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Thomas, Reena Rosy

In silico Analysis of whole-Genome of Solanum lycopersicum for Alpha-Crystallin Domains Associated with Heat Stress Tolerance

Abstract Views :358 | PDF Views:115

Authors

M. K. Chandra Prakash ¹, Reena Rosy Thomas ¹, Papiya Mondal ¹

Affiliations
1 Section of Economics and Statistics, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru - 560089, IN

Source

Journal of Horticultural Sciences, Vol 10, No 2 (2015), Pagination: 143-146

Abstract

Living organisms alter their gene-expression patterns to withstand stressful conditions. Drought, salinity, heat and chilling are potent abiotic stresses causing an alteration in gene expression. Among these, high temperature stress stimulates Heat Shock Transcription Factors (HSF) which activate heat shock promoters, thus turning on the heat shock genes. Heat shock proteins are, therefore, products of heat shock genes and are classified as per their molecular weight, including small heat shock proteins (sHsps). Hsps are chaperones playing an important role in stress tolerance. These consist of a conserved domain, flanked by N- and C-terminal regions termed the alphacrystallin domain (ACD), and are widely distributed in living beings. Their role as chaperones is to help the other proteins in protein-folding and prevent irreversible protein aggregation. The conserved domains in sHsps are essential for heat-stress tolerance and for their molecular chaperone activity, enabling plant survival under increasing temperatures, leading to adaptations needed for coping with extremes climatic conditions. The present study focusses on identification of ACDs in the whole-genome of Solanum lycopersicum. A multinational consortium, International Tomato Annotation Group (ITAG), funded in part by the EU-SOL Project, provides annotation of the whole genome of S. lycopersicum available in the public domain. We used several in silico methods for exploring alpha-crystallin domains in all the chromosomes of S. lycopersicum. Surprisingly, these ACDs were found to be present in all the chromosomes excepting Chromosome 4; these are highly conserved in sHsps and are related to heat tolerance.

Keywords

Solanum lycopersicum, Alpha-Crystallin Domain (ACD), Small Heat Shock Proteins (sHsps), in silico, Heat Stress

Full Text

References

Chandraprakash, M.K., Reena Rosy Thomas, Krishna Reddy, M. and Sukhada Mohandas. 2013.Molecular evolutionary conservedness of small heat shock protein sequences in Solanaceae crops using in silico methods. J. Hortl. Sci., 8:82-87

Eisenhardt, B.D. 2013. Small heat shock proteins: recent developments. Biomol. Concepts,4:583-595

Franz Narberhaus. 2002. Alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. Microbiol. Mol. Biol. Rev., 66:64-93

Jakob, U., Gaestel, M., Engel, K. and Buchner, J. 1993. Small heat shock proteins are molecular chaperones. J. Biol. Chem., 268:1517-20

Jorg Becker and Elizabeth A. Craig. 1994. Heat-shock proteins as molecular chaperones. European J. Biochem., 219:11-23

Kappé, G., Franck, E., Verschuure, P., Boelens, W.C., Leunissen, J.A.M. and de Jong, W.W. 2003. The human genome encodes 10 α-crystallin-related small heat shock proteins: HspB1-10. Cell Stress Chaperones, 8:53-61

Kumar, R.R., Singh, G.P., Sharma, S.K., Singh, K., Goswami, S. and Rai, R.D. 2012. Molecular cloning of HSP17 gene (sHSP) and their differential expression under exogenous putrescine and heat shock in wheat (Triticum aestivum). African J. Biotech., 11:16800 -16808

Liberek, K., Lewandowska, A. and Zietkiewicz, S. 2008. Chaperones in control of protein disaggregation. EMBO J., 27:328-335

MacRae, T.H. 2000. Structure and function of small heat shock/alpha-crystallin proteins: established concepts and emerging ideas. Cell Mol. Life Sci., 57:899-913

Nagar, A. and Hahsler, M. 2013. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC Bioinformatics, 14 Suppl., 11:S2

Parsell, D.A. and Lindquist, S. 1993. The function of heat shock proteins in stress tolerance: degradation and reactivation of damaged proteins. Annu. Rev. Genet., 27:437-497

Reena Rosy Thomas, Chandraprakash, M.K., Krishna Reddy, M., Sukhada Mohandas and Riaz Mahmood. 2013. Microsatellite identification in Solanaceae crops associated with Nucleoside Diphosphate Kinase (NDK) specific to abiotic stress tolerance through in silico analysis. J. Hortl. Sci., 8:195-198

Tariq Mahmood, Waseem Safdar, Bilal Haider Abbasi and Saqlan Naqvi, S.M. 2010. An overview on the small heat shock proteins. African J. Biotech., 9:927-939

Tyedmers, J., Mogk, A. and Bukau, B. 2010. Cellular strategies for controlling protein aggregation. Nat’l. Rev. Mol. Cell Biol., 11:777-788

Whitham, S.A., Anderberg, R.J., Chrisholm, S.T. and Carrington, J.C. 2000. Arabidopsis RTM2 gene is necessary for specific restriction of Tobacco Etch Virus and encodes an unusual small heat shock like protein. Pl. Cell, 12:569-582

Evidence for Molecular Evolutionary Conservedness of Small Heat-Shock Protein Sequence in Solanaceaeous Crops Using in silico Methods

