Browsing by Author "Chattopadhyay, Sudip"

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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.
A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of of blue light-mediate photomorphogenic growth
(American Society of Plant Biologists, 2005) Yadav, Vandana; Mallappa, Chandrashekara; Gangappa, Sreeramaiah N.; Bhatia, Shikha; Chattopadhyay, Sudip
This work is supported by Department of Biotechnology and Department of Science and Technology grants to S.C. V.Y., C.M., and S.N.G. are recipients of Council of Scientific and Industrial Research fellowships from the government of India.
A basic leucine zipper transcription factor, G-box-binding factor 1, regulates blue light-mediated photomorphogenic growth in Arabidopsis
(The American Society for Biochemistry and Molecular Biology, Inc., 2006) Mallappa, Chandrashekara; Yadav, Vandana; Negi, Prem; Chattopadhyay, Sudip
Several transcriptional regulators have been identified and demonstrated to play either positive or negative regulatory roles in seedling development. However, the regulatory coordination between hypocotyl elongation and cotyledon expansion during early seedling development in plants remains unknown. We report the identification of a Z-box binding factor (ZBF2) and its functional characterization in cryptochrome-mediated blue light signaling. ZBF2 encodes a G-box binding factor (GBF1), which is a basic leucine zipper transcription factor. Our DNA- protein interaction studies reveal that ZBF2/GBF1 also interacts with the Z-box light-responsive element of light-regulated promoters. Genetic analyses of gbf1 mutants and overexpression studies suggest that GBF1 acts as a repressor of blue light-mediated inhibition in hypocotyl elongation, however, it acts as a positive regulator of cotyledon expansion during photomorphogenic growth. Furthermore, whereas GBF1 acts as a positive regulator of lateral root formation, it differentially regulates the expression of light-inducible genes. Taken together, these results demonstrate that GBF1 is a unique transcriptional regulator of photomorphogenesis in blue light.
Calmodulin7 plays an important role as transcriptional regulator in Arabidopsis seedling development
(American Society of Plant Biologists, 2008) Kushwaha, Ritu; Singh, Aparna; Chattopadhyay, Sudip
Although calmodulin (CaM) is known to play multiple regulatory roles in eukaryotes, its direct function as transcriptional regulator is unknown. Furthermore, the physiological functions of CaM are largely unknown in plants. Here, we show that one of the four Arabidopsis thaliana CaM isoforms, CAM7, is a transcriptional regulator that directly interacts with the promoters of light-inducible genes and promotes photomorphogenesis. CAM7 overexpression causes hyperphotomorphogenic growth and an increase in the expression of light-inducible genes. Mutations in CAM7 produce no visible effects on photomorphogenic growth, indicating likely redundant gene functions. However, cam7 mutants display reduced expression of light-inducible genes, and cam7 hy5 double mutants show an enhancement of the hy5 phenotype. Moreover, over- expression of CAM7 can partly suppress the hy5 phenotype, indicating that the two factors work together to control light- induced seedling development. The mutational and transgenic studies, together with physiological analyses, illustrate the concerted function of CAM7 and HY5 basic leucine zipper transcription factor in Arabidopsis seedling development.
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.
Functional interconnection of MYC2 and SPA1 in the photomorphogenic seedling development of Arabidopsis
(American Society of Plant Biologists, 2010) Gangappa, Sreeramaiah N.; Prasad, V. Babu Rajendra; Chattopadhyay, Sudip
MYC2 is a basic helix-loop-helix transcription factor that cross talks with light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. Here, we have shown that Arabidopsis (Arabidopsis thaliana) MYC2 directly binds to the G-box present in the SUPPRESSOR OF PHYTOCHROME A1 (SPA1) promoter and that it controls the expression of SPA1 in a COP1-dependent manner. Analyses of atmyc2 spa1 double mutants suggest that whereas MYC2 and SPA1 act redundantly to suppress photomorphogenic growth in the dark, they function synergistically for the suppression of photomorphogenic growth in the light. Our studies have also revealed that MYC2-mediated ABA and JA responses are further modulated by SPA1. Taken together, this study demonstrates the molecular and physiological interrelations of MYC2 and SPA1 in light, ABA, and JA signaling pathways.
Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development
(BMC, 2012) Prasad, Babu Rajendra V; Kumar, Selva V; Nandi, Ashis; Chattopadhyay, Sudip
Arabidopsis seedling development is controlled by many regulatory genes involved in multiple signaling pathways. The functional relationships of these genes working in multiple signaling cascades have started to be unraveled. Arabidopsis HY1/HO1 is a rate-limiting enzyme involved in biosynthesis of phytochrome chromophore. HY5 (a bZIP protein) promotes photomorphogenesis, however ZBF1/MYC2 (a bHLH protein) works as a negative regulator of photomorphogenic growth and light regulated gene expression. Further, MYC2 and HY1 have been shown to play important roles in jasmonic acid (JA) signaling pathways. Here, we show the genetic interactions of HY1 with two key transcription factor genes of light signaling, HY5 and MYC2, in Arabidopsis seedling development. Our studies reveal that although HY1 acts in an additive manner with HY5, it is epistatic to MYC2 in light-mediated seedling growth and gene expression. This study further demonstrates that HY1 additively or synergistically functions with HY5, however it works upstream to MYC2 in JA signaling pathways. Taken together, this study demonstrates the functional interrelations of HY1, MYC2 and HY5 in light and JA signaling pathways.
