Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site

Nucleic Acids Research

Volumn 35, Issue 5, 2007, Pages 1514-1521

  Nishiyama, Takashi ^a   Yamamoto, Hiroshi ^b   Uchiumi, Toshio ^b   Nakashima, Nobuhiko ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b NIIGATA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EXPORTIN 1; MUTANT PROTEIN; PROTEIN S 5; PROTEIN S25; RIBOSOME PROTEIN; RIBOSOME RNA; RNA 18S; RNA 40S; SPACER DNA; UNCLASSIFIED DRUG; URIDINE;

ARTICLE; CONTROLLED STUDY; ELECTRON MICROSCOPY; EUKARYOTE; INTERNAL RIBOSOME ENTRY SITE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SITE DIRECTED MUTAGENESIS;

ANIMALS; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; DROSOPHILA PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROTEIN BINDING; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSOMAL PROTEINS; RIBOSOMES; RNA VIRUSES; RNA, RIBOSOMAL, 18S; RNA, VIRAL; URIDINE;

EUKARYOTA; PROKARYOTA;

EID: 34247105689     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1121     Document Type: Article

References (39)

1. Christian,P., Carstens,E., Domier,L., Johnson,L., Johnson,K., Nakashima,N., Scotti,P. and van der Wilk,F. (2005). Dicistroviridae. In Fauquet,CM, Mayo,MA, Maniloff,J, Desselberger,U and Ball,LA (eds), Virus Taxonomy VIII Elsevier Academic Press, San Diego, pp. 783-788.
2. Sasaki,J. and Nakashima,N. (1999) Translation initiation at the CUU codon is mediated by the internal ribosome entry site of an insect picorna-like virus in vitro. J. Virol., 73, 1219-1226.
3. Sasaki,J. and Nakashima,N. (2000) Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc. Natl. Acad. Sci. U.S.A., 97, 1512-1515.
4. Wilson,J.E., Pestova,T.V., Hellen,C.U.T. and Sarnow,P. (2000) Initiation of protein synthesis from the A site of the ribosome. Cell, 102 511-520.
5. Kanamori,Y. and Nakashima,N. (2001) A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA, 7, 266-274.
6. Pestova,T.V., Kolupaeva,V.G., Lomakin,I.B., Pilipenko,E.V., Shatsky,I.N., Agol,V.I. and Hellen,C.U.T. (2001) Molecular mechanisms of translation initiation in eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 98, 7029-7036.
7. Jan,E. and Sarnow,P. (2002) Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J. Mol. Biol., 324, 889-892.
8. Pestova,T.V. and Hellen,C.U.T. (2003) Translation elongation after assembly of ribosomes on the cricket paralysis virus internal ribosome entry site without initiation factors or initiator tRNA. Genes Dev. 17, 181-186.
9. Nishiyama,T., Yamamoto,H., Shibuya,N., Hatakeyama,Y., Hachimori,A., Uchiumi,T. and Nakashima,N. (2003) Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res., 31, 2434-2442.
10. Pestova,T.V., Lomakin,I.B. and Hellen,C.U.T. (2004) Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly. EMBO Rep., 5, 906-913.
11. Shibuya,N., Nishiyama,T., Kanamori,Y., Saito,H. and Nakashima,N. (2003) Conditional rather than absolute requirements of the capsid coding sequence for initiation of methionine-independent translation in Plautia stali intestine virus. J. Virol., 77, 12002-12010.
12. Spahn,C.M.T., Jan,E., Mulder,A., Grassucci,R.A., Sarnow,P. and Frank,J. (2004) Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: The IRES functions as an RNA-based translation factor. Cell, 118, 465-475.
13. Bradford,C.T. and Sullivan,D.T. (1981) Isolation of polysomes from larval and adult Drosophila melanogaster. Anal. Biochem., 112, 176-181.
14. Blobel,G. and Sabatini,D. (1971) Dissociation of mammalian polyribosomes into subunits by puromycin. Proc. Natl. Acad. Sci. U.S.A., 68, 390-394.
15. Nakashima,N., Sasaki,J. and Toriyama,S. (1999) Determining the nucleotide sequence and capsid-coding region of himetobi P virus: A member of a novel group of RNA viruses that infect insects. Arch. Virol., 144, 2051-2058.
16. Dubreuil,Y.L., Expert-Bezançon,A. and Favre,A. (1991) Conformation and structural fluctuations of a 218 nucleotides long rRNA fragment: 4-thiouridine as an intrinsic photolabelling probe. Nucleic Acids Res., 19, 3653-3660.
