A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col-0 and Ws.
Arabidopsis thaliana
Columbia Col-0 ecotype
TMT labeling
Wassilewskija ecotype
quantitative proteomics
shoot
Journal
Proteomics
ISSN: 1615-9861
Titre abrégé: Proteomics
Pays: Germany
ID NLM: 101092707
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
revised:
10
02
2021
received:
24
11
2020
accepted:
07
04
2021
pubmed:
24
4
2021
medline:
9
10
2021
entrez:
23
4
2021
Statut:
ppublish
Résumé
Arabidopsis has become a powerful model to study morphogenesis, plant growth, development but also plant response to environmental conditions. Over 1000 Arabidopsis genomes are available and show natural genetic variations. Among them, the main reference accessions Wassilewskija (Ws) and Columbia (Col-0), originally growing at contrasted altitudes and temperatures, are widely studied, but data contributing to their molecular phenotyping are still scarce. A global quantitative proteomics approach using isobaric stable isotope labeling (Tandem Mass Tags, TMT) was performed on Ws and Col-0. Plants have been hydroponically grown at 16 h/8 h (light/dark cycle) at 23°C day/19°C night for three weeks. A TMT labeling of the proteins extracted from their shoots has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several proteins families possibly involved in the differential responses observed for Ws and Col-0 during plant development and upon environmental changes. In particular, Ws and Col-0 mainly differ in photosynthesis, cell wall-related proteins, plant defense/stress, ROS scavenging enzymes/redox homeostasis and DNA/RNA binding/transcription/translation/protein folding.
Identifiants
pubmed: 33891803
doi: 10.1002/pmic.202000293
doi:
Substances chimiques
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2000293Informations de copyright
© 2021 The Authors. Proteomics published by Wiley-VCH GmbH.
Références
Alonso-Blanco, C., & Koornneef, M. (2000). Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics. Trends in Plant Science, 5, 22-29.
Weigel, D. (2012). Natural variation in Arabidopsis: from molecular genetics to ecological genomics1,[W][OA]. Plant Physiology, 158, 2-22.
Passardi, F., Dobias, J., Valério, L., Guimil, S., Penel, C., & Dunand, C. (2007). Morphological and physiological traits of three major Arabidopsis thaliana accessions. Journal of Plant Physiology, 164, 980-992.
Bolle, C., Schneider, A., & Leister, D. (2011). Perspectives on systematic analyses of gene function in Arabidopsis thaliana: New tools, topics and trends. Current Genomics, 12, 1-14.
Aukerman, M. J., Hirschfeld, M., Wester, L., Weaver, T. C., Clack, T., Amasino, R. M., & Sharrock, R. A. (1997). A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing. The Plant Cell, 9, 1317-1326.
Pouteau, S., Ferret, V., Gaudin, V., Lefebvre, D., Sabar, M., Zhao, G., & Prunus, F. (2004). Extensive phenotypic variation in early flowering mutants of Arabidopsis. Plant Physiology, 135, 201-211.
Aceves-García, P., Álvarez-Buylla, E. R., Garay-Arroyo, A., García-Ponce, B., Muñoz, R., & Sánchez, M. De La P. (2016). Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana. Frontiers in Plant Science, 7, 858.
Beemster, G. T., & Baskin, T. I. (1998). Analysis of cell division and elongation underlying the developmental acceleration of root growth in Arabidopsis thaliana. Plant Physiology, 116, 1515-1526.
Yang, S., & Hua, J. (2004). A haplotype-specific resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. The Plant Cell, 16, 1060-1071.
Bartels, S., Anderson, J. C., González Besteiro, M. A., Carreri, A., Hirt, H., Buchala, A., Métraux, J.-P., Peck, S. C., & Ulm, R. (2009). MAP kinase phosphatase1 and protein tyrosine phosphatase1 are repressors of salicylic acid synthesis and SNC1-mediated responses in Arabidopsis. The Plant Cell, 21, 2884-2897.
Gómez-Gómez, L., Felix, G., & Boller, T. (1999). A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana. The Plant Journal, 18, 277-284.
