Surveying cereal-infecting geminiviruses in Germany-Diagnostics and direct sequencing using rolling circle amplification

Virus Research

Volumn 127, Issue 1, 2007, Pages 61-70

  Schubert, Jörg ^a   Habekuß, Antje ^a   Kazmaier, Katja ^b   Jeske, Holger ^b  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Mastrevirus; Nomenclature; Phylogeny

Indexed keywords

GENOMIC DNA; POLYCLONAL ANTIBODY;

ARTICLE; CEREAL; CONTROLLED STUDY; DNA SEQUENCE; DNA VIRUS; ENZYME LINKED IMMUNOSORBENT ASSAY; GEMINIVIRUS; GENE AMPLIFICATION; GERMANY; HOST RANGE; IMMUNOLOGICAL PROCEDURES; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; ROLLING CIRCLE AMPLIFICATION; VIRUS CLASSIFICATION; VIRUS DETECTION; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS ISOLATION;

CEREALS; DNA, CIRCULAR; DNA, VIRAL; GEMINIVIRIDAE; GERMANY; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TOBACCO;

BACTERIA (MICROORGANISMS); GEMINIVIRIDAE; HORDEUM; MASTREVIRUS;

EID: 34249001105     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2007.03.018     Document Type: Article

References (61)

1. Accotto G.P., Donson J., and Mullineaux P.M. Mapping of digitaria streak virus transcripts reveals different RNA species from the same transcription unit. EMBO J. 8 (1989) 1033-1039
2. Andersen M.T., Richardson K.A., Harbison S.A., and Morris B.A.M. Nucleotide sequence of the geminivirus chloris striate mosaic virus. Virology 164 (1988) 443-449
3. Bendahmane M., Schalk H.J., and Gronenborn B. Identification and characterization of wheat dwarf virus from France using a rapid method for geminivirus DNA preparation. Phytopathology 85 (1995) 1449-1455
4. Biebricher C.K., and Eigen M. What is a quasispecies?. Curr. Top. Microbiol. Immunol. 299 (2006) 1-31
5. Bosque-Perez N.A. Eight decades of maize streak virus research. Virus Res. 71 (2000) 107-121
6. Büchen-Osmond, C., 2006. International Commitee on Taxonomy of Viruses (ICTV) database. http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm.
7. Chatani M., Matsumoto Y., Mizuta H., Ikegami M., Boulton M., and Davies J.W. The nucleotide sequence and genome structure of the geminivirus Miscanthus streak virus. J. Gen. Virol. 72 (1991) 2325-2331
8. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res. 31 (2003) 3497-3500
9. Clark M.F., and Adams A.N. Characteristics of the micro plate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J. Gen. Virol. 34 (1977) 475-483
10. Commandeur U., and Huth W. Differentiation of strains of wheat dwarf virus in infected wheat and barley plants by means of polymerase chain reaction. Z. Pflanzenkr. Pflanzensch. 106 (1999) 550-552
11. Dekker E.L., Woolston C.J., Xue Y., Cox B.S., and Mullineaux P.M. Transcript mapping reveals different expression strategies for the bicistronic RNAs of the geminivirus wheat dwarf virus. Nucleic Acids Res. 19 (1991) 4075-4081
12. Donson J., Accotto G.P., Boulton M.I., Mullineaux P., and Davies J.W. The nucleotide sequence of a geminivirus from Digitaria sanguinalis. Virology 161 (1987) 160-169
13. Eigen M. On the nature of virus quasispecies. Trends Microbiol. 4 (1996) 216-218
14. Fauquet C.M., Bisaro D.M., Briddon R.W., Brown J.K., Harrison B.D., Rybicki E.P., Stenger D.C., and Stanley J. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Arch. Virol. 148 (2003) 405-421
15. Fauquet C.M., Maxwell D.P., Gronenborn B., and Stanley J. Revised proposal for naming geminiviruses. Arch. Virol. 145 (2000) 1743-1761
16. Fauquet C.M., and Stanley J. Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Arch. Virol. 150 (2005) 2151-2179
17. Gutierrez C., Ramirez-Parra E., Mar Castellano M., Sanz-Burgos A.P., Luque A., and Missich R. Geminivirus DNA replication and cell cycle interactions. Vet. Microbiol. 98 (2004) 111-119
18. Haible D., Kober S., and Jeske H. Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J. Virol. Methods 135 (2006) 9-16
