Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato

English version

Autoři: Sarina Bao ^aff001; Robert A. Owens ^aff002; Qinghua Sun ^aff001; Hui Song ^aff001; Yanan Liu ^aff001; Andrew Leigh Eamens ^aff003; Hao Feng ^aff001; Hongzhi Tian ^aff001; Ming-Bo Wang ^aff004; Ruofang Zhang ^aff001
Působiště autorů: School of Life Sciences, Inner Mongolia University, Hohhot, China ^aff001; Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, Maryland, United States of America ^aff002; Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Australia ^aff003; CSIRO Plant Industry, Canberra, Australia ^aff004
Vyšlo v časopise: Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato. PLoS Pathog 15(12): e32767. doi:10.1371/journal.ppat.1008110
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008110

Souhrn

Viroids are small, non-protein-coding RNAs which can induce disease symptoms in a variety of plant species. Potato (Solanum tuberosum L.) is the natural host of Potato spindle tuber viroid (PSTVd) where infection results in stunting, distortion of leaves and tubers and yield loss. Replication of PSTVd is accompanied by the accumulation of viroid-derived small RNAs (sRNAs) proposed to play a central role in disease symptom development. Here we report that PSTVd sRNAs direct RNA silencing in potato against StTCP23, a member of the TCP (teosinte branched1/Cycloidea/Proliferating cell factor) transcription factor family genes that play an important role in plant growth and development as well as hormonal regulation, especially in responses to gibberellic acid (GA). The StTCP23 transcript has 21-nucleotide sequence complementarity in its 3ʹ untranslated region with the virulence-modulating region (VMR) of PSTVd strain RG1, and was downregulated in PSTVd-infected potato plants. Analysis using 3ʹ RNA ligase-mediated rapid amplification of cDNA ends (3ʹ RLM RACE) confirmed cleavage of StTCP23 transcript at the expected sites within the complementarity with VMR-derived sRNAs. Expression of these VMR sRNA sequences as artificial miRNAs (amiRNAs) in transgenic potato plants resulted in phenotypes reminiscent of PSTVd-RG1-infected plants. Furthermore, the severity of the phenotypes displayed was correlated with the level of amiRNA accumulation and the degree of amiRNA-directed down-regulation of StTCP23. In addition, virus-induced gene silencing (VIGS) of StTCP23 in potato also resulted in PSTVd-like phenotypes. Consistent with the function of TCP family genes, amiRNA lines in which StTCP23 expression was silenced showed a decrease in GA levels as well as alterations to the expression of GA biosynthesis and signaling genes previously implicated in tuber development. Application of GA to the amiRNA plants minimized the PSTVd-like phenotypes. Taken together, our results indicate that sRNAs derived from the VMR of PSTVd-RG1 direct silencing of StTCP23 expression, thereby disrupting the signaling pathways regulating GA metabolism and leading to plant stunting and formation of small and spindle-shaped tubers.

Klíčová slova:

Genetically modified plants – Gibberellins – Leaves – Phenotypes – Potato – Small interfering RNAs – Transcription factors – Tubers

Zdroje

1. Diener TO. Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA. Virology. 1971;45:411–28. doi: 10.1016/0042-6822(71)90342-4 5095900

2. Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, et al. Nucleotide sequence and secondary structure of Potato spindle tuber viroid. Nature. 1978;273:203–8. doi: 10.1038/273203a0 643081

3. Wang Y, Ding B. Viroids: small probes for exploring the vast universe of RNA trafficking in plants. J Integr Plant Biol. 2010;52:28–39. doi: 10.1111/j.1744-7909.2010.00900.x 20074138

4. Schultz ES, Folsom D. Transmission, variation, and control of certain degeneration diseases of Irish potatoes. J Agric Res. 1923;25:43–118.

5. Diener TO. Origin and evolution of viroids and viroid-like satellite RNAs. Virus Genes. 1995;11:119–31. doi: 10.1007/bf01728653 8828140

6. Lebas BSM, Clover GRG, Ochoa-Corona FM, Elliott DR, Tang Z, Alexander BJR. Distribution of Potato spindle tuber viroid in New Zealand glasshouse crops of capsicum and tomato. Austral Plant Pathol. 2005;34:129–33.

7. Manzer FE, Merriam D. Field transmission of the Potato spindle tuber virus and virus X by cultivating and hilling equipment. Am Potato J. 1961;38:346–52.

8. Verhoeven JTJ, Hüner L, Marn MV, Plesko IM, Roenhorst JW. Mechanical transmission of Potato spindle tuber viroid between plants of Brugmansia suaveoles, Solanum jasminoides and potatoes and tomatoes. Eur J Plant Pathol. 2010;128:417–21.

