1
|
Yasmin T, Thekke-Veetil T, Hobbs HA, Nelson BD, McCoppin NK, Lagos-Kutz D, Hartman GL, Lambert KN, Walker DR, Domier LL. Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales. J Gen Virol 2020; 101:105-111. [PMID: 31769392 DOI: 10.1099/jgv.0.001355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A novel picorna-like virus, provisionally named Aphis glycines virus 1 (ApGlV1) was discovered by high-throughput sequencing of soybean total RNAs and detected in suction trap-collected Aphis glycines. The ApGlV1 genome contains two large ORFs organized similar to those of dicipiviruses in the Picornaviridae where ORFs 1 and 2 encode structural and nonstructural proteins, respectively. Both ORFs are preceded by internal ribosome entry site (IRES) elements. The 5' IRES was more active in dual luciferase activity assays than the IRES in the intergenic region. The ApGlV1 genome was predicted to encode a serine protease instead of a cysteine protease and showed very low aa sequence identities to recognized members of the Picornavirales. In phylogenetic analyses based on capsid protein and RNA-dependent RNA polymerase sequences, ApGlV1 consistently clustered with a group of unclassified bicistronic picorna-like viruses discovered from arthropods and plants that may represent a novel family in the order Picornavirales.
Collapse
Affiliation(s)
- Tuba Yasmin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | | - Houston A Hobbs
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Berlin D Nelson
- Deptartment of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Nancy K McCoppin
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Doris Lagos-Kutz
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Glen L Hartman
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Kris N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - David R Walker
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.,Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA
| |
Collapse
|
2
|
Wang SL, Cheng RL, Lu JB, Yu XP, Zhang CX. A Cripavirus in the brown planthopper, Nilaparvata lugens. J Gen Virol 2016; 97:706-714. [PMID: 26746854 DOI: 10.1099/jgv.0.000394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A Cripavirus-like long unique sequence was identified during transcriptome sequencing of the brown planthopper (BPH), Nilaparvata lugens. This unique sequence demonstrated high similarity with the whole-genome sequence of cricket paralysis virus, including 5' and 3' untranslated regions; thus we considered it the whole genome of a new virus. We propose that the virus be named Nilaparvata lugens C virus (NlCV). The plus-strand RNA genome spanned 9144 nt, excluding a 3' poly(A) tail with two large ORFs encoding structural and non-structural proteins, respectively. Detection of NlCV in BPH honeydew raised the hypothesis of horizontal transmission of the virus. Honeydew from viruliferous BPHs was used to feed non-viruliferous insects, the results of which indicated that the BPH could acquire NlCV through feeding and that the virus could multiply in the insect body. A tissue-specific distribution test using real-time quantitative PCR demonstrated that NlCV was mainly present in the reproductive organs, and the virus was detected in eggs laid by viruliferous female insects using nested PCR, indicating the possibility of vertical transmission as well. As no significant symptom was detected in the viruliferous BPH, NlCV is considered a new commensal virus of BPH. Interestingly, this virus was also detected in two other hemipteran insects, the white-backed planthopper and the horned gall aphid, indicating that NlCV might be present in many other hemipteran insects and have a wide host range.
Collapse
Affiliation(s)
- Si-Liang Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Ruo-Lin Cheng
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Jia-Bao Lu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Xiao-Ping Yu
- College of Life Science, China Jiliang University, Hangzhou, Zhejiang 310018, PR China
| | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| |
Collapse
|
3
|
Abstract
The dicistrovirus is a positive-strand single-stranded RNA virus that possesses two internal ribosome entry sites (IRES) that direct translation of distinct open reading frames encoding the viral structural and nonstructural proteins. Through an unusual mechanism, the intergenic region (IGR) IRES responsible for viral structural protein expression mimics a tRNA to directly recruit the ribosome and set the ribosome into translational elongation. In this study, we explored the mechanism of host translational shutoff in Drosophila S2 cells infected by the dicistrovirus, cricket paralysis virus (CrPV). CrPV infection of S2 cells results in host translational shutoff concomitant with an increase in viral protein synthesis. CrPV infection resulted in the dissociation of eukaryotic translation initiation factor 4G (eIF4G) and eIF4E early in infection and the induction of deIF2alpha phosphorylation at 3 h postinfection, which lags after the initial inhibition of host translation. Forced dephosphorylation of deIF2alpha by overexpression of dGADD34, which activates protein phosphatase I, did not prevent translational shutoff nor alter virus production, demonstrating that deIF2alpha phosphorylation is dispensable for host translational shutoff. However, premature induction of deIF2alpha phosphorylation by thapsigargin treatment early in infection reduced viral protein synthesis and replication. Finally, translation mediated by the 5' untranslated region (5'UTR) and the IGR IRES were resistant to impairment of eIF4F or eIF2 in translation extracts. These results support a model by which the alteration of the deIF4F complex contribute to the shutoff of host translation during CrPV infection, thereby promoting viral protein synthesis via the CrPV 5'UTR and IGR IRES.
