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Giri J. Intraperitonial/ Subcutaneous delivery of fit autologous Mesenchymal Stromal cells effectively cure DSS induced colitis. Cytotherapy 2020. [DOI: 10.1016/j.jcyt.2020.03.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Khanal L, Giri J, Shah S, Koirala S, Rimal J. Influence of learning-style preferences in academic performance in the subject of human anatomy: an institution-based study among preclinical medical students. ADVANCES IN MEDICAL EDUCATION AND PRACTICE 2019; 10:343-355. [PMID: 31239799 PMCID: PMC6554476 DOI: 10.2147/amep.s198878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/23/2019] [Indexed: 06/03/2023]
Abstract
Purpose: The present study was conducted to find the preferred mode of learning among first-year preclinical students and compare the preferred mode of learning with sex, faculty of students, and academic performance of the students using the VARK questionnaire. Methods: A cross-sectional study was done among 142 first-year Bachelor of Medicine-Bachelor of Surgery and Bachelor of Dental Surgery students from February to May 2018. Demographic data and various academic performance marks were recorded for each individual. VARK (visual, aural, read/write and kinesthetic) questionnaire version 7.8 was administered to calculate the score of each component. Mean VARK scores were calculated and each student classified by their preferred mode of learning. The preferred mode of learning was compared with sex, nationality, faculty of students, and academic performance using χ 2, unpaired t-tests, and the Mann-Whitney U test. P<0.05 was taken as statistically significant for comparison. Results: A majority of the students (53.52%) were multimodal. The most common multimodal mode of preference was bimodal (26.06%), while the most common unimodal preference was kinesthetic (29.06%). Total V score, K score, and VARK score were higher among males, while A and R scores were higher among females. The K score (7.96±2.35 in males and 6.96±2.43 in females) differed significantly (P=0.019) between male and female subjects. More subjects with higher scores in the theory exam of anatomy were unimodal learners (53.8%) compared to multimodal learners (46.2%). Conclusion: From this study, it can be concluded that undergraduate students were diverse in their learning styles, but most were multimodal. Though learning styles were found to vary by sex, nationality, and academic performance, differences were not statistically significant.
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Mehra P, Pandey BK, Verma L, Giri J. A novel glycerophosphodiester phosphodiesterase improves phosphate deficiency tolerance in rice. PLANT, CELL & ENVIRONMENT 2019; 42:1167-1179. [PMID: 30307043 DOI: 10.1111/pce.13459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/07/2018] [Indexed: 06/08/2023]
Abstract
Soil phosphate (Pi) deficiency is major constraint for rice cultivation worldwide. Cellular membranes account for one third of cellular organic phosphorus (P) in the form of phospholipids. Therefore, remobilization of Pi from membrane phospholipids under Pi deficiency can be an important strategy to improve phosphorus use efficiency. Glycerophosphodiester phosphodiesterases (GDPDs) hydrolyse intermediate product of phospholipid catabolism, glycerophosphodiesters to glycerol-3-phosphate, a precursor for P and non P-lipid biosynthesis. Here, we show that OsGDPD2 is a Pi deficiency responsive gene, which is transcriptionally regulated by OsPHR2. In silico analysis of active site residues and enzymatic assays confirmed phosphodiesterase activity of OsGDPD2. All overexpression lines showed higher GDPD activity, Pi content, root growth, and biomass accumulation as compared with wild type. Conversely, silencing of OsGDPD2 led to decreased GDPD activity and Pi content. Notably, most of the P-containing metabolites and fatty acids were elevated in transgenic lines. Further, quantitative analysis of polar lipids revealed higher accumulation of several classes of phospholipids and galactolipids in overexpression lines indicating a potential role of OsGDPD2 in de novo glycerolipid biosynthesis. Thus, present study provides insights into novel physiological roles of OsGDPD2 in low Pi acclimation in rice.
