1887

Abstract

The chromosome was fractionated with the enzymes and and genomic fragments were separated by PFGE and used for mapping a collection of 40 genes. This permitted the localization of 8 genes previously mapped and of 32 genes which had not been mapped. We showed that a careful search of databases and identification of sequences that were homologous to known genes could be used to design and synthesize DNA probes for the mapping of homologues by Southern hybridization with genomic fragments, resulting in definition of the locations of the and genetic markers. In addition, a combination of distinct DNA sources were utilized as radioactively labelled probes, including specific restriction fragments of the cloned genes ( DNA fragments prepared by PCR, and single-stranded DNA prepared from phagemid libraries that had been randomly sequenced. We used a PCR approach to clone fragments of the putative and genes. Random sequencing of DNA from phagemid libraries and database searching permitted the cloning of sequences from the and gene homologues. The described genomic methods permit the rapid mapping of the genome without linkage analysis.

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1996-01-01
2021-04-10
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References

  1. Amabile-Cuevas C. F., Demple B. 1991; Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon. Nucleic Acids Res 19:4479–4484
    [Google Scholar]
  2. Beall B., Lowe M., Lutkenhaus J. 1988; Cloning and characterization of Bacillus subtilis homologues of Escherichia coli cell division genes ftsZ and ftsA. J Bacteriol 170:4855–4864
    [Google Scholar]
  3. Bell A., Hancock R. E. W. 1989; Outer membrane protein HI of Pseudomonas aeruginosa: purification of the protein and cloning and nucleotide sequence of the gene. J Bacteriol 171:3211–3217
    [Google Scholar]
  4. Benvenisti L, Koby S, Rutman A, Giladi H, Yura T., Oppenheim A. B. 1995; Cloning and primary sequence of the rpoH gene from Pseudomonas aeruginosa. Gene 155:73–76
    [Google Scholar]
  5. Birren B., Lai E. 1993 Pulsed Field Gel Electrophoresis. A Practical Approach New York: Academic Press;
    [Google Scholar]
  6. Buck D. W., Spencer M. E., Guest J. R. 1985; Primary structure of the succinyl-CoA synthetase of Escherichia coli. Biochemistry 24:6245–6252
    [Google Scholar]
  7. Burland V, Plunkett G III, Daniels D. L., Blattner F. R. 1993; DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16:551–561
    [Google Scholar]
  8. Cuskey S. M., Phibbs P. V. 1985; Chromosomal mapping of mutations affecting glycerol and glucose metabolism in Pseudomonas aeruginosa and Pseudomonas putida. J Bacteriol 162:872–880
    [Google Scholar]
  9. Eriani G, Delarue M, Poch O., Gangloff J., Moras D. 1990; Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203–206
    [Google Scholar]
  10. Hassett D. J., Woodruff W. A., Wozniak D. J., Vasil M. L., Cohen M. S., Ohman D. E. 1993; Cloning and characterization of the Pseudomonas aeruginosa sodA and sodB genes encoding manganese- and iron-cofactored superoxide dismutase: demonstration of increased manganese superoxide dismutase activity in alginate-producing bacteria. J Bacteriol 175:7658–7665
    [Google Scholar]
  11. Holloway B. W., Rómling U., Tümmler B. 1994; Genomic mapping of Pseudomonas aeruginosa PAO. Microbiology 140:2907–2929
    [Google Scholar]
  12. Huang H., Siehnel R. J., Bellido F., Rawling E., Hancock R. E. W. 1992; Analysis of two gene regions involved in the expression of the imipenem-specific, outer membrane porin protein OprD of Pseudomonas aeruginosa. FEMS Microbiol Eett 76:267–273
