scholarly journals Splitting of RNA-dependent RNA Polymerase is Common in Narnaviridae: Identification of a type II Divided-RdRp from Deep-Sea Fungal Isolates

2021 ◽  
Author(s):  
Yuto Chiba ◽  
Sayoko Oiki ◽  
Zhao Yanjie ◽  
Yuriko Nagano ◽  
Syun-ichi Urayama ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Deep Sea ◽  
Rna Viruses ◽  
Essential Gene ◽  
Type I ◽  
Type Ii ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
Division Site ◽  
Untapped Resource

Abstract Until recently, it was accepted that RNA-dependent RNA polymerase (RdRp) is the only essential gene for non-retro RNA viruses and is encoded by a single open reading frame (ORF) in their genomes. However, divided-RdRps that are coded by two ORFs were discovered in fungal RNA viruses in a few independent reports. This discovery showed higher plasticity of viral RdRp than was expected. Among these divided-RdRps, the division site was common; specifically, the first part of the RdRp contains motifs F, A, and B, whereas the latter part possesses motifs C and D. These RdRps are designated as type I divided-RdRp and have been limited to viruses in a specific clade of Narnaviridae. In this study, to further understand the plasticity of RdRp, we explored viruses from deep sea-derived fungal strains as an untapped resource with a focus on Aspergillus section Versicolores. Seven strains were found to be infected by total of 13 viruses, and the viral RNA genomes were determined by FLDS technology. Among them, six strains belong to Narnaviridae. One of the strains, Aspergillus tennesseensis narnavirus 1, which infects an Aspergillus tennesseensis, has a divided RdRp with a new division site (referred to as type II divided-RdRp). A couple of sequences for possible type II divided-RdRps were also detected in public metagenomic datasets. Our findings reveal that different types of division in RdRp are present in the virosphere, and two types of RdRp splitting occurred independently within Narnaviridae.

scholarly journals An exploration of ambigrammatic sequences in narnaviruses

2019 ◽  
Author(s):  
Joseph L. DeRisi ◽  
Greg Huber ◽  
Amy Kistler ◽  
Hanna Retallack ◽  
Michael Wilkinson ◽  
...  
Keyword(s):  
De Novo ◽  
Rna Viruses ◽  
Nucleotide Substitutions ◽  
Rna Dependent Rna Polymerase ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Reverse Complement ◽  
Positive Sense ◽  
Reverse Strand ◽  
Coding Strategy

ABSTRACTNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

scholarly journals An exploration of ambigrammatic sequences in narnaviruses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Joseph L. DeRisi ◽  
Greg Huber ◽  
Amy Kistler ◽  
Hanna Retallack ◽  
Michael Wilkinson ◽  
...  
Keyword(s):  
De Novo ◽  
Rna Viruses ◽  
Nucleotide Substitutions ◽  
Rna Dependent Rna Polymerase ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Reverse Complement ◽  
Positive Sense ◽  
Reverse Strand ◽  
Coding Strategy

AbstractNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

scholarly journals Sequences at the 3′ Untranslated Region of Bamboo Mosaic Potexvirus RNA Interact with the Viral RNA-Dependent RNA Polymerase

2001 ◽  
Vol 75 (6) ◽  
pp. 2818-2824 ◽  
Author(s):  
Cheng-Yen Huang ◽  
Yih-Leh Huang ◽  
Menghsiao Meng ◽  
Yau-Heiu Hsu ◽  
Ching-Hsiu Tsai
Keyword(s):  
Rna Polymerase ◽  
Untranslated Region ◽  
Rna Binding ◽  
Bovine Liver ◽  
Viral Rna ◽  
Mobility Shift ◽  
Rna Dependent Rna Polymerase ◽  
Stem Loop ◽  
Competition Analysis ◽  
Reading Frame

ABSTRACT The 3′ untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a pseudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase (C.-P. Cheng and C.-H. Tsai, J. Mol. Biol. 288:555–565, 1999). Electrophoretic mobility shift and competition assays have now been used to demonstrate that theEscherichia coli-expressed RNA-dependent RNA polymerase domain (Δ893) derived from BaMV open reading frame 1 could specifically bind to the 3′ UTR of BaMV RNA. No competition was observed when bovine liver tRNAs or poly(I)(C) double-stranded homopolymers were used as competitors, and the cucumber mosaic virus 3′ UTR was a less efficient competitor. Competition analysis with different regions of the BaMV 3′ UTR showed that Δ893 binds to at least two independent RNA binding sites, stem-loop D and the poly(A) tail. Footprinting analysis revealed that Δ893 could protect the sequences at loop D containing the potexviral conserved hexamer motif and part of the stem of domain D from chemical cleavage.

