Isolation and Single Nucleotide Polymorphisms Analysis of Caffeic Acid O-methyltransferase (LkCOMT) in Larix kaempferi

YI Min; ZHANG Shou-gong; XIE Yun-hui; SUN Xiao-mei

Volume 26 Issue S1

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Isolation and Single Nucleotide Polymorphisms Analysis of Caffeic Acid O-methyltransferase (LkCOMT) in Larix kaempferi

1.
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2013-08-20

Abstract

The ESTs sequences of caffeic acid O-methyltransferase from Larix kaempferi transcriptome database, an cDNA clone encoding COMT, was isolated from L. kaempferi by gene-specific PCR amplification. The COMT clone was 1 350 bp in length with an open reading frame (ORF, 1 092 bp) which would be capable to encode a protein of 364 AA. The sequence indicated that the deduced amino acid contained five highly conserved regions of COMT family, and shared 94% identity with PpCOMT from Pinus pinaster. The genomic sequences of LkCOMT in 40 individuals were sequenced, and single nucleotide polymorphisms (SNPs) diversity of LkCOMT was analyzed using the software DnaSP5.0. A total of 92 SNPs were detected, and the frequency and diversity of SNPs (πT) were 1/17 bp and 0.007 80, respectively. There were 65 transition and 27 transversion of mutation types. A total of 58 SNPs were detected in the coding regions of LkCOMT, of which 15 were synonymous mutation and 37 were missense mutation.
- Larix kaempferi,
- caffeic acid O-methyltransferase,
- gene cloning,
- single nucleotide polymorphism

