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Kniert J, Lin QF, Shmulevitz M. Captivating Perplexities of Spinareovirinae 5' RNA Caps. Viruses 2021; 13:v13020294. [PMID: 33668598 PMCID: PMC7918360 DOI: 10.3390/v13020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.
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Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses. J Virol 2020; 94:JVI.00854-20. [PMID: 32999026 DOI: 10.1128/jvi.00854-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
We conducted an exhaustive search for three-dimensional structural homologs to the proteins of 20 key phylogenetically distinct nucleocytoplasmic DNA viruses (NCLDV). Structural matches covered 429 known protein domain superfamilies, with the most highly represented being ankyrin repeat, P-loop NTPase, F-box, protein kinase, and membrane occupation and recognition nexus (MORN) repeat. Domain superfamily diversity correlated with genome size, but a diversity of around 200 superfamilies appeared to correlate with an abrupt switch to paralogization. Extensive structural homology was found across the range of eukaryotic RNA polymerase II subunits and their associated basal transcription factors, with the coordinated gain and loss of clusters of subunits on a virus-by-virus basis. The total number of predicted endonucleases across the 20 NCLDV was nearly quadrupled from 36 to 132, covering much of the structural and functional diversity of endonucleases throughout the biosphere in DNA restriction, repair, and homing. Unexpected findings included capsid protein-transcription factor chimeras; endonuclease chimeras; enzymes for detoxification; antimicrobial peptides and toxin-antitoxin systems associated with symbiosis, immunity, and addiction; and novel proteins for membrane abscission and protein turnover.IMPORTANCE We extended the known annotation space for the NCLDV by 46%, revealing high-probability structural matches for fully 45% of the 9,671 query proteins and confirming up to 98% of existing annotations per virus. The most prevalent protein families included ankyrin repeat- and MORN repeat-containing proteins, many of which included an F-box, suggesting extensive host cell modulation among the NCLDV. Regression suggested a minimum requirement for around 36 protein structural superfamilies for a viable NCLDV, and beyond around 200 superfamilies, genome expansion by the acquisition of new functions was abruptly replaced by paralogization. We found homologs to herpesvirus surface glycoprotein gB in cytoplasmic viruses. This study provided the first prediction of an endonuclease in 10 of the 20 viruses examined; the first report in a virus of a phenolic acid decarboxylase, proteasomal subunit, or cysteine knot (defensin) protein; and the first report of a prokaryotic-type ribosomal protein in a eukaryotic virus.
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Biswas P, Kundu A, Ghosh AK. Genome segment 4 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes RNA triphosphatase and methyltransferases. J Gen Virol 2014; 96:95-105. [PMID: 25228490 DOI: 10.1099/vir.0.069716-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cloning and sequencing of Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) genome segment S4 showed that it consists of 3410 nt with a single ORF of 1110 aa which could encode a protein of ~127 kDa (p127). Bioinformatics analysis showed the presence of a 5' RNA triphosphatase (RTPase) domain (LRDR), a S-adenosyl-l-methionine (SAM)-binding (GxGxG) motif and the KDKE tetrad of 2'-O-methyltransferase (MTase), which suggested that S4 may encode RTPase and MTase. The ORF of S4 was expressed in Escherichia coli as a His-tagged fusion protein and purified by nickel-nitrilotriacetic acid affinity chromatography. Biochemical analysis of recombinant p127 showed its RTPase as well as SAM-dependent guanine N(7)-and ribose 2'-O-MTase activities. A MTase assay using in vitro transcribed AmCPV S2 RNA having a 5' G*pppG end showed that guanine N(7) methylation occurred prior to the ribose 2'-O methylation to yield a m(7)GpppG/m(7)GpppGm RNA cap. Mutagenesis of the SAM-binding (GxGxG) motif (G831A) completely abolished N(7)- and 2'-O-MTase activities, indicating the importance of these residues for capping. From the kinetic analysis, the Km values of N(7)-MTase for SAM and RNA were calculated as 4.41 and 0.39 µM, respectively. These results suggested that AmCPV S4-encoded p127 catalyses RTPase and two cap methylation reactions for capping the 5' end of viral RNA.
