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Databases for Genes Involved in Stress Mechanism in PlantsBY: Dr. Dhammaprakash P Wankhede | Category: Bioinformatics | Submitted: 2016-06-18 18:43:51
Article Summary: "Different Biotic and abiotic stresses are among the major constraints in improving crop productivity. Several genes involved in stress tolerance mechanisms have been identified in plants and databases developed for stress responsive genes and stress conditions. This article gives information about important databases dedicated f.."
Databases for genes involved in stress mechanism in plants
Authors: Dhammaprakash P Wankhede, Vikender Kaur, J. Aravind, Ankit Saroha
ICAR-National Bureau of Plant Genetic Resources, Pusa campus, New Delhi
Plants being sessile are exposed number of biotic and abiotic stresses in field conditions. Performance of crop plants in terms of yield is often depends on how plants cope with array of stress conditions. With the advancement in the field of molecular biology, DNA sequencing technologies and bioinformatics several genes involved in stress tolerance mechanism in different plants have been identified. The flow of available information with respect to stress related genes especially in model plants have resulted in development of number of databases. This article gives information about important stress related databases available in public domain. This information will likely help researchers involved in the areas of plant stress biology.
This database gives an inclusive list of different biotic and abiotic stress responsive genes in model plants Arabidopsis and rice. The probable Transcription Factor Binding Sites in promoter regions of stress responsive genes also can also be identified. The database comprises biotic stressors such as plant pathogenic bacteria, fungi, and viruses as well as abiotic stressors including ABA, drought, cold, salinity, dehydration, UV-B, high light, heat, heavy metals etc. Based on available information on transcription factor families involved in certain stress conditions, HMM based models have been used to identify respective transcription factor binding element in genes. Results of this approach have been validated using available literature (Naika et al. 2013; Shameer et al. 2009; Ambikaet al. 2008)
Plant Stress Proteins Database gives list of plants proteins involved in Biotic and Abiotic stresses. The database includes 30 different types of stress proteins and 2064 manually curated proteins from UniProt. Further it has integrated Tools from NCBI BLAST, ClustalW, NJPLOT and Hmmer. The database is updated every month with new protein entries and every six month with manually curetted peptides (Anil Kumar et al. 2014).
Plant Stress Gene Database gives information about stress related genes (259) in eleven plant species ( Arabidopsis thaliana, Arachis hypogaea, Glycine max, Hordeum vulgare, Oryza sativa, Pennisetum glaucum, Phaseolus vulgaris, Saccharum officinarum, Solanum lycopersicum, Triticum aestivum and Zea mays). Information on their orthologs and paralogs of the stress related genes, ESTs have also been given. The database can be searched using species name, genes name or stress conditions. The database also gives link/information of other important databases for genes and proteins (Prabha et al. 2011)
This database gives information on metal stress tolerance genes in Arabidopsis thaliana based on published reports. There are 637 gene entries related to stress responses associated with around 50 stress conditions. Genes involved in cross tolerance have also been included. The nucleotide, protein sequences can be searched, compared and retrieved. There is also option to search similar sequences (nucleotide and protein) using BLAST search. Further, additional information such as gene info, gene investigator, gene family profiler and pubmed reference are also provided (Borkotoky et al. 2013)
Drought stress gene database gives details of genes involved in drought stress mechanism such as drought avoidance and drought tolerance. It provides crucial information with respect to genes such as their identifier, organism with reference to publication, function, phenotype, reference-PMID, orthologous groups and sequence information. The interactive pathway browser is also provided which facilitate simplified interactive interface to the pathways for molecular and physiological adaptation (Svenja et al. 2014)
The Rice Stress-Responsive Transcription Factor Database (RiceSRTFDB) provides comprehensive information on the expression patterns of rice Transcription factors in water-deficit and salinity stress conditions at various stages of development. A curated set of 99 Affymetrix GeneChip Rice Genome arrays having representation from 18 different drought and salinity stress treatments constitute the stress responsive expression data in the database. The expression viewer gives stress and developmental stages specific expression of selected transcription factor with graphical representations. Salt and drought induced differential expression of all the data transcription factors or specific TF family in rice can be downloaded. The information about the cis-regulatory elements in the promoters of TFs and Tos17 mutant information have also been provided. The comprehensive drought and salt responsive expression of transcription factors in rice at different tissues and developmental stages provided in the database gives elaborate understanding about regulatory networks of rice transcription factors in drought and salinity stress (Priya and Jain, 2013).
Naika M, Shameer K, Mathew OK, 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(2):e8(1-15).
Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R (2009) STIFDB-Arabidopsis Stress Responsive Transcription Factor DataBase.Int J Plant Genomics. 2009; 2009: 583429
Ambika S, Varghese SM, Shameer K, Udayakumar M, Sowdhamini R (2008) STIF: Hidden Markov Model-based search algorithm for the recognition of binding sites of Stress-upregulated TranscrIption Factors and genes in Arabidopsis thaliana. Bioinformation, 2(10):431-437
Anil Kumar S, Hima Kumari P, Sundararajan VS , Suravajhala P, Kanagasabai R, Kavi Kishor PB (2014) PSPDB: Plant Stress Protein Database. Plant Molecular Biology Reporter 32,4: 940-942
Prabha R, Ghosh I, Singh DP (2011) Plant Stress Gene Database: A Collection of Plant Genes Responding to Stress Condition. ARPN Journal of Science and Technology, 1, 1:28-3
Borkotoky S, Saravanan V, Jaiswal A, et al. (2013) The Arabidopsis Stress Responsive Gene Database, International Journal of Plant Genomics, vol. 2013, Article ID 949564, 3 pages, 2013. doi:10.1155/2013/949564
Svenja Alter, Kai C. Bader, Manuel Spannagl, Yu Wang, Eva Bauer, Chris-Carolin Schon, Klaus F.X. Mayer (2014) DroughtDB: An expert-curated compilation of plant drought stress genes and their homologs in nine species.
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.
About Author / Additional Info:
I am working as a scientist in ICAR-National Bureau of Plant Genetics Resources, New Delhi , India
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