• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of embojLink to Publisher's site
EMBO J. Dec 20, 1989; 8(13): 4081–4089.
PMCID: PMC401585

A physical genome map of Pseudomonas aeruginosa PAO.


A complete macrorestriction map of the 5.9 Mb genome of Pseudomonas aeruginosa PAO (DSM 1707) was constructed by the combination of various one- and two-dimensional pulsed field gel electrophoresis techniques. A total of 51 restriction sites (36 SpeI sites, 15 DpnI sites) were placed on the physical map yielding an average resolution of 110 kb. Several genes encoding virulence factors and enzymes of metabolic pathways were located on the anonymous map by Southern hybridization. Distances between the gene loci were similar on the genetic and physical maps, suggesting an even distribution of genome mobility throughout the bacterial chromosome. The four rRNA operons were organized in pairs of inverted repeats. The two-dimensional macro-restriction techniques described herein are generally applicable for the genome mapping of any prokaryote and lower eukaryote which yields resolvable fragment patterns on two-dimensional pulsed field gels.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.1M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Sanderson KE, Roth JR. Linkage map of Salmonella typhimurium, Edition VI. Microbiol Rev. 1983 Sep;47(3):410–453. [PMC free article] [PubMed]
  • Bautsch W. Rapid physical mapping of the Mycoplasma mobile genome by two-dimensional field inversion gel electrophoresis techniques. Nucleic Acids Res. 1988 Dec 23;16(24):11461–11467. [PMC free article] [PubMed]
  • Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. [PMC free article] [PubMed]
  • Boehm TL, Drahovsky D. Two-dimensional restriction mapping by digestion with restriction endonucleases of DNA in agarose and polyacrylamide gels. J Biochem Biophys Methods. 1984 May;9(2):153–161. [PubMed]
  • Brewer BJ. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell. 1988 Jun 3;53(5):679–686. [PubMed]
  • Burke DT, Carle GF, Olson MV. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science. 1987 May 15;236(4803):806–812. [PubMed]
  • Carle GF, Frank M, Olson MV. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science. 1986 Apr 4;232(4746):65–68. [PubMed]
  • Chang M, Hadero A, Crawford IP. Sequence of the Pseudomonas aeruginosa trpI activator gene and relatedness of trpI to other procaryotic regulatory genes. J Bacteriol. 1989 Jan;171(1):172–183. [PMC free article] [PubMed]
  • Chu G, Vollrath D, Davis RW. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986 Dec 19;234(4783):1582–1585. [PubMed]
  • Church GM, Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. [PMC free article] [PubMed]
  • Crawford IP, Wilde A, Yelverton EM, Figurski D, Hedges RW. Structure and regulation of the anthranilate synthase genes in Pseudomonas aeruginosa: II. Cloning and expression in Escherichia coli. Mol Biol Evol. 1986 Sep;3(5):449–458. [PubMed]
  • Douglas CM, Guidi-Rontani C, Collier RJ. Exotoxin A of Pseudomonas aeruginosa: active, cloned toxin is secreted into the periplasmic space of Escherichia coli. J Bacteriol. 1987 Nov;169(11):4962–4966. [PMC free article] [PubMed]
  • Ellwood M, Nomura M. Chromosomal locations of the genes for rRNA in Escherichia coli K-12. J Bacteriol. 1982 Feb;149(2):458–468. [PMC free article] [PubMed]
  • Ely B, Gerardot CJ. Use of pulsed-field-gradient gel electrophoresis to construct a physical map of the Caulobacter crescentus genome. Gene. 1988 Sep 7;68(2):323–333. [PubMed]
  • Fan JB, Chikashige Y, Smith CL, Niwa O, Yanagida M, Cantor CR. Construction of a Not I restriction map of the fission yeast Schizosaccharomyces pombe genome. Nucleic Acids Res. 1989 Apr 11;17(7):2801–2818. [PMC free article] [PubMed]
  • Feinberg AP, Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. [PubMed]
  • Feingold J, Bellofatto V, Shapiro L, Amemiya K. Organization and nucleotide sequence analysis of an rRNA and tRNA gene cluster from Caulobacter crescentus. J Bacteriol. 1985 Jul;163(1):155–166. [PMC free article] [PubMed]
  • Festl H, Ludwig W, Schleifer KH. DNA hybridization probe for the Pseudomonas fluorescens group. Appl Environ Microbiol. 1986 Nov;52(5):1190–1194. [PMC free article] [PubMed]
  • Guidi-Rontani C, Collier RJ. Exotoxin A of Pseudomonas aeruginosa: evidence that domain I functions in receptor binding. Mol Microbiol. 1987 Jul;1(1):67–72. [PubMed]
  • Haas D, Watson J, Krieg R, Leisinger T. Isolation of an Hfr donor of Pseudomonas aeruginosa PAO by insertion of the plasmid RP1 into the tryptophan synthase gene. Mol Gen Genet. 1981;182(2):240–244. [PubMed]
