Browsing by Author "Sopory, Sudhir K."

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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.
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.
Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium
(John Wiley & Sons, 2014) Kaur, Charanpreet; Mustafiz, Ananda; Sarkar, Ananda K.; Ariyadasa, Thilini U.; Singla-Pareek, Sneh L.; Sopory, Sudhir K.
ETHYLMALONIC ENCEPHALOPATHY PROTEIN 1 (ETHE1) encodes sulfur dioxygenase (SDO) activity regulating sulfide levels in living organisms. It is an essential gene and mutations in ETHE1 leads to ethylmalonic encephalopathy (EE) in humans and embryo lethality in Arabidopsis. At present, very little is known regarding the role of ETHE1 beyond the context of EE and almost nothing is known about factors affecting its regulation in plant systems. In this study, we have identified, cloned and characterized OsETHE1, a gene encoding ETHE1-like protein from Oryza sativa. ETHE1 proteins in general are most similar to glyoxalase II (GLYII) and hence OsETHE1 has been earlier annotated as OsGLYII1, a putative GLYII gene. Here we show that OsETHE1 lacks GLYII activity and is instead an ETHE1 homolog being localized in mitochondria like its human and Arabidopsis counterparts. We have isolated and analyzed 1618 bp OsETHE1 promoter (pOsETHE1) to examine the factors affecting OsETHE1 expression. For this, transcriptional promoter pOsETHE1: 5-bromo-5-chloro-3-indolyl-β-D-glucuronide (GUS) fusion construct was made and stably transformed into rice. GUS expression pattern of transgenic pOsETHE1:GUS plants reveal a high root-specific expression of OsETHE1. The pOsETHE1 activity was stimulated by Ca(II) and required light for induction. Moreover, pOsETHE1 activity was induced under various abiotic stresses such as heat, salinity and oxidative stress, suggesting a potential role of OsETHE1 in stress response.
Light mediated regulation defines a minimal promoter region of TOP2
(Oxford University Press, 2003) Hettiarachchi, G. H. C. M.; Yadav, Vandana; Reddy, M. K.; Chattopadhyay, Sudip; Sopory, Sudhir K.
Light signaling has been demonstrated to be an important factor for plant growth and development; however, its role in the regulation of DNA replication and cell cycle has just started to be unraveled. In this work, we have demonstrated that the TOP2 promoter of Pisum sativum (pea) is activated by a broad spectrum of light including far-red light (FR), red light (RL) and blue light (BL). Deletion analyses of the TOP2 promoter in transformed plants, Arabidopsis thaliana and Nicotiana tobaccum (tobacco), de®ne a minimal promoter region that is induced by RL, FR and BL, and is essential and suficient for light-mediated activation. The minimal promoter of TOP2 follows the phytochromemediated low- ̄uence response similar to complex light regulated promoters. DNA±protein interaction studies reveal the presence of a DNA binding activity speci®c to a 106 bp region of the minimal promoter that is crucial for light-mediated activation. These results altogether indicate a direct involvement of light signaling in the regulation of expression of TOP2, one of the components of the DNA replication/cell cycle machinery.
Regulation of TOP2 by various abiotic stresses including cold and salinity in pea and transgenic tobacco plants
(Oxford University Press, 2005) Hettiarachchi, Gardhi H. C. M.; Reddy, Malireddy K.; Sopory, Sudhir K.; Chattopadhyay, Sudip
Although abiotic stress affects plant growth and development, demonstration of its direct effect on regulation of the components of the DNA replication machinery is largely unknown. In this work, we demonstrate that the expression of TOP2 (encoding topoisomerase II) is up-regulated by various abiotic stresses including salinity and low temperature, and phytohormones such as ABA (abscisic acid) and SA (salicylic acid). Transgenic studies with different deletion versions of the TOP2 promoter in tobacco define several promoter determinants responsible for specific abiotic stress responsiveness. Taken together, these results demonstrate a direct involvement of stress in the transcriptional regulation of TOP2.