1887

Abstract

To further understand the genomic diversity and genetic architecture of phytoplasmas, a physical and genetic map of the sweet potato little leaf (SPLL) strain V4 phytoplasma chromosome was determined. PFGE was used to determine the size of the SPLL-V4 genome, which was estimated to be 622 kb. A physical map was prepared by two-dimensional reciprocal digestions using the restriction endonucleases HII, I, I and I-I. Sixteen cleavage sites were located on the map. Southern hybridizations of digested SPLL-V4 chromosomal DNA were done using random clones and PCR-amplified genes as probes. This confirmed fragment positions and located the two rRNA operons and the linked / genes encoding elongation factors G and Tu, respectively, on the physical map. An inversion of one of the rRNA operons was observed from hybridization data. Sequence analysis of one of the random clones identified a gene encoding a glucose-inhibited division protein. Digestions of the tomato big bud (TBB) phytoplasma chromosome with the same four enzymes revealed genome heterogeneity when compared to the closely related SPLL-V4, and a preliminary chromosome size for the TBB phytoplasma of 662 kb was estimated. This mapping information has revealed that significant genome diversity exists within the phytoplasmas.

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2000-04-01
2019-10-16
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References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. ( 1990; ). Basic local alignment search tool. J Mol Biol 215, 403-410.[CrossRef]
    [Google Scholar]
  2. Amikan, D., Razin, S. & Glaser, G. ( 1982; ). Ribosomal RNA genes in Mycoplasmas. Nucleic Acids Res 10, 4215-4222.[CrossRef]
    [Google Scholar]
  3. Barbara, D. J., Davies, D. L. & Clark, M. F. (1998). Cloning and sequencing of a major membrane protein from chlorante (aster yellows) phytoplasma. 12th International Organisation of Mycoplasmology Conference, 22–28 July 1998, Sydney, Australia (programme and abstracts), poster G.04.
  4. Bautsch, W. ( 1988; ). Rapid physical mapping of the Mycoplasma mobile genome by two-dimensional field inversion gel electrophoresis techniques. Nucleic Acids Res 16, 11461-11467.[CrossRef]
    [Google Scholar]
  5. Berg, M. & Seemuller, E. ( 1999; ). Chromosomal organization and nucleotide sequence of the genes coding for the elongation factors G and Tu of the apple proliferation phytoplasma. Gene 226, 103-109.[CrossRef]
    [Google Scholar]
  6. Bhugra, B., Voelker, L. L., Zou, N. X., Yu, H. L. & Dybvig, K. ( 1995; ). Mechanism of antigenic variation in Mycoplasma pulmonis – interwoven, site-specific DNA inversions. Mol Microbiol 18, 703-714.[CrossRef]
    [Google Scholar]
  7. Carle, P., Laigret, F., Tully, J. G. & Bové, J. M. ( 1995; ). Heterogeneity of genome sizes within the genus Spiroplasma. Int J Syst Bacteriol 45, 178-181.[CrossRef]
    [Google Scholar]
  8. Davis, M. J., Tsai, J. H., Cox, R. L., McDaniel, L. L. & Harrison, N. A. ( 1988; ). Cloning of chromosomal and extrachromosomal DNA of the mycoplasmalike organism that causes maize bushy stunt disease. Mol Plant–Microbe Interact 1, 295-302.[CrossRef]
    [Google Scholar]
  9. Davis, R. E., Lee, I.-M., Douglas, S. M. & Dally, E. L. ( 1990; ). Molecular cloning and detection of chromosomal and extrachromosomal DNA of the mycoplasmalike organism associated with little leaf disease in periwinkle (Catharanthus roseus). Phytopathology 80, 789-793.[CrossRef]
    [Google Scholar]
  10. Davis, R. I., Schneider, B. & Gibb, K. S. ( 1997; ). Detection and differentiation of phytoplasmas in Australia. Aust J Agric Res 48, 535-544.[CrossRef]
    [Google Scholar]
  11. Firrao, G., Scott, S., Smart, C., Carraro, L., Chang, C.-J., Seemüller, E. & Kirkpatrick, B. C. ( 1996a; ). Serological and molecular genetic characterization of five members of the X-disease phytoplasma clade. Inst Organ Mycoplasmol Lett 4, 278-279.
    [Google Scholar]
  12. Firrao, G., Smart, C. D. & Kirkpatrick, B. C. ( 1996b; ). Physical map of the western X-disease phytoplasma chromosome. J Bacteriol 178, 3985-3988.
    [Google Scholar]
  13. Fraser, C. M., Gocayne, J. D., White, O. & 26 other authors ( 1995; ). The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.[CrossRef]
    [Google Scholar]
  14. Guindy, Y. S., Samuelsson, T. & Johanssen, T.-I. ( 1989; ). Unconventional codon reading by Mycoplasma mycoides tRNAs as revealed by partial sequence analysis. Biochem J 258, 869-873.
