, Camellia sinensis. J. Plant Physiol. 170, 272-282.
10. de Morais R. F., Quedsds D. M., Reis V. M., Urquiaga S., Alves B. J. R. and Boddet R. M. 2011 Contribution of biological nitrogen fixation to elephant grass (Pennisetum purpureum Schum.)Plant Soil356, 23-34.
11. Dixon R. A., Chen F., Guo D. and Parvathi K. 2001 The biosynthesis of monolignols: a 'metabolic grid', or independent pathways to guaiacyl and syringyl units?Phytochemistry57, 1069-1084.
12. Doyle J. and Doyle J. L. 1987 A rapid DNA isolation method for small quantities of fresh tissues. Phytochem. Bull. 19, 11-15.
13. Emanuelsson O., Nielsen H., Brunak S. and von Heijne G. 2000 Predicting subcellular localization of proteins based on their Nterminal amino acid sequence. J. Mol. Biol. 300, 1005-1016.
14. Eudes A., Pollet B., Sibout R., Do C. T., Séguin A., Lapierre C. et al. 2006 Evidence for a role of AtCAD 1 in lignification of elongating stems of Arabidopsis thaliana. Planta 225, 23-39.
15. Eudes A., George A., Mukerjee P., Kim J. S., Pollet B., Benke P. I. et al. 2012 Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol. J. 10, 609-620.
16. Finn R. D., Mistry J., Tate P., Coggill P., Hegar A., Pollington J. E. et al. 2010 The pfam protein families database. Nucleic Acids Res. 38, 211-222.
17. Fu C., Xiao X., Xi Y., Ge Y., Chen F., Bouton J. et al. 2009 Downregulation of cinnamyl alcohol dehydrogenase (CAD) leads to improved saccharification efficiency in switchgrass. Bioenerg. Res. 4, 153-164.
18. Fu C, Mielenz J. R., Xiao X., Ge Y., Hamilton C. Y., Rodriguez M. et al. 2011 Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc. Natl. Acad. Sci. USA108, 3803-3808.
19. Fornalé S., Capellades M., Encina A., Wang K., Irar S., Lapierre C. et al. 2012 Altered lignin biosynthesis improves cellulosic bioethanol production in transgenic maize plants down-regulated for cinnamyl alcohol dehydrogenase. Mol. Plant. 5, 817-830.
20. Galliano H., Cabane M., Eckerskorn C., Lottspeich F., Sandermann H. and 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. 23, 145-156.
21. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M. R., Appel R. D. et al. 2005 Protein identification and analysis tools on the ExPASy Server. The Proteomics Protocols Handbook, 571-607.
22. Goffner D., van Doorsselaere J., Yahiaoui N., Samaj J., Grima-Pettenati J. and Boudet A. M. 1998 A novel aromatic alcohol dehydrogenase in higher plants: Molecular cloning and expression. Plant Mol. Biol. 36, 755-765.
23. Gouet P., Courcelle E., Stuart D. I. and Métoz F. 1999 ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305-308.
24. Guo D. M., Ran J. H. and Wang X. Q. 2010 Evolution of the cinnamyl/sinapyl alcohol dehydrogenase(CAD/SAD) gene family: The emergence of real Lignin is associated with the origin of bona fide CAD. J. Mol. Evol. 71, 202-218.
25. Halpin C., Knight M. E., Grima-Pettenati J., Goffner D., Boudet A. and Schuch W. 1992 Purification and characterization of cinnamyl alcohol dehydrogenase from tobacco stems. Plant Physiol. 98, 12-16.
26. Hirano K., Aya K., Kondo M., Okuno A., Morinak Y. and Matasuoka M. 2012 OsCAD2 is the major CAD gene responsible for monolignol biosynthesis in rice culm. Plant Cell Rep. 31, 91-101.
27. Hisano H., Nandakumar R. and Wang Z. Y. 2009 Genetic modification of lignin biosynthesis for improved biofuel production. In Vitro Cell. Dev. Biol.-Plant45, 306-313.
