Conserved Sequence Motifs for Nucleoside Triphosphate Binding Unique to Turreted
            <i>Reoviridae</i>
            Members and Coltiviruses

Nibert, Max L.; Kim, Jong-Hwa

doi:10.1128/jvi.78.10.5528-5530.2004

Cited by 26 publications

(22 citation statements)

References 36 publications

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“…Other similarities identified by FASTA 3 included those found between MYRV-1/Cp9B21 S6 and a Nilaparvata lugens virus (NLRV) inner core protein with the purine-binding motif (Nakashima et al, 1996) (identity, 22?1 %; optimal score, 110; overlap, 340 aa). Such a domain was recently described as being unique to turreted members of the family Reoviridae and coltiviruses (Nibert & Kim, 2004). Both motifs A and B described in that study were identified in MYRV-1/Cp9B21 (Fig.…”

Section: Sequences Of Myrv-1/cp9b21 Segments S4-s11supporting

confidence: 56%

Complete genome sequence of Mycoreovirus-1/Cp9B21, a member of a novel genus within the family Reoviridae, isolated from the chestnut blight fungus Cryphonectria parasitica

Suzuki

Supyani

Maruyama

et al. 2004

Journal of General Virology

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Mycoreovirus 1 (MYRV-1) is the type species of the newly described genus Mycoreovirus of the large virus family Reoviridae. The virus was isolated from a hypovirulent strain (9B21) of the chestnut blight fungus, Cryphonectria parasitica. A previous study showed that double-shelled particles introduced to fungal spheroplasts resulted in stably infected colonies. Of the 11 double-stranded RNA genomic segments (S1-S11), the three largest (S1-S3) were sequenced previously and shown to have moderate levels of similarity to the homologous segments of mammal-pathogenic coltiviruses (Eyach virus and Colorado tick fever virus) and another fungus-infecting reovirus, Mycoreovirus 3 of Rosellinia necatrix strain W370 (MYRV-3/RnW370). The sequences of the remaining segments (S4-S11) are reported here. All of the segments have single ORFs on their positive strands and the terminal sequences 59-GAUCA----GCAGUCA-39 are conserved among currently and previously sequenced segments. Oligo-cap analysis showed that the positive strands of the genomic segments are capped, whereas the negative strands are not. Similarities among the four evolutionarily related viruses include low or moderate levels of amino acid sequence identity (14?7-34?2 %) and isoelectric points among equivalent polypeptides, e.g. proteins encoded by segments S4 and S5 of the four viruses. Phylogenetic analysis indicated that MYRV-1/Cp9B21 is related more closely to MYRV-3/RnW370 than to the coltiviruses. An interesting dissimilarity is found in codon-choice pattern among the four viruses, i.e. MYRV-1/Cp9B21 segments have a lower frequency of [XYG+XYC] than corresponding segments of the other viruses, suggesting a possible adjustment of virus codon usage to their host environments.

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Section: Sequences Of Myrv-1/cp9b21 Segments S4-s11supporting

confidence: 56%

Complete genome sequence of Mycoreovirus-1/Cp9B21, a member of a novel genus within the family Reoviridae, isolated from the chestnut blight fungus Cryphonectria parasitica

Suzuki

Supyani

Maruyama

et al. 2004

Journal of General Virology

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“…The N-terminal domain is formed by two small β-sheets and several α-helices and the main body of the C-terminal domain is a Walker-A α/β motif, a well-known NTP-binding motif found in the P-loop kinase family of proteins. Sequence analysis predicted an NTP binding site in VP4 (Refs 14,15). Indeed, the VP4 structure contains a GTP molecule at the predicted NTP binding site of the C-terminal domain (Fig.…”

mentioning

confidence: 99%

“…But, remarkably, bluetongue virus VP4 is an RNA capping enzyme and its α/β domain does not bind GTP (Ref 16). CPV VP4 and its homologs in other dsRNA viruses have been speculated to function as an NTPase, as an RNA 5′-triphosphatase (RTPase) or as a helicase 14,17,18 . Our structure supports VP4 as an NTPase but shows no interaction with dsRNA, suggesting that VP4 is unlikely a helicase.…”

mentioning

confidence: 99%

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

Zhang

Ding

et al. 2015

Nature

111

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Summary Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented dsRNAs inside the viral capsid and carry out endogenous mRNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoEM and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the total 10 segmented dsRNAs in CPV are organized with 10 TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. TEC consists of two extensively-interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes significant conformational change when converted from q-CPV to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An N-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.

