Phân tích in Silico họ gen Glutamate dehydrogenase ở cây đậu tương (Glycine max L.)
Main Article Content
Abstract
Glutamate dehydrogenase (GDH, EC 1.4.1.2~4) là enzyme xúc tác phản ứng thuận nghịch khử amin hóa glutamate tới a-ketoglutarate hoặc 2-oxoglutarate. Chúng tôi xác định được mười gen mã hóa GDH trong hệ gen của cây đậu tương. Các protein GDH suy diễn có kích thước 637 hoặc 411 amino acid, ngoại trừ GmGDH06. Phân tích cây phả hệ được xây dựng từ các GHD của đậu tương và các cây khác cho thấy các GDH của đậu tương được xếp vào hai nhóm, hai gen nhóm I và tám gen nhóm II. Các protein nhóm II có motif bảo thủ tín hiệu khu trú ti thể, motif bảo thủ gắn cơ chất đặc hiệu a-ketoglutarate và vùng gắn đặc hiệu coenzyme NADH. Các protein nhóm I cũng có vùng gắn cơ chất đặc hiệu nhưng có vùng gắn coenzyme NADPH. Sự biểu hiện của các gen GDH của cây đậu tương khác nhau ở các mô khác nhau. Bốn gen GmGDH03, GmGDH04, GmGDH05và GmGDH07 biểu hiện ở tất cả các mô ở tất cả các giai đoạn phát triển được nghiên cứu. Các GmGDH biểu hiện ở mô sinh sản mạnh hơn ở mô sinh dưỡng, ngoại trừ GmGDH06, gen biểu hiện đặc hiệu ở nốt sần.
Keywords:
Glutamate dehydrogenase, biểu hiện gen, cây phả hệ, đặc trưng của gen, đậu tương
References
[1] M. Friedman and D. L. Brandon, Nutritional and health benefits of soy proteins, J Agric Food Chem 49 (2001) 1069-86.
[2] K. Liu, Soybeans as functional foods and ingredients, AOCS Publishing (2005).
[3] J. Schmutz, S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, et al., Genome sequence of the palaeopolyploid soybean, Nature, 463 (2010) 178-183.
[4] F. Dubois, T. Tercé-Laforgue, M.-B. Gonzalez-Moro, J.-M. Estavillo, R. Sangwan, A. Gallais, et al., Glutamate dehydrogenase in plants: is there a new story for an old enzyme?, Plant Physiol and Biochem 41 (2013) 565-576.
[5] B. G. Forde and P. J. Lea, Glutamate in plants: metabolism, regulation, and signalling, in J Exp Bot 58 (2007) 2339-58.
[6] B. G. Forde, Glutamate signalling in roots, in J Exp Bot. 65 (2014) 779-787.
[7] J. X. Fontaine, T. Terce-Laforgue, P. Armengaud, G. Clement, J. P. Renou, S. Pelletier, et al., Characterization of a NADH-dependent glutamate dehydrogenase mutant of Arabidopsis demonstrates the key role of this enzyme in root carbon and nitrogen metabolism, in Plant Cell 24 (2012) 4044-4065.
[8] P. J. Baker, K. L. Britton, P. C. Engel, G. W. Farrants, K. S. Lilley, D. W. Rice, et al., Subunit assembly and active site location in the structure of glutamate dehydrogenase, Proteins 12 (1992) 75-86.
[9] K. A. Loulakakis and K. A. Roubelakis-Angelakis, Plant NAD(H)-Glutamate Dehydrogenase Consists of Two Subunit Polypeptides and Their Participation in the Seven Isoenzymes Occurs in an Ordered Ratio, Plant Physiol 97 (1991) 104-111.
[10] F. J. Turano, S. S. Thakkar, T. Fang, and J. M. Weisemann, Characterization and expression of NAD(H)-dependent glutamate dehydrogenase genes in Arabidopsis, Plant Physiol 113 (1997) 1329-1341.
