Omics-based Databases on Plant Stresses as Information Resources
DOI:
https://doi.org/10.30732/ijbbb.20160103002Keywords:
Plant stress, Stress database, Abiotic, Biotic, Agriculture.Abstract
In natural ecology and cultivated condition, plants and crop species are subjected to numerous stresses which influence their growth and development. Stress in plants can be regarded as an alteration in growth phage which causes interruption in metabolic homeostasis. Plant pathogens correspond to biotic stresses while different environmental factors accounts for abiotic stresses. Plants take action towards these stresses and evolved improved adaptation by triggering their machinery. Currently, a number of studies are going on for better understanding of plants adaptation and survival in different stresses and this is resulting in a large amount of data. Therefore, there is need of proper management, investigation and interpretation of this data for decoding plant strategies towards stresses. This has led to development of various databases and resources upholding information and details about stresses in numerous crops and plants. In this article, we are providing a brief detail of different resources which provides valuable information in the field of plant stresses.
References
[1] Rodziewicz, P., Swarcewicz, B., Chmielewska, K., Wojakowska, A., Stobiecki, M., 2014. Influence of abiotic stresses on plant proteome and metabolome changes. Acta Physiologiae Plantarum, 36, 1-19.
[2] Hirt, H., Shinozaki, K., 2004, Plant responses to abiotic stress. Berlin Heidelberg: Springer.
[3] Rejeb, I.B., Pastor, V., Mauch-Mani, B., 2014, Plant responses to simultaneous biotic and abiotic stress: molecular mechanisms. Plants, 3, 458-475.
[4] Shrivastava, P., Kumar, R., 2015, Soil salinity: A serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci, 22, 123–131.
[5] Atkinson, N.J., Urwin, P.E., 2012, The interaction of plant biotic and abiotic stresses: from genes to the field. doi:10.1093/jxb/ers100.
[6] Upadhyaya, H., Sahoo, L., Panda, S.K., 2013, Molecular physiology of osmotic stress in plants. In: Molecular Stress Physiology of Plants G.R. Rout, A.B. Das (ed.), Springer, pp 179-192.
[7] Bray, E.A., Bailey-Serres, J., Weretilnyk, E., 2000, Responses to abiotic stresses. In: Biochemistry and Molecular Biology of Plants, W. Gruissem, B. Buchannan, R. Jones (ed.), American Society of Plant Physiologists, Rockville, MD, 1158–1249.
[8] Mantri, N., Patade, V., Penna, S., Ford, R., Pang, E., 2012, Abiotic stress responses in plants: Present and future. In: Abiotic Stress Responses in Plants, P. Ahmad, M.N.V. Prasad (ed.), 1-19.
[9] Bilgin, D.D., Zavala, J.A., Zhu, J., Clough, S.J., Ort, D.R., DeLucia, E.H., 2010, Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ, 33, 1597-613.
[10] Prabha, R., Singh, D.P., Keshri, V., Sevyaa, Sharma, A.K., 2014, Bioinformatics resources for the management of biological information on plant responses towards stresses. In: Approaches to Plant Stress and their Management R.K. Gaur, P. Sharma (ed.), Springer, 365-382.
[11] Dorantes-Acosta, A.E., Sánchez-Hernández, C.V., Arteaga-Vázquez, M.A., 2012, Biotic stress in plants: life lessons from your parents and grandparents. Front Genet, 3, 256.
[12] Osakabe, Y., Arinaga, N., Umezawa, T., Katsura, S., Nagamachi, K., Tanaka, H., 2013. Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis. Plant Cell 25, 609–624.
[13] Hirayama, T., Shinozaki, K., 2010, Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J., 61, 1041-52.
[14] Mahajan, S., Tuteja, N., 2005, Cold, salinity and drought stresses: An overview. Archives of Biochemistry and Biophysics, 444, 139–158.
[15] Vinocur, B., Altman, A., 2005, Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol, 16, 123-132.
