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Functional & Integrative Genomics

, Volume 19, Issue 3, pp 437–452 | Cite as

Leaf rust (Puccinia triticina) mediated RNAi in wheat (Triticum aestivum L.) prompting host susceptibility

  • Summi Dutta
  • Shailendra Kumar Jha
  • Kumble Vinod Prabhu
  • Manish Kumar
  • Kunal MukhopadhyayEmail author
Original Article

Abstract

Significance of microRNAs in regulating gene expression in higher eukaryotes as well as in pathogens like fungi to suppress host defense is a well-established phenomenon. The present study focuses on leaf rust fungi Puccinia triticina (Pathotype 77-5) mediated RNAi to make wheat (Triticum aestivum L.) more susceptible. To reach such conclusions, we first confirmed the presence of argonaute (AGO) and dicer-like protein (DCL) family sequences in Puccinia. Bioinformatic tools were applied to retrieve the sequences from Puccinia genome followed by cloning and sequencing from P. triticina pathotype 77-5 cDNA to obtain the specific sequences. Their homologs were searched in other 14 Puccinia races to relate them with pathogenesis. Further, precursor sequences for three miRNA-like RNA molecules (milRs) were cloned from P. triticina cDNA. Their target genes like MAP kinase were successfully predicted and validated through degradome mapping and qRT-PCR. Gradual increase in milR2 (milR and milR*) expression over progressive time point of infection and positive expression for all the milRs within 77-5 urediniospores confirmed a complete host- independent RNAi activity by P. triticina.

Keywords

Leaf rust Puccinia triticina pathotype 77-5 Wheat Triticum aestivum L. RNAi miRNA-like RNA molecules Argonaute Dicer-like protein 

Notes

Acknowledgements

This work was supported by Centre of Excellence, Technical Education Quality Improvement Program-II (grant no. NPIU/TEQIP II/FIN/31/158). The authors are thankful to BTISNet SubDIC (BT/BI/04/065/04) for providing bioinformatics facilities. S.D. acknowledges Innovation in Science Pursuit for Inspired Research (INSPIRE), Government of India, Ministry of Science and Technology, New Delhi (IF140725) for providing fellowships. The authors acknowledge Dr. Dhananjay Kumar for preparing sRNA and degradome libraries.

Supplementary material

10142_2019_655_MOESM1_ESM.docx (1.1 mb)
ESM 1 (DOCX 1102 kb)