[11] X. Qiu, W. Xie, X. Lian, and Q. Zhang, Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation, Plant Cell Rep 28 (2009) 1115-1126.
[12] G. Ferraro, S. Bortolotti, P. Mortera, A. Schlereth, M. Stitt, F. Carrari, et al., Novel glutamate dehydrogenase genes show increased transcript and protein abundances in mature tomato fruits, in J Plant Physiol. 169 (2012) 899-907.
[13] F. M. Restivo, Molecular cloning of glutamate dehydrogenase genes of Nicotiana plumbaginifolia: structure analysis and regulation of their expression by physiological and stress conditions, Plant Science 166 (2004) 971-982.
[14] Y. Miyashita and A. G. Good, NAD(H)-dependent glutamate dehydrogenase is essential for the survival of Arabidopsis thaliana during dark-induced carbon starvation, in J Exp Bot, 59 (2008) 667-680.
[15] G. Tsilikochrisos, G. Tsaniklidis, C. Delis, N. Nikoloudakis, and G. Aivalakis, Glutamate dehydrogenase is differentially regulated in seeded and parthenocarpic tomato fruits during crop development and postharvest storage, Scientia Horticulturae 181 (2015) 34-42.
[16] A. J. Severin, J. L. Woody, Y. T. Bolon, B. Joseph, B. W. Diers, A. D. Farmer, et al., RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome, BMC Plant Biol 10 (2010) 160.
[17] M. P. Purnell, D. S. Skopelitis, K. A. Roubelakis-Angelakis, and J. R. Botella, Modulation of higher-plant NAD(H)-dependent glutamate dehydrogenase activity in transgenic tobacco via alteration of beta subunit levels, Planta 222 (2005) 167-180.
[18] R. Inokuchi, K. I. Kuma, T. Miyata, and M. Okada, Nitrogen-assimilating enzymes in land plants and algae: phylogenic and physiological perspectives, in Physiol Plant. 116 (2002) 1-11.
[19] K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol 28 (2011) 2731-2739.
[20] K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol 30 (2013) 772-780.
[21] E. Gasteiger, C. Hoogland, A. Gattiker, M. R. Wilkins, R. D. Appel, and A. Bairoch, Protein identification and analysis tools on the ExPASy server, in The proteomics protocols handbook, Springer, (2005) 571-607.
[22] A. Y. Guo, Q. H. Zhu, X. Chen, and J. C. Luo, GSDS: a gene structure display server, Yi Chuan 29 (2007) 1023-1026.
[23] R. Inokuchi, K. Motojima, Y. Yagi, K. Nakayama, and M. Okada, Bryopsis maxima (Chlorophyta) glutamate dehydrogenase: multiple genes and isozymes, Journal of Phycology 35 (1999) 1013-1024.
[24] A. Ficarelli, F. Tassi, and F. M. Restivo, Isolation and characterization of two cDNA clones encoding for glutamate dehydrogenase in Nicotiana plumbaginifolia, Plant Cell Physiol 40 (1999) 339-342.
[2] K. Liu, Soybeans as functional foods and ingredients, AOCS Publishing (2005).
[3] J. Schmutz, S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, et al., Genome sequence of the palaeopolyploid soybean, Nature, 463 (2010) 178-183.
[4] F. Dubois, T. Tercé-Laforgue, M.-B. Gonzalez-Moro, J.-M. Estavillo, R. Sangwan, A. Gallais, et al., Glutamate dehydrogenase in plants: is there a new story for an old enzyme?, Plant Physiol and Biochem 41 (2013) 565-576.
[5] B. G. Forde and P. J. Lea, Glutamate in plants: metabolism, regulation, and signalling, in J Exp Bot 58 (2007) 2339-58.
[6] B. G. Forde, Glutamate signalling in roots, in J Exp Bot. 65 (2014) 779-787.
[7] J. X. Fontaine, T. Terce-Laforgue, P. Armengaud, G. Clement, J. P. Renou, S. Pelletier, et al., Characterization of a NADH-dependent glutamate dehydrogenase mutant of Arabidopsis demonstrates the key role of this enzyme in root carbon and nitrogen metabolism, in Plant Cell 24 (2012) 4044-4065.
