1887

Abstract

The combination of PFGE and hybridization approaches was used to study the genome of neotype strain ATCC 4356. PFGE analysis of chromosomal DNA after digestion with each of the rare-cutting restriction enzymes I-I, I, I, I, I and AI allowed the size of the circular chromosome of to be estimated at 2·061 Mbp. The physical map contained 86 restriction sites for the six enzymes employed, with intervals between the sites varying from 1 to 88 kbp (∼0·05–4·3 % of the chromosome). Based on the physical map, a genetic map was constructed via Southern blot analyses of DNA using specific gene probes. A total of 73 probes representing key genes, including 12 rRNA () genes, were positioned on the latter map. Mapping analysis also indicated the presence of four operons () on the chromosome, each containing a single copy of each of the three genes 16S (), 23S () and 5S (). Operon was inverted in orientation with respect to the others and contained a long 16S–23S intergenic spacer region with tRNA and tRNA genes, whereas the other operons contained a short spacer lacking any tRNA genes. The high-resolution physical/genetic map constructed in this study provides a platform for genomic and genetic studies of species and for improving industrial and probiotic strains.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27134-0
2005-03-01
2019-10-14
Loading full text...

Full text loading...

/deliver/fulltext/micro/151/3/mic1510875.html?itemId=/content/journal/micro/10.1099/mic.0.27134-0&mimeType=html&fmt=ahah