Divalent cation-activated RNA synthesis in toluene-treated Escherichia coli

1981 ◽  
Vol 59 (7) ◽  
pp. 511-518
Author(s):  
William B. Helfman ◽  
Sheldon S. Hendler ◽  
Douglas W. Smith
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Divalent Cation ◽  
Rna Synthesis ◽  
Actinomycin D ◽  
Low Molecular Weight ◽  
Type I ◽  
Type Ii ◽  
Relative Resistance ◽  
Strict Requirement

Novel RNA polymerase activities (termed type II reaction) can be found in toluene-treated Escherichia coli with Ca2+, Fe2+, or endogenously bound cations, probably Mg2+. These activities are distinguishable from the well characterized DNA-dependent RNA polymerase (type I reaction) by: (i) their divalent cation requirements, i.e., the classical enzyme is activated by exogenously added Mn2+, Mg2+, or Co2+ ions; (ii) their relative resistance to inhibition by actinomycin D, rifampicin, and streptolydigin; (iii) their selective synthesis of low molecular weight RNA; (iv) their sensitivity to inhibition by arabinonucleoside 5′-triphosphates or deoxyribonucleoside 5′-triphosphates; and (v) the strict requirement for ATP in Ca2+ and bound cation-activated reactions. The Ca2+-activated and endogenous RNA polymerase activities are inhibited by orthophosphate. The properties of the type II RNA polymerase(s) are compared with those of polynucleotide phosphorylase, the dnaG gene product, and the RNA polymerase described by Ohasa and Tsugita.

scholarly journals Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses

2020 ◽  
Author(s):  
Yuto Chiba ◽  
Takashi Yaguchi ◽  
Syun-ichi Urayama ◽  
Daisuke Hagiwara
Keyword(s):  
Rna Polymerase ◽  
Rna Viruses ◽  
Current Knowledge ◽  
Single Gene ◽  
Rna Seq ◽  
Rna Dependent Rna Polymerase ◽  
Independent Manner ◽  
Viral Genomes ◽  
True Diversity ◽  
Fungal Viruses

AbstractBy identifying variations in viral RNA genomes, cutting-edge metagenome technology has potential to reshape current concepts about the evolution of RNA viruses. This technology, however, cannot process low-homology genomic regions properly, leaving the true diversity of RNA viruses unappreciated. To overcome this technological limitation we applied an advanced method, Fragmented and Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses from 155 fungal isolates, which allowed us to obtain complete viral genomes in a homology-independent manner. We created a high-quality catalog of 19 RNA viruses (12 viral species) that infect Aspergillus isolates. Among them, nine viruses were not detectable by the conventional methodology involving agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections. Segmented genome structures were determined in 42% of the viruses. Some RNA viruses had novel genome architectures; one contained a dual methyltransferase domain and another had a separated RNA-dependent RNA polymerase (RdRp) gene. A virus from a different fungal taxon (Pyricularia) had an RdRp sequence that was separated on different segments, suggesting that a divided RdRp is widely present among fungal viruses, despite the belief that all RNA viruses encode RdRp as a single gene. These findings illustrate the previously hidden diversity and evolution of RNA viruses, and prompt reconsideration of the structural plasticity of RdRp. By highlighting the limitations of conventional surveillance methods for RNA viruses, we showcase the potential of FLDS technology to broaden current knowledge about these viruses.Author SummaryThe development of RNA-seq technology has facilitated the discovery of RNA viruses in all types of biological samples. However, it is technically difficult to detect highly novel viruses using RNA-seq. We successfully reconstructed the genomes of multiple novel fungal RNA viruses by screening host fungi using a new technology, FLDS. Surprisingly, we identified two viral species whose RNA-dependent RNA polymerase (RdRp) proteins were separately encoded on different genome segments, overturning the commonly accepted view of the positional unity of RdRp proteins in viral genomes. This new perspective on divided RdRp proteins should hasten the discovery of viruses with unique RdRp structures that have been overlooked, and further advance current knowledge and understanding of the diversity and evolution of RNA viruses.

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 Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

2020 ◽  
Author(s):  
Feroza Begum ◽  
Debica Mukherjee ◽  
Sandeepan Das ◽  
Dluya Thagriki ◽  
Prem Prakash Tripathi ◽  
...  
Keyword(s):  
Protein Structure ◽  
Rna Polymerase ◽  
Rna Replication ◽  
Viral Rna ◽  
Rna Dependent Rna Polymerase ◽  
Stem Loop ◽  
Reading Frame ◽  
Replication Complex ◽  
Structural Modifications ◽  
Mutation Analyses

1.AbstractThe open reading frame (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase (RdRp); helicase and 3’-5’ exonuclease. Sequence analyses of ORF1ab unravelled emergence of mutations especially in the viral RdRp and helicase at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp (at position 4715 in the context of the polyprotein/ at position 323 of RdRp) leads to rigidification of structure and that mutation in the helicase (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp better for therapeutic intervention.

