@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 {128071, title = {Begomoviral beta C1 orchestrates organellar genomic instability to augment viral infection}, journal = {PLANT JOURNAL }, year = {2023}, month = {05/2023}, abstract = {

Chloroplast is the site for transforming light energy to chemical energy. It also acts as a production unit for a variety of defense-related molecules. These defense moieties are necessary to mount a successful counter defense against pathogens, including viruses. Previous studies indicated disruption of chloroplast homeostasis as a basic strategy of Begomovirus for its successful infection leading to the production of vein-clearing, mosaic, and chlorotic symptoms in infected plants. Although begomoviral pathogenicity determinant protein Beta C1 (beta C1) was implicated for pathogenicity, the underlying mechanism was unclear. Here we show that, begomoviral beta C1 directly interferes with the host plastid homeostasis. beta C1 induced DPD1, an organelle-specific nuclease, implicated in nutrient salvage and senescence, as well as modulated the function of a major plastid genome maintainer protein RecA1, to subvert plastid genome. We show that beta C1 was able to physically interact with bacterial RecA and its plant homolog RecA1, resulting in its altered activity. We observed that knocking-down DPD1 during virus infection significantly reduced virus-induced necrosis. These results indicate the presence of a strategy in which a viral protein alters host defense by targeting modulators of chloroplast DNA. We predict that the mechanism identified here might have similarities in other plant-pathogen interactions.

}, doi = {10.1111/tpj.16186}, author = {Nair, Ashwin and Harshith, Chitthavalli Y. Y. and Narjala, Anushree and Shivaprasad, P V} } @article {126670, title = {Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection.}, journal = {Plant J}, year = {2023}, month = {2023 Mar 14}, abstract = {

Chloroplast is the site for transforming light energy to chemical energy. It also acts as a production unit for a variety of defense-related molecules. These defense moieties are necessary to mount a successful counter defense against pathogens, including viruses. Previous studies indicated disruption of chloroplast homeostasis as a basic strategy of Begomovirus for its successful infection leading to the production of vein-clearing, mosaic, and chlorotic symptoms in infected plants. Although begomoviral pathogenicity determinant protein Beta C1 (βC1) was implicated for pathogenicity, the underlying mechanism was unclear. Here we show that, begomoviral βC1 directly interferes with the host plastid homeostasis. βC1 induced DPD1, an organelle-specific nuclease, implicated in nutrient salvage and senescence, as well as modulated the function of a major plastid genome maintainer protein RecA1, to subvert plastid genome. We show that βC1 was able to physically interact with bacterial RecA and its plant homolog RecA1, resulting in its altered activity. We observed that knocking-down DPD1 during virus infection significantly reduced virus-induced necrosis. These results indicate the presence of a strategy in which a viral protein alters host defense by targeting modulators of chloroplast DNA. We predict that the mechanism identified here might have similarities in other plant-pathogen interactions.

}, issn = {1365-313X}, doi = {10.1111/tpj.16186}, author = {Nair, Ashwin and Harshith, Chitthavalli Y and Narjala, Anushree and Shivaprasad, Padubidri V} } @article {135859, title = {Novel regulators of mitochondrial genome integrity.}, journal = {J Biosci}, volume = {48}, year = {2023}, month = {2023}, abstract = {

Mitochondrial genomes are unusual in that they have very low mutation rates in coding sequences when compared with animals, yeast, and bacteria. It has been proposed that the mitochondrial (mt) DNA damage is preferentially repaired by homologous recombination (HR). In this short review, we summarize and discuss the well-established and recently identified pathways that help in maintaining the integrity of plant mitochondrial genomes.

}, keywords = {Animals, DNA, Mitochondrial, Genome, Mitochondrial, Genome, Plant, Homologous Recombination, Mitochondria, Plants, Saccharomyces cerevisiae}, issn = {0973-7138}, author = {Nair, Ashwin and Shivaprasad, P V} } @article {99103, title = {Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions.}, journal = {New Phytol}, year = {2021}, month = {2021 Aug 27}, abstract = {

RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α- and β-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and non-coding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities, and their contribution to the regulation of gene expression.

