scholarly journals Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3′ stem–loop structure is not required for replication

2007 ◽  
Vol 88 (6) ◽  
pp. 1738-1747 ◽  
Author(s):  
Patrícia A. G. C. Silva ◽  
Richard Molenkamp ◽  
Tim J. Dalebout ◽  
Nathalie Charlier ◽  
Johan H. Neyts ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Molecular Mechanisms ◽  
Yellow Fever Virus ◽  
Animal Cell ◽  
Fever Virus ◽  
Loop Structure ◽  
Animal Cells ◽  
Pn Sequence ◽  
Stem Loop ◽  
Stem Loop Structure

The pentanucleotide (PN) sequence 5′-CACAG-3′ at the top of the 3′ stem–loop structure of the flavivirus genome is well conserved in the arthropod-borne viruses but is more variable in flaviviruses with no known vector. In this study, the sequence requirements of the PN motif for yellow fever virus 17D (YFV) replication were determined. In general, individual mutations at either the second, third or fourth positions were tolerated and resulted in replication-competent virus. Mutations at the fifth position were lethal. Base pairing of the nucleotide at the first position of the PN motif and a nucleotide four positions downstream of the PN (ninth position) was a major determinant for replication. Despite the fact that the majority of the PN mutants were able to replicate efficiently, they were outcompeted by parental YFV-17D virus following repeated passages in double-infected cell cultures. Surprisingly, some of the virus mutants at the first and/or the ninth position that maintained the possibility of forming a base pair were found to have a similar fitness to YFV-17D under these conditions. Overall, these experiments suggest that YFV is less dependent on sequence conservation of the PN motif for replication in animal cells than West Nile virus. However, in animal cell culture, YFV has a preference for the wt CACAG PN sequence. The molecular mechanisms behind this preference remain to be elucidated.

scholarly journals Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3′ stem–loop structure is not required for replication

2007 ◽  
Vol 88 (8) ◽  
pp. 2361-2361
Author(s):  
Patrícia A. G. C. Silva ◽  
Richard Molenkamp ◽  
Tim J. Dalebout ◽  
Nathalie Charlier ◽  
Johan H. Neyts ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Fever Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

scholarly journals Size Heterogeneity in the 3′ Noncoding Region of South American Isolates of Yellow Fever Virus

2005 ◽  
Vol 79 (6) ◽  
pp. 3807-3821 ◽  
Author(s):  
Juliet E. Bryant ◽  
Pedro F. C. Vasconcelos ◽  
Rene C. A. Rijnbrand ◽  
J. P. Mutebi ◽  
Stephen Higgs ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Growth Kinetics ◽  
Yellow Fever Virus ◽  
Biological Significance ◽  
Fever Virus ◽  
Noncoding Region ◽  
South American ◽  
Genotype I ◽  
Stem Loop ◽  
Size Heterogeneity

ABSTRACT The 3′ noncoding region (3′ NCR) of flaviviruses contains secondary and tertiary structures essential for virus replication. Previous studies of yellow fever virus (YFV) and dengue virus have found that modifications to the 3′ NCR are sometimes associated with attenuation in vertebrate and/or mosquito hosts. The 3′ NCRs of 117 isolates of South American YFV have been examined, and major deletions and/or duplications of conserved RNA structures have been identified in several wild-type isolates. Nineteen isolates (designated YF-XL isolates) from Brazil, Trinidad, and Venezuela, dating from 1973 to 2001, exhibited a 216-nucleotide (nt) duplication, yielding a tandem repeat of conserved hairpin, stem-loop, dumbbell, and pseudoknot structures. YF-XL isolates were found exclusively within one subclade of South American genotype I YFV. One Brazilian isolate exhibited, in addition to the 216-nt duplication, a deletion of a 40-nt repeated hairpin (RYF) motif (YF-XL-ΔRYF). To investigate the biological significance of these 3′ NCR rearrangements, YF-XL-ΔRYF and YF-XL isolates, as well as other South American YFV isolates, were evaluated for three phenotypes: growth kinetics in cell culture, neuroinvasiveness in suckling mice, and ability to replicate and produce disseminated infections in Aedes aegypti mosquitoes. YF-XL-ΔRYF and YF-XL isolates showed growth kinetics and neuroinvasive characteristics comparable to those of typical South American YFV isolates, and mosquito infectivity trials demonstrated that both types of 3′ NCR variants were capable of replication and dissemination in a laboratory-adapted colony of A. aegypti.