References

  1. Arikit S, Xia R, Kakrana A, Huang K, Jixian Zhai J, Yan Z, Valdés-López O (2014) An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. Plant Cell 26:4584–4601CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bi G, Zhou JM (2017) MAP kinase signaling pathways: a hub of plant–microbe interactions. Cell Host Microbe 21:270–273CrossRefPubMedGoogle Scholar
  4. Bolton MD, Kolmer JA, Garvin DF (2008) Wheat leaf rust caused by Puccinia triticina. Mol Plant Pathol 9:563–575CrossRefPubMedGoogle Scholar
  5. Cao JY, Xu YP, Li W, Li SS, Rahman H, Cai XZ (2016) Genome-wide identification of dicer-like, Argonaute, and RNA-dependent RNA polymerase gene families in Brassica species and functional analyses of their Arabidopsis homologs in resistance to Sclerotinia sclerotiorum. Front Plant Sci 7:1614PubMedPubMedCentralGoogle Scholar
  6. Carmell MA, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16:2733–2742CrossRefPubMedGoogle Scholar
  7. Cerutti H, Casas-Mollano JA (2006) On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet 50:81–99CrossRefPubMedPubMedCentralGoogle Scholar
  8. Chai L, Tudor RL, Poulter NS, Wilkins KA, Eaves DJ, Franklin FC, Franklin-Tong VE (2017) MAP kinase PrMPK9-1 contributes to the self-incompatibility response. Plant Physiol 174(2):1226–1237CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chang SS, Zhang Z, Liu Y (2012) RNA interference pathways in fungi: mechanisms and functions. Annu Rev Microbiol 66:305–323CrossRefPubMedPubMedCentralGoogle Scholar
  10. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159CrossRefPubMedPubMedCentralGoogle Scholar
  11. Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, … Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol. 13:414–430Google Scholar
  12. Dutta S, Kumar D, Jha S, Prabhu KV, Kumar M, Mukhopadhyay K (2017) Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L). Planta 246:939–957CrossRefPubMedGoogle Scholar
  13. Fei Q, Zhang Y, Xia R, Meyers BC (2016) Small RNAs add zing to the zig-Zag-zig model of plant defences. Mol Plant-Microbe Interact 29:165–169CrossRefPubMedGoogle Scholar
  14. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, … Salazar GA (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44:D279–85Google Scholar
  15. Glazebrook J, Ton J (2007) Biotic interactions recurring themes and expanding scales. Curr Opin Plant Biol 10:331–334CrossRefGoogle Scholar
  16. Gupta SK, Charpe A, Koul S, Haque QMR, Prabhu KV (2006) Development and validation of SCAR markers co-segregating with an Agropyron elongatum derived leaf rust resistance gene Lr24 in wheat. Euphytica 150:233–240CrossRefGoogle Scholar
  17. Hasabnis SN, Shinde VK, Ilhe BM (2006) Virulence population of leaf rust of wheat in warmer areas of India during 2000–01. Agric Sci Dig 26:35–38Google Scholar
  18. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531CrossRefGoogle Scholar
  19. Hutvagner G, Simard MJ (2008) Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9:22–32CrossRefPubMedGoogle Scholar
  20. Iki T (2017) Messages on small RNA duplexes in plant. J Plant Res 130:7–16CrossRefPubMedGoogle Scholar
  21. Inal B, Türktaş M, Eren H, Ilhan E, Okay S, Atak M, Erayman M, Unver T (2014) Genome-wide fungal stress responsive miRNA expression in wheat. Planta 240:1287–1298CrossRefPubMedGoogle Scholar
  22. Jangid A, Chandel V, Jesse MI, Srivastava A, Rishi N (2017) In-silico interaction of RNA silencing suppressors of velvet bean severe mosaic virus with DICER domains. Arch Phytopathol Plant Protect 18:1–9Google Scholar
  23. Jaubert M, Bhattacharjee S, Mello AF, Perry KL, Moffett P (2011) ARGONAUTE2 mediates RNA-silencing antiviral defenses against potato virus X in Arabidopsis. Plant Physiol 156:1556–1564CrossRefPubMedPubMedCentralGoogle Scholar
  24. Johnson NR, Yeoh JM, Coruh C, Axtell MJ (2016) Improved placement of multi-mapping small RNAs. G3 (Bethesda) 6:2103–2111CrossRefGoogle Scholar
  25. Kang K, Zhong J, Jiang L, Liu G, Gou CY, Wu Q, Wang Y, Luo J, Gou D (2013) Identification of microRNA-like RNAs in the filamentous fungus Trichoderma reesei by Solexa sequencing. PLoS One 8:e76288CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kiran K, Rawal HC, Dubey H, Jaswal R, Devanna BN, Gupta DK, … Balasubramanian P (2016) Draft genome of the wheat rust pathogen (Puccinia triticina) unravels genome-wide structural variations during evolution. Genome Biol Evol. 8:2702–2721Google Scholar
  27. Klein M, Chandradoss SD, Depken M, Joo C (2017) Why Argonaute is needed to make microRNA target search fast and reliable. Semin Cell Dev Biol 65:20–28CrossRefPubMedGoogle Scholar