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Singh V, Singh AP, Bhadoria J, Giri J, Singh J, T V V, Sharma PC. Differential expression of salt-responsive genes to salinity stress in salt-tolerant and salt-sensitive rice (Oryza sativa L.) at seedling stage. PROTOPLASMA 2018; 255:1667-1681. [PMID: 29740721 DOI: 10.1007/s00709-018-1257-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/01/2018] [Indexed: 05/14/2023]
Abstract
The understanding of physio-biochemical and molecular attributes along with morphological traits contributing to the salinity tolerance is important for developing salt-tolerant rice (Oryza sativa L.) varieties. To explore these facts, rice genotypes CSR10 and MI48 with contrasting salt tolerance were characterized under salt stress (control, 75 and 150 mM NaCl) conditions. CSR10 expressed higher rate of physio-biochemical parameters, maintained lower Na/K ratio in shoots, and restricted Na translocation from roots to shoots than MI48. The higher expression of genes related to the osmotic module (DREB2A and LEA3) and ionic module (HKT2;1 and SOS1) in roots of CSR10 suppresses the stress, enhances electrolyte leakage, promotes the higher compatible solute accumulation, and maintains cellular ionic homeostasis leading to better salt stress tolerance than MI48. This study further adds on the importance of these genes in salt tolerance by comparing their behaviour in contrasting rice genotypes and utilizing specific marker to identify salinity-tolerant accessions/donors among germplasm; overexpression of these genes which accelerate the selection procedure precisely has been shown.
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Soda N, Verma L, Giri J. CRISPR-Cas9 based plant genome editing: Significance, opportunities and recent advances. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:2-11. [PMID: 29103811 DOI: 10.1016/j.plaphy.2017.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/02/2017] [Accepted: 10/26/2017] [Indexed: 05/21/2023]
Abstract
Precise genome editing is a quantum leap in the field of plant sciences. Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated Cas9 protein have emerged as a powerful tool for precise genome editing. CRISPR-Cas9 system introduces small heritable mutations (indels) in the genome of an organism. This system also enables precise gene characterization in plants with complex genomes. Besides, it offers new opportunities of trait stacking, where addition of desirable traits or removal of undesirable traits can be achieved simultaneously in a single event. With CRISPR-Cas9 RNPs technology, raising transgene free genetically modified plants is within realm of possibility which would be helpful in addressing regulatory concerns of transgenic plants. Several new advancements have been made in this technology which has extended its applications in almost every aspect of plant science. For example, recently developed catalytically inactive dCas9 fused with transcriptional effector domains allows targeted activation or silencing of the gene of interest. Apart from this, dCas9 fused with fluorescent labels is a budding tool in chromatin imaging studies. In this review, we summarize these recent advancements in CRISPR/Cas system and methods for analyzing the induced mutations, and its implementations in crop improvement.
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Huang G, Liang W, Sturrock CJ, Pandey BK, Giri J, Mairhofer S, Wang D, Muller L, Tan H, York LM, Yang J, Song Y, Kim YJ, Qiao Y, Xu J, Kepinski S, Bennett MJ, Zhang D. Rice actin binding protein RMD controls crown root angle in response to external phosphate. Nat Commun 2018; 9:2346. [PMID: 29892032 PMCID: PMC5995806 DOI: 10.1038/s41467-018-04710-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/01/2018] [Indexed: 11/12/2022] Open
Abstract
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
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Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ. Author Correction: Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun 2018; 9:1810. [PMID: 29717128 PMCID: PMC5931545 DOI: 10.1038/s41467-018-04280-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article omitted the following from the Acknowledgements:'We also thank DBT-CREST BT/HRD/03/01/2002.'This has been corrected in both the PDF and HTML versions of the Article.
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Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun 2018; 9:1408. [PMID: 29650967 PMCID: PMC5897452 DOI: 10.1038/s41467-018-03850-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2018] [Indexed: 11/09/2022] Open
Abstract
Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice. Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.