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Affiliation(s)
- Poulomi Biswas
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Anirban Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ananta Kumar Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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Markussen T, Dahle MK, Tengs T, Løvoll M, Finstad ØW, Wiik-Nielsen CR, Grove S, Lauksund S, Robertsen B, Rimstad E. Sequence analysis of the genome of piscine orthoreovirus (PRV) associated with heart and skeletal muscle inflammation (HSMI) in Atlantic salmon (Salmo salar). PLoS One 2013; 8:e70075. [PMID: 23922911 PMCID: PMC3726481 DOI: 10.1371/journal.pone.0070075] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/16/2013] [Indexed: 12/20/2022] Open
Abstract
Piscine orthoreovirus (PRV) is associated with heart- and skeletal muscle inflammation (HSMI) of farmed Atlantic salmon (Salmo salar). We have performed detailed sequence analysis of the PRV genome with focus on putative encoded proteins, compared with prototype strains from mammalian (MRV T3D)- and avian orthoreoviruses (ARV-138), and aquareovirus (GCRV-873). Amino acid identities were low for most gene segments but detailed sequence analysis showed that many protein motifs or key amino acid residues known to be central to protein function are conserved for most PRV proteins. For M-class proteins this included a proline residue in μ2 which, for MRV, has been shown to play a key role in both the formation and structural organization of virus inclusion bodies, and affect interferon-β signaling and induction of myocarditis. Predicted structural similarities in the inner core-forming proteins λ1 and σ2 suggest a conserved core structure. In contrast, low amino acid identities in the predicted PRV surface proteins μ1, σ1 and σ3 suggested differences regarding cellular interactions between the reovirus genera. However, for σ1, amino acid residues central for MRV binding to sialic acids, and cleavage- and myristoylation sites in μ1 required for endosomal membrane penetration during infection are partially or wholly conserved in the homologous PRV proteins. In PRV σ3 the only conserved element found was a zinc finger motif. We provide evidence that the S1 segment encoding σ3 also encodes a 124 aa (p13) protein, which appears to be localized to intracellular Golgi-like structures. The S2 and L2 gene segments are also potentially polycistronic, predicted to encode a 71 aa- (p8) and a 98 aa (p11) protein, respectively. It is concluded that PRV has more properties in common with orthoreoviruses than with aquareoviruses.
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Affiliation(s)
- Turhan Markussen
- Department of Laboratory Services, National Veterinary Institute, Oslo, Norway
| | - Maria K. Dahle
- Department of Laboratory Services, National Veterinary Institute, Oslo, Norway
| | - Torstein Tengs
- Department of Laboratory Services, National Veterinary Institute, Oslo, Norway
| | - Marie Løvoll
- Department of Laboratory Services, National Veterinary Institute, Oslo, Norway
| | - Øystein W. Finstad
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, Oslo, Norway
| | | | - Søren Grove
- Department of Laboratory Services, National Veterinary Institute, Oslo, Norway
| | - Silje Lauksund
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Børre Robertsen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Espen Rimstad
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, Oslo, Norway
- * E-mail:
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Broome virus, a new fusogenic Orthoreovirus species isolated from an Australian fruit bat. Virology 2010; 402:26-40. [PMID: 20350736 DOI: 10.1016/j.virol.2009.11.048] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 10/16/2009] [Accepted: 11/26/2009] [Indexed: 11/22/2022]
Abstract
This report describes the discovery and characterization of a new fusogenic orthoreovirus, Broome virus (BroV), isolated from a little red flying-fox (Pteropus scapulatus). The BroV genome consists of 10 dsRNA segments, each having a 3' terminal pentanucleotide sequence conserved amongst all members of the genus Orthoreovirus, and a unique 5' terminal pentanucleotide sequence. The smallest genome segment is bicistronic and encodes two small nonstructural proteins, one of which is a novel fusion associated small transmembrane (FAST) protein responsible for syncytium formation, but no cell attachment protein. The low amino acid sequence identity between BroV proteins and those of other orthoreoviruses (13-50%), combined with phylogenetic analyses of structural and nonstructural proteins provide evidence to support the classification of BroV in a new sixth species group within the genus Orthoreovirus.
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Xu W, Coombs KM. Conserved structure/function of the orthoreovirus major core proteins. Virus Res 2009; 144:44-57. [PMID: 19720241 DOI: 10.1016/j.virusres.2009.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 03/25/2009] [Accepted: 03/31/2009] [Indexed: 11/18/2022]
Abstract
Orthoreoviruses are infectious agents with genomes of 10 segments of double-stranded RNA. Detailed molecular information is available for all 10 segments of several mammalian orthoreoviruses, and for most segments of several avian orthoreoviruses (ARV). We, and others, have reported sequences of the L2, all S-class, and all M-class genome segments of two different avian reoviruses, strains ARV138 and ARV176. We here determined L1 and L3 genome segment nucleotide sequences for both strains to complete full genome characterization of this orthoreovirus subgroup. ARV L1 segments were 3958 nucleotides long and encode lambda A major core shell proteins of 1293 residues. L3 segments were 3907 nucleotides long and encode lambda C core turret proteins of 1285 residues. These newly determined ARV segments were aligned with all currently available homologous mammalian reovirus (MRV) and aquareovirus (AqRV) genome segments. Identical and conserved amino acid residues amongst these diverse groups were mapped into known mammalian reovirus lambda 1 core shell and lambda 2 core turret proteins to predict conserved structure/function domains. Most identical and conserved residues were located near predicted catalytic domains in the lambda-class guanylyltransferase, and forming patches that traverse the lambda-class core shell, which may contribute to the unusual RNA transcription processes in this group of viruses.
