PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

Byun, Yanga; Han, Kyungsook

doi:10.1093/nar/gkl210

Cited by 87 publications

(61 citation statements)

References 14 publications

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“…RNA secondary structures were predicted using the mfold online server (33,34). The pknotsRG (35,36) and PseudoViewer3 (37,38) online versions were used to predict and illustrate, respectively, the RNA structures containing pseudoknots.…”

Section: Methodsmentioning

confidence: 99%

Novel cis -Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

Liu

Jiang

et al. 2013

J Virol

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c cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5= cyclization sequence (5=CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5=CS, and the presence of DCS-PK facilitates the formation of 5=-3= RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution. T he flavivirus genus contains numerous important agents of human infectious diseases, including dengue virus (DENV), West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever virus (YFV), and tick-borne encephalitis virus (TBEV). Human infection by flaviviruses can result in symptoms ranging from mild fever to severe encephalitis and hemorrhagic fever. Due to lack of effective vaccines and specific medicines against many flaviviruses, they pose a significant threat to human health around the world.Flaviviruses are enveloped RNA viruses with single-stranded, positive-sense genomes. Their 5= capped viral genome RNA (vRNA) is approximately 10 to 11 kb and contains a single open reading frame (ORF) flanked by 5= and 3= untranslated regions (UTRs). The ORF encodes a polyprotein with more than 3,000 residues, which is cotranslationally and/or posttranslationally proteolytically processed into three structural proteins (capsid, pre-membrane/membrane, and envelope) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) by viral and cellular proteases. NS3 and NS5 perform essential enzyme activities required for vRNA replication. The C-terminal domain of NS3 has helicase/NTPase (1) and RNA triphosphatase activities (2, 3). The N-terminal domain of NS5 encodes guanylyltransferase (4) and methyltransferase activities (5, 6), whereas the C-terminal domain of NS5 has RNA-dependent RNA polymerase (RdRp) activity. These enzyme activities are involved in vRNA synthesis, 5= capping, and internal adenosine methylation (7).The 5=UTR, 3=UTR, and capsid-coding sequence are involved in vRNA replication, translation, and perhaps encapsidation, and many cis-acting elements have ...

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Section: Methodsmentioning

confidence: 99%

Novel cis -Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

Liu

Jiang

et al. 2013

J Virol

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“…The alignment is available on request. Exemplarily one placozoan ITS2 secondary structure was plotted with PseudoViewerIII (Byun & Han 2006) (Fig. 5).…”

Section: Methodsmentioning

confidence: 99%

Placozoa: at least two

et al. 2007

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It was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE -a tool for synchronous RNA sequence and secondary structure alignment and editing -in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is "no longer a phylum of one".

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“…The ITS2PAM50 matrix was used to predict the secondary structure of G. diakidnus using the ITS2 database. The predicted folding results from the Mfold and ITS2 database analyses were viewed with Pseudoviewer version 3 (Byun & Han, 2006).…”

Section: Comparative Dna Analysesmentioning

confidence: 99%

Gynichthys diakidnus n. g., n. sp. (Digenea: Cryptogonimidae) from the grunt Plectorhinchus gibbosus (Lacépède, 1802) (Perciformes: Haemulidae) off the Great Barrier Reef, Australia

Miller

Cribb

2009

Syst Parasitol

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Gynichthys diakidnus n. g., n. sp. (Digenea: Cryptogonimidae) is described from the fish Plectorhinchus gibbosus (Lacépède) (Perciformes: Haemulidae) off Heron and Lizard Islands on the Great Barrier Reef, Australia. The monotypic Gynichthys n. g. is distinguished from all other cryptogonimid genera by the combination of a fusiform body, the lack of oral spines, a forebody that occupies approximately half or more of the body length, a deeply lobed ovary, opposite to slightly oblique testes, a seminal vesicle that is confined mainly in the forebody and the presence of multiple gonotyls in the form of two small slightly muscular pores or pseudosucker-like structures in the mid-line well anterior to the ventral sucker. Bayesian inference analysis of LSU rDNA data revealed that G. diakidnus n. sp. grouped relatively distant to species of the cryptogonimid genus Oligogonotylus Watson, 1976, which also have multiple gonotyls, suggesting that the presence of multiple gonotyls is homoplasious and has thus at least evolved twice in the family. The secondary structure of the internal transcribed spacer 2 (ITS2) rDNA region was inferred for G. diakidnus using minimum free energy and homology modelling algorithms. A four helix model was inferred with helices I and IV being relatively short (<30 nucleotides) and helix three being the longest; this structure is homologous with that observed for other digeneans and eukaryotes in general.

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PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

Cited by 87 publications

References 14 publications

Novel cis -Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

Novel cis -Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

Placozoa: at least two

Gynichthys diakidnus n. g., n. sp. (Digenea: Cryptogonimidae) from the grunt Plectorhinchus gibbosus (Lacépède, 1802) (Perciformes: Haemulidae) off the Great Barrier Reef, Australia

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