A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana

English version

Autoři: Jian Wu ^aff001; Neocles B. Leontis ^aff002; Craig L. Zirbel ^aff003; David M. Bisaro ^aff001; Biao Ding ^aff001
Působiště autorů: Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Infectious Diseases Institute, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, United States of ^aff001; Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America ^aff002; Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio, United States of America ^aff003
Vyšlo v časopise: A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana. PLoS Pathog 15(10): e32767. doi:10.1371/journal.ppat.1008147
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008147

Souhrn

Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177–182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.

Klíčová slova:

Histones – Leaves – RNA extraction – RNA structure – Sequence motif analysis – RNA stem-loop structure – Viroids – Palisade mesophyll

Zdroje

1. Lucas WJ, Ham B-K, Kim J-Y. Plasmodesmata- bridging the gap between neighboring plant cells. Trends Cell Biol. 2009;19:495–503. doi: 10.1016/j.tcb.2009.07.003 19748270

2. Hyun TK, Uddin MN, Rim Y, Kim J-Y. Cell-to-cell trafficking of RNA and RNA silencing through plasmodesmata. Protoplasma. 2011;248:101–16. doi: 10.1007/s00709-010-0225-6 21042816

3. Ham B-K, Lucas WJ. Phloem-mobile RNAs as systemic signaling agents. Annu Rev Plant Biol. 2017;68:173–95. doi: 10.1146/annurev-arplant-042916-041139 28125282

4. Banerjee AK, Chatterjee M, Yu Y, Suh S-G, Miller WA, Hannapel DJ. Dynamics of a mobile RNA of potato involved in a long-distance signaling pathway. The Plant Cell. 2006;18:3443–57. doi: 10.1105/tpc.106.042473 17189340

5. Mahajan A, Bhogale S, Kang IH, Hannapel DJ, Banerjee AK. The mRNA of a Knotted1-like transcription factor of potato is phloem-mobile. Plant Molecular Biology. 2012;79:595–608. doi: 10.1007/s11103-012-9931-0 22638904

6. Lin T, Sharma P, Gonzalez DH, Viola IL, Hannapel DJ. The impact of long-distance transport of a Bel-1-like messenger RNA on development. Plant Physiol. 2013;161:760–72. doi: 10.1104/pp.112.209429 23221774

7. Kim M, Canio W, Kessler S, Sinha N. Developmental changes due to long-distance movement of a homeobox fusion transcript in tomato. Science. 2001;293:287–9. doi: 10.1126/science.1059805 11452121

8. Haywood V, Yu TS, Huang NC, Lucas WJ. Phloem long-distance trafficking of GIBBERELLIC ACID-INSENSITIVE RNA regulates leaf development. Plant J. 2005;42:49–68. doi: 10.1111/j.1365-313X.2005.02351.x 15773853

9. Deeken R, Ache P, Kajahn I, Klinkenberg J, Bringmann G, Hedrich R. Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments. Plant J. 2008;55:746–59. doi: 10.1111/j.1365-313X.2008.03555.x 18485061

10. Guo S, Zhang J, Sun H, Salse J, Lucas WJ, al. e. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet. 2013;45:51–8. doi: 10.1038/ng.2470 23179023

11. Zhang Z, Zheng Y, Ham BK, Chen J, Yoshida A, Kochian LV, et al. Vascular-mediated signalling involved in early phosphate stress response in plants. Nat Plants. 2016;2:16033. doi: 10.1038/nplants.2016.33 27249565

12. Yoo BC, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee YM, et al. A systemic small RNA signaling system in plants. The Plant Cell. 2004;16:1979–2000. doi: 10.1105/tpc.104.023614 15258266

13. Buhtz A, Springer F, Chappell L, Baulcombe DC, Kehr J. Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J. 2008;53:739–49. doi: 10.1111/j.1365-313X.2007.03368.x 18005229

14. Ham B-K, Li G, Jia W, Leary JA, Lucas WJ. Systemic delivery of siRNA in pumpkin by a plant PHLOEM SMALL RNA-BINDING PROTEIN 1-ribonucleoprotein complex. Plant J. 2014;80:683–94. doi: 10.1111/tpj.12662 25227635

15. Chitwood DH, Nogueira FTS, Howell MD, Montgomery TA, Carrington JC, Timmermans MCP. Pattern formation via small RNA mobility. Genes Dev. 2009;23:549–54. doi: 10.1101/gad.1770009 19270155

16. Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, et al. Small RNA duplexes function as mobile silencing signals between plant cells. Science. 2010;328:912–6. doi: 10.1126/science.1185880 20413458

17. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science. 2010;328:872–5. doi: 10.1126/science.1187959 20413459