References

  1. Abs EL-Osta, Y. G., Hillier, A. J., Davidson, B. E. & Dobos, M. ( 2002; ). Pulsed field gel electrophoretic analysis of the chromosome of Lactobacillus gasseri ATCC33323. Electrophoresis 23, 3321–3331.[CrossRef]
    [Google Scholar]
  2. Albertsen, H. M., Le Paslier, D., Abderrahim, H., Dausset, J., Cann, H. & Cohen, D. ( 1989; ). Improved control of partial DNA restriction enzyme digest in agarose using limiting concentrations of Mg++. Nucleic Acids Res 174, 808.
    [Google Scholar]
  3. Anderson, D. G. & Mckay, L. L. ( 1983; ). Simple and rapid method for isolating plasmid DNA from lactic streptococci. Appl Environ Microbiol 46, 549–552.
    [Google Scholar]
  4. Bentley, R. W., Leigh, J. A. & Collins, M. D. ( 1991; ). Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41, 487–494.[CrossRef]
    [Google Scholar]
  5. Birnboim, H. C. & Doly, J. ( 1979; ). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7, 1513–1523.[CrossRef]
    [Google Scholar]
  6. Boot, H. J., Kolen, C. P., Andreadaki, F. J., Leer, R. J. & Pouwels, P. H. ( 1996; ). The Lactobacillus acidophilus S-layer protein gene expression site comprises two consensus promoter sequences, one of which directs transcription of stable mRNA. J Bacteriol 178, 5388–5394.
    [Google Scholar]
  7. Branny, P., De La Torre, F. & Garel, J. R. ( 1998; ). An operon encoding three glycolytic enzymes in Lactobacillus delbrueckii subsp. bulgaricus: glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase. Microbiology 144, 905–914.[CrossRef]
    [Google Scholar]
  8. Canard, B. & Cole, S. T. ( 1989; ). Genome organization of the anaerobic pathogen Clostridium perfringens. Proc Natl Acad Sci U S A 86, 6676–6680.[CrossRef]
    [Google Scholar]
  9. Chevallier, B., Hubert, J. C. & Kammerer, B. ( 1994; ). Determination of chromosome size and number of rrn loci in Lactobacillus plantarum by pulsed-field gel electrophoresis. FEMS Microbiol Lett 120, 51–56.[CrossRef]
    [Google Scholar]
  10. Cole, S. T. & Saint Girons, I. ( 1994; ). Bacterial genomics. FEMS Microbiol Rev 14, 139–160.[CrossRef]
    [Google Scholar]
  11. Collins, M. D., Rodrigues, U., Ash, C., Aguirre, M., Farrow, J. A. E., Martinez-Murica, A., Phillips, B. A., Williams, A. M. & Wallbanks, S. ( 1991; ). Phylogenetic analysis of the genes Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77, 5–12.[CrossRef]
    [Google Scholar]
  12. Davidson, B. E., Kordias, N., Dobos, M. & Hillier, A. J. ( 1996; ). Genomic organisation of lactic acid bacteria. Antonie Van Leeuwenhoek 70, 161–183.[CrossRef]
    [Google Scholar]
  13. De Man, J. C., Rogosa, M. & Sharpe, E. ( 1960; ). A medium for the cultivation of lactobacilli. J Appl Bacteriol 23, 130–135.[CrossRef]
    [Google Scholar]
  14. De Vuyst, L. & Vandamme, E. J. ( 1994; ). Bacteriocins of Lactic Acid Bacteria, 1st edn. Glasgow, UK: Chapman & Hall.
  15. Doherty, J. P., Lindeman, R., Trent, R. J., Graham, M. W. & Woodcock, D. M. ( 1993; ). Escherichia coli host strains SURETM and SRB fail to preserve a palindrome cloned in lambda phage: improved alternate host strains. Gene 124, 29–35.[CrossRef]
    [Google Scholar]
  16. Dower, W. J., Miller, J. F. & Ragsdale, C. W. ( 1988; ). High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16, 6127–6145.[CrossRef]
    [Google Scholar]
  17. Dudez, A. M., Chaillou, S., Hissler, L., Stentz, R., Champomier-Verges, M. C., Alpert, C. A. & Zagorec, M. ( 2002; ). Physical and genetic map of the Lactobacillus sakei 23K chromosome. Microbiology 148, 421–431.
    [Google Scholar]
  18. Feinberg, A. P. & Vogelstein, B. ( 1984; ). A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 137, 266–267.[CrossRef]
    [Google Scholar]
  19. Garcia-Martinez, J., Acinas, S. G., Anton, A. I. & Rodriguez-Valera, F. ( 1999; ). Use of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36, 55–64.[CrossRef]
    [Google Scholar]
  20. Gilliland, S. E. ( 1990; ). Health and nutritional benefits from lactic acid bacteria. FEMS Microbiol Rev 87, 175–188.[CrossRef]
    [Google Scholar]
  21. Goldin, B. R. ( 1998; ). Health benefits of probiotics. Br J Nutr 80, S203–S207.
    [Google Scholar]
