Archana N. Rai

Molecular evolution of plant P5CS gene involved in proline biosynthesis

The P5CS ({Delta} 1-Pyrroline–5-Carboxylate Synthetase) gene encodes for a bifunctional enzyme that catalyzes the rate limiting reaction in proline biosynthesis in living organisms. A wide range of multifunctional roles of proline have now been shown in stress defense. The proline biosynthetic genes, especially, P5CS is commonly used in metabolic engineering for proline overproduction conferring stress tolerance in plants. The gene is functionally well characterized at the molecular level, but there is more to learn about its evolutionary path in the plant kingdom, particularly the drive behind functional (osmoprotective and developmental) divergence of duplication of P5CS genes. In this review, we present the current understanding of the evolutionary trail of plant P5CS gene which plays a key role in stress tolerance.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintocks original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Membrane Topology and Predicted RNA-Binding Function of the ‘Early Responsive to Dehydration (ERD4)’ Plant Protein

Functional annotation of uncharacterized genes is the main focus of computational methods in the post genomic era. These tools search for similarity between proteins on the premise that those sharing sequence or structural motifs usually perform related functions, and are thus particularly useful for membrane proteins. Early responsive to dehydration (ERD) genes are rapidly induced in response to dehydration stress in a variety of plant species. In the present work we characterized function of Brassica juncea ERD4 gene using computational approaches. The ERD4 protein of unknown function possesses ubiquitous DUF221 domain (residues 312–634) and is conserved in all plant species. We suggest that the protein is localized in chloroplast membrane with at least nine transmembrane helices. We detected a globular domain of 165 amino acid residues (183–347) in plant ERD4 proteins and expect this to be posited inside the chloroplast. The structural-functional annotation of the globular domain was arrived at using fold recognition methods, which suggested in its sequence presence of two tandem RNA-recognition motif (RRM) domains each folded into βαββαβ topology. The structure based sequence alignment with the known RNA-binding proteins revealed conservation of two non-canonical ribonucleoprotein sub-motifs in both the putative RNA-recognition domains of the ERD4 protein. The function of highly conserved ERD4 protein may thus be associated with its RNA-binding ability during the stress response. This is the first functional annotation of ERD4 family of proteins that can be useful in designing experiments to unravel crucial aspects of stress tolerance mechanism.

Calcium Signaling and Its Significance in Alleviating Salt Stress in Plants

Environmental stresses such as salinity, temperature, drought and heavy metals negatively impact the agricultural productivity. Of these, salinity stands as a major problem mainly in the developing countries. Calcium is an essential nutrient that regulates the plant growth and development and it has evolved as a ubiquitous secondary messenger in mediating complex responses towards various developmental and environmental cues. Thus, understanding the calcium signaling and consequent calcium-dependent events is essential to improve plant productivity under extreme environment. The first step in calcium signaling is the induction of [Ca2+]cyt-transient/signatures which is defined as the repetitive oscillations or spiking of [Ca2+]cyt level. This in turn activates a set of calcium binding proteins including Ca2+ sensors/decoders, protein kinases and transcription factors. The interplay between Ca2+ signatures and these proteins together contributes towards the stimulus specificity. Various efforts have been made to manipulate calcium signaling events either by exogenous calcium supplementation or by genetic modification of calcium signaling related genes in many plant species and considerable progress has been made in managing the plant responses toward salt stress. Additionally, these studies also help in understanding the effect of salt stress on the process of calcium signaling. The present review deals with the basic steps of calcium signaling process and its possible modulations that can lead to the enhanced salt tolerance in plants.

Brassica RNA binding protein ERD4 is involved in conferring salt, drought tolerance and enhancing plant growth in Arabidopsis.

Abstract‘Early responsive to dehydration’ (ERD) genes are a group of plant genes having functional roles in plant stress tolerance and development. In this study, we have isolated and characterized a Brassica juncea ‘ERD’ gene (BjERD4) which encodes a novel RNA binding protein. The expression pattern of ERD4 analyzed under different stress conditions showed that transcript levels were increased with dehydration, sodium chloride, low temperature, heat, abscisic acid and salicylic acid treatments. The BjERD4 was found to be localized in the chloroplasts as revealed by Confocal microscopy studies. To study the function, transgenic Arabidopsis plants were generated and analyzed for various morphological and physiological parameters. The overexpressing transgenic lines showed significant increase in number of leaves with more leaf area and larger siliques as compared to wild type plants, whereas RNAi:ERD4 transgenic lines showed reduced leaf number, leaf area, dwarf phenotype and delayed seed germination. Transgenic Arabidopsis plants overexpressing BjERD4 gene also exhibited enhanced tolerance to dehydration and salt stresses, while the knockdown lines were susceptible as compared to wild type plants under similar stress conditions. It was observed that BjERD4 protein could bind RNA as evidenced by the gel-shift assay. The overall results of transcript analysis, RNA gel-shift assay, and transgenic expression, for the first time, show that the BjERD4 is involved in abiotic stress tolerance besides offering new clues about the possible roles of BjERD4 in plant growth and development.

