Biotechnology, Agricultural and Biological Sciences, Plant Science, Molecular Biology
8
Scopus Publications
319
Scholar Citations
7
Scholar h-index
5
Scholar i10-index
Scopus Publications
Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership Sabnam Parbin, Subha Damodharan, Purusharth I. Rajyaguru Yeast, 2021 Posttranslational modifications play a crucial role in regulating gene expression. Among these modifications, arginine methylation has recently attracted tremendous attention due to its role in multiple cellular functions. This review discusses the recent advances that have established arginine methylation as a major player in determining cytoplasmic messenger RNA (mRNA) fate. We specifically focus on research that implicates arginine methylation in regulating mRNA translation, decay, and RNA granule dynamics. Based on this research, we highlight a few emerging future avenues that will lead to exciting discoveries in this field.
Tuning of SlARF10A dosage by sly-miR160a is critical for auxin-mediated compound leaf and flower development Subha Damodharan, Shira Corem, Suresh Kumar Gupta, Tzahi Arazi Plant Journal, 2018 miR160 adjusts auxin-mediated development by post-transcriptional regulation of the auxin response factors ARF10/16/17. In tomato, knockdown of miR160 (sly-miR160) suggested that it is required for auxin-driven leaf blade outgrowth, but whether additional developmental events are adjusted by sly-miR160 is not clear. Here, the SlMIR160 genes and the genes of its SlARFs targets were edited by CRISPR/Cas9 resulting in the isolation of loss-of-function mutants. In addition, hypomorphic mutants that accumulate variable reduced levels of sly-miR160a were isolated. We found that the loss-of-function mutants in SlMIR160a (CR-slmir160a-6/7) produced only four wiry leaves, whereas the hypomorphic mutants developed leaves and flowers with graded developmental abnormalities. Phenotypic severity correlated with the upregulation of SlARF10A. Consistent with that, double mutants in SlMIR160a and SlARF10A restored leaf and flower development indicating that over-accumulation of SlARF10A underlay the developmental abnormalities exhibited in the CR-slmir160a mutants. Phenotype severity also correlated with the upregulation of the SHOOT MERISTEMLESS homolog Tomato Knotted 2, which in turn activated the transcription of the cytokinin biosynthesis genes SlIPT2 and SlIPT4. However, no change in Tomato Knotted 2 was detected in the absence of SlARF10A, suggesting that it is upregulated due to auxin signaling suppression by SlARF10A. Knockout of sly-miR160a-targeted SlARFs showed that whereas SlARF10A is indispensable for leaf blade outgrowth and floral organ patterning, the functions of SlARF16A and SlARF17 are redundant. Taken together our results suggest that sly-miR160a promotes blade outgrowth as well as leaf and leaflet initiation and floral organ development through the quantitative regulation of its major target SlARF10A.
A common miRNA160-based mechanism regulates ovary patterning, floral organ abscission and lamina outgrowth in tomato Subha Damodharan, Dazhong Zhao, Tzahi Arazi Plant Journal for Cell and Molecular Biology, 2016 Plant microRNAs play vital roles in auxin signaling via the negative regulation of auxin response factors (ARFs). Studies have shown that targeting of ARF10/16/17 by miR160 is indispensable for various aspects of development, but its functions in the model crop tomato (Solanum lycopersicum) are unknown. Here we knocked down miR160 (sly-miR160) using a short tandem target mimic (STTM160), and investigated its roles in tomato development. Northern blot analysis showed that miR160 is abundant in developing ovaries. In line with this, its down-regulation perturbed ovary patterning as indicated by the excessive elongation of the proximal ends of mutant ovaries and thinning of the placenta. Following fertilization, these morphological changes led to formation of elongated, pear-shaped fruits reminiscent of those of the tomato ovate mutant. In addition, STTM160-expressing plants displayed abnormal floral organ abscission, and produced leaves, sepals and petals with diminished blades, indicating a requirement for sly-miR160 for these auxin-mediated processes. We found that sly-miR160 depletion was always associated with the up-regulation of SlARF10A, SlARF10B and SlARF17, of which the expression of SlARF10A increased the most. Despite the sly-miR160 legitimate site of SlARF16A, its mRNA levels did not change in response to sly-miR160 down-regulation, suggesting that it may be regulated by a mechanism other than mRNA cleavage. SlARF10A and SlARF17 were previously suggested to function as inhibiting ARFs. We propose that by adjusting the expression of a group of ARF repressors, of which SlARF10A is a primary target, sly-miR160 regulates auxin-mediated ovary patterning as well as floral organ abscission and lateral organ lamina outgrowth.
