1887

Microbiology Society logo

Volume 143, Issue 4

Directed introduction of DNA cleavage sites to produce a high-resolution genetic and physical map of the Acinetobacter sp. strain ADP1 (BD413UE) chromosome Free

Abstract

The natural transformability of the soil bacterium sp. ADP1 (BD413UE), formerly classified as has facilitated previous physiological and biochemical investigations. In the present studies, the natural transformation system was exploited to generate a physical and genetic map of this strain's 3780·191 kbp circular chromosome. Previously isolated Acinetobacter genes were modified to incorporate a recognition sequence for the restriction endonuclease l. Following transformation of the wild-type strain by the modified DNA, homologous recombination placed each engineered l cleavage site at the chromosomal location of the corresponding gene. This allowed precise gene localization and orientation of more than 40 genes relative to a physical map which was constructed with transverse alternating field electrophoresis (TAFE) and Southern hybridization methods. The positions of l, l and l- l recognition sites were determined, and the latter enzyme identified the presence of seven ribosomal RNA operons. Multiple chromosomal copies of insertion sequence IS were indicated by hybridization. Several of these copies were concentrated in one region of the chromosome in which a spontaneous deletion of approximately 100 kbp occurred. Moreover, contrary to previous reports, ColE1-based plasmids appeared to replicate autonomously in sp. ADP1.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Acinetobacter , genome , map , PFGE (pulsed-field gel electrophoresis) and TAFE (transverse alternating-field electrophoresis)
© Society for General Microbiology 1997
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-143-4-1345
1997-04-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/micro/143/4/mic-143-4-1345.html?itemId=/content/journal/micro/10.1099/00221287-143-4-1345&mimeType=html&fmt=ahah