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Affiliation(s)
- Wanhong Xu
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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Tran AT, Xu W, Racine T, Silaghi DA, Coombs KM. Assignment of avian reovirus temperature-sensitive mutant recombination groups E, F, and G to genome segments. Virology 2008; 375:504-13. [PMID: 18353422 DOI: 10.1016/j.virol.2008.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 12/13/2007] [Accepted: 02/06/2008] [Indexed: 11/28/2022]
Abstract
Avian reoviruses (ARV) are less well understood than their mammalian counterparts. ARV are ubiquitous in commercial poultry and frequently isolated from acutely infected chickens. We previously described isolation of ARV temperature-sensitive (ts) mutants after nitrosoguanidine mutagenesis of wild-type ARV138, their assignment to 7 recombination groups (A-G), and genetic mapping of mutants in groups A-D to specific gene segments. For this study, wild-type serotype ARV176 was crossed with ts mutants tsE158 (Group E), tsF206 (Group F), or tsG247 (Group G) and reassortant progenies analyzed. Reassortant temperature-sensitivities were determined by efficiency of plating at permissive and non-permissive temperatures. Mapping results indicated tsE158, tsF206, and tsG247 mapped to the L1, S4, and L3 genes, respectively, which encode the lambdaA core shell, sigmaNS non-structural, and lambdaC core spike proteins, respectively. Specific amino acid substitutions in each mutant were determined and locations of structural protein alterations were placed within the 3-dimensional structure of homologous mammalian reovirus proteins. Mapping recombination groups E-G marks completion of gene assignments for all seven ts mutant groups previously generated.
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Affiliation(s)
- Anh T Tran
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
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Conformational changes accompany activation of reovirus RNA-dependent RNA transcription. J Struct Biol 2008; 162:277-89. [PMID: 18321727 DOI: 10.1016/j.jsb.2008.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 12/07/2007] [Accepted: 01/17/2008] [Indexed: 12/28/2022]
Abstract
Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known three-dimensional structures of major core proteins.
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Affiliation(s)
- Wolfgang Karl Bill Joklik
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Kim J, Tao Y, Reinisch KM, Harrison SC, Nibert ML. Orthoreovirus and Aquareovirus core proteins: conserved enzymatic surfaces, but not protein-protein interfaces. Virus Res 2004; 101:15-28. [PMID: 15010214 DOI: 10.1016/j.virusres.2003.12.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Orthoreoviruses and Aquareoviruses constitute two respective genera in the family Reoviridae of double-stranded RNA viruses. Orthoreoviruses infect mammals, birds, and reptiles and have a genome comprising 10 RNA segments. Aquareoviruses infect fish and have a genome comprising 11 RNA segments. Despite these differences, recent structural and nucleotide sequence evidence indicate that the proteins of Orthoreoviruses and Aquareoviruses share many similarities. The focus of this review is on the structure and function of the Orthoreovirus core proteins lambda1, lambda2, lambda3, and sigma2, for which X-ray crystal structures have been recently reported. The homologous core proteins in Aquareoviruses are VP3, VP1, VP2, and VP6, respectively. By mapping the locations of conserved residues onto the Orthoreovirus crystal structures, we have found that enzymatic surfaces involved in mRNA synthesis are well conserved between these two groups of viruses, whereas several surfaces involved in protein-protein interactions are not well conserved. Other evidence indicates that the Orthoreovirus mu2 and Aquareovirus VP5 proteins are homologous, suggesting that VP5 is a core protein as mu2 is known to be. These findings provide further evidence that Orthoreoviruses and Aquareoviruses have diverged from a common ancestor and contribute to a growing understanding of the functions of the core proteins in viral mRNA synthesis.
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Affiliation(s)
- Jonghwa Kim
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02115, USA
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Kim J, Zhang X, Centonze VE, Bowman VD, Noble S, Baker TS, Nibert ML. The hydrophilic amino-terminal arm of reovirus core shell protein lambda1 is dispensable for particle assembly. J Virol 2002; 76:12211-22. [PMID: 12414960 PMCID: PMC136864 DOI: 10.1128/jvi.76.23.12211-12222.2002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The reovirus core particle is a molecular machine that mediates synthesis, capping, and export of the viral plus strand RNA transcripts. Its assembly and structure-function relationships remain to be well understood. Following the lead of previous studies with other Reoviridae family members, most notably orbiviruses and rotaviruses, we used recombinant baculoviruses to coexpress reovirus core proteins lambda1, lambda2, and sigma2 in insect cells. The resulting core-like particles (CLPs) were purified and characterized. They were found to be similar to cores with regard to their sizes, morphologies, and protein compositions. Like cores, they could also be coated in vitro with the two major outer-capsid proteins, micro 1 and sigma3, to produce virion-like particles. Coexpression of core shell protein lambda1 and core nodule protein sigma2 was sufficient to yield CLPs that could withstand purification, whereas expression of lambda1 alone was not, indicating a required role for sigma2 as a previous study also suggested. In addition, CLPs that lacked lambda2 (formed from lambda1 and sigma2 only) could not be coated with micro 1 and sigma3, indicating a required role for lambda2 in the assembly of these outer-capsid proteins into particles. To extend the use of this system for understanding the core and its assembly, we addressed the hypothesis that the hydrophilic amino-terminal region of lambda1, which adopts an extended arm-like conformation around each threefold axis in the reovirus core crystal structure, plays an important role in assembling the core shell. Using a series of lambda1 deletion mutants, we showed that the amino-terminal 230 residues of lambda1, including its zinc finger, are dispensable for CLP assembly. Residues in the 231-to-259 region of lambda1, however, were required. The core crystal structure suggests that residues in the 231-to-259 region are necessary because they affect the interaction of lambda1 with the threefold and/or fivefold copies of sigma2. An effective system for studies of reovirus core structure, assembly, and functions is hereby established.