[16] Ramakrishna, A., Ravishankar, G.A., 2011, Influence of abiotic stress signals on secondary metabolites in plants. Plant Signal Behav, 6, 1720–1731.
[17] Crane, T.A., Roncoli, C., Hoogenboom, G., 2011, Adaptation to climate change and climate variability: The importance of understanding agriculture as performance. NJAS - Wageningen Journal of Life Sciences, 57, 179–185.
[18] Hilker, M., Schwachtje, J., Baier, M., Balazadeh, S., Bäurle, I., Geiselhardt, S., Hincha, D., Kunze, R., Mueller-Roeber, B., Rillig, M.C., Rolff, J., Romeis, T., Schmülling, T., Steppuhn, A., van Dongen, J., Whitcomb, S.J., Wurst, S., Zuther, E., Kopka, J., 2015, Priming and memory of stress responses in organisms lacking a nervous system. Biological Reviews, DOI: 10.1111/brv.12215
[19] Osakabe, Y., Osakabe, K., Shinozaki, K., Tran L-S.P., 2014, Response of plants to water stress. Front Plant Sci, 5, 86.
[20] Li, Z., Wakao, S., Fischer, B. B., Niyogi, K. K., 2009, Sensing and responding to excess light. Annu. Rev. Plant Biol. 60, 239–260.
[21] Pareek, A., Sopory, S.K., Bohnert, H., Govindjee, 2010, Abiotic stress adaptation in plants: physiological, molecular and genomic foundation. Springer. ISBN 978-90-481-3112-9
[22] Bäurle, I., 2016, Plant heat adaptation: priming in response to heat stress. F1000Research, 5(F1000 Faculty Rev), 694.
[23] Bui, E., 2013, Possible role of soil alkalinity in plant breeding for salt-tolerance. Biol Lett, 9, 20130566.
[24] Bromham, L., Haris, Saslis-Lagoudakis, C,, Bennett, T.H., Flowers, T.J., 2013, Soil alkalinity and salt tolerance: adapting to multiple stresses. Biology Letters, DOI: 10.1098/rsbl.2013.0642.
[25] Emamverdian, A., Ding, Y., Mokhberdoran, F., Xie, Y., 2015, Heavy metal stress and some mechanisms of plant defense response. The Scientific World Journal, 2015, 1-18.
[26] Rorison IH (1986) The response of plants to acid soils. Experientia. 42: 357-362.
[27] Edmeades, D.C., Blamey, F.P.C., Farina, M.P.W., 1995, Techniques for assessing plant responses on acid soils. In: Plant-Soil Interactions at Low pH, Date, R.A. et al (ed.), 221-233.
[28] Munns, R., Tester, M., 2008, Mechanisms of salinity tolerance. Annu Rev Plant Biol, 59, 651–681
[29] Silva, P., Facanha, A.R., Tavares, R.M., Geros, H., 2010, Role of tonoplast proton pumps and Na+/H+ antiport system in salt tolerance of Populus euphratica oliv. J Plant Growth Regul, 29, 23–34.
[30] Thomashow, M.F., 2010, Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol, 154, 571–577
[31] Balaji, J., Crouch, J.H., Petite, P.V., Hoisington, D.A., 2006, A database of annotated tentative orthologs from crop abiotic stress transcripts. Bioinformation, 1, 225-227.
[32] Wanchana, S., Thongjuea, S., Ulat, V.J., Anacleto, M., Mauleon, R., Conte, M., Rouard, M., Ruiz, M., Krishnamurthy, N., Sjolander, K., van Hintum, T., Bruskiewich, R.M., 2008, The Generation Challenge Programme comparative plant stress responsive gene catalogue. Nucleic Acids Res, 36, D943-D946.
[33] Shameer, K., Ambika, S., Varghese, S.M., Karaba, N., Udayakumar, M., Sowdhamini, R., 2009, STIFDB—Arabidopsis Stress Responsive Transcription Factor DataBase. International Journal of Plant Genomics, doi:10.1155/2009/583429.
