Publications of NIPGR Scientists

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    Genome-wide identification, in-silico characterisation and expression analysis of multiprotein bridging factor 1 gene family members in rice
    (Springer Nature Publishing AG, 2025) Bishnoi, Alka; Ram, Hasthi; Soni, Praveen
    The multiprotein bridging factor 1 (MBF1) proteins are evolutionarily conserved transcription co-factors. However, little is known about rice MBF1 gene family and its role. A genome-wide search led to the identification of two MBF1 genes in the rice genome. Their proteins contained characteristic MBF1 and helix-turn-helix domains. Phylogenetic analysis showed that they belong to two different groups. Exploration of publicly available rice transcriptome data revealed that OsMBF1b exhibits constitutively high transcript abundance in all tissues and developmental stages of rice with a little alteration in its expression. Contrarily, OsMBF1c exhibited a prominent alteration in its expression in response to environmental perturbations. Both OsMBF1s showed the highest expression in endosperm. Analysis of publicly-available rice transcriptome data also showed that both OsMBF1s have a role in response to different stresses, especially in heat. Transcript analysis using qRT-PCR confirmed heat inducibility of OsMBF1c in contrasting genotypes i.e. IR64 (heat sensitive) and Nagina 22 (heat tolerant). qRT-PCR also confirmed the drought inducibility of both genes in the IR64 genotype which is sensitive to drought stress also as revealed by analysis of different parameters. In-silico interaction study also indicated their role in heat response as a number of proteins required to cope with high temperatures were predicated to be their interacting partners. Several heat-responsive genes were found to co-express with OsMBF1s. In-silico promoter analysis revealed the occurrence of stress-responsive elements in their putative promoters. Interestingly, both OsMBF1s showed diurnal rhythmic expressions having peaks during the daytime when the temperature rises. Altogether, this study indicates an active role of OsMBF1s in thermotolerance in rice. This is the first report regarding the characterization of rice MBF1 members.
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    Molecular characterization, evolutionary analysis, and expression profiling of BOR genes in important cereals
    (MDPI AG, 2022) Sharma, Himanshu; Sharma, Alok; Rajput, Ruchika; Sidhu, Sukhjeet; Dhillon, Harpal; Verma, Praveen Chandra; Pandey, Ashutosh; Upadhyay, Santosh Kumar
    Boron (B) is an essential micronutrient of plants. Plants grapple with a narrow range of B between its toxicity and deficiency. B homeostasis mechanism is required to rescue plants from such a quagmire. B transporters are specialized proteins involved in the homeostasis of B. In the present study, a total of 29 BOR genes were identified in five major cereals, including three BORs in each Brachypodium distachyon and Sorghum bicolor, four in Oryza sativa, six in Zea mays, and 13 in Triticum aestivum. Multiple sequence alignments, domain structure analyses, and phylogenetic analysis indicated the conserved nature of the BOR protein family. Duplication events and Ka/Ks analysis of TaBORs showed the role of segmental duplication events and purifying selection in the expansion of the BOR family in T. aestivum. Furthermore, in silico expression and co-expression analyses under biotic and abiotic stress conditions depicted their involvement in combating such conditions. Moreover, qRT-PCR of TaBORs in B treatment suggested the roles of BOR genes in B stress management. The present study hints at the conserved nature of BOR proteins and their different aspects. The study will lay down a way for several crop improvement programs.
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    Expression profiling of miRNAs indicates crosstalk between phytohormonal response and rhizobial infection in chickpea
    (Springer Nature Publishing AG, 2020) Tiwari, Manish; Bhatia, Sabhyata
    Legumes develop root nodules in which bacteria fix nitrogen for plants. The phytohormones auxin and cytokinin regulate nodule organogenesis by recruiting various genes to effect symbiosis. Moreover, these genes are regulated by the action of microRNAs also. To understand the complex regulatory network involving miRNAs in response to phytohormones and rhizobial interactions in chickpea roots, a miRNA expression profiling was performed. Indole acetic acid and 6-benzylaminopurine at concentrations of 0.1, 1 and 10 lM were used for auxin and cytokinin exogenous treatment and Mesorhizobium ciceri to study rhizobial interaction with chickpea root. Expression profiling of a set of 11 miRNAs was performed. Further, the targets of the candidate miRNAs were identified, followed by functional annotation. This analysis revealed that cat-miR160, cat-miR164, cat-miR396 and cat-miR398 were responsive to auxin and cytokinin. cat-miR319 was found to be only auxin responsive and is known to regulate auxin signalling by targeting TEOSINTE BRANCHED/ CYCLOIDEA/PCF (TCP) which interacts with auxin inducible genes. Further, cytokinin elicited a response at very low concentration of 0.1 lM, and most of the miRNAs investigated were responsive to cytokinin. Interactome analysis revealed that cat-miR164 and cat-miR168 work in conjunction to regulate auxin signalling. Interestingly, cat-miR169 and cat-miR482 were low expressing during auxin treatment and M. ciceri infection but their expression spiked during cytokinin treatment, indicating a cytokinin mediated mode of action. The miRNA expression profiling in response to phytohormones and rhizobia and the reported function of their target genes suggested a crosstalk among the phytohormonal responses during chickpea nodulation.
