1
|
Gibbs AJ. Viral taxonomy needs a spring clean; its exploration era is over. Virol J 2013; 10:254. [PMID: 23938184 PMCID: PMC3751428 DOI: 10.1186/1743-422x-10-254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/07/2013] [Indexed: 11/10/2022] Open
Abstract
The International Committee on Taxonomy of Viruses has recently changed its approved definition of a viral species, and also discontinued work on its database of virus descriptions. These events indicate that the exploration era of viral taxonomy has ended; over the past century the principles of viral taxonomy have been established, the tools for phylogenetic inference invented, and the ultimate discriminatory data required for taxonomy, namely gene sequences, are now readily available. Further changes would make viral taxonomy more informative. First, the status of a ‘taxonomic species’ with an italicized name should only be given to viruses that are specifically linked with a single ‘type genomic sequence’ like those in the NCBI Reference Sequence Database. Secondly all approved taxa should be predominately monophyletic, and uninformative higher taxa disendorsed. These are ‘quality assurance’ measures and would improve the value of viral nomenclature to its users. The ICTV should also promote the use of a public database, such as Wikipedia, to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are ‘Open Access’.
Collapse
Affiliation(s)
- Adrian J Gibbs
- Australian National University Emeritus Faculty, Canberra ACT 0200, Australia.
| |
Collapse
|
2
|
Liu Z, Liu H, Xie X, He J, Luo T, Teng Y. Evaluation of a loop-mediated isothermal amplification assay for rapid diagnosis of soft-shelled turtle iridovirus. J Virol Methods 2011; 173:328-33. [PMID: 21392535 DOI: 10.1016/j.jviromet.2011.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Revised: 02/24/2011] [Accepted: 03/01/2011] [Indexed: 11/28/2022]
Abstract
Softshelled turtle iridovirus (STIV) is the first Asian iridovirus isolated from reptiles, which infects soft-shelled turtles severely and leads to "Red neck disease" associated with high mortality. A set of four specific primers was designed by targeting the STIV Thymidine kinase (TK) gene and amplified STIV DNA specifically under optimized amplification conditions at 63°C for 60 min. The sensitivity of the loop-mediated isothermal amplification (LAMP) assay was found to be 20 copies/μl of STIV DNA. To evaluate the application of the LAMP assay for detection of STIV in clinical samples, 223 samples suspected of STIV infection from turtle tissues were tested by the LAMP assay and by cell-based virus isolation. A 78.5% concordance was observed between the results of the two methods. In this study, a robust and simple LAMP assay for rapid detection of STIV was developed and evaluated, which is the first suitable for potential diagnosis and helping to monitor STIV infections in the aquaculture industry.
Collapse
Affiliation(s)
- Zongxiao Liu
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | | | | | | | | | | |
Collapse
|
3
|
Abstract
African swine fever virus (ASFV) is a large, intracytoplasmically-replicating DNA arbovirus and the sole member of the family Asfarviridae. It is the etiologic agent of a highly lethal hemorrhagic disease of domestic swine and therefore extensively studied to elucidate the structures, genes, and mechanisms affecting viral replication in the host, virus-host interactions, and viral virulence. Increasingly apparent is the complexity with which ASFV replicates and interacts with the host cell during infection. ASFV encodes novel genes involved in host immune response modulation, viral virulence for domestic swine, and in the ability of ASFV to replicate and spread in its tick vector. The unique nature of ASFV has contributed to a broader understanding of DNA virus/host interactions.
Collapse
Affiliation(s)
- E R Tulman
- Department of Pathobiology and Veterinary Science, Center of Excellence for Vaccine Research, University of Connecticut, Storrs 06269, USA.
| | | | | | | |
Collapse
|
4
|
Coupar BEH, Goldie SG, Hyatt AD, Pallister JA. Identification of a Bohle iridovirus thymidine kinase gene and demonstration of activity using vaccinia virus. Arch Virol 2005; 150:1797-812. [PMID: 15883656 DOI: 10.1007/s00705-005-0544-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 03/16/2005] [Indexed: 10/25/2022]
Abstract
In recent years interest in the family Iridoviridae has been renewed by the identification of a number of viruses, particularly from the genus Ranavirus, associated with disease in a range of poikilotherms. Ranaviruses have been isolated from amphibian, piscine and reptilian species. Here we describe an open reading frame (ORF) identified in the genome of Bohle iridovirus (BIV) which contains a nucleotide binding motif conserved within the thymidine kinase (TK) genes of iridoviruses from other genera (lymphocystis disease virus, LCDV, type species of the genus Lymphocystivirus; Chilo iridescent virus, CIV, type species of the genus Iridovirus). The ability of this putative gene to express a functional TK was confirmed by rescue of a TK negative mutant vaccinia virus in the presence of selective media, when expression was controlled by a vaccinia virus promoter. The sequence of the BIV TK was compared with the homologous sequences from epizootic haematopoietic necrosis virus (EHNV), a virus associated with disease in fish, from Wamena iridovirus (WIV) associated with systemic disease in green pythons, and from frog virus 3 (FV3) the ranavirus type species. Comparisons between these sequences and those available from other ranaviruses, other iridoviruses, other DNA viruses and cellular TKs are presented.