18. Ding S-W, Voinnet O. Antiviral immunity directed by small RNAs. Cell. 2007;130:413–26. doi: 10.1016/j.cell.2007.07.039 17693253

19. Raja P, Wolf JN, Bisaro DM. RNA silencing directed against geminiviruses: post-transcriptional and epigenetic components. Biochim Biophys Acta. 2010;1799:337–51. doi: 10.1016/j.bbagrm.2010.01.004 20079472

20. Matzke MA, Mosher RA. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet. 2014;15:394–408. doi: 10.1038/nrg3683 24805120

21. Roney JK, Khatibi PA, Westwood JH. Cross-species translocation of mRNA from host plants into the parasitic plant dodder. Plant Physiol. 2007;143:1037–43. doi: 10.1104/pp.106.088369 17189329

22. Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science. 2014;345:808–11. doi: 10.1126/science.1253122 25124438

23. Weiberg A, Wang M, Lin F-M, Zhao H, Zhang Z, Kaloshian I, et al. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science. 2013;342:118–23. doi: 10.1126/science.1239705 24092744

24. Zhang T, Zhao YL, Zhao JH, Wang S, Jin Y, Chen ZQ, et al. Cotton plants export microRNAs to inhibit virulence gene expression in a fungal pathogen. Nat Plants. 2016;2:16153. doi: 10.1038/nplants.2016.153 27668926

25. Lucas WJ. Plant viral movement proteins: Agents for cell-to-cell trafficking of viral genomes. Virology. 2006;344:169–84. doi: 10.1016/j.virol.2005.09.026 16364748

26. Ding B, Itaya A. Viroid: a useful model for studying the basic principles of infection and RNA biology. Molecular Plant-Microbe Interactions. 2007;20:7–20. doi: 10.1094/MPMI-20-0007 17249418

27. Ding B. The biology of viroid-host interactions. Annual Review of Phytopathology. 2009;47:105–31. doi: 10.1146/annurev-phyto-080508-081927 19400635

28. Flores R, Gago-Zachert S, Serra P, Sanjuán R, Elena SF. Viroids: Survivors from the RNA world? Annu Rev Microbiol. 2014;68:395–414. doi: 10.1146/annurev-micro-091313-103416 25002087

29. Qi Y, Pelissier T, Itaya A, Hunt E, Wassenegger M, Ding B. Direct role of a viroid RNA motif in mediating directional RNA trafficking across a specific cellular boundry. The Plant Cell. 2004;16:1741–52. doi: 10.1105/tpc.021980 15194818

30. Zhong X, Tao X, Stombaugh J, Leontis N, Ding B. Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking. The EMBO Journal. 2007;26:3836–46. doi: 10.1038/sj.emboj.7601812 17660743

31. Takeda R, Petrov AI, Leontis NB, Ding B. A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. The Plant Cell. 2011;23:258–72. doi: 10.1105/tpc.110.081414 21258006

32. Jiang D, Wang M, Li S. Functional analysis of a viroid RNA motif mediating cell-to-cell movement in Nicotiana benthamiana. Journal of General Virology. 2017;98:121–5. doi: 10.1099/jgv.0.000630 27902342

33. Takeda R, Zirbel CL, Leontis NB, Wang Y, Ding B. Allelic RNA motifs in regulating systemic trafficking of Potato spindle tuber viroid. Viruses. 2018;10:160. doi: 10.3390/v10040160 29601476

34. Williams AS, Ingledue III TC, Kay BK, Marzluff WF. Changes in the stem-loop at the 3’ terminus of histone mRNA affects its nucleocytoplasmic transport and cytoplasmic regulation. Nucleic Acids Research. 1994;22:4660–6. doi: 10.1093/nar/22.22.4660 7984415

35. Zanier K, Luyten I, Crombie C, Müller B, Schümperli D, Linge JP, et al. Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression. RNA. 2002;8:29–46. doi: 10.1017/s1355838202014061 11871659

36. Skrajna A, Yang X-C, Bucholc K, Zhang J, Tanaka Hall TM, Dadlez M, et al. U7 snRNP is recruited to histone pre-mRNA in a FLASH-dependent manner by two separate regions of stem-loop binding protein. RNA. 2017;23:938–51. doi: 10.1261/rna.060806.117 28289156

37. Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. Nucleic Acids Research. 2016;44:W320–W7. doi: 10.1093/nar/gkw453 27235417

38. Flores R, Hernández C, Martínez de Alba AE, Daròs J-A, Di Serio F. Viroids and viroid-host interactions. Annual Review of Phytopathology. 2005;43:117–39. doi: 10.1146/annurev.phyto.43.040204.140243 16078879