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Affiliation(s)
- Jonghwa Kim
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Lunardi C, Bason C, Leandri M, Navone R, Lestani M, Millo E, Benatti U, Cilli M, Beri R, Corrocher R, Puccetti A. Autoantibodies to inner ear and endothelial antigens in Cogan's syndrome. Lancet 2002; 360:915-21. [PMID: 12354474 DOI: 10.1016/s0140-6736(02)11028-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND Cogan's syndrome is a chronic inflammatory disease of unknown origin, characterised by sensorineural hearing loss, episcleritis, and vasculitis. An autoimmune origin has been suggested but not proven. Our aim was to establish whether or not an autoimmune process is the cause of the disease. METHODS We used pooled IgG immunoglobulins derived from eight patients with Cogan's syndrome to screen a random peptide library to identify disease relevant autoantigen peptides. Among the identified peptides, one was recognised by all the patients' sera. Antibodies against peptides were affinity purified from patients' sera and used to characterise the autoantigen, to stain human cochlea, and to transfer the features of Cogan's disease into animals. FINDINGS We identified an immunodominant peptide that shows similarity with autoantigens such as SSA/Ro and with the reovirus III major core protein lambda 1. The peptide sequence shows similarity also with the cell-density enhanced protein tyrosine phosphatase-1 (DEP-1/CD148), which is expressed on the sensory epithelia of the inner ear and on endothelial cells. IgG antibodies against the peptide, purified from the patients' sera, recognised autoantigens and DEP-1/CD148 protein, bound human cochlea, and inhibited proliferation of cells expressing DEP-1/CD148. The same antibodies bound connexin 26, gene mutations of which lead to congenital inner-ear deafness. Furthermore, these antibodies were able to induce the features of Cogan's disease in mice. INTERPRETATION Our results indicate that Cogan's syndrome is an autoimmune disease, characterised by the presence of autoantibodies able to induce tissue damage on binding of cell-surface molecules present on the sensory epithelia of the inner ear and on endothelial cells.
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Affiliation(s)
- Claudio Lunardi
- Department of Clinical and Experimental Medicine, University of Verona, Verona, Italy.
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Harrison SJ, Farsetta DL, Kim J, Noble S, Broering TJ, Nibert ML. Mammalian reovirus L3 gene sequences and evidence for a distinct amino-terminal region of the lambda1 protein. Virology 1999; 258:54-64. [PMID: 10329567 DOI: 10.1006/viro.1999.9707] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To complement evidence for nucleoside triphosphate phosphohydrolase (NTPase), RNA helicase, RNA 5' triphosphate phosphohydrolase, and nucleic acid-binding activities by the core shell protein lambda1 of mammalian orthoreoviruses (reoviruses), we determined nucleotide sequences of the lambda1-encoding L3 gene segments from three isolates: type 1 Lang (T1L), type 2 Jones (T2J), and type 3 Dearing (T3D). The T1L and T3D L3 gene sequences and deduced lambda1 protein sequences shared high levels of identity (97.7% and 99.3%, respectively). The lambda1 sequences differed at only 9 of 1275 amino acids. Two single-nucleotide insertions relative to a previously published sequence for T3D L3 extended the lambda1 open reading frame to within 60 nucleotides of the plus-strand 3' end for T3D and the other isolates sequenced, in keeping with the short 3' nontranslated regions of the other nine gene segments. Seven of the nine amino acid differences between T1L and T3D lambda1 were located within the amino-terminal 500 residues of lambda1, a region with putative sequence similarities to NTPases and RNA helicases. The T2J L3 and lambda1 sequences were found to be more divergent, especially within the amino-terminal 180 residues of lambda1, preceding the putative CCHH zinc finger motif. The T2J L3 sequence, along with partial sequences for L3 genes from three other reovirus isolates, suggested that one or more of the polymorphisms at amino acids 71, 215, 500, 1011, and/or 1100 in lambda1 contribute to the L3-determined differences in ATPase activities by T1L and T3D cores. The findings contribute to our ongoing efforts to elucidate sequence-structure-function relationships for the lambda1 core protein.
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Affiliation(s)
- S J Harrison
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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Hazelton PR, Coombs KM. The reovirus mutant tsA279 L2 gene is associated with generation of a spikeless core particle: implications for capsid assembly. J Virol 1999; 73:2298-308. [PMID: 9971813 PMCID: PMC104475 DOI: 10.1128/jvi.73.3.2298-2308.1999] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/1998] [Accepted: 11/23/1998] [Indexed: 11/20/2022] Open
Abstract
Previous studies which used intertypic reassortants of the wild-type reovirus serotype 1 Lang and the temperature-sensitive (ts) serotype 3 mutant clone tsA279 identified two ts lesions; one lesion, in the M2 gene segment, was associated with defective transmembrane transport of restrictively assembled virions (P. R. Hazelton and K. M. Coombs, Virology 207:46-58, 1995). In the present study we show that the second lesion, in the L2 gene segment, which encodes the lambda2 protein, is associated with the accumulation of a core-like particle defective for the lambda2 pentameric spike. Physicochemical, biochemical, and immunological studies showed that these structures were deficient for genomic double-stranded RNA, the core spike protein lambda2, and the minor core protein micro2. Core particles with the lambda2 spike structure accumulated after temperature shift-down from a restrictive to a permissive temperature in the presence of cycloheximide. These data suggest the spike-deficient, core-like particle is an assembly intermediate in reovirus morphogenesis. The existence of this naturally occurring primary core structure suggests that the core proteins lambda1, lambda3, and sigma2 interact to initiate the process of virion capsid assembly through a dodecahedral mechanism. The next step in the proposed capsid assembly model would be the association of the minor core protein mu2, either preceding or collateral to the condensation of the lambda2 pentameric spike at the apices of the primary core structure. The assembly pathway of the reovirus double capsid is further elaborated when these observations are combined with structures identified in other studies.