    [Google Scholar]
  15. Inamine, J. M., Loechel, S. & Hu, P.-C. ( 1989; ). Nucleotide sequence of the tuf gene from Mycoplasma gallisepticum. Nucleic Acids Res 17, 10126.[CrossRef]
    [Google Scholar]
  16. Jarausch, W., Saillard, C., Dosba, F. & Bové, J. M. ( 1994; ). Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO. Appl Environ Microbiol 60, 2916-2923.
    [Google Scholar]
  17. Katayama, S., Dupuy, B., Garnier, T. & Cole, S. T. ( 1995; ). Rapid expansion of the physical and genetic map of the chromosome of Clostridium perfringens cpn50. J Bacteriol 177, 5680-5685.
    [Google Scholar]
  18. Kirkpatrick, B. C., Smart, C. D., Gardner, S. L. & 9 other authors ( 1994; ). Phylogenetic relationships of plant pathogenic MLOs established by 16/23S rDNA spacer sequences. Inst Organ Mycoplasmol Lett 3, 228–229.
    [Google Scholar]
  19. Kollar, A. & Seemüller, E. ( 1989; ). Base composition of the DNA of the mycoplasma-like organisms associated with various plant diseases. J Phytopathol 127, 177-186.[CrossRef]
    [Google Scholar]
  20. Kuboyama, T., Huang, C. C., Lu, X., Sawayanagi, T., Kanazawa, T., Kagami, T., Matsuda, I., Tsuchizaki, T. & Namba, S. ( 1998; ). A plasmid isolated from phytopathogenic onion yellows phytoplasma and its heterogeneity in the pathogenic phytoplasma mutant. Mol Plant–Microbe Interact 11, 1031-1037.[CrossRef]
    [Google Scholar]
  21. 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]
  22. Ladefoged, S. A. & Christiansen, G. ( 1992; ). Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis. J Bacteriol 174, 2199-2207.
    [Google Scholar]
  23. Lauer, U. & Seemüller, E. (1998). Physical map of the apple proliferation phytoplasma genome. 12th International Organisation of Mycoplasmology Conference, 22–28 July 1998, Sydney, Australia (programme and abstracts), poster D.59.
  24. Lim, P.-O. & Sears, B. B. ( 1992; ). Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences. J Bacteriol 174, 2606-2611.
    [Google Scholar]
  25. Lindahl, L. & Zengel, J. M. ( 1986; ). Ribosomal genes in Escherichia coli. Annu Rev Genet 20, 297-326.[CrossRef]
    [Google Scholar]
  26. Liu, S.-L. & Sanderson, K. E. ( 1995; ). I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J Bacteriol 177, 3355-3357.
    [Google Scholar]
  27. Lysnyansky, I., Rosengarten, R. & Yogev, D. ( 1996; ). Phenotypic switching of variable surface lipoproteins in Mycoplasma bovis involves high-frequency chromosomal rearrangements. J Bacteriol 178, 5395-5401.
    [Google Scholar]
  28. Marcone, C., Neimark, H., Ragozzino, A., Lauer, U. & Seemuller, E. ( 1999; ). Chromosome sizes of phytoplasmas composing major phylogenetic groups and subgroups. Phytopathology 89, 805-810.[CrossRef]
    [Google Scholar]
  29. Neimark, H. & Kirkpatrick, B. C. ( 1993; ). Isolation and characterisation of full-length chromosomes from non-culturable plant-pathogenic mycoplasma-like organisms. Mol Microbiol 7, 21-28.[CrossRef]
    [Google Scholar]
  30. Neimark, H. C. & Lange, C. S. ( 1990; ). Pulse-field electrophoresis indicates full-length mycoplasma chromosomes range widely in size. Nucleic Acids Res 18, 5443-5448.[CrossRef]
    [Google Scholar]
  31. Ojaimi, C., Davidson, B. E., Saint Girons, I. & Old, I. G. ( 1994; ). Conservation of gene arrangement and an unusual organization of rRNA genes in the linear chromosomes of the Lyme disease spirochaetes Borrelia burgdorferi, B. garinii and B. afzelii. Microbiology 140, 2931-2940.[CrossRef]
    [Google Scholar]
  32. Peterson, S. N., Lucier, T., Heitzman, K., Smith, E. A., Bott, K. F., Hu, P.-C. & Hutchison, C. A.III ( 1995; ). Genetic map of the Mycoplasma genitalium chromosome. J Bacteriol 177, 3199-3204.
    [Google Scholar]
  33. Post, L. E. & Nomura, M. ( 1980; ). DNA sequences from the str operon of Escherichia coli. J Biol Chem 255, 4660-4666.