References

  1. Averhoff B., Gregg-Jolly L. A., Elsemore D. A., Ornston L. N. 1992; Genetic analysis of supraoperonic clustering by use of natural transformation in Acinetobacter calcoaceticus.. J Bacteriol 174:200–204
     [Google Scholar]
  2. Baumann P., Doudoroff M., Stanier R. Y. 1968; A study of Moraxella group I1 : oxidase negative species (genus Acinetobacter).. J Bacteriol 95:1520–1541
     [Google Scholar]
  3. Bergogne-Bérézin E. 1994; Acinetobacter spp., saprophytic organisms of increasing pathogenic importance.. Zentralbl Bakteriol 281:389–405
     [Google Scholar]
  4. Condon C., Liveris D., Squires C., Schwartz J., Squires C. L. 1995; rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation.. J Bacteriol 177:4152–4156
     [Google Scholar]
  5. Doten R. C., Ngai K.-L., Mitchell D. J., Ornston L. N. 1987; Cloning and genetic organization of the pcaG gene cluster from Acinetobacter calcoaceticus.. J Bacteriol 169:3168–3174
     [Google Scholar]
  6. Dryden S.C., Kaplan S. 1990; Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides.. Nucleic Acids Res 18:7267–7277
     [Google Scholar]
  7. Ellwood M., Nomura M. 1982; Chromosomal location of the genes for rRNA in E . coli K-12.. J Bacteriol 149:458–468
     [Google Scholar]
  8. Elsemore D. A., Ornston L. N. 1994; The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate-shikimate dehydrogenase.. J Bacteriol 176:7659–7666
     [Google Scholar]
  9. Eraso J. M., Kaplan S. 1994; prrA, a putative response regulator involved in oxygen regulation of photosynthetic gene expression in Rhodobacter sphaeroides.. J Bacteriol 176:32–43
     [Google Scholar]
  10. Fonstein M., Haselkorn R. 1995; Physical mapping of bacterial genomes.. J Bacteriol 177:3361–3369
     [Google Scholar]
  11. Geissdörfer W., Frosch S. C., Haspel G., Ehrt S., Hillen W. 1995; Two genes encoding proteins with similarities to rubredoxin and rubredoxin reductase are required for conversion of dodecane to lauric acid in Acinetobacter calcoaceticus ADP1.. Microbiology 141:1425–1432
     [Google Scholar]
  12. Gerischer U., Ornston L. N. 1995; Spontaneous mutations in pcaH and -G structural genes for protocatechuate 3,4-dioxygenase in Acinetobacter calcoaceticus.. J Bacteriol 177:1336–1347
     [Google Scholar]
  13. Gerischer U., D’Argenio D., Ornston L. N. 1996; IS1236, a newly discovered member of the IS3 family, exhibits varied patterns of insertion into the Acinetobacter calcoaceticus chromosome.. Microbiology 142:1825–1831
     [Google Scholar]
  14. Gerner-Smidt P. 1994; Acinetobacter : epidemiological and taxonomic aspects.. Acta Pathol Microbiol lmmunol Scand Suppl 47:102–541
     [Google Scholar]
  15. Gralton E. M. 1996; Physical and genetic map of Acinetobacter calcoaceticus strain BD413 (ADPI). MS thesis, . University of Georgia, Athens, GA.
     [Google Scholar]
  16. Gregg-Jolly, L. A., Ornston L. N. 1990; Recovery of DNA from the Acinetobacter calcoaceticus chromosome by gap repair.. J Bacteriol 172:6169–6172
     [Google Scholar]
  17. Gregg-Jolly L. A., Ornston L. N. 1994; Properties of Acinetobacter calcoaceticus recA and its contribution to intracellular gene conversion.. Mol Microbiol 12:985–992
     [Google Scholar]
  18. Harwood C. S., Parales R. E. 1996; Thep-ketoadipate pathway and the biology of self-identity.. Annu Rev Microbiol 50:553–590
     [Google Scholar]
  19. Haspel G.,, Hunger M., Schmucker R., Hillen W. 1990; Identification and nucleotide sequence of the Acinetobacter calcoaceticus encoded trpE gene.. Mol Gen Genet 220:475–477
     [Google Scholar]
  20. Haspel G., Kishan V., Hillen W. 1991; Organisation, potential regulatory elements and evolution of trp genes in Acinetobacte. In The Biology of Acinetobacter, Edited by K. J. Towner, E. Bergogne-Bérézin & C. A. Fewson.. New York: Plenum Press.239–249
     [Google Scholar]
  21. Holloway B. W., Dharmsthiti S., Krishnapillai V., Morgan A., Obeyesekere V., Ratnaningsih E., Sinclair M., Strom D., Zhang C. 1990; Patterns of gene linkages in Pseudomonas species. In The Bacterial Chromosome, Edited by K. Drlica & M. Riley. . Washington, DC: American Society for Micro biology.97–105
     [Google Scholar]
  22. Holloway B. W., Escuadra M. D., Morgan A. F., Saffery R., Krishnapillai V. . 1992; The new approaches to whole genome analysis of bacteria.. FEMS Microbiol Lett 100:101–106
     [Google Scholar]
  23. Hunger M., Schmucker R., Kishan V., Hillen W. 1990; Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids.. Gene 87:45–51
     [Google Scholar]
  24. Juni E. 1972; Interspecies transformation of Acinetobacter : genetic evidence for a ubiquitous genus.. J Bacteriol 112:917–931
     [Google Scholar]
