Browsing by Author "Citu"

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Complex networks of prion-like proteins reveal cross talk between stress and memory pathways in plants
(Frontiers Media S.A., 2021) Garai, Sampurna; Citu; Singla-Pareek, Sneh L.; Sopory, Sudhir K.; Kaur, Charanpreet; Yadav, Gitanjali
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its “prionome.” In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
Complex networks reveal biological functions of START domains in rice: Insights from computational systems biology
(Springer Nature Publishing AG, 2022) Mahtha, Sanjeet Kumar; Citu; Prasad, Abhishek; Yadav, Gitanjali
With the advancement of high throughput technologies, there has been a massive surge in the omics data generation and there is a growing need to integrate this data gain insights into the patterns that shape biological interactions. Complex networks not only enable representation of such interactions, but also offer a mechanism for visualization and understanding of big data at a systems level. In this work, we use a complex network approach to investigate functions of the plant amplified StAR-related lipid transfer (START) domains in rice. We analyse the data at three levels; namely the transcriptome, proteome, and regulome. Each of these distinct datasets was superimposed after generation of the respective co-expression, protein-protein interaction, and gene regulatory networks for rice START genes, to reveal domain specific features in the family. This work thus serves as a protocol for network-based approaches to understand biological processes of genes and to complement experimental strategy.