Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food...
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doaj-1a743e6e97d543048a6eccc5b07911832020-11-25T00:58:53ZengFrontiers Media S.A.Frontiers in Chemistry2296-26462017-12-01510.3389/fchem.2017.00115307529Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance ImprovementShikha Mittal0Mallana Gowdra Mallikarjuna1Atmakuri R. Rao2Prashant A. Jain3Prasanta K. Dash4Nepolean Thirunavukkarasu5Division of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, IndiaDivision of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, IndiaCentre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR), New Delhi, IndiaDepartment of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, IndiaICAR-National Research Centre on Plant Biotechnology, New Delhi, IndiaDivision of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, IndiaCalcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.http://journal.frontiersin.org/article/10.3389/fchem.2017.00115/fullCDPKdifferential expressiondrought3-D protein structurefunctional mechanism |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shikha Mittal Mallana Gowdra Mallikarjuna Atmakuri R. Rao Prashant A. Jain Prasanta K. Dash Nepolean Thirunavukkarasu |
spellingShingle |
Shikha Mittal Mallana Gowdra Mallikarjuna Atmakuri R. Rao Prashant A. Jain Prasanta K. Dash Nepolean Thirunavukkarasu Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement Frontiers in Chemistry CDPK differential expression drought 3-D protein structure functional mechanism |
author_facet |
Shikha Mittal Mallana Gowdra Mallikarjuna Atmakuri R. Rao Prashant A. Jain Prasanta K. Dash Nepolean Thirunavukkarasu |
author_sort |
Shikha Mittal |
title |
Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement |
title_short |
Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement |
title_full |
Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement |
title_fullStr |
Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement |
title_full_unstemmed |
Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement |
title_sort |
comparative analysis of cdpk family in maize, arabidopsis, rice, and sorghum revealed potential targets for drought tolerance improvement |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Chemistry |
issn |
2296-2646 |
publishDate |
2017-12-01 |
description |
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species. |
topic |
CDPK differential expression drought 3-D protein structure functional mechanism |
url |
http://journal.frontiersin.org/article/10.3389/fchem.2017.00115/full |
work_keys_str_mv |
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