  25. Juni E. (1978); Genetics and physiology of Acinetobacter.. Annu Rev Microbiol 32:349–371
     [Google Scholar]
  26. Juni E., Janik A. 1969; Transformation of Acinetobacter calcoaceticus (Bacterium anitratum).. J Bacteriol 98:281–288
     [Google Scholar]
  27. Kaplan J. B., Goncharoff P., Seibold A. M., Nichols B. P. 1984; Nucleotide sequence of the Acinetobacter calcoaceticus trpGDC gene cluster.. Mol Biol Evol 1:456–472
     [Google Scholar]
  28. Kloos D.-U., DiMarco A. A., Elsemore D. A., Timmis K., Ornston L. N. 1995; Distance between alleles as a determinant of linkage in Acinetobacter calcoaceticus.. J Bacteriol 177:6015–6017
     [Google Scholar]
  29. Kok R. 1995; Lipolytic enzymes in Acinetobacter calcoaceticus. PhD thesis, University of Amsterdam..
    [Google Scholar]
  30. Kok R. G., Christoffels V. M., Vosman B., Hellingwerf K. J. 1993; Growth-phase-dependent expression of the lipolytic system of Acinetobacter calcoaceticus BD413 : cloning of a gene encoding one of the esterases.. J Gen Microbiol 139:2329–2342
     [Google Scholar]
  31. 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 USA 90:6874–4878
     [Google Scholar]
  32. Neidle E. L., Shapiro M. K., Ornston L. N. 1987; Cloning and expression in Escherichia coli of Acinetobacter calcoaceticus genes for benzoate degradation.. J Bacteriol 169:5496–5503
     [Google Scholar]
  33. Neidle E. L., Hartnett C., Ornston L. N. 1989; Characterization of Acinetobacter calcoaceticus catM, a repressor gene homologous in sequence to transcriptional activator genes. . J Bacteriol 171:5410–5421
     [Google Scholar]
  34. Ornston L. N., Neidle E. L. 1991; Evolution of genes for the pketoadipate pathway in Acinetobacter calcoaceticus. In The Biology of Acinetobacter. Edited by K. J. Towner, E. Bergogne-Bérézin & C. A. Fewson. . New York: Plenum Press.201–237
     [Google Scholar]
  35. Rainey F. A., Lang E., Stackebrandt E. 1994; The phylogenetic structure of the genus Acinetobacter.. FEMS Microbiol Lett 124:349–354
     [Google Scholar]
  36. Ross C. M., Kaplan J. B., Winkler M. E., Nichols B. P. 1990; An evolutionary comparison of Acinetobacter calcoaceticus trpF with trpF genes of several organisms.. Mol Gen Genet 7:74–81
     [Google Scholar]
  37. Sambrook J., Fritsch E. F., Maniatis T. 1989; Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory..
    [Google Scholar]
  38. Schmidt K. D., Tummler B., Romling U. 1996; Comparative genome mapping of Pseudomonas aeruginosa P A 0 with P. aeruginosa C, which belongs to a major clone in cystic fibrosis patients and aquatic habitats.. J Bacteriol 178:85–93
     [Google Scholar]
  39. Shanley M. S., Neidle E. L., Parales R. E., Ornston L. N. 1986; Cloning and expression of Acinetobacter calcoaceticus catBCDE genes in Pseudomonas putida and Escherichia coli. . J Bacteriol 165:557–563
     [Google Scholar]
  40. Smith C. L., Cantor C. R. 1987; Purification, specific fragmentation and separation of large DNA molecules.. Methods Enzymol 155:449–467
     [Google Scholar]
  41. Stark M. 1996; PhD thesis, Tel-Aviv University..
    [Google Scholar]
  42. Stratz M., Mau M., Timmis K. N. 1996; System to study horizontal gene exchange among microorganisms without cultivation of recipients.. Mol Microbiol 22:207–215
     [Google Scholar]
  43. Suwanto A., Kaplan S. 1989; Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome : genome size, fragment identification and gene localization.. J Bacteriol 171:5840–5849
     [Google Scholar]
  44. Towner K. J. 1978; Chromosome mapping in Acinetobacter calcoaceticus.. J Gen Microbiol 104:175–180
     [Google Scholar]
  45. Towner K. J., Bergogne-BBrBzin E., Fewson C. A. 1991; Acinetobacter: portrait of a genus. In The Biology of Acinetobacter, pp. Edited by K. J. Towner, E. Bergogne-Bérézin & C. A. Fewson. . New York: Plenum Press1–24
     [Google Scholar]
  46. Yanisch-Perron C., Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains : nucleotide sequences of the M13mp18 and pUC19 vectors.. Gene 33:103–119
     [Google Scholar]
  47. Zhang C., Huang M., Holloway B. W. 1993; Mapping of the berz, ant and cat genes of Pseudomonas aeruginosa and evolutionary relationship of the ben region of P. aeruginosa and P. putida.. FEMS Microbiol Lett 108:303–310
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-143-4-1345
Loading
Directed introduction of DNA cleavage sites to produce a high-resolution genetic and physical map of the Acinetobacter sp. strain ADP1 (BD413UE) chromosome
Microbiology 143, 1345 (1997); https://doi.org/10.1099/00221287-143-4-1345
/content/journal/micro/10.1099/00221287-143-4-1345
/content/journal/micro/10.1099/00221287-143-4-1345
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