Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3ï¿½-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome.

The formation and modification of chromatin-like structure of human parvovirus B19 regulate viral genome replication and RNA processing

Virus Research ◽

10.1016/j.virusres.2017.03.001 ◽

2017 ◽

Vol 232 ◽

pp. 134-138 ◽

Cited By ~ 1

Author(s):

Huanzhou Xu ◽

Sujuan Hao ◽

Junmei Zhang ◽

Zhen Chen ◽

Hanzhong Wang ◽

...

Keyword(s):

Rna Processing ◽

Viral Genome ◽

Parvovirus B19 ◽

Genome Replication ◽

Human Parvovirus B19 ◽

NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing

Journal of Virology ◽

10.1128/jvi.02618-15 ◽

2015 ◽

Vol 90 (4) ◽

pp. 1718-1728 ◽

Cited By ~ 19

Author(s):

Olufemi O. Fasina ◽

Yanming Dong ◽

David J. Pintel

Keyword(s):

Rna Processing ◽

Alternative Polyadenylation ◽

Genome Replication ◽

Coding Region ◽

Content Type ◽

Mrna Transcripts ◽

Minute Virus ◽

Polyadenylation Sites ◽

The Right

ABSTRACTMinute virus of canines (MVC) is an autonomous parvovirus in the genusBocaparvovirus. It has a single promoter that generates a single pre-mRNA processed via alternative splicing and alternative polyadenylation to produce at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another complex site, (pA)p, within the capsid-coding region. During viral infection, the mRNAs must extend through (pA)p and undergo additional splicing of the immediately upstream 3D∕3A intron to access the capsid gene. MVC NP1 is a 22-kDa nuclear phosphoprotein unique to the genusBocaparvovirusof theParvovirinaewhich we have shown governs suppression of (pA)p independently of viral genome replication. We show here that in addition to suppression of (pA)p, NP1 is also required for the excision of the MVC 3D∕3A intron, independently of its effect on alternative polyadenylation. Mutations of the arginine∕serine (SR) di-repeats within the intrinsically disordered amino terminus of NP1 are required for splicing of the capsid transcript but not suppression of polyadenylation at (pA)p. 3′-end processing of MVC mRNAs at (pA)p is critical for viral genome replication and the optimal expression of NP1 and NS1. Thus, a finely tuned balance between (pA)p suppression and usage is necessary for efficient virus replication. NP1 is the first parvovirus protein implicated in RNA processing. Its characterization reveals another way that parvoviruses govern access to their capsid protein genes, namely, at the RNA level, by regulating the essential splicing of an intron and the suppression of an internal polyadenylation site.IMPORTANCETheParvovirinaeare small nonenveloped icosahedral viruses that are important pathogens in many animal species, including humans. Although parvoviruses have only subtle early-to-late expression shifts, they all regulate access to their capsid genes. Minute virus of canines (MVC) is an autonomous parvovirus in the genusBocaparvovirus. It has a single promoter generating a single pre-mRNA which is processed via alternative splicing and alternative polyadenylation to generate at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another, (pA)p, within the capsid-coding region. It had not been clear how the potent internal polyadenylation motif is suppressed to allow processing, export, and accumulation of the spliced capsid protein-encoding mRNAs. We show here that MVC NP1, the first parvovirus protein to be implicated in RNA processing, governs access to the MVC capsid gene by facilitating splicing and suppressing internal polyadenylation of MVC pre-mRNAs.

Autophagy inhibits viral genome replication and gene expression stages in West Nile virus infection

Virus Research ◽

10.1016/j.virusres.2014.07.016 ◽

2014 ◽

Vol 191 ◽

pp. 83-91 ◽

Cited By ~ 24

Author(s):

Shintaro Kobayashi ◽

Yasuko Orba ◽

Hiroki Yamaguchi ◽

Kenta Takahashi ◽

Michihito Sasaki ◽

...

Keyword(s):

Gene Expression ◽

West Nile Virus ◽

Virus Infection ◽

Viral Genome ◽

West Nile Virus Infection ◽

Genome Replication ◽

West Nile ◽

Dimerisation of the influenza virus RNA polymerase during viral genome replication

Access Microbiology ◽

10.1099/acmi.ac2019.po0145 ◽

2019 ◽

Vol 1 (1A) ◽

Author(s):

Alexander Walker ◽

Haitian Fan ◽

Loic Carrique ◽

Jeremy Keown ◽

David Bauer ◽

...

