Biology subjects

Giri, J.

Publications and source records attributed to Giri, J..

5 recordsLinked to original sources

bioRxiv2025

The EXS domain of rice PHOSPHATE1 (OsPHO1;2) reduces the low phosphate response through jasmonate signaling

Phosphorus (P) is a vital macronutrient essential for plant growth, and its deficiency significantly hampers agricultural productivity. The PHOSPHATE 1 (PHO1) protein family, characterized by an N-terminal SPX domain, four transmembrane (4TM) domains, and a C-terminal EXS domain, is pivotal in transporting phosphate (Pi) from roots to shoots. Rice, PHO1;2 plays a crucial role in the Pi export process, and defects in this gene cause severe growth retardation and Pi deficiency symptoms even when external Pi levels are adequate. This study examined the roles of the EXS domain and the combined 4TM+EXS domains of OsPHO1;2 in supporting plant growth responses, independent of Pi transport activity, as well as their influence on hormone signaling and gene regulation. Using CRISPR/Cas9, rice lines expressing specific OsPHO1;2 domains (EXS or 4TM+EXS) were created by targeted deletion of particular domain-coding regions. Phenotypic analysis under Pi-sufficient and deficient conditions, as well as phosphate profiling, revealed that EXS lines exhibited notably better growth than loss-of-function mutants, ospho1;2, during early development, despite having similar shoot Pi levels to the null mutant. These lines showed lower levels of defense hormones (jasmonic acid) than ospho1;2 but were comparable to those in the wild type. Conversely, 4TM+EXS lines exhibited growth patterns similar to ospho1;2 mutants. RNA sequencing indicated that the phosphate starvation response (PSR) and defense pathways were less pronounced in the EXS lines compared to ospho1;2 mutants. However, both EXS and 4TM+EXS lines showed seed development defects and reduced total phosphorus content in seeds, mirroring the ospho1;2 phenotype. Heterozygous plants carrying one functional OsPHO1;2 allele displayed normal growth and seed development, indicating the mutations recessive nature. The findings suggest that the EXS domain of OsPHO1;2 can promote plant growth independently of Pi transport by decreasing PSR and modulating defense hormone pathways. This further suggests a signaling role for PHO1 domains beyond direct Pi translocation. Overall, these results enhance our understanding of Pi homeostasis and may help form strategies for breeding P-efficient crops.

molecular biology↗

bioRxiv2025

Identification of the Best Filter-based Feature Selection Techniques for Microarray Datasets

This article basically explores the impact of univariate & multivariate filter-based feature selection methodologies on enhancing the classification performance for the real-life classification problems. Our study considers two univariate filter-based feature selection techniques, namely, Chi-square and Fisher score, as well as two multivariate filter-based feature selection techniques, viz., Symmetrical Uncertainty and Minimum Redundancy-Maximum Relevance (mRMR). These methods are applied to feature selection from Five diverse collections of datasets, including datasets related to Mixed-lineage Leukaemia (MLL), Lung Cancer, Ovarian Cancer, Central Nervous System (CNS), and Colon Cancer. For each feature, fitness values are calculated using the four aforementioned feature selection methods. After that, a stratified 10-fold cross-validation procedure is conducted using Support Vector Machines (SVM) and Multilayer Perceptrons (MLP) to determine the classification accuracy for each feature. A set of five microarray datasets was used in this evaluation in order to assess the effectiveness of the filter methods. The results of this study represent the first comprehensive analysis and comparison of gene expression datasets filtered using a variety of ranking strategies. Among these approaches, entropy-based methods (e.g., mRMR) emerge as the most effective. The mRMR method demonstrates Outstanding performance outcomes of accuracy, F1-score, and Root Mean Square Error (RMSE). When comparing classifier performance, the F1-score, which combines precision and recall, is particularly useful, while the RMSE measures prediction accuracy. Chi-square, Fisher Score, and Symmetrical Uncertainty (SU) follow as the second, third, and fourth best approaches, respectively. Although the SVM classifier demonstrates superior performance, the difference in accuracy between SVM and the MLP classifier is marginal. Key PointsO_LIOur study considers two univariate filter-based feature selection techniques, namely, Chi-square and Fisher score, as well as two multivariate filter-based feature selection techniques, viz., Symmetrical Uncertainty and Minimum Redundancy-Maximum Relevance (mRMR). C_LIO_LIThese methods are applied to feature selection from Five diverse collections of datasets, including datasets related to Mixed-lineage Leukaemia (MLL), Lung Cancer, Ovarian Cancer, Central Nervous System (CNS), and Colon Cancer. C_LIO_LIAfter that, a stratified 10-fold cross-validation procedure is conducted using Support Vector Machines (SVM) and Multilayer Perceptrons (MLP) to determine the classification accuracy for each feature. C_LIO_LIAmong these approaches, entropy-based methods (e.g., mRMR) emerge as the most effective. The mRMR method demonstrates Outstanding performance outcomes of accuracy, F1-score, and Root Mean Square Error (RMSE). C_LI