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    Interplay between auxin and cytokinin and its impact on mitogen activated protein kinase (MAPK)
    (Springer, 2017) Singh, Pallavi; Sinha, Alok Krishna
    Plant physiology, in particular, is governed by a repertoire of endogenous as well as environmental cues. Auxin and cytokinin constitute an indispensable phytohormonal system required for plant growth and development. Another pivotal aspect of plant physiological process that thoroughly affects various plant growth and developmental attributes is the signaling network, majorly comprising the canonical mitogen activated protein kinase (MAPK) cascade. Striking a fine balance between the phytohormonal and signaling components could be adopted as an intricate strategy by plants to counteract various stresses in question. Thus, a brief understanding of this multifaceted complex could be of use for delineating numerous plant physiological and developmental phenomena. Thus, the present section discusses the various MAPK related assays in context to auxin and cytokinin crosstalk. Briefly, this chapter outlines the discrete MAPK methods to better understand the fundamentals of MAPK signaling network in auxin and cytokinin treated rice seedlings. Further, various phenotypic, genomic as well as proteomic protocols are discussed for a better understanding of MAPK networks in the backdrop of auxin and cytokinin interplay.
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    A multi-step phosphorelay two-component system impacts on tolerance against dehydration stress in common wheat
    (Springer, 2014) Gahlaut, Vijay; Mathur, Saloni; Dhariwal, Raman; Khurana, Jitendra P.; Tyagi, Akhilesh K.; Balyan, Harindra S.; Gupta, Pushpendra K.
    Wheat is an important staple crop, and its productivity is severely constrained by drought stress (DS). An understanding of the molecular basis of drought tolerance is necessary for genetic improvement of wheat for tolerance to DS. The two-component system (TCS) serves as a common sensor-regulator coupling mechanism implicated in the regulation of diverse biological processes (including response to DS) not only in prokaryotes, but also in higher plants. In the latter, TCS generally consists of two signalling elements, a histidine kinase (HK) and a response regulator (RR) associated with an intermediate element called histidine phosphotransferase (HPT). Keeping in view the possible utility of TCS in developing water use efficient (WUE) wheat cultivars, we identified and characterized 62 wheat genes encoding TCS elements in a silico study; these included 7 HKs, 45 RRs along with 10 HPTs. Twelve of the 62 genes showed relatively higher alterations in the expression under drought. The quantitative RT-PCR (qRT-PCR)-based expression analysis of these 12 TCS genes was carried out in wheat seedlings of a drought sensitive (HD2967) and a tolerant (Dharwar Dry) cultivar subjected to either dehydration stress or cytokinin treatment. The expression of these 12 genes under dehydration stress differed in sensitive and tolerant genotypes, even though for individual genes, both showed either up-regulation or down-regulation. In response to the treatment of cytokinin, the expression of type-A RR genes was higher in the tolerant genotype, relative to that in the sensitive genotype, the situation being reverse for the type-B RRs. These results have been discussed in the context of the role of TCS elements in drought tolerance in wheat.
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    Eugenol-induced suppression of biofilm-forming genes in Streptococcus mutans: An approach to inhibit biofilms
    (Elsevier B.V., 2014) Adil, Mohd; Singh, Kunal; Verma, Praveen K.; Khan, Asad U.
    Streptococcus mutans is well documented as a major aetiological agent of dental caries. The ability to form a biofilm on tooth surfaces is the major virulence factor of this bacterium. The objective of this study was to evaluate the effect of eugenol on suppression of biofilm- and quorum sensing (QS)-related genes of S. mutans and to determine its putative mode of action. Eugenol was evaluated for its inhibitory activity against virulence properties such as adherence and biofilm formation. Morphological changes in the architecture of S. mutans and in the biofilm were analysed and observed using confocal laser scanning microscopy and transmission electron microscopy. The effects of eugenol on expression of biofilm- and QS-related genes (gtfB, gtfC, comDE, smu630, vicR, brpA, ftf, relA, gbpB and spaP) were checked by quantitative real-time PCR (qRT-PCR). The present data revealed that eugenol at a sub-minimum inhibitory concentration (sub-MIC) significantly downregulated the expression of tested genes but did not affect bacterial growth. These results suggest that a sub-MIC of eugenol can effectively suppress virulence genes. Thus, the results indicated that eugenol can inhibit caries-associated biofilm and showed its therapeutic potential against oral biofilm.