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.
GBF 1, a transcription factor of blue light signaling in Arabidopsis, is degraded in the dark by a proteasome-mediated pathway independent of COP 1 and SPA 1
(The American Society for Biochemistry and Molecular Biology, Inc., 2008) Mallappa, Chandrashekara; Singh, Aparna; Ram, Hathi; Chattopadhyay, Sudip
Arabidopsis GBF1/ZBF2 is a bZIP transcription factor that plays dual but opposite regulatory roles in cryptochrome-mediated blue light signaling. Here, we show the genetic and molecular interrelation of GBF1 with two well characterized negative regulators of light signaling, COP1 and SPA1, in photomorphogenic growth and light-regulated gene expression. Our results further reveal that GBF1 protein is less abundant in the dark- grown seedlings and is degraded by a proteasome-mediated pathway independent of COP1 and SPA1. Furthermore, COP1 physically interacts with GBF1 and is required for the optimum accumulation of GBF1 protein in light-grown seedlings. Taken together, this study provides a mechanistic view of concerted function of three important regulators in Arabidopsis seedling development.
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.
HY1 genetically interacts with GBF1 and regulates the activity of the Z-box containing promoters in light signaling pathways in Arabidopsis thaliana
(Elsevier, 2012) Prasad, V. Babu Rajendra; Gupta, Nisha; Nandi, Ashis; Chattopadhyay, Sudip
Arabidopsis HY1/HO1, heme oxygenase enzyme, catalyses the oxygenation of heme to produce biliverdin, an essential step in the phytochrome-chromophore biosynthesis pathway. GBF1/ZBF2 is a G/Z-box binding bZIP protein that plays a dual but opposite regulatory roles in blue light-mediated seedling development and gene expression. Here, we show the genetic interactions of HY1 and GBF1 in seedling photomorphogenesis, and the role of HY1 in the regulation of promoters containing the Z-box light responsive element. Our results indicate that whereas the additional mutation in GBF1 does not affect the phenotype of hy1 mutant seedlings in red or far-red light, the additional mutation in HY1 suppresses the hyper photomorphogenic phenotype of gbf1 in BL. Further, transgenic studies using promoter-reporter constructs indicate that functional HY1 is essential for the optimal induction of Z-box containing synthetic and native promoters at various stages of Arabidopsis growth and development. Thus, this study establishes a functional relation of HY1 with GBF1, and HY1-mediated regulation of Z-box containing promoters in Arabidopsis seedling development.
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.
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.
Light regulated modulation of Z-box containing promoters by photoreceptor and downstream regulatory components, COP1 and HY5 in Arabidopsis thaliana
(Wiley-Blackwell, 2002) Yadav, Vandana; Kundu, Snehangshu; Chattopadhyay, Debasis; Negi, Prem; Wei, Ning; Deng, Xing-Wang; Chattopadhyay, Sudip
The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA±protein interaction studies reveal the presence of a DNA-binding activity that is speci®c to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.
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.
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.
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.
Molecular interactions of GBF1 with HY5 and HYH during light-mediated seedling development in Arabidopsis thaliana
(American Society for Biochemistry and Molecular Biology, 2012) Singh, Aparna; Ram, Hathi; Abbas, Nazia; Chattopadhyay, Sudip
Arabidopsis bZIP transcription factor, GBF1, acts as a differential regulator of cryptochrome-mediated blue light signaling. Whereas the bZIP proteins, HY5 (elongated hypocotyl 5) and HYH (HY5 homologue), are degraded by COP1-mediated proteasomal pathways, GBF1 is degraded by a proteasomal pathway independent of COP1. In this study, we have investigated the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development. The genetic studies using double and triple mutants reveal that GBF1 largely acts antagonistically with HY5 and HYH in Arabidopsis seedling development. Further, GBF1 and HY5 play more important roles than HYH in blue light-mediated photomorphogenic growth. This study reveals that GBF1 is able to form a G-box-binding heterodimer with HY5 but not with HYH. The in vitro and in vivo studies demonstrate that GBF1 co-localizes with HY5 or HYH in the nucleus and physically interacts with both of the proteins. The protein-protein interaction studies further reveal that the bZIP domain of GBF1 is essential and sufficient for the interaction with HY5 or HYH. Taken together, these data demonstrate the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development.
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.
MYC2, a bHLH transcription factor, modulates the adult phenotype of SPA1
(Landes Bioscience, 2010) Gangappa, Sreeramaiah N.; Chattopadhyay, Sudip
MYC2 and SPA1 are two key regulatory proteins that negatively regulate light-controlled Arabidopsis seedling development. We have recently demonstrated the genetic and molecular relationships of MYC2 and SPA1 in light and JA (jasmonic acid) signaling pathways. Here, we have further shown the genetic interactions between these two proteins in flowering time and lateral root development.