Characterization of the lysogenic repressor (C) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112

Virology

Volumn 272, Issue 1, 2000, Pages 85-97

  Salmon, Kirsty A ^a   Freedman, Orit ^a   Ritchings, Bruce W ^b   DuBow, Michael S ^a  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REPRESSOR PROTEIN; TRANSPOSASE;

ARTICLE; BACTERIOPHAGE; NONHUMAN; NORTHERN BLOTTING; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; REPRESSOR GENE; SITE DIRECTED MUTAGENESIS; START CODON;

PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0034691156     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.2000.0341     Document Type: Article

References (63)

1. Akhverdian V. Z., Khrenova E. A., Bogush V. G., Gerasimova T. V., Kirsanov N. B., Krylov V. N. Wide distribution of transposable phages in natural populations of Pseudomonas aeruginosa. Genetika. 20:1984;1612-1619.
2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
3. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Strhl K. Current Protocols in Molecular Biology. 1989;Green and Wiley-Interscience, New York.
4. Autexier C., Wragg-Légaré S., DuBow M. S. Characterization of the Pseudomonas aeruginosa transposable phage D3112 left-end regulatory region. Biochim. Biophys. Acta. 1088:1991;147-150.
5. Bidnenko E. M., Akhverdian V. Z., Krylov V. N. Cloning and studying the expression of the cip1 gene of Pseudomonas aeruginosa transposable phage D3112 in the homologous host and in Escherichia coli. Genetika. 32:1996;914-921.
6. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 2:1977;95-113.
7. Branden C., Tooze J. Introduction to Protein Structure. 1991;Garland Publishing, Inc. New York.
8. Cai J., DuBow M. S. Expression of the Escherichia coli chromosomal ars operon. Can. J. Microbiol. 42:1996;662-671.
9. Court D., Oppenheim A. B. Phage lambda's accessory genes. Hendrix R. W., Roberts J. W., Stahl F. W., Weisberg R. A. Lambda II. 1983;251-277 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
10. Darzins A., Casadaban M. J. Mini-D3112 bacteriophage transposable elements for genetic analysis of Pseudomonas aeruginosa. J. Bacteriol. 171:1989a;3909-3916.
11. Darzins A., Casadaban M. J. In vivo cloning of Pseudomonas aeruginosa genes with mini-D3112 transposable bacteriophage. J. Bacteriol. 171:1989b;3917-3925.
12. Deretic V., Gill J. F., Chakrabarty A. M. Gene algD coding for GDPmannose dehydrogenase is transcriptionally activated in mucoid Pseudomonas aeruginosa. J. Bacteriol. 169:1987;351-358.
13. DuBow M. S. Mu and related bacteriophages. Webster R. G., Granoff A. Encyclopedia of Virology. 1994;868-876 Academic Press, London.
14. Farinha M. A., Allan B. J., Gertman E. M., Ronald S. L., Kropinski A. M. Cloning of the early promoters of Pseudomonas aeruginosa bacteriophage D3: Sequence of the immunity region of D3. J. Bacteriol. 176:1994;4809-4815.
15. Farinha M. A., Kropinski A. M. High efficiency electroporation of Pseudomonas aeruginosa using frozen cell suspensions. FEMS Lett. 70:1990;221-226.
16. Freese E., Bautz E., Freese E. B. The chemical and mutagenic specificity of hydroxylamine. Genetics. 47:1961a;845-855.
17. Freese E., Freese E. B., Bautz E. Hydroxylamine as a mutagenic and inactivating agent. J. Mol. Biol. 3:1961b;133-143.
18. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9:1981;6505-6525.
19. Garner M. M., Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9:1981;3047-3060.
20. Gerasimov V. A., Yanenko A. S., Akhverdian V. Z., Krylov V. N. Interaction between transposable phages: cip locus of prophage D3112, responsible for inhibition of integration and transposition of the related phage B39 of Pseudomonas aeruginosa. Genetika. 21:1985;1634-1642.
21. Glisin V., Crkvenjakov R., Byus C. Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry. 13:1974;2633-2637.
22. Gray T. M., Mathews B. W. Structural analysis of the temperature-sensitive mutant of bacteriophage T4 lysozyme, glycine 156-aspartic acid. J. Biol. Chem. 262:1987;16848-16864.
23. Groisman E. A., Castilho B. A., Casadaban M. J. In vivo DNA cloning and adjacent gene fusing with a mini-Mu-lac bacteriophage containing a plasmid replicon. Proc. Natl. Acad. Sci USA. 81:1984;1480-1483.
24. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:1983;557-580.
25. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:1983;2237-2255.
26. Holloway B. W. Genetics of Pseudomonas. Bacteriol. Rev. 33:1969;419-433.
27. Krause H. M., Rothwell M. R., Higgins N. P. The early promoter of bacteriophage Mu: definition of the site of transcript initiation. Nucleic Acids Res. 11:1983;5483-5495.
28. Krylov V. N., Bogush V. G., Shapiro J. Bacteriophages of Pseudomonas aeruginosa, the DNA structure of which is similar to the structure of phage Mu1 DNA. Genetika. 16:1980a;824-832.
29. Krylov V. N., Bogush V. G., Yanenko A. S., Kirsanov N. B. Pseudomonas aeruginosa bacteriophage with DNA similar in structure to that of phage Mu1. Genetika. 16:1980b;975-984.