bioinformatics↗

bioRxiv2024

Editing cis-elements of OsPHO1;2 improved phosphate transport and yield in rice

Increasing grain yield is the main aim of crop improvement, which is globally impacted by the low availability of soil phosphate (Pi). Overexpressing Pi transporters for increasing Pi uptake often result in Pi toxicity and growth retardation. Despite advancements in genetic engineering, targeting cis-regulatory motifs of Pi transporters remains underexplored for understanding plant mechanisms and improving Pi status. Here, we demonstrated that the excision of the transcription inhibitor motif from the promoter of Pi transporter, OsPHO1;2, enhanced its expression and increased root-to-shoot Pi transport, leading to improved grain yield. Using, in-silico and DNA-protein interaction studies, we show the role of OsWRKY6 transcription factor in the negative regulation of OsPHO1;2 expression by binding to the cis-regulatory element (W-box) present in its promoter. oswrky6 knockout lines displayed a higher OsPHO1;2 expressions, and improved shoot Pi levels. Further, we engineered the OsPHO1;2 promoter for precisely removing the W-box and enhancing OsPHO1;2 expression. The phenotypic and physiological evaluation at the vegetative stage shows that OsPHO1;2 promoter edited (OsPHO1;2:PE) lines have increased shoot length, plant biomass and more root-shoot Pi export under low and normal P conditions. Notably, the 33Pi uptake assay reveals that OsPHO1;2:PE lines exhibited enhanced root Pi uptake, supported by higher root-associated Pi transporters (OsPHTs) expression. An extensive agronomical assessment revealed that OsPHO1;2:PE lines acquire increased seed and panicle numbers, thereby increasing yield without affecting seed quality. Our findings offer valuable insight into the potential of promoter editing to raise plants with better Pi use and improved crop yield.

plant biology↗

bioRxiv2023

Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea

Jasmonates (JAs) form a group of oxylipin-derived phytohormones involved in multiple biotic and abiotic stress responses and regulate plant development. JAs are perceived by the receptor proteins, COI (coronatine insensitive). These JA receptors encoding F-box protein, form SCFCOI ubiquitin ligase complex (Skp, Cullin, F-box) and activate JA signaling by facilitating degradation of the transcriptional repressor (JAZ; Jasmonate associated ZIM domain containing) proteins through 26S proteasomal pathway. However, JA signaling is poorly understood in chickpea, a vital legume plant. Here, we first identified two putative chickpea JA receptor named CaCOI1, CaCOI2 and demonstrated CaCOI2 as a functional JA receptor. Further subcellular localization studies revealed that CaCOI2 is localized to extra-nuclear region and move to the nucleus on JA perception to activate JA signaling. Using domain swapping (between CaCOI1 and CaCOI2) experiments, we have demonstrated that the LRR region of JA receptors, which interact with bioactive JA i.e., JA-Ile, also plays a critical role in regulating subcellular localization of CaCOI proteins. We report that an acidic amino acid in F-box region of COI proteins (AtCOI1T29) stabilizes COI-InsP8 (1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6) tetrakisphosphate) interaction. This interaction is found to be critical for COI-JAZ interaction and therefore, their functionality. Our study thus identified a functional JA receptor in chickpea and revealed novel aspects of JA signaling and perception, which might also have implications in other plants.

plant biology↗

bioRxiv2018

OsJAZ9 overexpression improves potassium deficiency tolerance in rice by modulating jasmonic acid levels and signaling

Potassium (K) which makes around 2-10% of plants total dry biomass, when become deficient, makes the plants highly susceptible to both abiotic and biotic stresses. Recent evidences suggest overlapping transcriptional responses to K deficiency and Jasmonate (JA) treatment in plants. However, a link between these responses was missing. Notably, K deficiency and JA application produce similar phenotypic and transcriptional responses. Here, we used molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis, K deficiency and sheath blight resistance. We raised OsJAZ9 overexpression, knockdown, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis and OsJAZ9 as a critical component of JA signaling for K deficiency response. OsJAZ9 overexpression and knockdown provide K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Furthermore, RNA Seq and JA profiling revealed an elevation of JA responsive genes and JA levels in OsJAZ9 OE lines under K deficiency. Our data provide clear evidence on the crucial role of JAZ repressor, OsJAZ9 in improving K deficiency tolerance in rice by altering JA levels and signaling.

plant biology↗