9. Bai J, Chen X, Lu X, Guo H, Xin X, Zhang Z. Can cryopreservation eliminate the potato virus X (PVX) and Potato spindle tuber viroid (PSTVd)?. Biosci Methods. 2012;3:34–40.

10. Singh RP. Seed transmission of Potato spindle tuber virus in tomato and potato. Am Potato J. 1970;47:225–7.

11. Wang MB, Bian XY, Wu LM, Liu LX, Smith NA, Isenegger D, et al. On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci U S A. 2004;101:3275–80. doi: 10.1073/pnas.0400104101 14978267

12. Ivanova D, Milev I, Vachev T, Baev V, Yahubyan G, Minkov G, et al. Small RNA analysis of Potato spindle tuber viroid infected Phelipanche ramosa. Plant Physiol Biochem. 2014;74:276–82. doi: 10.1016/j.plaphy.2013.11.019 24326144

13. Tsushima D, Tsushima T, Sano T. Molecular dissection of a dahlia isolate of Potato spindle tuber viroid inciting a mild symptoms in tomato. Virus Res. 2016;214:11–8. doi: 10.1016/j.virusres.2015.12.018 26732488

14. Dingley AJ, Steger G, Esters B, Riesner D, Grzesiek S. Structural characterization of the 69 nucleotide Potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis. J Mol Biol. 2003;334:751–67. doi: 10.1016/j.jmb.2003.10.015 14636600

15. Smith NA, Eamens AL, Wang MB. Viral small interfering RNAs target host genes to mediate disease symptoms in plants. PLoS Pathog. 2011;7:e1002022. doi: 10.1371/journal.ppat.1002022 21573142

16. Diener TO: Structure and associated biological functions of viroids. New York, NY: Plenum Press; 1987.

17. Sano T, Candresse T, Hammond RW, Diener TO, Owens RA. Identification of multiple structural domains regulating viroid pathogenicity. Proc Natl Acad Sci U S A. 1992;89:10104–8. doi: 10.1073/pnas.89.21.10104 1332029

18. Qi Y, Ding B. Inhibition of cell growth and shoot development by a specific nucleotide sequence in a noncoding viroid RNA. Plant Cell. 2003;15:1360–74. doi: 10.1105/tpc.011585 12782729

19. Eamens AL, Smith NA, Dennis ES, Wassenegger M, Wang MB. In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes. Virology. 2014;450–451:266–77. doi: 10.1016/j.virol.2013.12.019 24503090

20. Adkar-Purushothama CR, Brosseau C, Giguere T, Sano T, Moffett P, Perreault JP. Small RNA Derived from the virulence modulating region of the Potato spindle tuber viroid silences callose synthase genes of tomato plants. Plant Cell. 2015;27:2178–94. doi: 10.1105/tpc.15.00523 26290537

21. Adkar-Purushothama CR, Perreault JP. Alterations of the viroid regions that interact with the host defense genes attenuate viroid infection in host plant. RNA Biol. 2018;15:955–66. doi: 10.1080/15476286.2018.1462653 29683389

22. Katsarou K, Wu Y, Zhang R, Bonar N, Morris J, Hedley PE, et al. Insight on genes affecting tuber development in potato upon Potato spindle tuber viroid (PSTVd) infection. PLoS One. 2016;11:e0150711. doi: 10.1371/journal.pone.0150711 26937634

23. Gruner R, Fels A, Qu F, Zimmat R, Steger G, Riesner D. Interdependence of pathogenicity and replicability with Potato spindle tuber viroid. Virology. 1995;209:60–9. doi: 10.1006/viro.1995.1230 7747485

24. Adkar-Purushothama CR, Bru P, Perreault JP. 3' RNA ligase mediated rapid amplification of cDNA ends for validating viroid induced cleavage at the 3' extremity of the host mRNA. J Virol Methods. 2017;250:29–33. doi: 10.1016/j.jviromet.2017.09.023 28947148

25. Zuber H, Scheer H, Joly AC, Gagliardi D. Respective contributions of URT1 and HESO1 to the uridylation of 5' fragments produced from RISC-cleaved mRNAs. Front Plant Sci. 2018;9:1438. doi: 10.3389/fpls.2018.01438 30364210

26. Hooker WJ, Nimnoi PN, Tai W, Young TC. Germination reduction in PSTVd infected tomato pollen. Am Potato J. 1978;55:378.