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Affiliation(s)
- P R Hazelton
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0W3
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15
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Yue Z, Shatkin AJ. Enzymatic and control functions of reovirus structural proteins. Curr Top Microbiol Immunol 1998; 233:31-56. [PMID: 9599920 DOI: 10.1007/978-3-642-72092-5_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Z Yue
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854-5638, USA
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16
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Affiliation(s)
- K M Coombs
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
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17
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Affiliation(s)
- M L Nibert
- Institute for Molecular Virology, Graduate School, University of Wisconsin-Madison 53706, USA
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18
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Dryden KA, Farsetta DL, Wang G, Keegan JM, Fields BN, Baker TS, Nibert ML. Internal/structures containing transcriptase-related proteins in top component particles of mammalian orthoreovirus. Virology 1998; 245:33-46. [PMID: 9614865 DOI: 10.1006/viro.1998.9146] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of mammalian orthoreovirus top component particles, which are profoundly deficient in the content of double-stranded RNA genome, was determined at 30 A resolution by transmission cryoelectron microscopy and three-dimensional image reconstruction. Previously undetected, ordered densities, appearing primarily as pentameric flowers in the reconstruction, were seen to extend 65 A inwardly from the inner capsid at the icosahedral fivefold axes. Identically positioned but lower density elements were observed in two types of partially uncoated top component particles obtained by limited proteolysis. The levels of three inner-capsid proteins-lamda 1, lamda 3, and mu 2-were reduced in concert with the internal densities during proteolytic uncoating. Since lamda 3 contains the catalytic regions of the viral RNA polymerase and since both lamda 1 and mu 2 appear to play roles in transcription or mRNA capping, the internal structures are concluded to be complexes of the viral transcriptase-related enzymes. The findings have implications for the mechanisms of transcription and mRNA capping by orthoreovirus particles.
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Affiliation(s)
- K A Dryden
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Abstract
All eight reovirus structural proteins were resolved in a new tris, glycine, and urea (TGU) electrophoretic gel system. The specific identities of proteins were determined immunologically, biochemically, and genetically. Structural proteins of reovirus type 1 Lang had different mobilities in the TGU gel than did type 3 Dearing proteins. Intertypic reassortant viruses that contained various combinations of parental genes were used to identify each of the viral protein bands. Type 1 Lang virions were metabolically-labelled with either 3H-amino acids or 35S-methionine/cysteine and gradient purified. Aliquots of purified virions were treated to generate infectious subviral particles (ISVPs) and core particles. Radiolabelled virus, ISVP, and core proteins were resolved in the TGU gel and protein band intensities were used to determine copy numbers of each structural protein. These studies confirmed the copy numbers and locations of most reovirus proteins. However, important new findings include the discovery that virions contain approximately 120 copies of major core protein sigma 2 and 20 copies of the polymerase cofactor protein mu 2, and ISVP particles contain about 24 copies of mu 1 C that has not been processed to the delta peptide. These data are used to generate a new model of the arrangement of structural proteins with the reovirus particle.
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Affiliation(s)
- K M Coombs
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada.
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20
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Bisaillon M, Lemay G. Characterization of the reovirus lambda1 protein RNA 5'-triphosphatase activity. J Biol Chem 1997; 272:29954-7. [PMID: 9368073 DOI: 10.1074/jbc.272.47.29954] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Characterization of the phosphohydrolytic activities of recombinant reovirus lambda1 protein demonstrates that, in addition to the previously reported nucleoside triphosphate phosphohydrolase and helicase activities, the protein also possesses RNA 5'-triphosphatase activity. This activity was absolutely dependent on the presence of a divalent cation, Mg2+ or Mn2+, and specifically removes the 5'-gamma-phosphate at the end of triphosphate-terminated RNAs. Kinetic competition analysis showed that nucleoside triphosphate phosphohydrolase and RNA 5'-triphosphatase reactions are carried out at a common active site. These results strongly support the idea that, in addition to its role as an RNA helicase during transcription of the viral genome, lambda1 also participates during formation of the cap structure at the 5' end of newly synthesized reovirus mRNAs. The lambda1 protein represents only the third RNA triphosphatase whose primary structure is known and the first described in a double-stranded RNA virus.