Collapse
|
4
|
Czibener C, Alvarez D, Scodeller E, Gamarnik AV. Characterization of internal ribosomal entry sites of Triatoma virus. J Gen Virol 2005; 86:2275-2280. [PMID: 16033975 DOI: 10.1099/vir.0.80842-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Triatoma virus (TrV) belongs to a new family of RNA viruses known as Dicistroviridae. Nucleotide sequence comparisons between different dicistroviruses allowed two putative internal ribosomal entry sites (IRESs) in the TrV RNA to be defined: the 5'UTR IRES of 548 nt and the intergenic region (IGR) IRES of 172 nt. Using monocistronic and bicistronic RNAs, it was shown that the TrV genome contains two functional IRESs that mediate translation initiation in a cap-independent manner. In addition, it was found that the two TrV IRESs were able to direct efficient translation of reporter genes in microinjected Xenopus oocytes, suggesting minimum requirements for host factors. The IGR IRES begins with a non-canonical CUC; however, mutations of this triplet to AUG or CCU did not impair IRES function, indicating that the CUC is not essential for the initiation process. Furthermore, translation efficiency from two TrV IRESs was differentially modulated by IFN-alpha and viral infection.
Collapse
Affiliation(s)
- Cecilia Czibener
- Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Diego Alvarez
- Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Eduardo Scodeller
- Centro de Virología Animal CEVAN, Serrano 669, 3er piso, Buenos Aires 1414, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
| |
Collapse
|
5
|
Dhar AK, Cowley JA, Hasson KW, Walker PJ. Genomic organization, biology, and diagnosis of Taura syndrome virus and yellowhead virus of penaeid shrimp. Adv Virus Res 2004; 63:353-421. [PMID: 15530565 PMCID: PMC7127055 DOI: 10.1016/s0065-3527(04)63006-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Arun K Dhar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | | | | | | |
Collapse
|
6
|
Abstract
As invading viruses do not harbor functional ribosomes in their virions, successful amplification of the viral genomes requires that viral mRNAs compete with cellular mRNAs for the host cell translation apparatus. Several RNA viruses have evolved remarkable strategies to recruit the host translation initiation factors required for the first steps in translation initiation by host cell mRNAs. This review describes the ways that three families of RNA viruses effectively usurp limiting translation initiation factors from the host.
Collapse
Affiliation(s)
- Martin Bushell
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305, USA
| | | |
Collapse
|
7
|
Abstract
Picorna-like insect virus RNAs direct an unorthodox form of translation initiation at a non-AUG-related codon, without involvement of initiator tRNA. This seems to involve a special type of mRNA pseudoknot structure which allows bypassing of the usual P-site-dependent mechanism.
Collapse
Affiliation(s)
- J E McCarthy
- Department of Biomolecular Sciences, UMIST, Manchester M60 1QD, UK.
| |
Collapse
|
8
|
Wilson JE, Powell MJ, Hoover SE, Sarnow P. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 2000; 20:4990-9. [PMID: 10866656 PMCID: PMC85949 DOI: 10.1128/mcb.20.14.4990-4999.2000] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cricket paralysis virus is a member of a group of insect picorna-like viruses. Cloning and sequencing of the single plus-strand RNA genome revealed the presence of two nonoverlapping open reading frames, ORF1 and ORF2, that encode the nonstructural and structural proteins, respectively. We show that each ORF is preceded by one internal ribosome entry site (IRES). The intergenic IRES is located 6,024 nucleotides from the 5' end of the viral RNA and is more active than the IRES located at the 5' end of the RNA, providing a mechanistic explanation for the increased abundance of structural proteins relative to nonstructural proteins in infected cells. Mutational analysis of this intergenic-region IRES revealed that ORF2 begins with a noncognate CCU triplet. Complementarity of this CCU triplet with sequences in the IRES is important for IRES function, pointing to an involvement of RNA-RNA interactions in translation initiation. Thus, the cricket paralysis virus genome is an example of a naturally occurring, functionally dicistronic eukaryotic mRNA whose translation is controlled by two IRES elements located at the 5' end and in the middle of the mRNA. This finding argues that eukaryotic mRNAs can express multiple proteins not only by polyprotein processing, reinitiation and frameshifting but also by using multiple IRES elements.
Collapse
Affiliation(s)
- J E Wilson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | |
Collapse
|
9
|
Characterization of a picornavirus isolated from Pseudoplusia includens (Lepidoptera: Noctuidae). J Invertebr Pathol 1986. [DOI: 10.1016/0022-2011(86)90094-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
|
11
|
Reavy B, Moore NF. The gene organisation of a small RNA-containing insect virus: comparison with that of mammalian picornaviruses. Virology 1983; 131:551-4. [PMID: 6659369 DOI: 10.1016/0042-6822(83)90520-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The coding regions of an insect virus, cricket paralysis virus, have been mapped using pactamycin. The results suggest that the genome of this virus functions as a polycistronic mRNA, the structural proteins being encoded by the 5' end of the RNA in an order similar to those of mammalian picornaviruses. High-molecular-weight proteins of unknown function map at the 3' end of the genome.
