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Ivanov KA, Hertzig T, Rozanov M, Bayer S, Thiel V, Gorbalenya AE, Ziebuhr J. Major genetic marker of nidoviruses encodes a replicative endoribonuclease. Proc Natl Acad Sci U S A 2004; 101:12694-9. [PMID: 15304651 PMCID: PMC514660 DOI: 10.1073/pnas.0403127101] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Indexed: 11/18/2022] Open
Abstract
Coronaviruses are important pathogens that cause acute respiratory diseases in humans. Replication of the approximately 30-kb positive-strand RNA genome of coronaviruses and discontinuous synthesis of an extensive set of subgenome-length RNAs (transcription) are mediated by the replicase-transcriptase, a barely characterized protein complex that comprises several cellular proteins and up to 16 viral subunits. The coronavirus replicase-transcriptase was recently predicted to contain RNA-processing enzymes that are extremely rare or absent in other RNA viruses. Here, we established and characterized the activity of one of these enzymes, replicative nidoviral uridylate-specific endoribonuclease (NendoU). It is considered a major genetic marker that discriminates nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) from all other RNA virus families. Bacterially expressed forms of NendoU of severe acute respiratory syndrome coronavirus and human coronavirus 229E were revealed to cleave single-stranded and double-stranded RNA in a Mn(2+)-dependent manner. Single-stranded RNA was cleaved less specifically and effectively, suggesting that double-stranded RNA is the biologically relevant NendoU substrate. Double-stranded RNA substrates were cleaved upstream and downstream of uridylates at GUU or GU sequences to produce molecules with 2'-3' cyclic phosphate ends. 2'-O-ribose-methylated RNA substrates proved to be resistant to cleavage by NendoU, indicating a functional link with the 2'-O-ribose methyltransferase located adjacent to NendoU in the coronavirus replicative polyprotein. A mutagenesis study verified potential active-site residues and allowed us to inactivate NendoU in the full-length human coronavirus 229E clone. Substitution of D6408 by Ala was shown to abolish viral RNA synthesis, demonstrating that NendoU has critical functions in viral replication and transcription.
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Affiliation(s)
- Konstantin A Ivanov
- Institute of Virology and Immunology, University of Würzburg, Versbacher Strasse 7, 97078 Würzburg, Germany
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Abstract
The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined reference genotypes exist for three major viral pathogens: human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and hepatitis B virus (HBV). User-defined reference sequences can be used at the same time. The query sequence is broken into segments for comparison to the reference so that the mosaic organization of recombinant sequences could be revealed. The results are displayed graphically using color-coded genotypes. Therefore, the genotype(s) of any portion of the query can quickly be determined. The Genotyping tool can be found at: http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi.
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Affiliation(s)
- Mikhail Rozanov
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Building 38A, Room S602, 8600 Rockville Pike, Bethesda, MD 20892, USA
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Affiliation(s)
- Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LLM, Guan Y, Rozanov M, Spaan WJM, Gorbalenya AE. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 2003; 331:991-1004. [PMID: 12927536 PMCID: PMC7159028 DOI: 10.1016/s0022-2836(03)00865-9] [Citation(s) in RCA: 933] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The genome organization and expression strategy of the newly identified severe acute respiratory syndrome coronavirus (SARS-CoV) were predicted using recently published genome sequences. Fourteen putative open reading frames were identified, 12 of which were predicted to be expressed from a nested set of eight subgenomic mRNAs. The synthesis of these mRNAs in SARS-CoV-infected cells was confirmed experimentally. The 4382- and 7073 amino acid residue SARS-CoV replicase polyproteins are predicted to be cleaved into 16 subunits by two viral proteinases (bringing the total number of SARS-CoV proteins to 28). A phylogenetic analysis of the replicase gene, using a distantly related torovirus as an outgroup, demonstrated that, despite a number of unique features, SARS-CoV is most closely related to group 2 coronaviruses. Distant homologs of cellular RNA processing enzymes were identified in group 2 coronaviruses, with four of them being conserved in SARS-CoV. These newly recognized viral enzymes place the mechanism of coronavirus RNA synthesis in a completely new perspective. Furthermore, together with previously described viral enzymes, they will be important targets for the design of antiviral strategies aimed at controlling the further spread of SARS-CoV.