Collapse
Affiliation(s)
- B E H Coupar
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Vic., Australia.
| | | | | | | |
Collapse
|
5
|
Bercovier H, Fishman Y, Nahary R, Sinai S, Zlotkin A, Eyngor M, Gilad O, Eldar A, Hedrick RP. Cloning of the koi herpesvirus (KHV) gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis. BMC Microbiol 2005; 5:13. [PMID: 15774009 PMCID: PMC1079851 DOI: 10.1186/1471-2180-5-13] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2004] [Accepted: 03/17/2005] [Indexed: 11/25/2022] Open
Abstract
Background Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV). Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary. Results A robust and sensitive PCR assay based on a defined gene sequence of KHV was developed to improve the diagnosis of KHV infection. From a KHV genomic library, a hypothetical thymidine kinase gene (TK) was identified, subcloned and expressed as a recombinant protein. Preliminary characterization of the recombinant TK showed that it has a kinase activity using dTTP but not dCTP as a substrate. A PCR assay based on primers selected from the defined DNA sequence of the TK gene was developed and resulted in a 409 bp amplified fragment. The TK based PCR assay did not amplify the DNAs of other fish herpesviruses such as Herpesvirus cyprini (CHV) and the channel catfish virus (CCV). The TK based PCR assay was specific for the detection of KHV and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions. The TK based PCR was compared to previously described PCR assays and to viral culture in diseased fish and was shown to be the most sensitive method of diagnosis of KHV infection. Conclusion The TK based PCR assay developed in this work was shown to be specific for the detection of KHV. The TK based PCR assay was more sensitive for the detection of KHV than previously described PCR assays; it was as sensitive as virus isolation which is the golden standard method for KHV diagnosis and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions.
Collapse
Affiliation(s)
- Herve Bercovier
- Institute of Microbiology, Department of Clinical Microbiology, The Hebrew University-Hadassah Medical School, Ein Karen, Jerusalem, Israel
| | - Yolanta Fishman
- Institute of Microbiology, Department of Clinical Microbiology, The Hebrew University-Hadassah Medical School, Ein Karen, Jerusalem, Israel
| | - Ronen Nahary
- Institute of Microbiology, Department of Clinical Microbiology, The Hebrew University-Hadassah Medical School, Ein Karen, Jerusalem, Israel
| | - Sharon Sinai
- Institute of Microbiology, Department of Clinical Microbiology, The Hebrew University-Hadassah Medical School, Ein Karen, Jerusalem, Israel
| | - Amir Zlotkin
- Department of Infectious diseases, Sheba medical center, Tel Hashomer, 52621, Israel
| | - Marina Eyngor
- Department of Poultry and Fish Diseases, The Kimron Veterinary Institute, Beit Dagan, Israel
| | - Oren Gilad
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Avi Eldar
- Department of Poultry and Fish Diseases, The Kimron Veterinary Institute, Beit Dagan, Israel
| | - Ronald P Hedrick
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| |
Collapse
|
6
|
Tsai MF, Yu HT, Tzeng HF, Leu JH, Chou CM, Huang CJ, Wang CH, Lin JY, Kou GH, Lo CF. Identification and characterization of a shrimp white spot syndrome virus (WSSV) gene that encodes a novel chimeric polypeptide of cellular-type thymidine kinase and thymidylate kinase. Virology 2000; 277:100-10. [PMID: 11062040 DOI: 10.1006/viro.2000.0597] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
From previously constructed genomic libraries of a Taiwan WSSV isolate, a putative WSSV tk-tmk gene was identified. Uniquely, the open reading frame (ORF) of this gene was predicted to encode a novel chimeric protein of 388 amino acids with significant homology to two proteins: thymidine kinase (TK) and thymidylate kinase (TMK). Northern blot analysis with a WSSV tk-tmk-specific riboprobe detected a major transcript of 1.6 kb. When healthy adult Penaeus monodon shrimp were inoculated with WSSV, the tk-tmk gene transcript was first detected by RT-PCR analysis at 4 h postinfection and transcription levels continued to increase over the first 18 h. The gene's major in vitro transcription and translation product, equivalent to the predicted size (43 kDa), is a single chimeric protein that includes both the TK and TMK functional motifs. Evidence for phylogenetic analysis and sequence alignment suggested that the gene may have resulted from the fusion of a cellular-type TK gene and a cellular-type TMK gene. Its unique arrangement may also provide a valuable gene marker for WSSV.
Collapse
Affiliation(s)
- M F Tsai
- Department of Zoology, Institute of Biochemistry, Taipei, 106, Taiwan, Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Oliveros M, García-Escudero R, Alejo A, Viñuela E, Salas ML, Salas J. African swine fever virus dUTPase is a highly specific enzyme required for efficient replication in swine macrophages. J Virol 1999; 73:8934-43. [PMID: 10515998 PMCID: PMC112924 DOI: 10.1128/jvi.73.11.8934-8943.1999] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The African swine fever virus (ASFV) gene E165R, which is homologous to dUTPases, has been characterized. A multiple alignment of dUTPases showed the conservation in ASFV dUTPase of the motifs that define this protein family. A biochemical analysis of the purified recombinant enzyme showed that the virus dUTPase is a trimeric, highly specific enzyme that requires a divalent cation for activity. The enzyme is most probably complexed with Mg(2+), the preferred cation, and has an apparent K(m) for dUTP of 1 microM. Northern and Western blotting, as well as immunofluorescence analyses, indicated that the enzyme is expressed at early and late times of infection and is localized in the cytoplasm of the infected cells. On the other hand, an ASFV dUTPase-deletion mutant (vDeltaE165R) has been obtained. Growth kinetics showed that vDeltaE165R replicates as efficiently as parental virus in Vero cells but only to 10% or less of parental virus in swine macrophages. Our results suggest that the dUTPase activity is dispensable for virus replication in dividing cells but is required for productive infection in nondividing swine macrophages, the natural host cell for the virus. The viral dUTPase may play a role in lowering the dUTP concentration in natural infections to minimize misincorporation of deoxyuridine into the viral DNA and ensure the fidelity of genome replication.
