Publications of NIPGR Scientists

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    Genomic survey, gene expression, and interaction analysis suggest diverse roles of ARF and Aux/IAA proteins in Solanaceae
    (Springer, 2015) Kumar, Rahul; Agarwal, Priyanka; Pareek, Amit; Tyagi, Akhilesh K.; Sharma, Arun K.
    Auxin response factor (ARF) and Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are the foremost regulators of auxin action and play an essential role in the coordination of many aspects of plant growth and development. Though many members of both ARF and Aux/IAA gene families have been identified and characterized in tomato, they are less studied in other Solanaceae species. In the present study, we focused on gaining insights into their functional conservation as well as diversification during auxin-mediated responses in Solanaceae. First, we identified their full complement in tomato, potato, pepper, Nicotiana benthamiana, eggplant, and petunia and found that both the gene families have expanded in N. benthamiana. We also looked into the structural variations associated with all the members of these two classes of genes in tomato and showed that huge natural variation exists in their sequence in wild relatives. The comprehensive gene expression analysis provided evidence of high conservation in the expression of orthologous ARFs and Aux/IAAs during fruit development and ripening in tomato and pepper. Furthermore, the molecular changes caused by exogenous plant hormones and abiotic stress conditions on their transcript levels were investigated which showed that many members of both the gene families may participate in various hormone- and stress-mediated responses in tomato and potato. Some of these genes may play a role in linking the hormone-controlled plant growth and stress-related signaling pathways. Finally, we demonstrate that single tomato ARF can interact with multiple Aux/IAA proteins and vice versa. Overall, our study will be very helpful in establishing both conserved as well as non-conserved functions of these genes in Solanaceae.
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    Differential expression and interaction specificity of heterotrimeric G-protein family in Brassica nigra reveal their developmental-and condition-specific roles
    (Oxford University Press, 2014) Kumar, Roshan; Arya, Gulab C.; Bisht, Naveen C.
    Heterotrimeric G-proteins, comprised of α, β and γ subunits, are important signal transducers across phyla. The G-proteins are well characterized in the model plants Arabidopsis and rice, and their inventories are possible from a few other plant species; however, information about the roles played by G-proteins in regulating various growth and developmental traits particularly from polyploid crops is still awaited. In this study, we have isolated one Gα (BniB.Gα1), three Gβ (BniB.Gβ1-BniB.Gβ3) and four Gγ (BniB.Gγ1-BniB.Gγ4) coding sequences from the paleopolyploid Brassica nigra, a major condiment crop of the Brassicaceae family. Sequence and phylogenetic analysis revealed that whole-genome triplication events in the Brassica lineage had proportionally increased the inventory of the Gβ subunit, but not of the Gα and Gγ subunits in B. nigra. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis showed that members of the G-protein subunit genes have distinct temporal and spatial expression patterns and were differentially altered in response to various stress and phytohormone treatments, thereby suggesting differential transcriptional regulation of G-protein genes in B. nigra. Interestingly, specific members of G-protein subunits were co-expressed across plant developmental stages, and in response to different elicitor treatments. Yeast-based interaction screens further predicted that the B. nigra G-protein subunits interacted in most of the possible combinations, although showing a high degree of interaction specificity between different G-protein subunits. Our data on physical interactions coupled with the co-expression pattern of the multiple G-protein subunit genes suggested that tissue- and condition-specific functional combinations of Gαβγ heterotrimers may exist in paleopolyploid B. nigra, to control diverse growth and development processes.