Sequence analysis of two plasmids from the phytoplasma beet leafhopper-transmitted virescence agent

References

1. Ahrens U., Seemüller E. 1992; Detection of DNA of plant pathogenic mycoplasma-like organisms by a polymerase chain reaction that amplifies a sequence of the 16S rRNA gene. Phytopathology 82:828–832 [CrossRef]
   [Google Scholar]
2. Altschul S. F., Madden T. L., Zhang J., Zhang Z., Miller W., Lipman D. L., Schäffer A. A. 1997; Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
   [Google Scholar]
3. Aravind L., Leipe D. D., Koonin E. U. 1998; Toprim – a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res 26:4205–4213 [CrossRef]
   [Google Scholar]
4. Benson G. 1999; Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580 [CrossRef]
   [Google Scholar]
5. del Solar G., Giraldo R., Espinosa M., Ruiz-Echevarría M. J., Díaz-Orejas R. 1998; Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62:434–464
   [Google Scholar]
6. Denes A. S., Sinha R. C. 1992; Alteration of clover phyllody mycoplasma DNA after in vitro culturing of phyllody-diseased clover. Can J Plant Pathol 14:189–196 [CrossRef]
   [Google Scholar]
7. Eberhard W. G. 1990; Evolution in bacterial plasmids and levels of selection. Q Rev Biol 65:3–22 [CrossRef]
   [Google Scholar]
8. Feinberg A. P., Vogelstein B. 1983; A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6–13 [CrossRef]
   [Google Scholar]
9. Golino D. A., Oldfield G. N., Gumpf D. J. 1987; Transmission characterisitics of the beet leafhopper transmitted virescence agent. Phytopathology 77:954–957 [CrossRef]
   [Google Scholar]
10. Golino D. A., Oldfield G. N., Gumpf D. J. 1988; Induction of flowering through infection by beet leafhopper transmitted virescence agent. Phytopathology 78:285–288 [CrossRef]
    [Google Scholar]
11. Golino D. A., Oldfield G. N., Gumpf D. J. 1989; Experimental hosts of the beet leafhopper-transmitted virescence agent. Plant Dis 73:850–854 [CrossRef]
    [Google Scholar]
12. Ilyina T. V., Koonin E. V. 1992; Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eukaryotes and archaebacteria. Nucleic Acids Res 20:3279–3285 [CrossRef]
    [Google Scholar]
13. Ilyina T. V., Gorbalenya A. E., Koonin E. V. 1992; Organization and evolution of bacterial and bacteriophage primase-helicase systems. J Mol Evol 34:351–357 [CrossRef]
    [Google Scholar]
14. Kirkpatrick B. C. 1992; Mycoplasma-like organisms – plant and invertebrate pathogens. In The Prokaryotes vol. IV, 2nd edn. pp. 4050–4068 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. New York: Springer;
    [Google Scholar]
15. Kirkpatrick B. C., Stenger D. C., Morris T. J., Purcell A. H. 1987; Cloning and detection of DNA from a nonculturable plant pathogenic mycoplasma-like organism. Science 238:197–200 [CrossRef]
    [Google Scholar]
16. Koch A. L. 1981; Evolution of antibiotic resistance gene function. Microbiol Rev 45:355–378
    [Google Scholar]
17. Kuske C. R., Kirkpatrick B. C. 1990; Identification and characterization of plasmids from the western aster yellows mycoplasmalike organism. J Bacteriol 172:1628–1633
    [Google Scholar]
18. Lukashin A., Borodovsky M. 1998; GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115 [CrossRef]
    [Google Scholar]
19. Nakashima K., Hayashi T. 1995; Extrachromosomal DNAs of rice yellow dwarf and sugarcane white leaf phytoplasmas. Ann Phytopathol Soc Jpn 61:456–462 [CrossRef]
    [Google Scholar]
20. Nakashima K., Hayashi T. 1997; Sequence analysis of extrachromosomal DNA of sugarcane white leaf phytoplasma. Ann Phytopathol Soc Jpn 63:21–25 [CrossRef]
    [Google Scholar]