Collapse
Affiliation(s)
- M Oliveros
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
8
|
Moore DM, Zsak L, Neilan JG, Lu Z, Rock DL. The African swine fever virus thymidine kinase gene is required for efficient replication in swine macrophages and for virulence in swine. J Virol 1998; 72:10310-5. [PMID: 9811782 PMCID: PMC110620 DOI: 10.1128/jvi.72.12.10310-10315.1998] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1998] [Accepted: 09/02/1998] [Indexed: 11/20/2022] Open
Abstract
African swine fever virus (ASFV) replicates in the cytoplasm of infected cells and contains genes encoding a number of enzymes needed for DNA synthesis, including a thymidine kinase (TK) gene. Recombinant TK gene deletion viruses were produced by using two highly pathogenic isolates of ASFV through homologous recombination with an ASFV p72 promoter-beta-glucuronidase indicator cassette (p72GUS) flanked by ASFV sequences targeting the TK region. Attempts to isolate double-crossover TK gene deletion mutants on swine macrophages failed, suggesting a growth deficiency of TK- ASFV on macrophages. Two pathogenic ASFV isolates, ASFV Malawi and ASFV Haiti, partially adapted to Vero cells, were used successfully to construct TK deletion viruses on Vero cells. The selected viruses grew well on Vero cells, but both mutants exhibited a growth defect on swine macrophages at low multiplicities of infection (MOI), yielding 0.1 to 1.0% of wild-type levels. At high MOI, the macrophage growth defect was not apparent. The Malawi TK deletion mutant showed reduced virulence for swine, producing transient fevers, lower viremia titers, and reduced mortality. In contrast, 100% mortality was observed for swine inoculated with the TK+ revertant virus. Swine surviving TK- ASFV infection remained free of clinical signs of African swine fever following subsequent challenge with the parental pathogenic ASFV. The data indicate that the TK gene of ASFV is important for growth in swine macrophages in vitro and is a virus virulence factor in swine.
Collapse
Affiliation(s)
- D M Moore
- Plum Island Animal Disease Center, Agricultural Research Service, U. S. Department of Agriculture, Greenport, New York 11944-0848, USA.
| | | | | | | | | |
Collapse
|
9
|
Tidona CA, Darai G. Molecular anatomy of lymphocystis disease virus. ARCHIVES OF VIROLOGY. SUPPLEMENTUM 1997; 13:49-56. [PMID: 9413525 DOI: 10.1007/978-3-7091-6534-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Lymphocystis disease (LD) has been reported to occur in over one hundred different species of fish worldwide. The disease is caused by lymphocystis disease virus (LCDV), a member of the iridovirus family. Numerous fish species that play an important role in fishery and fish farming are highly susceptible to LCDV infection. The infected animals develop disseminated clusters of aberrant hypertrophied cells within their connective tissue, the so-called lymphocystis cells. In the cytoplasm of these cells a massive accumulation of virions can be observed. As a first step towards understanding the mechanisms of viral infection and pathogenesis the complete genomic nucleotide sequence of lymphocystis disease virus type 1 (LCDV-1; flounder isolate) was determined. LCDV-1 is the type species of the genus Lymphocystivirus within the family Iridoviridae. The virions contain a single linear double-stranded DNA molecule that is circularly permuted, terminally redundant and heavily methylated. Since there is no convenient cell system for virus replication we determined the complete nucleotide sequence of the viral genome (102,653 base pairs). Computer assisted analyses of 195 potential open reading frames resulted in the identification of a number of putative gene products with significant homology to functionally characterized proteins of other species.
Collapse
Affiliation(s)
- C A Tidona
- Institut für Medizinische Virologie, Universität Heidelberg, Federal Republic of Germany
| | | |
Collapse
|
10
|
Oliveros M, Yáñez RJ, Salas ML, Salas J, Viñuela E, Blanco L. Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair. J Biol Chem 1997; 272:30899-910. [PMID: 9388236 DOI: 10.1074/jbc.272.49.30899] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
African swine fever virus (ASFV) encodes a novel DNA polymerase, constituted of only 174 amino acids, belonging to the polymerase (pol) X family of DNA polymerases. Biochemical analyses of the purified enzyme indicate that ASFV pol X is a monomeric DNA-directed DNA polymerase, highly distributive, lacking a proofreading 3'-5'-exonuclease, and with a poor discrimination against dideoxynucleotides. A multiple alignment of family X DNA polymerases, together with the extrapolation to the crystal structure of mammalian DNA polymerase beta (pol beta), showed the conservation in ASFV pol X of the most critical residues involved in DNA binding, nucleotide binding, and catalysis of the polymerization reaction. Therefore, the 20-kDa ASFV pol X most likely represents the minimal functional version of an evolutionarily conserved pol beta-type DNA polymerase core, constituted by only the "palm" and "thumb" subdomains. It is worth noting that such an "unfingered" DNA polymerase is able to handle templated DNA polymerization with a considerable high fidelity at the base discrimination level. Base excision repair is considered to be a cellular defense mechanism repairing modified bases in DNA. Interestingly, the fact that ASFV pol X is able to conduct filling of a single nucleotide gap points to a putative role in base excision repair during the ASFV life cycle.
Collapse
Affiliation(s)
- M Oliveros
- Centro de Biología Molecular "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
11
|
Martín Hernández AM, Camacho A, Prieto J, Menéndez del Campo AM, Tabarés E. Isolation and characterization of TK-deficient mutants of African swine fever virus. Virus Res 1995; 36:67-75. [PMID: 7625127 DOI: 10.1016/0168-1702(94)00098-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
African swine fever virus induces the synthesis of thymidine kinase (TK) in BHK TK-negative cells as an immediate early protein. The TK gene is not essential for growth of ASFV in cell culture and a stable viral strain deficient in TK has been isolated (E70NTKp). The genetic lesion of this ASFV TK- strain was identified by TK gene nucleotide sequencing, showing a nucleotide deletion leading to a -1 frameshift and a nonsense codon residue downstream of the deletion. The availability of this viable ASFV variant deficient in TK activity allows the insertion of foreign genes in the ASFV genome for genetic and biochemical studies.
