The terminal loop of a 3' proximal hairpin plays a critical role in replication and the structure of the 3' region of Turnip crinkle virus.
Plus-strand RNA viruses serve as templates for translation and then transcription by newly synthesized RdRp. A ribosome-binding tRNA-shaped structure (TSS) and upstream hairpin H4 in the 3' UTR of Turnip crinkle virus (TCV) play key roles in translation and transcription. Second-site mutations generated to compensate for altering the critical asymmetric internal loop of H4 included a three- to two-base alteration in the terminal loop of a 3' proximal hairpin (Pr) located downstream of the TSS. Unlike the non-deleterious three-base alteration, single mutations in Pr loop were detrimental for RdRp transcription while enhancing translation and RdRp binding. One deleterious mutation in the Pr loop altered the structures of both the TSS and H4. These complex interactions in the 3' UTR support a compact structural arrangement likely permitting RdRp access to a number of residues within a 195-base region including the 3' end that are necessary for efficient transcription initiation.
Yuan
Xuefeng
X
Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA.
Shi
Kerong
K
Young
Megan Y L
MY
Simon
Anne E
AE
D001483:Base Sequence; D019184:Carmovirus / Q000235:genetics / Q000502:physiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017354:Point Mutation; D014176:Protein Biosynthesis; D012330:RNA, Double-Stranded / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic; D014779:Virus Replication
D012330:RNA, Double-Stranded; D012367:RNA, Viral
J Virol. 2005 Jun;79(11):6631-43
15890901
Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1113-8
9037015
Biochim Biophys Acta. 2009 Sep-Oct;1789(9-10):571-83
19501200
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903
11296253
Virology. 2006 Aug 15;352(1):39-51
16757010
EMBO J. 2003 Oct 15;22(20):5602-11
14532132
RNA. 2009 Oct;15(10):1849-64
19656866
Virology. 2006 Aug 1;351(2):476-88
16682064
EMBO J. 1986 Dec 20;5(13):3423-8
16453740
Biochimie. 2006 Aug;88(8):993-9
16889885
J Virol. 1999 Dec;73(12):10104-12
10559325
J Virol. 2002 Feb;76(4):1707-17
11799166
J Mol Biol. 1995 Nov 17;254(1):6-14
7473759
J Gen Virol. 2006 Oct;87(Pt 10):3013-3022
16963760
RNA. 2007 Feb;13(2):267-80
17185361
Plant Cell. 1997 Nov;9(11):2051-63
9401127
Biochim Biophys Acta. 2009 Sep-Oct;1789(9-10):495-517
19781674
Virus Res. 2006 Jul;119(1):43-51
16307817
J Virol. 2006 Sep;80(18):9181-91
16940529
Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1385-90
20080629
Annu Rev Phytopathol. 2007;45:221-43
17417941
PLoS Pathog. 2009 Mar;5(3):e1000323
19266082
Annu Rev Phytopathol. 2006;44:447-67
16704356
J Virol. 2004 Jul;78(14):7619-33
15220437
Virus Res. 2009 Feb;139(2):230-9
18703097
J Virol. 2008 Sep;82(18):9008-22
18614633
Arch Virol. 1998;143(1):173-80
9505975
J Virol. 1999 Nov;73(11):8982-8
10516004
RNA. 2009 Sep;15(9):1740-52
19605533
J Virol. 2009 Jan;83(2):927-39
19004956
RNA. 2008 Nov;14(11):2379-93
18824512
Genes Dev. 1998 Aug 1;12(15):2293-304
9694795
Nucleic Acids Res. 1998 May 15;26(10):2426-32
9580696
J Virol. 2008 Sep;82(17):8706-20
18579599
RNA. 2004 Oct;10(10):1637-52
15383680
Virology. 2006 Feb 20;345(2):305-16
16298411
Virology. 1992 Jan;186(1):1-8
1727594
J Virol. 2000 Feb;74(3):1085-93
10627518