[34] Prabha, R., Ghosh, I., Singh, D.P., 2011, Plant Stress Gene Database: A collection of plant genes responding to stress condition. ARPN Journal of Science and Technology, 1, 28–31.
[35] Smita, S., Lenka, S.K., Katiyar, A., Jaiswal, P., Preece, J., Bansal, K.C., 2011, QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database, doi:10.1093/database/bar037
[36] Ali, M., Khalid, R.R., Nawaz, M., Qamar, N., 2011, Development of a tool for the analysis of plant stress proteins. Int J Bioautomation, 15, 261-266.
[37] Naika, M., Shameer, K., Mathew, O.K., Gowda, R., Sowdhamini, R., 2013, STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol, 54, e8.
[38] Borkotoky, S., Saravanan, V., Jaiswal, A., Das, B., Selvaraj, S., Murali, A., Lakshmi, P.T.V., 2013, The Arabidopsis Stress Responsive Gene Database. International Journal of Plant Genomics, 2013. http://dx.doi.org/10.1155/2013/949564.
[39] Zhang, S., Yue, Y., Sheng, L., Wu, Y., Fan, G., Li, A., Hu, X., ShangGuan, M., Wei, C., 2013, PASmiR: A literature-curated database for miRNA molecular regulation in plant response to abiotic stress. BMC Plant Biol, 13, 33.
[40] Priya, P., Jain, M., 2013, RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database,2013, bat027.
[41] Alter, S., Bader, K.C., Spannagl, M., Wang, Yu., Bauer, E., Schön, C., Mayer, K.F.X., 2014, DroughtDB: An expert-curated compilation of plant drought stress genes and their homologs in nine species. doi: 10.1093/database/bav046.
[42] Kumar S.A., Kumari P.H., Sundararajan V.S., Suravajhala P., Kanagasabai R., Kishor P.B.K., 2014, PSPDB: Plant Stress Protein Database. Plant Molecular Biology Reporter, 32, 940-942.
[43] Mousavi, S.A., Pouya, F.M., Ghaffari, M.R., Mirzaei, M., Ghaffari, A., Alikhani, M., Ghareyazie, M., Komatsu, S., Haynes, P.A., Salekdeh, G.H., 2016, PlantPReS: A database for plant proteome response to stress. Journal of Proteomics, 143, 69-72.
[2] Hirt, H., Shinozaki, K., 2004, Plant responses to abiotic stress. Berlin Heidelberg: Springer.
[3] Rejeb, I.B., Pastor, V., Mauch-Mani, B., 2014, Plant responses to simultaneous biotic and abiotic stress: molecular mechanisms. Plants, 3, 458-475.
[4] Shrivastava, P., Kumar, R., 2015, Soil salinity: A serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci, 22, 123–131.
[5] Atkinson, N.J., Urwin, P.E., 2012, The interaction of plant biotic and abiotic stresses: from genes to the field. doi:10.1093/jxb/ers100.
[6] Upadhyaya, H., Sahoo, L., Panda, S.K., 2013, Molecular physiology of osmotic stress in plants. In: Molecular Stress Physiology of Plants G.R. Rout, A.B. Das (ed.), Springer, pp 179-192.
[7] Bray, E.A., Bailey-Serres, J., Weretilnyk, E., 2000, Responses to abiotic stresses. In: Biochemistry and Molecular Biology of Plants, W. Gruissem, B. Buchannan, R. Jones (ed.), American Society of Plant Physiologists, Rockville, MD, 1158–1249.
[8] Mantri, N., Patade, V., Penna, S., Ford, R., Pang, E., 2012, Abiotic stress responses in plants: Present and future. In: Abiotic Stress Responses in Plants, P. Ahmad, M.N.V. Prasad (ed.), 1-19.
