메뉴 건너뛰기




Volumn 139, Issue 2, 2009, Pages 148-156

Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures

Author keywords

Dicistroviridae; Internal ribosome entry; IRES; Pseudoknot; RNA structure; Translation initiation; X ray crystallography

Indexed keywords

INITIATION FACTOR; SPACER DNA; TRANSFER RNA; VIRUS RNA;

EID: 59949086458     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2008.07.007     Document Type: Article
Times cited : (14)

References (52)
  • 2
    • 27644484907 scopus 로고    scopus 로고
    • Structure of the hepatitis C Virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES
    • Boehringer D., Thermann R., Ostareck-Lederer A., Lewis J.D., and Stark H. Structure of the hepatitis C Virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Structure 13 (2005) 1695-1706
    • (2005) Structure , vol.13 , pp. 1695-1706
    • Boehringer, D.1    Thermann, R.2    Ostareck-Lederer, A.3    Lewis, J.D.4    Stark, H.5
  • 3
    • 34447538279 scopus 로고    scopus 로고
    • Viral RNA pseudoknots: versatile motifs in gene expression and replication
    • Brierley I., Pennell S., and Gilbert R.J. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat. Rev. Microbiol. 5 (2007) 598-610
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 598-610
    • Brierley, I.1    Pennell, S.2    Gilbert, R.J.3
  • 4
    • 0042353728 scopus 로고    scopus 로고
    • Vaccinia virus transcription
    • Broyles S.S. Vaccinia virus transcription. J. Gen. Virol. 84 (2003) 2293-2303
    • (2003) J. Gen. Virol. , vol.84 , pp. 2293-2303
    • Broyles, S.S.1
  • 6
    • 11144247914 scopus 로고    scopus 로고
    • Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp
    • Cevallos R.C., and Sarnow P. Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J. Virol. 79 (2005) 677-683
    • (2005) J. Virol. , vol.79 , pp. 677-683
    • Cevallos, R.C.1    Sarnow, P.2
  • 7
    • 33846279049 scopus 로고    scopus 로고
    • Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
    • Cochrane J.C., Lipchock S.V., and Strobel S.A. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14 (2007) 97-105
    • (2007) Chem. Biol. , vol.14 , pp. 97-105
    • Cochrane, J.C.1    Lipchock, S.V.2    Strobel, S.A.3
  • 9
    • 13944276301 scopus 로고    scopus 로고
    • A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs
    • Costantino D., and Kieft J.S. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA 11 (2005) 332-343
    • (2005) RNA , vol.11 , pp. 332-343
    • Costantino, D.1    Kieft, J.S.2
  • 12
    • 36749042932 scopus 로고    scopus 로고
    • Translation initiation by viral internal ribosome entry sites
    • Mathews M.B., Sonenberg N., and Hershey J.W.B. (Eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Doudna J.A., and Sarnow P. Translation initiation by viral internal ribosome entry sites. In: Mathews M.B., Sonenberg N., and Hershey J.W.B. (Eds). Translational Control in Biology and Medicine (2007), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 129-153
    • (2007) Translational Control in Biology and Medicine , pp. 129-153
    • Doudna, J.A.1    Sarnow, P.2
  • 13
    • 33846951996 scopus 로고    scopus 로고
    • Translation initiation via cellular internal ribosome entry sites.
    • Mathews M.B., Sonenberg N., and Hershey J. (Eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Elroy-Stein O., and Merrick W.C. Translation initiation via cellular internal ribosome entry sites. In: Mathews M.B., Sonenberg N., and Hershey J. (Eds). Translational Control in Biology and Medicine (2007), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 155-172
    • (2007) Translational Control in Biology and Medicine , pp. 155-172
    • Elroy-Stein, O.1    Merrick, W.C.2
  • 14
    • 33749330704 scopus 로고    scopus 로고
    • Functional association between viral and cellular transcription during influenza virus infection
    • Engelhardt O.G., and Fodor E. Functional association between viral and cellular transcription during influenza virus infection. Rev. Med. Virol. 16 (2006) 329-345
    • (2006) Rev. Med. Virol. , vol.16 , pp. 329-345
    • Engelhardt, O.G.1    Fodor, E.2
  • 15
