scholarly journals Comparative analysis of protein evolution and RNA structural changes in the genome of pre-epidemic and epidemic Zika virus

2016 ◽  
Author(s):  
Arunachalam Ramaiah ◽  
Lei Dai ◽  
Deisy Contreras ◽  
Sanjeev Sinha ◽  
Ren Sun ◽  
...  
Keyword(s):  
Virus Replication ◽  
Protein Evolution ◽  
Zika Virus ◽  
Structural Changes ◽  
Yellow Fever Virus ◽  
Rna Structures ◽  
Stem Loop ◽  
Human Host ◽  
Genome Wide ◽  
Poor Pregnancy Outcome

ABSTRACTZika virus (ZIKV) infection is associated with microcephaly, neurological disorders and poor pregnancy outcome1-3and no vaccine is available. Although ZIKV was first discovered in 1947, the exact mechanism of virus replication and pathogenesis still remains unknown. Recent outbreaks of Zika virus in the Americas clearly suggest a better adaptation of viral strains to human host. Understanding the conserved and adaptive features in the evolution of ZIKV genome will reveal the molecular mechanism of virus replication and host adaptation. Here, we show comprehensive analysis of protein evolution and changes in RNA secondary structures of ZIKV strains including the current 2015-16 outbreak. To identify the constraints on ZIKV evolution, selection pressure at individual codons, immune epitopes, co-evolving sites, and RNA structures were analyzed. The proteome of current 2015/16 epidemic ZIKV strains of Asian genotype is found to be genetically conserved due to genome-wide negative selection on codons, with limited positive selection. Predicted RNA structures at the 5’ and 3’ ends of ZIKV strains reveal substantial changes such as an additional stem loop which makes it similar to that of Yellow Fever Virus. Concisely, the targeted changes at both the amino acid and the RNA levels contribute to the better adaptation of ZIKV strains to human host with an enhanced neurotropism.

scholarly journals Wolbachia wStri Blocks Zika Virus Growth at Two Independent Stages of Viral Replication

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
M. J. Schultz ◽  
A. L. Tan ◽  
C. N. Gray ◽  
S. Isern ◽  
S. F. Michael ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Viral Replication ◽  
Yellow Fever ◽  
Virus Replication ◽  
Zika Virus ◽  
Chikungunya Virus ◽  
Yellow Fever Virus ◽  
Rna Viruses ◽  
Content Type ◽  
Infected Cells

ABSTRACTMosquito-transmitted viruses are spread globally and present a great risk to human health. Among the many approaches investigated to limit the diseases caused by these viruses are attempts to make mosquitos resistant to virus infection. Coinfection of mosquitos with the bacteriumWolbachia pipientisfrom supergroup A is a recent strategy employed to reduce the capacity for major vectors in theAedesmosquito genus to transmit viruses, including dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV). Recently, a supergroup BWolbachia wStri, isolated fromLaodelphax striatellus, was shown to inhibit multiple lineages of ZIKV inAedes albopictuscells. Here, we show thatwStri blocks the growth of positive-sense RNA viruses DENV, CHIKV, ZIKV, and yellow fever virus by greater than 99.9%.wStri presence did not affect the growth of the negative-sense RNA viruses LaCrosse virus or vesicular stomatitis virus. Investigation of the stages of the ZIKV life cycle inhibited bywStri identified two distinct blocks in viral replication. We found a reduction of ZIKV entry intowStri-infected cells. This was partially rescued by the addition of a cholesterol-lipid supplement. Independent of entry, transfected viral genome was unable to replicate inWolbachia-infected cells. RNA transfection and metabolic labeling studies suggested that this replication defect is at the level of RNA translation, where we saw a 66% reduction in mosquito protein synthesis inwStri-infected cells. This study’s findings increase the potential for application ofwStri to block additional arboviruses and also identify specific blocks in viral infection caused byWolbachiacoinfection.IMPORTANCEDengue, Zika, and yellow fever viruses are mosquito-transmitted diseases that have spread throughout the world, causing millions of infections and thousands of deaths each year. Existing programs that seek to contain these diseases through elimination of the mosquito population have so far failed, making it crucial to explore new ways of limiting the spread of these viruses. Here, we show that introduction of an insect symbiont,Wolbachia wStri, into mosquito cells is highly effective at reducing yellow fever virus, dengue virus, Zika virus, and Chikungunya virus production. Reduction of virus replication was attributable to decreases in entry and a strong block of virus gene expression at the translational level. These findings expand the potential use ofWolbachia wStri to block viruses and identify two separate steps for limiting virus replication in mosquitos that could be targeted via microbes or other means as an antiviral strategy.