[9] Bilgin, D.D., Zavala, J.A., Zhu, J., Clough, S.J., Ort, D.R., DeLucia, E.H., 2010, Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ, 33, 1597-613.
[10] Prabha, R., Singh, D.P., Keshri, V., Sevyaa, Sharma, A.K., 2014, Bioinformatics resources for the management of biological information on plant responses towards stresses. In: Approaches to Plant Stress and their Management R.K. Gaur, P. Sharma (ed.), Springer, 365-382.
[11] Dorantes-Acosta, A.E., Sánchez-Hernández, C.V., Arteaga-Vázquez, M.A., 2012, Biotic stress in plants: life lessons from your parents and grandparents. Front Genet, 3, 256.
[12] Osakabe, Y., Arinaga, N., Umezawa, T., Katsura, S., Nagamachi, K., Tanaka, H., 2013. Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis. Plant Cell 25, 609–624.
[13] Hirayama, T., Shinozaki, K., 2010, Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J., 61, 1041-52.
[14] Mahajan, S., Tuteja, N., 2005, Cold, salinity and drought stresses: An overview. Archives of Biochemistry and Biophysics, 444, 139–158.
[15] Vinocur, B., Altman, A., 2005, Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol, 16, 123-132.
[16] Ramakrishna, A., Ravishankar, G.A., 2011, Influence of abiotic stress signals on secondary metabolites in plants. Plant Signal Behav, 6, 1720–1731.
[17] Crane, T.A., Roncoli, C., Hoogenboom, G., 2011, Adaptation to climate change and climate variability: The importance of understanding agriculture as performance. NJAS - Wageningen Journal of Life Sciences, 57, 179–185.
[18] Hilker, M., Schwachtje, J., Baier, M., Balazadeh, S., Bäurle, I., Geiselhardt, S., Hincha, D., Kunze, R., Mueller-Roeber, B., Rillig, M.C., Rolff, J., Romeis, T., Schmülling, T., Steppuhn, A., van Dongen, J., Whitcomb, S.J., Wurst, S., Zuther, E., Kopka, J., 2015, Priming and memory of stress responses in organisms lacking a nervous system. Biological Reviews, DOI: 10.1111/brv.12215
[19] Osakabe, Y., Osakabe, K., Shinozaki, K., Tran L-S.P., 2014, Response of plants to water stress. Front Plant Sci, 5, 86.
[20] Li, Z., Wakao, S., Fischer, B. B., Niyogi, K. K., 2009, Sensing and responding to excess light. Annu. Rev. Plant Biol. 60, 239–260.
[21] Pareek, A., Sopory, S.K., Bohnert, H., Govindjee, 2010, Abiotic stress adaptation in plants: physiological, molecular and genomic foundation. Springer. ISBN 978-90-481-3112-9
[22] Bäurle, I., 2016, Plant heat adaptation: priming in response to heat stress. F1000Research, 5(F1000 Faculty Rev), 694.
[23] Bui, E., 2013, Possible role of soil alkalinity in plant breeding for salt-tolerance. Biol Lett, 9, 20130566.
[24] Bromham, L., Haris, Saslis-Lagoudakis, C,, Bennett, T.H., Flowers, T.J., 2013, Soil alkalinity and salt tolerance: adapting to multiple stresses. Biology Letters, DOI: 10.1098/rsbl.2013.0642.
[25] Emamverdian, A., Ding, Y., Mokhberdoran, F., Xie, Y., 2015, Heavy metal stress and some mechanisms of plant defense response. The Scientific World Journal, 2015, 1-18.
[26] Rorison IH (1986) The response of plants to acid soils. Experientia. 42: 357-362.
[27] Edmeades, D.C., Blamey, F.P.C., Farina, M.P.W., 1995, Techniques for assessing plant responses on acid soils. In: Plant-Soil Interactions at Low pH, Date, R.A. et al (ed.), 221-233.