    [Google Scholar]
  13. Huang M., Oppermann F. B., Steinbuechel A. 1994; Molecular characterization of the Pseudomonas putida 2,3-butanediol-catabolic pathway. FEMS Microbiol Eett 124:141–150
    [Google Scholar]
  14. Joris B, Ledent P, Dideberg O., Fonzé E., Lamotte-Brasseur J., Kelly J. A., Ghuysen J. M., Frère J.-M. 1991; Comparison of the sequences of class A β-lactamases and of the secondary structure elements of penicillin-recognizing proteins. Antimicrob Agents Chemother 35:2294–2301
    [Google Scholar]
  15. Kawamukai M, Matsuda H, Fujii W., Utsumi R., Komano T. 1989; Nucleotide sequences of fic and fic-1 genes involved in cell filamentation induced by cyclic AMP in Escherichia coli. J Bacteriol 171:4525–529
    [Google Scholar]
  16. Kwon D., Lu C., Walthall D, Brown J, Houghton J., Abdelal A. 1994; Structure and regulation of the carAB operon in Pseudomonas aeruginosa and Pseudomonas stutzeri. J Bacteriol 176:2532–2542
    [Google Scholar]
  17. Lightfoot J., Lam J. S. 1993; Chromosomal mapping, expression and synthesis of lipopolysaccharide in Pseudomonas aeruginosa: a role for guanosine diphospho(GDP)-D-mannose. Mol Microbiol 8:771–782
    [Google Scholar]
  18. Lodge J. M., Minchin S. D., Piddock L. J. V., Busby S. J. 1990; Cloning, sequencing and analysis of the structural gene and regulatory region of the Pseudomonas aeruginosa chromosomal ampC β -lactamase. Biochem J 272:627–631
    [Google Scholar]
  19. Margolin W., Corbo J. C., Long S. R. 1991; Cloning and characterization of a Rhizobium meliloti homologue of the Escherichia coli cell division gene ftsZ. J Bacteriol 173:5822–5830
    [Google Scholar]
  20. Martin P. R., Hobbs M., Free P. D., Jeske Y., Mattick J. S. 1993; Characterization of pilQ, a new gene required for the biogenesis of type 4 fimbriae in Pseudomonas aeruginosa. Mol Microbiol 9:857–868
    [Google Scholar]
  21. Michaud C, Parquet C, Flouret B., Blanot D., Van Heijenoort J. 1990; Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetylmuramyl-tripeptide synthetase of Escherichia coli. Biochem J 269:277–278
    [Google Scholar]
  22. Miller H. I. 1984; Primary structure of the him A gene of Escherichia coli: homology with DNA-binding protein HU and association with the phenylalanyl-tRNA synthetase operon. Cold Spring Harbor Symp Quant Biol 49:691–698
    [Google Scholar]
  23. Mohr C. D., Sonsteby S. K., Deretic V. 1994; The Pseudomonas aeruginosa homologs of hemC and hemD are linked to the gene encoding the regulator of mucoidy algR. Mol & Gen Genet 242:177–184
    [Google Scholar]
  24. Nakamura M., Maruyama I. N., Soma M, Kato J, Suzuki H., Hirota Y. 1983; On the process of cellular division in Escherichia coli: nucleotide sequence of the gene for penicillin-binding protein 2. Mol & Gen Genet 191:1–9
    [Google Scholar]
  25. Poole K, Krebes K, McNally C., Neshat S. 1993; Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon. J Bacteriol 175:7363–7372
    [Google Scholar]
  26. Ratnaningsih E, Dharmsthiti S, Krishnapillai V, Morgan A, Sinclair M., Holloway B. W. 1990; A combined physical and genetic map of Pseudomonas aeruginosa PAO. J Gen Microbiol 136:2351–2357
    [Google Scholar]
  27. Robinson A. C., Kenan D. J., Hatfull G. F., Sullivan N. F., Spielgelberg R., Donachie W. D. 1984; DNA sequence and transcriptional organization of essential cell division genes ftsQ and ftsA of Escherichia coli: evidence for overlapping transcriptional units. J Bacteriol 160:546–555
    [Google Scholar]
  28. Robison K., Gilbert W., Church G. M. 1994; Large scale bacterial gene discovery by similarity search. Nat Genet 7:205–214
