A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana.
Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.
Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210, USA.
Ryuta
R
Takeda
Anton I
AI
Petrov
Neocles B
NB
Leontis
Biao
B
Ding
D001483:Base Sequence; D058503:Mesophyll Cells / Q000821:virology*; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D010942:Plant Viruses / Q000235:genetics / Q000502:physiology*; D012367:RNA, Viral / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D014026:Nicotiana / Q000821:virology*; D014772:Viroids / Q000235:genetics / Q000502:physiology*
D012367:RNA, Viral
Biochim Biophys Acta. 2007 Jan;1775(1):181-232
17137717
J Mol Biol. 1998 Dec 4;284(3):591-608
9826501
Nucleic Acids Res. 2002 Aug 15;30(16):3497-531
12177293
Plant Cell. 2006 Dec;18(12):3443-57
17189340
Curr Opin Struct Biol. 2006 Jun;16(3):279-87
16713707
J Virol. 2009 Apr;83(8):3540-8
19193810
BMC Microbiol. 2006 Mar 06;6:24
16519798
Plant Cell. 2004 Aug;16(8):1979-2000
15258266
Virus Res. 2009 Sep;144(1-2):209-14
19442691
Development. 1999 Oct;126(20):4405-19
10498677
J Phys Chem B. 2009 Feb 12;113(6):1743-55
19152254
Science. 2005 Sep 2;309(5740):1508-14
16141058
Plant Cell. 2007 Apr;19(4):1179-91
17416731
Curr Opin Plant Biol. 2010 Feb;13(1):40-5
19796985
Annu Rev Phytopathol. 2005;43:117-39
16078879
J Mol Biol. 1996 Oct 11;262(5):652-70
8876645
Science. 2010 May 14;328(5980):872-5
20413459
Science. 1999 Jan 1;283(5398):94-8
9872750
PLoS One. 2009 Jun 19;4(6):e5980
19543387
J Mol Biol. 1990 Dec 5;216(3):585-610
2258934
Science. 2010 May 14;328(5980):912-6
20413458
Nat Rev Mol Cell Biol. 2008 Mar;9(3):242-53
18292779
Mol Plant Pathol. 2007 Sep;8(5):549-60
20507521
Mol Plant Microbe Interact. 2007 Jan;20(1):7-20
17249418
Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
19920124
Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
17130148
Virology. 2002 Oct 25;302(2):445-56
12441088
Nat Struct Mol Biol. 2007 Aug;14(8):727-32
17660832
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7
15215472
Trends Cell Biol. 2009 Oct;19(10):495-503
19748270
Nature. 2010 Sep 23;467(7314):415-9
20864994
BMC Plant Biol. 2010 Apr 13;10:64
20388194
DNA Cell Biol. 2009 Feb;28(2):51-6
19105595
J Biol Chem. 2010 Jun 4;285(23):17442-52
20353945
Plant Cell. 2004 Jul;16(7):1741-52
15194818
Science. 2001 Jul 13;293(5528):287-9
11452121
Biochimie. 2002 Sep;84(9):961-73
12458088
J Mol Biol. 1986 Feb 5;187(3):399-416
2422386
Annu Rev Phytopathol. 2009;47:105-31
19400635
EMBO J. 2007 Aug 22;26(16):3836-46
17660743
Curr Opin Plant Biol. 2010 Feb;13(1):59-65
19783199
Nucleic Acids Res. 2009 Apr;37(7):2294-312
19240142
Q Rev Biophys. 1998 Nov;31(4):399-455
10709244
Annu Rev Genet. 2007;41:305-30
17645412
Biol Cell. 2008 Jan;100(1):13-26
18072941
Bioinformatics. 2006 Sep 1;22(17):2168-70
16820430
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337
EMBO J. 2010 May 19;29(10):1699-712
20414198
J Mol Endocrinol. 2008 Apr;40(4):151-9
18372404
J Gen Virol. 1997 Jun;78 ( Pt 6):1199-206
9191908
Nat Cell Biol. 2007 Jun;9(6):654-9
17486113
Nature. 2010 May 20;465(7296):316-21
20410882
Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6328-33
20304794
Plant Cell Physiol. 1998 Aug;39(8):895-7
9787465
J Exp Bot. 2006;57(12):3183-93
16936221
Plant Physiol. 2008 Jun;147(2):732-46
18390805
Plant J. 2008 Mar;53(5):739-49
18005229
Genes Dev. 2009 Aug 15;23(16):1971-9
19684116
Bioinformatics. 2009 May 1;25(9):1189-91
19151095
New Phytol. 2008;179(4):1133-1141
18631294
BMC Plant Biol. 2010 Aug 04;10:159
20682080
Trends Plant Sci. 2005 Aug;10(8):376-82
16023398
Plant J. 2008 Mar;53(5):731-8
17988220
Bioessays. 2007 Jul;29(7):654-67
17563084
Plant Physiol. 2009 May;150(1):378-87
19261735
J Integr Plant Biol. 2010 Jan;52(1):40-52
20074139
RNA. 2010 Oct;16(10):1915-24
20699302
Annu Rev Plant Biol. 2009;60:207-21
19025382
Genes Dev. 2009 Mar 1;23(5):549-54
19270155
J Integr Plant Biol. 2010 Jan;52(1):28-39
20074138
Virology. 2006 Aug 1;351(2):455-65
16697024
Virology. 2001 Jan 5;279(1):69-77
11145890
Cell. 2007 Aug 10;130(3):413-26
17693253
Curr Opin Cell Biol. 2009 Aug;21(4):575-81
19442504
J Exp Bot. 2008;59(1):85-92
17905731
Cell Microbiol. 2008 Nov;10(11):2168-79
18764915
Virology. 2006 Jan 5;344(1):169-84
16364748
BMC Bioinformatics. 2008 Apr 25;9:212
18439255
J Math Biol. 2008 Jan;56(1-2):215-52
17694311
RNA. 2001 Apr;7(4):499-512
11345429
Plant J. 2005 Apr;42(1):49-68
15773853
Plant Cell. 2008 Jan;20(1):35-47
18178767
Plant J. 2008 Sep;55(5):746-59
18485061
Curr Opin Plant Biol. 2008 Dec;11(6):687-94
18977685
Plant Cell. 2009 Jan;21(1):197-215
19122103
Plant Physiol. 2007 Feb;143(2):1037-43
17189329
Plant Physiol. 2009 Dec;151(4):1831-43
19783647
J Mol Biol. 1998 Oct 30;283(3):571-83
9784367
Nucleic Acids Res. 2010 Jan;38(3):970-80
19923230
J Virol. 2006 Sep;80(17):8566-81
16912306
Plant J. 2009 Sep;59(6):921-9
19453448
J Exp Bot. 2007;58(13):3645-56
17928373