[28] Munns, R., Tester, M., 2008, Mechanisms of salinity tolerance. Annu Rev Plant Biol, 59, 651–681
[29] Silva, P., Facanha, A.R., Tavares, R.M., Geros, H., 2010, Role of tonoplast proton pumps and Na+/H+ antiport system in salt tolerance of Populus euphratica oliv. J Plant Growth Regul, 29, 23–34.
[30] Thomashow, M.F., 2010, Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol, 154, 571–577
[31] Balaji, J., Crouch, J.H., Petite, P.V., Hoisington, D.A., 2006, A database of annotated tentative orthologs from crop abiotic stress transcripts. Bioinformation, 1, 225-227.
[32] Wanchana, S., Thongjuea, S., Ulat, V.J., Anacleto, M., Mauleon, R., Conte, M., Rouard, M., Ruiz, M., Krishnamurthy, N., Sjolander, K., van Hintum, T., Bruskiewich, R.M., 2008, The Generation Challenge Programme comparative plant stress responsive gene catalogue. Nucleic Acids Res, 36, D943-D946.
[33] Shameer, K., Ambika, S., Varghese, S.M., Karaba, N., Udayakumar, M., Sowdhamini, R., 2009, STIFDB—Arabidopsis Stress Responsive Transcription Factor DataBase. International Journal of Plant Genomics, doi:10.1155/2009/583429.
[34] Prabha, R., Ghosh, I., Singh, D.P., 2011, Plant Stress Gene Database: A collection of plant genes responding to stress condition. ARPN Journal of Science and Technology, 1, 28–31.
[35] Smita, S., Lenka, S.K., Katiyar, A., Jaiswal, P., Preece, J., Bansal, K.C., 2011, QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database, doi:10.1093/database/bar037
[36] Ali, M., Khalid, R.R., Nawaz, M., Qamar, N., 2011, Development of a tool for the analysis of plant stress proteins. Int J Bioautomation, 15, 261-266.
[37] Naika, M., Shameer, K., Mathew, O.K., Gowda, R., Sowdhamini, R., 2013, STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol, 54, e8.
[38] Borkotoky, S., Saravanan, V., Jaiswal, A., Das, B., Selvaraj, S., Murali, A., Lakshmi, P.T.V., 2013, The Arabidopsis Stress Responsive Gene Database. International Journal of Plant Genomics, 2013. http://dx.doi.org/10.1155/2013/949564.
[39] Zhang, S., Yue, Y., Sheng, L., Wu, Y., Fan, G., Li, A., Hu, X., ShangGuan, M., Wei, C., 2013, PASmiR: A literature-curated database for miRNA molecular regulation in plant response to abiotic stress. BMC Plant Biol, 13, 33.
[40] Priya, P., Jain, M., 2013, RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database,2013, bat027.
[41] Alter, S., Bader, K.C., Spannagl, M., Wang, Yu., Bauer, E., Schön, C., Mayer, K.F.X., 2014, DroughtDB: An expert-curated compilation of plant drought stress genes and their homologs in nine species. doi: 10.1093/database/bav046.
[42] Kumar S.A., Kumari P.H., Sundararajan V.S., Suravajhala P., Kanagasabai R., Kishor P.B.K., 2014, PSPDB: Plant Stress Protein Database. Plant Molecular Biology Reporter, 32, 940-942.
[43] Mousavi, S.A., Pouya, F.M., Ghaffari, M.R., Mirzaei, M., Ghaffari, A., Alikhani, M., Ghareyazie, M., Komatsu, S., Haynes, P.A., Salekdeh, G.H., 2016, PlantPReS: A database for plant proteome response to stress. Journal of Proteomics, 143, 69-72.
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2016-12-30
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Prabha, R., & Singh, D. P. (2016). Omics-based Databases on Plant Stresses as Information Resources. CSVTU International Journal of Biotechnology, Bioinformatics and Biomedical, 1(3), 42–49. https://doi.org/10.30732/ijbbb.20160103002
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