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Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R. A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun 2018; 9:1409. [PMID: 29651114 PMCID: PMC5897496 DOI: 10.1038/s41467-018-03851-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2018] [Indexed: 12/27/2022] Open
Abstract
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
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Ajmera I, Shi J, Giri J, Wu P, Stekel DJ, Lu C, Hodgman TC. Regulatory feedback response mechanisms to phosphate starvation in rice. NPJ Syst Biol Appl 2018; 4:4. [PMID: 29354282 PMCID: PMC5758793 DOI: 10.1038/s41540-017-0041-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 11/14/2017] [Accepted: 11/24/2017] [Indexed: 01/31/2023] Open
Abstract
Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses. Food security is a global priority. One aspect of this is the ability to grow crops in poorer soils with less fertilizer input, of which phosphate is both essential and resource limited. This study provides a quantitative understanding of the genetic regulation of phosphate uptake in rice upon its deficiency. The mathematical models developed in this article lead to three hypotheses for the gaps identified in current knowledge. One of these hypotheses has previously only been reported in animals while the other prompted laboratory experiments, revealing an extra level of regulation at short timescales. These models provide the basis for crop systems biologists to study other aspects of phosphate regulation, including its internal utilisation, external availability and foraging, and, more crucially, in response to other stresses.
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Bhadouria J, Singh AP, Mehra P, Verma L, Srivastawa R, Parida SK, Giri J. Identification of Purple Acid Phosphatases in Chickpea and Potential Roles of CaPAP7 in Seed Phytate Accumulation. Sci Rep 2017; 7:11012. [PMID: 28887557 PMCID: PMC5591292 DOI: 10.1038/s41598-017-11490-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/21/2017] [Indexed: 11/09/2022] Open
Abstract
Purple acid phosphatases (PAPs) play important roles in phosphate (Pi) acquisition and utilization. These PAPs hydrolyze organic Phosphorus (P) containing compounds in rhizosphere as well as inside the plant cell. However, roles of PAPs in one of the most widely cultivated legumes, chickpea (Cicer arietnum L.), have not been unraveled so far. In the present study, we identified 25 putative PAPs in chickpea (CaPAPs) which possess functional PAP motifs and domains. Differential regulation of CaPAPs under different nutrient deficiencies revealed their roles under multiple nutrient stresses including Pi deficiency. Interestingly, most of the CaPAPs were prominently expressed in flowers and young pods indicating their roles in flower and seed development. Association mapping of SNPs underlying CaPAPs with seed traits revealed significant association of low Pi inducible CaPAP7 with seed weight and phytate content. Biochemical characterization of recombinant CaPAP7 established it to be a functional acid phosphatase with highest activity on most abundant organic-P substrate, phytate. Exogenous application of recombinant CaPAP7 enhanced biomass and Pi content of Arabidopsis seedlings supplemented with phytate as sole P source. Taken together, our results uncover the PAPs in chickpea and potential roles of CaPAP7 in seed phytate accumulation.
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Mehra P, Pandey BK, Giri J. Improvement in phosphate acquisition and utilization by a secretory purple acid phosphatase (OsPAP21b) in rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1054-1067. [PMID: 28116829 PMCID: PMC5506657 DOI: 10.1111/pbi.12699] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/04/2017] [Accepted: 01/18/2017] [Indexed: 05/07/2023]
Abstract
Phosphate (Pi) deficiency in soil system is a limiting factor for rice growth and yield. Majority of the soil phosphorus (P) is organic in nature, not readily available for root uptake. Low Pi-inducible purple acid phosphatases (PAPs) are hypothesized to enhance the availability of Pi in soil and cellular system. However, information on molecular and physiological roles of rice PAPs is very limited. Here, we demonstrate the role of a novel rice PAP, OsPAP21b in improving plant utilization of organic-P. OsPAP21b was found to be under the transcriptional control of OsPHR2 and strictly regulated by plant Pi status at both transcript and protein levels. Biochemically, OsPAP21b showed hydrolysis of several organophosphates at acidic pH and possessed sufficient thermostability befitting for high-temperature rice ecosystems with acidic soils. Interestingly, OsPAP21b was revealed to be a secretory PAP and encodes a distinguishable major APase (acid phosphatase) isoform under low Pi in roots. Further, OsPAP21b-overexpressing transgenics showed increased biomass, APase activity and P content in both hydroponics supplemented with organic-P sources and soil containing organic manure as sole P source. Additionally, overexpression lines depicted increased root length, biomass and lateral roots under low Pi while RNAi lines showed reduced root length and biomass as compared to WT. In the light of these evidences, present study strongly proposes OsPAP21b as a useful candidate for improving Pi acquisition and utilization in rice.