  22. Gorbach, S. L. ( 2000; ). Probiotics and gastrointestinal health. Am J Gastroenterol 95 (Suppl 1), S2–S4.
    [Google Scholar]
  23. Gürtler, V. & Stanisich, V. A. ( 1996; ). New approaches to typing and identification of bacteria using the 16–23 rDNA spacer. Microbiology 142, 3–16.[CrossRef]
    [Google Scholar]
  24. Hammes, W. P. & Vogel, R. F. ( 1995; ). The genus Lactobacillus. In The Genera of Lactic Acid Bacteria, vol. 1, pp. 18–54. Edited by B. J. B. Wood & W. H. Holzapfel. Glasgow, UK: Blackie.
  25. Hanahan, D. ( 1983; ). Studies of transformation of Escherichia coli with plasmids. J Mol Biol 166, 557–580.[CrossRef]
    [Google Scholar]
  26. Hartmann, R. K., Toschka, H. Y., Ulbrich, N. & Erdmann, V. A. ( 1986; ). Genomic organization of rDNA in Pseudomonas aeruginosa. FEBS Lett 195, 187–193.[CrossRef]
    [Google Scholar]
  27. Hunt, M. L., Ruffolo, C. G., Rajakumar, K. & Adler, B. ( 1998; ). A physical and genetic map of the Pasteurella multocida A : 1 chromosome. J Bacteriol 180, 6054–6058.
    [Google Scholar]
  28. Itaya, M. ( 1997; ). Physical map of the Bacillus subtilis 166 genome: evidence for the inversion of an approximately 1900 kb continuous DNA segment, the translocation of an approximately 100 kb segment and the duplication of a 5 kb segment. Microbiology 143, 3723–3732.[CrossRef]
    [Google Scholar]
  29. Kandler, O. & Weiss, H. ( 1986; ). Regular, nonsporing gram-positive rods. In Bergey's Manual of Systematic Bacteriology, vol. 2. Edited by P. H. A. Sneath and others. Baltimore: William & Wilkins.
  30. Klaenhammer, T. R. ( 1995; ). Genetics of intestinal lactobacilli. Int Dairy J 5, 1019–1058.[CrossRef]
    [Google Scholar]
  31. Kleerebezem, M., Boekhorst, J., van Kranenburg, R. & 17 other authors ( 2003; ). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 100, 1990–1995.[CrossRef]
    [Google Scholar]
  32. Kolsto, A. B., Gronstad, A. & Oppegaard, H. ( 1990; ). Physical map of the Bacillus cereus chromosome. J Bacteriol 172, 3821–3825.
    [Google Scholar]
  33. Le Bourgeois, P., Lautier, M., Mata, M. & Ritzenthaler, P. ( 1992; ). Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1402. J Bacteriol 174, 6752–6762.
    [Google Scholar]
  34. Lee, J. J., Smith, H. O. & Redfield, R. J. ( 1989; ). Organisation of the Haemophilus influenzae Rd genome. J Bacteriol 171, 3016–3024.
    [Google Scholar]
  35. Leong-Morgenthaler, P., Ruettener, C., Mollet, B. & Hottinger, H. ( 1990; ). Construction of the physical map of Lactobacillus bulgaricus. Proc Third Symp Lactic Acid Bact A28.
    [Google Scholar]
  36. Lezhava, A., Mizukami, T., Kajitani, T., Kameoka, D., Redenbach, M., Shinkawa, H., Nimi, O. & Kinashi, H. ( 1995; ). Physical map of the linear chromosome of Streptomyces griseus. J Bacteriol 177, 6492–6498.
    [Google Scholar]
  37. Liu, S. L., Hessel, A. & Sanderson, K. E. ( 1993; ). Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 90, 6874–6878.[CrossRef]
    [Google Scholar]
  38. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  39. McKay, L. L. & Baldwin, K. A. ( 1990; ). Applications for biotechnology: present and future improvements in lactic acid bacteria. FEMS Microbiol Rev 87, 3–14.[CrossRef]
    [Google Scholar]
  40. Mercenier, A., Dutot, P., Kleinpeter, P., Aguirre, M., Paris, P., Reymund, J. & Slos, P. ( 1996; ). Development of lactic acid bacteria as live vectors for oral or local vaccines. Adv Food Sci 18, 73–77.
    [Google Scholar]
  41. Mercenier, A., Pavan, S. & Pot, B. ( 2003; ). Probiotics as biotherapeutic agents: present knowledge and future prospects. Curr Pharm Des 9, 175–191.[CrossRef]
    [Google Scholar]
  42. Nour, M. ( 1998; ). 16S–23S and 23S–5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res Microbiol 149, 433–448.[CrossRef]
    [Google Scholar]
  43. Ogasawara, N. & Yoshikawa, H. ( 1992; ). Genes and their organisation in the replication origin region of the bacterial chromosome. Mol Microbiol 6, 629–634.[CrossRef]
    [Google Scholar]
  44. 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 chromosome of the Lyme disease spirochaetes Borrelia burgdorferi, B. garinii and B. afzelii. Microbiology 140, 2931–2940.[CrossRef]
