Publications of NIPGR Scientists

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Author: search.filters.author.Thakur, Jitendra K.Subject: search.filters.subject.Mediator subunit

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    MediatorWeb: a protein-protein interaction network database for the RNA polymerase II Mediator complex
    (John Wiley & Sons, 2024) Maji, Sourobh; Waseem, Mohd; Sharma, Manish Kumar; Singh, Maninder; Singh, Anamika; Dwivedi, Nidhi; Thakur, Pallabi; Cooper, David G.; Bisht, Naveen C.; Fassler, Jan S.; Subbarao, Naidu; Khurana, Jitendra P.; Bhavesh, Neel Sarovar; Thakur, Jitendra K.
    The protein-protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue-level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.
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    Characterization of mediator complex and its associated proteins from rice
    (Springer, 2017) Samanta, Subhasis; Thakur, Jitendra K.
    The Mediator complex is a multi-protein complex that acts as a molecular bridge conveying transcriptional messages from the cis element-bound transcription factor to the RNA Polymerase II machinery. It is found in all eukaryotes including members of the plant kingdom. Increasing number of reports from plants regarding different Mediator subunits involved in a multitude of processes spanning from plant development to environmental interactions have firmly established it as a central hub of plant regulatory networks. Routine isolation of Mediator complex in a particular species is a necessity because of many reasons. First, composition of the Mediator complex varies from species to species. Second, the composition of the Mediator complex in a particular species is not static under all developmental and environmental conditions. Besides this, at times, Mediator complex is used in in vitro transcription systems. Rice, a staple food crop of the world, is used as a model monocot crop. Realizing the need of a reliable protocol for the isolation of Mediator complex from plants, we describe here the isolation of Mediator complex from rice.
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    Role of plant mediator complex in stress response
    (Springer, 2015) Samanta, Subhasis; Thakur, Jitendra K.
    Class II gene loci of eukaryotes are transcribed by RNA Polymerase II, which functions in coordination with several other proteins like transcription factors, general transcription factors, and cofactors. Recently, Mediator complex, a multi-subunit, megadalton size protein complex has gained lots of attention as an important component of RNA pol II transcriptional machinery because of its essentiality in the regulation of most of the class II genes. Like yeast and other metazoans, plants also possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Recent times have experienced a flurry of scientific papers containing the functional information of individual Mediator subunits in plants, although many were reported earlier without consideration of their association with the Mediator complex. Among its diverse functional aspects, several reports have established the Mediator complex as an important integrative hub of different biotic and abiotic stress signaling pathways, which have been discussed in this chapter from the functional genomics perspectives. Although reports are emerging in support of its inclusion as a component of the basic transcriptional machinery, the gene selective roles of the individual Mediator subunits are proven and indisputably accepted.