39. Visvader JE, Gould AR, Bruening GE, Symons RH. Cirus exocortis viroid: Nucleotide sequence and secondary structure of an Australian isolate. FEBS Lett. 1982;137:288–92. doi: 10.1016/0014-5793(82)80369-4 15768484

40. Spieker RL. The molecular structure of Iresene viroid, a new viroid species from Iresine herbstii (‘beefsteak plant’). Journal of General Virology. 1996;77:2631–5. doi: 10.1099/0022-1317-77-10-2631 8887500

41. Nie X. Analysis of sequence polymorphism and population structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in viroid-infected tomato plants. Viruses. 2012;4:940–53. doi: 10.3390/v4060940 22816033

42. Leontis NB, Stombaugh J, Westhof E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Research. 2002;30:3497–531. doi: 10.1093/nar/gkf481 12177293

43. Gast FU, Kempe D, Spieker RL, Sänger HL. Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base pairs, large A-rich loops, and a terminal branch. Journal of Molecular Biology. 1996;262:652–70. doi: 10.1006/jmbi.1996.0543 8876645

44. Giguere T, Adkar-Purushothama CR, Perreault JP. Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae. PLoS One. 2014;9:e98655. doi: 10.1371/journal.pone.0098655 24897295

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

46. Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB. Characterizing RNA structures in vitro and in vivo with selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Methods. 2016;103:34–48. doi: 10.1016/j.ymeth.2016.04.002 27064082

47. López-Carrasco A, Flores R. Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A “naked” rod-like confomation similar but not identical; to that observed in vitro. RNA Biol. 2017;14:1046–54. doi: 10.1080/15476286.2016.1223005 27574720

48. Liang Y-H, Lavoie M, Comeau M-A, Elena SA, Ji X. Structure of a eukaryotic RNase III postcleavage complex reveals a doubler-ruler mechanism for substrate selection. Mol Cell. 2014;54:431–44. doi: 10.1016/j.molcel.2014.03.006 24703949

49. Noller HF. RNA structure: Reading the ribosome. Science. 2005;309:1508–14. doi: 10.1126/science.1111771 16141058

50. Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008;9:242–53. doi: 10.1038/nrm2352 18292779

51. Baumstark T, Schröder AR, Riesner D. Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. The EMBO Journal. 1997;16:599–610. doi: 10.1093/emboj/16.3.599 9034342

52. Müller K, Lindauer A, Brüderlein M, Schmitt R. Organization and transcription of Volvox histone-encoding genes: similarities between algal and animal genes. Gene. 1990;93:167–75. doi: 10.1016/0378-1119(90)90221-c 2227431

53. Fabry S, Müller K, Lindauer A, Park PB, Cornelius T, Schmitt R. The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes. Curr Genet. 1995;28:333–45. doi: 10.1007/bf00326431 8590479

54. Zhong X, Archual AJ, Amin AA, Ding B. A genomic map of viroid RNA motifs critical for replication and systemic trafficking. The Plant Cell. 2008;20:35–47. doi: 10.1105/tpc.107.056606 18178767

55. Lucas WJ, Yoo BC, Kragler F. RNA as a long-distance information macromolecule in plants. Nat Rev Mol Cell Biol. 2001;2:849–57. doi: 10.1038/35099096 11715051

56. Ding B, Itaya A, Qi Y. Symplastic protein and RNA traffic: Regulatory points and regulatory factors. Current Opinion in Plant Biology. 2003;6:596–602. doi: 10.1016/j.pbi.2003.09.010 14611959

57. Ding B, Kwon M-O, Hammond R, Owens R. Cell-to-cell movement of potato spindle tuber viroid. Plant J. 1997;12:931–6. doi: 10.1046/j.1365-313x.1997.12040931.x 9375403

58. Lee J-Y, Lu H. Plasmodesmata: the battleground against intruders. Trends Plant Sci. 2011;16:201–10. doi: 10.1016/j.tplants.2011.01.004 21334962

59. Burch-Smith TM, Zambryski PC. Plasmodesmata paradigm shift: regulation from without versus within. Annu Rev Plant Biol. 2012;63. doi: 10.1146/annurev-arplant-042811-105453 22136566

60. Wu S-W, Kumar R, Iswanto ABB, Kim J-Y. Callose balancing at plasmodesmata. J Exp Bot. 2018;69:5325–39. doi: 10.1093/jxb/ery317 30165704

61. Muhlbach HP, Sanger HL. Viroid replication is inhibited by alpha-amanitin. Nature. 1979;278:185–8. doi: 10.1038/278185a0 763366

62. Schindler IM, Mühlbach HP. Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication:a reevaluation. Plant Science. 1992;84:221–9. doi: 10.1016/0168-9452(92)90138-C