21. Nishigawa H., Miyata S., Oshima K., Sawayanagi T., Komoto A., Kuboyama T., Matsuda I., Tsuchizaki T., Namba S. 2001; In planta expression of a protein encoded by the extrachromosomal DNA of a phytoplasma and related to geminivirus replication proteins. Microbiology 147:507–513
    [Google Scholar]
22. Nishigawa H., Oshima K., Kakizawa S., Jung H., Kuboyama T., Miyata S., Ugaki M., Namba S. 2002a; A plasmid from a non-insect-transmissible line of a phytoplasma lacks two open reading frames that exist in the plasmid from the wild-type line. Gene 298:195–201 [CrossRef]
    [Google Scholar]
23. Nishigawa H., Oshima K., Kakizawa S., Jung H., Kuboyama T., Miyata S., Ugaki M., Namba S. 2002b; Evidence of intermolecular recombination between extrachromosomal DNAs in phytoplasma: a trigger for the biological diversity of phytoplasma?. Microbiology 148:1389–1396
    [Google Scholar]
24. Nishigawa H., Oshima K., Miyata S., Ugaki M., Namba S. 2003; Complete set of extrachromosomal DNAs from three pathogenic lines of onion yellows phytoplasma and use of PCR to differentiate each line. J Gen Plant Pathol 69:194–198
    [Google Scholar]
25. Oshima K., Shiomi T., Kuboyama T., Sawayanagi T., Nishigawa H., Kakizawa S., Miyata S., Ugaki M., Namba S. 2001; Isolation and characterization of derivative lines of the onion yellows phytoplasma that do not cause stunting or phloem hyperplasia. Phytopathology 91:1024–1029 [CrossRef]
    [Google Scholar]
26. O'Sullivan T., van Sinderen D., Fitzgerald G. 1999; Structural and functional analysis of pCI65st, a 6·5 kb plasmid from Streptococcus thermophilus NDI-6. Microbiology 145:127–134 [CrossRef]
    [Google Scholar]
27. Pansegrau W., Lanka E. 1992; A common sequence motif among prokaryotic DNA primases. Nucleic Acids Res 20:4931 [CrossRef]
    [Google Scholar]
28. Rekab D., Carraro L., Schneider B., Chen J., Chang C.-J., Locci R., Firrao G., Seemüller E. 1999; Geminivirus-related extrachromosomal DNAs of the X-clade phytoplasmas share high sequence similarity. Microbiology 145:1453–1459 [CrossRef]
    [Google Scholar]
29. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
30. Saraste M., Sibbald P. R., Wittinghofer A. 1990; The P-loop – a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 15:430–434 [CrossRef]
    [Google Scholar]
31. Shaw M. E. 1991; Biological and molecular characterization of virescence agents infecting herbaceous crops in California. PhD thesis University of California; Davis, USA:
32. Shaw M. E., Kirkpatrick B. C., Golino D. A. 1990; Infection of radish in Idaho by leafhopper-transmitted virescence agent. Plant Dis 74:252
    [Google Scholar]
33. Shaw M. E., Kirkpatrick B. C., Golino D. A. 1993; The beet leafhopper-transmitted virescence agent is the causal agent of tomato big bud disease in California. Plant Dis 77:290–295 [CrossRef]
    [Google Scholar]
34. Smart C. D., Thompson S. V., Flint K., Kirkpatrick B. C. 1993; The beet leafhopper-transmitted virescence agent is associated with diseased potatoes in Utah. Phytopathology 83:1399
    [Google Scholar]
35. Strack B., Lessl M., Calendar R., Lanka E. 1992; The common sequence motif, -E-G-Y-A-T-A-, identified within the primase domains of plasmid-encoded I- and P-type DNA primases and the α protein of the Escherichia coli satellite phage P4. J Biol Chem 267:13062–13072
    [Google Scholar]
36. Tatusova T. A., Madden T. L. 1999; Blast 2 sequences – a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250 [CrossRef]
    [Google Scholar]
37. Versalovic J., Lupski J. R. 1993; The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Gene 136:281–286 [CrossRef]
    [Google Scholar]
38. Zünd P., Lebak G. 1980; Generation time-prolonging R plasmids: correlation between increases in the generation time of Escherichia coli caused by R plasmids and their molecular size. Plasmid 3:65–69 [CrossRef]
    [Google Scholar]