    • 31044449305 scopus 로고    scopus 로고
    • Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation
    • Fernandez-Miragall O., Ramos R., Ramajo J., and Martinez-Salas E. Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA 12 (2006) 223-234
    • (2006) RNA , vol.12 , pp. 223-234
    • Fernandez-Miragall, O.1    Ramos, R.2    Ramajo, J.3    Martinez-Salas, E.4
  • 16
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre'-D'Amare' A.R., Zhou K., and Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395 (1998) 567-574
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre'-D'Amare', A.R.1    Zhou, K.2    Doudna, J.A.3
  • 17
    • 1942437439 scopus 로고    scopus 로고
    • Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts
    • Hatakeyama Y., Shibuya N., Nishiyama T., and Nakashima N. Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA 10 (2004) 779-786
    • (2004) RNA , vol.10 , pp. 779-786
    • Hatakeyama, Y.1    Shibuya, N.2    Nishiyama, T.3    Nakashima, N.4
  • 18
    • 0032419548 scopus 로고    scopus 로고
    • New developments in structure determination of pseudoknots
    • Hilbers C.W., Michiels P.J., and Heus H.A. New developments in structure determination of pseudoknots. Biopolymers 48 (1998) 137-153
    • (1998) Biopolymers , vol.48 , pp. 137-153
    • Hilbers, C.W.1    Michiels, P.J.2    Heus, H.A.3
  • 19
    • 33646791554 scopus 로고    scopus 로고
    • Divergent IRES elements in invertebrates
    • Jan E. Divergent IRES elements in invertebrates. Virus Res. 119 (2006) 16-28
    • (2006) Virus Res. , vol.119 , pp. 16-28
    • Jan, E.1
  • 20
    • 0037073485 scopus 로고    scopus 로고
    • Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus
    • Jan E., and Sarnow P. Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J. Mol. Biol. 324 (2002) 889-902
    • (2002) J. Mol. Biol. , vol.324 , pp. 889-902
    • Jan, E.1    Sarnow, P.2
  • 21
    • 0346103682 scopus 로고    scopus 로고
    • Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis
    • Jan E., Kinzy T.G., and Sarnow P. Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 15410-15415
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 15410-15415
    • Jan, E.1    Kinzy, T.G.2    Sarnow, P.3
  • 22
    • 0035788058 scopus 로고    scopus 로고
    • Initiator Met-tRNA-independent translation mediated by an internal ribosome entry site element in cricket paralysis virus-like insect viruses
    • Jan E., Thompson S.R., Wilson J.E., Pestova T.V., Hellen C.U., and Sarnow P. Initiator Met-tRNA-independent translation mediated by an internal ribosome entry site element in cricket paralysis virus-like insect viruses. Cold Spring Harb. Symp. Quant. Biol. 66 (2001) 285-292
    • (2001) Cold Spring Harb. Symp. Quant. Biol. , vol.66 , pp. 285-292
    • Jan, E.1    Thompson, S.R.2    Wilson, J.E.3    Pestova, T.V.4    Hellen, C.U.5    Sarnow, P.6
  • 23
    • 0035259873 scopus 로고    scopus 로고
    • A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation
    • Kanamori Y., and Nakashima N. A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 7 (2001) 266-274
    • (2001) RNA , vol.7 , pp. 266-274
    • Kanamori, Y.1    Nakashima, N.2
  • 24
    • 46549086974 scopus 로고    scopus 로고
    • Viral IRES RNA structures and ribosome interactions
    • Kieft J.S. Viral IRES RNA structures and ribosome interactions. Trends Biochem. Sci. 33 (2008) 274-283
    • (2008) Trends Biochem. Sci. , vol.33 , pp. 274-283
    • Kieft, J.S.1
  • 25
    • 0036237981 scopus 로고    scopus 로고
    • Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation
    • Kieft J.S., Zhou K., Grech A., Jubin R., and Doudna J.A. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struct. Biol. 9 (2002) 370-374
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 370-374
    • Kieft, J.S.1    Zhou, K.2    Grech, A.3    Jubin, R.4    Doudna, J.A.5
  • 26
    • 0033600934 scopus 로고    scopus 로고
    • The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold
    • Kieft J.S., Zhou K., Jubin R., Murray M.G., Lau J.Y., and Doudna J.A. The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J. Mol. Biol. 292 (1999) 513-529
