Papers by Jitendra Thakur
Photosynthesis and Abiotic Stress in Plants
Biotic and Abiotic Stress Tolerance in Plants
The kinase module of the Mediator complex: an important signalling processor for the development and survival of plants
Journal of Experimental Botany
Mediator, a multisubunit protein complex, is a signal processor that conveys regulatory informati... more Mediator, a multisubunit protein complex, is a signal processor that conveys regulatory information from transcription factors to RNA polymerase II and therefore plays an important role in the regulation of gene expression. This megadalton complex comprises four modules, namely, the head, middle, tail, and kinase modules. The first three modules form the core part of the complex, whereas association of the kinase module is facultative. The kinase module is able to alter the function of Mediator and has been established as a major transcriptional regulator of numerous developmental and biochemical processes. The kinase module consists of MED12, MED13, CycC, and kinase CDK8. Upon association with Mediator, the kinase module can alter its structure and function dramatically. In the past decade, research has established that the kinase module is very important for plant growth and development, and in the fight against biotic and abiotic challenges. However, there has been no comprehensi...
Genome‐wide analysis of polymorphisms identified domestication‐associated long low‐diversity region carrying important rice grain size/weight quantitative trait loci
The Plant Journal
Genetic diversity provides foundation for plant breeding and genetic research. As part of the 3K ... more Genetic diversity provides foundation for plant breeding and genetic research. As part of the 3K Rice Genome Project, over 3000 rice genomes were recently sequenced. We added four Indian rice accessions to it and made original panel of 3004 accessions. However, large set of germplasms are difficult to preserve and evaluate. Construction of core and mini-core collections is an efficient method for managing genetic resources. This study aims to designing of mini-core comprised of 520 accessions representing original panel. The designed mini-core captured most of the SNPs and represented all phenotypes and geographical regions. The mini-core was validated using different statistical analyses and had representation from all major groups including japonica, indica, aus/boro and aromatic/basmati. GWAS analyses with mini-core panel efficiently reproduced the marker-traits association identified among original 3004 panel. Expression analysis of trait-associated genes highlights the relevanc...
GC-MS-Based Analysis of Methanol: Chloroform-extracted Fatty Acids from Plant Tissues
BIO-PROTOCOL
Scientific reports, Jan 2, 2017
The KIX domain has emerged in the last two decades as a critical site of interaction for transcri... more The KIX domain has emerged in the last two decades as a critical site of interaction for transcriptional assembly, regulation and gene expression. Discovered in 1994, this conserved, triple helical globular domain has been characterised in various coactivator proteins of yeast, mammals and plants, including the p300/CBP (a histone acetyl transferase), MED15 (a subunit of the mediator complex of RNA polymerase II), and RECQL5 helicases. In this work, we describe the first rigorous meta analysis of KIX domains across all forms of life, leading to the development of KIXBASE, a predictive web server and global repository for detection and analysis of KIX domains. To our knowledge, KIXBASE comprises the largest online collection of KIX sequences, enabling assessments at the level of both sequence and structure, incorporating PSIPRED and MUSTER at the backend for further annotation and quality assessment. In addition, KIXBASE provides useful information about critical aspects of KIX domai...
Plant signaling & behavior, Feb 17, 2018
Med15 is an important subunit of Mediator tail module and is characterized by a KIX domain presen... more Med15 is an important subunit of Mediator tail module and is characterized by a KIX domain present in the amino terminal. In yeast and metazoans, Med15 KIX domain has been found to interact with various transcription factors, regulating several processes including carbohydrate metabolism, lipogenesis, stress response and multidrug resistance. Mechanism of Med15 functioning in Arabidopsis is largely unknown. In this study, interactome of Arabidopsis Med15, AtMed15a, was characterized. We found 45 proteins that interact with AtMed15a KIX domain, including 11 transcription factors, 3 single strand nucleic acid-binding proteins and 1 splicing factor. The third helix of the KIX domain was found to be involved in most of the interactions. Mapping of the regions participating in the interactions revealed that the activation domain of a transcription factor, UKTF1 interacted with AtMed15a KIX domain. Thus, our results suggest that in Arabidopsis, activation domain of transcription factors t...