Molecular modeling and in-silico engineering of Cardamom mosaic virus coat protein for the presentation of immunogenic epitopes of Leptospira LipL32 Vikram Kumar, S. Damodharan, Eswari P.J. Pandaranayaka, Madanan G. Madathiparambil, Jebasingh Tennyson Journal of Biomolecular Structure and Dynamics, 2016 Expression of Cardamom mosaic virus (CdMV) coat protein (CP) in E. coli forms virus-like particles. In this study, the structure of CdMV CP was predicted and used as a platform to display epitopes of the most abundant surface-associated protein, LipL32 of Leptospira at C, N, and both the termini of CdMV CP. In silico, we have mapped sequential and conformational B-cell epitopes from the crystal structure of LipL32 of Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 using IEDB Elipro, ABCpred, BCPRED, and VaxiJen servers. Our results show that the epitopes displayed at the N-terminus of CdMV CP are promising vaccine candidates as compared to those displayed at the C-terminus or at both the termini. LipL32 epitopes, EP2, EP3, EP4, and EP6 are found to be promising B-cell epitopes for vaccine development. Based on the type of amino acids, length, surface accessibility, and docking energy with CdMV CP model, the order of antigenicity of the LipL32 epitopes was found to be EP4 > EP3 > EP2 > EP6.
Global and local perturbation of the tomato microRNA pathway by a trans -activated DICER-LIKE 1 mutant Michael Kravchik, Ramanjulu Sunkar, Subha Damodharan, Ran Stav, Matat Zohar, Tal Isaacson, Tzahi Arazi Journal of Experimental Botany, 2014 DICER-like 1 (DCL1) is a major player in microRNA (miRNA) biogenesis and accordingly, its few known loss-of-function mutants are either lethal or display arrested development. Consequently, generation of dcl1 mutants by reverse genetics and functional analysis of DCL1 in late-developing organs are challenging. Here, these challenges were resolved through the unique use of trans-activated RNA interference. Global, as well as organ-specific tomato DCL1 (SlDCL1) silencing was induced by crossing the generated responder line (OP:SlDCL1IR) with the appropriate driver line. Constitutive trans-activation knocked down SlDCL1 levels by ~95%, resulting in severe abnormalities including post-germination growth arrest accompanied by decreased miRNA and 21-nucleotide small RNA levels, but prominently elevated levels of 22-nucleotide small RNAs. The increase in the 22-nucleotide small RNAs was correlated with specific up-regulation of SlDCL2b and SlDCL2d, which are probably involved in their biogenesis. Leaf- and flower-specific OP:SlDCL1IR trans-activation inhibited blade outgrowth, induced premature bud senescence and produced pale petals, respectively, emphasizing the importance of SlDCL1-dependent small RNAs in these processes. Together, these results establish OP:SlDCL1IR as an efficient tool for analysing processes regulated by SlDCL1-mediated gene regulation in tomato.
Expression and immunological characterization of cardamom mosaic virus coat protein displaying HIV gp41 epitopes Subha Damodharan, Ravindra Gujar, Sathyamurthy Pattabiraman, Manohar Nesakumar, Luke Elizabeth Hanna, Ramanathan D Vadakkuppattu, Ramakrishnan Usha Microbiology and Immunology, 2013 The coat protein of cardamom mosaic virus (CdMV), a member of the genus Macluravirus, assembles into virus‐like particles when expressed in an Escherichia coli expression system. The N and C‐termini of the coat protein were engineered with the Kennedy peptide and the 2F5 and 4E10 epitopes of gp41 of HIV. The chimeric proteins reacted with sera from HIV positive persons and also stimulated secretion of cytokines by peripheral blood mononuclear cells from these persons. Thus, a system based on the coat protein of CdMV can be used to display HIV‐1 antigens.