Targeting Viral RNA-Dependent RNA Polymerases as an Antiviral Therapy

2021 ◽  
Vol 28 ◽  
Author(s):  
Daniel Miranda ◽  
David Jesse Sanchez
Keyword(s):  
Clinical Trials ◽  
Global Health ◽  
Rna Polymerase ◽  
Biomedical Research ◽  
Rna Viruses ◽  
Standard Of Care ◽  
Rna Dependent Rna Polymerase ◽  
Viral Pathogens ◽  
Relevant Topic ◽  
Target Rna

Abstract: Progressive globalization of our society brings not only worldwide integration, it increases and promotes our exposure to new viral pathogens with evident impacts on our global health. Especially with the emergence of SARS-CoV-2, our biomedical research infrastructure has never been more compelled to rapidly develop antiviral regimens that demonstrate improved efficacy against these pathogens. Here we showcase 3 poignant antivirals against the lucrative target, RNA-dependent RNA polymerase (RdRP) of RNA viruses – a timely and relevant topic given the present efforts against COVID-19. While effective drug designs against RdRP are important, their benefit and potential as a standard of care truly relies on them standing out in well-designed clinical trials.

scholarly journals Proteinase-Polymerase Precursor as the Active Form of Feline Calicivirus RNA-Dependent RNA Polymerase

2001 ◽  
Vol 75 (3) ◽  
pp. 1211-1219 ◽  
Author(s):  
Lai Wei ◽  
Jason S. Huhn ◽  
Aaron Mory ◽  
Harsh B. Pathak ◽  
Stanislav V. Sosnovtsev ◽  
...  
Keyword(s):  
Amino Acids ◽  
Rna Polymerase ◽  
Active Form ◽  
Polymerase Activity ◽  
Feline Calicivirus ◽  
Amino Terminus ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
Catalytically Active ◽  
Catalytic Cysteine

ABSTRACT The objective of this study was to identify the active form of the feline calicivirus (FCV) RNA-dependent RNA polymerase (RdRP). Multiple active forms of the FCV RdRP were identified. The most active enzyme was the full-length proteinase-polymerase (Pro-Pol) precursor protein, corresponding to amino acids 1072 to 1763 of the FCV polyprotein encoded by open reading frame 1 of the genome. Deletion of 163 amino acids from the amino terminus of Pro-Pol (the Val-1235 amino terminus) caused a threefold reduction in polymerase activity. Deletion of an additional one (the Thr-1236 amino terminus) or two (the Ala-1237 amino terminus) amino acids produced derivatives that were 7- and 175-fold, respectively, less active than Pro-Pol. FCV proteinase-dependent processing of Pro-Pol in the interdomain region preceding Val-1235 was not observed in the presence of a catalytically active proteinase; however, processing within the polymerase domain was observed. Inactivation of proteinase activity by changing the catalytic cysteine-1193 to glycine permitted the production and purification of intact Pro-Pol. Biochemical analysis of Pro-Pol showed that this enzyme has properties expected of a replicative polymerase, suggesting that Pro-Pol is an active form of the FCV RdRP.

scholarly journals Products of Oxidative Guanine Damage Form Base Pairs with Guanine

2020 ◽  
Vol 21 (20) ◽  
pp. 7645
Author(s):  
Katsuhito Kino ◽  
Taishu Kawada ◽  
Masayo Hirao-Suzuki ◽  
Masayuki Morikawa ◽  
Hiroshi Miyazawa
Keyword(s):  
Carboxylic Acid ◽  
Rna Polymerase ◽  
Rna Viruses ◽  
Antiviral Agents ◽  
Present Knowledge ◽  
Base Pairs ◽  
Rna Dependent Rna Polymerase ◽  
Novel Coronavirus

Among the natural bases, guanine is the most oxidizable base. The damage caused by oxidation of guanine, commonly referred to as oxidative guanine damage, results in the formation of several products, including 2,5-diamino-4H-imidazol-4-one (Iz), 2,2,4-triamino-5(2H)-oxazolone (Oz), guanidinoformimine (Gf), guanidinohydantoin/iminoallantoin (Gh/Ia), spiroiminodihydantoin (Sp), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), urea (Ua), 5-guanidino-4-nitroimidazole (NI), spirodi(iminohydantoin) (5-Si and 8-Si), triazine, the M+7 product, other products by peroxynitrite, alkylated guanines, and 8,5′-cyclo-2′-deoxyguanosine (cG). Herein, we summarize the present knowledge about base pairs containing the products of oxidative guanine damage and guanine. Of these products, Iz is involved in G-C transversions. Oz, Gh/Ia, and Sp form preferably Oz:G, Gh/Ia:G, and Sp:G base pairs in some cases. An involvement of Gf, 2Ih, Ua, 5-Si, 8-Si, triazine, the M+7 product, and 4-hydroxy-2,5-dioxo-imidazolidine-4-carboxylic acid (HICA) in G-C transversions requires further experiments. In addition, we describe base pairs that target the RNA-dependent RNA polymerase (RdRp) of RNA viruses and describe implications for the 2019 novel coronavirus (SARS-CoV-2): When products of oxidative guanine damage are adapted for the ribonucleoside analogs, mimics of oxidative guanine damages, which can form base pairs, may become antiviral agents for SARS-CoV-2.

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