Nature communications, Nov 16, 2017
Invasion of human erythrocytes by Plasmodium falciparum merozoites involves multiple interactions... more Invasion of human erythrocytes by Plasmodium falciparum merozoites involves multiple interactions between host receptors and their merozoite ligands. Here we report human Cyclophilin B as a receptor for PfRhopH3 during merozoite invasion. Localization and binding studies show that Cyclophilin B is present on the erythrocytes and binds strongly to merozoites. We demonstrate that PfRhopH3 binds to the RBCs and their treatment with Cyclosporin A prevents merozoite invasion. We also show a multi-protein complex involving Cyclophilin B and Basigin, as well as PfRhopH3 and PfRh5 that aids the invasion. Furthermore, we report identification of a de novo peptide CDP3 that binds Cyclophilin B and blocks invasion by up to 80%. Collectively, our data provide evidence of compounded interactions between host receptors and merozoite surface proteins and paves the way for developing peptide and small-molecules that inhibit the protein-protein interactions, individually or in toto, leading to abrog...
The Journal of biological chemistry, Jul 5, 2017
Persistent or chronic infection with the hepatitis B virus represents one of the most common vira... more Persistent or chronic infection with the hepatitis B virus represents one of the most common viral diseases in humans. The hepatitis B virus deploys the Hepatitis B Virus X Protein (HBx) as a suppressor of host defenses consisting of RNAi-based silencing of viral genes. Because of its critical role in countering host defenses, HBx represents an attractive target for antiviral drugs. Here, we developed and optimized a loss-of-function screening procedure, which identified a potential pharmacophore that abrogated HBxs RNAi suppression activity. In a survey of 14,400 compounds in the Maybridge Screening Collection, we prioritized candidate compounds via high-throughput screening based on reversal of green fluorescent protein (GFP) reported, RNAi-mediated silencing in a HepG2/GFP-shRNA RNAi sensor line. The screening yielded a pharmacologically active compound, N (2,4 difluorophenyl) N [3 (1H imidazol 1 yl) propyl] thiourea (IR415), which blocked HBx mediated RNAi suppression indicated ...
Scientific Reports, 2016
Mediator, a multiprotein complex involved in transcription of class II genes, was first discovere... more Mediator, a multiprotein complex involved in transcription of class II genes, was first discovered in yeast and then characterized in many metazoans revealing a striking structural conservation of the complex. However, sequences of Mediator subunits are not well conserved raising a question on the functional conservation of these individual subunits. In this study, expression of Med15 of Arabidopsis (AtMed15) in gal11∆ yeast could not complement the function of ScGal11 in galactose metabolism and resistance against cycloheximide. Surprisingly, AtMed15 changed the morphology of the yeast cells. The cells adhered strongly on the surface of the agar media, and showed robust flocculation in the liquid media without affecting the growth. The AtMed15-induced adhesion and flocculation were observed in different carbon sources. Calcium-assisted cell wall-bound mannan-binding proteins were found to be involved in this flocculation, which was unaffected by wide fluctuation of pH or temperatures revealing its constitutive robust nature. Expression of few flocculation related Flo genes was up-regulated in these cells. Interestingly, there was significant increase in ethanol production by the yeast expressing AtMed15. Robust and constitutive flocculation and increased ethanol production by yeast cells harbouring AtMed15 indicate an opportunity of its important usage in biotechnology industries. In higher eukaryotes, transcriptional programme of a protein coding gene is dependent on the regulatory elements present within or outside the gene. These regulatory elements are recognized by specific transcription factors which have the ability to respond to specific developmental and environmental signals. The transcription factors perceive the signal and then communicate with the transcriptional machinery either directly or indirectly through the precisely orchestrated recruitment of cofactors 1-3. The Mediator complex or Mediator is one such cofactor, and is required for basal and induced expression of almost all RNA polymerase II-dependent genes 4-7. Mediator is a large complex made up of 25 or more subunits arranged in a way to provide modular interfaces for several intermolecular interactions 8. Some of these subunits can interact with transcription factors whereas some other subunits can interact with components of RNA pol II transcriptional machinery, suggesting that Mediator functions as a communication bridge that can relay regulatory signals from transcription factors bound to the regulatory elements to the RNA pol II machinery bound to the promoter of the gene 4,6,9,10. Combination of genetic, structural and biochemical studies of yeast and metazoan Mediator complexes suggest that the subunits of the complex form four distinct modules designated as head, middle, tail and kinase 1,4,8,11,12. The head, middle and tail modules form the relatively stable core structure, whereas the kinase module associates reversibly with the core structure. It is suggested that the kinase module sterically blocks the RNA Pol II interactions with the core Mediator, and thus exert a repressive function 13,14. The head and middle modules are involved in interactions with the core RNA Pol II machinery 15,16 , whereas subunits of the tail modules interact with DNA-bound transcription activators and repressors 17-21. The tail module includes the Med2, Med3, Med14, Med15 and Med16 subunits. The Med15 protein is an interesting example of a category of the Mediator subunits which have a large intrinsic disordered region 22 and has evolved to process transcriptional signals for regulating distinct cellular processes. The Med15 gene was initially identified in yeast as a positive regulator of the genes encoding proteins that are involved in galactose metabolism,
Mediator Subunit Gall 1 p/MED15 Is Required for Fatty Acid-dependent Gene Activation by Yeast Transcription Factor Oaf1 p
The Journal of Biological Chemistry, 2009
Scientific reports, Jan 22, 2016
The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for unders... more The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for understanding the complex genetic architecture of grain size/weight quantitative trait in rice. The targeted multiplex amplicon resequencing of 55 MED genes annotated from whole rice genome in 384 accessions discovered 3971 SNPs, which were structurally and functionally annotated in diverse coding and non-coding sequence-components of genes. Association analysis, using the genotyping information of 3971 SNPs in a structured population of 384 accessions (with 50-100 kb linkage disequilibrium decay), detected 10 MED gene-derived SNPs significantly associated (46% combined phenotypic variation explained) with grain length, width and weight in rice. Of these, one strong grain weight-associated non-synonymous SNP (G/A)-carrying OsMED4_2 gene was validated successfully in low- and high-grain weight parental accessions and homozygous individuals of a rice mapping population. The seed-specific express...
