scholarly journals Late Male-Killing Viruses in Homona magnanima Identified as Osugoroshi Viruses, Novel Members of Partitiviridae

2021 ◽  
Vol 11 ◽  
Author(s):  
Ryosuke Fujita ◽  
Maki N. Inoue ◽  
Takumi Takamatsu ◽  
Hiroshi Arai ◽  
Mayu Nishino ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Rna Polymerase ◽  
Rna Viruses ◽  
Rna Virus ◽  
Horizontal Transmission ◽  
Rna Dependent Rna Polymerase ◽  
Double Stranded Rna ◽  
First Report ◽  
Male Killing ◽  
Male Specific

Late male-killing, a male-specific death after hatching, is a unique phenotype found in Homona magnanima, oriental tea tortrix. The male-killing agent was suspected to be an RNA virus, but details were unknown. We herein successfully isolated and identified the putative male-killing virus as Osugoroshi viruses (OGVs). The three RNA-dependent RNA polymerase genes detected were phylogenetically related to Partitiviridae, a group of segmented double-stranded RNA viruses. Purified dsRNA from a late male-killing strain of H. magnanima revealed 24 segments, in addition to the RdRps, with consensus terminal sequences. These segments included the previously found male-killing agents MK1068 (herein OGV-related RNA16) and MK1241 (OGV-related RNA7) RNAs. Ultramicroscopic observation of purified virions, which induced late male-killing in the progeny of injected moths, showed sizes typical of Partitiviridae. Mathematical modeling showed the importance of late male-killing in facilitating horizontal transmission of OGVs in an H. magnanima population. This study is the first report on the isolation of partiti-like virus from insects, and one thought to be associated with late male-killing, although the viral genomic contents and combinations in each virus are still unknown.

scholarly journals Functions of Conserved Motifs in the RNA-Dependent RNA Polymerase of a Yeast Double-Stranded RNA Virus

1998 ◽  
Vol 72 (5) ◽  
pp. 4427-4429 ◽  
Author(s):  
Eric Routhier ◽  
Jeremy A. Bruenn
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Virus ◽  
Rna Dependent Rna Polymerase ◽  
Conserved Motifs ◽  
Double Stranded Rna ◽  
Conserved Regions

ABSTRACT At least eight conserved motifs are visible in the totivirus RNA-dependent RNA polymerase (RDRP). We have systematically altered each of these in the Saccharomyces cerevisiaedouble-stranded RNA virus ScVL1 by substituting the conserved motifs from a giardiavirus. The results help define the conserved regions of the RDRP involved in polymerase function and those essential for other reasons.

scholarly journals NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

2022 ◽  
Author(s):  
Shoichi Sakaguchi ◽  
Syun-ichi Urayama ◽  
Yoshihiro Takaki ◽  
Hong Wu ◽  
Youichi Suzuki ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Viruses ◽  
Rna Virus ◽  
Sequence Similarity ◽  
Virus Detection ◽  
Detection Methods ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Rna Dependent Rna Polymerase ◽  
Multiple Sequence

RNA viruses are distributed in various environments, and most RNA viruses have been recently identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify their sequences. Therefore, this study generated a dataset of RNA-dependent RNA polymerase (RdRp) domains essential for all RNA viruses belonging to Orthornavirae. Also, the collected genes with RdRp domains from various RNA viruses were clustered by amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than five. Using the 1,467 HMM profiles, we detected RdRp domains in the RefSeq RNA virus sequences, combined the hit sequences with the RdRp domains, and reconstructed the HMM profiles. As a result, 2,234 HMM profiles were generated from 12,316 RdRp domain sequences, and the dataset was named NeoRdRp. Additionally, using the UniProt dataset, we confirmed that almost all NeoRdRp HMM profiles could specifically detect RdRps in Orthornavirae. Furthermore, we compared the NeoRdRp dataset with two previously reported RNA virus detection methods to detect RNA virus sequences from metatranscriptome sequencing data. Our methods can identify most of the RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. The NeoRdRp can be improved by repeatedly adding new RdRp sequences and can be expected to be widely applied as a system for detecting various RNA viruses from metatranscriptome data.

scholarly journals A Narnavirus -Like Element from the Trypanosomatid Protozoan Parasite Leptomonas seymouri

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Lon-Fye Lye ◽  
Natalia S. Akopyants ◽  
Deborah E. Dobson ◽  
Stephen M. Beverley
Keyword(s):  
Rna Polymerase ◽  
Rna Virus ◽  
Protozoan Parasite ◽  
Database Search ◽  
Genome Sequences ◽  
Rna Dependent Rna Polymerase ◽  
First Report

Genome sequences were determined for a novel RNA virus, Leptomonas seymouri Narna-like virus 1 (LepseyNLV1). A 2.9-kb segment encodes an RNA-dependent RNA polymerase (RdRp), while a smaller 1.5-kb segment showed no database search matches. This is the first report of bisegmented Narnaviridae from insect trypanosomatids.

