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Dicer 1 of Candida albicans cleaves plant viral dsRNA in vitro and provides tolerance in plants against virus infection

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Abstract

Most of the viral diseases of plants are caused by RNA viruses which drastically reduce crop yield. In order to generate resistance against RNA viruses infecting plants, we isolated the dicer 1 protein (CaDcr1), a member of RNAse III family (enzyme that cleaves double stranded RNA) from an opportunistic fungus Candida albicans. In vitro analysis revealed that the CaDcr1 cleaved dsRNA of the coat protein gene of cucumber mosaic virus (genus Cucumovirus, family Bromoviridae). Furthermore, we developed transgenic tobacco plants (Nicotiana tabacum cv. Xanthi) over-expressing expressing CaDcr1 by Agrobacterium mediated transformation. Transgenic tobacco lines were able to suppress infection of an Indian isolate of potato virus X (genus Potexvirus, family Alphaflexiviridae). The present study demonstrates that CaDcr1 can cleave double stranded replicative intermediate and provide tolerance to plant against RNA viruses.

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References

  1. Aravind L, Koonin EV. A natural classification of ribonucleases. Methods Enzymol. 2001;341:3–28.

    Article  CAS  PubMed  Google Scholar 

  2. Bernsteina DA, Vyasa VK, Weinberga DE, Drinnenberga IA, Bartela DP, Finka GR. Candida albicans Dicer (CaDcr1) is required for efficient ribosomal and spliceosomal RNA maturation. PNAS USA. 2012;109:523–8.

    Article  Google Scholar 

  3. Braun BR, van het Hoog M, d’Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Rosa Z, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Köhler G, Morschhäuser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A. A human-curated annotation of the Candida albicans genome. PLoS Genet. 2005;1(1):36–57.

    Article  CAS  PubMed  Google Scholar 

  4. Chanfreau G, Rotondo G, Legrain P, Jacquier A. Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J. 1998;17:3726–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Conrad C, Rauhut R. Ribonuclease III: new sense from nuisance. Int J Biochem Cell Biol. 2002;34:116–29.

    Article  CAS  PubMed  Google Scholar 

  6. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: version II. Plant Mol Biol Rep. 1983;1:19–21.

    Article  CAS  Google Scholar 

  7. Ding SW, Voinnet O. Antiviral immunity directed by small RNAs. Cell. 2007;130:413–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP. RNAi in budding yeast. Science. 2009;326:544–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Elela SA, Igel H, Ares M. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell. 1996;85:115–24.

    Article  CAS  PubMed  Google Scholar 

  10. Filippov V, Solovyev V, Filippova M, Gill SS. A novel type of RNase III family proteins in eukaryotes. Gene. 2000;245:213–21.

    Article  CAS  PubMed  Google Scholar 

  11. Geetanjali AS, Kumar R, Srivastava PS, Mandal B. Biological and molecular characterization of two distinct tomato strains of Cucumber mosaic virus based on complete RNA-3 genome and subgroup specific diagnosis. Indian J Virol. 2011;22:117–26.

    Article  Google Scholar 

  12. Giuseppe R, David F. Purification and characterization of the Pac1 ribonuclease of Schizosaccharomyces pombe. Nucleic Acids Res. 1996;24(12):2377–86.

    Article  Google Scholar 

  13. Horsch RB, Rogers SG, Fraley RT. Transgenic plants. Cold Spring Harb Symp Quant Biol. 1985;50:433–7.

    Article  CAS  PubMed  Google Scholar 

  14. Jacobsen SE, Running MP, Meyerowitz EM. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development. 1999;126:5231–43.

    CAS  PubMed  Google Scholar 

  15. Iino Y, Sugimoto A, Yamamoto M. Schizosachraomyces pombe pac1+ , whose overexpression inhibits sexual development, encodes a ribonuclease III-like RNase. EMBO J. 1991;10:221–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kiyota E, Okada R, Kondo N, Hiraguri A, Moriyama H, Fukuhara T. Arabidopsis RNase III-like protein, AtRTL2, cleaves double-stranded RNA in vitro. J Plant Res. 2001;124:405–14.

    Article  CAS  Google Scholar 

  17. Kumari P, Singh AK, Sharma VK, Chattopadhyay B, Chakraborty S. A novel recombinant tomato-infecting begomovirus capable of trans-complementing heterologous DNA-B components. Arch Virol. 2001;156:769–83.

    Article  CAS  Google Scholar 

  18. Lamontagne B, Trembley A, Elela SA. The N-Terminal domain that distinguishes yeast from bacterial RNase III contains dimerization signal required for efficient double-stranded RNA cleavage. Mol Cell Biol. 2000;20:1104–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lamontagne B, Elela SA. Purification and characterization of Saccharomyces cerevisiae Rnt1p nuclease. Methods Enzymol. 2001;342:159–67.

    Article  CAS  PubMed  Google Scholar 

  20. Langenberg WG, Zhang L, Court D, Giunchedi L, Mirtra A. Transgenic tobacco plants expressing the bacterial rnc gene resist virus infection. Mol Breed. 1997;3:391–9.

    Article  CAS  Google Scholar 

  21. Li H, Nicholson AW. Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical foot printing using catalytically inactive RNase III mutants. EMBO J. 1996;15:1421–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. MacRae IJ, Doudna JA. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol. 2007;17:138–45.

