A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.

Szczegóły
Abstrakt

Tytuł:: A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.
Autorzy:: Koirala D; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Shao Y; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Koldobskaya Y; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Fuller JR; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Watkins AM; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Shelke SA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Pilipenko EV; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Rice PA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
Piccirilli JA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .; Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. .
Źródło:: Nature communications [Nat Commun] 2019 Aug 09; Vol. 10 (1), pp. 3629. Date of Electronic Publication: 2019 Aug 09.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Język:: English
Imprint Name(s):: Original Publication: [London] : Nature Pub. Group
MeSH Terms:: Conserved Sequence*
Internal Ribosome Entry Sites/*physiology
Nucleotide Motifs/*physiology
Picornaviridae/*physiology
RNA, Viral/*chemistry
RNA, Viral/*physiology
Base Sequence ; Foot-and-Mouth Disease Virus/genetics ; Foot-and-Mouth Disease Virus/metabolism ; Hepatitis A virus ; Internal Ribosome Entry Sites/immunology ; Molecular Chaperones ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Viral/metabolism ; Ribosomes/chemistry ; Ribosomes/metabolism
References:: Curr Opin Struct Biol. 2009 Jun;19(3):267-76. (PMID: 19362464)
RNA. 2006 Oct;12(10):1755-85. (PMID: 16957278)
EMBO J. 1997 Jul 1;16(13):4107-16. (PMID: 9233819)
Science. 1999 May 14;284(5417):1171-4. (PMID: 10325228)
J Virol. 1994 Aug;68(8):5253-63. (PMID: 8035522)
Nat Struct Mol Biol. 2016 Sep;23(9):859-64. (PMID: 27525590)
Science. 2016 Jun 17;352(6292):1413-6. (PMID: 27313038)
J Gen Virol. 2004 Sep;85(Pt 9):2555-2565. (PMID: 15302949)
Annu Rev Microbiol. 2013;67:21-42. (PMID: 23682606)
Int J Mol Sci. 2017 Jan 04;18(1):. (PMID: 28054974)
RNA. 2008 Jan;14(1):134-47. (PMID: 18025255)
Nat Methods. 2010 Apr;7(4):291-4. (PMID: 20190761)
Virus Res. 2006 Jul;119(1):76-88. (PMID: 16303201)
J Virol. 1995 Jul;69(7):4399-406. (PMID: 7769702)
Q Rev Biophys. 2013 Aug;46(3):223-64. (PMID: 23915736)
Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):82-7. (PMID: 18162543)
Nucleic Acids Res. 1989 Jul 25;17(14):5701-11. (PMID: 2548167)
J Biol Chem. 2009 May 22;284(21):14189-202. (PMID: 19276085)
RNA. 2003 Mar;9(3):355-63. (PMID: 12592009)
Methods. 2001 Mar;23(3):201-5. (PMID: 11243833)
J Mol Biol. 2016 Oct 9;428(20):4100-4114. (PMID: 27593161)
Sci Adv. 2018 May 25;4(5):eaar5316. (PMID: 29806027)
Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9611-9616. (PMID: 28827335)
Curr Opin Virol. 2011 Nov;1(5):373-80. (PMID: 22440838)
J Virol. 1994 Feb;68(2):1066-74. (PMID: 8289336)
Structure. 2011 Jun 8;19(6):868-80. (PMID: 21645857)
Oncogene. 2016 Feb 25;35(8):1015-24. (PMID: 25961916)
Cold Spring Harb Protoc. 2013 Nov 01;2013(11):. (PMID: 24184761)
