Journal article
Transcriptome-wide identification of host genes targeted by tomato spotted wilt virus-derived small interfering RNAs
Virus research, Vol.238, pp.13-23
06/15/2017
Handle:
https://hdl.handle.net/2376/110061
PMID: 28545854
Abstract
•TSWV derived vsiRNAs potentially target 11898 sites on tomato transcripts.•Tomato cultivars exhibit differential expression of selected target transcripts.•Differential response of cultivars to TSWV could be its ability to overcome vsiRNA targeting.•First interactome map between TSWV derived siRNAs and tomato transcriptome.
RNA silencing mechanism functions as a major defense against invading viruses. The caveat in the RNA silencing mechanism is that the effector small interfering RNAs (siRNAs) act on any RNA transcripts with sequence complementarity irrespective of target’s origin. A subset of highly expressed viral small interfering RNAs (vsiRNAs) derived from the tomato spotted wilt virus (TSWV; Tospovirus: Bunyaviridae) genome was analyzed for their propensity to downregulate the tomato transcriptome. A total of 11898 putative target sites on tomato transcripts were found to exhibit a propensity for down regulation by TSWV-derived vsiRNAs. In total, 2450 unique vsiRNAs were found to have potential cross-reacting capability with the tomato transcriptome. VsiRNAs were found to potentially target a gamut of host genes involved in basal cellular activities including enzymes, transcription factors, membrane transporters, and cytoskeletal proteins. KEGG pathway annotation of targets revealed that the vsiRNAs were mapped to secondary metabolite biosynthesis, amino acids, starch and sucrose metabolism, and carbon and purine metabolism. Transcripts for protein processing, hormone signalling, and plant-pathogen interactions were the most likely targets from the genetic, environmental information processing, and organismal systems, respectively. qRT-PCR validation of target gene expression showed that none of the selected transcripts from tomato cv. Marglobe showed up regulation, and all were down regulated even upto 20 folds (high affinity glucose transporter). However, the expression levels of transcripts from cv. Red Defender revealed differential regulation as three among the target transcripts showed up regulation (Cc-nbs-lrr, resistance protein, AP2-like ethylene-responsive transcription factor, and heat stress transcription factor A3). Accumulation of tomato target mRNAs of corresponding length was proved in both tomato cultivars using 5′ RACE analysis. The TSWV-tomato interaction at the sRNA interface points to the ability of tomato cultivars to overcome vsiRNA-mediated targeting of NBS-LRR class R genes. These results suggest the prevalence of vsiRNA-induced RNA silencing of host transcriptome, and the interactome scenario is the first report on the interaction between tospovirus genome-derived siRNAs and tomato transcripts, and provide a deeper understanding of the role of vsiRNAs in pathogenicity and in perturbing host machinery.
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Details
- Title
- Transcriptome-wide identification of host genes targeted by tomato spotted wilt virus-derived small interfering RNAs
- Creators
- Shunmugiah V Ramesh - Department of Plant Pathology, Washington State University, Pullman, WA 99164, USASarah Williams - Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, AustraliaMadhu Kappagantu - Department of Plant Pathology, Washington State University, Pullman, WA 99164, USANeena Mitter - Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, AustraliaHanu R Pappu - Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
- Publication Details
- Virus research, Vol.238, pp.13-23
- Academic Unit
- Plant Pathology, Department of
- Publisher
- Elsevier B.V
- Identifiers
- 99900547118401842
- Language
- English
- Resource Type
- Journal article