    [Google Scholar]
  29. Römling U., Tömmler B. 1991; The impact of two-dimensional pulsed-field gel electrophoresis techniques for the consistent and complete mapping of bacterial genomes: refined physical map of Pseudomonas aeruginosa PAO. Nucleic Acids Res 12:3199–3206
    [Google Scholar]
  30. Rómling U, Grothues D, Bautsch W., TUmmler B. 1989; A physical genome map of Pseudomonas aeruginosa PAO. EMBO J 8:4081–4089
    [Google Scholar]
  31. Rómling U, Duchène M, Essar D. W., Galloway D., Guidi-Rontani C., Hill D., Lazdunski A, Millet R. V., Scheifer K. H., Smith D. W., Toschka H. Y., Tümmler B. 1992; Localization of alg, opr, phn, 45S RNA, 6S RNA, tox, trp and xcp genes, rrn operons, and the chromosomal origin on the physical genome map of Pseudomonas aeruginosa PAO. J Bacteriol 174:327–330
    [Google Scholar]
  32. Rothmel R. K., Aldrich T. L., Houghton J. E., Coco W. M., Ornston L. N., Chakrabarty A. M. 1990; Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the lysR family. J Bacteriol 172:922–931
    [Google Scholar]
  33. Saint-Onge A, Romeyer F, Lebel P., Masson L., Brousseau R. 1992; Specificity of the Pseudomonas aeruginosa PAOl lipoprotein I gene as a DNA probe and PCR target region within the Pseudomonadaceae. J Gen Microbiol 138:733–741
    [Google Scholar]
  34. Sambrook J., Maniatis T., Fritsch E. F. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  35. Sanangelantoni A. M., Calogero R. C., Buttarelli F. R., Gualerzi C. O., Tiboni O. 1990; Organization and nucleotide sequence of the genes for ribosomal protein and elongation factor Ts in Spirulina platensis. FEMS Microbiol Lett 66:141–146
    [Google Scholar]
  36. Sano Y, Matsui H, Kobayashi M., Kageyama M. 1993; Molecular structures and functions of pyocins SI and S2 in Pseudomonas aeruginosa. J Bacteriol 175:2907–2916
    [Google Scholar]
  37. Schweizer H. P., Po C. 1994; Cloning and nucleotide sequence of the glpD gene encoding sn-glycerol-3-phosphate dehydrogenase of Pseudomonas aeruginosa. J Bacteriol 176:2184–2193
    [Google Scholar]
  38. Siehnel R. J., Worobec E. A., Hancock R. E. 1988; Regulation of components of the Pseudomonas aeruginosa phosphate-starvation-inducible regulon in Escherichia coli. Mol Microbiol 2:347–352
    [Google Scholar]
  39. Siehnel R. J., Martin N. L., Hancock R. E. W. 1990; Sequence and relatedness in other bacteria of the Pseudomonas aeruginosa oprP gene coding for the phosphate-specific porin p. Mol Microbiol 4:831–838
    [Google Scholar]
  40. Siehnel R. J., Egli C., Hancock R. E. W. 1992; Polyphosphate-selective porin OprO of Pseudomonas aeruginosa: expression, purification and sequence. Mol Microbiol 6:2319–2326
    [Google Scholar]
  41. Sofia H. J., Burland V., Daniels D. L., Plunkett G. III, Blattner F. R. 1994; Analysis of the Escherichia coli genome V DNA sequence of the region from 76·0 to 81·5 minutes. Nucleic Acids Res 22:2576–2586
    [Google Scholar]
  42. Spratt B. G., Cromie K. D. 1988; Penicillin-binding proteins of Gram-negative bacteria. Rev Infect Dis 10:699–711
    [Google Scholar]
  43. Vieira J., Messing J. 1987; Production of single-stranded plasmid DNA. Methods Enzymol 153:3–11
    [Google Scholar]
  44. West S. E., Iglewski B. H. 1988; Codon usage in Pseudomonas aeruginosa. Nucleic Acids Res 16:9323–9335
    [Google Scholar]
  45. Woodruff W. A., Parr T. R., Hancock R. E. W., Hanne L., Nicas T. I., Iglewski B. 1986; Expression in Escherichia coli and function of Pseudomonas aeruginosa outer membrane protein. J Bacteriol 167:473–479
    [Google Scholar]
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