19. Harris R.S., and Liddament M.T. Retroviral restriction by APOBEC proteins. Nat. Rev. Immunol. 4 (2004) 868-876
20. Hofer J.M.I., Dekker E.L., Reynolds H.V., Woolston C.J., Cox B.S., and Mullineaux P.M. Coordinate regulation of replication and virion sense gene expression in wheat dwarf virus. Plant Cell 4 (1992) 213-223
21. Huth W. Virus of Gramineae in Germany-a short overview. J. Plant Dis. Protect. 107 (2000) 406-414
22. Inoue-Nagata A.K., Albuquerque L.C., Rocha W.B., and Nagata T. A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J. Virol. Methods 116 (2004) 209-211
23. Kammann M., Schalk H.J., Matzeit V., Schaefer S., Schell J., and Gronenborn B. DNA replication of wheat dwarf virus, a geminivirus, requires two cis-acting signals. Virology 184 (1991) 786-790
24. Köklü G., Ramsell J.N.E., and Kvarnheden A. The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains. Virus Genes 34 (2007) 359-366
25. Kvarnheden A., Lindblad M., Lindsten K., and Valkonen J.P.T. Genetic diversity of Wheat dwarf virus. Arch. Virol. 147 (2002) 205-216
26. Laufs J., Jupin I., David C., Schumacher S., Heyraud-Nitschke F., and Gronenborn B. Geminivirus replications: genetic and biochemical characterization of Rep protein function, a review. Biochimie (Paris) 77 (1995) 765-773
27. Lazarowitz S.G. Infectivity and complete nucleotide sequence of the genome of a South African isolate of maize streak virus. Nucleic Acids Res. 16 (1988) 229-249
28. Lindsten K., and Vacke J. A possible barley adapted strain of wheat dwarf virus (WDV). Acta Phytopathol. Entomol. Hung. 26 (1991) 175-180
29. MacDowell S.W., Macdonald H., Hamilton W.D.O., Coutts R.H.A., and Buck K.W. The nucleotide sequence of cloned wheat dwarf virus DNA. EMBO J. 4 (1985) 2173-2180
30. Manurung B., Witsack W., Mehner S., Gruntzig M., and Fuchs E. The epidemiology of Wheat dwarf virus in relation to occurrence of the leafhopper Psammotettix alienus in Middle-Germany. Virus Res. 100 (2004) 109-113
31. Martin D.P., van der Walt E., Posada D., and Rybicki E.P. The evolutionary value of recombination is constrained by genome modularity. PLoS Genet. 1 (2005) 475-479
32. Martin D.P., Willment J.A., Billharz R., Velders R., Odhiambo B., Njuguna J., James D., and Rybicki E.P. Sequence diversity and virulence in Zea mays of maize streak virus isolates. Virology 288 (2001) 247-255
33. Mehner S., Manurung B., Grüntzig M., Habekuß A., Witsack W., and Fuchs E. Investigations into the ecology of the Wheat dwarf virus (WDV) in Saxony-Anhalt, Germany. J. Plant Dis. Protect. 110 (2003) 313-323
34. Milne I., Wright F., Rowe G., Marshall D.F., Husmeier D., and McGuire G. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20 (2004) 1806-1807
35. Morris-Krsinich B.A.M., Mullineaux P.M., Donson J., Boulton M.I., Markham P.G., Short M.N., and Davies J.W. Bidirectional transcription of maize streak virus DNA and identification of the coat protein gene. Nucleic Acids Res. 13 (1985) 7237-7256
36. Mullineaux P.M., Guerineau F., and Accotto G.P. Processing of complementary sense RNAs of digitaria streak virus in its host and in transgenic tobacco. Nucleic Acids Res. 18 (1990) 7259-7265
37. Owor B.E., Shepherd D.N., Taylor N.J., Edema R., Monjane A.L., Thomson J.A., Martin D.P., and Varsani A. Successful application of FTA classic card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J. Virol. Methods 140 (2007) 100-105
38. Palmer K.E., Schnippenkoetter W.H., and Rybicki E.P. Geminivirus isolation and DNA extraction. Methods Mol. Biol. 81 (1998) 41-52
39. Peterschmitt M., Granier M., Frutos R., and Reynaud B. Infectivity and complete nucleotide sequence of the genome of a genetically distinct strain of maize streak virus from Reunion Island. Arch. Virol. 141 (1996) 1637-1650