Collapse
Affiliation(s)
- A M Martín Hernández
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
| | | | | | | | | |
Collapse
|
12
|
Rodríguez JM, Yáñez RJ, Rodríguez JF, Viñuela E, Salas ML. The DNA polymerase-encoding gene of African swine fever virus: sequence and transcriptional analysis. Gene 1993; 136:103-10. [PMID: 8293992 DOI: 10.1016/0378-1119(93)90453-a] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The putative DNA polymerase-encoding gene of African swine fever virus has been sequenced. The gene, designated G1207R, is located in the central region of the viral genome, and encodes a protein of 1207 amino acids (aa) with a predicted M(r) of 139,835. The gene is transcribed at both early and late stages of infection into a 4.1-kb RNA. Transcription is initiated at tsp, 8 nucleotides (nt) upstream from the start codon. Open reading frame (ORF) G1207R contains four direct repeats in tandem close to the 3'-end. Each repeat consists of 12 nt, coding for the reiterated sequence, K/NPAG. The deduced aa sequence of G1207R shows significant similarity with DNA polymerases from cellular and viral origin, belonging to the alpha-like family of DNA polymerases. In particular, the G1207R protein presents a colinear arrangement of all the 3'-->5' exonuclease and polymerization highly conserved aa regions characteristic of this group of DNA-dependent DNA polymerases.
Collapse
Affiliation(s)
- J M Rodríguez
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | | | | | | | | |
Collapse
|
13
|
Freije JM, Laín S, Viñuela E, López-Otín C. Nucleotide sequence of a nucleoside triphosphate phosphohydrolase gene from African swine fever virus. Virus Res 1993; 30:63-72. [PMID: 8266720 DOI: 10.1016/0168-1702(93)90016-g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A putative nucleoside triphosphate phosphohydrolase (NTPase) gene of African swine fever virus was identified by using a degenerate oligonucleotide probe derived from the nucleoside triphosphate binding motif, which is highly conserved among viral and cellular NTPases. The probe hybridized with fragments SalI E and EcoRI Q, which is entirely contained in the former one. Sequencing of this region revealed an open reading frame, designated Q706L, coding for a protein of 706 amino acids, with a calculated molecular weight of 80,283. The deduced amino acid sequence of this open reading frame has significant similarity with the putative helicase encoded by the killer plasmid pGKL2 of Kluyveromyces lactis as well as with the NTPase I of vaccinia virus and entomopoxvirus and a subunit of the early transcription factor of vaccinia and fowlpox virus. The protein encoded by this open reading frame contains the sequence features characteristic of helicases of the superfamily II. According to this, we propose the inclusion of the product of this ASF virus gene in this superfamily.
Collapse
Affiliation(s)
- J M Freije
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Spain
| | | | | | | |
Collapse
|
14
|
Roberts PC, Lu Z, Kutish GF, Rock DL. Three adjacent genes of African swine fever virus with similarity to essential poxvirus genes. Arch Virol 1993; 132:331-42. [PMID: 8397501 DOI: 10.1007/bf01309543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nucleotide sequencing of the right end of the SalIj fragment of the highly virulent Malawi Lil20/1 strain of African swine fever virus (ASFV) has revealed three adjacent genes with similarity to: serine-threonine protein kinases; members of the putative helicase superfamily SF2; and the vaccinia virus 56 kDa abortive late protein. All three genes are transcribed to the left with respect to the orientation of the ASFV genome. Gene L19IL predicts a protein similar to serine-threonine protein kinases including vaccinia virus gene B1R. Gene L19KL predicts a protein that is likely to be a nucleic acid-dependent ATPase, as it has similarity to both the poxvirus 70 kDa early transcription factor subunit and the poxvirus nucleoside triphosphatase I gene. Gene L19LL has extensive similarity to the vaccinia virus 56 kDa abortive late protein.
Collapse
Affiliation(s)
- P C Roberts
- Plum Island Animal Disease Center, USDA, ARS, NAA, Greenport, New York
| | | | | | | |
Collapse
|
15
|
Baylis SA, Banham AH, Vydelingum S, Dixon LK, Smith GL. African swine fever virus encodes a serine protein kinase which is packaged into virions. J Virol 1993; 67:4549-56. [PMID: 8331722 PMCID: PMC237839 DOI: 10.1128/jvi.67.8.4549-4556.1993] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nucleotide sequencing of the SalI j region of the virulent Malawi (LIL20/1) strain of African swine fever virus (ASFV) identified an open reading frame (ORF), designated j9L, with extensive similarity to the family of protein kinases. This ORF encodes a 35.1-kDa protein of 299 amino acids which shares 24.6% amino acid identity with the human pim-1 proto-oncogene and 21.0% identity with the vaccinia virus B1R-encoded protein kinase. The ASFV ORF contains the motifs characteristic of serine-threonine protein kinases, with the exception of the presumed ATP-binding site, which is poorly conserved. The ORF was expressed to high levels in Escherichia coli, and the recombinant enzyme phosphorylated a calf thymus histone protein on serine residues in vitro. An antibody raised to an amino-terminal peptide of the ASFV protein kinase was reactive with the recombinant protein in Western immunoblot analyses and was used to demonstrate the presence of the protein kinase in ASF virions.