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Affiliation(s)
- M Bisaillon
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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21
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Noble S, Nibert ML. Core protein mu2 is a second determinant of nucleoside triphosphatase activities by reovirus cores. J Virol 1997; 71:7728-35. [PMID: 9311857 PMCID: PMC192124 DOI: 10.1128/jvi.71.10.7728-7735.1997] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
NTPase activities in mammalian reovirus cores were examined under various conditions that permitted several new differences to be identified between strains type 1 Lang (T1L) and type 3 Dearing (T3D). One difference concerned the ratio (at pH 8.5) of ATP hydrolysis at 50 degrees C to that at 35 degrees C. A genetic analysis using T1L x T3D reassortant viruses implicated the L3 and M1 gene segments in this difference, with M1 influencing ATPase activity most strongly at high temperatures. L3 and M1 encode the core proteins lambda1 and mu2, respectively. Another difference concerned the absolute levels of GTP hydrolysis by cores at 45 degrees C and pH 6.5. A genetic analysis using T1L x T3D reassortants implicated the M1 gene as the sole determinant of this difference. The results of these experiments, coupled with previous findings (S. Noble and M. L. Nibert, J. Virol. 71:2182-2191, 1997), suggest either that a single type of NTPase in cores is strongly influenced by two different core proteins--lambda1 and mu2--or that cores contain two different types of NTPase influenced by the two proteins. The findings appear relevant for understanding the complex functions of reovirus cores in RNA synthesis and capping.
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Affiliation(s)
- S Noble
- Institute for Molecular Virology, Graduate School, and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 52706, USA
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22
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Affiliation(s)
- M Bisaillon
- Département de Microbiologie et Immunologie, Université de Montréal, Station Centre-ville, Montréal, Québec, H3C 3J7, Canada
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23
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Bisaillon M, Bergeron J, Lemay G. Characterization of the nucleoside triphosphate phosphohydrolase and helicase activities of the reovirus lambda1 protein. J Biol Chem 1997; 272:18298-303. [PMID: 9218469 DOI: 10.1074/jbc.272.29.18298] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Previous studies have shown that the reovirus lambda1 core protein harbors a putative nucleotide-binding motif and exhibits an affinity for nucleic acids. In addition, a nucleoside triphosphate phosphohydrolase activity present in reovirus cores has been recently assigned to lambda1 using gene reassortment analysis. In this study, it was demonstrated that the recombinant lambda1 protein, expressed in the yeast Pichia pastoris, is able to hydrolyze nucleoside 5'-triphosphates or deoxynucleoside 5'-triphosphates. This activity was absolutely dependent on the presence of a divalent cation, Mg2+ or Mn2+. The protein can also unwind double-stranded nucleic acid molecules in the presence of a nucleoside 5'-triphosphate or deoxynucleoside 5'-triphosphate. These results provide the first biochemical evidence that the reovirus lambda1 protein is a nucleoside triphosphate phosphohydrolase/helicase and strongly support the idea that lambda1 participates in transcription of the viral genome.
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Affiliation(s)
- M Bisaillon
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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24
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Noble S, Nibert ML. Characterization of an ATPase activity in reovirus cores and its genetic association with core-shell protein lambda1. J Virol 1997; 71:2182-91. [PMID: 9032352 PMCID: PMC191325 DOI: 10.1128/jvi.71.3.2182-2191.1997] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A previously identified nucleoside triphosphatase activity in mammalian reovirus cores was further characterized by comparing two reovirus strains whose cores differ in their efficiencies of ATP hydrolysis. In assays using a panel of reassortant viruses derived from these strains, the difference in ATPase activity at standard conditions was genetically associated with viral genome segment L3, encoding protein lambda1, a major constituent of the core shell that possesses sequence motifs characteristic of other ATPases. The ATPase activity of cores was affected by several other reaction components, including temperature, pH, nature and concentration of monovalent and divalent cations, and nature and concentration of anions. A strain difference in the response of core ATPase activity to monovalent acetate salts was also mapped to L3/lambda1 by using reassortant viruses. Experiments with different nucleoside triphosphates demonstrated that ATP is the preferred ribonucleotide substrate for cores of both strains. Other experiments suggested that the ATPase is latent in reovirus virions and infectious subviral particles but undergoes activation during production of cores in close association with the protease-mediated degradation of outer-capsid protein mu1 and its cleavage products, suggesting that mu1 may play a role in regulating the ATPase.
