1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 6

The –––– gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation Free

Abstract

The – operon or operon is a classic bacterial gene cluster, which codes for proteins K, A, J and L of the large ribosomal subunit, as well as proteins B ( subunit) and C (′ subunit) of RNA polymerase. In the early 1990s, the operon was obtained as a 2.6 kbp DNA fragment (In-2.6) by random cloning of DNA from periwinkle plants infected with the Poona (India) strain of the huanglongbing agent, later named ‘ () Liberibacter asiaticus’. DNA from periwinkle plants infected with the Nelspruit strain (South Africa) of ‘ L. africanus’ was amplified with a primer pair designed from In-2.6 and yielded, after cloning and sequencing, a 1.7 kbp DNA fragment (AS-1.7) of the operon of ‘ L. africanus’. The operon of the American liberibacter, as well as the three upstream genes (, , ), have now also been obtained by the technique of chromosome walking and extend over 4673 bp, comprising the following genes: , , , , , , and . The sequence of the operon was also determined for a Brazilian strain of ‘ L. asiaticus’, from to (3025 bp), and was found to share 99 % identity with the corresponding operon sequences of an Indian and a Japanese strain. Finally, the operon sequence of ‘ L. africanus’ was extended from 1673 bp ( to ) to 3013 bp ( to ), making it possible to compare the operon sequences of the African, Asian and American liberibacters over a length of ∼3000 bp, from to . While ‘. L. africanus’ and ‘. L. asiaticus’ shared 81.2 % sequence identity, the percentage for ‘. L. americanus’ and ‘. L. africanus’ was only 72.2 %, and identity for ‘. L. americanus’ and ‘. L. asiaticus’ was only 71.4 %. The ∼3000 bp – sequence was also used to construct a phylogenetic tree, and this tree was found to be identical to the known 16S rRNA gene sequence-based tree. These results confirm earlier findings that ‘. L. americanus’ is a distinct liberibacter, more distantly related to ‘. L. africanus’ and ‘. L. asiaticus’ than ‘. L. africanus’ is to ‘. L. asiaticus’. The dates of speciation have also been estimated.

  • Published Online:
Keyword(s): HLB, huanglongbing
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65641-0
2008-06-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/58/6/1414.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65641-0&mimeType=html&fmt=ahah

