Browsing by Author "Ram, Hathi"

Now showing 1 - 5 of 5

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.
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.