Retraction note to: Brassica RNA binding protein ERD4 is involved in conferring salt, drought tolerance and enhancing plant growth in Arabidopsis

‘Early responsive to dehydration’ (ERD) genes are a group of plant genes having functional roles in plant stress tolerance and development. In this study, we have isolated and characterized a Brassica juncea ‘ERD’ gene (BjERD4) which encodes a novel RNA binding protein. The expression pattern of ERD4 analyzed under different stress conditions showed that transcript levels were increased with dehydration, sodium chloride, low temperature, heat, abscisic acid and salicylic acid treatments. The BjERD4 was found to be localized in the chloroplasts as revealed by Confocal microscopy studies. To study the function, transgenic Arabidopsis plants were generated and analyzed for various morphological and physiological parameters. The overexpressing transgenic lines showed significant increase in number of leaves with more leaf area and larger siliques as compared to wild type plants, whereas RNAi:ERD4 transgenic lines showed reduced leaf number, leaf area, dwarf phenotype and delayed seed germination. Transgenic Arabidopsis plants overexpressing BjERD4 gene also exhibited enhanced tolerance to dehydration and salt stresses, while the knockdown lines were susceptible as compared to wild type plants under similar stress conditions. It was observed that BjERD4 protein could bind RNA as evidenced by the gel-shift assay. The overall results of transcript analysis, RNA gel-shift assay, and transgenic expression, for the first time, show that the BjERD4 is involved in abiotic stress tolerance besides offering new clues about the possible roles of BjERD4 in plant growth and development.

Salt-induced stress responses of Brassica (Brassica juncea L.) genotypes

The effects of salt stress were evaluated in two Brassica juncea cultivars, Varuna and TM2, in relation to growth, osmolyte accumulation and antioxidant enzymes at 50, 100 and 200 mmol l−1 NaCl concentration. In general, significant reduction in shoot and root growth and relative water content was observed under salt stress.Among the varieties, extent of reduction for these parameters was more pronounced and significant in the case of Varuna than TM2. Significant accumulation of glycine betaine was observed in Varuna and TM2 in 100 and 200 mmol l−1 salt stress treatments than control but the magnitude of increase was significantly higher in TM2. In general, salt stress led to increased activities of Superoxid dismutase, Catalase and Guaiacol peroxidase. The SOD activity was significantly higher in Varuna than TM2. Catalase activity showed an increase up to 100 mmol l−1 NaCl concentration whereas it decreased at 200 mmol l−1 in both the cultivars. Based on the results, TM2 appears to have higher salt tolerance than Varuna. It is also suggestive that osmotic adjustment and antioxidant enzymes play an important role in contributing to salinity tolerance in Brassica juncea L.

Aliphatic glucosinolate synthesis and gene expression changes in gamma-irradiated cabbage.

Glucosinolates, found principally in the plant order Brassicales, are modulated by different post-harvest processing operations. Among these, ionizing radiation, a non-thermal process, has gained considerable interest for ensuring food security and safety. In gamma-irradiated cabbage, enhanced sinigrin, a major glucosinolate, has been reported. However, the molecular basis of such a radiation induced effect is not known. Herein, the effect of radiation processing on the expression of glucosinolate biosynthetic genes was investigated. RT-PCR based expression analysis of seven glucosinolate biosynthetic pathway genes (MYB28, CYP79F1, CYP83A1, SUR1, UGT74B1, SOT18 and TGG1) showed that CYP83A1, MYB28, UGT74B1, CYP79F1 and SUR1 were up-regulated in irradiated cabbage. The content of jasmonates, signalling molecules involved in glucosinolate induction was, however, unaffected in irradiated cabbage suggesting their non-involvement in glucosinolate induction during radiation processing. This is the first report on the effect of gamma irradiation on the expression of glucosinolate biosynthetic genes in vegetables.