Comparative structural studies of bovine viral diarrhea virus IRES RNA

被引：6

作者：

Burks, Jody M. ^{[1
]}

Zwieb, Christian ^{[2
]}

Mueller, Florian ^{[3
]}

Wower, Iwona K. ^{[1
]}

Wower, Jacek ^{[1
]}

机构：

[1] Auburn Univ, Dept Anim Sci, Auburn, AL 36849 USA

[2] Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX 78229 USA

[3] PENTAFOLIUM SOFT, D-21224 Rosengarten, Germany

来源：

VIRUS RESEARCH | 2011年 / 160卷 / 1-2期

基金：

美国国家科学基金会;

关键词：

BVDV; IRES RNA; Comparative Sequence Analysis; RNA secondary structure; RNA model; HEPATITIS-C-VIRUS; RIBOSOMAL ENTRY SITE; SWINE-FEVER VIRUS; 5' NONTRANSLATED REGION; TRANSLATION INITIATION; DOMAIN-II; NUCLEOTIDE-SEQUENCE; MOLECULAR-CLONING; INTERNAL INITIATION; PSEUDOKNOT UPSTREAM;

D O I：

10.1016/j.virusres.2011.06.002

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

The internal ribosomal entry site (IRES) RNA of bovine viral diarrhea virus (BVDV) has been implicated in virus propagation. To gain insight into the structure and potential function of the BVDV IRES RNA, we collected and aligned 663 of its sequences. Compensatory Watson-Crick and wobble G.U pairs were investigated to establish phylogenetically supported secondary structures for each of the BVDV IRES RNA sequences. The extensively folded BVDV IRES RNAs were composed of helices 2, 3 and 4. Helix 2 consisted of five helical sections. Helix 3 contained sections 3a to 3j as well as six helical insertions 3.1-3.6. Sections 3a and 3b together with helices 3.6 and 4 formed an RNA pseudoknot. Two highly variable regions corresponded to hairpins 3j and 3.4. Three-dimensional modeling of the BVDV-1b strain Osloss IRES RNA predicted an elongated structure with approximate dimensions of 170 angstrom by 65 angstrom by 90 angstrom. The model of the IRES RNA-ribosome complex suggested proximity between helix 2 of the BVDV IRES and ribosomal proteins S5 and S25. Published by Elsevier B.V.

引用

页码：136 / 142

页数：7

共 78 条

[1] PSI-BLAST pseudocounts and the minimum description length principle [J].

Altschul, Stephen F. ;

Gertz, E. Michael ;

Agarwala, Richa ;

Schaffer, Alejandro A. ;

Yu, Yi-Kuo .

NUCLEIC ACIDS RESEARCH, 2009, 37 (03) :815-824

[2] Semiautomated improvement of RNA alignments [J].

Andersen, Ebbe S. ;

Lind-Thomsen, Allan ;

Knudsen, Bjarne ;

Kristensen, Susie E. ;

Havgaard, Jakob H. ;

Torarinsson, Elfar ;

Larsen, Niels ;

Zwieb, Christian ;

Sestoft, Peter ;

Kjems, Jorgen ;

Gorodkin, Jan .

RNA, 2007, 13 (11) :1850-1859

[3]

[Anonymous], NUCL ACIDS RES

[4]

[Anonymous], 2011, FIELDS VIROLOGY

[5] Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome [J].

Babaylova, Elena ;

Graifer, Dmitri ;

Malygin, Alexey ;

Stahl, Joachim ;

Shatsky, Ivan ;

Karpova, Galina .

NUCLEIC ACIDS RESEARCH, 2009, 37 (04) :1141-1151

[6] THE CLINICAL MANIFESTATIONS OF BOVINE VIRAL DIARRHEA INFECTION [J].

BAKER, JC .

VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE, 1995, 11 (03) :425-&

[7] Crystal Structure of the Eukaryotic Ribosome [J].

Ben-Shem, Adam ;

Jenner, Lasse ;

Yusupova, Gulnara ;

Yusupov, Marat .

SCIENCE, 2010, 330 (6008) :1203-1209

[8]

Benson D. A., 2009, GenBank. Nucleic Acids Res., V38, P046

[9] The Protein Data Bank [J].

Berman, HM ;

Battistuz, T ;

Bhat, TN ;

Bluhm, WF ;

Bourne, PE ;

Burkhardt, K ;

Iype, L ;

Jain, S ;

Fagan, P ;

Marvin, J ;

Padilla, D ;

Ravichandran, V ;

Schneider, B ;

Thanki, N ;

Weissig, H ;

Westbrook, JD ;

Zardecki, C .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :899-907

[10] The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit [J].

Berry, Katherine E. ;

Waghray, Shruti ;

Doudna, Jennifer A. .

RNA, 2010, 16 (08) :1559-1569

← 1 2 3 4 5 6 7 8 →