RNA Conformational Changes in the Life Cycles of RNA Viruses, Viroids, and Virus-associated RNAs

Overview

Journal Biochim Biophys Acta

Specialties Biochemistry
Biophysics

Date 2009 Jun 9

PMID 19501200

Citations 27

Authors

Anne E Simon

Lee Gehrke

Affiliations

Soon will be listed here.

Abstract

The rugged nature of the RNA structural free energy landscape allows cellular RNAs to respond to environmental conditions or fluctuating levels of effector molecules by undergoing dynamic conformational changes that switch on or off activities such as catalysis, transcription or translation. Infectious RNAs must also temporally control incompatible activities and rapidly complete their life cycle before being targeted by cellular defenses. Viral genomic RNAs must switch between translation and replication, and untranslated subviral RNAs must control other activities such as RNA editing or self-cleavage. Unlike well characterized riboswitches in cellular RNAs, the control of infectious RNA activities by altering the configuration of functional RNA domains has only recently been recognized. In this review, we will present some of these molecular rearrangements found in RNA viruses, viroids and virus-associated RNAs, relating how these dynamic regions were discovered, the activities that might be regulated, and what factors or conditions might cause a switch between conformations.

Citing Articles

Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency.

Endoh T, Sugimoto N Molecules. 2019; 24(8).

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RNA Structural Differentiation: Opportunities with Pattern Recognition.

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SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants.

Bayne C, Widawski M, Gao F, Masab M, Chattopadhyay M, Murawski A Virology. 2018; 520:137-152.

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Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

Lin L, McKerrow W, Richards B, Phonsom C, Lawrence C BMC Bioinformatics. 2018; 19(1):82.

PMID: 29506466 PMC: 5836418. DOI: 10.1186/s12859-018-2078-5.

Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch.

Le M, Kasprzak W, Kim T, Gao F, Young M, Yuan X Elife. 2017; 6.

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References

Hsue B, Masters P . A bulged stem-loop structure in the 3' untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J Virol. 1997; 71(10):7567-78. PMC: 192104. DOI: 10.1128/JVI.71.10.7567-7578.1997. View

Houwing C, Jaspars E . Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus. Biochemistry. 1978; 17(14):2927-33. DOI: 10.1021/bi00607a035. View

Paillart J, Dettenhofer M, Yu X, Ehresmann C, Ehresmann B, Marquet R . First snapshots of the HIV-1 RNA structure in infected cells and in virions. J Biol Chem. 2004; 279(46):48397-403. DOI: 10.1074/jbc.M408294200. View

Chao L, Rang C, Wong L . Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage phi6. J Virol. 2002; 76(7):3276-81. PMC: 136006. DOI: 10.1128/jvi.76.7.3276-3281.2002. View

Uzri D, Gehrke L . Nucleotide sequences and modifications that determine RIG-I/RNA binding and signaling activities. J Virol. 2009; 83(9):4174-84. PMC: 2668486. DOI: 10.1128/JVI.02449-08. View

Song C, Simon A . Requirement of a 3'-terminal stem-loop in in vitro transcription by an RNA-dependent RNA polymerase. J Mol Biol. 1995; 254(1):6-14. DOI: 10.1006/jmbi.1995.0594. View

Tinoco Jr I, Bustamante C . How RNA folds. J Mol Biol. 1999; 293(2):271-81. DOI: 10.1006/jmbi.1999.3001. View

Lai M, Cavanagh D . The molecular biology of coronaviruses. Adv Virus Res. 1997; 48:1-100. PMC: 7130985. View

Guogas L, Filman D, Hogle J, Gehrke L . Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication. Science. 2004; 306(5704):2108-11. PMC: 1500904. DOI: 10.1126/science.1103399. View

10.

Bamming D, Horvath C . Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem. 2009; 284(15):9700-12. PMC: 2665091. DOI: 10.1074/jbc.M807365200. View

11.

Schroder A, Riesner D . Detection and analysis of hairpin II, an essential metastable structural element in viroid replication intermediates. Nucleic Acids Res. 2002; 30(15):3349-59. PMC: 137078. DOI: 10.1093/nar/gkf454. View

12.

DSouza V, Summers M . Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature. 2004; 431(7008):586-90. DOI: 10.1038/nature02944. View

13.

Landick R . The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans. 2006; 34(Pt 6):1062-6. DOI: 10.1042/BST0341062. View

14.

Vilfan I, Candelli A, Hage S, Aalto A, Poranen M, Bamford D . Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate. Nucleic Acids Res. 2008; 36(22):7059-67. PMC: 2602768. DOI: 10.1093/nar/gkn836. View

15.

Olsthoorn R, Mertens S, Brederode F, Bol J . A conformational switch at the 3' end of a plant virus RNA regulates viral replication. EMBO J. 1999; 18(17):4856-64. PMC: 1171557. DOI: 10.1093/emboj/18.17.4856. View

16.

Fukuyama K, Abdel-Meguid S, Rossmann M . Crystallization of alfalfa mosaic virus coat protein as a T = 1 aggregate. J Mol Biol. 1981; 150(1):33-41. DOI: 10.1016/0022-2836(81)90323-5. View

17.

Lai M . The molecular biology of hepatitis delta virus. Annu Rev Biochem. 1995; 64:259-86. DOI: 10.1146/annurev.bi.64.070195.001355. View

18.

Boyce M, Scott F, Guogas L, Gehrke L . Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex. J Mol Recognit. 2005; 19(1):68-78. DOI: 10.1002/jmr.759. View

19.

Alvarez D, Lodeiro M, Luduena S, Pietrasanta L, Gamarnik A . Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol. 2005; 79(11):6631-43. PMC: 1112138. DOI: 10.1128/JVI.79.11.6631-6643.2005. View

20.

Zhang J, Stuntz R, Simon A . Analysis of a viral replication repressor: sequence requirements for a large symmetrical internal loop. Virology. 2004; 326(1):90-102. DOI: 10.1016/j.virol.2004.05.006. View