Collapse
Affiliation(s)
- S A Baylis
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | | | | | | | | |
Collapse
|
16
|
Neilan JG, Lu Z, Afonso CL, Kutish GF, Sussman MD, Rock DL. An African swine fever virus gene with similarity to the proto-oncogene bcl-2 and the Epstein-Barr virus gene BHRF1. J Virol 1993; 67:4391-4. [PMID: 8389936 PMCID: PMC237812 DOI: 10.1128/jvi.67.7.4391-4394.1993] [Citation(s) in RCA: 142] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
An open reading frame, LMW5-HL, in the African swine fever virus genome displays a high degree of similarity to the proto-oncogene bcl-2 and, to a lesser degree, the Epstein-Barr virus gene BHRF1. A highly conserved central region is found in all three proteins. LMW5-HL encodes a protein of 18 kDa that is present in infected porcine macrophages at both early and late times postinfection. The similarity of LMW5-HL to bcl-2 and BHRF1 suggests a role for it in cell maintenance during productive or persistent viral infection.
Collapse
Affiliation(s)
- J G Neilan
- Plum Island Animal Disease Center, U.S. Department of Agriculture, Greenport, New York 11944-0848
| | | | | | | | | | | |
Collapse
|
17
|
Yáñez RJ, Boursnell M, Nogal ML, Yuste L, Viñuela E. African swine fever virus encodes two genes which share significant homology with the two largest subunits of DNA-dependent RNA polymerases. Nucleic Acids Res 1993; 21:2423-7. [PMID: 8506138 PMCID: PMC309542 DOI: 10.1093/nar/21.10.2423] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A random sequencing strategy applied to two large SalI restriction fragments (SB and SD) of the African swine fever virus (ASFV) genome revealed that they might encode proteins similar to the two largest RNA polymerase subunits of eukaryotes, poxviruses and Escherichia coli. After further mapping by dot-blot hybridization, two large open reading frames (ORFs) were completely sequenced. The first ORF (NP1450L) encodes a protein of 1450 amino acids with extensive similarity to the largest subunit of RNA polymerases. The second one (EP1242L) codes for a protein of 1242 amino acids similar to the second largest RNA polymerase subunit. Proteins NP1450L and EP1242L are more similar to the corresponding subunits of eukaryotic RNA polymerase II than to those of vaccinia virus, the prototype poxvirus, which shares many functional characteristics with ASFV. ORFs NP1450L and EP1242L are mainly expressed late in ASFV infection, after the onset of DNA replication.
Collapse
Affiliation(s)
- R J Yáñez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | | | | | | | | |
Collapse
|
18
|
Muñoz M, Freije JM, Salas ML, Viñuela E, López-Otín C. Structure and expression in E. coli of the gene coding for protein p10 of African swine fever virus. Arch Virol 1993; 130:93-107. [PMID: 8503790 DOI: 10.1007/bf01318999] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The gene encoding protein p10, a structural protein of African swine fever (ASF) virus, has been mapped, sequenced and expressed in E. coli. Protein p10 was purified from dissociated virus by reverse-phase HPLC, and its NH2-terminal end identified by automated Edman degradation. To map the gene encoding protein p10, a mixture of 20-mer oligonucleotides based upon a part of the amino acid sequence was hybridized to cloned ASF virus restriction fragments. This allowed the localization of the gene in fragment Eco RI K of the ASF virus genome. The nucleotide sequence obtained from this region revealed an open reading frame encoding 78 amino acids, with a high content of Ser and Lys residues. Several of the Ser residues are found in Ser-rich regions, which are also found in some nucleic acid-binding proteins. The gene coding for protein p10 has been inserted in an expression vector which contains the promoter for T7 RNA polymerase. The recombinant plasmid was used to produce the ASF virus protein in E. coli. The bacterially produced p10 protein shows a strong DNA binding activity with similar affinity for both double-stranded and single-stranded DNA.
Collapse
Affiliation(s)
- M Muñoz
- Departamento de Biología Funcional Facultad de Medicina, Universidad de Oviedo, Spain
| | | | | | | | | |
Collapse
|
19
|
Mettraux C, Ackermann M, Tratschin JD, Kihm U. Approaches to the identification of non-essential genes of African swine fever virus. Vet Microbiol 1992; 33:101-15. [PMID: 1481351 DOI: 10.1016/0378-1135(92)90039-v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It is poorly understood why vaccines could not be developed for the control and prevention of African swine fever (ASF) virus infection. The aim of our study was to identify genes non-essential for ASF virus replication because there were indications that certain viral gene products, which apparently are non-essential for viral replication, conferred protection from death due to ASF. A cosmid library representing the genome of ASF virus strain France 64 was established and characterized. Then, in order to inactivate viral genes by insertion, the beta-galactosidase (beta-gal) gene was introduced either randomly or at specific locations of selected cloned DNA fragments. These constructions were transfected into cells which had been previously infected with a cell-culture-adapted viral strain in order to allow the generation of recombinant progeny virus. Viable recombinant progeny was identified by at least one of the following means: (1) expression of beta-gal; (2) detection of beta-gal specific DNA by plaque hybridization, and (3) absence of a functional product of the inactivated gene. Presently, we are characterizing a recombinant virus with an insertionally inactivated thymidine kinase gene.
Collapse
Affiliation(s)
- C Mettraux
- Institute for Viral Diseases, Basel, Switzerland
| | | | | | | |
Collapse
|
20
|
Sussman MD, Lu Z, Kutish G, Afonso CL, Roberts P, Rock DL. Identification of an African swine fever virus gene with similarity to a myeloid differentiation primary response gene and a neurovirulence-associated gene of herpes simplex virus. J Virol 1992; 66:5586-9. [PMID: 1323711 PMCID: PMC289119 DOI: 10.1128/jvi.66.9.5586-5589.1992] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Here we describe an open reading frame (LMW23-NL) in the African swine fever virus genome that possesses striking similarity to a murine myeloid differentiation primary response gene (MyD116) and the neurovirulence-associated gene (ICP34.5) of herpes simplex virus. In all three proteins, a centrally located acidic region precedes a highly conserved, hydrophilic 56-amino-acid domain located at the carboxy terminus. LMW23-NL predicts a highly basic protein of 184 amino acids with an estimated molecular mass of 21.3 kDa. The similarity of LMW23-NL to genes involved in myeloid cell differentiation and viral host range suggests a role for it in African swine fever virus host range.
