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Transcriptome Profiling of the Response of Arabidopsis Suspension Culture Cells to Suc Starvation
Open accessAbstract
Upon encountering nutrient stress conditions, plant cells undergo extensive metabolic changes and induce nutrient recycling pathways for their continued survival. The role of nutrient mobilization in the response of Arabidopsis suspension cells to Suc starvation was examined. Vacuolar autophagy was induced within 24 h of starvation, with increased expression of vacuolar proteases that are likely to be required for degradation of cytoplasmic components delivered to the vacuole, and thus for nutrient recycling. After 48 h of starvation, culture viability began to decrease, and substantial cell death was evident by 72 h. To provide further insight into the pathways required for survival during Suc deficit, transcriptional profiling during Suc starvation was performed using the ATH1 GeneChip array containing 22,810 probe sets. A significant increase in transcript levels was observed for 343 genes within 48 h of starvation, indicating a response to nutrient stress that utilizes the recycling of cellular components and nutrient scavenging for maintaining cell function, the protection of the cell from death through activation of various defense and stress response pathways, and regulation of these processes by specific protein kinases and transcription factors. These physiological and molecular data support a model in which plant cells initiate a coordinated response of nutrient mobilization at the onset of Suc depletion that is able to maintain cell viability for up to 48 h. After this point, genes potentially involved in cell death increase in expression, whereas those functioning in translation and replication decrease, leading to a decrease in culture viability and activation of cell death programs.
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Citations
Cites
MYB transcription factors in Arabidopsis
Dubos, C., Stracke, R., Grotewold, E., Weisshaar, B., Martin, C., & Lepiniec, L. (2010) · Trends in Plant Science · doi:10.1016/j.tplants.2010.06.005 · Cited by 4,865
Antimicrobial Autophagy: A Conserved Innate Immune Response in Drosophila
Moy, R. H., & Cherry, S. (2013) · Journal of Innate Immunity · doi:10.1159/000350326 · Cited by 3,539
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
Higo, K., Ugawa, Y., Iwamoto, M., & Korenaga, T. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.297 · Cited by 3,381
Seed Germination and Dormancy.
Bewley, J. D. (1997) · The Plant Cell · doi:10.1105/tpc.9.7.1055 · Cited by 3,137
The WRKY superfamily of plant transcription factors
Eulgem, T., Rushton, P. J., Robatzek, S., & Somssich, I. E. (2000) · Trends in Plant Science · doi:10.1016/s1360-1385(00)01600-9 · Cited by 3,035
A ubiquitin-like system mediates protein lipidation
Ichimura, Y., Kirisako, T., Takao, T., Satomi, Y., Shimonishi, Y., Ishihara, N., Mizushima, N., Tanida, I., Kominami, E., Ohsumi, M., et al. (2000) · Nature · doi:10.1038/35044114 · Cited by 2,059
Dual action of the active oxygen species during plant stress responses
Dat, J., Vandenabeele, S., Vranov�, E., Van Montagu, M., Inz� *, D., & Van Breusegem, F. (2000) · Cellular and Molecular Life Sciences (CMLS) · doi:10.1007/s000180050041 · Cited by 1,904
bZIP transcription factors in Arabidopsis
Jakoby, M., Weisshaar, B., Dröge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., & Parcy, F. (2002) · Trends in Plant Science · doi:10.1016/s1360-1385(01)02223-3 · Cited by 1,849
CARBOHYDRATE-MODULATED GENE EXPRESSION IN PLANTS
Koch, K. E. (1996) · Annual Review of Plant Physiology and Plant Molecular Biology · doi:10.1146/annurev.arplant.47.1.509 · Cited by 1,766
A protein conjugation system essential for autophagy
Mizushima, N., Noda, T., Yoshimori, T., Tanaka, Y., Ishii, T., George, M. D., Klionsky, D. J., Ohsumi, M., & Ohsumi, Y. (1998) · Nature · doi:10.1038/26506 · Cited by 1,699
Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses
Garg, A. K., Kim, J.-K., Owens, T. G., Ranwala, A. P., Choi, Y. D., Kochian, L. V., & Wu, R. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252637799 · Cited by 1,346
Regulation of an ATG7 - beclin 1 Program of Autophagic Cell Death by Caspase-8
Yu, L., Alva, A., Su, H., Dutt, P., Freundt, E., Welsh, S., Baehrecke, E. H., & Lenardo, M. J. (2004) · Science · doi:10.1126/science.1096645 · Cited by 1,220
Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,010
Kirisako, T., Ichimura, Y., Okada, H., Kabeya, Y., Mizushima, N., Yoshimori, T., Ohsumi, M., Takao, T., Noda, T., & Ohsumi, Y. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.151.2.263 · Cited by 980
Chen, W., Provart, N. J., Glazebrook, J., Katagiri, F., Chang, H.-S., Eulgem, T., Mauch, F., Luan, S., Zou, G., Whitham, S. A., et al. (2002) · The Plant Cell · doi:10.1105/tpc.010410 · Cited by 968
Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response
Dong, J., Chen, C., & Chen, Z. (2003) · Plant Molecular Biology · doi:10.1023/a:1020780022549 · Cited by 889
Formation Process of Autophagosome Is Traced with Apg8/Aut7p in Yeast
Kirisako, T., Baba, M., Ishihara, N., Miyazawa, K., Ohsumi, M., Yoshimori, T., Noda, T., & Ohsumi, Y. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.147.2.435 · Cited by 881
Metabolic repression of transcription in higher plants.