28. Hofmann K. and Stoffel W. 1993 TMbase-A database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler374, 166.
29. Jackson L. A., Shadle G. L., Zhou R., Nakashima J., Chen F. and Dixon C. R. 2008 Improving saccharification efficiency of alfalfa stems through modification of the terminal stages of monolignol biosynthesis. Bioenerg. Res. 1, 180-192.
30. Kim S. J., Kim M. R., Bedgar D. L., Moinuddin S. G. A., Cardenas, C. L., Davin L. B. et al. 2004 Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc. Natl. Acad. Sci. USA101, 1455-1460.
31. Kim S. J., Kim K. W., Cho M. H., Franceschi V. R., Davin L. B. and Lewis N. G. 2007 Expression of cinnamyl alcohol dehydrogenase and their putative homologues during Arabidopsis thaliana growth and development: lessons for database annotation?Phytochemistry68, 1957-1974.
32. Knight M. E., Halpin C. and Schuch W. 1992 Identification and characterization of cDNA clones encoding cinnamyl alcohol dehydrogenase from tobacco. Plant Mol. Biol. 19, 739-810.
33. Li L. G., Cheng X. F., Leshkevich J., Umezawa T., Harding S. A. and Chiang V. L. 2001 The last step of syringyl monolignol biosynthesis in angiosperms is regulated by a novel gene encoding sinapyl alcohol dehydrogenase. Plant Cell13, 1567-1585.
34. Li X., Yang Y., Yao J., Chen G., Li X. H., Zhang Q. et al. 2009 FLEXIBLE CULM 1 encoding a cinnamyl-alcohol dehydrogenase controls culm mechanical strength in rice. Plant Mol. Biol. 69, 685-697.
35. Lynch D., Lidgett A., Mclnnes R., Huxley H., Jones E., Mahoney N. et al. 2002 Isolation and characterisation of three cinnamyl alcohol dehydrogenase homologue cDNAs from perennial ryegrass (Lolium perenne L.)J. Plant Physiol. 159, 653-660.
36. Ma Q. H. 2010 Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J. Exp. Bot. 61, 2735-2744.
37. MacKay J. J., O'Malley D. M, Presnell T., Booker F. L., Campbell M. M., Whetten R. W. et al. 1997 Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase. Proc. Natl. Acad. Sci. USA94, 8255-8260.
38. Madakadze I. C., Masamvu T. M., Radiotis T., Li J. and Smith D. L. 2010 Evaluation of pulp and paper making characteristics of elephant grass (Pennisetum purpureum Schum.) and switchgrass (Panicum virgatum L.)Afr. J. Environ. Sci. Techonol. 4, 465-470.
39. Matthews-Amune O. C. and Kakulu S. 2012 Determination of heavy metals in forage grasses (carpet grass (Axonopus ompressus), guinea grass (Panicum maximum) and elephant grass (Pennisetum purpureum)) in the vicinity of Itakpe Iron Ore Mine, Nigeria. Int. J. Pure Appl. Sci. Technol. 13, 16-25.
40. Mansell R. L., Gross G. G., Stoeckigt J., Franke H. and Zenk M. H. 1974 Purification and properties of cinnamyl alcohol dehydrogenase from higher plants involved in lignin biosynthesis. Phytochemistry13, 2427-2436.
41. O'Malley D. M., Porter S. and Sederoff R. R. 1992 Purification, characterization, and cloning of cinnamyl alcohol dehydrogenase in loblolly pine (Pinus taeda L). Plant Physiol. 98, 1364-1371.
42. Pandey B., Pandey V. P. and Dwivedi U. N. 2011 Cloning, expression, functional validation and modeling of cinnamyl alcohol dehydrogenase isolated from xylem of Leucaena leucocephala. Protein Expr. Purif. 79, 197-203.
43. Peter G. and Neale D. 2004 Molecular basis for the evolution of xylem lignification. Curr. Opin. Plant Biol. 7, 737-742.
44. Petersen T. N., Brunak S., von Heijine G. and Nielson H. 2011 SignalP 4. 0: discriminating signal peptides from transmembrane region. Nat. Methods8, 785-786.