References

[1]	Vanholme R, Morreel K, Ralph J, et al. Lignin engineering[J]. Curr Opin Plant Biol,2008,11(3): 1-228
[2]	Brodeur-Campbell S E, Vucetich J A, mRichter D L, et al. Insect herbivory on low-lignin transgenic aspen[J].Environ Entomol,2006,35:1696-1701
[3]	Guo D J, Chen F, Inoue K, et al. Downregulation of caffeic acid 3-O-methyltransferase and caffeoyl CoA 3-O-methyltransferase in transgenic alfalfa: Impacts on lignin structure and implications for the biosynthesis of G and S lignin[J]. Plant Cell, 2001, 13: 73-88
[4]	Bose S K, Francis R C, Govender M, et al. Lignin content versus syringyl to guaiacyl ratio amongst poplars[J].Bioresour Technol, 2009,100(4):1628-1633
[5]	Sticklen M B. Plant genetic engineering for biofuel production:towards affordable cellulosic ethanol[J].Nature Reviews Genetics,2008,9:433-443
[6]	Whetten R, Sederoff R. Lignin biosynthesis[J].Plant Cell,1995,7(25):1001-1013
[7]	Shi R, Sun Y H, Li Q Z, et al. Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes[J]. Plant Cell Physiol,2010, 51(1): 144-163
[8]	Davin L B. Dirigent proteins and dirigent sites explain the mystery of specificity of radical precursor coupling in lignin and lignin biosynthesis[J].Plant Physiol, 2001, 123: 453-466
[9]	Bugos R C, Chiang V L C, Campell W H. cDNA clonging,sequence analysis and seasonal expression of ligninbispecific caffeic/5-hydroxyferulic acid O-methyltransferase of aspen[J].Plant Molecular Biology, 1991,17(6):1203-1215
[10]	Zhang H, Wang J, Goodman H M. An Arabidopsis gene encoding a putative 14-3-3-interacting protein, caffeic acid/5-hydroxyferulic acid O-methyltransferase[J].Biochim Biophys Acta,1997,1353(3):199-202
[11]	Zein I, Wenzel G, Andersen J R, et al. Low level of linkage disequilibrium at the COMT(caffeic acid O-methyltransferase)locus in European maize (Zea mays)[J].Genetic Resources and Crop Evolution,2007,54(1):139-148
[12]	Ye Z H, Varner J E. Differential expression of two O-methyltransferase in lignin biosynthesis in Zinnia elegans[J].Plant Physiol,1995,108:459-467
[13]	Gowri G, Bugos R C, Campbell W H, et al. Stress responses in alfalfa (Medicago sativa L) molecular cloning and expression of S-adenosyl-L-methionine:caffeic acid 3-0-methyltransferase a key enzyme of lignin biosynthesis[J].Plant Physiology,1991,97:7-14
[14]	Li L G, Osakabe Y, Joshi C P, et al. Secondary xylem-specific expression of caffeoyl-coenzyme A 3-O-methyltransferase plays an important role in the methylation pathway associated with lignin biosynthesis in loblolly pine[J].Plant Mol Biol, 1999,40:555-565
[15]	Ibrahim R K, Bruneau A, Bantignies B. Plant O-methyltransferases: molecular analysis, common signature and classification[J]. Plant Molecular Biology, 1998, 36(1): 1-10
[16]	Jouanin L, Goujon T, de Nadai V, et al. Lignification in transgenic poplars with extremely reduced caffeic acid O-methyltransferase activity[J]. Plant Physiol,2000, 123(4), 1363-1374
[17]	Lapierre C, Pollet B, Petit-Conil M, et al. Structural alterations of lignins in transgenic poplars with depressed cinnamylalcohol dehydrogenase or caffeic acid O-methyltransferase activity have an opposite impact on the efficiency of industrial kraft pulping[J]. Plant Physiol,1999,119(1): 153-164
[18]	马常耕, 孙晓梅. 我国落叶松遗传改良现状及发展方向[J].世界林业研究,2008,21(3) :58-63
[19]	孙晓梅, 张守攻, 李时元, 等. 日本落叶松纸浆材优良家系多性状联合选择[J].林业科学,2005,41(4) :48-54
[20]	许晨璐. 落叶松基因挖掘及基因差异表达与杂种优势形成机制探讨[D].北京:中国林业科学研究院,2013
[21]	Zubieta C, He X Z, Dixon R A, et al. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases[J].Nature Structural Biology, 2001, 8(3): 271-279
[22]	Kim B G, Kim D H, Hur H G, et al. O-Methyltransferases from Arabidopsis thaliana[J].Agric Chem Biotechnol,2005, 48:113-119
[23]	刘希华. 欧洲黑杨幼苗氮高效基因型及SNPs标记筛选研究[D].南京:南京林业大学,2010
[24]	郭琦, 王保垒, 王博文, 等. 毛白杨 PtDREB2A基因的克隆、表达及单核苷酸多态性分析[J].林业科学,2011,47(4):49-56
[25]	Kim B G, Lee Y J, Park Y H, et al. Caffeic Acid O-Methyltransferase from Populus deltoides: functional expression and characterization[J]. Journal of Plant Biology, 2006, 49(1) : 55-60
[26]	谷振军, 张党权, 黄青云. 木质素合成关键酶基因与造纸植物转基因改良应用研究[J].中南林业科技大学学报,2010,30(3):67-74
[27]	Boerjan W, Ralph J, Baucher M. Lignin biosynthesis[J]. Annual Review of Plant Biology,2003, 54(1):519-546
[28]	Zubieta C, Kota P, Ferrer J L, et al. Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase[J].The Plant Cell,2002,14:1265-1277
[29]	Zhang D Q, Zhang Z Y. Single nucleotidepolymorphisms discovery and linkage disequilibrium[J]. Forestry Studies in China, 2005,7:1-14
[30]	褚延广, 苏晓华. 单核苷酸多态性在林木中的研究进展[J].遗传,2008,30(10):1272-1278
[31]	Yu X Q, Bai G H, Liu S W, et al. Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions[J]. Journal of Experimental Botany,2013,64(6):1537-1551
[32]	Dvornyk V, Sirvio A, Mikkonen M, et al. Low nudeotide diversity at the pal/locus in the widely distributed Pinus sylvestris[J].Mol Biol Evo,2003,19:179-188
[33]	Suha Y, Vijg J. SNP discovery in associating genetic variation with human disease phenotypes[J]. Mutation Research, 2005,573: 41-53
[34]	Krutovsky K V, Neale D B. Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality-related candidate genes in douglas fir[J].Genetics, 2005,171(4): 2029-2041
[35]	Pot D, McMillan L, Echt C, et al.Nucleotide variation in genes involved in wood formation in two pine species[J].New Phytologist, 2005,167:101-112