30. Krylov V. N., Plotnikova T. G., Kulakov L. A., Fedorova T. V., Eremenko E. N. Integration of the genome of Mu-like bacteriophage D3112 of Pseudomonas aeruginosa into plasmid RP4 and its introduction within the hybrid plasmid into Pseudomonas putida and Escherichia coli. Genetika. 18:1982;5-12.
31. Kukolj G., DuBow M. S. Characterization of the lysogenic repressor c from transposable Mu-like bacteriophage D108. Nucleic Acids Res. 19:1991;5949-5956.
32. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:1970;68-685.
33. Levin D. B., DuBow M. S. Regulation of repressor and early gene expression in Mu-like transposable bacteriophage D108. Mol. Gen. Genet. 217:1989;392-400.
34. Lim H. M., Pene J. J. Optimal conditions for supercoil DNA sequencing with the Escherichia coli DNA polymerase I large fragment. Gene Anal. Tech. 5:1988;32-39.
35. Ljundquist E., Bukhari A. I. State of prophage Mu DNA upon induction. Proc. Natl. Acad. Sci. USA. 74:1977;3143-3147.
36. Lukashin A., Borodovsky M. GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res. 26:1998;1107-1115.
37. Mahmoudi M., Lin V. K. Comparison of two different hybridization systems in Northern transfer analysis. BioTechniques. 7:1989.
38. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:1980;499-560.
39. McClelland J. L., Rumelhart D. E. Explorations in Parallel Distributed Processing. 1988;MIT Press, Cambridge.
40. Miller J. A Short Course in Bacterial Genetics. 1972;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
41. Neidhart F. C., Ingraham J. L., Schaechter M. Physiology of the Bacterial Cell. A Molecular Approach. 1990;Sinauer Associates, Inc. Sunderland.
42. Nelson H. C., Hecht M. H., Sauer R. T. Mutations defining the operator-binding sites of bacteriophage λ repressor. Cold Spring Harb. Symp. Quant. Biol. 47:1983;441-449.
43. Nishi K., Müller M., Schnier J. Spontaneous missense mutations in the rplx gene for ribosomal protein L24 from Escherichia coli. J. Bacteriol. 169:1987;4854-4856.
44. Pabo C. O. The operator-binding domain of λ repressor: Structure and DNA recognition. Nature. 298:1982;443-447.
45. Pato M. L. Bacteriophage Mu. Berg D. E., Howe M. M. Mobile DNA. 1989;23-52 American Society for Microbiology, Washington.
46. Plotnikova T. G., Akhverdian V. Z., Reulets M. A., Gorbunova S. A., Krylov V. N. Multiplicity of integration sites of Mu-like bacteriophages in the chromosome and plasmid of Pseudomonas aeruginosa. Genetika. 19:1983;1604-1610.
47. Reese, M. G. 1994, Diploma thesis, German Cancer Research Center, Heidelberg.
48. Reese, M. G, and, Eeckman, F. H. 1995, Novel neural network algorithms for improved eukaryotic promoter site recognition, The Seventh International Genome Sequencing and Analysis Conference, Hilton Head Island, South Carolina.
49. Reese, M. G, Harris, N. L, and, Eeckman, F. H. 1996, Large scale sequencing specific neural networks for promoter and splice site recognition, In, Biocomputing: Proceedings of the 1996, Pacific Symposium, (, Hunter, L, and Klein, T. E, Eds.), World Scientific Publishing Co. Singapore.
50. Rhemat S., Shapiro J. A. Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112. Mol. Gen. Genet. 192:1983;416-423.
51. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
52. Schumm J. W., Moore D. D., Blattner F. R., Howe M. M. Correlation of the genetic and physical maps in the central region of the bacteriophage Mu genome. Virology. 105:1980;185-195.
53. Shine J., Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA. 71:1974;1342-1346.
54. Snyder L., Kaufman G. T4 exclusion. Drake J. W., Kreuzer K. N., Mosig G., Hall D. H., Eiserling F. A., Black L. W., Spicer E. K., Kutter E., Carlson K., Miller E. S. Molecular Biology of Bacteriophage T4. 1994;391-396 American Society for Microbiology, Washington.
55. Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189:1986;113-130.
56. Tessman I., Ishiwa H., Kumar S. Mutagenic effects of hydroxylamine in vivo. Science. 148:1967;504-513.
57. Totten P. A., Lory S. Characterization of the type A flagellin gene from Pseudomonas aeruginosa PAK. J. Bacteriol. 172:1990;7188-7199.
58. Ulycznyj P. I., Salmon K. A., Douillard H., DuBow M. S. Characterization of the Pseudomonas aeruginosa transposable bacteriophage D3112 A and B genes. Biochim. Biophys. Acta. 1264:1995;249-253.
59. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 153:1987;3-11.
60. Vogel J. L., Li Z. J., Howe M. M., Toussaint A., Higgins N. P. Temperature sensitive mutations in the bacteriophage Mu c repressor locate a 63-amino-acid binding domain. J. Bacteriol. 173:1991;6568-6577.
61. Yanenko A. S., Bekkarevich A. O., Gerasimov V. A., Krylov V. N. Genetic map of the transposable phage D3112 of Pseudomonas aeruginosa. Genetika. 24:1988;2120-2126.
62. Yanenko A. S., Bogush V. G., Kirsanov N. B., Lyapin M. N., Krylov V. N. Use of deletion mutants of the RP4::D3112 plasmid for genetic analysis of Pseudomonas aeruginosa bacteriophage D3112. Genetika. 19:1983;1760-1768.
63. Yu M.-H., King J. Single amino acid substitutions influencing the folding pathway of phage P22 tail spike endorhamnosidase. Proc. Natl. Acad. Sci. USA. 81:1984;65854-65858.