    [Google Scholar]
  45. O'Sullivan, D. J. & Klaenhammer, T. R. ( 1993; ). Rapid mini-prep isolation of high-quality plasmid DNA from Lactococcus and Lactobacillus spp. Appl Environ Microbiol 59, 2730–2733.
    [Google Scholar]
  46. Pouwels, P. H., Vriesema, A., Martinez, B., Tielen, F. J., Seegers, J. F., Leer, R. J., Jore, J. & Smit, E. ( 2001; ). Lactobacilli as vehicles for targeting antigens to mucosal tissues by surface exposition of foreign antigens. Methods Enzymol 336, 369–389.
    [Google Scholar]
  47. Pridmore, R. D., Berger, B., Desiere, F. & 12 other authors ( 2004; ). The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci U S A 101, 2512–2527.[CrossRef]
    [Google Scholar]
  48. Raman, V., Woodcock, D. & Hill, R. J. ( 1997; ). Typical unstable long tandem repeats in Escherichia coli show increased stability in strain PMC 107 and are stable when incorporated into the Drosophilia melanogaster genome. Anal Biochem 245, 242–245.[CrossRef]
    [Google Scholar]
  49. Reed, K. C. & Mann, D. A. ( 1985; ). Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res 13, 7207–7221.[CrossRef]
    [Google Scholar]
  50. Rolfe, R. D. ( 2000; ). The role of probiotic cultures in the control of gastrointestinal health. J Nutr 130, 396S–402S.
    [Google Scholar]
  51. Römling, U., Grothues, D., Bautsch, W. & Tummler, B. ( 1989; ). A physical genome map of Pseudomonas aeruginosa PAO. EMBO J 8, 4081–4089.
    [Google Scholar]
  52. Roussel, Y., Colmin, C., Simonet, J. M. & Decaris, B. ( 1993; ). Strain characterization, genome size and plasmid content in the Lactobacillus acidophilus group (Hansen and Mocquot). J Appl Bacteriol 74, 549–556.
    [Google Scholar]
  53. Roussel, Y., Pebay, M., Guedon, G., Simonet, J. M. & Decaris, B. ( 1994; ). Physical and genetic map of Streptococcus thermophilus A054. J Bacteriol 176, 7413–7422.
    [Google Scholar]
  54. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  55. Scheppler, L., Vogel, M., Zuercher, A. W., Zuercher, M., Germond, J. E., Miescher, S. M. & Stadler, B. M. ( 2002; ). Recombinant Lactobacillus johnsonii as a mucosal vaccine delivery vehicle. Vaccine 20, 2913–2920.[CrossRef]
    [Google Scholar]
  56. Seegers, J. F. ( 2002; ). Lactobacilli as live vaccine delivery vectors: progress and prospects. Trends Biotechnol 20, 508–515.[CrossRef]
    [Google Scholar]
  57. Smith, C. L., Econome, J. G., Schutt, A., Klco, S. & Cantor, C. R. ( 1997; ). A physical map of the Escherichia coli K12 genome. Nature 236, 1448–1453.
    [Google Scholar]
  58. Stiles, M. E. ( 1996; ). Biopreservation by lactic acid bacteria. Antonie Van Leeuwenhoek 70, 331–345.[CrossRef]
    [Google Scholar]
  59. Tulloch, D. L., Finch, L. R., Hillier, A. J. & Davidson, B. E. ( 1991; ). Physical map of the chromosome of Lactococcus lactis subsp. lactis DL11 and localization of six putative rRNA operons. J Bacteriol 173, 2768–2775.
    [Google Scholar]
  60. Vandamme, P., Pot, B., Gillis, M., de Vos, P., Kersters, P. & Swings, J. ( 1996; ). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438.
    [Google Scholar]
  61. Vaughan, E. E., Mollet, B. & de Vos, W. M. ( 1999; ). Functionality of probiotics and intestinal lactobacilli: light in the intestinal tract tunnel. Curr Opin Biotechnol 10, 505–510.[CrossRef]
    [Google Scholar]
  62. Wagner, R. ( 1994; ). The regulation of ribosomal RNA synthesis and bacterial cell growth. Microbiology 161, 100–109.
    [Google Scholar]
  63. Walker, D. C., Girgis, H. S. & Klaenhammer, T. R. ( 1999; ). The groESL chaperone operon of Lactobacillus johnsonii. Appl Environ Microbiol 65, 3033–3041.
    [Google Scholar]
  64. Wells, J. M., Robinson, K., Chamberlain, L. M., Schofield, K. M. & Le Page, R. W. F. ( 1996; ). Lactic acid bacteria as vaccine delivery vehicles. Antonie Van Leeuwenhoek 70, 317–330.[CrossRef]
    [Google Scholar]
  65. Yanisch-Perron, C., Vieire, J. & Messing, J. ( 1985; ). Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33, 103–119.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27134-0
Loading
/content/journal/micro/10.1099/mic.0.27134-0
Loading

Data & Media loading...

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