scholarly journals Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

Nature ◽  
2010 ◽  
Vol 463 (7282) ◽  
pp. 818-822 ◽  
Author(s):  
Alexander Karlas ◽  
Nikolaus Machuy ◽  
Yujin Shin ◽  
Klaus-Peter Pleissner ◽  
Anita Artarini ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Replication ◽  
Rnai Screen ◽  
Host Factors ◽  
Human Host ◽  
Genome Wide ◽  
Influenza Virus Replication ◽  
Human Host Factors

scholarly journals Genome-wide discovery of local RNA structural elements in Zika virus

2018 ◽  
Author(s):  
Ryan J Andrews ◽  
Julien Roche ◽  
Walter N Moss
Keyword(s):  
Zika Virus ◽  
Genome Replication ◽  
Rna Structures ◽  
Coding Region ◽  
Step Size ◽  
Base Pairs ◽  
Local Structures ◽  
Genome Wide ◽  
Viral Polyprotein ◽  
Functional Rna

In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. In the presented approach, all base pairs from all analysis windows are considered and weighted by favorable folding metrics throughout all windows. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. This approach was applied to the Zika virus (ZIKV) genome. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain-Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. Our approach is able to successfully identify and model the structures of these regions, while also finding additional regions likely to form functional RNA structures throughout the viral polyprotein coding region. All data for the ZIKV genome have been archived at the RNAStructuromeDB, a repository of RNA folding data for humans and their pathogens.

scholarly journals ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6136 ◽  
Author(s):  
Ryan J. Andrews ◽  
Julien Roche ◽  
Walter N. Moss
Keyword(s):  
Zika Virus ◽  
Genome Replication ◽  
Rna Structures ◽  
Step Size ◽  
Base Pairs ◽  
Rna Motifs ◽  
Tertiary Structures ◽  
Local Structures ◽  
Genome Wide ◽  
Functional Rna

In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.

scholarly journals Genome-wide discovery of local RNA structural elements in Zika virus

2018 ◽  
Author(s):  
Ryan J Andrews ◽  
Julien Roche ◽  
Walter N Moss
Keyword(s):  
Zika Virus ◽  
Genome Replication ◽  
Rna Structures ◽  
Coding Region ◽  
Step Size ◽  
Base Pairs ◽  
Local Structures ◽  
Genome Wide ◽  
Viral Polyprotein ◽  
Functional Rna

In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. In the presented approach, all base pairs from all analysis windows are considered and weighted by favorable folding metrics throughout all windows. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. This approach was applied to the Zika virus (ZIKV) genome. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain-Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. Our approach is able to successfully identify and model the structures of these regions, while also finding additional regions likely to form functional RNA structures throughout the viral polyprotein coding region. All data for the ZIKV genome have been archived at the RNAStructuromeDB, a repository of RNA folding data for humans and their pathogens.