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Affiliation(s)
- S Noble
- Department of Biochemistry, University of Wisconsin-Madison, 53706, USA
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25
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Joklik WK, Roner MR. Molecular recognition in the assembly of the segmented reovirus genome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:249-81. [PMID: 8650305 DOI: 10.1016/s0079-6603(08)60147-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- W K Joklik
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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26
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Coombs KM, Mak SC, Petrycky-Cox LD. Studies of the major reovirus core protein sigma 2: reversion of the assembly-defective mutant tsC447 is an intragenic process and involves back mutation of Asp-383 to Asn. J Virol 1994; 68:177-86. [PMID: 8254727 PMCID: PMC236276 DOI: 10.1128/jvi.68.1.177-186.1994] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The reovirus group C temperature-sensitive mutant tsC447, whose defect maps to the S2 gene, which encodes the major core protein sigma 2, fails to assemble core particles at the nonpermissive temperature. To identify other proteins that may interact with sigma 2 during assembly, we generated and examined 10 independent revertants of the mutant. To determine which gene(s) carried a compensatory suppressor mutation(s), we generated intertypic reassortants between wild-type reovirus serotype 1 Lang and each revertant and determined the temperature sensitivities of the reassortants by efficiency-of-plating assays. Results of the efficiency-of-plating analyses indicated that reversion of the tsC447 defect was an intragenic process in all revertants. To identify the region(s) of sigma 2 that had reverted, we determined the nucleotide sequences of the S2 genes. In all revertant sequences examined, the G at nucleotide position 1166 in tsC447 had reverted to the A present in the wild-type sequence. This reversion leads to the restoration of a wild-type asparagine (in place of a mutant aspartic acid) at amino acid 383 in the sigma 2 sequence. These results collectively indicate that the functional lesion in tsC447 is Asp-383 and that this lesion cannot be corrected by alterations in other core proteins. These observations suggest that this region of sigma 2, which may be important in mediating assembly of the core particle, does not interact significantly with other reovirus proteins.
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Affiliation(s)
- K M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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27
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Dermody TS, Schiff LA, Nibert ML, Coombs KM, Fields BN. The S2 gene nucleotide sequences of prototype strains of the three reovirus serotypes: characterization of reovirus core protein sigma 2. J Virol 1991; 65:5721-31. [PMID: 1920614 PMCID: PMC250232 DOI: 10.1128/jvi.65.11.5721-5731.1991] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The S2 gene nucleotide sequences of prototype strains of the three reovirus serotypes were determined to gain insight into the structure and function of the S2 translation product, virion core protein sigma 2. The S2 sequences of the type 1 Lang, type 2 Jones, and type 3 Dearing strains are 1,331 nucleotides in length and contain a single large open reading frame that could encode a protein of 418 amino acids, corresponding to sigma 2. The deduced sigma 2 amino acid sequences of these strains are very conserved, being identical at 94% of the sequence positions. Predictions of sigma 2 secondary structure and hydrophobicity suggest that the protein has a two-domain structure. A larger domain is suggested to be formed from the amino-terminal three-fourths of sigma 2 sequence, which is separated from a smaller carboxy-terminal domain by a turn-rich hinge region. The carboxy-terminal domain includes sequences that are more hydrophilic than those in the rest of the protein and contains sequences which are predicted to form an alpha-helix. A region of striking similarity was found between amino acids 354 and 374 of sigma 2 and amino acids 1008 and 1031 of the beta subunit of the Escherichia coli DNA-dependent RNA polymerase. We suggest that the regions with similar sequence in sigma 2 and the beta subunit form amphipathic alpha-helices which may play a related role in the function of each protein. We have also performed experiments to further characterize the double-stranded RNA-binding activity of sigma 2 and found that the capacity to bind double-stranded RNA is a property of the sigma 2 protein of prototype strains and of the S2 mutant tsC447.
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Affiliation(s)
- T S Dermody
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts
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28
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Nibert ML, Furlong DB, Fields BN. Mechanisms of viral pathogenesis. Distinct forms of reoviruses and their roles during replication in cells and host. J Clin Invest 1991; 88:727-34. [PMID: 1885768 PMCID: PMC295447 DOI: 10.1172/jci115369] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- M L Nibert
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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29
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Coombs KM, Fields BN, Harrison SC. Crystallization of the reovirus type 3 Dearing core. Crystal packing is determined by the lambda 2 protein. J Mol Biol 1990; 215:1-5. [PMID: 2398494 DOI: 10.1016/s0022-2836(05)80089-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Core particles of reovirus type 3 Dearing (T3D) crystallized in the face-centered cubic space group F432 with dimensions of 1270 A along each edge of the unit cell. Core particles of reovirus type 1 Lang (T1L) did not crystallize. Experiments with core particles derived from 27 different T1L x T3D reassortant viruses indicated that the L2 genome segment determined the capacity of cores to crystallize. This finding indicates important differences in the surface topography of the L2-translation product, the lambda 2 protein, of these two isolates, and suggests that important crystal contacts are mediated by this protein. These data are used to generate a model of the packing of reovirus core particles within the unit cell.
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Affiliation(s)
- K M Coombs
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
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30
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Affiliation(s)
- D L Nuss
- Department of Molecular Oncology and Virology, Roche Research Center, Nutley, New Jersey 07110
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31
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Anzola JV, Dall DJ, Xu ZK, Nuss DL. Complete nucleotide sequence of wound tumor virus genomic segments encoding nonstructural polypeptides. Virology 1989; 171:222-8. [PMID: 2525838 DOI: 10.1016/0042-6822(89)90529-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sequence analysis of the genomic segments which encode the five wound tumor virus nonstructural polypeptides has been completed. The complete nucleotide sequence of segments S4 (2565 bp), S6 (1700 bp), S9 (1182 bp), and S10 (1172 bp) are presented in this report while the sequence of segment S12 (851 bp) has been described previously (T. Asamizu, D. Summers, M. B. Motika, J. V. Anzola, and D. L. Nuss, 1985, Virology 144, 398-409). Comparison of the only published sequence for another member of the genus Phytoreovirus, that of rice dwarf virus segment S10, with the combined available wound tumor virus sequence data revealed similarity with WTV segment S10: 54.9 and 30.6% at the nucleotide and amino acid level, respectively. Although wound tumor virus and rice dwarf virus differ in plant host range, tissue specificity, vector range, and disease symptom expression, the level of sequence similarity shared by the two segments suggests a common origin for these viruses. The potential use of a phytoreovirus sequence database for predicting functions of viral encoded gene products is considered.