Collapse
Affiliation(s)
- M D Sussman
- Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, New York 11944
| | | | | | | | | | | |
Collapse
|
21
|
Hammond JM, Kerr SM, Smith GL, Dixon LK. An African swine fever virus gene with homology to DNA ligases. Nucleic Acids Res 1992; 20:2667-71. [PMID: 1614852 PMCID: PMC336905 DOI: 10.1093/nar/20.11.2667] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Sequence analysis of the SalI g region of the genome of a virulent isolate of ASFV (Malawi Lil 20/1) has revealed an open reading frame with the potential to encode a 48 kilodalton (kD) polypeptide which has significant homology with eukaryotic and prokaryotic DNA ligases. This ASFV encoded gene also contains the putative active site region of DNA ligases including the lysine residue which is necessary for enzyme-adenylate adduct formation, but lacks the C-terminal basic region conserved in other eukaryotic DNA ligases. A novel [32P]-labelled potential DNA ligase-adenylate adduct of M(r) 45 kD was observed upon incubation of ASFV infected cell cytoplasmic extracts with alpha-[32P]-ATP and subsequent analysis of products by SDS/PAGE. These data together suggest that ASFV encodes its own DNA ligase.
Collapse
Affiliation(s)
- J M Hammond
- AFRC Institute for Animal Health, Pirbright Laboratory, Woking, Surrey, UK
| | | | | | | |
Collapse
|
22
|
García-Beato R, Freije JM, López-Otín C, Blasco R, Viñuela E, Salas ML. A gene homologous to topoisomerase II in African swine fever virus. Virology 1992; 188:938-47. [PMID: 1316688 DOI: 10.1016/0042-6822(92)90558-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A putative topoisomerase II gene of African swine fever virus was mapped using a degenerate oligonucleotide probe derived from a region highly conserved in type II topoisomerases. The gene is located within EcoRI fragments P and H of the African swine fever virus genome. Sequencing of this region has revealed a long open reading frame, designated P1192R, encoding a protein of 1192 amino acids, with a predicted molecular weight of 135,543. Open reading frame P1192R is transcribed late after infection into a 4.6-kb RNA. The deduced amino acid sequence of this open reading frame shares significant similarity with topoisomerase II sequences from different sources, with percentages of identity between 23 and 29%. The evolutionary relationships among the topoisomerase II sequences of ASF virus, eukaryotes and prokaryotes were analyzed and a phylogenetic tree was established. The tree indicates that the ASF virus topoisomerase II gene was present in the virus genome before protozoa, yeasts, and metazoa diverged.
Collapse
Affiliation(s)
- R García-Beato
- Centro de Biología Molecular, (CSIC-UAM), Facultad de Ciencias, Universidad Autónoma, Madrid, Spain
| | | | | | | | | | | |
Collapse
|
23
|
Rodríguez JM, Almazán F, Viñuela E, Rodriguez JF. Genetic manipulation of African swine fever virus: construction of recombinant viruses expressing the beta-galactosidase gene. Virology 1992; 188:67-76. [PMID: 1566585 DOI: 10.1016/0042-6822(92)90735-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Homologous recombination is shown to be specifically induced in Vero cells by infection with African swine fever (ASF) virus. The frequency of recombination induced by ASF virus infection between cotransfecting plasmids is comparable to that found after infection with the prototype poxvirus, vaccinia virus. The induction of recombination is accompanied by replication of the plasmid templates in the ASF virus-infected cells. An ASF virus insertion/expression plasmid vector containing the Escherichia coli reporter gene beta-galactosidase (beta-gal) fused to a viral promoter sequence was constructed. Recombination between homologous sequences present in both the plasmid vector and the virus genome led to the generation of recombinant viruses expressing the beta-gal gene. Visual screening of beta-gal+ plaques allowed the isolation and plaque purification of recombinant ASF viruses. The characterization of a beta-gal+ virus isolate showed that the beta-gal gene had been stably inserted into the thymidine kinase locus of the virus genome, thus demonstrating that controlled genetic manipulation of ASF virus can be achieved by homologous recombination in infected cells.
Collapse
Affiliation(s)
- J M Rodríguez
- Centro de Biología Molecular (C.S.I.C.-U.A.M.), Facultad de Ciencias, Universidad Autónoma, Cantoblanco, Madrid, Spain
| | | | | | | |
Collapse
|
24
|
Koonin EV, Senkevich TG. Evolution of thymidine and thymidylate kinases: the possibility of independent capture of TK genes by different groups of viruses. Virus Genes 1992; 6:187-96. [PMID: 1317076 DOI: 10.1007/bf01703067] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phylogenetic analysis of viral and cellular thymidine and thymidylate kinases was performed using computer-assisted methods. Multiple alignments and tentative phylogenetic trees were generated for the two families of these enzymes, which include a) thymidine kinases (TK) of mammals, poxviruses, African swine fever virus, E. coli, and bacteriophage T4; and b) thymidylate kinases (ThyK) of yeast and poxviruses and distantly related herpesvirus proteins with both enzymatic activities. Analysis of the alignment of the TKs of the first family highlighted three strongly conserved segments. Two of these corresponded to the A and B motifs of the purine NTP-binding pattern. The third, C-terminal segment, showing the highest conservation, encompassed a modified Zn finger motif. It is speculated that this motif might be involved in TK oligomerization. Phylogenetic trees constructed by three different methods suggested that cellular TK genes could be captured independently by T4 bacteriophage, African swine fever virus, fowlpox virus, and the other poxviruses. The observed tree topologies appear to contradict the popular virus-host coevolution schemes and to imply that different subdivisions of poxviruses diverged at earlier stages of evolution than their hosts did. It was shown that deoxynucleoside monophosphate kinase of bacteriophage T4 is related to the ThyK family. Phylogenetic analysis suggested that ThyK genes probably have been acquired independently by phage T4, poxviruses, and herpes-viruses.