Sheen, J. (1990) · The Plant Cell · doi:10.1105/tpc.2.10.1027 · Cited by 720
TOR controls translation initiation and early G1 progression in yeast.
Barbet, N. C., Schneider, U., Helliwell, S. B., Stansfield, I., Tuite, M. F., & Hall, M. N. (1996) · Molecular Biology of the Cell · doi:10.1091/mbc.7.1.25 · Cited by 715
MCM Proteins in DNA Replication
Tye, B. K. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.649 · Cited by 664
Doelling, J. H., Walker, J. M., Friedman, E. M., Thompson, A. R., & Vierstra, R. D. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204630200 · Cited by 606
The target of rapamycin (TOR) proteins
Raught, B., Gingras, A.-C., & Sonenberg, N. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.121145898 · Cited by 605
Hanaoka, H., Noda, T., Shirano, Y., Kato, T., Hayashi, H., Shibata, D., Tabata, S., & Ohsumi, Y. (2002) · Plant Physiology · doi:10.1104/pp.011024 · Cited by 595
The TOR signaling cascade regulates gene expression in response to nutrients
Cardenas, M. E., Cutler, N. S., Lorenz, M. C., Di Como, C. J., & Heitman, J. (1999) · Genes & Development · doi:10.1101/gad.13.24.3271 · Cited by 582
Eulgem, T. (1999) · The EMBO Journal · doi:10.1093/emboj/18.17.4689 · Cited by 555
Controlled cell death, plant survival and development
Lam, E. (2004) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1358 · Cited by 554
A New Protein Conjugation System in Human
Mizushima, N., Sugita, H., Yoshimori, T., & Ohsumi, Y. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.51.33889 · Cited by 513
Cytokinesis in the Arabidopsis Embryo Involves the Syntaxin-Related KNOLLE Gene Product
Lukowitz, W., Mayer, U., & Jürgens, G. (1996) · Cell · doi:10.1016/s0092-8674(00)80993-9 · Cited by 509
The Arabidopsis KNOLLE Protein Is a Cytokinesis-specific Syntaxin
Lauber, M. H., Waizenegger, I., Steinmann, T., Schwarz, H., Mayer, U., Hwang, I., Lukowitz, W., & Jürgens, G. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.139.6.1485 · Cited by 495
Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene
Menand, B., Desnos, T., Nussaume, L., Berger, F., Bouchez, D., Meyer, C., & Robaglia, C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092141899 · Cited by 493
Schluepmann, H., Pellny, T., van Dijken, A., Smeekens, S., & Paul, M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1132018100 · Cited by 490
SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements
Prestridge, D. S. (1991) · Bioinformatics · doi:10.1093/bioinformatics/7.2.203 · Cited by 489
Wu, P., Ma, L., Hou, X., Wang, M., Wu, Y., Liu, F., & Deng, X. W. (2003) · Plant Physiology · doi:10.1104/pp.103.021022 · Cited by 488
Vacuolar Import of Proteins and Organelles From The Cytoplasm
Klionsky, D. J., & Ohsumi, Y. (1999) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.15.1.1 · Cited by 465
Kagaya, Y., Ohmiya, K., & Hattori, T. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.470 · Cited by 462
Willekens, H., Inzé, D., Van Montagu, M., & van Camp, W. (1995) · Molecular Breeding · doi:10.1007/bf02277422 · Cited by 451
Powers, T., & Walter, P. (1999) · Molecular Biology of the Cell · doi:10.1091/mbc.10.4.987 · Cited by 392
Eastmond, P. J., Van Dijken, A. J. H., Spielman, M., Kerr, A., Tissier, A. F., Dickinson, H. G., Jones, J. D. G., Smeekens, S. C., & Graham, I. A. (2002) · The Plant Journal · doi:10.1046/j.1365-313x.2002.01220.x · Cited by 380
Programmed Cell Death (PCD): Apoptosis, Autophagic PCD, or Others?