}, issn = {1469-8137}, doi = {10.1111/nph.17700}, author = {Jha, Vikram and Narjala, Anushree and Basu, Debjani and Sujith, T N and Pachamuthu, Kannan and Chenna, Swetha and Nair, Ashwin and Shivaprasad, Padubidri V} } @article {73040, title = {A conserved sequence signature is essential for robust plant miRNA biogenesis.}, journal = {Nucleic Acids Res}, year = {2020}, month = {2020 Feb 06}, abstract = {

Micro (mi)RNAs are 20-22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.

}, issn = {1362-4962}, doi = {10.1093/nar/gkaa077}, author = {Narjala, Anushree and Nair, Ashwin and Tirumalai, Varsha and G Vivek Hari Sundar and Shivaprasad, Padubidri V} } @article {74442, title = {Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs.}, journal = {Plant Reprod}, volume = {33}, year = {2020}, month = {2020 Mar}, pages = {59-73}, abstract = {

KEY MESSAGE: In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indica AGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.

}, issn = {2194-7961}, doi = {10.1007/s00497-020-00386-w}, author = {Das, Soumita and Swetha, Chenna and Pachamuthu, Kannan and Nair, Ashwin and Shivaprasad, P V} } @article {79800, title = {A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer.}, journal = {Nat Commun}, volume = {11}, year = {2020}, month = {2020 Jul 17}, pages = {3598}, abstract = {

Genetic variation at the 8q24 locus is linked with the greater susceptibility to prostate cancer in men of African ancestry. One such African ancestry specific rare variant, rs72725854 (A\>G/T) (~6\% allele frequency) has been associated with a ~2-fold increase in prostate cancer risk. However, the functional relevance of this variant is unknown. Here we show that the variant rs72725854 is present in a prostate cancer-specific enhancer at 8q24 locus. Chromatin-conformation capture and dCas9 mediated enhancer blocking establish a direct regulatory link between this enhancer and lncRNAs PCAT1, PRNCR1 and PVT1. The risk allele ({\textquoteright}T{\textquoteright}) is associated with higher expression of PCAT1, PVT1 and c-myc in prostate tumors. Further, enhancer with the risk allele gains response to androgen stimulation by recruiting the transcription factor SPDEF whereas, non-risk alleles remain non-responsive. Elevated expression of these lncRNAs and c-myc in risk allele carriers may explain their greater susceptibility to prostate cancer.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-17325-y}, author = {Walavalkar, Kaivalya and Saravanan, Bharath and Singh, Anurag Kumar and Jayani, Ranveer Singh and Nair, Ashwin and Farooq, Umer and Islam, Zubairul and Soota, Deepanshu and Mann, Rajat and Shivaprasad, Padubidri V and Freedman, Matthew L and Sabarinathan, Radhakrishnan and Haiman, Christopher A and Notani, Dimple} } @article {81664, title = {Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions.}, journal = {BMC Biol}, volume = {18}, year = {2020}, month = {2020 Aug 31}, pages = {110}, abstract = {

BACKGROUND: To successfully invade new hosts, plant viruses must break host resistance and be competent to move within and between plant cells. As a means, viral proteins known as pathogenicity determinants have evolved to coordinate a network of protein interactions. The βC1 protein encoded by specific geminiviral satellites acts as a key pathogenicity determinant for this disease-causing family of plant viruses. Post-translational modifications (PTMs) such as ubiquitination and phosphorylation of the βC1 protein have been shown to occur in diverse viruses. However, the relevance of these and other layers of PTMs in host-geminiviral interactions has not been fully understood.

