Browsing by Author "Pandey, Amita"

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Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development
(Oxford University Press, 2014) Sharma, Manisha; Singh, Amarjeet; Shankar, Alka; Pandey, Amita; Baranwal, Vinay; Kapoor, Sanjay; Tyagi, Akhilesh K.; Pandey, Girdhar K.
Genes in the Armadillo (ARM)-repeat superfamily encode proteins with a range of developmental and physiological processes in unicellular and multicellular eukaryotes. These 42 amino acid, long tandem repeat-containing proteins have been abundantly recognized in many plant species. Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis. In this study, we performed a computational analysis in the rice genome (Oryza sativa L. subsp. japonica), and identified 158 genes of Armadillo superfamily. Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them. An in-depth analysis of gene expression through microarray and Q-PCR revealed a number of ARM proteins expressing differentially in abiotic stresses and developmental conditions, suggesting a potential roles of this superfamily in development and stress signalling. Comparative phylogenetic analysis between Arabidopsis and rice Armadillo genes revealed a high degree of evolutionary conservation between the orthologues in two plant species. The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection. This genome-wide identification and expression analysis provides a basis for further functional analysis of Armadillo genes under abiotic stress and reproductive developmental condition in the plant lineage.
Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice
(PLOS, 2013) Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K.; Sopory, Sudhir K.; Kapoor, Sanjay; Pandey, Girdhar K.
BACKGROUND: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. METHODOLOGY/PRINCIPAL FINDINGS: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. CONCLUSION/SIGNIFICANCE: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future.
Editorial: Abiotic stress signaling in plants: Functional genomic intervention
(Frontiers Media S.A., 2016) Pandey, Girdhar K.; Pandey, Amita; Prasad, Manoj; Böhmer, Maik
Editorial on Research Topic: Abiotic Stress Signaling in Plants: Functional Genomic Intervention. The major challenge before the plant scientists is to develop strategies to increase the productivity of crop plants so as to feed the rapidly increasing global population. The increased anthropogenic activities have resulted in radical decrease of fertile land available for agricultural practices, and in addition, the impact of climate change, which poses environmental stress resulting in drastic decrease in crop productivity are major concerns for plant biologists.
Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice
(John Wiley & Sons, 2014) Singh, Amarjeet; Kanwar, Poonam; Yadav, Akhilesh K.; Mishra, Manali; Jha, Saroj K.; Baranwal, Vinay; Pandey, Amita; Kapoor, Sanjay; Tyagi, Akhilesh K.; Pandey, Girdhar K.
Ca²⁺ homeostasis is required to maintain a delicate balance of cytosolic Ca²⁺ during normal and adverse growth conditions. Various Ca²⁺ transporters actively participate to maintain this delicate balance especially during abiotic stresses and developmental events in plants. In this study, we present a genome-wide account, detailing expression profiles, subcellular localization and functional analysis of rice Ca²⁺ transport elements. Exhaustive in silico data mining and analysis resulted in the identification of 81 Ca²⁺ transport element genes, which belong to various groups such as Ca²⁺-ATPases (pumps), exchangers, channels, glutamate receptor homologs and annexins. Phylogenetic analysis revealed that different Ca²⁺ transporters are evolutionarily conserved across different plant species. Comprehensive expression analysis by gene chip microarray and quantitative RT-PCR revealed that a substantial proportion of Ca²⁺ transporter genes were expressed differentially under abiotic stresses (salt, cold and drought) and reproductive developmental stages (panicle and seed) in rice. These findings suggest a possible role of rice Ca²⁺ transporters in abiotic stress and development triggered signaling pathways. Subcellular localization of Ca²⁺ transporters from different groups in Nicotiana benthamiana revealed their variable localization to different compartments, which could be their possible sites of action. Complementation of Ca²⁺ transport activity of K616 yeast mutant by Ca²⁺-ATPase OsACA7 and involvement in salt tolerance verified its functional behavior. This study will encourage detailed characterization of potential candidate Ca²⁺ transporters for their functional role in planta.
A protein phosphatase 2C, AP2C1 interacts with and negatively regulates the function of CIPK9 under potassium deficient conditions in Arabidopsis
(Oxford University Press, 2018) Singh, Amarjeet; Yadav, Akhilesh K.; Kaur, Kanwaljeet; Sanyal, Sibaji K.; Jha, Saroj K.; Fernandes, Joel L.; Sharma, Pankhuri; Tokas, Indu; Pandey, Amita; Luan, Sheng; Pandey, Girdhar K.
Potassium (K+) is a major macronutrient required for plant growth. In response to low- K+ condition, an adaptive mechanism entails activation of the Ca2+ signaling network consisting of calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs) in plants. The CBL-interacting protein kinase 9 (CIPK9) is previously implicated in low-K+ responses in Arabidopsis thaliana. Here, we report a protein phosphatase 2C (PP2C), AP2C1, as an interactor of CIPK9. Fluorescence resonance energy transfer (FRET), bimolecular fluorescence complementation (BiFC) and co-localization analyses revealed that CIPK9 and AP2C1 interact in the cytoplasm. AP2C1 dephosphorylates the auto-phosphorylated form of CIPK9 in vitro, presenting a regulatory mechanism for CIPK9 function. Furthermore, genetic and molecular analysis revealed that ap2c1 null mutants (ap2c1-1 and ap2c1-2) are tolerant to low-K+ conditions, retained higher K+ content and showed higher expression of K+ deficiency related genes contrary to cipk9 mutants (cipk9-1 and cipk9-2). In contrast, transgenic plants overexpressing AP2C1 were sensitive to low-K+ conditions. Thus, this study shows that AP2C1 and CIPK9 interact to regulate K+-deficiency responses in Arabidopsis. CIPK9 functions as positive regulator whereas, AP2C1 acts as a negative regulator of Arabidopsis root growth and seedling development under low-K+ conditions.