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Key Words
- nidovirus
- genome organization
- subgenomic mrna synthesis
- replicase
- rna processing
- sars-cov, severe acute respiratory syndrome coronavirus
- orf, open reading frame
- sg, subgenomic
- bcov, bovine coronavirus
- etov, equine torovirus
- hcov, human coronavirus
- mhv, mouse hepatitis coronavirus
- pl1pro, papain-like proteinase 1
- ibv, avian infectious bronchitis coronavirus
- sud, sars-cov unique domain
- trs, transcription-regulating sequence
- xendou, poly(u)-specific endoribonuclease
- exon, 3′-to-5′ exonuclease
- 2′-o-mt, s-adenosylmethionine-dependent ribose 2′-o-methyltransferase
- adrp, adenosine diphosphate-ribose 1″-phosphatase
- cpd, cyclic phosphodiesterase
- snorna, small nucleolar rna
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Affiliation(s)
- Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Room L4-34, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
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Balkanov V, Belolaptikov I, Bezrukov L, Chensky A, Budnev N, Danilchenko I, Dzhilkibaev ZA, Domogatsky G, Doroshenko A, Fialkovsky S, Gaponenko O, Garus A, Gress T, Karle A, Klabukov A, Klimov A, Klimushin S, Koshechkin A, Kulepov V, Kuzmichev L, Lubsandorzhiev B, Lovzov S, Mikolajski T, Milenin M, Mirgazov R, Moroz A, Moseiko N, Nikiforov S, Osipova E, Pandel D, Panfilov A, Parfenov Y, Pavlov A, Petukhov D, Pokhil P, Pokolev P, Popova E, Rozanov M, Rubzov V, Sokalski I, Spiering C, Streicher O, Tarashansky B, Thon T, Wischnewski R, Yashin I. In situ measurements of optical parameters in Lake Baikal with the help of a Neutrino telescope. Appl Opt 1999; 38:6818-6825. [PMID: 18324221 DOI: 10.1364/ao.38.006818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present results of an experiment performed in Lake Baikal at a depth of approximately 1 km. The photomultipliers of an underwater neutrino telescope under construction at this site were illuminated by a distant laser. The experiment not only provided a useful cross-check of the time calibration of the detector but also allowed us to determine inherent optical parameters of the water in a way that was complementary to standard methods. In 1997 we measured an absorption length of 22 m and an asymptotic attenuation length of 18 m. The effective scattering length was measured as 480 m. By use of (cos theta) = 0.95 (0.90) for the average scattering angle, this length corresponds to a geometric scattering length of 24 (48) m.
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Affiliation(s)
- V Balkanov
- Institute for Nuclear Research, Russian Academy of Sciences, 60-th October Anniversary Prospect 7a, 117312 Moscow, Russia
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Kadaré G, Rozanov M, Haenni AL. Expression of the turnip yellow mosaic virus proteinase in Escherichia coli and determination of the cleavage site within the 206 kDa protein. J Gen Virol 1995; 76 ( Pt 11):2853-7. [PMID: 7595394 DOI: 10.1099/0022-1317-76-11-2853] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The large non-structural polyprotein (206 kDa) of turnip yellow mosaic tymovirus (TYMV) undergoes auto-cleavage, producing N- and C-terminal proteins. Here we show that the viral proteinase responsible for this event is active when produced in Escherichia coli, as monitored in Western blots by examining the generation of the C-terminal cleavage product after induction by IPTG. The outer boundaries and critical amino acids of the proteinase domain were characterized by deletion analysis and site-directed mutagenesis. A miniproteinase of 273 residues resulting from combined N- and C-terminal deletions still performed efficient cleavage. Sequence analysis of the bacterially-purified C-terminal cleavage product indicated that cleavage occurs between Ala1259 and Thr1260 of the non-structural protein.
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Affiliation(s)
- G Kadaré
- Institut Jacques Monod, Paris, France
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Ohira K, Namba S, Rozanov M, Kusumi T, Tsuchizaki T. Complete sequence of an infectious full-length cDNA clone of citrus tatter leaf capillovirus: comparative sequence analysis of capillovirus genomes. J Gen Virol 1995; 76 ( Pt 9):2305-9. [PMID: 7561769 DOI: 10.1099/0022-1317-76-9-2305] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The complete nucleotide sequence of citrus tatter leaf capillovirus (CTLV lily strain) was determined. It is 6496 nucleotides long, excluding the 3'-terminal poly(A) tract, and contains two putative overlapping open reading frames (ORFs). ORF1 (positions 37-6354) encodes a potential polyprotein of molecular mass 242 kDa. ORF2 (positions 4788-5750) codes for a 36 kDa protein. The 242 kDa polypeptide contains several non-structural protein domains (i.e. methyltransferase, NTP-binding helicase, papain-like proteinase and polymerase) and, at its C terminus, the putative coat protein. The N-terminal region of the 36 kDa protein displays sequence similarity to the cell-to-cell movement proteins of the '30 K superfamily'. Such a genome structure is conserved between CTLV and apple stem grooving capillovirus. Capped transcripts from a plasmid containing the complete sequence of CTLV, with a T7 RNA promoter, successfully infected Chenopodium quinoa plants and caused symptoms characteristic of CTLV. Uncapped transcripts were noninfectious.
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Affiliation(s)
- K Ohira
- Laboratory of Bioresource Technology, Graduate School, University of Tokyo, Japan
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