scholarly journals Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles

2015 ◽  
Vol 90 (5) ◽  
pp. 2446-2454 ◽  
Author(s):  
Enzo Z. Poirier ◽  
Bryan C. Mounce ◽  
Kathryn Rozen-Gagnon ◽  
Peter Jan Hooikaas ◽  
Kenneth A. Stapleford ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Viruses ◽  
Rna Virus ◽  
Point Mutations ◽  
Viral Fitness ◽  
Dependent Manner ◽  
Rna Dependent Rna Polymerase ◽  
Live Attenuated Vaccine ◽  
Defective Interfering Particles

ABSTRACTLow-fidelity RNA-dependent RNA polymerases for many RNA virus mutators have been shown to confer attenuated phenotypes, presumably due to increased mutation rates. Additionally, for many RNA viruses, replication to high titers results in the production of defective interfering particles (DIs) that also attenuate infection. We hypothesized that fidelity, recombination, and DI production are tightly linked. We show that a Sindbis virus mutator replicating at a high multiplicity of infection manifests an earlier and greater accumulation of DIs than its wild-type counterpart. The isolated DIs interfere with the replication of full-length virus in a dose-dependent manner. Importantly, the ability of the mutator virus to overproduce DIs could be linked to an increased recombination frequency. These data confirm that RNA-dependent RNA polymerase fidelity and recombination are inversely correlated for this mutator. Our findings suggest that defective interference resulting from higher recombination rates may be more detrimental to RNA virus mutators than the increase in mutational burden.IMPORTANCEReplication, adaptation, and evolution of RNA viruses rely in large part on their low-fidelity RNA-dependent RNA polymerase. Viruses artificially modified in their polymerases to decrease fidelity (mutator viruses) are attenuatedin vivo, demonstrating the important role of fidelity in viral fitness. However, attenuation was attributed solely to the modification of the viral mutation rate and the accumulation of detrimental point mutations. In this work, we described an additional phenotype of mutator viruses: an increased recombination rate leading to defective interfering particle (DI) overproduction. Because DIs are known for their inhibitory effect on viral replication, our work suggests that fidelity variants may be attenuatedin vivovia several mechanisms. This has important implications in the development of fidelity variants as live attenuated vaccine strains.

scholarly journals Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus  6 from De Novo Initiation to Elongation

2011 ◽  
Vol 86 (5) ◽  
pp. 2837-2849 ◽  
Author(s):  
S. Wright ◽  
M. M. Poranen ◽  
D. H. Bamford ◽  
D. I. Stuart ◽  
J. M. Grimes
Keyword(s):  
Rna Polymerase ◽  
De Novo ◽  
Rna Virus ◽  
Rna Dependent Rna Polymerase ◽  
Double Stranded Rna

scholarly journals Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Natalie D. Collins ◽  
Andrew S. Beck ◽  
Steven G. Widen ◽  
Thomas G. Wood ◽  
Stephen Higgs ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Rna Viruses ◽  
Rna Virus ◽  
Infectious Clone ◽  
Vaccine Virus ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Replication Complex

ABSTRACT One paradigm to explain the complexity of viral RNA populations is that the low fidelity of the RNA-dependent RNA polymerase (RdRp) drives high mutation rates and consequently genetic diversity. Like most RNA viruses, wild-type yellow fever virus (YFV) replication is error-prone due to the lack of proofreading by the virus-encoded RdRp. However, there is evidence that replication of the live attenuated YF vaccine virus 17D, derived from wild-type strain Asibi, is less error-prone than wild-type RNA viruses. Recent studies comparing the genetic diversity of wild-type Asibi and 17D vaccine virus found that wild-type Asibi has the typical heterogeneous population of an RNA virus, while there is limited intra- and interpopulation variability of 17D vaccine virus. Utilizing chimeric and mutant infectious clone-derived viruses, we show that high and low genetic diversity profiles of wild-type Asibi virus and vaccine virus 17D, respectively, are multigenic. Introduction of either structural (pre-membrane and envelope) genes or NS2B or NS4B substitutions into the Asibi and 17D backbone resulted in altered variant population, nucleotide diversity, and mutation frequency compared to the parental viruses. Additionally, changes in genetic diversity of the chimeric and mutant viruses correlated with the phenotype of multiplication kinetics in human alveolar A549 cells. Overall, the paradigm that only the error-prone RdRp controls genetic diversity needs to be expanded to address the role of other genes in genetic diversity, and we hypothesize that it is the replication complex as a whole and not the RdRp alone that controls genetic diversity. IMPORTANCE With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity can contribute to both attenuation and virulence and the paradigm is that this is controlled by the error-prone RNA-dependent RNA polymerase (RdRp). Since wild-type yellow fever virus (YFV) strain Asibi has genetic diversity typical of a wild-type RNA virus, while 17D virus vaccine has limited diversity, it provides a unique opportunity to investigate RNA population theory in the context of a well-characterized live attenuated vaccine. Utilizing infectious clone-derived viruses, we show that genetic diversity of RNA viruses is complex and that multiple genes, including structural genes and NS2B and NS4B genes also contribute to genetic diversity. We suggest that the replication complex as a whole, rather than only RdRp, drives genetic diversity, at least for YFV.

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