Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Geisler-Lee, J., Geisler, M., Coutinho, P. M., Segerman, B., Nishikubo, N., Takahashi, J., Aspeborg, H., Djerbi, S., Master, E., Andersson-Gunneras, S., Sundberg, B., Karpinski, S., Teeri, T. T., Kleczkowski, L. A., Henrissat, B., & Mellerowicz, E. J. Plant Physiology, 140(3):946–962, March, 2006. Place: Rockville Publisher: Amer Soc Plant Biologists WOS:000235868900014doi abstract bibtex Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.
@article{geisler-lee_poplar_2006,
title = {Poplar carbohydrate-active enzymes. {Gene} identification and expression analyses},
volume = {140},
issn = {0032-0889},
doi = {10/bj9bkd},
abstract = {Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.\&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.},
language = {English},
number = {3},
journal = {Plant Physiology},
author = {Geisler-Lee, J. and Geisler, M. and Coutinho, P. M. and Segerman, B. and Nishikubo, N. and Takahashi, J. and Aspeborg, H. and Djerbi, S. and Master, E. and Andersson-Gunneras, S. and Sundberg, B. and Karpinski, S. and Teeri, T. T. and Kleczkowski, L. A. and Henrissat, B. and Mellerowicz, E. J.},
month = mar,
year = {2006},
note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900014},
keywords = {arabidopsis, callose synthase, cell-walls, cellulose, family, hybrid aspen, multiple sequence alignment, pectin methylesterases, populus, sucrose},
pages = {946--962},
}
Downloads: 0
{"_id":"rsANhxWFehPkeKnAm","bibbaseid":"geislerlee-geisler-coutinho-segerman-nishikubo-takahashi-aspeborg-djerbi-etal-poplarcarbohydrateactiveenzymesgeneidentificationandexpressionanalyses-2006","author_short":["Geisler-Lee, J.","Geisler, M.","Coutinho, P. M.","Segerman, B.","Nishikubo, N.","Takahashi, J.","Aspeborg, H.","Djerbi, S.","Master, E.","Andersson-Gunneras, S.","Sundberg, B.","Karpinski, S.","Teeri, T. T.","Kleczkowski, L. A.","Henrissat, B.","Mellerowicz, E. J."],"bibdata":{"bibtype":"article","type":"article","title":"Poplar carbohydrate-active enzymes. Gene identification and expression analyses","volume":"140","issn":"0032-0889","doi":"10/bj9bkd","abstract":"Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.","language":"English","number":"3","journal":"Plant Physiology","author":[{"propositions":[],"lastnames":["Geisler-Lee"],"firstnames":["J."],"suffixes":[]},{"propositions":[],"lastnames":["Geisler"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Coutinho"],"firstnames":["P.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Segerman"],"firstnames":["B."],"suffixes":[]},{"propositions":[],"lastnames":["Nishikubo"],"firstnames":["N."],"suffixes":[]},{"propositions":[],"lastnames":["Takahashi"],"firstnames":["J."],"suffixes":[]},{"propositions":[],"lastnames":["Aspeborg"],"firstnames":["H."],"suffixes":[]},{"propositions":[],"lastnames":["Djerbi"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Master"],"firstnames":["E."],"suffixes":[]},{"propositions":[],"lastnames":["Andersson-Gunneras"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Sundberg"],"firstnames":["B."],"suffixes":[]},{"propositions":[],"lastnames":["Karpinski"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Teeri"],"firstnames":["T.","T."],"suffixes":[]},{"propositions":[],"lastnames":["Kleczkowski"],"firstnames":["L.","A."],"suffixes":[]},{"propositions":[],"lastnames":["Henrissat"],"firstnames":["B."],"suffixes":[]},{"propositions":[],"lastnames":["Mellerowicz"],"firstnames":["E.","J."],"suffixes":[]}],"month":"March","year":"2006","note":"Place: Rockville Publisher: Amer Soc Plant Biologists WOS:000235868900014","keywords":"arabidopsis, callose synthase, cell-walls, cellulose, family, hybrid aspen, multiple sequence alignment, pectin methylesterases, populus, sucrose","pages":"946–962","bibtex":"@article{geisler-lee_poplar_2006,\n\ttitle = {Poplar carbohydrate-active enzymes. {Gene} identification and expression analyses},\n\tvolume = {140},\n\tissn = {0032-0889},\n\tdoi = {10/bj9bkd},\n\tabstract = {Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.\\&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.},\n\tlanguage = {English},\n\tnumber = {3},\n\tjournal = {Plant Physiology},\n\tauthor = {Geisler-Lee, J. and Geisler, M. and Coutinho, P. M. and Segerman, B. and Nishikubo, N. and Takahashi, J. and Aspeborg, H. and Djerbi, S. and Master, E. and Andersson-Gunneras, S. and Sundberg, B. and Karpinski, S. and Teeri, T. T. and Kleczkowski, L. A. and Henrissat, B. and Mellerowicz, E. J.},\n\tmonth = mar,\n\tyear = {2006},\n\tnote = {Place: Rockville\nPublisher: Amer Soc Plant Biologists\nWOS:000235868900014},\n\tkeywords = {arabidopsis, callose synthase, cell-walls, cellulose, family, hybrid aspen, multiple sequence alignment, pectin methylesterases, populus, sucrose},\n\tpages = {946--962},\n}\n\n","author_short":["Geisler-Lee, J.","Geisler, M.","Coutinho, P. M.","Segerman, B.","Nishikubo, N.","Takahashi, J.","Aspeborg, H.","Djerbi, S.","Master, E.","Andersson-Gunneras, S.","Sundberg, B.","Karpinski, S.","Teeri, T. T.","Kleczkowski, L. A.","Henrissat, B.","Mellerowicz, E. J."],"key":"geisler-lee_poplar_2006","id":"geisler-lee_poplar_2006","bibbaseid":"geislerlee-geisler-coutinho-segerman-nishikubo-takahashi-aspeborg-djerbi-etal-poplarcarbohydrateactiveenzymesgeneidentificationandexpressionanalyses-2006","role":"author","urls":{},"keyword":["arabidopsis","callose synthase","cell-walls","cellulose","family","hybrid aspen","multiple sequence alignment","pectin methylesterases","populus","sucrose"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/zotero/upscpub","dataSources":["9cGcv2t8pRzC92kzs","fvfkWcShg3Mybjoog","Tu3jPdZyJF3j547xT"],"keywords":["arabidopsis","callose synthase","cell-walls","cellulose","family","hybrid aspen","multiple sequence alignment","pectin methylesterases","populus","sucrose"],"search_terms":["poplar","carbohydrate","active","enzymes","gene","identification","expression","analyses","geisler-lee","geisler","coutinho","segerman","nishikubo","takahashi","aspeborg","djerbi","master","andersson-gunneras","sundberg","karpinski","teeri","kleczkowski","henrissat","mellerowicz"],"title":"Poplar carbohydrate-active enzymes. Gene identification and expression analyses","year":2006}