Institutional Publications

Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11

Browse

Author: search.filters.author.Chattopadhyay, SudipHas files: Yes

Search Results

Now showing 1 - 10 of 25
  • Thumbnail Image
    Item
    MKKK20 works as an upstream triple-kinase of MKK3-MPK6-MYC2 module in Arabidopsis seedling development
    (Cell Press, 2023) Ojha, Madhusmita; Verma, Deepanjali; Chakraborty, Nibedita; Pal, Abhideep; Bhagat, Prakash Kumar; Singh, Anshuman; Verma, Neetu; Sinha, Alok Krishna; Chattopadhyay, Sudip
    The mitogen-activated protein kinase (MAPK) cascade is involved in several signal transduction processes in eukaryotes. Here, we report a mechanistic function of MAP kinase kinase kinase 20 (MKKK20) in light signal transduction pathways. We show that MKKK20 acts as a negative regulator of photomorphogenic growth at various wavelengths of light. MKKK20 not only regulates the expression of light signaling pathway regulatory genes but also gets regulated by the same pathway genes. The atmyc2 mkkk20 double mutant analysis shows that MYC2 works downstream to MKKK20 in the regulation of photomorphogenic growth. MYC2 directly binds to the promoter of MKKK20 to modulate its expression. The protein-protein interaction study indicates that MKKK20 physically interacts with MYC2, and this interaction likely suppresses the MYC2-mediated promotion of MKKK20 expression. Further, the protein phosphorylation studies demonstrate that MKKK20 works as the upstream kinase of MKK3-MPK6-MYC2 module in photomorphogenesis.
  • Thumbnail Image
    Item
    Functional relationship of GBF1 with HY5 and HYH in genome-wide gene expression in Arabidopsis
    (Springer, 2016) Ram, Hathi; Jain, Mukesh; Singh, Aparna; Chattopadhyay, Sudip
    Transcriptional networks play important roles in the regulation of biological processes through coordinated activation or repression of downstream target genes. Arabidopsis bZIP transcription factors, GBF1, HY5, and HYH, interact and heterodimerize with each other to form the regulatory network in photomorphogenesis. The genome-wide direct target genes of GBF1 and the roles of HY5 and HYH in controlling GBF1’s genome-wide DNA binding ability have been shown earlier. However, the GBF1 regulated genes at global scale, and how HY5 and HYH modulate GBF1-mediated genome-wide gene expression remain unknown. Here, we report the genome-wide gene expression profile in gbf1, gbf1 hy5, and gbf1 hyh mutants. Our results suggest that HY5 and HYH antagonistically regulate GBF1-mediated global gene expression. We validated the microarray analysis with independent qPCR analyses. Functional analysis of GBF1-regulated genes validates previously known roles of GBF1 in important biological processes. Furthermore, the data also highlight possible novel role of GBF1 in several other biological processes. The previous ChIP-chip results and this transcriptome data together demonstrate the complex transcriptional regulatory mechanism of these transcription factors, GBF1, HY5, and HYH, in photomorphogenesis.
  • Thumbnail Image
    Item
    A mitogen-activated protein kinase cascade module, MKK3-MPK6 and MYC2, is involved in blue light-mediated seedling development in Arabidopsis
    (American Society of Plant Biologists, 2014) Sethi, Vishmita; Raghuram, Badmi; Sinha, Alok Krishna; Chattopadhyay, Sudip
    Mitogen-activated protein kinase (MAPK) pathways are involved in several signal transduction processes in eukaryotes. Light signal transduction pathways have been extensively studied in plants; however, the connection between MAPK and light signaling pathways is currently unknown. Here, we show that MKK3-MPK6 is activated by blue light in a MYC2-dependent manner. MPK6 physically interacts with and phosphorylates a basic helix-loop-helix transcription factor, MYC2, and is phosphorylated by a MAPK kinase, MKK3. Furthermore, MYC2 binds to the MPK6 promoter and regulates its expression in a feedback regulatory mechanism in blue light signaling. We present mutational and physiological studies that illustrate the function of the MKK3-MPK6-MYC2 module in Arabidopsis thaliana seedling development and provide a revised mechanistic view of photomorphogenesis.
  • Thumbnail Image
    Item
    Genome-wide DNA binding of GBF1 is modulated by its heterodimerizing protein partners, HY5 and HYH
    (Elsevier B.V., 2014) Ram, Hathi; Priya, Pushp; Jain, Mukesh; Chattopadhyay, Sudip