Keyword(s):

Influenza Virus ◽

Rna Polymerase ◽

Viral Genome ◽

Genome Replication ◽

Virus Rna ◽

Mosquito metabolomics reveal that dengue virus replication requires phospholipid reconfiguration via the remodeling cycle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015095117 ◽

2020 ◽

Vol 117 (44) ◽

pp. 27627-27636

Author(s):

Thomas Vial ◽

Wei-Lian Tan ◽

Eric Deharo ◽

Dorothée Missé ◽

Guillaume Marti ◽

...

Keyword(s):

Dengue Virus ◽

Viral Genome ◽

De Novo ◽

Genome Replication ◽

Mosquito Vector ◽

Phospholipid Biosynthesis ◽

Replication Complex ◽

Mosquito Cells ◽

Blood Meals

Dengue virus (DENV) subdues cell membranes for its cellular cycle by reconfiguring phospholipids in humans and mosquitoes. Here, we determined how and why DENV reconfigures phospholipids in the mosquito vector. By inhibiting and activating the de novo phospholipid biosynthesis, we demonstrated the antiviral impact of de novo–produced phospholipids. In line with the virus hijacking lipids for its benefit, metabolomics analyses indicated that DENV actively inhibited the de novo phospholipid pathway and instead triggered phospholipid remodeling. We demonstrated the early induction of remodeling during infection by using isotope tracing in mosquito cells. We then confirmed in mosquitoes the antiviral impact of de novo phospholipids by supplementing infectious blood meals with a de novo phospholipid precursor. Eventually, we determined that phospholipid reconfiguration was required for viral genome replication but not for the other steps of the virus cellular cycle. Overall, we now propose that DENV reconfigures phospholipids through the remodeling cycle to modify the endomembrane and facilitate formation of the replication complex. Furthermore, our study identified de novo phospholipid precursor as a blood determinant of DENV human-to-mosquito transmission.

Adenovirus Late-Phase Infection Is Controlled by a Novel L4 Promoter

Journal of Virology ◽

10.1128/jvi.00107-10 ◽

2010 ◽

Vol 84 (14) ◽

pp. 7096-7104 ◽

Cited By ~ 22

Author(s):

Susan J. Morris ◽

Gillian E. Scott ◽

Keith N. Leppard

Keyword(s):

Gene Expression ◽

Intermediate Phase ◽

Expression Patterns ◽

Late Phase ◽

Adenovirus Vector ◽

Human Adenovirus ◽

Late Gene ◽

Genome Replication ◽

Late Gene Expression ◽

ABSTRACT During human adenovirus 5 infection, a temporal cascade of gene expression leads ultimately to the production of large amounts of the proteins needed to construct progeny virions. However, the mechanism for the activation of the major late gene that encodes these viral structural proteins has not been well understood. We show here that two key positive regulators of the major late gene, L4-22K and L4-33K, previously thought to be expressed under the control of the major late promoter itself, initially are expressed from a novel promoter that is embedded within the major late gene and dedicated to their expression. This L4 promoter is required for late gene expression and is activated by a combination of viral protein activators produced during the infection, including E1A, E4 Orf3, and the intermediate-phase protein IVa2, and also by viral genome replication. This new understanding redraws the long-established view of how adenoviral gene expression patterns are controlled and offers new ways to manipulate that gene expression cascade for adenovirus vector applications.

Dual Role of a Viral Polymerase in Viral Genome Replication and Particle Self-Assembly

mBio ◽

10.1128/mbio.01242-18 ◽

2018 ◽

Vol 9 (5) ◽

Cited By ~ 2

Author(s):

Xiaoyu Sun ◽

Serban L. Ilca ◽

Juha T. Huiskonen ◽

Minna M. Poranen

Keyword(s):