40. Petty I.T.D., Coutts R.H.A., and Buck K.W. Geminivirus coat protein gene promoter sequences can function in Escherichia coli. Nucleic Acids Res. 14 (1986) 5113
41. Rabenstein F., Sukhacheva E., Habekuß A., and Schubert J. Differentiation of Wheat dwarf virus isolates from wheat, triticale, and barley by means of a monoclonal antibody. Proceedings of the X Conference on Viral Diseases of Gramineae in Europe (2005) 60
42. Ray, S., 1999. SimPlot, 2.5 ed. John Hopkins University School of Medicine, Baltimore. www.welch.jhu.edu/∼sray.
43. Redinbaugh M.G. Transmission of Maize streak virus by vascular puncture inoculation with unit-length genomic DNA. J. Virol. Methods 109 (2003) 95-98
44. Redinbaugh M.G., Louie R., Ngwira P., Edema R., Gordon D.T., and Bisaro D.M. Transmission of viral RNA and DNA to maize kernels by vascular puncture inoculation. J. Virol. Methods 98 (2001) 135-143
45. Rigden J.E., Dry I.B., Krake L.R., and Rezaian M.A. Plant virus DNA replication processes in agrobacterium: insight into the origins of geminiviruses?. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 10280-10284
46. Rybicki E.P., and Pietersen G. Plant virus disease problems in the developing world. Adv. Virus Res. 53 (1999) 127-175
47. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Press, Cold Spring Harbor, NY
48. Schalk H.J., Matzeit V., Schiller B., Schell J., and Gronenborn B. Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO J. 8 (1989) 359-364
49. Schnippenkoetter W.H., Martin D.P., Hughes F.L., Fyvie M., Willment J.A., James D., von Wechmar M.B., and Rybicki E.P. The relative infectivities and genomic characterisation of three distinct mastreviruses from South Africa. Arch. Virol. 146 (2001) 1075-1088
50. Schubert J., Habekuß A., and Rabenstein F. Investigation of differences between wheat and barley forms of Wheat dwarf virus and their distribution in host plants. Plant Protect. Sci. 38 (2002) 43-48
51. Selth L.A., Randles J., and Rezaian M.A. Agrobacterium tumefaciens supports DNA replication of diverse geminivirus types. FEBS Lett. 516 (2002) 179-182
52. Shepherd D.N., Martin D.P., McGivern D.R., Boulton M.I., Thomson J.A., and Rybicki E.P. A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding. J. Gen. Virol. 86 (2005) 803-813
53. Stanley J., Bisaro D.M., Briddon R.W., Brown J.K., Fauquet C.M., Harrison B.D., Rybicki E.P., and Stenger D.C. Geminiviridae. In: Ball L.A. (Ed). Virus Taxonomy. VIII Report of the International Committee on Taxonomy of Viruses (2005), Elsevier/Academic Press, London 301-326.
54. Tóbiás L., Kiss B., and Palkovics L. The nucleotide sequence of two Hungarian isolates of Wheat dwarf virus. Acta Phytopathol. Entomol. Hungarica 41 (2006) 47-52
55. Vacke J. Wheat dwarf virus disease. Biol. Plant. Praha 3 (1961) 228-233
56. Vacke J., and Cibulka R. Comparison of DAS-ELISA and enzyme amplified ELISA for detection of Wheat dwarf virus in host plants and leafhopper vectors. Plant Protect. Sci. 36 (2000) 41-45
57. Willment J.A., Martin D.P., and Rybicki E.P. Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data. J. Virol. Methods 93 (2001) 75-87
58. Willment J.A., Martin D.P., van der Walt E., and Rybicki E.P. Biological and genomic sequence characterization of Maize streak virus isolates from wheat. Phytopathology 92 (2002) 81-86
59. Wright E.A., Heckel T., Groenendijk J., Davies J.W., and Boulton M.I. Splicing features in maize streak virus virion- and complementary-sense gene expression. Plant J. 12 (1997) 1285-1297
60. Xie J., Wang X., Liu Y., Peng Y., and Zhou G. First report of the occurrence of Wheat dwarf virus in wheat in China. Plant Dis. 91 (2007) 111
61. Zhang W., Olson N.H., Baker T.S., Faulkner L., Agbandje-McKenna M., Boulton M., Davies J.W., and McKenna R. Structure of the maize streak virus geminate particle. Virology 279 (2001) 471-477