63. Rackwitz HR, Rohde W, Sanger HL. DNA-dependent RNA polymerase II of plant origin transcribes viroid RNA into full-length copies. Nature. 1981;291:297–301. doi: 10.1038/291297a0 7231549

64. Bojić T, Beeharry Y, Zhang DJ, Pelchat M. Tomato RNA polymerase II interacts with the rod-like conformation of the left terminal domain of the potato spindle tuber viroid positive RNA genome. Journal of General Virology. 2012;93:1591–600. doi: 10.1099/vir.0.041574-0 22422064

65. Wang Y, Qu J, Ji S, Wallace AJ, Wu J, Li Y, et al. A land plant-specific transcription factor directly enhances transcription of a pathogenic noncoding RNA template by DNA-dependent RNA polymerase II. The Plant Cell. 2016;28:1094–107. doi: 10.1105/tpc.16.00100 27113774

66. Hammond MC, Wachter A, Breaker RR. A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol. 2009;16:541–9. doi: 10.1038/nsmb.1588 19377483

67. Eiras M, Nohales MA, Katajima EW, Flores R, Daros JA. Ribosomal protein L5 and transcription factor IIIA from Arabidopsis thaliana bind in vitro specifically Potato spindle tuber viroid RNA. Archives of Virology. 2011;156:529–33. doi: 10.1007/s00705-010-0867-x 21153748

68. Jiang J, Smith HN, Ren D, Dissanayaka Mudiyanselage SD, Dawe AL, Wang L, et al. Potato spindle tuber viroid modulates its replication through a direct interaction with a splicing regulator. Journal of Virology. 2018;92:e01004–18. doi: 10.1128/JVI.01004-18 30068655

69. Gozmanova M, Denti MA, Minkov IN, Tsagris M, Tabler M. Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1. Nucleic Acids Research. 2003;31:5534–43. doi: 10.1093/nar/gkg777 14500815

70. Kalantidis K, Denti MA, Tzortzakaki S, Marinou E, Tabler M, Tsagris M. Virp1 is a host protein with a major role in Potato spindle tuber viroid infection in Nicotiana plants. Journal of Virology. 2007;81:12872–80. doi: 10.1128/JVI.00974-07 17898061

71. Wang Y, Zirbel CL, Leontis NB, Ding B. RNA 3-dimensional structural motifs as a critical constraint of viroid evolution. PLoS Pathog. 2018;14:e1006801. doi: 10.1371/journal.ppat.1006801 29470541

72. Tijerina P, Mohr S, Russell R. DMS footprinting of structured RNAs and RNA-protein complexes. Nature Protocols. 2007;2:2608–23. doi: 10.1038/nprot.2007.380 17948004

73. Karabiber F, McGinnis JL, Favorov OV, Weeks KM. QuShape: Rapid, accurate, and best-practices quantitation of nucleic acid probing information, resolved by capillary electrophoresis. RNA. 2013;19:63–73. doi: 10.1261/rna.036327.112 23188808

74. Reuter JS, Mathews DH. RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010;11:129-2105-11-129.

75. Hu Y, Feldstein PA, Hammond J, Hammond RW, Bottino PJ, Owens RA. Destabilization of potato spindle tuber viroid by mutations in the left terminal loop Journal of General Virology. 1997;78:1199–206. doi: 10.1099/0022-1317-78-6-1199 9191908

76. Qi Y, Ding B. Replication of Potato spindle tuber viroid in cultured cells of tobacco and Nicotiana benthamiana: the role of specific nucleotides in determining replication levels for host adaptation. Virology. 2002;302:445–56. doi: 10.1006/viro.2002.1662 12441088

77. Beaudry D, Perreault JP. An efficient strategy for the synthesis of circular RNA molecules. Nucleic Acids Research. 1995;23:3064–6. doi: 10.1093/nar/23.15.3064 7544891

78. Negrutiu I, Shillito R, Potrykus I, Biasini G, Sala F. Hybrid genes in the analysis of transformation conditions I. Setting up a simple method for direct gene transfer in plant protoplasts. Plant Molecular Biology. 1987;8:363–73. doi: 10.1007/BF00015814 24301258

79. Zhong X, Leontis N, Qian S, Itaya A, Qi Y, Boris-Lawrie K, et al. Tertiary structural and functional analysis of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication. Journal of Virology. 2006;80:8566–81. doi: 10.1128/JVI.00837-06 16912306

80. Zhu Y, Green L, Woo Y-M, Owens RA, Ding B. Cellular basis of Potato spindle tuber viroid systemic movement. Virology. 2001;279:69–77. doi: 10.1006/viro.2000.0724 11145890

81. Traas J. Whole-mount in situ hybridization of RNA probes to plant tissues. CSH Protocols. 2008;3: doi: 10.1101/pdb.prot4944 21356775