    [Google Scholar]
  34. Pyle, L. E., Corcoran, L. N., Cocks, B. G., Bergemann, A. D., Whitley, J. C. & Finch, L. R. ( 1988; ). Pulse-field electrophoresis indicates larger-than-expected sizes for mycoplasma genomes. Nucleic Acids Res 16, 6015-6025.[CrossRef]
    [Google Scholar]
  35. Pyle, L. E., Taylor, T. & Finch, L. R. ( 1990; ). Genomic maps of some strains within the Mycoplasma mycoides cluster. J Bacteriol 172, 7265-7268.
    [Google Scholar]
  36. Rasmussen, O. F. & Christiansen, C. ( 1987; ). Identification of the proton ATPase operon in Mycoplasma strain PG50 by heterologous hybridization. Isr J Med Sci 23, 393-397.
    [Google Scholar]
  37. Rasmussen, O. F. & Christiansen, C. ( 1990; ). A 23 kb region of the Mycoplasma strain PG50 genome with three identified genetic structures. Zentbl Bakteriol Suppl 20, 315-323.
    [Google Scholar]
  38. Razin, S., Knyszynski, A. & Lifshitz, Y. ( 1964; ). Nucleases of mycoplasma. J Gen Microbiol 36, 323-331.[CrossRef]
    [Google Scholar]
  39. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  40. Samuelsson, T., Elias, P., Lustig, F. & Guindy, Y. S. ( 1985; ). Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides. Biochem J 232, 223-338.
    [Google Scholar]
  41. Schneider, B. & Seemüller, E. ( 1994; ). Presence of two sets of ribosomal genes in phytopathogenic mollicutes. Appl Environ Microbiol 60, 3409-3412.
    [Google Scholar]
  42. Schneider, B., Gibb, K. S. & Seemüller, E. ( 1997; ). Sequence and RFLP analysis of the elongation factor Tu gene used in differentiation and classification of phytoplasmas. Microbiology 143, 3381-3389.[CrossRef]
    [Google Scholar]
  43. Schneider, B., Gibb, K. S., Padovan, A., Davis, R. I. & De La Rue, S. ( 1998; ). Comparison and characterization of tomato big bud- and sweet potato little leaf-group phytoplasmas. J Phytopathol 147, 1-64.
    [Google Scholar]
  44. Sears, B. B., Lim, P.-O., Holland, N., Kirkpatrick, B. C. & Klomparens, K. L. ( 1989; ). Isolation and characterisation of DNA from a mycoplasmalike organism. Mol Plant–Microbe Interact 2, 175-180.[CrossRef]
    [Google Scholar]
  45. Seemüller, E., Marcone, C., Lauer, U., Ragozzino, A. & Göschl, M. ( 1998; ). Current status of molecular classification of the phytoplasmas. J Plant Pathol 80, 3-26.
    [Google Scholar]
  46. Toda, T. & Itaya, M. ( 1995; ). I-CeuI recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmarks for genome analysis. Microbiology 141, 1937-1945.[CrossRef]
    [Google Scholar]
  47. Whatling, C. A. & Thomas, C. M. ( 1993; ). Preelectrophoresis of agarose plugs containing bacterial chromosomal DNA prepared for analysis by pulsed field gel electrophoresis can improve the clarity of restriction patterns. Anal Biochem 210, 98-101.[CrossRef]
    [Google Scholar]
  48. Whitley, J. C., Muto, A. & Finch, L. R. ( 1990; ). A physical map for Mycoplasma capricolum cal. Kid with loci for all known tRNA species. Nucleic Acids Res 19, 399-400.
    [Google Scholar]
  49. Yasumoto, K., Liu, H. T., Jeong, S. M., Ohashi, Y., Kakinuma, S., Tanaka, K., Kawamura, F., Yoshikawa, H. & Takahashi, H. ( 1996; ). Sequence analysis of a 50 kb region between spoOH and rrnH on the Bacillus subtilis chromosome. Microbiology 142, 3039-3046.[CrossRef]
    [Google Scholar]
  50. Ye, F., Laigret, F., Carle, P. & Bové, J. M. ( 1995; ). Chromosomal heterogeneity among various strains of Spiroplasma citri. Int J Syst Bacteriol 45, 729-734.[CrossRef]
    [Google Scholar]
  51. Ye, F., Melcher, U., Rascoe, J. E. & Fletcher, J. ( 1996; ). Extensive chromosome aberrations in Spiroplasma citri strain BR3. Biochem Genet 34, 269-286.[CrossRef]
    [Google Scholar]
  52. Yu, Y.-L., Yeh, K.-W. & Lin, C.-P. ( 1998; ). An antigenic protein gene of a phytoplasma associated with sweet potato witches’ broom. Microbiology 144, 1257-1262.[CrossRef]
    [Google Scholar]
  53. Zreik, L., Carle, P., Bové, J. M. & Garnier, M. ( 1995; ). Characterization of the mycoplasmalike organism associated with witches’-broom disease of lime and proposition of a Candidatus taxon for the organism, ‘‘Candidatus Phytoplasma aurantifolia’’. Int J Syst Bacteriol 45, 449-453.[CrossRef]
    [Google Scholar]
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