Literature DB >> 11680841

Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots.

R C Olsthoorn1, J F Bol.   

Abstract

Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3' noncoding region (3' NCR) directly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that includes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conserved sequences CS2 and RCS2. In yellow fever virus RNAs that contain one CS2 motif, only one copy of this pseudoknotted structure was found. The conserved pseudoknotted element is absent from the 3' NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different from that of mosquito-borne virus RNAs. The strong conservation of the pseudoknot in mosquito-borne flavivirus RNAs implies a stronger relationship between these viruses than concluded from previous secondary structure analyses. The role of the (tandem) pseudoknots in flavivirus replication is discussed.

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Year:  2001        PMID： 11680841      PMCID： PMC1370180     

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


  17 in total

1.  RNA secondary structure prediction based on free energy and phylogenetic analysis.

Authors:  V Juan; C Wilson
Journal:  J Mol Biol       Date:  1999-06-18       Impact factor: 5.469

2.  Essential role of cyclization sequences in flavivirus RNA replication.

Authors:  A A Khromykh; H Meka; K J Guyatt; E G Westaway
Journal:  J Virol       Date:  2001-07       Impact factor: 5.103

3.  Sequence of the genes encoding the structural proteins of the low-virulence tick-borne flaviviruses Langat TP21 and Yelantsev.

Authors:  C W Mandl; L Iacono-Connors; G Wallner; H Holzmann; C Kunz; F X Heinz
Journal:  Virology       Date:  1991-12       Impact factor: 3.616

4.  Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to replication and translation.

Authors:  F C Lahser; L E Marsh; T C Hall
Journal:  J Virol       Date:  1993-06       Impact factor: 5.103

5.  Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein.

Authors:  T J Chambers; R C Weir; A Grakoui; D W McCourt; J F Bazan; R J Fletterick; C M Rice
Journal:  Proc Natl Acad Sci U S A       Date:  1990-11       Impact factor: 11.205

6.  Antigenic relationships between flaviviruses as determined by cross-neutralization tests with polyclonal antisera.

Authors:  C H Calisher; N Karabatsos; J M Dalrymple; R E Shope; J S Porterfield; E G Westaway; W E Brandt
Journal:  J Gen Virol       Date:  1989-01       Impact factor: 3.891

7.  Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences.

Authors:  C S Hahn; Y S Hahn; C M Rice; E Lee; L Dalgarno; E G Strauss; J H Strauss
Journal:  J Mol Biol       Date:  1987-11-05       Impact factor: 5.469

Review 8.  On finding all suboptimal foldings of an RNA molecule.

Authors:  M Zuker
Journal:  Science       Date:  1989-04-07       Impact factor: 47.728

9.  Secondary structure model for the last two domains of single-stranded RNA phage Q beta.

Authors:  M J Beekwilder; R Nieuwenhuizen; J van Duin
Journal:  J Mol Biol       Date:  1995-04-14       Impact factor: 5.469

10.  A novel in vitro replication system for Dengue virus. Initiation of RNA synthesis at the 3'-end of exogenous viral RNA templates requires 5'- and 3'-terminal complementary sequence motifs of the viral RNA.

Authors:  S You; R Padmanabhan
Journal:  J Biol Chem       Date:  1999-11-19       Impact factor: 5.157
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  46 in total

1.  Identification of cis-acting elements in the 3'-untranslated region of the dengue virus type 2 RNA that modulate translation and replication.

Authors:  Mark Manzano; Erin D Reichert; Stephanie Polo; Barry Falgout; Wojciech Kasprzak; Bruce A Shapiro; Radhakrishnan Padmanabhan
Journal:  J Biol Chem       Date:  2011-04-22       Impact factor: 5.157

2.  Genetic relationships and evolution of genotypes of yellow fever virus and other members of the yellow fever virus group within the Flavivirus genus based on the 3' noncoding region.

Authors:  John-Paul Mutebi; René C A Rijnbrand; Heiman Wang; Kate D Ryman; Eryu Wang; Lynda D Fulop; Rick Titball; Alan D T Barrett
Journal:  J Virol       Date:  2004-09       Impact factor: 5.103

3.  Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3' UTR structures.

Authors:  Alex Michael Ward; Katell Bidet; Ang Yinglin; Siok Ghee Ler; Kelly Hogue; Walter Blackstock; Jayantha Gunaratne; Mariano A Garcia-Blanco
Journal:  RNA Biol       Date:  2011-11-01       Impact factor: 4.652

Review 4.  Recent advances in deciphering viral and host determinants of dengue virus replication and pathogenesis.

Authors:  Karen Clyde; Jennifer L Kyle; Eva Harris
Journal:  J Virol       Date:  2006-08-23       Impact factor: 5.103

5.  Interplay of RNA elements in the dengue virus 5' and 3' ends required for viral RNA replication.

Authors:  Peter Friebe; Eva Harris
Journal:  J Virol       Date:  2010-03-31       Impact factor: 5.103

6.  Overlapping local and long-range RNA-RNA interactions modulate dengue virus genome cyclization and replication.

Authors:  Luana de Borba; Sergio M Villordo; Nestor G Iglesias; Claudia V Filomatori; Leopoldo G Gebhard; Andrea V Gamarnik
Journal:  J Virol       Date:  2015-01-14       Impact factor: 5.103

7.  Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.

Authors:  Zhong-Yu Liu; Xiao-Feng Li; Tao Jiang; Yong-Qiang Deng; Hui Zhao; Hong-Jiang Wang; Qing Ye; Shun-Ya Zhu; Yang Qiu; Xi Zhou; E-De Qin; Cheng-Feng Qin
Journal:  J Virol       Date:  2013-04-10       Impact factor: 5.103

Review 8.  Functions of the 3' and 5' genome RNA regions of members of the genus Flavivirus.

Authors:  Margo A Brinton; Mausumi Basu
Journal:  Virus Res       Date:  2015-02-13       Impact factor: 3.303

9.  Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and Mammalian cells.

Authors:  Esther Schnettler; Mark G Sterken; Jason Y Leung; Stefan W Metz; Corinne Geertsema; Rob W Goldbach; Just M Vlak; Alain Kohl; Alexander A Khromykh; Gorben P Pijlman
Journal:  J Virol       Date:  2012-10-03       Impact factor: 5.103

10.  3' cis-acting elements that contribute to the competence and efficiency of Japanese encephalitis virus genome replication: functional importance of sequence duplications, deletions, and substitutions.

Authors:  Sang-Im Yun; Yu-Jeong Choi; Byung-Hak Song; Young-Min Lee
Journal:  J Virol       Date:  2009-06-03       Impact factor: 5.103
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