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

Microbiology

Volumn 143, Issue 4, 1997, Pages 1345-1357

  Gralton, Elizabeth M ^a,b   Campbell, Alan L ^a   Neidle, Ellen L ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNITED STATES MILITARY ACADEMY   (United States)

Author keywords

Acinetobacter; Genome; Map; PFGE (pulsed field gel electrophoresis); TAFE (transverse alternating field electrophoresis)

Indexed keywords

RESTRICTION ENDONUCLEASE;

ACINETOBACTER; ARTICLE; BACTERIAL GENE; CHROMOSOME MAP; CONTROLLED STUDY; DNA CLEAVAGE; DNA RECOMBINATION; GENE INSERTION SEQUENCE; GENE LOCATION; GENE MAPPING; NONHUMAN; OPERON; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SOIL MICROFLORA; SOUTHERN BLOTTING;

ACINETOBACTER; ACINETOBACTER CALCOACETICUS; ACINETOBACTER SP.; BACTERIA (MICROORGANISMS);

EID: 0031011542     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-143-4-1345     Document Type: Article

References (47)

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.
2. Baumann, P., Doudoroff, M. & Stanier, R. Y. (1968). A study of Moraxella group II: oxidase negative species (genus Acinetobacter). J Bacteriol 95, 1520-1541.
3. Bergogne-Bérézin, E. (1994). Acinetobacter spp., saprophytic organisms of increasing pathogenic importance. Zentralbl Bakteriol 281, 389-405.
4. Condon, C., Liveris, D., Squires, C., Schwartz, I. & Squires, C. L. (1995). rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J Bacteriol 177, 4152-4156.
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.
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.
7. Ellwood, M. & Nomura, M. (1982). Chromosomal location of the genes for rRNA in E. coli K-12. J Bacteriol 149, 458-468.
8. Elsemore, D. A. & Ornston, L. N. (1994). The pca-pob supra-operonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate-shikimate dehydrogenase. J Bacteriol 176, 7659-7666.
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.
10. Fonstein, M. & Haselkorn, R. (1995). Physical mapping of bacterial genomes. J Bacteriol 177, 3361-3369.
11. Geissdörfer, W., Frosch, S. C., Haspel, G., Ehrt, S. & Hillen, W. (1995). Two genes encoding proteins with similarities to rub-redoxin and rubredoxin reductase are required for conversion of dodecane to lauric acid in Acinetobacter calcoaceticus ADP1. Microbiology 141, 1425-1432.
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.
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.
14. Gerner-Smidt, P. (1994). Acinetobacter: epidemiological and taxonomic aspects. Acta Pathol Microbiol Immunol Scand Suppl 47 102, 5-41.
15. Gralton, E. M. (1996). Physical and genetic map of Acinetobacter calcoaceticus strain BD413 (ADP1). MS thesis, University of Georgia, Athens, GA.
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.
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.
18. Harwood, C. S. & Parales, R. E. (1996). The β-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50, 553-590.
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.
20. Haspel, G., Kishan, V. & Hillen, W. (1991). Organisation, potential regulatory elements and evolution of trp genes in Acinetobacter. In The Biology of Acinetobacter, pp. 239-249. Edited by K. J. Towner, E. Bergogne-Berezin & C. A. Fewson. New York: Plenum Press.
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, pp. 97-105. Edited by K. Drlica & M. Riley. Washington, DC: American Society for Microbiology.
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.
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.
24. Juni, E. (1972). Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus. J Bacteriol 112, 917-931.
25. Juni, E. (1978). Genetics and physiology of Acinetobacter. Annu Rev Microbiol 32, 349-371.
26. Juni, E. & Janik, A. (1969). Transformation of Acinetobacter calcoaceticus (Bacterium anitratum). J Bacteriol 98, 281-288.
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.
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.
29. Kok, R. (1995). Lipolytic enzymes in Acinetobacter calcoaceticus. PhD thesis, University of Amsterdam.
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.
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, 6874-6878.
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.
33. Neidle, E. L., Hartnett, C. & Ornston, L. N. (1989). Characterization of Acinetobacter calcoaceticus catM, a represser gene homologous in sequence to transcriptional activator genes. J Bacteriol 171, 5410-5421.
34. Ornston, L. N. & Neidle, E. L. (1991). Evolution of genes for the β-ketoadipate pathway in Acinetobacter calcoaceticus. In The Biology of Acinetobacter, pp. 201-237. Edited by K. J. Towner, E. Bergogne-Bérézin & C. A. Fewson. New York: Plenum Press.
35. Rainey, F. A., Lang, E. & Stackebrandt, E. (1994). The phylogenetic structure of the genus Acinetobacter. FEMS Microbiol Lett 124, 349-354.
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.
37. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
38. Schmidt, K. D., Tummler, B & Romling, U. (1996). Comparative genome mapping of Pseudomonas aeruginosa PAO with P. aeruginosa C, which belongs to a major clone in cystic fibrosis patients and aquatic habitats. J Bacteriol 178, 85-93.
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.
40. Smith, C. L. & Cantor, C. R. (1987). Purification, specific fragmentation and separation of large DNA molecules. Methods Enzymol 155, 449-467.
41. Stark, M. (1996). PhD thesis, Tel-Aviv University.
42. Strätz, M., Mau, M. & Timmis, K. N. (1996). System to study horizontal gene exchange among microorganisms without cultivation of recipients. Mol Microbiol 22, 207-215.
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.
44. Towner, K. J. (1978). Chromosome mapping in Acinetobacter calcoaceticus. J Gen Microbiol 104, 175-180.
45. Towner, K. J., Bergogne-Bérézin, E. & Fewson, C. A. (1991). Acinetobacter: portrait of a genus. In The Biology of Acinetobacter, pp. 1-24. Edited by K. J. Towner, E. Bergogne-Bérézin & C. A. Fewson. New York: Plenum Press.
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.
47. Zhang, C., Huang, M. & Holloway, B. W. (1993). Mapping of the ben, 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.