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Pandey BK, Mehra P, Verma L, Bhadouria J, Giri J. OsHAD1, a Haloacid Dehalogenase-Like APase, Enhances Phosphate Accumulation. PLANT PHYSIOLOGY 2017; 174:2316-2332. [PMID: 28637831 PMCID: PMC5543963 DOI: 10.1104/pp.17.00571] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/17/2017] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) deficiency limits plant growth and yield. Since plants can absorb only the inorganic form of P (Pi), a large portion of soil P (organic and inorganic P complexes) remains unused. Here, we identified and characterized a PHR2-regulated, novel low-Pi-responsive haloacid dehalogenase (HAD)-like hydrolase, OsHAD1 While OsHAD1 is a functional HAD protein having both acid phosphatase and phytase activities, it showed little homology with other known low-Pi-responsive HAD superfamily members. Recombinant OsHAD1 is active at acidic pH and dephosphorylates a broad range of organic and inorganic P-containing substrates, including phosphorylated serine and sodium phytate. Exogenous application of recombinant OsHAD1 protein in growth medium supplemented with phytate led to marked increases in growth and total P content of Pi-deficient wild-type rice (Oryza sativa) seedlings. Furthermore, overexpression of OsHAD1 in rice resulted in enhanced phosphatase activity, biomass, and total and soluble P contents in Pi-deficient transgenic seedlings treated with phytate as a restricted Pi source. Gene expression and metabolite profiling revealed enhanced Pi starvation responses, such as up-regulation of multiple genes involved in Pi uptake and solubilization, accumulation of organic acids, enhanced secretory phosphatase activity, and depletion of ATP in overexpression lines as compared with the wild type. To elucidate the underlying regulatory mechanisms of OsHAD1, we performed in vitro pull-down assays, which revealed the association of OsHAD1 with protein kinases such as OsNDPKs. We conclude that, besides dephosphorylation of cellular organic P, OsHAD1 in coordination with kinases may regulate the phosphorylation status of downstream targets to accomplish Pi homeostasis under limited Pi supply.
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Bandyopadhyay T, Mehra P, Hairat S, Giri J. Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice. Funct Integr Genomics 2017; 17:565-581. [DOI: 10.1007/s10142-017-0556-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
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Mehra P, Giri J. Rice and chickpea GDPDs are preferentially influenced by low phosphate and CaGDPD1 encodes an active glycerophosphodiester phosphodiesterase enzyme. PLANT CELL REPORTS 2016; 35:1699-1717. [PMID: 27108120 DOI: 10.1007/s00299-016-1984-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/13/2016] [Indexed: 06/05/2023]
Abstract
Rice and chickpea GDPD s are transcriptionally influenced by mineral deficiencies; especially, by phosphate starvation and CaGDP1 encodes an active glycerophosphodiester phosphodiesterase enzyme. Glycerophosphodiester phosphodiesterases (GDPDs) are enzymes involved in the degradation of glycerophosphodiesters into sn-glycerol-3-phosphate and corresponding alcohols. These phospholipid remodeling genes have been suggested to play important roles in phosphate homeostasis. However, comprehensive information about the role of GDPDs under low phosphate (P) and other nutrient deficiencies (N, K, Fe, Zn) in rice and chickpea is missing. Here, we identified 13 OsGDPDs and 6 CaGDPDs in rice and chickpea, respectively, and partly characterized their roles in multiple nutrient stresses. Expression profiling after 7 and 15 days of deficiency treatments revealed unique and overlapping differential expression patterns of OsGDPDs and CaGDPDs under different nutrient stresses. Principal component analysis on the expression patterns of OsGDPDs and CaGDPDs revealed their preferential role in P starvation. Some of the GDPDs were also induced by N, K, Fe and Zn deficiency in temporal manner in both crops suggesting their roles in multiple nutrient stresses. Biochemical characterization of highly responsive chickpea GDPD, CaGDPD1, confirmed its in vitro GDPD activity and revealed its optimal temperature, pH and cofactor requirements. Further, CaGDPD1 showed its accumulation in ER and endomembranes. We hereby propose CaGDPD1 and various OsGDPDs as low P responsive marker genes in chickpea and rice, respectively. Our data uphold role of GDPDs in multinutrient responses and suggest them as candidates for rice and chickpea improvement for tolerance to various nutrient deficiencies.