  28. Kumar D, Dutta S, Singh D, Prabhu KV, Kumar M, Mukhopadhyay K (2017) Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L) using high-throughput sequencing and prediction of their targets through degradome analysis. Planta 245:161–182CrossRefPubMedGoogle Scholar
  29. Liu T, Hu J, Zuo Y, Jin Y, Hou J (2016) Identification of microRNA-like RNAs from Curvularia lunata associated with maize leaf spot by bioinformation analysis and deep sequencing. Mol Gen Genomics 291:587–596CrossRefGoogle Scholar
  30. Liu W, Meng J, Cui J, Luan Y (2017) Characterization and function of MicroRNA*s in plants. Front Plant Sci 8:2200CrossRefPubMedPubMedCentralGoogle Scholar
  31. Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S et al (2016) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203CrossRefPubMedPubMedCentralGoogle Scholar
  32. Meng H, Wang Z, Wang Y, Zhu H, Huang B (2017) Dicer and Argonaute genes involved in RNA interference in the entomopathogenic fungus Metarhizium robertsii. Appl Environ Microbiol 83:e03230–e03216CrossRefPubMedPubMedCentralGoogle Scholar
  33. Mueth NA, Ramachandran SR, Hulbert SH (2015) Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f sp tritici). BMC Genomics 16:718CrossRefPubMedPubMedCentralGoogle Scholar
  34. Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J et al (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science 333:596–601CrossRefPubMedPubMedCentralGoogle Scholar
  35. Nunes CC, Gowda M, Sailsbery J, Xue M, Chen F, Brown DE, Oh YY, Mitchell TK, Dean RA (2011) Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics 12:288CrossRefPubMedPubMedCentralGoogle Scholar
  36. Panwar V, Jordan M, McCallum B, Bakkeren G (2017) Host-induced silencing of essential genes in Puccinia triticina through transgenic expression of RNAi sequences reduces severity of leaf rust infection in wheat. Plant Biotechnol J.  https://doi.org/10.1111/pbi.12845
  37. Parent JS, Bouteiller N, Elmayan T, Vaucheret H (2015) Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant J 81:223–232CrossRefGoogle Scholar
  38. Poovaiah BW, Du L, Wang H, Yang T (2013) Recent advances in calcium/calmodulin-mediated signaling with an emphasis on plant–microbe interactions. Plant Physiol 163:531–542CrossRefPubMedPubMedCentralGoogle Scholar
  39. Reis RS (2017) The entangled history of animal and plant microRNAs. Funct Integr Genomics 17:127–134CrossRefPubMedGoogle Scholar
  40. Salomon WE, Jolly SM, Moore MJ, Zamore PD, Serebrov V (2015) Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. Cell 162:84–95CrossRefPubMedPubMedCentralGoogle Scholar
  41. Song MS, Rossi JJ (2017) Molecular mechanisms of dicer: endonuclease and enzymatic activity. Biochem J 474:1603–1618CrossRefPubMedPubMedCentralGoogle Scholar
  42. Van Kleeff PJ, Galland M, Schuurink RC, Bleeker PM (2016) Small RNAs from Bemisia tabaci are transferred to Solanum lycopersicum phloem during feeding. Front Plant Sci 7:1759PubMedPubMedCentralGoogle Scholar
  43. Wang HLV, Chekanova JA (2016) Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants. WIREs RNA 7:356–381CrossRefPubMedGoogle Scholar
  44. Wang B, Sun Y, Song N, Zhao M, Liu R, Feng H, Wang X, Kang Z (2017) Puccinia striiformis f sp tritici microRNA-like RNA 1 (Pst-milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis-related 2 gene. New Phytol 215:338–350CrossRefPubMedGoogle Scholar
  45. Weiberg A, Jin H (2015) Small RNAs—the secret agents in the plant–pathogen interactions. Curr Opin Plant Biol 26:87–94CrossRefPubMedPubMedCentralGoogle Scholar
  46. Weiberg A, Wang M, Lin FM, Zhao H, Zhang Z, Kaloshian I, Huang HD, Jin H (2013) Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342:118–123CrossRefPubMedPubMedCentralGoogle Scholar
  47. Weiberg A, Wang M, Bellinger M, Jin H (2014) Small RNAs: a new paradigm in plant–microbe interactions. Annu Rev Phytopathol 52:495–516CrossRefPubMedGoogle Scholar
  48. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134CrossRefPubMedPubMedCentralGoogle Scholar
  49. Yuan P, Jauregui E, Du L, Tanaka K, Poovaiah BW (2017) Calcium signatures and signaling events orchestrate plant–microbe interactions. Curr Opin Plant Biol 38:173–183CrossRefPubMedGoogle Scholar
  50. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63:246–254CrossRefPubMedGoogle Scholar
  51. Zhou J, Fu Y, Xie J, Li B, Jiang D, Li G, Cheng J (2012) Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing. Mol Gen Genomics 287:275–282CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Bio-EngineeringBirla Institute of TechnologyRanchiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia

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