45. Raes J., Rohde A., Christensen J. H., van de Peer Y., Boerjan W. 2003 Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 133, 1051-1071.
46. Ragauskas A., Williams C., Davison B., Britovsek G., Cairney J. and Eckert C. A. 2006 The path forward for biofuels and biomaterials. Science311, 484-489.
47. Rossmann M. G., Moras D. and Olsen K. W. 1974 Chemical and biological evolution of a nucleotide-binding protein. Nature250, 194-199.
48. Saathoff A. J., Hargrove M. S., Haas E. J., Tobias C. M., Twigg P., Sattler S. et al. 2012 Switchgrass PviCAD1: Understanding residues important for substrate preferences and activity. Appl. Biochem. Biotechnol. 168, 1086-1100.
49. Saathoff A. J., Tobias C. M., Sattler S. E, Haase J., Twigg P. and Sarath G. 2011 Switchgrass contains two cinnamyl alcohol dehydrogenases involved in lignin formation. Bioenerg. Res. 4, 120-133.
50. Saballos A., Ejeta G., Sanchez E., Kang C. and Vermerris W. 2009 A genome-wide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the brown midrib6 gene. Genetics181, 783-795.
51. Sibout R., Eudes A., Pollet B., Goujon T., Mila I., Granier F. et al. 2003 Expression pattern of two paralogs encoding cinnamyl alcohol dehydrogenases in Arabidopsis. Isolation and characterization of the corresponding mutants. Plant Physiol. 132, 848-860.
52. Sibout R., Eudes A., Mouille G., Pollet B., Lapierre C., Jouanin L. et al. 2005 CINNAMYL ALCOHOL DEHYDROGENASEC and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17, 2059-2076.
53. + oxidoreductase. Proc. Natl. Acad. Sci. USA93, 14199-14203.
54. Tavares C. M., Aubourg S., Lecharny A. and kreis M. 2000 Organization and structural evolution of four multigene families in Arabidopsis thaliana, AtLCAD, AtLGT, AtMYST and AtHD-GL2. Plant Mol. Biol. 42: 703-717.
55. Tobias C. M. and Chow E. K. 2005 Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification. Planta220, 678-688.
56. Tsuruta S., Ebina M., Nakagawa H., Kawamura O. and Akashi R. 2007 Isolation and characterization of cDNA encoding cinnamyl alcohol dehydrogenase (CAD) in sorghum (Sorghum bicolor (L.) Moench). Grassland Sci. 53, 103-109.
57. van Doorsselaere J., Baucher M., Feuillet C., Boudet A. M., van Montagu M. and Inzé D. 1995 Isolation of cinnamyl alcohol dehydrogenase cDNAs from two important economic species: alfalfa and poplar. Demonstration of a high homology of the gene within angiosperms. Plant Physiol. Biochem. 33, 105-109.
58. Videira S. S., Oliveira D. M. D, de Morais R. F., Borges W. L., Baldani V. L. and Baldani J. I. 2012 Genetic diversity and plant growth promoting traits of diazotrophic bacteria isolated from two Pennisetum purpureum Schum. genotypes grown in the field. Plant Soil356, 51-66.
59. Weng J. K. and Chapple C. 2010 The origin and evolution of lignin biosynthesis. New Phytol. 187, 273-285.
60. Xie X. M., Zhou F, Zhang X. Q. and Zhang J. M. 2009 Genetic variability and relationship between MT-1 elephant grass and closely related cultivars assessed by SRAP marker. J. Genet. 88, 281-290.
61. Youn B., Camacho R., Moinuddin S. G. A., Lee C., Davin L. B., Lewis N. G. et al. 2006 Crystal structures and catalytic mechanism of the Arabidopsiscinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4. Org. Biomol. Chem. 4, 1687-1697.
62. Zhang K., Qian Q., Huang Z., Wang Y., Li M., Hong L. et al. 2006 GOLD HULL AND INTERNODE2 encodes a primarily multifunctional cinnamyl alcohol dehydrogenase in rice. Plant Physiol. 140, 972-983.