The P-MAPA immunomodulator partially prevents apoptosis induced by Zika virus infection in THP-1 cells

2020 ◽  
Vol 21 ◽  
Author(s):  
Morganna C. Lima ◽  
Elisa A. N. Azevedo ◽  
Clarice N. L. de Morais ◽  
Larissa I. O. de Sousa ◽  
Bruno M. Carvalho ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cell Death ◽  
Virus Infection ◽  
Virus Replication ◽  
Zika Virus ◽  
Mammalian Cells ◽  
Caspase 3 ◽  
Neurological Complications ◽  
Zika Virus Infection

Background: Zika virus is an emerging arbovirus of global importance. ZIKV infection is associated with a range of neurological complications such as the Congenital Zika Syndrome and Guillain Barré Syndrome. Despite the magnitude of recent outbreaks, there is no specific therapy to prevent or to alleviate disease pathology. Objective: To investigate the role of P-MAPA immunomodulator in Zika-infected THP-1 cells. Methods: THP-1 cells were subjected at Zika virus infection (Multiplicity of Infection = 0.5) followed by treatment with P-MAPA for until 96 hours post-infection. After that, the cell death was analyzed by annexin+/ PI+ and caspase 3/ 7+ staining by flow cytometry. In addition, the virus replication and cell proliferation were accessed by RT-qPCR and Ki67 staining, respectively. Results: We demonstrate that P-MAPA in vitro treatment significantly reduces Zika virus-induced cell death and caspase-3/7 activation on THP-1 infected cells, albeit it has no role in virus replication and cell proliferation. Conclusions: Our study reveals that P-MAPA seems to be a satisfactory alternative to inhibits the effects of Zika virus infection in mammalian cells.

Valosin‐containing protein ATPase activity regulates the morphogenesis of Zika virus replication organelles and virus‐induced cell death

2021 ◽  
Author(s):  
Anaïs Anton ◽  
Clément Mazeaud ◽  
Wesley Freppel ◽  
Claudia Gilbert ◽  
Nicolas Tremblay ◽  
...  
Keyword(s):  
Cell Death ◽  
Atpase Activity ◽  
Virus Replication ◽  
Zika Virus

scholarly journals Interactions between highly conserved U2 small nuclear RNA structures and Prp5p, Prp9p, Prp11p, and Prp21p proteins are required to ensure integrity of the U2 small nuclear ribonucleoprotein in Saccharomyces cerevisiae.

1994 ◽  
Vol 14 (9) ◽  
pp. 6337-6349 ◽  
Author(s):  
S E Wells ◽  
M Ares
Keyword(s):  
Synthetic Lethality ◽  
Small Nuclear Rna ◽  
Rna Structures ◽  
Stem Loop ◽  
U2 Snrna ◽  
Small Nuclear Ribonucleoprotein ◽  
U2 Snrnp ◽  
Nuclear Rna ◽  
Nuclear Ribonucleoprotein

Binding of U2 small nuclear ribonucleoprotein (snRNP) to the pre-mRNA is an early and important step in spliceosome assembly. We searched for evidence of cooperative function between yeast U2 small nuclear RNA (snRNA) and several genetically identified splicing (Prp) proteins required for the first chemical step of splicing, using the phenotype of synthetic lethality. We constructed yeast strains with pairwise combinations of 28 different U2 alleles with 10 prp mutations and found lethal double-mutant combinations with prp5, -9, -11, and -21 but not with prp3, -4, -8, or -19. Many U2 mutations in highly conserved or invariant RNA structures show no phenotype in a wild-type PRP background but render mutant prp strains inviable, suggesting that the conserved but dispensable U2 elements are essential for efficient cooperative function with specific Prp proteins. Mutant U2 snRNA fails to accumulate in synthetic lethal strains, demonstrating that interaction between U2 RNA and these four Prp proteins contributes to U2 snRNP assembly or stability. Three of the proteins (Prp9p, Prp11p, and Prp21p) are associated with each other and pre-mRNA in U2-dependent splicing complexes in vitro and bind specifically to synthetic U2 snRNA added to crude splicing extracts depleted of endogenous U2 snRNPs. Taken together, the results suggest that Prp9p, -11p, and -21p are U2 snRNP proteins that interact with a structured region including U2 stem loop IIa and mediate the association of the U2 snRNP with pre-mRNA.

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