27. Grasmick ME, Slack SA. Effect of Potato spindle tuber viroid on sexual reproduction and viroid transmission in true potato seed. Can J Bot. 1986;64:336–40.

28. Lebas B, Clover G, Ochoa-Corona F, Elliott D, Tang Z, Alexander B. Distribution of Potato spindle tuber viroid in New Zealand glasshouse crops of capsicum and tomato. Plant Pathol. 2005;34:129–33.

29. Simmons HE, Ruchti TB, Munkvold GP. Frequencies of seed infection and transmission to seedlings by Potato spindle tuber viroid (a pospiviroid) in tomato. J Plant Pathol Microbiol. 2015;6:275.

30. Viola RT, Oparka KM. Meristem activation in potato: impact on tuber formation, development and dormancy. Plant Biochem Cell Biol. 2000;2001:99–102.

31. Hartmann A, Senning M, Hedden P, Sonnewald U, Sonnewald S. Reactivation of meristem activity and sprout growth in potato tubers require both cytokinin and gibberellin. Plant Physiol. 2011;155:776–96. doi: 10.1104/pp.110.168252 21163959

32. Fernie AR, Willmitzer L. Molecular and biochemical triggers of potato tuber development. Plant Physiol. 2001;127:1459–65. 11743089

33. Kloosterman B, Navarro C, Bijsterbosch G, Lange T, Prat S, Visser RG, et al. StGA2ox1 is induced prior to stolon swelling and controls GA levels during potato tuber development. Plant J. 2007;52:362–73. doi: 10.1111/j.1365-313X.2007.03245.x 17764503

34. Nicolas M, Cubas P. TCP factors: new kids on the signaling block. Curr Opin Plant Biol. 2016;33:33–41. doi: 10.1016/j.pbi.2016.05.006 27310029

35. Abelenda JA, Navarro C, Prat S. Flowering and tuberization: a tale of two nightshades. Trends Plant Sci. 2014;19:115–22. doi: 10.1016/j.tplants.2013.09.010 24139978

36. Sonnewald S, Sonnewald U. Regulation of potato tuber sprouting. Planta. 2014;239:27–38. doi: 10.1007/s00425-013-1968-z 24100410

37. Hannapel DJ, Banerjee AK. Multiple mobile mRNA signals regulate tuber development in potato. Plants (Basel). 2017;6:E8.

38. Li ZY, Li B, Dong AW. The Arabidopsis transcription factor AtTCP15 regulates endoreduplication by modulating expression of key cell-cycle genes. Mol Plant. 2012;5:270–80. doi: 10.1093/mp/ssr086 21992944

39. Resentini F, Felipo-Benavent A, Colombo L, Blazquez MA, Alabadi D, Masiero S. TCP14 and TCP15 mediate the promotion of seed germination by gibberellins in Arabidopsis thaliana. Mol Plant. 2015;8:482–5. doi: 10.1016/j.molp.2014.11.018 25655823

40. de Lucas M, Daviere JM, Rodriguez-Falcon M, Pontin M, Iglesias-Pedraz JM, Lorrain S, et al. A molecular framework for light and gibberellin control of cell elongation. Nature. 2008;451:480–4. doi: 10.1038/nature06520 18216857

41. Gallego-Bartolome J, Minguet EG, Marin JA, Prat S, Blazquez MA, Alabadi D. Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis. Mol Biol Evol. 2010;27:1247–56. doi: 10.1093/molbev/msq012 20093430

42. Daviere JM, Achard P. Gibberellin signaling in plants. Development. 2013;140:1147–51. doi: 10.1242/dev.087650 23444347

43. Lee S, Cheng H, King KE, Wang W, He Y, Hussain A, et al. Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes Dev. 2002;16:646–58. doi: 10.1101/gad.969002 11877383

44. Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, et al. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 2004;135:1008–19. doi: 10.1104/pp.104.039578 15173565

45. Ueguchi-Tanaka M, Nakajima M, Katoh E, Ohmiya H, Asano K, Saji S, et al. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. Plant Cell. 2007;19:2140–55. doi: 10.1105/tpc.106.043729 17644730

46. Wang H, Pan J, Li Y, Lou D, Hu Y, Yu D. The DELLA-CONSTANS transcription factor cascade integrates gibberellic acid and photoperiod signaling to regulate flowering. Plant Physiol. 2016;172:479–88. doi: 10.1104/pp.16.00891 27406167

47. Matsushita Y, Tsuda S. Seed transmission of Potato spindle tuber viroid, tomato chlorotic dwarf viroid, tomato apical stunt viroid, and Columnea latent viroid in horticultural plants. Eur J Plant Pathol. 2016;145:1007–11.