Nucleic Acids Research, 2015
Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit ... more Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms.
Frontiers in Plant Science, 2015
Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either ... more Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.
Role of Plant Mediator Complex in Stress Response
Elucidation of Abiotic Stress Signaling in Plants, 2015
Plant Biotechnology and Molecular Markers, 2005
Plant Signaling & Behavior, 2013
Mediator was discovered in yeast as a necessary component for transcription of a protein coding g... more Mediator was discovered in yeast as a necessary component for transcription of a protein coding gene. 1,2 Later on, Mediator was purified and characterized to be a gigantic multiprotein complex required by RNA polymerase II for the transcription of its target genes. 3-5 It was found to play important role in facilitating the assembly of the preinitiation complex. 6-8 Genetic, biochemical and bioinformatic analyses revealed its existence in all the eukaryotes ranging from simple unicellular yeast to complex multicellular mammals and plants. 8-11 In yeast, there are 25 subunits which make Mediator, whereas in animals and plants the number is higher. 11,12 Biochemical and biophysical studies in fungi and metazoans confirmed the modular structure of this complex, wherein the subunits compose four different modules namely Head, Middle, Tail and Kinase. 5,8,13-15 Head, Middle and Tail constitute the core part of the complex, whereas the Kinase module reversibly associates with the core part. Subunits constituting the Head and Middle modules are found to interact with RNA pol II and components of transcriptional machinery, whereas subunits of Tail module establish contact with diverse transcription factors. 13,16-18 Thus, Mediator provides an interface to relay the regulatory signals from the transcriptional regulators to the transcriptional machinery. The subunits of Kinase module can interact with the subunits of the Head and Middle modules, and so affect the interaction between the complex and the RNA pol II. That is why in many cases, presence of Kinase module in the Mediator was found to be associated with the repression of the gene expression. 19 Mediator is a gigantic multiprotein complex required for transcription of almost all the protein coding genes. In this report, we have analyzed the transcript abundance of 31 Med genes in different tissues of Arabidopsis. Our analysis revealed the tissue specific differential expression profile of many Med subunit genes suggesting they might be contributing in the formation, maturation or function of that specific tissue. Moreover, we also found increase or decrease in the expression level of several Med subunits during the same duration of specific processes (for example flowering) indicating probable enrichment of a particular arrangement of selected subunits during that process. Thus, this study suggests that not only specific Med subunits have functional relevance in specific processes, but specific arrangements of Med subunits might also play significant role in some processes in Arabidopsis or other plants.
Plant Signaling & Behavior, 2012
Nucleic Acids Research, 2014
The kinase-inducible domain interacting (KIX) domain is a highly conserved independently folding ... more The kinase-inducible domain interacting (KIX) domain is a highly conserved independently folding three-helix bundle that serves as a docking site for transcription factors, whereupon promoter activation and target specificity are achieved during gene regulation. This docking event is a harbinger of an intricate multi-protein assembly at the transcriptional apparatus and is regulated in a highly precise manner in view of the critical role it plays in multiple cellular processes. KIX domains have been characterized in transcriptional coactivators such as p300/CREB-binding protein and mediator of RNA polymerase II transcription subunit 15, and even recQ protein-like 5 helicases in various organisms. Their targets are often intrinsically disordered regions within the transactivation domains of transcription factors that attain stable secondary structure only upon complexation with KIX. In this article, we review the KIX domain in terms of its sequence and structure and present the vario...
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Papers by Jitendra Thakur