    • (1999) J. Mol. Biol. , vol.292 , pp. 513-529
    • Kieft, J.S.1    Zhou, K.2    Jubin, R.3    Murray, M.G.4    Lau, J.Y.5    Doudna, J.A.6
  • 27
    • 33748325570 scopus 로고    scopus 로고
    • Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    • Klein D.J., and Ferre-D'Amare A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756
    • (2006) Science , vol.313 , pp. 1752-1756
    • Klein, D.J.1    Ferre-D'Amare, A.R.2
  • 28
    • 0033744387 scopus 로고    scopus 로고
    • A potential RNA drug target in the hepatitis C virus internal ribosomal entry site
    • Klinck R., Westhof E., Walker S., Afshar M., Collier A., and Aboul-Ela F. A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. RNA 6 (2000) 1423-1431
    • (2000) RNA , vol.6 , pp. 1423-1431
    • Klinck, R.1    Westhof, E.2    Walker, S.3    Afshar, M.4    Collier, A.5    Aboul-Ela, F.6
  • 29
    • 33846959081 scopus 로고    scopus 로고
    • HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly
    • Locker N., Easton L.E., and Lukavsky P.J. HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly. EMBO J. 26 (2007) 795-805
    • (2007) EMBO J. , vol.26 , pp. 795-805
    • Locker, N.1    Easton, L.E.2    Lukavsky, P.J.3
  • 31
    • 0033673387 scopus 로고    scopus 로고
    • Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function
    • Lukavsky P.J., Otto G.A., Lancaster A.M., Sarnow P., and Puglisi J.D. Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Nat. Struct. Biol. 7 (2000) 1105-1110
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1105-1110
    • Lukavsky, P.J.1    Otto, G.A.2    Lancaster, A.M.3    Sarnow, P.4    Puglisi, J.D.5
  • 32
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary contacts distant from the active site prime a ribozyme for catalysis
    • Martick M., and Scott W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126 (2006) 309-320
    • (2006) Cell , vol.126 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 34
    • 34247103448 scopus 로고    scopus 로고
    • The tmRNA system for translational surveillance and ribosome rescue
    • Moore S.D., and Sauer R.T. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76 (2007) 101-124
    • (2007) Annu. Rev. Biochem. , vol.76 , pp. 101-124
    • Moore, S.D.1    Sauer, R.T.2
  • 35
    • 0038750886 scopus 로고    scopus 로고
    • Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes
    • Nishiyama T., Yamamoto H., Shibuya N., Hatakeyama Y., Hachimori A., Uchiumi T., and Nakashima N. Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res. 31 (2003) 2434-2442
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2434-2442
    • Nishiyama, T.1    Yamamoto, H.2    Shibuya, N.3    Hatakeyama, Y.4    Hachimori, A.5    Uchiumi, T.6    Nakashima, N.7
  • 37
    • 33846991130 scopus 로고    scopus 로고
    • The mechanism of translation initiation in eukaryotes
    • Mathews M.B., Sonenberg N., and Hershey J.W.B. (Eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Pestova T., Lorsch J.R., and Hellen C.U. The mechanism of translation initiation in eukaryotes. In: Mathews M.B., Sonenberg N., and Hershey J.W.B. (Eds). Translational Control in Biology and Medicine (2007), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 87-128
    • (2007) Translational Control in Biology and Medicine , pp. 87-128
    • Pestova, T.1    Lorsch, J.R.2    Hellen, C.U.3
  • 38
    • 0037439060 scopus 로고    scopus 로고
    • Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA
    • Pestova T.V., and Hellen C.U. Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev. 17 (2003) 181-186
    • (2003) Genes Dev. , vol.17 , pp. 181-186
    • Pestova, T.V.1    Hellen, C.U.2
  • 39
    • 13944271964 scopus 로고    scopus 로고
    • Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly
    • Pestova T.V., Lomakin I.B., and Hellen C.U. Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly. EMBO Rep. 5 (2004) 906-913
    • (2004) EMBO Rep. , vol.5 , pp. 906-913
    • Pestova, T.V.1    Lomakin, I.B.2    Hellen, C.U.3
  • 40
    • 33845335508 scopus 로고    scopus 로고
    • Structural basis for ribosome recruitment and manipulation by a viral IRES RNA