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Affiliation(s)
- J V Anzola
- Department of Cell and Developmental Biology, Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110
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32
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Wiener JR, Bartlett JA, Joklik WK. The sequences of reovirus serotype 3 genome segments M1 and M3 encoding the minor protein mu 2 and the major nonstructural protein mu NS, respectively. Virology 1989; 169:293-304. [PMID: 2523177 DOI: 10.1016/0042-6822(89)90154-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The sequences of the M1 and M3 genome segments of reovirus serotype 3 strain Dearing, which encode protein mu 2, a minor capsid, component, and protein mu NS, one of the two nonstructural proteins, are reported. They are 2304 and 2235 base pairs long, respectively, and proteins mu 2 and mu NS comprise 736 and 719 amino acids, respectively. This completes the sequencing of the reovirus serotype 3 genome: it comprises 23,549 basepairs. Neither protein mu 2 nor protein mu NS possesses any sequence similarity to any protein sequence in gene banks, nor any of the commonly recognized motifs indicative of specialized function. Protein mu 2 has a higher alpha-helix content (36%) than other capsid proteins; for it, the ratio of amino acids in alpha-helix/beta-sheet configuration is 1.2, whereas that of typical reovirus capsid proteins ranges from 0.5 to 0.9. Thus it is not a typical capsid protein. Protein mu NS has a very high alpha-helix content (about 50%; alpha-helix/beta-sheet ratio 2.5), which is very similar to that of the other nonstructural reovirus protein, protein sigma NS. The C-terminal regions of mu NS and various myosins exhibit periodic sequence similarity elements indicative of helical structure. Protein mu NS exists in two forms in infected cells: protein mu NS and a protein, mu NSC, which lacks a region of about 5 kDa at its N-terminus. Pulse-chase analysis in vivo suggests that protein mu NSC is not a cleavage product of protein mu NS; further, protein mu NSC is formed along with protein mu NS in in vitro protein synthesizing systems, whereas protein mu 1C, the cleavage product of protein mu 1, is not. It is likely, therefore, that protein mu NSC is a primary translation product, formed either by ribosomes reading through the first initiation codon of m1 messenger RNA at position 14 and initiating at codon 42, or by de novo internal initiation at this codon.
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Affiliation(s)
- J R Wiener
- Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
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33
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Wiener JR, Joklik WK. The sequences of the reovirus serotype 1, 2, and 3 L1 genome segments and analysis of the mode of divergence of the reovirus serotypes. Virology 1989; 169:194-203. [PMID: 2922925 DOI: 10.1016/0042-6822(89)90055-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report the sequence of the L1 genome segment of reovirus serotype 3 strain Dearing, which encodes the minor core component protein lambda 3. It is 3854 bp long, with a long open reading frame starting at position 19 that is 1267 codons long. Protein lambda 3 is not detectably related to any other protein, nor does it appear to possess motifs indicative of recognized specialized functions. We have also sequenced the L1 genome segments of reovirus serotypes 1 and 2. The serotype 1 and 3 L1 genome segments are extremely closely related; there are only 154 mismatches (4.1%), 80% of which are in third base codon positions, so that these two lambda 3 proteins are 98.3% related (only 22 mismatches out of 1267). The serotype 2 L1 genome segment is only 75% related to the serotype 1 and 3 genome segments, and the serotype 2 lambda 3 protein is 92% related to the serotype 1 and 3 lambda 3 proteins. We have also analyzed the divergence patterns by which the various reovirus genome segments evolved into the three serotype forms. It appears that serotype 2 separated from the serotype 1/3 precursor long before serotypes 1 and 3 themselves diverged. In all cases the third base codon positions in the various genome segments have diverged about 80% toward randomness. The first and second base codon positions have diverged much less and to varying degree, depending, presumably, on each protein's ability to accept changes without significant loss of function. For the separation into the serotype 1 and 3 forms, the extent of divergence of the various genome varies over a very wide range. The S1 genome segments have again diverged most extensively, the extent of divergence in the first, second, and third base codon positions being about 50, 35 and 75%, respectively. For seven other genome segments that we examined the extent of third base codon position divergence is 56, 53, 48, 29, 22, 13, and 6%, whereas first and second base codon position divergence ranges from no more than 6 to 2 and 3 to less than 1%, respectively. The most likely explanation of these patterns is that the separation of the various genome segments into the present-day serotype 1 and 3 associated forms occurred at different times during evolution, from progenitors that were genome segment reassortants with survival rates as high as or higher than those of homologous genome segment sets.
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Affiliation(s)
- J R Wiener
- Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
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