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Kothari KS, Dansana PK, Giri J, Tyagi AK. Rice Stress Associated Protein 1 (OsSAP1) Interacts with Aminotransferase (OsAMTR1) and Pathogenesis-Related 1a Protein (OsSCP) and Regulates Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:1057. [PMID: 27486471 PMCID: PMC4949214 DOI: 10.3389/fpls.2016.01057] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/06/2016] [Indexed: 05/19/2023]
Abstract
Stress associated proteins (SAPs) are the A20/AN1 zinc-finger containing proteins which can regulate the stress signaling in plants. The rice SAP protein, OsSAP1 has been shown to confer abiotic stress tolerance to plants, when overexpressed, by modulating the expression of endogenous stress-related genes. To further understand the mechanism of OsSAP1-mediated stress signaling, OsSAP1 interacting proteins were identified using yeast two-hybrid analysis. Two novel proteins, aminotransferase (OsAMTR1) and a SCP/TAPS or pathogenesis-related 1 class of protein (OsSCP) were found to interact with OsSAP1. The genes encoding OsAMTR1 and OsSCP were stress-responsive and showed higher expression upon abiotic stress treatments. The role of OsAMTR1 and OsSCP under stress was analyzed by overexpressing them constitutively in Arabidopsis and responses of transgenic plants were assessed under salt and water-deficit stress. The OsAMTR1 and OsSCP overexpressing plants showed higher seed germination, root growth and fresh weight than wild-type plants under stress conditions. Overexpression of OsAMTR1 and OsSCP affected the expression of many known stress-responsive genes which were not affected by the overexpression of OsSAP1. Moreover, the transcript levels of OsSCP and OsAMTR1 were also unaffected by the overexpression of OsSAP1. Hence, it was concluded that OsSAP1 regulates the stress responsive signaling by interacting with these proteins which further regulate the downstream stress responsive gene expression.
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Mehra P, Pandey BK, Giri J. Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes. Sci Rep 2015; 5:13090. [PMID: 26278778 PMCID: PMC4538390 DOI: 10.1038/srep13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 07/17/2015] [Indexed: 12/30/2022] Open
Abstract
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
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Sharma G, Giri J, Tyagi AK. Rice OsiSAP7 negatively regulates ABA stress signalling and imparts sensitivity to water-deficit stress in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 237:80-92. [PMID: 26089154 DOI: 10.1016/j.plantsci.2015.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 05/19/2023]
Abstract
Stress associated protein (SAP) genes in plants regulate abiotic stress responses. SAP gene family consists of 18 members in rice. Although their abiotic stress responsiveness is well established, the mechanism of their action is poorly understood. OsiSAP7 was chosen to investigate the mechanism of its action based on the dual nature of its sub-cellular localization preferentially in the nucleus or sub-nuclear speckles upon transient expression in onion epidermal cells. Its expression was down-regulated in rice seedlings under abiotic stresses. OsiSAP7 was localized evenly in the nucleus under unstressed conditions and in sub-nuclear speckles on MG132 treatment. OsiSAP7 exhibits E3 ubiquitin ligase activity in vitro. Abiotic stress responses of OsiSAP7 were assessed by its overexpression in Arabidopsis under the control of a stress inducible promoter rd29A. Stress response assessment was done at seed germination and advanced stages of development. Transgenics were ABA insensitive at seed germination stage and sensitive to water-deficit stress at advanced stage as compared to wild type (WT). They were also impaired in ABA and stress-responsive gene expression. Our study suggests that OsiSAP7 acts as a negative regulator of ABA and water-deficit stress signalling by acting as an E3 ubiquitin ligase.