    • Pfingsten J.S., Costantino D.A., and Kieft J.S. Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science 314 (2006) 1450-1454
    • (2006) Science , vol.314 , pp. 1450-1454
    • Pfingsten, J.S.1    Costantino, D.A.2    Kieft, J.S.3
  • 41
    • 34250223454 scopus 로고    scopus 로고
    • Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes
    • Pfingsten J.S., Costantino D.A., and Kieft J.S. Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J. Mol. Biol. 370 (2007) 856-869
    • (2007) J. Mol. Biol. , vol.370 , pp. 856-869
    • Pfingsten, J.S.1    Costantino, D.A.2    Kieft, J.S.3
  • 42
    • 45749123968 scopus 로고    scopus 로고
    • RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes
    • Pfingsten J.S., and Kieft J.S. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. RNA 14 (2008) 1255-1263
    • (2008) RNA , vol.14 , pp. 1255-1263
    • Pfingsten, J.S.1    Kieft, J.S.2
  • 43
    • 5144229241 scopus 로고    scopus 로고
    • Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites
    • Rijnbrand R., Thiviyanathan V., Kaluarachchi K., Lemon S.M., and Gorenstein D.G. Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites. J. Mol. Biol. 343 (2004) 805-817
    • (2004) J. Mol. Biol. , vol.343 , pp. 805-817
    • Rijnbrand, R.1    Thiviyanathan, V.2    Kaluarachchi, K.3    Lemon, S.M.4    Gorenstein, D.G.5
  • 44
    • 0032927056 scopus 로고    scopus 로고
    • Translation initiation at the CUU codon is mediated by the internal ribosome entry site of an insect picorna-like virus in vitro
    • Sasaki J., and Nakashima N. 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 (1999) 1219-1226
    • (1999) J. Virol. , vol.73 , pp. 1219-1226
    • Sasaki, J.1    Nakashima, N.2
  • 45
    • 0034652349 scopus 로고    scopus 로고
    • Methionine-independent initiation of translation in the capsid protein of an insect RNA virus
    • Sasaki J., and Nakashima N. Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 1512-1515
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 1512-1515
    • Sasaki, J.1    Nakashima, N.2
  • 48
    • 4644247805 scopus 로고    scopus 로고
    • Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes; the IRES functions as an RNA-based translation factor
    • Spahn C.M., Jan E., Mulder A., Grassucci R.A., Sarnow P., and Frank J. 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 (2004) 465-475
    • (2004) Cell , vol.118 , pp. 465-475
    • Spahn, C.M.1    Jan, E.2    Mulder, A.3    Grassucci, R.A.4    Sarnow, P.5    Frank, J.6
  • 49
    • 22744455135 scopus 로고    scopus 로고
    • Pseudoknots: RNA structures with diverse functions
    • Staple D.W., and Butcher S.E. Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3 (2005) e213
    • (2005) PLoS Biol. , vol.3
    • Staple, D.W.1    Butcher, S.E.2
  • 50
    • 0034682720 scopus 로고    scopus 로고
    • Initiation of protein synthesis from the A site of the ribosome
    • Wilson J.E., Pestova T.V., Hellen C.U., and Sarnow P. Initiation of protein synthesis from the A site of the ribosome. Cell 102 (2000) 511-520
    • (2000) Cell , vol.102 , pp. 511-520
    • Wilson, J.E.1    Pestova, T.V.2    Hellen, C.U.3    Sarnow, P.4
  • 51
    • 0033920258 scopus 로고    scopus 로고
    • Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites
    • Wilson J.E., Powell M.J., Hoover S.E., and Sarnow P. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol. Cell Biol. 20 (2000) 4990-4999
    • (2000) Mol. Cell Biol. , vol.20 , pp. 4990-4999
    • Wilson, J.E.1    Powell, M.J.2    Hoover, S.E.3    Sarnow, P.4
  • 52
    • 34247185278 scopus 로고    scopus 로고
    • Binding mode of the first aminoacyl-tRNA in translation initiation mediated by Plautia stali intestine virus internal ribosome entry site
    • Yamamoto H., Nakashima N., Ikeda Y., and Uchiumi T. Binding mode of the first aminoacyl-tRNA in translation initiation mediated by Plautia stali intestine virus internal ribosome entry site. J. Biol. Chem. 282 (2007) 7770-7776
    • (2007) J. Biol. Chem. , vol.282 , pp. 7770-7776
    • Yamamoto, H.1    Nakashima, N.2    Ikeda, Y.3    Uchiumi, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.