@article {162685, title = {Loss of function of chromatin remodeler OsCLSY4 leads to RdDM-mediated mis-expression of endosperm-specific genes affecting grain qualities.}, journal = {PLoS Genet}, volume = {21}, year = {2025}, month = {2025 Dec}, pages = {e1011956}, abstract = {

In plants, RNA-directed DNA methylation (RdDM) sequence-specifically targets transposable elements (TEs) and repeats, often in a tissue-specific manner. In triploid endosperm tissue, RdDM also acts as a parental dosage regulator, mediating spatio-temporal expression of genes required for its development. It is unclear how RdDM is initiated and established in endosperm. Rice endosperm-specific imprinted chromatin remodeler OsCLSY3 recruits RNA polymerase IV to specific genomic sites for silencing and optimal gene expression. Here we show that, in addition to OsCLSY3, ubiquitously expressed OsCLSY4 is also crucial for proper reproductive growth and endosperm development. Loss of function of OsCLSY4 led to reproductive and nutrient-filling defects in endosperm. Using genetic and molecular analysis, we show that both OsCLSY3 and OsCLSY4 play overlapping and unique silencing roles in rice endosperm, by targeting specific and shared genomic regions such as TEs, repeats and genic regions. These results indicate the importance of optimal expression of two OsCLSYs in regulating endosperm-specific gene expression, genomic imprinting and suppression of specific TEs. Results presented here provide new insights into the functions of rice CLSYs as upstream RdDM regulators in rice endosperm development, and we propose that functions of their homologs might be conserved across monocots.

}, keywords = {Chromatin Assembly and Disassembly, DNA Methylation, DNA Transposable Elements, Edible Grain, Endosperm, Gene Expression Regulation, Plant, Genomic Imprinting, Oryza, Plant Proteins}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1011956}, author = {Pal, Avik Kumar and Rana, Saumyapriya and Dey, Riju and Shivaprasad, Padubidri V} } @article {160480, title = {OsWRKY53 dictates wound responses in rice through fine-tuning crosstalk between PEP and PSK-mediated signalling.}, journal = {Plant J}, volume = {123}, year = {2025}, month = {2025 Sep}, pages = {e70481}, abstract = {

Wounding is a major event during the multitude of stresses that plants face in their natural environment. Wound response is very dynamic and involves the integration of various regulatory networks culminating in successful wound-induced downstream signalling. Plants depend on endogenous molecular signals predominantly, small peptides, to initiate wound responses. Transcriptional response is paramount in dictating a successful wound response. Here we show the involvement of a WRKY transcription factor (TF) named OsWRKY53 that is upregulated upon wounding as well as wound-derived plant elicitor peptide (PEP), OsPep2 treatments. OsWRKY53 is involved in the positive regulation of gene expression of OsPep2-responsive genes. OsWRKY53 displays altered DNA occupancy in response to OsPep2 treatment over time, correlating with the altered gene expression. OsWRKY53 undergoes phosphorylation upon OsPep2 perception, and this contributes to the enhanced stability of the protein. Further, OsWRKY53 is involved in the simultaneous activation and suppression of OsPep2-responsive and phytosulfokine (PSK)-responsive genes, respectively. In agreement with these findings, perturbed expression of OsWRKY53 leads to compromised transcriptional responses post-wounding. Collectively, we establish that OsWRKY53 acts at the intersection of PEP and PSK-mediated transition of wound responses.

}, keywords = {Gene Expression Regulation, Plant, Oryza, Phosphorylation, Plant Proteins, Signal Transduction, Transcription Factors}, issn = {1365-313X}, doi = {10.1111/tpj.70481}, author = {Harshith, Chitthavalli Y and Palchaudhuri, Dipasmit and Dey, Riju and Raju, Steffi and Shivaprasad, Padubidri V} } @article {147285, title = {Wound-induced small-peptide-mediated signaling cascade, regulated by OsPSKR, dictates balance between growth and defense in rice.}, journal = {Cell Rep}, volume = {43}, year = {2024}, month = {2024 Jul 23}, pages = {114515}, abstract = {

Wounding is a general stress in plants that results from various pest and pathogenic infections in addition to environment-induced mechanical damages. Plants have sophisticated molecular mechanisms to recognize and respond to wounding, with those of monocots being distinct from dicots. Here, we show the involvement of two distinct categories of temporally separated, endogenously derived peptides, namely, plant elicitor peptides (PEPs) and phytosulfokine (PSK), mediating wound responses in rice. These peptides trigger a dynamic signal relay in which a receptor kinase involved in PSK perception named OsPSKR plays a major role. Perturbation of OsPSKR expression in rice leads to compromised development and constitutive autoimmune phenotypes. OsPSKR regulates the transitioning of defense to growth signals upon wounding. OsPSKR displays mutual antagonism with the OsPEPR1 receptor involved in PEP perception. Collectively, our work indicates the presence of a stepwise peptide-mediated signal relay that regulates the transition from defense to growth upon wounding in monocots.

}, keywords = {Gene Expression Regulation, Plant, Oryza, Peptides, Plant Diseases, Plant Proteins, Signal Transduction}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.114515}, author = {Harshith, Chitthavalli Y and Pal, Avik and Chakraborty, Monoswi and Nair, Ashwin and Raju, Steffi and Shivaprasad, Padubidri V} } @article {124206, title = {A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance.}, journal = {Sci Rep}, volume = {13}, year = {2023}, month = {2023 Feb 07}, pages = {2195}, abstract = {

Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group.\ The miRNA-miRNA* duplex region is completely conserved across eleven\ Oryza\ species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the {\textquoteright}A{\textquoteright} allele may promote better processing vis-{\`a}-vis the structure conferred by {\textquoteright}G{\textquoteright} allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.

}, keywords = {MicroRNAs, Oryza, Polymorphism, Single Nucleotide, Salt-Tolerant Plants}, issn = {2045-2322}, doi = {10.1038/s41598-023-28836-1}, author = {Jaganathan, Deepa and Rajakani, Raja and Doddamani, Dadakhalandar and Saravanan, Divya and Pulipati, Shalini and Vivek Hari Sundar G and Sellamuthu, Gothandapani and Jayabalan, Shilpha and Kumari, Kumkum and Parthasarathy, Pavithra and S, Punitha and Ramalingam, Sivaprakash and Shivaprasad, Padubidri V and Venkataraman, Gayatri} }