BURSCH, W., ELLINGER, A., GERNER, C., FRÖHWEIN, U., & SCHULTE‐HERMANN, R. (2000) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2000.tb05594.x · Cited by 309
Gene Expression in Autumn Leaves
Bhalerao, R., Keskitalo, J., Sterky, F., Erlandsson, R., Björkbacka, H., Birve, S. J., Karlsson, J., Gardeström, P., Gustafsson, P., Lundeberg, J., et al. (2003) · Plant Physiology · doi:10.1104/pp.012732 · Cited by 305
Vascular Factors in Cognitive Impairment‐Where Are We Now?
HACHINSKI, V., & MUNOZ, D. (2000) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2000.tb06343.x · Cited by 297
Molecular regulation of leaf senescence
Yoshida, S. (2003) · Current Opinion in Plant Biology · doi:10.1016/s1369526602000092 · Cited by 296
Carbon Catabolite Repression Regulates Glyoxylate Cycle Gene Expression in Cucumber.
Graham, I. A., Denby, K. J., & Leaver, C. J. (1994) · The Plant Cell · doi:10.1105/tpc.6.5.761 · Cited by 293
Kametaka, S., Okano, T., Ohsumi, M., & Ohsumi, Y. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.35.22284 · Cited by 275
Meyers, B. C., Morgante, M., & Michelmore, R. W. (2002) · The Plant Journal · doi:10.1046/j.1365-313x.2002.01404.x · Cited by 272
Lu, C.-A., Ho, T.-H. D., Ho, S.-L., & Yu, S.-M. (2002) · The Plant Cell · doi:10.1105/tpc.001735 · Cited by 266
Aubert, S., Gout, E., Bligny, R., Marty-Mazars, D., Barrieu, F., Alabouvette, J., Marty, F., & Douce, R. (1996) · The Journal of cell biology · doi:10.1083/jcb.133.6.1251 · Cited by 262
Pathways of straight and branched chain fatty acid catabolism in higher plants
Graham, I. A., & Eastmond, P. J. (2002) · Progress in Lipid Research · doi:10.1016/s0163-7827(01)00022-4 · Cited by 242
Hara, K., Yagi, M., Kusano, T., & Sano, H. (2000) · Molecular and General Genetics MGG · doi:10.1007/pl00008673 · Cited by 233
Cellular and Genetic Responses of Plants to Sugar Starvation
Yu, S.-M. (1999) · Plant Physiology · doi:10.1104/pp.121.3.687 · Cited by 211
Surpin, M., Zheng, H., Morita, M. T., Saito, C., Avila, E., Blakeslee, J. J., Bandyopadhyay, A., Kovaleva, V., Carter, D., Murphy, A., et al. (2003) · The Plant Cell · doi:10.1105/tpc.016121 · Cited by 210
Pnueli, L., Hallak‐Herr, E., Rozenberg, M., Cohen, M., Goloubinoff, P., Kaplan, A., & Mittler, R. (2002) · The Plant Journal · doi:10.1046/j.1365-313x.2002.01364.x · Cited by 210
Genetic Analysis of Yeast RPA1 Reveals Its Multiple Functions in DNA Metabolism
Umezu, K., Sugawara, N., Chen, C., Haber, J. E., & Kolodner, R. D. (1998) · Genetics · doi:10.1093/genetics/148.3.989 · Cited by 206
Autophagy in Tobacco Suspension-Cultured Cells in Response to Sucrose Starvation
Moriyasu, Y., & Ohsumi, Y. (1996) · Plant Physiology · doi:10.1104/pp.111.4.1233 · Cited by 199
Autophagy in Yeast: A Review of the Molecular Machinery.
Huang, W.-P., & Klionsky, D. J. (2002) · Cell Structure and Function · doi:10.1247/csf.27.409 · Cited by 193
Biochemical changes during sucrose deprivation in higher plant cells.