48. Hadidi A, Flores R, Randles J, Palukaitis P: Viroids and satellites. London, UK: Sara Tenney; 2017.

49. Hammond RW. Analysis of the virulence modulating region of Potato spindle tuber viroid (PSTVd) by site-directed mutagenesis. Virology. 1992;187:654–62. doi: 10.1016/0042-6822(92)90468-5 1546460

50. Wassenegger M, Spieker RL, Thalmeir S, Gast FU, Riedel L, Sanger HL. A single nucleotide substitution converts Potato spindle tuber viroid (PSTVd) from a noninfectious to an infectious RNA for nicotiana tabacum. Virology. 1996;226:191–7. doi: 10.1006/viro.1996.0646 8955038

51. Avina-Padilla K, de la Vega OM, Rivera-Bustamante R, Martinez-Soriano JP, Owens RA, Hammond RW, et al. In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection. Gene. 2015;564:197–205. doi: 10.1016/j.gene.2015.03.076 25862922

52. Adkar-Purushothama CR, Iyer PS, Perreault JP. Potato spindle tuber viroid infection triggers degradation of chloride channel protein CLC-b-like and ribosomal protein S3a-like mRNAs in tomato plants. Sci Rep. 2017;7:8341. doi: 10.1038/s41598-017-08823-z 28827569

53. Adkar-Purushothama CR, Kasai A, Sugawara K, Yamamoto H, Yamazaki Y, He Y-H, et al. RNAi mediated inhibition of viroid infection in transgenic plants expressing viroid-specific small RNAs derived from various functional domains. Sci Rep. 2015;5:17949. doi: 10.1038/srep17949 26656294

54. Koyama T, Furutani M, Tasaka M, Ohme-Takagi M. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell. 2007;19:473–84. doi: 10.1105/tpc.106.044792 17307931

55. Koyama T, Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M. TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell. 2010;22:3574–88. doi: 10.1105/tpc.110.075598 21119060

56. Martin-Trillo M, Cubas P. TCP genes: a family snapshot ten years later. Trends Plant Sci. 2010;15:31–9. doi: 10.1016/j.tplants.2009.11.003 19963426

57. Ma J, Wang Q, Sun R, Xie F, Jones DC, Zhang B. Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii. Sci Rep. 2014;4:6645. doi: 10.1038/srep06645 25322260

58. Braun N, de Saint Germain A, Pillot JP, Boutet-Mercey S, Dalmais M, Antoniadi I, et al. The pea TCP transcription factor PsBRC1 acts downstream of strigolactones to control shoot branching. Plant Physiol. 2012;158:225–38. doi: 10.1104/pp.111.182725 22045922

59. Balsemao-Pires E, Andrade LR, Sachetto-Martins G. Functional study of TCP23 in Arabidopsis thaliana during plant development. Plant Physiol Biochem. 2013;67:120–5. doi: 10.1016/j.plaphy.2013.03.009 23562796

60. Faivre-Rampant O, Bryan GJ, Roberts AG, Milbourne D, Viola R, Taylor MA. Regulated expression of a novel TCP domain transcription factor indicates an involvement in the control of meristem activation processes in Solanum tuberosum. J Exp Bot. 2004;55:951–3. doi: 10.1093/jxb/erh082 14990618

61. Nicolas M, Rodriguez-Buey ML, Franco-Zorrilla JM, Cubas P. A Recently Evolved Alternative Splice Site in the BRANCHED1a Gene Controls Potato Plant Architecture. Curr Biol. 2015;25:1799–809. doi: 10.1016/j.cub.2015.05.053 26119747

62. Daviere JM, Wild M, Regnault T, Baumberger N, Eisler H, Genschik P, et al. Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Curr Biol. 2014;24:1923–8. doi: 10.1016/j.cub.2014.07.012 25127215

63. Daviere JM, Achard P. A pivotal role of DELLAs in regulating multiple hormone signals. Mol Plant. 2016;9:10–20. doi: 10.1016/j.molp.2015.09.011 26415696

64. Marin-de la Rosa N, Sotillo B, Miskolczi P, Gibbs DJ, Vicente J, Carbonero P, et al. Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners. Plant Physiol. 2014;166:1022–32. doi: 10.1104/pp.114.244723 25118255

65. Park J, Nguyen KT, Park E, Jeon JS, Choi G. DELLA proteins and their interacting RING finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis. Plant Cell. 2013;25:927–43. doi: 10.1105/tpc.112.108951 23482857