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Singh AP, Pandey BK, Deveshwar P, Narnoliya L, Parida SK, Giri J. JAZ Repressors: Potential Involvement in Nutrients Deficiency Response in Rice and Chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:975. [PMID: 26617618 PMCID: PMC4639613 DOI: 10.3389/fpls.2015.00975] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/25/2015] [Indexed: 05/20/2023]
Abstract
Jasmonates (JA) are well-known phytohormones which play important roles in plant development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA regulates both biotic and abiotic stress responses in plants; however, its role in nutrient deficiency responses is very elusive. Although, JA is well-known for root growth inhibition, little is known about behavior of JAZ genes in response to nutrient deficiencies, under which root architectural alteration is an important adaptation. Using protein sequence homology and a conserved-domains approach, here we identify 10 novel JAZ genes from the recently sequenced Chickpea genome, which is one of the most nutrient efficient crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners. Many of which are preferentially expressed in root. Our analysis further showed differential expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of specificity toward type of nutrient deficiency, generally majority of them showed induction under K deficiency. Generally, JAZ genes showed an induction at early stages of stress and expression declined at later stages of macro-nutrient deficiency. Our results suggest that JAZ genes might play a role in early nutrient deficiency response both in monocot and dicot roots, and information generated here can be further used for understanding the possible roles of JA in root architectural alterations for nutrient deficiency adaptations.
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Mehra P, Pandey BK, Giri J. Comparative Morphophysiological Analyses and Molecular Profiling Reveal Pi-Efficient Strategies of a Traditional Rice Genotype. FRONTIERS IN PLANT SCIENCE 2015; 6:1184. [PMID: 26779218 PMCID: PMC4700128 DOI: 10.3389/fpls.2015.01184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/10/2015] [Indexed: 05/20/2023]
Abstract
Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
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Tyagi H, Jha S, Sharma M, Giri J, Tyagi AK. Rice SAPs are responsive to multiple biotic stresses and overexpression of OsSAP1, an A20/AN1 zinc-finger protein, enhances the basal resistance against pathogen infection in tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:68-76. [PMID: 25017161 DOI: 10.1016/j.plantsci.2014.05.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 05/22/2023]
Abstract
Eukaryotic A20/AN1 zinc-finger proteins (ZFPs) play an important role in the regulation of immune and stress response. After elucidation of the role of first such protein, OsSAP1, in abiotic stress tolerance, 18 rice stress associated protein (SAP) genes have been shown to be regulated by multiple abiotic stresses. In the present study, expression pattern of all the 18 OsSAP genes have been analysed in response to different biotic stress simulators, in order to get insights into their possible involvement in biotic stress tolerance. Our results showed the upregulation of OsSAP1 and OsSAP11 by all biotic stress simulator treatments. Furthermore, the functional role of OsSAP1 in plant defence responses has been explored through overexpression in transgenic plants. Constitutive expression of OsSAP1 in transgenic tobacco resulted into enhanced disease resistance against virulent bacterial pathogen, together with the upregulation of known defence-related genes. Present investigation suggests that rice SAPs are responsive to multiple biotic stresses and OsSAP1 plays a key role in basal resistance against pathogen infection. This strongly supports the involvement of rice SAPs in cross-talk between biotic and abiotic stress signalling pathways, which makes them ideal candidate to design strategies for protecting crop plants against multiple stresses.
