Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 2, 2015, Pages 319-325

  Fuchs, Gabriele ^a   Petrov, Alexey N ^a   Marceau, Caleb D ^a   Popov, Lauren M ^a   Chen, Jin ^a,b   OLeary, Seán E ^a   Wang, Richard ^a   Carette, Jan E ^a   Sarnow, Peter ^a   Puglisi, Joseph D ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

HCV IRES; Human ribosomes; Single molecule FRET; Translation initiation

Indexed keywords

PROTEIN TAG; RIBOSOME PROTEIN; VIRUS RNA; HYBRID PROTEIN; MESSENGER RNA; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; RPS25 PROTEIN, HUMAN;

40S RIBOSOME SUBUNIT; ARTICLE; COMPLEX FORMATION; CONFORMATION; CONTROLLED STUDY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; IN VITRO STUDY; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; RIBOSOME SUBUNIT; TRANSLATION INITIATION; AMINO ACID SEQUENCE; ANTAGONISTS AND INHIBITORS; BINDING SITE; CRISPR CAS SYSTEM; GENE INACTIVATION; GENETICS; HELA CELL LINE; HEPACIVIRUS; HOST PATHOGEN INTERACTION; KINETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PATHOGENICITY; RNA TRANSLATION; SMALL RIBOSOMAL SUBUNIT;

HEPATITIS C VIRUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; CRISPR-CAS SYSTEMS; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE KNOCKOUT TECHNIQUES; HELA CELLS; HEPACIVIRUS; HOST-PATHOGEN INTERACTIONS; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; O(6)-METHYLGUANINE-DNA METHYLTRANSFERASE; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RECOMBINANT FUSION PROTEINS; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, SMALL, EUKARYOTIC; RNA, MESSENGER; RNA, VIRAL;

EID: 84920949832     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1421328111     Document Type: Article

References (31)

1. Sonenberg N, Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: Mechanisms and biological targets. Cell 136(4):731-745.
2. Spilka R, Ernst C, Mehta AK, Haybaeck J (2013) Eukaryotic translation initiation factors in cancer development and progression. Cancer Lett 340(1):9-21.
3. Landry DM, Hertz MI, Thompson SR (2009) RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev 23(23):2753-2764.
4. Hertz MI, Landry DM, Willis AE, Luo G, Thompson SR (2013) Ribosomal protein S25 dependency reveals a common mechanism for diverse internal ribosome entry sites and ribosome shunting. Mol Cell Biol 33(5):1016-1026.
5. Marshall RA, Aitken CE, Puglisi JD (2009) GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell 35(1):37-47.
6. Tsai A, et al. (2012) Heterogeneous pathways and timing of factor departure during translation initiation. Nature 487(7407):390-393.
7. Zantema A, Maassen JA, Kriek J, Möller W (1982) Preparation and characterization of fluorescent 50S ribosomes. Specific labeling of ribosomal proteins L7/L12 and L10 of Escherichia coli. Biochemistry 21(13):3069-3076.
8. Hickerson R, Majumdar ZK, Baucom A, Clegg RM, Noller HF (2005) Measurement of internal movements within the 30 S ribosomal subunit using Förster resonance energy transfer. J Mol Biol 354(2):459-472.
9. Dorywalska M, et al. (2005) Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res 33(1):182-189.
10. Petrov A, Puglisi JD (2010) Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations. Nucleic Acids Res 38(13):e143.
11. Mali P, et al. (2013) RNA-guided human genome engineering via Cas9. Science 339(6121):823-826.
12. Carette JE, et al. (2011) Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature 477(7364):340-343.
13. Obrig TG, Culp WJ, McKeehan WL, Hardesty B (1971) The mechanism by which cycloheximide and related glutarimide antibiotics inhibit peptide synthesis on reticulocyte ribosomes. J Biol Chem 246(1):174-181.
14. Schneider-Poetsch T, et al. (2010) Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat Chem Biol 6(3):209-217.
15. Lukavsky PJ, Otto GA, Lancaster AM, Sarnow P, Puglisi JD (2000) Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Nat Struct Biol 7(12):1105-1110.
16. Ben-Shem A, et al. (2011) The structure of the eukaryotic ribosome at 3. 0 Å resolution. Science 334(6062):1524-1529.
17. Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H (2005) Structure of the hepatitis C virus IRES bound to the human 80S ribosome: Remodeling of the HCV IRES. Structure 13(11):1695-1706.
18. Fukushi S, et al. (2001) Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J Biol Chem 276(24):20824-20826.
19. Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD (2013) Coordinated conformational and compositional dynamics drive ribosome translocation. Nat Struct Mol Biol 20(6):718-727.
20. O'Leary SE, Petrov A, Chen J, Puglisi JD (2013) Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure 21(12):2197-2207.
21. Ciandrini L, Stansfield I, Romano MC (2013) Ribosome traffic on mRNAs maps to gene ontology: Genome-wide quantification of translation initiation rates and polysome size regulation. PLOS Comput Biol 9(1):e1002866.
22. Vassilenko KS, Alekhina OM, Dmitriev SE, Shatsky IN, Spirin AS (2011) Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation. Nucleic Acids Res 39(13):5555-5567.
23. Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB (2013) Rate-limiting steps in yeast protein translation. Cell 153(7):1589-1601.
24. Pérard J, Leyrat C, Baudin F, Drouet E, JaminM (2013) Structure of the full-length HCV IRES in solution. Nat Commun 4:1612.
25. Kieft JS, Zhou K, Jubin R, Doudna JA (2001) Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA 7(2):194-206.
26. Lukavsky PJ (2009) Structure and function of HCV IRES domains. Virus Res 139(2): 166-171.
27. Campeau E, et al. (2009) A versatile viral system for expression and depletion of proteins in mammalian cells. PLoS ONE 4(8):e6529.
28. Fuchs G, Diges C, Kohlstaedt LA, Wehner KA, Sarnow P (2011) Proteomic analysis of ribosomes: Translational control of mRNA populations by glycogen synthase GYS1. J Mol Biol 410(1):118-130.
29. McKenna SA, et al. (2007) Purification and characterization of transcribed RNAs using gel filtration chromatography. Nat Protoc 2(12):3270-3277.
30. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70-W74.
31. Marshall RA, Dorywalska M, Puglisi JD (2008) Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci USA 105(40): 15364-15369.