RNAi-Mediated Downregulation of Inositol Pentakisphosphate Kinase (IPK1) in Wheat Grains Decreases Phytic Acid Levels and Increases Fe and Zn Accumulation

Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species. Recently, we reported that functional wheat inositol pentakisphosphate kinase (TaIPK1) is involved in PA biosynthesis, however, the functional roles of the IPK1 gene in wheat remains elusive. In this study, RNAi-mediated gene silencing was performed for IPK1 transcripts in hexaploid wheat. Four non-segregating RNAi lines of wheat were selected for detailed study (S3-D-6-1; S6-K-3-3; S6-K-6-10 and S16-D-9-5). Homozygous transgenic RNAi lines at T4 seeds with a decreased transcript of TaIPK1 showed 28–56% reduction of the PA. Silencing of IPK1 also resulted in increased free phosphate in mature grains. Although, no phenotypic changes in the spike was observed but, lowering of grain PA resulted in the reduced number of seeds per spikelet. The lowering of grain PA was also accompanied by a significant increase in iron (Fe) and zinc (Zn) content, thereby enhancing their molar ratios (Zn:PA and Fe:PA). Overall, this work suggests that IPK1 is a promising candidate for employing genome editing tools to address the mineral accumulation in wheat grains

Diverse Functions of Plant Zinc-Induced Facilitator-like Transporter for Their Emerging Roles in Crop Trait Enhancement

The major facilitator superfamily (MFS) is a large and diverse group of secondary transporters found across all kingdoms of life. Zinc-induced facilitator-like (ZIFL) transporters are the MFS family members that function as exporters driven by the antiporter-dependent processes. The presence of multiple ZIFL transporters was shown in various plant species, as well as in bryophytes. However, only a few ZIFLs have been functionally characterized in plants, and their localization has been suggested to be either on tonoplast or at the plasma membrane. A subset of the plant ZIFLs were eventually characterized as transporters due to their specialized role in phytosiderophores efflux and auxin homeostasis, and they were also proven to impart tolerance to micronutrient deficiency. The emerging functions of ZIFL proteins highlight their role in addressing important traits in crop species. This review aims to provide insight into and discuss the importance of plant ZIFL in various tissue-specific functions. Furthermore, a spotlight is placed on their role in mobilizing essential micronutrients, including iron and zinc, from the rhizosphere to support plant survival. In conclusion, in this paper, we discuss the functional redundancy of ZIFL transporters to understand their roles in developing specific traits in crop

Gene Expression Pattern of Vacuolar-Iron Transporter-Like (VTL) Genes in Hexaploid Wheat during Metal Stress

Iron is one of the important micronutrients that is required for crop productivity and yield-related traits. To address the Fe homeostasis in crop plants, multiple transporters belonging to the category of major facilitator superfamily are being explored. In this direction, earlier vacuolar iron transporters (VITs) have been reported and characterized functionally to address biofortification in cereal crops. In the present study, the identification and characterization of new members of vacuolar iron transporter-like proteins (VTL) was performed in wheat. Phylogenetic distribution demonstrated distinct clustering of the identified VTL genes from the previously known VIT genes. Our analysis identifies multiple VTL genes from hexaploid wheat with the highest number genes localized on chromosome 2. Quantitative expression analysis suggests that most of the VTL genes are induced mostly during the Fe surplus condition, thereby reinforcing their role in metal homeostasis. Interestingly, most of the wheat VTL genes were also significantly up-regulated in a tissue-specific manner under Zn, Mn and Cu deficiency. Although, no significant changes in expression of wheat VTL genes were observed in roots under heavy metals, but TaVTL2, TaVTL3 and TaVTL5 were upregulated in the presence of cobalt stress. Overall, this work deals with the detailed characterization of wheat VTL genes that could provide an important genetic framework for addressing metal homeostasis in bread wheat

Additional file 2

This is the source code of HIVProtI webserver available under GNU GPL v3.0 (General Public License version 3

MOESM1 of HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors

Additional file 1. Supporting information including Table S1. Performance of QSAR predictive models on three times randomly picked ~ 10% independent/validation data. These models were developed using remaining ~ 90% data during training/testing respectively for each of the six datasets; Table S2. Details of statistical parameters used for the development of IC50 based QSAR models; Table S3. Details of statistical parameters used for the development of percent inhibition based QSAR models; Table S4. Details of chemical descriptors used in the development of IC50 based QSAR models; Table S5. Details of chemical descriptors used in the development of percent inhibition based QSAR models; Table S6. Details of slopes k (predicted vs. observed inhibition) and k’ (observed vs. predicted inhibition) of the regression lines for the QSAR models; Table S7. Details of Y-randomization test performed on the QSAR models; Figure S1. Chemical space analysis of QSAR studies (Table 5) for Protease (PR) (a, b), Reverse Transcriptase (RT) (c, d) and Integrase (IN) (e, f) respectively; Figure S2. Chemical space mapping outline of (a) Integrase (IN), (b) Protease (PR) and (c) Reverse Transcriptase (RT) inhibitors (percentage inhibition) with internal circle showing clustering and 3-D embedding of compounds, middle circle with exact (zoomed) superimposed cluster and outermost circle with specific MCS of each cluster; Figure S3. Scatter plot depicting the applicability domain for IC50 datasets of (a) Integrase (IN), (b) Protease (PR) and (c) Reverse Transcriptase (RT); Figure S4. Scatter plot depicting the applicability domain for percentage inhibition datasets of (a) Integrase (IN), (b) Protease (PR) and (c) Reverse Transcriptase (RT)

Genome-wide expression analysis id 1 entifies core components during iron starvation in hexaploid wheat

Iron is one of essential micronutrient for all organisms. Its deficiency 33 causes a severe loss in crops yield. Nevertheless, our current understanding on major crops response to Fe deficiency remains limited. Herein, we investigated the effect of Fe deprivation at both transcriptomic and metabolic levels in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent, analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc42 induced facilitator-like protein was noticed. Our transcriptomic data were in agreement with the GC-MS analysis that showed an enhancement of accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be linked for enhancing Fe-mobilization. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase both at transcriptional and enzymatic activity, which indicate the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops

Additional file 1

Additional file 1 containing Table S1 to S7 and Figure S1 to S

Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation

Iron is one of essential micronutrient for all organisms. Its deficiency 33 causes a severe loss in crops yield. Nevertheless, our current understanding on major crops response to Fe deficiency remains limited. Herein, we investigated the effect of Fe deprivation at both transcriptomic and metabolic levels in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent, analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc42induced facilitator-like protein was noticed. Our transcriptomic data were in agreement with the GC-MS analysis that showed an enhancement of accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be linked for enhancing Fe-mobilization. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase both at transcriptional and enzymatic activity, which indicate the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops

Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation

Iron is an essential micronutrient for all organisms. In crop plants, iron deficiency can decrease crop yield significantly, however our current understanding of how major crops respond to iron deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic levels in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differential expressed. Homoeolog and subgenome specific analysis unveiled induction bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc-induced facilitator-like protein was noticed. Expression of genes related to the strategy-II mode of Fe uptake was predominant as well. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be contributing to Fe-mobilization. Interestingly, Fe starvation leads to significant temporal increase of glutathione-S-transferase both at transcriptional and in enzymatic activity levels, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at molecular level and lays foundation to design new strategies for the improvement of Fe nutrition in crops