Abstract Views :154 | PDF Views:106

Authors

M. K. Chandra Prakash ¹, Reena Rosy Thomas ², M. Krishna Reddy ³, Sukhada Mohandas ⁴

Affiliations
1 Section of Economics and Statistics, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore - 560 089, IN
2 Project Co-ordinator (Tropical Fruits) Cell, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore - 560 089, IN
3 Division of Plant Pathology, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore - 560 089, IN
4 Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore - 560 089, IN

Source

Journal of Horticultural Sciences, Vol 8, No 1 (2013), Pagination: 82-87

Abstract

Drought and heat contribute to much of the yield decline in agricultural lands all over the world. The basic physiological responses developed against drought and heat stress overlie each other, as; both these stresses eventually lead to dehydration of the cell and to osmotic imbalance. To cope with abiotic stresses, it is necessary to understand plant responses to stresses that disturb homeostatic equilibrium at the cellular and molecular level. Although there has been remarkable progress in this with development of microarray-based expression profiling methods (together with genomic sequence data), understanding on ways to employ these data to engineer plants with improved stresstolerance is still at a nascent stage. However, these data can be used for discovering genes, functional microsatellites and regulatory elements using in silico methods. In this context, single nucleotide repeat marker sequences have been identified which is associated with small heat-shock protein sequence (sHSP) for heat tolerance in Capsicum annuum. These sHSP sequences have some structural features in common; its characteristic is that it is homologous and highly conserved. These sequences have been analyzed for molecular evolutionary conservedness in solanaceaeous crops and have been found to have a single nucleotide repeat sequence and a highly conserved sHSP sequence.

Keywords

Small Heat-Shock Protein (sHSP), Evolutionary, Conserved, Solanaceae, Markers.

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Microsatellite Identification in Solanaceae Crops Associated with Nucleoside Diphosphate Kinase (NDK) Specific to Abiotic Stress Tolerance through in silico Analysis

Abstract Views :187 | PDF Views:128

Authors

Reena Rosy Thomas ¹, M. K. Chandra Prakash ¹, M. Krishna Reddy ², Sukhada Mohandas ³, Riaz Mahmood ⁴

Affiliations
1 Section of Economics and Statistics, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore -560089, IN
2 Division of Plant Pathology, Indian Institute of Horticultural Research, Bangalore - 560 089, IN
3 Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore - 560 089, IN
4 Dept. of Biotechnology, Kuvempu University, Shimoga - 577 451, IN

Source

Journal of Horticultural Sciences, Vol 8, No 2 (2013), Pagination: 195-198

Abstract

Abiotic stress often causes a series of morphological, physiological, biochemical and molecular changes that affect plant growth, development and productivity. To cope with abiotic stresses, it is necessary to understand plant responses to stresses that disturb homeostatic equilibrium at the cellular and molecular level. Genomic information on Capsicum annuum has been explored to identify microsatellite markers associated with abiotic stress tolerance and assign them to cognate functional groups related to specific stress responses. Several in silico methods have been used to identify simple sequence repeats associated with stress responsive gene candidates in Capsicum annuum. In this study, a microsatellite marker has been identified in Capsicum annuum associated with Nucleoside Diphosphate Kinase (NDK) having multiple environmental stress tolerance (oxidative, high temperature and salt stress) and which is also highly conserved in crops of Solanaceae. These are house-keeping enzymes that maintain intracellular levels of all nucleoside triphosphates (NTP) with the exception of adenosine triphosphate (ATP). These are also involved in phytochrome A response, UV-B signaling, auxin responses and oxidative stress signaling.

Keywords

Nucleoside Diphosphate Kinase (NDK), Microsatellite, Abiotic Stress, Solanaceae.

Full Text

Market Information System for Horticultural Crops:Web Application Development for Interactive Graphs

Abstract Views :191 | PDF Views:110

Authors

M. K. Chandra Prakash ¹, Reena Rosy Thomas ², Sudha Mysore ¹, G. Vadivel ¹, Rasika Thaker ¹

Affiliations
1 Section of Economics and Statistics, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bangalore - 560 089, IN
2 IIHR, Bangalore, IN

Source

Journal of Horticultural Sciences, Vol 6, No 1 (2011), Pagination: 76-83

Abstract

Marketing information service has been recognized as key for success in marketing of perishable commodities. Effort has been made to improve access to market information to all stakeholders involved in marketing of horticultural crops. Current study is an attempt in this direction to review various modes of such information support and also to highlight the effort made by premier institution like Indian Institute of Horticultural Research.

Web application has been developed for Market information to display the data as Interactive graphs. Data for the study includes the month-wise arrival and price information of different horticultural commodities from different markets for a period of ten years. This is collected from primary sources such as District -wise, Marketwise and secondary sources such as NHB, NHRDF etc., the data were tabulated and uploaded to Microsoft SQL server database through customized CMS module. Further, the price arrival data has been translated to the Interactive Charts by programs developed using Microsoft Visual studio. NET technologies, which is a relatively new addition to IIHR website.

Interactive Charts are used for drilling down for more information on price and arrivals. It consists of several interactive components like zoom, compare etc. Zoom component of the chart enables the user to zoom the graph to read the price trend prevailed in market in detail, which cannot be possible on Basic Chart. The Compare option allows user to compare price data with several other markets. The farmers and traders will get the advantage of taking precise decisions regarding choice of time and place for sale of their produce using this information system. Further, lean, peak stabilization periods prevailing in various markets enable farmers to schedule the cultivation plans.

Keywords

Horticulture, Competitiveness, Comparative Advantage, Interactive Chart, Price, Arrival and Markets.

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