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    Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato
    (Elsevier B.V., 2021) Akash; Parida, Adwaita Prasad; Srivastava, Alok; Mathur, Saloni; Sharma, Arun Kumar; Kumar, Rahul
    F-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2–B) genes, PP2–B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.
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    Novel microRNAs regulating ripening-associated processes in banana fruit
    (Springer Nature Publishing AG, 2020) Lakhwani, Deepika; Sanchita; Pandey, Ashutosh; Sharma, Deepika; Asif, Mehar H.; Trivedi, Prabodh K.
    MicroRNAs (miRNAs) modulate gene expression and regulate various physiological and developmental processes in plants. During fruit ripening phase, several physiological and biochemical variations take place resulting changes in colour and texture, softening and production of aroma volatiles. A number of pathways leading to cell wall hydrolysis, ethylene signaling, biosynthesis of fatty acids, esters and a number of secondary plant products play important role during fruit ripening. However, detailed analysis of various processes regulated by miRNAs has not been studied in detailed in a number of fruits. In this study, we sequenced small RNA libraries from ripe and un-ripe fruit of Banana (Musa acuminata), an important and staple food crop, to identify miRNAs regulating fruit ripening. Our analysis identifed a number of novel miRNAs which are diferentially expressed during fruit ripening. These novel miRNAs were analyzed for their precursors, chromosome localization and targets. Some of these miRNAs were identifed to target genes involved in miRNA biogenesis, fruit softening and aroma biosynthesis. This study advances our knowledges in the area of fruit ripening process regulated by miRNAs.
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    Genome-wide identification and interactome analysis of members of two-component system in Banana
    (BioMed Central Ltd, 2019) Dhar, Yogeshwar V.; Lakhwani, Deepika; Pandey, Ashutosh; Singh, Shikha; Trivedi, Prabodh K.; Asif, Mehar H.
    BACKGROUND: Ethylene signal transduction in plants is conducted by the two-component system (TCS) which consists of histidine kinase (HK), histidine phosphotransferase (HPT) and response regulators (RRs). This system plays an important role in signal transduction during various cellular processes, including fruit ripening and response to multiple environmental cues. Though members of TCS have been identified in a few plants, no detailed analysis has been carried out in banana. RESULTS: Through genome-wide analysis, we identified a total of 80 (25 HK, 10 HPT and 45 RR) and 72 (25 HK, 5 HPT and 42 RR) TCS genes in Musa acuminata and Musa balbisiana respectively. The analysis of identified genes revealed that most of the genes are highly conserved however; there are subtle divergences among various members. Comparative expression analysis revealed an involvement of a set of TCS members during banana fruit ripening. Co-expression network analysis identified a working TCS module with direct interactions of HK-HPT and RR members. The molecular dynamics analysis of TCS module showed a significant change in structural trajectories of TCS proteins in the presence of ethylene. Analysis suggests possible interactions between the HK-HPTs and RRs as well as other members leading to banana fruit ripening. CONCLUSIONS: In this study, we identified and compared the members of TCS gene family in two banana species and showed their diversity, within groups on the basis of whole-genome duplication events. Our analysis showed that during banana fruit ripening TCS module plays a crucial role. We also demonstrated a possible interaction mechanism of TCS proteins in the presence and absence of ethylene by molecular dynamics simulations. These findings will help in understanding the functional mechanism of TCS proteins in plants in different conditions.
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    Insights into transcriptional regulation of β-D-N-acetylhexosaminidase, an N-glycan-processing enzyme involved in ripening-associated fruit softening
    (Oxford University Press, 2014) Irfan, Mohammad; Ghosh, Sumit; Kumar, Vinay; Chakraborty, Niranjan; Chakraborty, Subhra; Datta, Asis
    Tomato (Solanum lycopersicum) fruit ripening-specific N-glycan processing enzyme, β-D-N-acetylhexosaminidase (β-Hex), plays an important role in the ripening-associated fruit-softening process. However, the regulation of fruit ripening-specific expression of β-Hex is not well understood. We have identified and functionally characterized the fruit ripening-specific promoter of β-Hex and provided insights into its transcriptional regulation during fruit ripening. Our results demonstrate that RIPENING INHIBITOR (RIN), a global fruit ripening regulator, and ABSCISIC ACID STRESS RIPENING 1 (SlASR1), a poorly characterized ripening-related protein, are the transcriptional regulators of β-Hex. Both RIN and SlASR1 directly bound to the β-Hex promoter fragments containing CArG and C₂₋₃(C/G)A cis-acting elements, the binding sites for RIN and SlASR1, respectively. Moreover, β-Hex expression/promoter activity in tomato fruits was downregulated once expression of either RIN or SlASR1 was suppressed; indicating that RIN and SlASR1 positively regulate the transcription of β-Hex during fruit ripening. Interestingly, RIN could also bind to the SlASR1 promoter, which contains several CArG cis-acting elements, and SlASR1 expression was suppressed in rin mutant fruits, indicating that RIN also acts as a positive regulator of SlASR1 expression during fruit ripening. Taken together, these results suggest that RIN, both directly and indirectly, through SlASR1, regulates the transcription of β-Hex during fruit ripening. The fruit ripening-specific promoter of β-Hex could be a useful tool in regulating gene expression during fruit ripening.
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    Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato
    (Springer Science, 2012) Kumar, Rahul; Sharma, Manoj K.; Kapoor, Sanjay; Tyagi, Akhilesh K.; Sharma, Arun K.
    A thorough understanding of molecular mechanisms underlying ripening is the prerequisite for genetic manipulation of fruits for better shelf-life and nutritional quality. Mutation in LeMADS-RIN, a MADS-box gene, leads to non-ripening phenotype of rin fruits in tomato. Characterization of ripening-inhibitor (rin) mutant has elucidated important role of ethylene in the regulation of climacteric fruit ripening. A complete understanding of this mutation will unravel novel genetic regulatory mechanisms involved in fruit ripening. In this study, fruit transcriptomes of two genotypes, including a cultivated Indian cultivar Solanum lycopersicum cv. Pusa Ruby and a homozygous line harboring the rin mutation (LA1795) were compared to get better insight into RIN-regulated ethylene-dependent and ethylene-independent events during ripening. Cluster analysis of ripening-related genes indicated a major shift in their expression profiles in rin mutant fruit. A total of 112 genes, exhibiting expression patterns similar to that of LeMADS-RIN in wild-type fruits, showed down regulation of expression in the rin mutant. In silico analysis of putative promoters of these genes for the presence of CArG box along with ERE and ethylene inducibility of these genes revealed that genes lacking CArG box in their regulatory regions could be indirectly regulated by LeMADS-RIN. New regulators of ethylene-dependent aspect of ripening were also identified. In this study, we have made an attempt to distinguish between ethylene-dependent and ethylene-independent aspects of ripening, which will be useful for developing strategies to improve fruit-related agronomic traits in tomato and other crops.