  • Hartmann RK, Toschka HY, Ulbrich N, Erdmann VA. Genomic organization of rDNA in Pseudomonas aeruginosa. FEBS Lett. 1986 Jan 20;195(1-2):187–193. [PubMed]
  • Holloway BW, Morgan AF. Genome organization in Pseudomonas. Annu Rev Microbiol. 1986;40:79–105. [PubMed]
  • Jarvis ED, Widom RL, LaFauci G, Setoguchi Y, Richter IR, Rudner R. Chromosomal organization of rRNA operons in Bacillus subtilis. Genetics. 1988 Nov;120(3):625–635. [PMC free article] [PubMed]
  • Kleckner N. Translocatable elements in procaryotes. Cell. 1977 May;11(1):11–23. [PubMed]
  • Kohara Y, Akiyama K, Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. [PubMed]
  • Kokjohn TA, Miller RV. Characterization of the Pseudomonas aeruginosa recA analog and its protein product: rec-102 is a mutant allele of the P. aeruginosa PAO recA gene. J Bacteriol. 1987 Apr;169(4):1499–1508. [PMC free article] [PubMed]
  • Lee JJ, Smith HO, Redfield RJ. Organization of the Haemophilus influenzae Rd genome. J Bacteriol. 1989 Jun;171(6):3016–3024. [PMC free article] [PubMed]
  • Lehner AF, Harvey S, Hill CW. Mapping and spacer identification of rRNA operons of Salmonella typhimurium. J Bacteriol. 1984 Nov;160(2):682–686. [PMC free article] [PubMed]
  • McClelland M, Jones R, Patel Y, Nelson M. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res. 1987 Aug 11;15(15):5985–6005. [PMC free article] [PubMed]
  • Morgan EA, Ikemura T, Lindahl L, Fallon AM, Nomura M. Some rRNA operons in E. coli have tRNA genes at their distal ends. Cell. 1978 Feb;13(2):335–344. [PubMed]
  • Nomura M, Morgan EA. Genetics of bacterial ribosomes. Annu Rev Genet. 1977;11:297–347. [PubMed]
  • O'Hoy K, Krishnapillai V. Recalibration of the Pseudomonas aeruginosa strain PAO chromosome map in time units using high-frequency-of-recombination donors. Genetics. 1987 Apr;115(4):611–618. [PMC free article] [PubMed]
  • Phibbs PV, Jr, Feary TW, Blevins WT. Pyruvate carboxylase deficiency in pleiotropic carbohydrate-negative mutant strains of Pseudomonas aeruginosa. J Bacteriol. 1974 Jun;118(3):999–1009. [PMC free article] [PubMed]
  • Pyle LE, Finch LR. A physical map of the genome of Mycoplasma mycoides subspecies mycoides Y with some functional loci. Nucleic Acids Res. 1988 Jul 11;16(13):6027–6039. [PMC free article] [PubMed]
  • Sanderson KE, Roth JR. Linkage map of Salmonella typhimurium, Edition VI. Microbiol Rev. 1983 Sep;47(3):410–453. [PMC free article] [PubMed]
  • Smith CL, Econome JG, Schutt A, Klco S, Cantor CR. A physical map of the Escherichia coli K12 genome. Science. 1987 Jun 12;236(4807):1448–1453. [PubMed]
  • Southern EM, Anand R, Brown WR, Fletcher DS. A model for the separation of large DNA molecules by crossed field gel electrophoresis. Nucleic Acids Res. 1987 Aug 11;15(15):5925–5943. [PMC free article] [PubMed]
  • Thuring RW, Sanders JP, Borst P. A freeze-squeeze method for recovering long DNA from agarose gels. Anal Biochem. 1975 May 26;66(1):213–220. [PubMed]
  • Toschka HY, Höpfl P, Ludwig W, Schleifer KH, Ulbrich N, Erdmann VA. Complete nucleotide sequence of a 23S ribosomal RNA gene from Pseudomonas aeruginosa. Nucleic Acids Res. 1987 Sep 11;15(17):7182–7182. [PMC free article] [PubMed]
  • Villems R, Duggleby CJ, Broda P. Restriction endonuclease mapping of DNA using in situ digestion in two-dimensional gels. FEBS Lett. 1978 May 15;89(2):267–270. [PubMed]
  • Wang SK, Sa'-Correia I, Darzins A, Chakrabarty AM. Characterization of the Pseudomonas aeruginosa alginate (alg) gene region II. J Gen Microbiol. 1987 Aug;133(8):2303–2314. [PubMed]
  • Wenzel R, Herrmann R. Physical mapping of the Mycoplasma pneumoniae genome. Nucleic Acids Res. 1988 Sep 12;16(17):8323–8336. [PMC free article] [PubMed]
  • Woolf T, Lai E, Kronenberg M, Hood L. Mapping genomic organization by field inversion and two-dimensional gel electrophoresis: application to the murine T-cell receptor gamma gene family. Nucleic Acids Res. 1988 May 11;16(9):3863–3875. [PMC free article] [PubMed]
  • Yee T, Inouye M. Two-dimensional DNA electrophoresis applied to the study of DNA methylation and the analysis of genome size in Myxococcus xanthus. J Mol Biol. 1982 Jan 15;154(2):181–196. [PubMed]
  • Hildebrand M, Jurgenson JE, Ramage RT, Bourque DP. Derivation of a physical map of chloroplast DNA from Nicotiana tabacum by two-dimensional gel and computer-aided restriction analysis. Plasmid. 1985 Jul;14(1):64–79. [PubMed]
  • HOLLOWAY BW, JENNINGS PA. An infectious fertility factor for Pseudomonas aeruginosa. Nature. 1958 Mar 22;181(4612):855–856. [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...