Liu, Y., Beyer, A., & Aebersold, R. (2016). On the dependency of cellular protein levels on mRNA abundance. Cell, 165, 535-550.
Mergner, J., Frejno, M., Messerer, M., Lang, D., Samaras, P., Wilhelm, M., Mayer, K., Schwechheimer, C., & Kuster, B. (2020). Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis. Scientific Data, 7, 334.
Jamet, E., Roujol, D., San-Clemente, H., Irshad, M., Soubigou-Taconnat, L., Renou, J.-P., & Pont-Lezica, R. (2009). Cell wall biogenesis of Arabidopsis thaliana elongating cells: Transcriptomics complements proteomics. Bmc Genomics [Electronic Resource], 10, 505.
Minic, Z., Jamet, E., San-Clemente, H., Pelletier, S., Renou, J.-P., Rihouey, C., Okinyo, D. P., Proux, C., Lerouge, P., & Jouanin, L. (2009). Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes. BMC Plant Biology, 9, 6.
Turek, I., Wheeler, J. I., Gehring, C., Irving, H. R., & Marondedze, C. (2015). Quantitative proteome changes in Arabidopsis thaliana suspension-cultured cells in response to plant natriuretic peptides. Data in Brief, 4, 336-343.
Ward, J., Baker, J., Llewellyn, A., Hawkins, N., & Beale, M. (2011). Metabolomic analysis of Arabidopsis reveals hemiterpenoid glycosides as products of a nitrate ion-regulated, carbon flux overflow. Proceedings of the National Academy of Sciences USA, 108, 10762-10767.
Ma, J., Wang, D., She, J., Li, J., Zhu, J.-K., & She, Y.-M. (2016). Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis. New Phytologist, 212, 282-296.
Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72, 248-254.
The, M., Maccoss, M., Noble, W., & Käll, L. (2016). Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. Journal of the American Society for Mass Spectrometry, 27, 1719-1727.
San Clemente, H., Pont-Lezica, R., & Jamet, E. (2009). Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case. Bioinformatics and Biology Insights, 3, 15-28.
Perez-Riverol, Y., Csordas, A., Bai, J., Bernal-Llinares, M., Hewapathirana, S., Kundu, D. J., Inuganti, A., Griss, J., Mayer, G., Eisenacher, M., Pérez, E., Uszkoreit, J., Pfeuffer, J., Sachsenberg, T., Yılmaz, Ş., Tiwary, S., Cox, J., Audain, E., Walzer, M., Jarnuczak, A. F., Ternent, T., Brazma, A., & Vizcaíno, J. A. (2019). The PRIDE database and related tools and resources in 2019: Improving support for quantification data. Nucleic Acids Research, 47, D442-D450.
Stewart, J. J., Polutchko, S. K., Adams, W. W., & Demmig-Adams, B. (2017). Acclimation of Swedish and Italian ecotypes of Arabidopsis thaliana to light intensity. Photosynthesis Research, 134, 215-229.
van Rooijen, R., Aarts, M., & Harbinson, J. (2015). Natural genetic variation for acclimation of photosynthetic light use efficiency to growth irradiance in Arabidopsis. Plant Physiology, 167, 1412-1429.
Adams, W., Stewart, J., Cohu, C., Muller, O., & Demmig-Adams, B. (2016). Habitat Temperature and Precipitation of Arabidopsis thaliana Ecotypes Determine the Response of Foliar Vasculature, Photosynthesis, and Transpiration to Growth Temperature. Frontiers in Plant Science, 7, 1026.
Braidwood, L., Breuer, C., & Sugimoto, K. (2014). My body is a cage: Mechanisms and modulation of plant cell growth. New Phytologist, 201, 388-402.
Le Gall, H., Philippe, F., Domon, J- M., Gillet, F., Pelloux, J., Rayon, C. (2015). Cell wall metabolism in response to abiotic stress. Plants, 4, 112-166.