    Article  CAS  PubMed  Google Scholar 

  23. MacRae IJ, Zhou K, Doudna JA. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol. 2007;14:934–40.

    Article  CAS  PubMed  Google Scholar 

  24. Malone CD, Hannon GJ. Small RNAs as guardians of the genome. Cell. 2009;136:656–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Moore JT, Uppal A, Maley F, Maley GF. Overcoming inclusion body formation in a high-level expression system. Protein Express Purif. 1993;4:160–3.

    Article  CAS  Google Scholar 

  26. Nicholson AW. Structure, reactivity, and biology of double-stranded RNA. Prog Nucleic Acid Res Mol Biol. 1996;52:1–65.

    Article  CAS  PubMed  Google Scholar 

  27. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev. 1999;23:371–90.

    Article  CAS  PubMed  Google Scholar 

  28. Robaglia C, Tepfer M. Using nonviral genes to engineer virus resistance in plants. Biotechnol Annu Rev. 1996;2:185–204.

    Article  CAS  Google Scholar 

  29. Robertson HD, Webster RE, Zinder ND. Purification and properties of ribonuclease III from Escherichia coli. J Biol Chem. 1968;243(1):82–91.

    CAS  PubMed  Google Scholar 

  30. Rotondo G, Frendewey D. Purification and characterization of the Pac1 ribonuclease of Schizosaccharomyces pombe. Nucleic Acids Res. 1996;24:2377–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sambrook J, Russell D. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory; 2001.

    Google Scholar 

  32. Sano T, Nagayama A, Ogawa T, Ishida I, Okada Y. Transgenic potato expressing a double-stranded RNA-specific ribonuclease is resistant to potato spindle tuber viroid. Nat Biotechnol. 1997;15:1290–4.

    Article  CAS  PubMed  Google Scholar 

  33. Sharma K, Misra RS. Molecular approaches towards analyzing the viruses infecting maize (Zea mays L.). J Gen Mol Virol. 2011;3(1):1–17.

    Google Scholar 

  34. Varma A, Malathi VG. Emerging geminivirus problems: a serious threat to crop production. Ann Appl Biol. 2003;142:145–64.

    Article  CAS  Google Scholar 

  35. Watanabe Y, Ogawa T, Takahashi H, Ishida I, Takeuchi Y, Yamamoto M, Okada Y. Resistance against multiple plant viruses in plants mediated by a double-stranded RNA-specific ribonuclease. FEBS Lett. 1995;372:165–8.

    Article  CAS  PubMed  Google Scholar 

  36. Weinberg DE, Nakanishi K, Patel DJ, Bartel DP. The inside-out mechanism of Dicers from budding yeasts. Cell. 2011;146:262–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Xu HP, Riggs M, Rodgers L, Wigler MA. A gene from S. pombe with homology to E. coli RNAse III blocks conjugation and sporulation when overexpressed in wild type cells. Nucleic Acids Res. 1990;18(17):5304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Zamore PD, Haley B. Ribo-gnome: the big world of small RNAs. Science. 2005;309:1519–24.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Financial support from the Council for Scientific and Industrial Research, Govt. of India vide Grant No. 38(1300)/11/EMR-11 to SC is gratefully acknowledged.

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Author notes

  1. Equal contribution by Chaudhury Mashhood Alam and Garima Jain.

Authors and Affiliations

  1. Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Chaudhary Mashhood Alam, Garima Jain, Aarzoo Kausar, Ashish Kumar Singh & Supriya Chakraborty

  2. Department of Botany, Patna University, Patna, Bihar, 600005, India

    Chaudhary Mashhood Alam & Choudhary Sharfuddin

  3. Advanced Centre of Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India

    Bikash Mandal & Anupam Varma

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  1. Chaudhary Mashhood Alam
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Correspondence to Supriya Chakraborty.

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Fig. S1

Confirmation of the recombinant CaDcr1 protein by MALDI analysis (TIFF 548 kb)

Fig. S2

Secondary structure of the coat protein transcripts of CMV and free energy value using GeneBee software.(a) Secondary structure of transcript of CMV-AUR(-133.6 kcal/mol free energy) (b) Secondary structure of transcript of CMV-PUNE (-147.0 kcal/mol free energy) (TIFF 2794 kb)

Fig. S3

Hyperchromicity Graph for determination melting point of secondary structure of the coat protein transcripts of CMV using Poland Software.(a) AUR RNA (100 °C) and (b) PUNE RNA (100 °C) (TIFF 83 kb)

Fig. S4

Prediction of allergenicity of CaDcr1. Non-Allergic nature of CaDcr1 was established using the Structural database of Allergen Protein (SDAP) software. The allergenicity value ranges between 3 to 11% that are much lower than the required threshold value (35%) as set for known allergens (indicated as Red horizontal line) (TIFF 215 kb)

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Alam, C.M., Jain, G., Kausar, A. et al. Dicer 1 of Candida albicans cleaves plant viral dsRNA in vitro and provides tolerance in plants against virus infection. VirusDis. 30, 237–244 (2019). https://doi.org/10.1007/s13337-019-00520-x

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