    In today’s post-genomic era where direct targets of many transcription factors have been identified, it is becoming increasingly evident that transcriptional networks are very complex. Heterodimerization of transcription factors is one of the several methods by which these complex transcriptional networks are formed. By heterodimerization, DNA- binding specificity and affinity, transactivation properties, and ultimately cell physiology might be altered (Naar et al., 2001). The formation of heterodimers has the potential to recognize additional binding sites and increase the range of DNA-binding specificity (Foster et al., 1994). Further, heterodimerization also allows the production of new protein configurations. For example, the protein STF1 from soybean can dimerize with GBF proteins and this dimerization brings together the acidic region from STF1 and the proline-rich region of the GBF proteins into one binding element (Cheong et al., 1998). These results highlight the importance and/or consequences of heterodimerization of transcription factors at particular locus. However, to understand the complex transcriptional networks, it is important to investigate that how heterodimerization affects the whole-genome-wide binding and transcriptional properties of a transcription factor. Here in this study, we have investigated genome-wide DNA binding of bZIP transcription factor GBF1, and analyzed the importance of its heterodimerization with HY5 and HYH for its genome-wide binding. We have found that GBF1 binding sites are enriched within the 1-kb regions upstream to the transcription start sites of target genes. Moreover, the bindings of GBF1 to most of its targets are largely dependent on HY5, while HYH only affects the binding of GBF1 to some specific sites.
  • Thumbnail Image
    Item
    LeMYC2 acts as a negative regulator of blue light mediated photomorphogenic growth, and promotes the growth of adult tomato plants
    (BioMed Central Ltd, 2014) Gupta, Nisha; Prasad, V Babu Rajendra; Chattopadhyay, Sudip
    Background: Arabidopsis ZBF1/MYC2bHLH transcription factor is a repressor of photomorphogenesis, and acts as a point of cross talk in light, abscisic acid (ABA) and jasmonic acid (JA) signaling pathways. MYC2 also functions as a positive regulator of lateral root development and flowering time under long day conditions. However, the function of MYC2 in growth and development remains unknown in crop plants. Results: Here, we report the functional analyses of LeMYC2 in tomato (Lycopersicon esculentum). The amino acid sequence of LeMYC2 showed extensive homology with Arabidopsis MYC2, containing the conserved bHLH domain. To study the function of LeMYC2 in tomato, overexpression and RNA interference (RNAi) LeMYC2 tomato transgenic plants were generated. Examination of seedling morphology, physiological responses and light regulated gene expression has revealed that LeMYC2 works as a negative regulator of blue light mediated photomorphogenesis. Furthermore, LeMYC2 specifically binds to the G-box of LeRBCS-3A promoter. Overexpression of LeMYC2 has led to increased root length with more number of lateral roots. The tomato plants overexpressing LeMYC2 have reduced internode distance with more branches, and display the opposite morphology to RNAi transgenic lines. Furthermore, this study shows that LeMYC2 promotes ABA and JA responsiveness. Conclusions: Collectively, this study highlights that working in light, ABA and JA signaling pathways LeMYC2 works as an important regulator for growth and development in tomato plants.
  • Thumbnail Image
    Item
    Arabidopsis CAM7 and HY5 physically interact and directly bind to the HY5 promoter to regulate its expression and thereby promote photomorphogenesis
    (American Society of Plant Biologists, 2014) Abbas, Nazia; Maurya, Jay P.; Senapati, Dhirodatta; Gangappa, Sreeramaiah N.; Chattopadhyay, Sudip
    Arabidopsis thaliana CALMODULIN7 (CAM7), a unique member of the calmodulin gene family, plays a crucial role as a transcriptional regulator in seedling development. The elongated HYPOCOTYL5 (HY5) bZIP protein, an integrator of multiple signaling pathways, also plays an important role in photomorphogenic growth and light-regulated gene expression. CAM7 acts synergistically with HY5 to promote photomorphogenesis at various wavelengths of light. Although the genetic relationships between CAM7 and HY5 in light-mediated seedling development have been demonstrated, the molecular connectivity between CAM7 and HY5 is unknown. Furthermore, whereas HY5-mediated gene regulation has been fairly well investigated, the transcriptional regulation of HY5 is largely unknown. Here, we report that HY5 expression is regulated by HY5 and CAM7 at various wavelengths of light and also at various stages of development. In vitro and in vivo DNA-protein interaction studies suggest that HY5 and CAM7 bind to closely located T/G- and E-box cis-acting elements present in the HY5 promoter, respectively. Furthermore, CAM7 and HY5 physically interact and regulate the expression of HY5 in a concerted manner. Taken together, these results demonstrate that CAM7 and HY5 directly interact with the HY5 promoter to mediate the transcriptional activity of HY5 during Arabidopsis seedling development.
  • Thumbnail Image
    Item
