Browsing by Author "Bhattacharjee, Annapurna"

Now showing 1 - 9 of 9

Characterization of rice homeobox genes, OsHOX22 and OsHOX24, and over-expression of OsHOX24 in transgenic Arabidopsis suggest their role in abiotic stress response
(Frontiers Media S.A., 2016) Bhattacharjee, Annapurna; Khurana, Jitendra P.; Jain, Mukesh
Homeobox transcription factors are well known regulators of plant growth and development. In this study, we carried out functional analysis of two candidate stress-responsive HD-ZIP I class homeobox genes from rice, OsHOX22, and OsHOX24. These genes were highly up-regulated under various abiotic stress conditions at different stages of rice development, including seedling, mature and reproductive stages. The transcript levels of these genes were enhanced significantly in the presence of plant hormones, including abscisic acid (ABA), auxin, salicylic acid, and gibberellic acid. The recombinant full-length and truncated homeobox proteins were found to be localized in the nucleus. Electrophoretic mobility shift assay established the binding of these homeobox proteins with specific DNA sequences, AH1 (CAAT(A/T)ATTG) and AH2 (CAAT(C/G)ATTG). Transactivation assays in yeast revealed the transcriptional activation potential of full-length OsHOX22 and OsHOX24 proteins. Homo- and hetero-dimerization capabilities of these proteins have also been demonstrated. Further, we identified putative novel interacting proteins of OsHOX22 and OsHOX24 via yeast-two hybrid analysis. Over-expression of OsHOX24 imparted higher sensitivity to stress hormone, ABA, and abiotic stresses in the transgenic Arabidopsis plants as revealed by various physiological and phenotypic assays. Microarray analysis revealed differential expression of several stress-responsive genes in transgenic lines as compared to wild-type. Many of these genes were found to be involved in transcriptional regulation and various metabolic pathways. Altogether, our results suggest the possible role of OsHOX22/OsHOX24 homeobox proteins as negative regulators in abiotic stress responses.
Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses
(BioMed Central, 2010) Jain, Mukesh; Ghanashyam, Challa; Bhattacharjee, Annapurna
Glutathione S-transferases (GSTs) are the ubiquitous enzymes that play a key role in cellular detoxification. Although several GSTs have been identified and characterized in various plant species, the knowledge about their role in developmental processes and response to various stimuli is still very limited. In this study, we report genome-wide identification, characterization and comprehensive expression analysis of members of GST gene family in crop plant rice, to reveal their function(s).
Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development
(Am. Soc. of Plant Biologists, 2011) Garg, Rohini; Patel, Ravi K.; Jhanwar, Shalu; Priya, Pushp; Bhattacharjee, Annapurna; Yadav, Gitanjali; Bhatia, Sabhyata; Chattopadhyay, Debasis; Tyagi, Akhilesh K.; Jain, Mukesh
Chickpea (Cicer arietinum) is an important food legume crop but lags in the availability of genomic resources. In this study, we have generated about 2 million high-quality sequences of average length of 372 bp using pyrosequencing technology. The optimization of de novo assembly clearly indicated that hybrid assembly of long-read and short-read primary assemblies gave better results. The hybrid assembly generated a set of 34,760 transcripts with an average length of 1,020 bp representing about 4.8% (35.5 Mb) of the total chickpea genome. We identified more than 4,000 simple sequence repeats, which can be developed as functional molecular markers in chickpea. Putative function and Gene Ontology terms were assigned to at least 73.2% and 71.0% of chickpea transcripts, respectively. We have also identified several chickpea transcripts that showed tissue-specific expression and validated the results using real-time polymerase chain reaction analysis. Based on sequence comparison with other species within the plant kingdom, we identified two sets of lineage-specific genes, including those conserved in the Fabaceae family (legume specific) and those lacking significant similarity with any non chickpea species (chickpea specific). Finally, we have developed a Web resource, Chickpea Transcriptome Database, which provides public access to the data and results reported in this study. The strategy for optimization of de novo assembly presented here may further facilitate the transcriptome sequencing and characterization in other organisms. Most importantly, the data and results reported in this study will help to accelerate research in various areas of genomics and implementing breeding programs in chickpea.
Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea
(Springer, 2015) Garg, Rohini; Bhattacharjee, Annapurna; Jain, Mukesh
Chickpea is an important legume crop plant and various abiotic stresses are the major constraints affecting its overall productivity. For discovery of candidate genes involved in abiotic stress responses, we employed RNA sequencing for transcriptome profiling of roots and shoots of chickpea seedlings subjected to desiccation, salinity, and cold stresses. In total, we generated more than 250 million high-quality reads from non-stressed and stressed tissue samples. Data analyses provided a comprehensive view of the dynamic transcriptional response of chickpea tissues to different abiotic stresses. Differential expression analysis identified a total of 11,640 chickpea transcripts showing response to at least one of the stress conditions. The reference-based transcriptome assembly was generated and at least 3,536 previously unannotated gene loci differentially expressed under abiotic stress conditions were identified. We observed extensive transcriptional reprogramming of genes involved in transcription regulation, energy metabolism, photosynthesis, hormonal responses, secondary metabolite biosynthesis and osmoprotectant metabolism under stress conditions. In addition, genes involved in post-translational modifications, RNA metabolic processes, and epigenetic regulation were also significantly highlighted. The comprehensive transcriptome analyses presented in this study revealed several potential key regulators of plant response to abiotic stresses and open avenues to carry out functional and applied genomic studies for improving abiotic stress tolerance in chickpea.
Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling
(PLOS, 2015) Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, Mukesh
Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.
Homeobox genes as potential candidates for crop improvement under abiotic stress
(Springer, 2013) Bhattacharjee, Annapurna; Jain, Mukesh
Understanding the molecular basis of plant responses to the major abiotic stresses such as drought and salinity is very important for the biotechnological application of stress adaptation for crop improvement. In this context, thousands of stress-responsive genes have been identified and a few of them have been functionally characterized. Some of them have been proposed as suitable targets for genetic engineering in order to impart stress tolerance in plants. Amidst numerous genes analyzed, transcription factors are considered to be very good targets for studying the molecular mechanisms of abiotic stress response as they singularly or in conjunction regulate the expression of many downstream target genes. Among the various transcription factor encoding genes, homeobox genes, which are well known to be involved in diverse aspects of development, have also recently been implicated in abiotic stress responses. Through various overexpression and mutant studies, the versatility of homeobox genes in plants has been revealed. There are evidences where these genes have been found to confer stress tolerance in plants. This review highlights the importance of homeobox genes in abiotic stress responses and their potential for engineering stress tolerance for crop improvement.
Over-expression of OsHOX24 confers enhanced susceptibility to abiotic stresses in transgenic rice via modulating stress-responsive gene expression
(Frontiers Media S.A., 2017) Bhattacharjee, Annapurna; Sharma, Raghvendra; Jain, Mukesh
Homeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT). OsHOX24 over-expression rice seedlings showed reduced root and shoot growth under salinity and desiccation stress (DS) conditions. Various physiological and phenotypic assays confirmed higher susceptibility of rice transgenics toward abiotic stresses as compared to WT at mature and reproductive stages of rice development too. Global gene expression profiling revealed differential regulation of several genes in the transgenic plants under control and DS conditions. Many of these differentially expressed genes were found to be involved in transcriptional regulatory activities, besides carbohydrate, nucleic acid and lipid metabolic processes and response to abiotic stress and hormones. Taken together, our findings highlighted the role of OsHOX24 in regulation of abiotic stress responses via modulating the expression of stress-responsive genes in rice.
Transcription factor mediated abiotic stress signaling in rice
(Global Science Books, 2013) Bhattacharjee, Annapurna; Jain, Mukesh
Abiotic stresses are the major cause that limits productivity of crop plants worldwide. Plants respond to these stress conditions at physiological and molecular levels. At the molecular level, the expression of thousands of genes is altered in response to various abiotic stress conditions. Several studies have been performed to find out the role of these genes in abiotic stress signaling. However, among these, transcription factor encoding genes are most important because many of them act as ‘key or master regulators’ of gene expression. Transcription factors appear to be attractive targets to unravel the molecular mechanisms of abiotic stress responses and engineering abiotic stress tolerance in plants. However, the role of only a few transcription factors in abiotic stress responses have been elucidated in rice until now and require a detailed investigation for several such candidate genes. In this review, our endeavour is to develop a comprehensive understanding of the intricate regulatory network of transcription factors operative during abiotic stress responses with greater emphasis on rice.
Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses
(Nature Publishing Group, 2016) Shankar, Rama; Bhattacharjee, Annapurna; Jain, Mukesh
Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.