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“…5B), suggesting that RnMyRV3-S6 is preferentially diced. The protein encoded by RnMyRV3-S6 has conserved mu2-like nucleoside triphosphate (NTP)-binding motifs (59), and the mu2 protein of mammalian orthoreoviruses is associated with viral RNA synthesis (60). It is unclear whether the relatively high vsRNA abundance is associated with the potential gene function of RnMyRV3-S6.…”

Section: Discussionmentioning

confidence: 99%

Differential Inductions of RNA Silencing among Encapsidated Double-Stranded RNA Mycoviruses in the White Root Rot Fungus Rosellinia necatrix

Yaegashi

Shimizu

Ito

et al. 2016

J Virol

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RNA silencing acts as a defense mechanism against virus infection in a wide variety of organisms. Here, we investigated inductions of RNA silencing against encapsidated double-stranded RNA (dsRNA) fungal viruses (mycoviruses), including a partitivirus (RnPV1), a quadrivirus (RnQV1), a victorivirus (RnVV1), a mycoreovirus (RnMyRV3), and a megabirnavirus (RnMBV1) in the phytopathogenic fungus Rosellinia necatrix. Expression profiling of RNA silencing-related genes revealed that a dicer-like gene, an Argonaute-like gene, and two RNA-dependent RNA polymerase genes were upregulated by RnMyRV3 or RnMBV1 infection but not by other virus infections or by constitutive expression of dsRNA in R. necatrix. Massive analysis of viral small RNAs (vsRNAs) from the five mycoviruses showed that 19-to 22-nucleotide (nt) vsRNAs were predominant; however, their ability to form duplexes with 3= overhangs and the 5= nucleotide preferences of vsRNAs differed among the five mycoviruses. The abundances of 19-to 22-nt vsRNAs from RnPV1, RnQV1, RnVV1, RnMyRV3, and RnMBV1 were 6.8%, 1.2%, 0.3%, 13.0%, and 24.9%, respectively. Importantly, the vsRNA abundances and accumulation levels of viral RNA were not always correlated, and the origins of the vsRNAs were distinguishable among the five mycoviruses. These data corroborated diverse interactions between encapsidated dsRNA mycoviruses and RNA silencing. Moreover, a green fluorescent protein (GFP)-based sensor assay in R. necatrix revealed that RnMBV1 infection induced silencing of the target sensor gene (GFP gene and the partial RnMBV1 sequence), suggesting that vsRNAs from RnMBV1 activated the RNA-induced silencing complex. Overall, this study provides insights into RNA silencing against encapsidated dsRNA mycoviruses. IMPORTANCEEncapsidated dsRNA fungal viruses (mycoviruses) are believed to replicate inside their virions; therefore, there is a question of whether they induce RNA silencing. Here, we investigated inductions of RNA silencing against encapsidated dsRNA mycoviruses (a partitivirus, a quadrivirus, a victorivirus, a mycoreovirus, and a megabirnavirus) in Rosellinia necatrix. We revealed upregulation of RNA silencing-related genes in R. necatrix infected with a mycoreovirus or a megabirnavirus but not with other viruses, which was consistent with the relatively high abundances of vsRNAs from the two mycoviruses. We also showed common and different molecular features and origins of the vsRNAs from the five mycoviruses. Furthermore, we demonstrated the activation of RNA-induced silencing complex by mycoviruses in R. necatrix. Taken together, our data provide insights into an RNA silencing pathway against encapsidated dsRNA mycoviruses which is differentially induced among encapsidated dsRNA mycoviruses; that is, diverse replication strategies exist among encapsidated dsRNA mycoviruses. RNA silencing is a sequence-specific RNA degradation mechanism that is widely conserved among eukaryotic organisms, including animals, plants, and fungi (1-4). This mechanism is triggered by th...

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Conserved Sequence Motifs for Nucleoside Triphosphate Binding Unique to Turreted Reoviridae Members and Coltiviruses

Cited by 26 publications

References 36 publications

Complete genome sequence of Mycoreovirus-1/Cp9B21, a member of a novel genus within the family Reoviridae, isolated from the chestnut blight fungus Cryphonectria parasitica

Complete genome sequence of Mycoreovirus-1/Cp9B21, a member of a novel genus within the family Reoviridae, isolated from the chestnut blight fungus Cryphonectria parasitica

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

Differential Inductions of RNA Silencing among Encapsidated Double-Stranded RNA Mycoviruses in the White Root Rot Fungus Rosellinia necatrix

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