Shelly Praveen

Bio: Shelly Praveen is an academic researcher from Indian Agricultural Research Institute. The author has contributed to research in topics: Gene & RNA silencing. The author has an hindex of 20, co-authored 125 publications receiving 1611 citations. Previous affiliations of Shelly Praveen include Indian Council of Agricultural Research.

ICTV Virus Taxonomy Profile: Potyviridae.

Abstract: The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide. There are eight genera, distinguished by the host range, genomic features and phylogeny of the member viruses. Genomes range from 8.2 to 11.3 kb, with an average size of 9.7 kb. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Potyviridae, which is available at www.ictv.global/report/potyviridae.

Infection of tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus with betasatellites, results in enhanced level of helper virus components and antagonistic interaction between DNA B and betasatellites

Abstract: Tomato leaf curl New Delhi virus (ToLCNDV) (Geminiviridae) is an important pathogen that severely affects tomato production An extensive survey was carried out during 2003–2010 to study the diversity of begomoviruses found in tomato, potato, and cucurbits that showed symptoms of leaf puckering, distortion, curling, vein clearing, and yellow mosaic in various fields in different regions of India Ten begomovirus isolates were cloned from infected samples and identified as belonging to the species ToLCNDV A total of 44 % of the samples showed association of betasatellites, with CLCuMuB and LuLDB being the most frequent The ToLCNDV cloned component DNA A and DNA B were agroinoculated on Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with or without betasatellites, CLCuMuB or LuLDB The viral genome levels were then monitored by real-time polymerase chain reaction at different time points of disease development Plants co-inoculated with betasatellites showed enhanced symptom severity in both N benthamiana and tomato, as well as increases in helper viral DNA A and DNA B levels The DNA B and betasatellites acted antagonistically to each other, so that the level of DNA B was 16-fold greater in the presence of betasatellites, while accumulation of betasatellites, CLCuMuB and LuLDB, were reduced by 60 % in the presence of DNA B DNA B-mediated symptoms predominated in CLCuMuB-inoculated plants, whereas betasatellite-mediated leaf abnormalities were prominent in LuLDB-co-inoculated plants Inoculation with the cloned components will be a good biotechnological tool in resistance breeding program

Tomato Leaf Curl New Delhi Virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops

Abstract: The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution Important progress has also been made in control strategies to reduce disease damage This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants

MicroRNA regulated defense responses in Triticum aestivum L. during Puccinia graminis f.sp. tritici infection.

Abstract: Plants have evolved diverse mechanism to recognize pathogen attack and triggers defense responses. These defense responses alter host cellular function regulated by endogenous, small, non-coding miRNAs. To understand the mechanism of miRNAs regulated cellular functions during stem rust infection in wheat, we investigated eight different miRNAs viz. miR159, miR164, miR167, miR171, miR444, miR408, miR1129 and miR1138, involved in three different independent cellular defense response to infection. The investigation reveals that at the initiation of disease, accumulation of miRNAs might be playing a key role in hypersensitive response (HR) from host, which diminishes at the maturation stage. This suggests a possible host-fungal synergistic relation leading to susceptibility. Differential expression of these miRNAs in presence and absence of R gene provides a probable explanation of miRNA regulated R gene mediated independent pathways.

RNA binding is more critical to the suppression of silencing function of Cucumber mosaic virus 2b protein than nuclear localization

Abstract: Previously, we found that silencing suppression by the 2b protein and six mutants correlated both with their ability to bind to double-stranded (ds) small RNAs (sRNAs) in vitro and with their nuclear/nucleolar localization. To further discern the contribution to suppression activity of sRNA binding and of nuclear localization, we have characterized the kinetics of in vitro binding to a ds sRNA, a single-stranded (ss) sRNA, and a micro RNA (miRNA) of the native 2b protein and eight mutant variants. We have also added a nuclear export signal (NES) to the 2b protein and assessed how it affected subcellular distribution and suppressor activity. We found that in solution native protein bound ds siRNA, miRNA, and ss sRNA with high affinity, at protein:RNA molar ratios ~2:1. Of the four mutants that retained suppressor activity, three showed sRNA binding profiles similar to those of the native protein, whereas the remaining one bound ss sRNA at a 2:1 molar ratio, but both ds sRNAs with 1.5-2 times slightly lower affinity. Three of the four mutants lacking suppressor activity failed to bind to any sRNA, whereas the remaining one bound them at far higher ratios. NES-tagged 2b protein became cytoplasmic, but suppression activity in patch assays remained unaffected. These results support binding to sRNAs at molar ratios at or near 2:1 as critical to the suppressor activity of the 2b protein. They also show that cytoplasmically localized 2b protein retained suppressor activity, and that a sustained nuclear localization was not required for this function.

Identification of genes

Abstract: A method of identifying microorganisms with reduced adaptability to a particular environment, wherein (1) each microorganism is independent by insertional inactivation of a gene with a nucleic acid comprising a unique marker sequence. Mutating to provide a plurality of microorganisms, or clones of said microorganisms, such that each mutation has a different label sequence; (2) providing storage samples of each mutation produced by step (1), respectively, and providing storage nucleic acids each comprising a unique label sequence from each mutation; (3) introducing a plurality of mutations produced by step (1) into the specific environment such that the microorganisms capable of growing in the specific environment grow in the above environment; (4) recovering the microorganisms or selected portions thereof from the environment and separating nucleic acids from the recovered microorganisms; (5) comparing all label sequences in the nucleic acid isolated in step (4) with the unique label sequences of each of the stored mutations as in step (2); and (6) any label isolated in step (4). Screening for individual mutations that also do not have a sequence.

microRNAs as Master Regulators of the Plant NB-LRR Defense Gene Family via the Production of Phased, Trans-acting siRNAs

Abstract: Legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide (nt) "phased" intervals, a pattern formed by DICER-LIKE 4 (DCL4) processing. A search for phased siRNAs (phasiRNAs) found at least 114 Medicago loci, the majority of which were defense-related NB-LRR-encoding genes. We identified three highly abundant 22-nt microRNA (miRNA) families that target conserved domains in these NB-LRRs and trigger the production of trans-acting siRNAs. High levels of small RNAs were matched to >60% of all ∼540 encoded Medicago NB-LRRs; in the potato, a model for mycorrhizal interactions, phasiRNAs were also produced from NB-LRRs. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phasiRNAs, suggesting synchronization between silencing and pathogen defense pathways. In addition, a new example of apparent "two-hit" phasiRNA processing was identified. Our data reveal complex tasiRNA-based regulation of NB-LRRs that potentially evolved to facilitate symbiotic interactions and demonstrate miRNAs as master regulators of a large gene family via the targeting of highly conserved, protein-coding motifs, a new paradigm for miRNA function.