Journet, E., Bligny, R., & Douce, R. (1986) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)35767-8 · Cited by 191
Ahmed, S. U., Rojo, E., Kovaleva, V., Venkataraman, S., Dombrowski, J. E., Matsuoka, K., & Raikhel, N. V. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.149.7.1335 · Cited by 191
Schoof, H. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.91 · Cited by 180
Characterization of a zinc-dependent transcriptional activator from Arabidopsis
de Pater, S. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.23.4624 · Cited by 173
Identification of senescence-associated genes from daylily petals
Panavas, T., Pikula, A., Reid, P. D., Rubinstein, B., & Walker, E. L. (1999) · Plant Molecular Biology · doi:10.1023/a:1006146230602 · Cited by 172
Brouquisse, R., Gaudillère, J.-P., & Raymond, P. (1998) · Plant Physiology · doi:10.1104/pp.117.4.1281 · Cited by 160
Ito, M., Iwase, M., Kodama, H., Lavisse, P., Komamine, A., Nishihama, R., Machida, Y., & Watanabe, A. (1998) · The Plant Cell · doi:10.1105/tpc.10.3.331 · Cited by 159
Preiß, T., Baron-Benhamou, J., Ansorge, W. J., & Hentze, M. W. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1015 · Cited by 158
Chen, M., Liu, L., Chen, Y.-R., Wu, H., & Yu, S. (1994) · The Plant Journal · doi:10.1046/j.1365-313x.1994.6050625.x · Cited by 153
Nakashima, K., Satoh, R., Kiyosue, T., Yamaguchi‐Shinozaki, K., & Shinozaki, K. (1998) · PLANT PHYSIOLOGY · doi:10.1104/pp.118.4.1233 · Cited by 147
Miernyk, J. A. (2001) · Cell Stress and Chaperones · doi:10.1379/1466-1268(2001)006<0209:tjdpoa>2.0.co;2 · Cited by 142
Expression of the Arabidopsis thaliana invertase gene family
Tymowska‐Lalanne, Z., & Kreis, M. E. (1998) · Planta · doi:10.1007/s004250050481 · Cited by 139
Role of mTOR Signalling in the Control of Translation Initiation and Elongation by Nutrients
Proud, C. G. (2004) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-18930-2_13 · Cited by 122
Cyclin/cdk complexes: Their involvement in cell cycle progression and mitotic division
John, P. C. L., Mews, M., & Moore, R. H. (2001) · PROTOPLASMA · doi:10.1007/bf02673865 · Cited by 120
A Novel Acyl-CoA Oxidase That Can Oxidize Short-chain Acyl-CoA in Plant Peroxisomes
Hayashi, H., Bellis, L. D., Ciurli, A., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.18.12715 · Cited by 115
Stevens, R. G., Mariconti, L., Rossignol, P., Perennes, C., Cella, R., & Catherine Bergounioux, A. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205125200 · Cited by 85
Shimizu, S., & Mori, H. (1998) · Plant and Cell Physiology · doi:10.1093/oxfordjournals.pcp.a029365 · Cited by 84
Dieuaide‐Noubhani, M., Couée, I., Pradet, A., & Raymond, P. (1993) · Biochemical Journal · doi:10.1042/bj2960199 · Cited by 62
van der Knaap, E., Jagoueix, S., & Kende, H. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.18.9979 · Cited by 60
Effects of carbohydrate starvation on gene expression in citrus root
Li, C. Y., Weiss, D. W., & Goldschmidt, E. Ε. (2003) · Planta · doi:10.1007/s00425-002-0963-6 · Cited by 59
Identification of genes that are up‐regulated in concert during sugar depletion in Arabidopsis
LEE, E. ‐., Koizumi, N., & Sano, H. (2004) · Plant Cell & Environment · doi:10.1046/j.1365-3040.2004.01146.x · Cited by 38
Fujiki, Y., Ito, M. A., Itoh, T., Nishida, I., & Watanabe, A. (2002) · Plant and Cell Physiology · doi:10.1093/pcp/pcf032 · Cited by 34
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Baena-González, E., Rolland, F., Thevelein, J. M., & Sheen, J. (2007) · Nature · doi:10.1038/nature06069 · Cited by 1,520
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Foyer, C. H., & Noctor, G. (2009) · Antioxidants & Redox Signaling · doi:10.1089/ars.2008.2177 · Cited by 1,431
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Metadata
- Authors
- Contento, A. L., Kim, S.-J., & Bassham, D. C.
- Venue
- Plant Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-08-01
- Volume
- 135
- Issue
- 4
- Pages
- 2330-2347
- ISSN
- 0032-0889 (ISSN-L)
- 1532-2548
- OpenAlex
- W2028820728
- Cited by
- 254
- References
- 77
- FWCI
- 15.74
- Type
- journal article
- Language
- en
- Open access
- green
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