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Isolation and Single Nucleotide Polymorphisms Analysis of Caffeic Acid O-methyltransferase (LkCOMT) in Larix kaempferi

1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2013-08-20

Abstract: The ESTs sequences of caffeic acid O-methyltransferase from Larix kaempferi transcriptome database, an cDNA clone encoding COMT, was isolated from L. kaempferi by gene-specific PCR amplification. The COMT clone was 1 350 bp in length with an open reading frame (ORF, 1 092 bp) which would be capable to encode a protein of 364 AA. The sequence indicated that the deduced amino acid contained five highly conserved regions of COMT family, and shared 94% identity with PpCOMT from Pinus pinaster. The genomic sequences of LkCOMT in 40 individuals were sequenced, and single nucleotide polymorphisms (SNPs) diversity of LkCOMT was analyzed using the software DnaSP5.0. A total of 92 SNPs were detected, and the frequency and diversity of SNPs (πT) were 1/17 bp and 0.007 80, respectively. There were 65 transition and 27 transversion of mutation types. A total of 58 SNPs were detected in the coding regions of LkCOMT, of which 15 were synonymous mutation and 37 were missense mutation.

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Reference (35)

[1]	Vanholme R, Morreel K, Ralph J, et al. Lignin engineering[J]. Curr Opin Plant Biol,2008,11(3): 1-228
[2]	Brodeur-Campbell S E, Vucetich J A, mRichter D L, et al. Insect herbivory on low-lignin transgenic aspen[J].Environ Entomol,2006,35:1696-1701
[3]	Guo D J, Chen F, Inoue K, et al. Downregulation of caffeic acid 3-O-methyltransferase and caffeoyl CoA 3-O-methyltransferase in transgenic alfalfa: Impacts on lignin structure and implications for the biosynthesis of G and S lignin[J]. Plant Cell, 2001, 13: 73-88
[4]	Bose S K, Francis R C, Govender M, et al. Lignin content versus syringyl to guaiacyl ratio amongst poplars[J].Bioresour Technol, 2009,100(4):1628-1633
[5]	Sticklen M B. Plant genetic engineering for biofuel production:towards affordable cellulosic ethanol[J].Nature Reviews Genetics,2008,9:433-443
[6]	Whetten R, Sederoff R. Lignin biosynthesis[J].Plant Cell,1995,7(25):1001-1013
[7]	Shi R, Sun Y H, Li Q Z, et al. Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes[J]. Plant Cell Physiol,2010, 51(1): 144-163
[8]	Davin L B. Dirigent proteins and dirigent sites explain the mystery of specificity of radical precursor coupling in lignin and lignin biosynthesis[J].Plant Physiol, 2001, 123: 453-466
[9]	Bugos R C, Chiang V L C, Campell W H. cDNA clonging,sequence analysis and seasonal expression of ligninbispecific caffeic/5-hydroxyferulic acid O-methyltransferase of aspen[J].Plant Molecular Biology, 1991,17(6):1203-1215
[10]	Zhang H, Wang J, Goodman H M. An Arabidopsis gene encoding a putative 14-3-3-interacting protein, caffeic acid/5-hydroxyferulic acid O-methyltransferase[J].Biochim Biophys Acta,1997,1353(3):199-202
[11]	Zein I, Wenzel G, Andersen J R, et al. Low level of linkage disequilibrium at the COMT(caffeic acid O-methyltransferase)locus in European maize (Zea mays)[J].Genetic Resources and Crop Evolution,2007,54(1):139-148
[12]	Ye Z H, Varner J E. Differential expression of two O-methyltransferase in lignin biosynthesis in Zinnia elegans[J].Plant Physiol,1995,108:459-467
[13]	Gowri G, Bugos R C, Campbell W H, et al. Stress responses in alfalfa (Medicago sativa L) molecular cloning and expression of S-adenosyl-L-methionine:caffeic acid 3-0-methyltransferase a key enzyme of lignin biosynthesis[J].Plant Physiology,1991,97:7-14
