Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus

Tuplin, Andrew; Wood, Jonny; Evans, David; Patel, Arvind H.; Simmonds, Peter

doi:10.1017/s1355838202554066

Cited by 113 publications

(141 citation statements)

References 37 publications

Supporting

Mentioning

130

Contrasting

Order By: Relevance

“…4). The data presented here, together with the location of the cre in the coding region in most picornaviruses and with thermodynamic and phylogenetic evidence for RNA structures in other viruses, highlight the potential significance of RNA structures in coding regions (Mathews et al, 1999;Tuplin et al, 2002). Predicted structures in caliciviruses have been tested recently and their disruption affects virus replication .…”

Section: Discussionmentioning

confidence: 58%

“…SimPlot version 3.2 (Lole et al, 1999), using the Kimura two-parameter technique, was used to investigate possible recombination events. Synonymous codon variability was determined, using the Simmonics sequence editor (Tuplin et al, 2002), by measuring mean pair-wise distances at each codon position of the 17 complete sequences and 61 3D sequences. The analysis was restricted to codons where the encoded amino acids were the same in all sequences.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Evolution and conservation in human parechovirus genomes

Williams

Panayiotou

Girling

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

Human parechoviruses (HPeVs) are frequent pathogens with a seroprevalance of over 90 % in adults. Recent studies on these viruses have increased the number of HPeV types to eight. Here we analyse the complete genome of one clinical isolate, PicoBank/HPeV1/a, and VP1 and 3D protein sequences of PicoBank/HPeV6/a, isolated from the same individual 13 months later. PicoBank/HPeV1/a is closely related to other recent HPeV1 isolates but is distinct from the HPeV1 Harris prototype isolated 50 years ago. The availability of an increasing number of HPeV sequences has allowed a detailed analysis of these viruses. The results add weight to the observations that recombination plays a role in the generation of HPeV diversity. An important finding is the presence of unexpected conservation of codons utilized in part of the 3D-encoding region, some of which can be explained by the presence of a phylogenetically conserved predicted secondary structure domain. This suggests that in addition to the cis-acting replication element, RNA secondary structure domains in coding regions play a key role in picornavirus replication. INTRODUCTIONPicornaviruses are non-enveloped, positive-sense RNA viruses with icosahedral capsids, composed of 60 copies of three or four virus-encoded proteins (VP1-4 or VP0, VP1 and VP3) (Stanway et al., 2002(Stanway et al., , 2005. They have a genome of around 7000-8000 nt encoding one polyprotein which is cleaved by virus proteases to give the structural and non-structural (2A-C and 3A-D) proteins. Picornaviruses consist of economically and socially very important human and animal viruses such as polioviruses, other enteroviruses, rhinoviruses, hepatitis A virus, footand-mouth disease virus and parechoviruses. Currently, parechoviruses consist of two species: human parechovirus (HPeV) and Ljungan virus (LV) (Johansson et al., 2002;Joki-Korpela & Hyypiä, 2001;Stanway & Hyypiä, 1999;Stanway et al., 2000). HPeVs are frequent infectious agents and although they usually cause mild gastroenteritis and respiratory disease in young children, more serious cases, such as flaccid paralysis, encephalitis and myocarditis, have also been reported, particularly associated with HPeV3 infection (Baumgarte et al., 2008;Benschop et al., 2006a Benschop et al., , 2008bEhrnst & Eriksson, 1993;Figueroa et al., 1989;Harvala et al., 2008Harvala et al., , 2009Joki-Korpela & Hyypiä, 2001). Recently, HPeV1 has also been linked to otitis media (Tauriainen et al., 2008). With the isolation of several HPeV types in recent studies AlSunaidi et al., 2007;Baumgarte et al., 2008;Benschop et al., 2006b; Drexler et al., 2009;Ito et al., 2004;Li et al., 2009), eight types (1-8) of HPeVs are currently known.HPeVs have several distinctive features compared with other picornaviruses (Ghazi et al., 1998;Hyypiä et al., 1992;Stanway et al., 1994Stanway et al., , 2000. Post-translational cleavage of the polyprotein results in only three structural proteins (VP0, VP3 and VP1), as the cleavage of VP0 to VP4 and VP2 seen in other picornaviruses does n...

