1887

Abstract

Application of a promoter-trapping strategy to identify plant-inducible genes carried on an indigenous plasmid, pQBR103, revealed the presence of a putative oligoribonuclease () gene that encodes a highly conserved 3′ to 5′ exoribonuclease specific for small oligoribonucleotides. The deduced amino acid sequence of the plasmid-derived ( ) showed three conserved motifs characteristic of Orn from both prokaryotes and eukaryotes. Deletion of generated no observable phenotype, but inactivation of the chromosomal copy caused slow growth in KT2440. This defect was fully restored by complementation with from ( ). Plasmid-derived was capable of partially complementing the mutant, demonstrating functionality of . Phylogenetic analysis showed that plasmid-encoded Orn was distinct from Orn encoded by the chromosome of proteobacteria. A survey of from related plasmids showed a sporadic distribution but no sequence diversity. These data suggest that the was acquired by pQBR103 in a single gene-transfer event: the donor is unknown, but is unlikely to be a member of the .

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2004-09-01
2019-09-17
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References

  1. Bailey, M. J., Lilley, A. K., Thompson, I. P., Rainey, P. B. & Ellis, R. J. ( 1995; ). Site directed chromosomal marking of a fluorescent pseudomonad isolated from the phytosphere of sugar beet; stability and potential for marker gene transfer. Mol Ecol 4, 755–763.[CrossRef]
    [Google Scholar]
  2. Bailey, M. J., Rainey, P. B., Zhang, X. X. & Lilley, A. K. ( 2001; ). Population dynamics, gene transfer and gene expression in plasmids, the role of the horizontal gene pool in local adaptation at the plant surface. In Microbiology of Aerial Plant Surfaces, pp. 171–189. Edited by S. E. Lindow, E. I. Hecht-Poinar & V. J. Elliott. St Paul, MN: American Phytopathological Society Press.
  3. Baxevanis, A. D. & Ouellette, B. F. F. ( 2001; ). Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins, 2nd edn. New York: Wiley Interscience.
  4. Bloemberg, G. V. & Lugtenberg, B. J. J. ( 2001; ). Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4, 343–350.[CrossRef]
    [Google Scholar]
  5. Ditta, G., Stanfield, S., Corbin, D. & Helinski, D. R. ( 1980; ). Broad host range DNA cloning system for Gram negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci U S A 77, 7347–7351.[CrossRef]
    [Google Scholar]
  6. Favaro, R. & Deho, G. ( 2003; ). Polynucleotide phosphorylase-deficient mutants of Pseudomonas putida. J Bacteriol 185, 5279–5286.[CrossRef]
    [Google Scholar]
  7. Fellay, R., Frey, J. & Krisch, H. ( 1987; ). Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of Gram-negative bacteria. Gene 52, 147–154.[CrossRef]
    [Google Scholar]
  8. Gal, M., Preston, G. M., Massey, R. C., Spiers, A. J. & Rainey, P. B. ( 2003; ). Genes encoding a cellulose polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol Ecol 12, 3109–3121.[CrossRef]
    [Google Scholar]
  9. Ghosh, S. & Deutscher, M. P. ( 1999; ). Oligoribonuclease is an essential component of the mRNA decay pathway. Proc Natl Acad Sci U S A 96, 4372–4377.[CrossRef]
    [Google Scholar]
  10. Hanekamp, T. & Thorsness, P. E. ( 1999; ). YNT20, a bypass suppressor of yme1 yme2, encodes a putative 3′-5′ exonuclease localized in mitochondria of Saccharomyces cerevisiae. Curr Genet 34, 438–448.[CrossRef]
    [Google Scholar]
  11. Hartl, D. L., Dykhuizen, D. E. & Berg, D. E. ( 1984; ). Accessory DNA's in the bacterial gene pool: playground for coevolution. In Origins and Development of Adaptations (Ciba Foundation Symposium 102), pp. 233–245. London: Pitman Books.
  12. Heeb, S., Itoh, Y., Nishijyo, T., Schnider, U., Keel, C., Wade, J., Walsh, U., O'Gara, F. & Haas, D. ( 2000; ). Small, stable shuttle vectors based on the minimal pVS1 replicon for use in gram-negative, plant-associated bacteria. Mol Plant–Microbe Interact 13, 232–237.[CrossRef]
    [Google Scholar]
  13. Lilley, A. K. & Bailey, M. J. ( 1997a; ). The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 63, 1577–1583.
    [Google Scholar]
  14. Lilley, A. K. & Bailey, M. J. ( 1997b; ). Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of Pseudomonas fluorescens SBW25: burden and benefit. Appl Environ Microbiol 63, 1584–1587.
    [Google Scholar]
  15. Lilley, A. K., Bailey, M. J., Day, M. J. & Fry, J. C. ( 1996; ). Diversity of mercury resistance plasmid obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol Ecol 20, 211–227.[CrossRef]
    [Google Scholar]
  16. McClure, N. C., Fry, J. C. & Weightman, A. J. ( 1990; ). Gene transfer in activated sludge. In Bacterial Genetics in Natural Environments, pp. 111–129. Edited by J. C. Fry & M. J. Day. London: Chapman & Hall.
  17. Nakazawa, T. ( 2002; ). Travels of a Pseudomonas, from Japan around the world. Environ Microbiol 4, 782–786.[CrossRef]
    [Google Scholar]
  18. Nguyen, L. H., Erzberger, J. P., Root, J. & Wilson, D. M., III ( 2000; ). The human homolog of Escherichia coli Orn degrades small single-stranded RNA and DNA oligomers. J Biol Chem 275, 25900–25906.[CrossRef]
    [Google Scholar]
  19. Ohnishi, Y., Nishiyama, Y., Sato, R., Kameyama, S. & Horinouchi, S. ( 2000; ). An oligoribonuclease gene in Streptomyces griseus. J Bacteriol 182, 4647–4653.[CrossRef]
    [Google Scholar]
  20. Page, R. D. M. ( 1996; ). TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
    [Google Scholar]
  21. Palleroni, N. J. ( 1984; ). Pseudomonadaceae. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by N. R. Kreig & J. G. Holt. Baltimore: Williams & Wilkins.
  22. Rainey, P. B. ( 1999; ). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1, 243–257.[CrossRef]
    [Google Scholar]
  23. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 374–377.
    [Google Scholar]
  24. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  25. Spiers, A. J., Bohannon, J., Gerhrig, S. M. & Rainey, P. B. ( 2003; ). Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 50, 15–27.[CrossRef]
    [Google Scholar]
  26. Thomas, C. M. ( 2000; ). The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread. Amsterdam: Harwood Academic Publishers.
  27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  28. Viegas, C. A., Lilley, A. K., Bruce, K. B. & Bailey, M. J. ( 1997; ). Description of a novel plasmid replicative origin from a genetically distinct family of conjugative plasmids associated with phytosphere microflora. FEMS Microbiol Lett 149, 121–127.[CrossRef]
    [Google Scholar]
  29. Vivian, A., Murillo, J. & Jackson, R. W. ( 2001; ). The roles of plasmids in phytopathogenic bacteria: mobile arsenals? Microbiology 147, 763–780.
    [Google Scholar]
  30. Zhang, X., Zhu, L. & Deutscher, M. P. ( 1998; ). Oligoribonuclease is encoded by a highly conserved gene in the 3′-5′ exonuclease superfamily. J Bacteriol 180, 2779–2781.
    [Google Scholar]
  31. Zuo, Y. & Deutscher, M. P. ( 2001; ). Survey and summary: exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29, 1017–1026.[CrossRef]
    [Google Scholar]
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