Self Assembly ◽

Viral Genome ◽

Rna Viruses ◽

The Self ◽

Genome Replication ◽

Double Stranded Rna ◽

Polymerase Complex ◽

Dsrna Viruses

ABSTRACTDouble-stranded RNA (dsRNA) viruses package several RNA-dependent RNA polymerases (RdRp) together with their dsRNA genome into an icosahedral protein capsid known as the polymerase complex. This structure is highly conserved among dsRNA viruses but is not found in any other virus group. RdRp subunits typically interact directly with the main capsid proteins, close to the 5-fold symmetric axes, and perform viral genome replication and transcription within the icosahedral protein shell. In this study, we utilizedPseudomonasphage Φ6, a well-established virus self-assembly model, to probe the potential roles of the RdRp in dsRNA virus assembly. We demonstrated that Φ6 RdRp accelerates the polymerase complex self-assembly process and contributes to its conformational stability and integrity. We highlight the role of specific amino acid residues on the surface of the RdRp in its incorporation during the self-assembly reaction. Substitutions of these residues reduce RdRp incorporation into the polymerase complex during the self-assembly reaction. Furthermore, we determined that the overall transcription efficiency of the Φ6 polymerase complex increased when the number of RdRp subunits exceeded the number of genome segments. These results suggest a mechanism for RdRp recruitment in the polymerase complex and highlight its novel role in virion assembly, in addition to the canonical RNA transcription and replication functions.IMPORTANCEDouble-stranded RNA viruses infect a wide spectrum of hosts, including animals, plants, fungi, and bacteria. Yet genome replication mechanisms of these viruses are conserved. During the infection cycle, a proteinaceous capsid, the polymerase complex, is formed. An essential component of this capsid is the viral RNA polymerase that replicates and transcribes the enclosed viral genome. The polymerase complex structure is well characterized for many double-stranded RNA viruses. However, much less is known about the hierarchical molecular interactions that take place in building up such complexes. Using the bacteriophage Φ6 self-assembly system, we obtained novel insights into the processes that mediate polymerase subunit incorporation into the polymerase complex for generation of functional structures. The results presented pave the way for the exploitation and engineering of viral self-assembly processes for biomedical and synthetic biology applications. An understanding of viral assembly processes at the molecular level may also facilitate the development of antivirals that target viral capsid assembly.

Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication

Journal of Virology ◽

10.1128/jvi.00563-18 ◽

2018 ◽

Vol 92 (15) ◽

Cited By ~ 3

Author(s):

Paula F. Zamora ◽

Liya Hu ◽

Jonathan J. Knowlton ◽

Roni M. Lahr ◽

Rodolfo A. Moreno ◽

...

Keyword(s):

Virus Replication ◽

Viral Genome ◽

Nonstructural Protein ◽

Dsrna Virus ◽

Genome Replication ◽

Nonstructural Proteins ◽

Content Type ◽

The Family ◽

ABSTRACTViral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, usingin vitroand cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCEFollowing infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the familyReoviridaeencode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the familyReoviridaediverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Usingin vitroand cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the familyReoviridaeassort and replicate their genomes.

Hitchhiking of Viral Genomes on Cellular Chromosomes

Annual Review of Virology ◽

10.1146/annurev-virology-092818-015716 ◽

2019 ◽

Vol 6 (1) ◽

pp. 275-296 ◽

Cited By ~ 3

Author(s):

Tami L. Coursey ◽

Alison A. McBride

Keyword(s):

Viral Genome ◽

Viral Infections ◽

Genome Replication ◽

Mitotic Chromosomes ◽

Dna Viruses ◽

Viral Genomes ◽

Barr Virus ◽

Dividing Cells ◽

Epstein Barr

Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.

ER-Shaping Atlastin Proteins Act as Central Hubs to Promote Flavivirus Replication and Virion Assembly

Proceedings ◽

10.3390/proceedings2020050031 ◽

2020 ◽

Vol 50 (1) ◽

pp. 31

Author(s):

Christopher J Neufeldt ◽

Mirko Cortese ◽

Pietro Scaturro ◽

Berati Cerikan ◽

Jeremy Wideman ◽

...

Keyword(s):

Viral Genome ◽

Viral Assembly ◽

Host Factors ◽

Genome Replication ◽

Membrane Structures ◽

Virion Assembly ◽

Virus Particles ◽

Membrane Invagination ◽

Flavivirus Infection

Members of the Flavivirus genus rely extensively on the host cell endomembrane network to generate complex membranous replication organelles (ROs) that facilitate viral genome replication and the production of virus particles. For dengue virus and Zika virus, these ROs included vesicles which are formed through membrane invagination into the endoplasmic reticulum (ER) lumen, termed invaginated vesicles or vesicle packets (VPs), as well as large areas of bundled smooth ER, termed convoluted membranes. Though the morphology of these virus-induced membrane structures has been well characterized, the viral and host constituents that make up flaviviral ROs are still poorly understood. Here, we identified a subset of ER resident proteins (atlastins), normally required for maintaining ER tubule networks, as critical host factors for flavivirus infection. Specific changes in atlastin (ATL) levels had dichotomous effects on flaviviruses with ATL2 depletion, leading to replication organelle defects and ATL3 depletion to changes in viral assembly/release pathways. These different depletion phenotypes allowed us to exploit virus infection to characterize non-conserved functional domains between the three atlastin paralogues. Additionally, we established the ATL interactome and show how it is reprogrammed upon viral infection. Screening of specific ATL interactors confirmed non-redundant ATL functions and identified a role for ATL3 in vesicle trafficking. Our data demonstrate that ATLs are central host factors that coordinate the ER network and shape the ER during flavivirus infection.