    CAM7 and HY5 genetically interact to regulate root growth and abscisic acid responses
    (Taylor & Francis Group, 2014) Abbas, Nazia; Chattopadhyay, Sudip
    CAM7, a member of CaM family in Arabidopsis, acts as a transcriptional regulator and enhances photomorphogenic growth and light regulated gene expression under various light conditions. HY5, a bZIP transcription factor, promotes photomorphogenesis at multiple wavelengths of light including far red, red, and blue light. Very recently, it has been shown that CAM7 and HY5 directly interact with the HY5 promoter to regulate the transcriptional activity of HY5 during Arabidopsis seedling development. In this study, we have investigated the root phenotype of cam7 hy5 double mutants and shown that CAM7 and HY5 genetically interact to control the root growth. We have further shown an interdependent function of HY5 and CAM7 in abscisic acid (ABA) responsiveness.
  • Thumbnail Image
    Item
    Molecular interaction of bZIP domains of GBF1, HY5 and HYH in Arabidopsis seedling development
    (Taylor & Francis, 2013) Ram, Hathi; Chattopadhyay, Sudip
    The bZIP proteins, GBF1, HY5 and HYH, play important regulatory roles in Arabidopsis seedling development. Whereas GBF1 plays a dual regulatory role, HY5 and HYH act as positive regulators of photomorphogenesis. The molecular and functional relations of GBF1 with HY5 and HYH in photomorphogenesis have recently been demonstrated. However, the possible interaction of bZIP domain of each of these proteins remains to be investigated. In this study, our results suggest that bZIP domains of HY5 and HYH are able to interact with the bZIP domain of GBF1. Taken together with the earlier study, (9) these results suggest that the N-terminal domain of GBF1 has an inhibitory effect on its interaction with HY5 and HYH.
  • Thumbnail Image
    Item
    The regulation of the Z- and G-box containing promoters by light signaling components, SPA1 and MYC2, in Arabidopsis
    (PLOS, 2013) Gangappa, Sreeramaiah N.; Maurya, Jay P.; Yadav, Vandana; Chattopadhyay, Sudip
    Although many transcription factors and regulatory proteins have been identified and functionally characterized in light signaling pathways, photoperception to transcription remains largely fragmented. The Z-box is one of the LREs (Light responsive elements) that plays important role in the regulation of transcription during light-controlled Arabidopsis seedling development. The involvement of photoreceptors in the modulation of the activity of the Z-box containing promoters has been demonstrated. However, the role of downstream signaling components such as SPA1 and MYC2/ZBF1, which are functionally interrelated, remains unknown. In this study, we have investigated the regulation of the Z-box containing synthetic and native promoters by SPA1 and MYC2 by using stable transgenic lines. Our studies suggest that SPA1 negatively regulates the expression of CAB1 native promoter. MYC2 negatively regulates the activity of Z- and/or G-box containing synthetic as well as native promoters irrespective of light quality. Moreover, MYC2 negatively regulates the expression of Z/G-NOS101-GUS even in the darkness. Furthermore, analyses of tissue specific expression in adult plants suggest that MYC2 strongly regulates the activity of Z- and G-box containing promoters specifically in leaves and stems. In roots, whereas MYC2 positively regulates the activity of the Z-box containing synthetic promoter, it does not seem to control the activity of the G-box containing promoters. Taken together, these results provide insights into SPA1- and MYC2-mediated transcriptional regulation of the Z- and G-box containing promoters in light signaling pathways.
  • Thumbnail Image
    Item
    MYC2 differentially regulates GATA-box conaining promoters during seedling development in Arabidopsis
    (Landes Bioscience, 2013) Gangappa, Sreeramaiah N.; Chattopadhyay, Sudip
    MY C2 is an important transcription factor, which modulates transcription by directly binding to Z-, G- and E-box elements present in the promoters of light and different stress responsive genes. Very recently, we have shown that MY C2 plays a role in the regulation of Z- and/or G-box containing promoters during both seedling and adult plant growth. Although, MY C2 does not bind to the GATA box light responsive element (LRE ) in vitro as shown in DNA binding assays, its involvement in the regulation of GATA -box containing promoter in planta, if any, is not known. Here, we report that the promoter activity of GATA-NOS101 in atmyc2 mutant was found to be similar to wild-type in BL and dark grown seedlings, whereas it was found to be lower compared with wild-type as revealed from GUS staining results. Further, we will discuss the consequences of MY C2 regulating GATA -box containing promoter in combination with G-box containing promoters.