Collapse
Affiliation(s)
- E V Koonin
- Institute of Microbiology, USSR Academy of Sciences, Oktyabrya
| | | |
Collapse
|
25
|
Cistué C, Tabarés E. Expression in vivo and in vitro of the major structural protein (VP73) of African swine fever virus. Arch Virol 1992; 123:111-24. [PMID: 1550491 DOI: 10.1007/bf01317142] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The VP73 protein was produced by in vitro transcription and translation from the Xho I-Bam HI fragment located between the Cla I-N and Cla I-H fragments of the viral genome. This DNA fragment encodes a late mRNA of about 2.6 kb detected in infected MS monkey and BHK hamster cells. The transcript was initiated at a site within two bases upstream of the translation initiation codon. The in vitro synthesized polypeptide shows the same molecular weight as the in vivo synthesized polypeptide, suggesting that VP73 has no post-translational modification. There are two internal AUG initiation codons for in vitro translation, one of which is functional in vivo, as well as a possible GUG initiator codon detected by expression of the protein in E. coli cells.
Collapse
Affiliation(s)
- C Cistué
- Departamento de Microbiologia, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
| | | |
Collapse
|
26
|
Gruidl ME, Hall RL, Moyer RW. Mapping and molecular characterization of a functional thymidine kinase from Amsacta moorei entomopoxvirus. Virology 1992; 186:507-16. [PMID: 1733099 DOI: 10.1016/0042-6822(92)90016-i] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A thymidine kinase (TK) gene from the entomopoxvirus of Amsacta moorei (AmEPV) has been identified, mapped, cloned, and sequenced. The AmEPV TK was shown to be biologically functional as cloning of the gene into a TK-derivative of the orthopoxvirus vaccinia creates a TK+ virus. The gene has been localized to a 1.5-kb EcoRI-Q DNA fragment which maps to the far left end of the viral genome. Sequence analysis reveals an open reading frame (ORF) of 182 amino acids potentially encoding a polypeptide of 21.2 kDa. Amino acid homology comparisons indicate that the gene is most closely related to the TKs of a variety of poxviruses (approximately 45%) and less so to the TKs of vertebrates (approximately 40%). The TK from African swine fever virus (ASF) showed the least homology (31.4%) to the AmEPV TK gene, suggesting that these two viruses are not closely related although ASF shares some biological features of poxviruses, and both ASF and AmEPV can replicate within arthropod hosts.
Collapse
Affiliation(s)
- M E Gruidl
- Department of Immunology and Medical Microbiology, JHMHC, College of Medicine, University of Florida, Gainesville 32610
| | | | | |
Collapse
|
27
|
Boursnell M, Shaw K, Yáñez RJ, Viñuela E, Dixon L. The sequences of the ribonucleotide reductase genes from African swine fever virus show considerable homology with those of the orthopoxvirus, vaccinia virus. Virology 1991; 184:411-6. [PMID: 1871976 DOI: 10.1016/0042-6822(91)90860-e] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two African swine fever virus (ASFV) recombinant plasmids containing large inserts of DNA have been sequenced at random, and translations of the DNA sequence have been compared to libraries of vaccinia virus protein sequences. Among other genes identified by their extensive homology with vaccinia virus genes were the large and small subunits of ribonucleotide reductase. A 5.5-kb fragment from the Malawi (LIL20/1) strain of ASFV was identified as containing the genes for both these subunits. The fragment has been sequenced and the two genes have been found to be in a head-to-head orientation. The sequences are compared to other sequenced ribonucleotide reductase genes, and the evolutionary implications discussed.
Collapse
Affiliation(s)
- M Boursnell
- AFRC Institute for Animal Health, Pirbright Laboratory, Woking, Surrey, United Kingdom
| | | | | | | | | |
Collapse
|
28
|
Feller JA, Massung RF, Turner PC, Gibbs EP, Bockamp EO, Beloso A, Talavera A, Viñuela E, Moyer RW. Isolation and molecular characterization of the swinepox virus thymidine kinase gene. Virology 1991; 183:578-85. [PMID: 1853562 DOI: 10.1016/0042-6822(91)90986-l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Swinepox virus (SPV), the only member of the Suipoxvirus genus, shows little antigenic relatedness or DNA homology to members of the other poxvirus genera. A SPV thymidine kinase (TK) gene was detected and mapped to the left end of the HindIII G fragment using degenerate oligonucleotide probes. Cloning and sequencing of a 1.8-kb HindIII-BamHI fragment containing the SPV TK gene revealed an open reading frame (ORF) of 181 amino acids yielding a predicted polypeptide of Mr 20.6 kDa with significant homology to both poxvirus and vertebrate thymidine kinases. Comparison with other TK protein sequences showed that the SPV thymidine kinase was closely related to the TK genes of avipoxviruses (52.0%) and vertebrates (57.1-59.7%). The TK gene from African swine fever virus (ASF) showed little homology (30.5%) to the SPV TK gene suggesting that these two viruses are not closely related though they share many biochemical features and infect a single, common mammalian host (swine). The SPV TK gene, like that of other poxviruses, is transcribed early, and when cloned into a TK- strain of vaccinia converted the virus to a TK+ phenotype. BUdRR mutants of SPV contained frameshift, deletion, and missense mutations in the TK ORF.