RECENT SCHOLAR PUBLICATIONS
Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership S Parbin, S Damodharan, PI Rajyaguru Yeast 38 (8), 441-452 , 2021 2021 Citations: 5
Tuning of SlARF10A dosage by sly‐miR160a is critical for auxin‐mediated compound leaf and flower development S Damodharan, S Corem, SK Gupta, T Arazi The Plant Journal 96 (4), 855-868 , 2018 2018 Citations: 75
Characterization of S almonella typhi OmpC and OmpF porins engineered with HIV‐gp41 epitope on the surface loops M Thulasingam, S Damodharan, G Madhana Vigneshwari, ... Proteins: Structure, Function, and Bioinformatics 85 (4), 657-664 , 2017 2017 Citations: 7
A common mi RNA 160‐based mechanism regulates ovary patterning, floral organ abscission and lamina outgrowth in tomato S Damodharan, D Zhao, T Arazi The Plant Journal 86 (6), 458-471 , 2016 2016 Citations: 137
Molecular modeling and in-silico engineering of Cardamom mosaic virus coat protein for the presentation of immunogenic epitopes of Leptospira LipL32 V Kumar, S Damodharan, EPJ Pandaranayaka, MG Madathiparambil, ... Journal of Biomolecular Structure and Dynamics 34 (1), 42-56 , 2016 2016 Citations: 18
Generation and characterization of a tomato DCL3-silencing mutant M Kravchik, S Damodharan, R Stav, T Arazi Plant Science 221, 81-89 , 2014 2014 Citations: 35
Global and local perturbation of the tomato microRNA pathway by a trans -activated DICER-LIKE 1 mutant M Kravchik, R Sunkar, S Damodharan, R Stav, M Zohar, T Isaacson, ... Journal of experimental botany 65 (2), 725-739 , 2014 2014 Citations: 34
Expression and immunological characterization of cardamom mosaic virus coat protein displaying HIV gp41 epitopes S Damodharan, R Gujar, S Pattabiraman, M Nesakumar, LE Hanna, ... Microbiology and Immunology 57 (5), 374-385 , 2013 2013 Citations: 8
MOST CITED SCHOLAR PUBLICATIONS
A common mi RNA 160‐based mechanism regulates ovary patterning, floral organ abscission and lamina outgrowth in tomato S Damodharan, D Zhao, T Arazi The Plant Journal 86 (6), 458-471 , 2016 2016 Citations: 137
Tuning of SlARF10A dosage by sly‐miR160a is critical for auxin‐mediated compound leaf and flower development S Damodharan, S Corem, SK Gupta, T Arazi The Plant Journal 96 (4), 855-868 , 2018 2018 Citations: 75
Generation and characterization of a tomato DCL3-silencing mutant M Kravchik, S Damodharan, R Stav, T Arazi Plant Science 221, 81-89 , 2014 2014 Citations: 35
Global and local perturbation of the tomato microRNA pathway by a trans -activated DICER-LIKE 1 mutant M Kravchik, R Sunkar, S Damodharan, R Stav, M Zohar, T Isaacson, ... Journal of experimental botany 65 (2), 725-739 , 2014 2014 Citations: 34
Molecular modeling and in-silico engineering of Cardamom mosaic virus coat protein for the presentation of immunogenic epitopes of Leptospira LipL32 V Kumar, S Damodharan, EPJ Pandaranayaka, MG Madathiparambil, ... Journal of Biomolecular Structure and Dynamics 34 (1), 42-56 , 2016 2016 Citations: 18
Expression and immunological characterization of cardamom mosaic virus coat protein displaying HIV gp41 epitopes S Damodharan, R Gujar, S Pattabiraman, M Nesakumar, LE Hanna, ... Microbiology and Immunology 57 (5), 374-385 , 2013 2013 Citations: 8
Characterization of S almonella typhi OmpC and OmpF porins engineered with HIV‐gp41 epitope on the surface loops M Thulasingam, S Damodharan, G Madhana Vigneshwari, ... Proteins: Structure, Function, and Bioinformatics 85 (4), 657-664 , 2017 2017 Citations: 7
Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership S Parbin, S Damodharan, PI Rajyaguru Yeast 38 (8), 441-452 , 2021 2021 Citations: 5