Collapse
|
12
|
Heat shock used in combination with amino acid analogues and protease inhibitors to demonstrate the processing of proteins of an insect picornavirus (Drosophila C virus) in Drosophila melanogaster cells. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/s0769-2617(83)80001-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Reavy B, Moore NF. Cell-free translation of Drosophila C virus RNA: identification of a virus protease activity involved in capsid protein synthesis and further studies on in vitro processing of cricket paralysis virus specified proteins. Arch Virol 1983; 76:101-15. [PMID: 6307220 DOI: 10.1007/bf01311694] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Drosophila C virus RNA acted as mRNA in rabbit reticulocyte lysates and directed the synthesis of at least one capsid protein and a number of higher molecular weight proteins. Kinetic analysis by pulse-chase experiments showed that a number of high molecular weight products acted as precursors to the capsid protein(s). Various dilution experiments were performed which showed that the virus specified a protease activity essential for the correct processing of precursors to give the capsid protein(s). A similar result was obtained with Cricket paralysis virus, and mixing experiments showed that the protease activity specified by one virus could perform some of the cleavages resulting in the production of the capsid proteins of the other virus. Some of the cleavages involving the highest molecular weight precursors could not be performed by the protease activity of the other virus. We could find no evidence for intramolecular cleavage of the capsid precursors of either of the viruses.
Collapse
|
14
|
Translation of red clover necrotic mosaic virus RNA in rabbit reticulocyte lysate: Identification of the virus coat protein cistron on the larger rna strand of the bipartite genome. Virology 1983; 124:349-56. [DOI: 10.1016/0042-6822(83)90351-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/1982] [Accepted: 09/28/1982] [Indexed: 11/17/2022]
|
15
|
|
16
|
Pullin JS, Moore NF, Clewley JP, Avery RJ. Comparison of the genomes of two insect picornaviruses, cricket paralysis virus andDrosophilaC virus, by ribonuclease T1oligonucleotide fingerprinting. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb00070.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
17
|
Moore NF, Pullin JS, Crump WA, Plus N. The proteins expressed by different isolates of Drosophila C virus. Arch Virol 1982; 74:21-30. [PMID: 6297428 DOI: 10.1007/bf01320779] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isolates of Drosophila C virus (DCV) from Drosophila flies obtained in geographically different regions were adapted to growth in Drosophila tissue culture cells. The viruses, purified from tissue culture cells, were shown to be serologically related to one of the isolates ("O" from Ouarzazate, Morocco). Analysis of the structural proteins by polyacrylamide gel electrophoresis demonstrated differences between the isolates. Labelling intracellular proteins of infected Drosophila melanogaster cells with 35S-methionine at 28 degrees C demonstrated the presence of the virus structural proteins and their immediate precursors. Raising the temperature to 37 degrees C both before and during the pulse period inhibited the processing of the high molecular weight proteins and resulted in a greater "shut-off" of host cell proteins than viral induced proteins. This allowed the precursor proteins to be compared as well as the structural proteins of the different strains. It was possible to clearly distinguish differences between the isolates on the basis of the induced proteins, although limited proteolysis of corresponding proteins showed marked similarities. Hence it is possible to distinguish between different isolates of the "same" small RNA-virus of insects from geographically different regions.
Collapse
|
18
|
Moore NF, Pullin JS, Reavy B. The intracellular proteins induced by cricket paralysis virus in Drosophila cells: the effect of protease inhibitors and amino acid analogues. Arch Virol 1981; 70:1-9. [PMID: 6277280 DOI: 10.1007/bf01320788] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Treatment of Cricket paralysis virus infected Drosophila cells with iodoacetamide before radiolabelling with 35S-methionine results in the appearance of two high molecular weight polypeptides of approximately equal to 200,000 molecular weight, not apparent in untreated infected cells (17). To attempt to differentiate between the effects of iodoacetamide being attributable to either alteration of initial polyprotein or inhibition of the protease (either cellular or viral) the effects of a spectrum of protease inhibitors were examined. These included aprotinin, leupeptin, pepstatin, elevated zinc concentration, phenyl methyl sulphonyl-fluoride, N-tosyl-L-lysine chloromethyl ketone (TLCK) and N-tosyl-L-phenylalanine chloromethyl ketone (TPCK). TLCK and TPCK both inhibited the cleavage of proteins which demonstrates an inhibition of the protease activity. The introduction of amino acid analogues into the infected cells before pulsing also results in the appearance of higher molecular weight proteins. This could be attributed to alternation of the polyprotein making it nonsusceptible to digestion with pre-existing cellular protease or newly synthesized viral protease. The possibility that the presence of the amino acid analogues results in alteration of a viral coded protease cannot be eliminated.
Collapse
|