Abstract
Plants, being sessile, are vividly change with respect to gene expression profiling during stress conditions. Regulation of gene expression is controlled by many of the factors, in which ribonucleic acids interference (RNAi) mechanism has been proved to be an important regulator of both transcriptional and post-transcription controls of gene expression. RNAi mechanism provides the anti-viral resistance to plants, in which virus-derived small interfering RNAs (vsiRNAs) is a well-known component. Apart from some databases like siRNAdb, HIVsirDB and VIRsiRNAdb, which are available online pertaining to siRNAs as well as vsiRNAs generated during viral infection in humans, ‘PVsiRNAdb (http://www.nipgr.res.in/PVsiRNAdb)’, a manually curated plant-exclusive database having information related to vsiRNAs found in different virus-infected plants, collected by exhaustive data mining of published literature so far. This chapter describes the data retrieval and functioning of PVsiRNAdb. Major emphasis is also given to the tools available at this database and explanation of all the results output. The information in this plant exclusive database is very useful for the researcher to explore the complex plants and virus interaction and furthermore in the agriculture field, virus-resistant varieties of crops can be raised.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bos L. Crop losses caused by viruses. Crop Prot. 1982;1:263–82. https://doi.org/10.1016/0261-2194(82)90002-3.
Bucher E, Lohuis D, van Poppel PMJA, et al. Multiple virus resistance at a high frequency using a single transgene construct. J Gen Virol. 2006;87:3697–701. https://doi.org/10.1099/vir.0.82276-0.
Chalk AM, Warfinge RE, Georgii-Hemming P, Sonnhammer ELL. siRNAdb: a database of siRNA sequences. Nucleic Acids Res. 2004;33:D131–4. https://doi.org/10.1093/nar/gki136.
Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet. 2007;8:884–96. https://doi.org/10.1038/nrg2179.
Chen X. Small RNAs – secrets and surprises of the genome. Plant J. 2010;61:941–58. https://doi.org/10.1111/j.1365-313X.2009.04089.x.
Diener TO. Physiology of virus-infected plants. Annu Rev Phytopathol. 1963;1:197–218. https://doi.org/10.1146/annurev.py.01.090163.001213.
Ding S-W, Lu R. Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr Opin Virol. 2011;1:533–44. https://doi.org/10.1016/j.coviro.2011.10.028.
Donaire L, Wang Y, Gonzalez-Ibeas D, et al. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology. 2009;392:203–14. https://doi.org/10.1016/j.virol.2009.07.005.
Duan C-G, Wang C-H, Guo H-S. Application of RNA silencing to plant disease resistance. Silence. 2012;3:5. https://doi.org/10.1186/1758-907X-3-5.
Guo Q, Liu Q, Smith NA, et al. RNA silencing in plants: mechanisms, technologies and applications in horticultural crops. Curr Genomics. 2016;17:476–89. https://doi.org/10.2174/1389202917666160520103117.
Gupta N, Singh A, Zahra S, Kumar S. PtRFdb: a database for plant transfer RNA-derived fragments. Database. 2018;2018:63.
Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science (New York, NY). 1999;286:950–2.
Malpica-Opez N, Rajeswaran R, Beknazariants D, et al. Revisiting the roles of tobamovirus replicase complex proteins in viral replication and silencing suppression. MPMI. 2018;311094:125–44. https://doi.org/10.1094/MPMI-07-17-0164-R.
Mansoor S, Amin I, Hussain M, et al. Engineering novel traits in plants through RNA interference. Trends Plant Sci. 2006;11:559–65. https://doi.org/10.1016/J.TPLANTS.2006.09.010.
Moissiard G, Voinnet O. RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer-like proteins. Proc Natl Acad Sci. 2006;103:19593–8. https://doi.org/10.1073/pnas.0604627103.
Prins M, de Haan P, Luyten R, et al. Broad resistance to tospoviruses in transgenic tobacco plants expressing three tospoviral nucleoprotein gene sequences. Mol Plant-Microbe Interact. 1995;8:85–91. https://doi.org/10.1094/MPMI-8-0085.
Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform. 2010;11:129. https://doi.org/10.1186/1471-2105-11-129.
Rodríguez-Negrete EA, Carrillo-Tripp J, Rivera-Bustamante RF. RNA silencing against geminivirus: complementary action of posttranscriptional gene silencing and transcriptional gene silencing in host recovery. J Virol. 2009;83:1332–40. https://doi.org/10.1128/JVI.01474-08.
Shimizu T, Nakazono-Nagaoka E, Akita F, et al. Hairpin RNA derived from the gene for Pns9, a viroplasm matrix protein of Rice gall dwarf virus, confers strong resistance to virus infection in transgenic rice plants. J Biotechnol. 2012;157:421–7. https://doi.org/10.1016/j.jbiotec.2011.12.015.
Skums P, Artyomenko A, Glebova O, et al. Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinformatics. 2015;31:682–90. https://doi.org/10.1093/bioinformatics/btu726.
Stobbe AH, Roossinck MJ. Plant virus metagenomics: what we know and why we need to know more. Front Plant Sci. 2014;5:150. https://doi.org/10.3389/fpls.2014.00150.
Szittya G, Moxon S, Pantaleo V, et al. Structural and functional analysis of viral siRNAs. PLoS Pathog. 2010;6:e1000838. https://doi.org/10.1371/journal.ppat.1000838.
Thakur N, Qureshi A, Kumar M. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res. 2012;40:D230–6. https://doi.org/10.1093/nar/gkr1147.
Tyagi A, Ahmed F, Thakur N, et al. HIVsirDB: a database of HIV inhibiting siRNAs. PLoS One. 2011;6:e25917. https://doi.org/10.1371/journal.pone.0025917.
Vazquez F, Hohn T. Biogenesis and biological activity of secondary siRNAs in plants. Scientifica. 2013;2013:783253. https://doi.org/10.1155/2013/783253.
Velásquez AC, Chakravarthy S, Martin GB. Virus-induced gene silencing (VIGS) in Nicotiana benthamiana and tomato. JoVE. 2009; https://doi.org/10.3791/1292.
Zhang C, Wu Z, Li Y, Wu J. Biogenesis, function, and applications of virus-derived small RNAs in plants. Front Microbiol. 2015;6:1–12. https://doi.org/10.3389/fmicb.2015.01237.
Zhu H, Guo H. The role of virus-derived small interfering RNAs in RNA silencing in plants. Sci China Life Sci. 2012;55:119–25. https://doi.org/10.1007/s11427-012-4281-3.
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–15.
Acknowledgment
PVsiRNAdb database is developed by Dr. Shailesh Kumar research group (http://www.nipgr.res.in/research/dr_shailesh.php) at National Institute of Plant Genome Research (NIPGR), New Delhi, India.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Singh, A., Kumar, S. (2019). Study of Plant Exclusive Virus-Derived Small Interfering RNAs. In: Kumar, S., Egbuna, C. (eds) Phytochemistry: An in-silico and in-vitro Update. Springer, Singapore. https://doi.org/10.1007/978-981-13-6920-9_29
Download citation
DOI: https://doi.org/10.1007/978-981-13-6920-9_29
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-6919-3
Online ISBN: 978-981-13-6920-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)