Institutional Publications

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Sub-functionalization in rice gene families with regulatory roles in abiotic stress responses
(Taylor & Francis Group, 2017) Sharma, G.; Giri, Jitender; Tyagi, Akhilesh K.
Plants have developed intricate mechanisms to overcome abiotic stresses. The process of signal perception and activation of signaling cascades involves a large number of factors and molecules belonging to diverse classes of gene families. In comparison to animals, plants harbor larger multigene families along with the occurrence of plant-specific ones. Gene families with abiotic-stress-responsive members were analyzed and categorized into classes such as transcription factors, signal transduction components, transporters, epigenetic regulators, and other regulatory components. The number of members, phylogeny, family expansion, domain composition, subcellular localization, and expression profiling during varied abiotic stresses have been summarized. Candidate genes from families, functionally characterized for abiotic stress responses, have been described. Based on our compilation, the expansion of abiotic-stress-responsive gene families in rice has occurred via segmental and tandem duplication events to accommodate sub-functionalization needed for regulating diverse abiotic stress responses at expression, localization, and functional levels. The information documented here can be further utilized as a primer for selecting candidate genes for improvement of rice yield under abiotic stresses.
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.
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.

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