[14]	Li L G, Osakabe Y, Joshi C P, et al. Secondary xylem-specific expression of caffeoyl-coenzyme A 3-O-methyltransferase plays an important role in the methylation pathway associated with lignin biosynthesis in loblolly pine[J].Plant Mol Biol, 1999,40:555-565
[15]	Ibrahim R K, Bruneau A, Bantignies B. Plant O-methyltransferases: molecular analysis, common signature and classification[J]. Plant Molecular Biology, 1998, 36(1): 1-10
[16]	Jouanin L, Goujon T, de Nadai V, et al. Lignification in transgenic poplars with extremely reduced caffeic acid O-methyltransferase activity[J]. Plant Physiol,2000, 123(4), 1363-1374
[17]	Lapierre C, Pollet B, Petit-Conil M, et al. Structural alterations of lignins in transgenic poplars with depressed cinnamylalcohol dehydrogenase or caffeic acid O-methyltransferase activity have an opposite impact on the efficiency of industrial kraft pulping[J]. Plant Physiol,1999,119(1): 153-164
[18]	马常耕, 孙晓梅. 我国落叶松遗传改良现状及发展方向[J].世界林业研究,2008,21(3) :58-63
[19]	孙晓梅, 张守攻, 李时元, 等. 日本落叶松纸浆材优良家系多性状联合选择[J].林业科学,2005,41(4) :48-54
[20]	许晨璐. 落叶松基因挖掘及基因差异表达与杂种优势形成机制探讨[D].北京:中国林业科学研究院,2013
[21]	Zubieta C, He X Z, Dixon R A, et al. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases[J].Nature Structural Biology, 2001, 8(3): 271-279
[22]	Kim B G, Kim D H, Hur H G, et al. O-Methyltransferases from Arabidopsis thaliana[J].Agric Chem Biotechnol,2005, 48:113-119
[23]	刘希华. 欧洲黑杨幼苗氮高效基因型及SNPs标记筛选研究[D].南京:南京林业大学,2010
[24]	郭琦, 王保垒, 王博文, 等. 毛白杨 PtDREB2A基因的克隆、表达及单核苷酸多态性分析[J].林业科学,2011,47(4):49-56
[25]	Kim B G, Lee Y J, Park Y H, et al. Caffeic Acid O-Methyltransferase from Populus deltoides: functional expression and characterization[J]. Journal of Plant Biology, 2006, 49(1) : 55-60
[26]	谷振军, 张党权, 黄青云. 木质素合成关键酶基因与造纸植物转基因改良应用研究[J].中南林业科技大学学报,2010,30(3):67-74
[27]	Boerjan W, Ralph J, Baucher M. Lignin biosynthesis[J]. Annual Review of Plant Biology,2003, 54(1):519-546
[28]	Zubieta C, Kota P, Ferrer J L, et al. Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase[J].The Plant Cell,2002,14:1265-1277
[29]	Zhang D Q, Zhang Z Y. Single nucleotidepolymorphisms discovery and linkage disequilibrium[J]. Forestry Studies in China, 2005,7:1-14
[30]	褚延广, 苏晓华. 单核苷酸多态性在林木中的研究进展[J].遗传,2008,30(10):1272-1278
[31]	Yu X Q, Bai G H, Liu S W, et al. Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions[J]. Journal of Experimental Botany,2013,64(6):1537-1551
[32]	Dvornyk V, Sirvio A, Mikkonen M, et al. Low nudeotide diversity at the pal/locus in the widely distributed Pinus sylvestris[J].Mol Biol Evo,2003,19:179-188
[33]	Suha Y, Vijg J. SNP discovery in associating genetic variation with human disease phenotypes[J]. Mutation Research, 2005,573: 41-53
[34]	Krutovsky K V, Neale D B. Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality-related candidate genes in douglas fir[J].Genetics, 2005,171(4): 2029-2041
[35]	Pot D, McMillan L, Echt C, et al.Nucleotide variation in genes involved in wood formation in two pine species[J].New Phytologist, 2005,167:101-112

Isolation and Single Nucleotide Polymorphisms Analysis of Caffeic Acid O-methyltransferase (LkCOMT) in Larix kaempferi

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通讯作者: 陈斌, bchen63@163.com

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Isolation and Single Nucleotide Polymorphisms Analysis of Caffeic Acid O-methyltransferase (LkCOMT) in Larix kaempferi

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