References

  1. Battistuzzi, F. U., Feijao, A. & Hedges, S. B.(2004). A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 9, 44 [Google Scholar]
  2. Beattie, G. A. C., Mabberley, D. J., Holford, P., Broadbent, P. & De Barro, P.(2005). Huanglongbing: its possible origins, collaborative research in Southeast Asia, and developing incursion management plans for Australia. In Proceedings of the 2nd International Citrus Canker and Huanglongbing Research Workshop, H-5. Orlando, FL: Florida Citrus Mutual.
  3. Bové, J. M.(2006). Huanglongbing: a destructive, newly-emerging, century-old disease of citrus. J Plant Pathol 88, 7–37. [Google Scholar]
  4. Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G. & Little, E.(1996). Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470–477.[CrossRef] [Google Scholar]
  5. Dower, W. J., Miller, J. F. & Ragdsdale, C. W.(1988). High efficiency transformation of Escherichia coli by high voltage electroporation. Nucleic Acids Res 16, 6127–6145.[CrossRef] [Google Scholar]
  6. Garnier, M. & Bové, J. M.(1983). Transmission of the organism associated with citrus greening disease from sweet orange to periwinkle by dodder. Phytopathology73, 1358–1363.
  7. Hocquellet, A., Bové, J. M. & Garnier, M.(1997). Production and evaluation of non-radioactive probes for the detection of the two “Candidatus Liberobacter” species associated with citrus Huanglongbing (greening). Mol Cell Probes 11, 433–438.[CrossRef] [Google Scholar]
  8. Hocquellet, A., Bové, J. M. & Garnier, M.(1999). Isolation of DNA from uncultured “Candidatus Liberobacter” species associated with citrus Huanglongbing by RAPD. Curr Microbiol 38, 176–182.[CrossRef] [Google Scholar]
  9. Johnson, J. L.(1984). Nucleic acids in bacterial classification. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 8–11. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  10. Murray, M. G. & Thompson, W. F.(1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8, 4321–4325.[CrossRef] [Google Scholar]
  11. Ochman, H. & Wilson, A. C.(1987). Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26, 74–86.[CrossRef] [Google Scholar]
  12. Okuda, M., Matsumoto, M., Tanaka, Y., Subandiyah, S. & Iwanami, T.(2005). Characterization of the tufB-secE-nusG-rplKAJL-rpoB gene cluster of the citrus greening organism and detection by loop-mediated isothermal amplification. Plant Dis 89, 705–711.[CrossRef] [Google Scholar]
  13. Planet, P., Jagoueix, S., Bové, J. M. & Garnier, M.(1995). Detection and characterization of the African citrus greening Liberibacter by amplification, cloning and sequencing of the rplKAJL-rpoB operon. Curr Microbiol 30, 137–141.[CrossRef] [Google Scholar]
  14. Schiex, T., Gouzy, J., Moisan, A. & de Oliveira, Y.(2003). FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res 31, 3738–3741.[CrossRef] [Google Scholar]
  15. Tamura, K., Nei, M. & Kumar, S.(2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101, 11030–11035.[CrossRef] [Google Scholar]
  16. Tamura, K., Dudley, J., Nei, M. & Kumar, S.(2007).mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef] [Google Scholar]
  17. Teixeira, D. C., Ayres, A. J., Kitajima, E. W., Tanaka, F. A. O., Danet, J. L., Jagoueix-Eveillard, S., Saillard, C. & Bové, J. M.(2005a). First report of a huanglongbing-like disease of citrus in Sao Paulo State, Brazil, and association of a new liberibacter species, ‘Candidatus Liberibacter americanus’, with the disease. Plant Dis 89, 107 [Google Scholar]
  18. Teixeira, D. C., Danet, J. L., Eveillard, S., Martins, E. C., de Jesus, W. C., Jr, Yamamoto, P. T., Lopes, S. A., Bassanezi, R. B., Ayres, A. J. & other authors(2005b). Citrus huanglongbing in São Paulo State, Brazil: PCR detection of the ‘Candidatus Liberibacter’ species associated with the disease. Mol Cell Probes 19, 173–179.[CrossRef] [Google Scholar]
  19. Teixeira, D. C., Saillard, C., Couture, C., Martins, E. C., Wulff, N. A., Eveillard-Jagoueix, S., Yamamoto, P. T., Ayres, A. J. & Bové, J. M.(2008). Distribution and quantification of Candidatus Liberibacter americanus, agent of huanglongbing disease of citrus in São Paulo State, Brasil, in leaves of an affected sweet orange tree as determined by PCR. Mol Cell Probes 22, 139–150.[CrossRef] [Google Scholar]
  20. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  21. Villechanoux, S., Garnier, M., Renaudin, J. & Bové, J. M.(1992). Detection of several strains of the bacterium-like organism of citrus greening disease by DNA probes. Curr Microbiol 24, 89–95.[CrossRef] [Google Scholar]
  22. Villechanoux, S., Garnier, M., Laigret, F., Renaudin, J. & Bové, J. M.(1993). The genome of the non-cultured, bacterium-like organism associated with citrus greening disease contains the nusG-rplKAJL-rpoB gene cluster and the gene for a bacteriophage type DNA polymerase. Curr Microbiol 26, 161–166.[CrossRef] [Google Scholar]
  23. von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B. & Bork, P.(2007).string 7 – recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35, D358–D362.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65641-0
Loading
The tufB–secE–nusG–rplKAJL–rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation
Int J Syst Evol Microbiol 58, 1414 (2008); https://doi.org/10.1099/ijs.0.65641-0
/content/journal/ijsem/10.1099/ijs.0.65641-0
/content/journal/ijsem/10.1099/ijs.0.65641-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error