Collapse
Affiliation(s)
- J A Feller
- Department of Immunology and Medical Microbiology, College of Medicine, University of Florida, Gainesville 32610
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Schnitzler P, Handermann M, Szépe O, Darai G. The primary structure of the thymidine kinase gene of fish lymphocystis disease virus. Virology 1991; 182:835-40. [PMID: 2024501 DOI: 10.1016/0042-6822(91)90625-l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The DNA nucleotide sequence of the thymidine kinase (TK) gene of fish lymphocystis disease virus (FLDV) which has been localized between the coordinates 0.678 to 0.688 of the viral genome was determined. The analysis of the DNA nucleotide sequence located between the recognition sites of HindIII (0.669 map unit; nucleotide position 1) and AccI (nucleotide position 2032) revealed the presence of an open reading frame of 954 bp on the lower strand of this region between nucleotide positions 1868 (ATG) and 915 (TAA). It encodes for a protein of 318 amino acid residues. The evolutionary relationships of the TK gene of FLDV to the other known TK genes was investigated using the method of progressive sequence alignment. These analyses revealed a high degree of diversity between the protein sequence of FLDV TK gene and the amino acid composition of other TKs tested. However, significant conservations were detected at several regions of amino acid residues of the FLDV TK protein when compared to the amino acid sequence of TKs of African swine fever virus, fowlpox virus, shope fibroma virus, and vaccinia virus and to the amino acid sequences of the cellular cytoplasmic TK of chicken, mouse, and man.
Collapse
Affiliation(s)
- P Schnitzler
- Institut für Medizinische Virologie, Universität Heidelberg, Germany
| | | | | | | |
Collapse
|
30
|
Bockamp EO, Blasco R, Viñuela E. Escherichia coli thymidine kinase: nucleotide sequence of the gene and relationships to other thymidine kinases. Gene 1991; 101:9-14. [PMID: 2060797 DOI: 10.1016/0378-1119(91)90218-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The thymidine kinase (TK)-encoding gene (tdk) of Escherichia coli is located at min 27 of the E. coli genetic map. Sequence analysis of this region revealed an open reading frame of 205 codons. Identification of this region as the E. coli tdk gene was confirmed by its similarity to other TK-encoding genes. The E. coli amino acid (aa) sequence showed significant similarity to the corresponding TK polypeptides of vertebrates and large DNA viruses, but showed no similarity to known herpes virus TK enzymes. Mapping of highly conserved positions among all sequences indicates the importance of these residues for catalytic activity and may facilitate further functional studies. Using a distance matrix method, the evolutionary relationships among the TK aa sequence of poxviruses, eukaryotes and prokaryotes were analyzed and a potential phylogenetic tree was established.
Collapse
Affiliation(s)
- E O Bockamp
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | | | | |
Collapse
|
31
|
Abstract
Bacteriophage lambda and plasmid clones containing African swine fever virus (ASFV) DNA inserts, which together covered more than 90% of the genome of a Malawi ASFV isolate (LIL 20/1), were transfected into vaccinia virus (VV)-infected cells. Expression of ASFV-encoded proteins was assayed at late times after VV infection by immunoprecipitation of [35S]methionine-labeled proteins with hyperimmune serum from ASFV-infected pigs, separation of immunoprecipitated proteins by denaturing polyacrylamide gel electrophoresis, and detection by autoradiography. Synthesis of eight additional proteins not observed in control experiments was detected. Seven VV recombinants were constructed, each containing an ASFV DNA insert from a separate bacteriophage lambda clone ranging in size from 9 to 15 kb. BSC40 cells were infected with recombinant viruses and expression of ASFV-encoded proteins assayed at early and late times postinfection. Synthesis of additional proteins, not observed in control experiments, was detected by immunoprecipitation with ASFV antiserum both early and late postinfection with two of these recombinants. In these experiments VV promoters were not included upstream of individual ASFV genes.
Collapse
Affiliation(s)
- J M Hammond
- Institute for Animal Health, Pirbright Laboratory, Surrey, United Kingdom
| | | |
Collapse
|
32
|
Schnitzlein WM, Tripathy DN. Identification and nucleotide sequence of the thymidine kinase gene of swinepox virus. Virology 1991; 181:727-32. [PMID: 1840707 DOI: 10.1016/0042-6822(91)90907-s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Using degenerative oligonucleotide probes, representing two different conserved regions of poxvirus and mammalian thymidine kinase (TK) genes, the swinepox virus (SPV) TK gene was mapped to a 1.7-kb BamHI-HindIII fragment of the viral genome. Nucleotide sequencing of this DNA piece revealed that the SPV TK gene was encoded by an open reading frame (ORF) of 177 codons. Immediately downstream of the TK gene was a second ORF with homologues at the same location in both capripoxvirus and leporipoxvirus genomes. A similar gene had translocated to near the left hand terminus of the vaccinia virus (orthopoxvirus) genome. Flanking the two SPV genes were ORFs whose counterparts in other poxvirus genera are located at the same relative positions. SPV appeared to be most closely related to capripoxvirus, based on the organization of the four genes and on the percentage of identical amino acid residues of the respective encoded proteins.
Collapse
Affiliation(s)
- W M Schnitzlein
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana 61801
| | | |
Collapse
|
33
|
New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1990; 18:6467-71. [PMID: 2243814 PMCID: PMC332589 DOI: 10.1093/nar/18.21.6467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|