[8] P. J. Baker, K. L. Britton, P. C. Engel, G. W. Farrants, K. S. Lilley, D. W. Rice, et al., Subunit assembly and active site location in the structure of glutamate dehydrogenase, Proteins 12 (1992) 75-86.
[9] K. A. Loulakakis and K. A. Roubelakis-Angelakis, Plant NAD(H)-Glutamate Dehydrogenase Consists of Two Subunit Polypeptides and Their Participation in the Seven Isoenzymes Occurs in an Ordered Ratio, Plant Physiol 97 (1991) 104-111.
[10] F. J. Turano, S. S. Thakkar, T. Fang, and J. M. Weisemann, Characterization and expression of NAD(H)-dependent glutamate dehydrogenase genes in Arabidopsis, Plant Physiol 113 (1997) 1329-1341.
[11] X. Qiu, W. Xie, X. Lian, and Q. Zhang, Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation, Plant Cell Rep 28 (2009) 1115-1126.
[12] G. Ferraro, S. Bortolotti, P. Mortera, A. Schlereth, M. Stitt, F. Carrari, et al., Novel glutamate dehydrogenase genes show increased transcript and protein abundances in mature tomato fruits, in J Plant Physiol. 169 (2012) 899-907.
[13] F. M. Restivo, Molecular cloning of glutamate dehydrogenase genes of Nicotiana plumbaginifolia: structure analysis and regulation of their expression by physiological and stress conditions, Plant Science 166 (2004) 971-982.
[14] Y. Miyashita and A. G. Good, NAD(H)-dependent glutamate dehydrogenase is essential for the survival of Arabidopsis thaliana during dark-induced carbon starvation, in J Exp Bot, 59 (2008) 667-680.
[15] G. Tsilikochrisos, G. Tsaniklidis, C. Delis, N. Nikoloudakis, and G. Aivalakis, Glutamate dehydrogenase is differentially regulated in seeded and parthenocarpic tomato fruits during crop development and postharvest storage, Scientia Horticulturae 181 (2015) 34-42.
[16] A. J. Severin, J. L. Woody, Y. T. Bolon, B. Joseph, B. W. Diers, A. D. Farmer, et al., RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome, BMC Plant Biol 10 (2010) 160.
[17] M. P. Purnell, D. S. Skopelitis, K. A. Roubelakis-Angelakis, and J. R. Botella, Modulation of higher-plant NAD(H)-dependent glutamate dehydrogenase activity in transgenic tobacco via alteration of beta subunit levels, Planta 222 (2005) 167-180.
[18] R. Inokuchi, K. I. Kuma, T. Miyata, and M. Okada, Nitrogen-assimilating enzymes in land plants and algae: phylogenic and physiological perspectives, in Physiol Plant. 116 (2002) 1-11.
[19] K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol 28 (2011) 2731-2739.
[20] K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol 30 (2013) 772-780.
[21] E. Gasteiger, C. Hoogland, A. Gattiker, M. R. Wilkins, R. D. Appel, and A. Bairoch, Protein identification and analysis tools on the ExPASy server, in The proteomics protocols handbook, Springer, (2005) 571-607.
[22] A. Y. Guo, Q. H. Zhu, X. Chen, and J. C. Luo, GSDS: a gene structure display server, Yi Chuan 29 (2007) 1023-1026.
[23] R. Inokuchi, K. Motojima, Y. Yagi, K. Nakayama, and M. Okada, Bryopsis maxima (Chlorophyta) glutamate dehydrogenase: multiple genes and isozymes, Journal of Phycology 35 (1999) 1013-1024.
[24] A. Ficarelli, F. Tassi, and F. M. Restivo, Isolation and characterization of two cDNA clones encoding for glutamate dehydrogenase in Nicotiana plumbaginifolia, Plant Cell Physiol 40 (1999) 339-342.