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Shunmugavelu M, Giri J, Akhtar S, Shetty R, Asirvatham AJ. Clinical experience with insulin detemir, biphasic insulin aspart and insulin aspart in people with type 2 diabetes: Results from the Tamil Nadu cohort of the A1chieve study. Indian J Endocrinol Metab 2013; 17:S569-S573. [PMID: 24404506 PMCID: PMC3872914 DOI: 10.4103/2230-8210.122139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The A1chieve, a multicentric (28 countries), 24-week, non-interventional study evaluated the safety and effectiveness of insulin detemir, biphasic insulin aspart and insulin aspart in people with T2DM (n = 66,726) in routine clinical care across four continents. MATERIALS AND METHODS Data was collected at baseline, at 12 weeks and at 24 weeks. This short communication presents the results for patients enrolled from Tamil Nadu, India. RESULTS A total of 2221 patients were enrolled in the study. Four different insulin analogue regimens were used in the study. Patients had started on or were switched to biphasic insulin aspart (n = 1707), insulin detemir (n = 270), insulin aspart (n = 85), basal insulin plus insulin aspart (n = 79) and other insulin combinations (n = 80). At baseline glycaemic control was poor for both insulin naïve (mean HbA1c: 9.2%) and insulin user (mean HbA1c: 9.2%) groups. After 24 weeks of treatment, both the groups showed improvement in HbA1c (insulin naïve: -1.7%, insulin users: -1.7%). SADRs including major hypoglycaemic events did not occur in any of the study patients. CONCLUSION Starting or switching to insulin analogues was associated with improvement in glycaemic control with a low rate of hypoglycaemia.
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Giri J, Dansana PK, Kothari KS, Sharma G, Vij S, Tyagi AK. SAPs as novel regulators of abiotic stress response in plants. Bioessays 2013; 35:639-48. [PMID: 23640876 DOI: 10.1002/bies.201200181] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Stress associated proteins (SAPs), novel A20/AN1 zinc-finger domain-containing proteins, are fast emerging as potential candidates for biotechnological approaches in order to improve abiotic stress tolerance in plants - the ultimate aim of which is crop-yield protection. Until relatively recently, such proteins had only been identified in humans, where they had been shown to be key regulators of innate immunity. Their phylogenetic relationship and recruitment of diverse protein domains reflect an architectural and mechanistic diversity. Emerging evidence suggests that SAPs may act as ubiquitin ligase, redox sensor, and regulator of gene expression during stress. Here, we evaluate the new knowledge on SAPs with a view to understand their mechanism of action. Furthermore, we set an agenda for investigating hitherto unexplored roles of these proteins.
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Jasnis M, Giri J, Davel L. Nitric oxide is involved in stimulation of tumor growth. Oncol Rep 2012; 4:1107-11. [PMID: 21590206 DOI: 10.3892/or.4.5.1107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The immune system can inhibit or stimulate tumor growth. Peritoneal cells (PEG) from MM3 mammary tumor-bearing mice (TBM) displayed enhanced capacity to produce nitric oxide (NO) upon stimulation with LPS plus IFN-gamma, as compared to normal mice. The addition of L-Arginine (L-Arg) increased NO release by TBM-PEC but not by normal PEG; this increase could be reversed with N-G-nitro-L-arginine methyl ester (L-NAME). This inhibitor, given systemically, decreased MM3 tumor growth but not lung metastasis. Tumor retardation was associated with inhibition of angiogenesis induced by spleen cells. Conversely, L-Arg potentiated vascular response but not tumor growth. In conclusion, NO synthesis is up regulated in PEC during MM3 tumor progression sustaining tumor growth by mediating the angiogenic cascade.
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Abstract
The accumulation of osmolytes like glycinebetaine (GB) in cell is known to protect organisms against abiotic stresses via osmoregulation or osmoprotection. Transgenic plants engineered to produce GB accumulate very low concentration of GB, which might not be sufficient for osmoregulation. Therefore, other roles of GB like cellular macromolecule protection and ROS detoxification have been suggested as mechanisms responsible for abiotic stress tolerance in transgenic plants. In addition, GB influences expression of several endogenous genes in transgenic plants. The new insights gained about the mechanism of stress tolerance in GB accumulating transgenic plants are discussed.
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