show abstract

Section: Discussionmentioning

confidence: 58%

mentioning

confidence: 99%

Evolution and conservation in human parechovirus genomes

Williams

Panayiotou

Girling

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

show abstract

“…Most HCV isolates are therefore unlikely to support a frameshift, even within core codons 8-11. HCV-1 codons 8-11 contain the sequences A AAA AAA and A AAA AAC, which are consistent with the consensus ribosomal frameshift signal X XXY YYZ (X,Y,Z: any nucleotide), and are followed by conserved RNA stem-loops {SL47, SL87 (14,25,26)}. Choi et al (23) demonstrated the importance of the region predicted to form SL47 and SL87 (codons 15-53) in Figure 1.…”

Section: Alternative Forms Of Core11 Proteins Trans-lated By Frameshimentioning

confidence: 59%

“…Moreover, recent studies with the highly efficient cell culture HCV infection system based on JFH1 and chimeric H77/JFH1 genomes have shown that the insertion of nonsense mutations into the core11 ORF has no effect on viral replication, the production of viral proteins or the release of infectious virus particles (84). By contrast, the integrity of the RNA structure embedded in the core11 sequence has been shown to be important in that mutations designed to disrupt the predicted highly conserved RNA stem-loops SL47 (nt 388-425) and SL87 (nt 428-508) (14,25,26) impair HCV genome translation (84) and viral proliferation in cell culture and in vivo, in both HCV-infected chimpanzees and mice xenografted with primary human hepatocytes (84,85).…”

Section: Functional Properties Of Core11 Proteinsmentioning

confidence: 99%

The HCV ARFP/F/core+1 protein: Production and functional analysis of an unconventional viral product

Vassilaki

Mavromara

2009

IUBMB Life

View full text Add to dashboard Cite

Hepatitis C virus (HCV) is an enveloped positive‐strand RNA virus of the Flaviviridae family. It has a genome of about 9,600 nucleotides encoding a large polyprotein (about 3,000 amino acids) that is processed by cellular and viral proteases into at least 10 structural and nonstructural viral proteins. A novel HCV protein has also been identified by our laboratory and others. This protein—known as ARFP (alternative reading frame protein), F (for frameshift) or core+1 (to indicate the position) protein ‐ is synthesized by an open reading frame overlapping the core gene at nucleotide +1 (core+1 ORF). However, almost 10 years after its discovery, we still know little of the biological role of the ARFP/F/core+1 protein. Abolishing core+1 protein production has no affect on HCV replication in cell culture or uPA‐SCID mice, suggesting that core+1 protein is probably not important for the HCV reproductive cycle. However, the detection of specific anti‐core+1 antibodies and T‐cell responses in HCV‐infected patients, as reported by many independent laboratories, provides strong evidence that this protein is produced in vivo. Furthermore, analyses of the HCV sequences isolated from patients with hepatocellular carcinoma and in vitro studies have provided strong preliminary evidence to suggest that core+1 protein plays a role in advanced liver disease and liver cancer. The available in vitro data also suggest that certain core function proteins may depend on production of the core+1 protein. We describe here the discovery of the various forms of the core+1 protein and what is currently known about the mechanisms of their production and their biochemical and functional properties. We also provide a detailed summary of the results of patient‐based research. © 2009 IUBMB IUBMB Life, 61(7): 739–752, 2009

show abstract

“…There are, however, a number of wellknown exceptions to this rule. A variety of conserved secondary structure elements have been detected in computational surveys of single stranded RNA virus genomes [165,406,405,402,439]. A comparative study of 28 different species [195] provides evidence for wide-spread selection for local secondary structures in mRNAs, in particular in eubacteria.…”

Section: Rna Structures In Coding Regionsmentioning

confidence: 99%

Evolutionary patterns of non-coding RNAs

Bompfünewerer

Flamm

Fried

et al. 2005

Theory in Biosciences

View full text Add to dashboard Cite

A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and Manuscript January 2005RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution we attempt to provide at least a cursory overview of the diversity of non-coding RNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates, studies of the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of microRNAs in metazoans, which suggests an explosive increase in the microRNA repertoire in vertebrates. The analysis of the transcription of non-coding RNAs (ncRNAs) suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.

show abstract

Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus

Cited by 113 publications

References 37 publications

Evolution and conservation in human parechovirus genomes

Evolution and conservation in human parechovirus genomes

The HCV ARFP/F/core+1 protein: Production and functional analysis of an unconventional viral product

Evolutionary patterns of non-coding RNAs

Contact Info

Product

Resources

About