Duruflé, H., Ranocha, P., Balliau, T., Zivy, M., Albenne, C., Burlat, V., Déjean, S., Jamet, E., & Dunand, C. (2020). An integrative study showing the adaptation to sub-optimal growth conditions of natural populations of Arabidopsis thaliana: A focus on cell wall changes. Cells, 9, 2249.
Kuśnierczyk, A., Winge, P., Midelfart, H., Armbruster, W. S., Rossiter, J. T., & Bones, A. M. (2007). Transcriptional responses of Arabidopsis thaliana ecotypes with different glucosinolate profiles after attack by polyphagous Myzus persicae and oligophagous Brevicoryne brassicae. Journal of Experimental Botany, 58, 2537-2552.
Wang, Y., Yang, L., Zheng, Z., Grumet, R., Loescher, W., Zhu, J.-K., Yang, P., Hu, Y., & Chan, Z. (2013). Transcriptomic and physiological variations of three Arabidopsis ecotypes in response to salt stress. Plos One, 8, e69036.
Bouchabke, O., Chang, F., Simon, M., Voisin, R., Pelletier, G., & Durand-Tardif, M. (2008). Natural variation in Arabidopsis thaliana as a tool for highlighting differential drought responses. Plos One, 3, e1705.
Sharma, S., Lin, W., Villamor, J., & Verslues, P. (2013). Divergent low water potential response in Arabidopsis thaliana accessions Landsberg erecta and Shahdara. Plant, Cell and Environment, 36, 994-1008.
Wattier, C., Turbant, A., Sargos-Vallade, L., Pelloux, J., Rusterucci, C., & Cherqui, A. (2019). New insights into diet breadth of polyphagous and oligophagous aphids on two Arabidopsis ecotypes. Insect Science, 26, 753-769.
Kimura, S., Waszczak, C., Hunter, K., & Wrzaczek, M. (2017). Bound by fate: The role of reactive oxygen species in receptor-like kinase signaling. The Plant Cell, 29, 638-654.
Waszczak, C., Akter, S., Jacques, S., Huang, J., Messens, J., & Van Breusegem, F. (2015). Oxidative post-translational modifications of cysteine residues in plant signal transduction. Journal of Experimental Botany, 66, 2923-2934.
Schippers, J., Foyer, C., & van Dongen, J. (2016). Redox regulation in shoot growth, SAM maintenance and flowering. Current Opinion in Plant Biology, 29, 121-128.
Lu, J., & Holmgren, A. (2014). The thioredoxin antioxidant system. Free Radical Biology and Medicine, 66, 75-87.
Zhang, H., Zhang, T., Liu, H., Shi, D., Wang, M., Bie, X., Li, X., & Zhang, X. (2018). Thioredoxin-Mediated ROS Homeostasis Explains Natural Variation in Plant Regeneration. Plant Physiology, 176, 2231-2250.
Lorković, Z. J. (2009). Role of plant RNA-binding proteins in development, stress response and genome organization. Trends in Plant Science, 14, 229-236.
Alexandre, C., Urton, J., Jean-Baptiste, K., Huddleston, J., Dorrity, M., Cuperus, J., Sullivan, A., Bemm, F., Jolic, D., Arsovski, A., Thompson, A., Nemhauser, J., Fields, S., Weigel, D., Bubb, K., & Queitsch, C. (2017). Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. Molecular Biology and Evolution, 35, 837-854.
Marondedze, C., Thomas, L., Serrano, N. L., Lilley, K. S., & Gehring, C. (2016). The RNA-binding protein repertoire of Arabidopsis thaliana. Scientific Reports, 6, 28766.
Kim, W., Kim, J., Jung, H., Oh, S., Han, Y., & Kang, H. (2010). Comparative analysis of Arabidopsis zinc finger-containing glycine-rich RNA-binding proteins during cold adaptation. Plant Physiology and Biochemistry, 48, 866-872.
Zhang, H., Han, B., Wang, T., Chen, S., Li, H., Zhang, Y., & Dai, S. (2012). Mechanisms of plant salt response: insights from proteomics. Journal of Proteome Research, 11, 49-67.