scholarly journals Influence of the 5′-proximal elements of the 5′-untranslated region of classical swine fever virus on translation and replication

2011 ◽  
Vol 92 (5) ◽  
pp. 1087-1096 ◽  
Author(s):  
Ming Xiao ◽  
Yujing Wang ◽  
Zailing Zhu ◽  
Chengli Ding ◽  
Jialin Yu ◽  
...  
Keyword(s):  
Classical Swine Fever Virus ◽  
Untranslated Region ◽  
Classical Swine Fever ◽  
Fever Virus ◽  
Loop Structure ◽  
Terminal Sequence ◽  
Entry Site ◽  
Stem Loop ◽  
Internal Ribosome Entry ◽  
Stem Loop Structure

The 5′-terminal sequence spanning nt 1–29 of the 5′-untranslated region of classical swine fever virus (CSFV) forms a 5′-proximal stem–loop structure known as domain Ia. Deletions and replacement mutations were performed to examine the role of this domain. Deletion of the 5′-proximal nucleotides and disruption of the stem–loop structure greatly increased internal ribosome entry site-mediated translation but abolished the replication of the replicons. Internal deletions resulting in a change in the size of the loop of domain Ia, and even removal of the entire domain, did not substantially change the translation activity, but reduced the replication of CSFV replicons provided the replicons contained the extreme 5′-GUAU terminal sequence. Internal replacements leading to a change in the nucleotide sequence of the loop did not alter the translation and replication activities of the CSFV RNA replicon, and did not influence the rescue of viruses and growth characteristics of new viruses. These results may be important for our understanding of the regulation of translation, replication and encapsidation in CSFV and other positive-sense RNA viruses.

968: Gelsolin Gene Silencing Involving Unusual Chromatin Structures and a Novel Stem Loop Structure of the Promoter Region in Human Bladder Cancer

2004 ◽  
Vol 171 (4S) ◽  
pp. 256-257
Author(s):  
Kazunori Haga ◽  
Ataru Sazawa ◽  
Toru Harabayashi ◽  
Nobuo Shinohara ◽  
Minoru Nomoto ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Silencing ◽  
Promoter Region ◽  
Loop Structure ◽  
Human Bladder Cancer ◽  
Human Bladder ◽  
Stem Loop ◽  
Stem Loop Structure

Detection and sequence analysis of an imperfect stem-loop structure in cis activating gene element from SV40PolyA

2011 ◽  
Vol 33 (4) ◽  
pp. 337-346
Author(s):  
Hong-Gang WANG ◽  
Huan MA ◽  
Zhu LI ◽  
Bin ZHANG ◽  
Xiang-Yang JING ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
In Cis ◽  
Gene Element

scholarly journals Yellow fever virus outbreak in Brazil under current and future climate

2021 ◽  
Vol 6 ◽  
pp. 664-677
Author(s):  
Tara Sadeghieh ◽  
Jan M. Sargeant ◽  
Amy L. Greer ◽  
Olaf Berke ◽  
Guillaume Dueymes ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Fever Virus ◽  
Future Climate

scholarly journals Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

2021 ◽  
Vol 14 (2) ◽  
pp. 121
Author(s):  
André Miranda ◽  
Tiago Santos ◽  
Eric Largy ◽  
Carla Cruz
Keyword(s):  
Loop Structure ◽  
Binding Properties ◽  
Stem Loop ◽  
Affinity Ligand ◽  
Stem Loop Structure ◽  
Topology Maintenance ◽  
G Quadruplex ◽  
Dimeric Form ◽  
Biophysical Techniques ◽  
Melting Experiments

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

scholarly journals Yellow Fever Outbreak in Eastern Senegal, 2020–2021

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1475
Author(s):  
Moussa Moïse Diagne ◽  
Marie Henriette Dior Ndione ◽  
Alioune Gaye ◽  
Mamadou Aliou Barry ◽  
Diawo Diallo ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Mosquito Species ◽  
Virus Transmission ◽  
Genomic Analysis ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
World Health ◽  
Effective Vaccine ◽  
Ministry Of Health

Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3′UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal.

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