Cell. 2014 May 8;157(4):823-31. (PMID: 24792965)
Nat Chem Biol. 2014 Jan;10(1):56-60. (PMID: 24240507)
Science. 2016 Jan 15;351(6270):. (PMID: 26816383)
Gene. 2012 Jul 10;502(2):75-86. (PMID: 22555019)
J Virol. 1991 Nov;65(11):5828-38. (PMID: 1656072)
J Mol Biol. 2007 Sep 21;372(3):774-97. (PMID: 17681537)
Nat Rev Microbiol. 2019 Jan;17(2):110-123. (PMID: 30514982)
J Mol Biol. 2003 Jan 3;325(1):65-83. (PMID: 12473452)
Biochim Biophys Acta. 2009 Sep-Oct;1789(9-10):529-41. (PMID: 19439208)
Nature. 2015 Jan 1;517(7532):85-88. (PMID: 25327248)
Genes Dev. 2000 Aug 15;14(16):2028-45. (PMID: 10950867)
J Gen Virol. 2001 Apr;82(Pt 4):757-763. (PMID: 11257179)
RNA. 2000 Oct;6(10):1380-92. (PMID: 11073214)
Virology. 1989 Feb;168(2):201-9. (PMID: 2536978)
Nat Commun. 2015 Jul 08;6:7646. (PMID: 26155016)
Virology. 1997 Oct 13;237(1):129-36. (PMID: 9344915)
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002)
Microbiol Spectr. 2018 Jul;6(4):. (PMID: 29992899)
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. (PMID: 20124702)
Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716):. (PMID: 28138065)
Biochemistry. 2016 Aug 30;55(34):4748-63. (PMID: 27490953)
Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. (PMID: 29112718)
J Virol. 1987 Jan;61(1):50-9. (PMID: 3023706)
Nat Methods. 2009 Aug;6(8):606-12. (PMID: 19620974)
Annu Rev Virol. 2016 Sep 29;3(1):283-307. (PMID: 27501262)
Virus Res. 2015 Aug 3;206:62-73. (PMID: 25617758)
Mol Cell Biol. 2000 Aug;20(16):6019-29. (PMID: 10913184)
RNA. 1996 Dec;2(12):1199-212. (PMID: 8972770)
J Mol Biol. 2006 Apr 14;357(5):1566-74. (PMID: 16497332)
Curr Opin Virol. 2015 Jun;12:113-20. (PMID: 26004307)
Nat Rev Microbiol. 2007 Jan;5(1):29-38. (PMID: 17128284)
Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):13-20. (PMID: 8552589)
Nat Struct Mol Biol. 2011 Jan;18(1):100-6. (PMID: 21151117)
Nat Struct Mol Biol. 2006 Dec;13(12):1092-6. (PMID: 17115051)
Virology. 1993 Apr;193(2):842-52. (PMID: 8384758)
RNA. 2006 Jan;12(1):83-93. (PMID: 16373494)
Nature. 2015 Jan 1;517(7532):33-8. (PMID: 25409156)
Nat Chem Biol. 2014 Aug;10(8):686-91. (PMID: 24952597)
RNA Biol. 2013 Dec;10(12):1842-52. (PMID: 24253111)
J Virol. 2013 Feb;87(3):1872-83. (PMID: 23192876)
Nat Rev Drug Discov. 2002 Nov;1(11):867-81. (PMID: 12415247)
Science. 2006 Dec 1;314(5804):1450-4. (PMID: 17124290)
Nucleic Acids Res. 2018 Mar 16;46(5):2624-2635. (PMID: 29309709)
Methods. 2013 Mar 15;60(1):3-14. (PMID: 23280336)
Grant Information:: P41 GM103403 United States GM NIGMS NIH HHS; R01 AI081987 United States AI NIAID NIH HHS; R01 GM102489 United States GM NIGMS NIH HHS; R35 GM122579 United States GM NIGMS NIH HHS
Substance Nomenclature:: 0 (Internal Ribosome Entry Sites)
0 (Molecular Chaperones)
0 (RNA, Viral)
Entry Date(s):: Date Created: 20190811 Date Completed: 20191212 Latest Revision: 20210514
Update Code:: 20240104
PubMed Central ID:: PMC6689051
DOI:: 10.1038/s41467-019-11585-z
PMID:: 31399592
: Czasopismo naukowe

Full Text Finder

Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment-a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.

Informacja