17. Hardy,S.J., Kurland,C.G., Voynow,P. and Mora,G. (1969) The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry, 8, 2897-2905.
18. Wada,A. (1986) Analysis of Escherichia coli ribosomal proteins by an improved two dimensional gel electrophoresis. I Detection of four new proteins. J. Biochem. (Tokyo), 100, 1583-1594.
19. Moazed,D. and Noller,H.F. (1986) Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985-994.
20. Hatakeyama,Y., Shibuya,N., Nishiyama,T. and Nakashima,N. (2004) Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA, 10, 779-786.
21. Favre,A., Saintome,C., Fourrey,J.L., Clivio,P. and Laugaa,P. (1998) Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. J. Photochem. Photobiol. B., 42, 109-124.
22. Costantino,D. and Kieft,J.S. (2005) A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA, 11, 332-343.
23. van de Peer,Y., de Rijk,P., Wuyts,J., Winkelmans,T. and de Wachter,R. (2000) The European small subunit ribosomal RNA database. Nucleic Acids Res., 28, 175-176.
24. Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5 A ̊resolution. Science, 292, 868-869.
25. Fukushi,S., Okada,M., Stahl,J., Kageyama,T., Hoshino,H.B. and Katayama,K. (2001) Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J. Biol. Chem., 276 20824-20826.
26. Lancaster,A.M., Jan,E. and Sarnow,P. (2006) Initiation factor-independent translation mediated by the hepatitis C virus internal ribosome entry site. RNA, 12, 894-902.
27. Spahn,C.M.T., Kieft,J.S., Grassucci,R.A., Penczek,P.A., Zhou,K., Doudna,J.A. and Frank,J. (2001) Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit. Science, 291, 1959-1962.
28. Uchiumi,T., Terao,K. and Ogata,K. (1981) Identification of neighboring protein pairs cross-linked with dimethyl 3,3′-dithiobispropionimidate in rat liver 40S ribosomal subunits. J. Biochem. (Tokyo), 90, 185-193.
29. Schüler,M., Connell,S.R., Lescoute,A., Giesebrecht,J., Dabrowski,M., Schroeer,B., Mielke,T., Penczek,P.A., Westhof,E. et al. (2006) Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol., 13, 1092-1096.
30. Pfingsten,J.S., Costantino,D. and Kieft,J.S. (2006) Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science, 314, 1450-1454.
31. Jan,E., Kinzy,T.G. and Sarnow,P. (2003) Divergent tRNA-like element supports initiation, elongation and termination of protein biogenesis. Proc. Natl. Acad. Sci. U.S.A., 100, 15410-15415.
32. Pestova,T.V. and Hellen,C.U.T. (2005) Reconstitution of eukaryotic translation elongation in vitro following initiation by internal ribosomal entry. Methods, 36, 261-269.
33. Lehto,K. and Karentikov,A. (2005) Relicts and models of the RNA world. Int. J. Astrobiol., 4, 33-41.
34. Atkins,J.F., Gesteland,R.F., Jackson,R.J. and Wills,N.M. (2006)The shapely mRNA: Knotting ventured, knotting gained. In Gesteland,R.F., Cech,T.R. and Atkins,J.F. (eds), The RNA World, Third edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, pp. 437-467.
35. Otsuki,T., Sato,A., Watanabe,Y. and Watanabe,K. (2002) A unique serine-specific elongation factor Tu found in nematode mitochondria. Nat. Struct. Biol., 9, 669-673.
36. Zhao,F., Ohtsuki,T., Yamada,K., Yoshinari,S., Kita,K., Watanabe,Y. and Watanabe,K. (2005) Isolation and physiochemical properties of protein-rich nematode mitochondrial ribosomes. Biochemistry, 44 9232-9237.
37. Otto,G.A., Lukavsky,P.J., Lancaster,A.M., Sarnow,P. and Puglisi,J.D. (2002) Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction. RNA, 8, 913-923.
38. Laletina,E., Graifer,D., Malygin,A., Ivanov,A., Shatsky,I. and Karpova,G. (2006) Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit. Nucleic Acids Res., 34, 2027-2036.
39. Christian,P.D., Richards,A.R. and Williams,T. (2006) Differential adsorption of occluded and nonoccluded insect-pathogenic viruses to soil-forming minerals. Appl. Environ. Microbiol., 72, 4648-4652.