66. Bou-Torrent J, Martínez-García JF, García-Martínez JL, Prat S. Gibberellin A1 metabolism contributes to the control of photoperiod-mediated tuberization in potato. PLoS One. 2011;6:e24458. doi: 10.1371/journal.pone.0024458 21961036

67. Roumeliotis E, Kloosterman B, Oortwijn M, Lange T, Visser RG, Bachem CW. Down regulation of StGA3ox genes in potato results in altered GA content and affect plant and tuber growth characteristics. J Plant Physiol. 2013;170:1228–34. doi: 10.1016/j.jplph.2013.04.003 23683509

68. Roumeliotis E, Visser RG, Bachem CW. A crosstalk of auxin and GA during tuber development. Plant Signal Behav. 2012;7:1360–3. doi: 10.4161/psb.21515 22902700

69. Fukazawa J, Mori M, Watanabe S, Miyamoto C, Ito T, Takahashi Y. DELLA-GAF1 complex is a main component in gibberellin feedback regulation of GA20 oxidase 2. Plant Physiol. 2017;175:1395–406. doi: 10.1104/pp.17.00282 28916594

70. Viola IL, Manassero NGU, Ripoll R, Gonzalez DH. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 2011;435:143–55. doi: 10.1042/BJ20101019 21241251

71. Ma X, Ma J, Fan D, Li C, Jiang Y, Luo K. Genome-wide identification of TCP family transcription factors from Populus euphratica and their involvement in leaf shape regulation. Sci Rep. 2016;6:32795. doi: 10.1038/srep32795 27605130

72. Herve C, Dabos P, Bardet C, Jauneau A, Auriac MC, Ramboer A, et al. In vivo interference with AtTCP20 function induces severe plant growth alterations and deregulates the expression of many genes important for development. Plant Physiol. 2009;149:1462–77. doi: 10.1104/pp.108.126136 19091878

73. Owens RA, Tech KB, Shao JY, Sano T, Baker CJ. Global analysis of tomato gene expression during Potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling. Mol Plant Microbe Interact. 2012;25:582–98. doi: 10.1094/MPMI-09-11-0258 22217247

74. Hellens RP, Edwards EA, Leyland NR, Bean S, Mullineaux PM. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol Biol. 2000;42:819–32. doi: 10.1023/a:1006496308160 10890530

75. Chronis D, Chen S, Lang P, Tran T, Thurston D, Wang X. Potato transformation. Bio-Protocol. 2014;4:1–8.

76. Dong Y, Burch-Smith TM, Liu Y, Mamillapalli P, Dinesh-Kumar SP. A ligation-independent cloning tobacco rattle virus vector for high-throughput virus-induced gene silencing identifies roles for NbMADS4-1 and-2 in floral development. Plant Physiol. 2007;145:1161–70. doi: 10.1104/pp.107.107391 17932306

77. Shi B, Lin L, Wang S, Guo Q, Zhou H, Rong L, et al. Identification and regulation of host genes related to Rice stripe virus symptom production. New Phytol. 2016;209:1106–19. doi: 10.1111/nph.13699 26487490

78. Sha A, Zhao J, Yin K, Tang Y, Wang Y, Wei X, et al. Virus-based microRNA silencing in plants. Plant Physiol. 2014;164:36–47. doi: 10.1104/pp.113.231100 24296072

79. Padmanabhan M, Dinesh-Kumar SP. Virus-induced gene silencing as a tool for delivery of dsRNA into plants. Cold Spring Harb Protoc. 2009;2009:pdb.prot5139.

80. Li X. Infiltration of Nicotiana benthamiana protocol for transient expression via Agrobacterium. Bio-Protocol. 2011;1:e95.

81. Yang J, Gao MX, Hu H, Ding XM, Lin HW, Wang L, et al. OsCLT1, a CRT-like transporter 1, is required for glutathione homeostasis and arsenic tolerance in rice. New Phytol. 2016;211:658–70. doi: 10.1111/nph.13908 26918637

82. Feng J, Fan P, Jiang P, Lv S, Chen X, Li Y. Chloroplast-targeted Hsp90 plays essential roles in plastid development and embryogenesis in Arabidopsis possibly linking with VIPP1. Physiol Plant. 2014;150:292–307. doi: 10.1111/ppl.12083 23875936

83. Werner S, Wollmann H, Schneeberger K, Weigel D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr Biol. 2010;20:42–8. doi: 10.1016/j.cub.2009.10.073 20015654