RESULTS: Here we identified the significance of a novel layer of PTMs in the βC1 protein of Synedrella yellow vein clearing virus (SyYVCV), a newly identified member of the Begomovirus genus of Geminiviruses. This protein has conserved SUMOylation and SUMO-interacting motifs (SIMs), and we observed SUMOylation of SyYVCV βC1 in host plants as a defensive strategy against ubiquitin-mediated degradation. Counteracting this, SIMs encoded in βC1 mediate the degradation of βC1; however, both these PTMs are essential for the function of βC1 protein since SIM and SUMOylation motif mutants failed to promote pathogenicity and viral replication in vivo. SUMOylation in different motifs of βC1 led to functionally distinct outcomes, regulating the stability and function of the βC1 protein, as well as increased global SUMOylation of host proteins.

CONCLUSION: Our results indicate the presence of a novel mechanism mediating a fine balance between defence and counter-defence in which a SIM site is competitively sought for degradation and, as a counter-defence, βC1 undergoes SUMOylation to escape from its degradation.

}, issn = {1741-7007}, doi = {10.1186/s12915-020-00843-y}, author = {Nair, Ashwin and Chatterjee, Kiran Sankar and Jha, Vikram and Das, Ranabir and Shivaprasad, P V} } @article {68513, title = {Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies.}, journal = {PeerJ}, volume = {7}, year = {2019}, month = {2019}, pages = {e8058}, abstract = {

Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies-considered to be generalist predators-consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72\% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.

}, issn = {2167-8359}, doi = {10.7717/peerj.8058}, author = {Deb, Rittik and Nair, Ashwin and Agashe, Deepa} } @article {59710, title = {miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes.}, journal = {J Exp Bot}, year = {2019}, month = {2019 May 30}, abstract = {

MicroRNAs are a class of non-coding small RNAs involved in negative regulation of gene expression and playing critical roles in developmental and metabolic pathways. Studies in several plants have identified few microRNAs and other small (s) RNAs that target regulators of phenylpropanoid metabolic pathway called MYB transcription factors. However, it is not well-understood how sRNA mediated regulation of MYBs influences accumulation of specific secondary metabolites. Using sRNA-sequencing, degradome analysis, mRNA-seq and proteomic analysis, we establish that grape lines with high anthocyanin content express two abundant MYB-targeting miRNAs resulting in differential expression of specific MYB proteins. miR828 and miR858 target coding sequences of specific helix motifs in the mRNA sequences of MYB proteins. Targeting by miR828, caused MYB RNA decay and production of cascade secondary siRNAs that depend on RNA dependant RNA polymerase 6. MYB suppression and cascade silencing was more robust in grape lines with high anthocyanin content when compared to a flavonol-rich grape line. We establish that miRNA-mediated silencing targeted repressor class of MYBs to promote anthocyanin biosynthesis in grape lines with high anthocyanins. We propose that this process regulates expression of appropriate MYBs in grape lines to produce specific secondary metabolites.

}, issn = {1460-2431}, doi = {10.1093/jxb/erz264}, author = {Tirumalai, Varsha and Swetha, Chenna and Nair, Ashwin and Pandit, Awadhesh and Shivaprasad, P V} } @article {45303, title = {Major domestication-related phenotypes in indica rice are due to loss of miRNA-mediated laccase silencing.}, journal = {Plant Cell}, year = {2018}, month = {2018 Oct 19}, abstract = {

Domestication of rice included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key genes such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA mediated regulation. Analysis of small (s) RNA datasets from cultivated indica rice lines, a few landraces and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs coding for laccases to decay and induce robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, over-expression of miR397 induced de-domestication phenotypes. Interestingly, nearly 26 unknown QTLs previously implicated for rice yield overlapped with laccases and miR397 genes. These results suggest the involvement of miRNAs in rice domestication-associated phenotypes.

}, issn = {1532-298X}, doi = {10.1105/tpc.18.00472}, author = {Swetha, Chenna and Basu, Debjani and Pachamuthu, Kannan and Tirumalai, Varsha and Nair, Ashwin and Prasad, Melvin and Shivaprasad, Padubidri V} }