Summary
A system for detecting a spontaneous deletion in Escherichia coli was developed and the role of DNA gyrase in deletion formation was studied. A derivative of λplac5, λAM36, was isolated in which whole pBR322 DNA was inserted in the lacZ gene and 227 by of the lac gene duplicated at both sides of the pBR322 DNA. E. coli lac −strains lysogenized by λAM36 had a Lac− phenotype and segregated Lac– revertants. Sequence analyses showed that the revertant was formed by a deletion that eliminated the inserted pBR322 DNA and one copy of the duplicated segments. The frequency of lac – revertant formation was independent of recA function, was increased by oxolinic acid, an inhibitor of DNA gyrase, but was not increased in a lysogen of a nalidixic acid-resistant derivative. The reversion frequencies of temperature sensitive mutants of gyrA gene are 10 to 100 times lower than that of the wild-type strain. These results indicate that the DNA gyrase of E. coli participated in the in vivo deletion formation resulting from the direct repeats.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Albertini AM, Hofer M, Calos MP, Miller JH (1982) On the formation of spontaneous deletion: The importance of short sequence homologies in the generation of large deletions. Cell 29:319–328
Bergsma DJ, Olive DM, Hartzell SW, Byrne BJ, Subramanian KN (1982) Cyclization of linear chimeric plasmids in vivo by a novel end-to-end joining reaction or by intramolecular recombination: One of the products contains a 147-bp perfect palindrome stable in Escherichia coli. Gene 20:157–167
Brunier D, Michel B, Ehrlich SD (1988) Copy choice illegitimate DNA recombination. Cell 52:883–892
Collins J, Volckaert G, Nevers P (1982) Precise and nearly-precise symmetrical inverted repeats of Tn5: Common features of recA-independent deletion events in Escherichia coli. Gene 19:139–146
Farabaugh PJ, Schmeissner U, Fofer M, Miller JH (1978) Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J Mol Biol 126:847–857
Foster TJ, Lundblad V, Hanley-Way S, Halling SM, Kleckner N (1981) Three Tn10-associated excision events: Relationship to transposition and. role of direct and inverted repeats. Cell 23:215–227
Galas DL (1978) An analysis of sequence repeats in the lacI gene of Escherichia coli. J Mol Biol 126:858–863
Garaev MM, Bobkov AF, Bobkova AF, Kalinin VN, Smirnov VD, Khudakov YuE, Tikchonenko TI (1982) The site-specific deletion in plasmid pBR322. Gene 18:21–28
Gellert M, Mizuuchi K, O'Dea MH, Itoh T, Tomizawa J-I (1977) Nalidixic acid resistance: A second genetic character involved in DNA gyrase activity. Proc Natl Acad Sci USA 74:4772–4776
Goodchild J, Michniewicz J, Seto-Young D, Narang S (1985) A novel deletion found during cloning of a synthetic palindromic DNA. Gene 33:367–371
Greaves DR, Patient RK (1986) RecBC, sbcB independent, (AT)n- mediated deletion of sequences flanking a Xenopus laevis β globin gene on propagation in E. coli. Nucleic Acids Res 14:4147–4158
Ikeda H, Moriya K, Matsumoto T (1981) In vitro study of illegitimate recombination: Involvement of DNA gyrase. Cold Spring Harbor Symp Quant Biol 45:399–408
Ikeda H, Aoki K, Naito A (1982) Illegitimate recombination mediated in vitro by DNA gyrase of Escherichia coli: Structure of recombinant DNA molecules. Proc Natl Acad Sci USA 79:3724–3728
Jones IM, Primose SB, Ehrlich SD (1982) Recombination between short direct repeats in a recA Host. Mol Gen Genet 188:486–489
Kleckner N, Barker DF, Ross DG, Botstein D (1978) Properties of the translocatable tetracycline-resistance element Tn10 in Escherichia coli and bacteriophage lambda. Genetics 90:427–461
Kollek R, Oertel W, Goebel W (1980) Site-specific deletion at the replication origin of the antibiotic resistance factor R1. Mol Gen Genet 177:413–419
Kourilsky P, Perricaudet M, Gros D, Garapin A, Gottesman M, Fritsch A, Tiollais P (1978) Description and properties of bacteriophage lambda vectors useful for the cloning of EcoR1 DNA fragments. Biochimie 60:183–187
Kreuzer KN, McEntee K, Geballe AP, Cozzarelli NR (1978) Lambda trasducing phages for the nalA gene of Escherichia coli and conditional lethal nalA mutations. Mol Gen Genet 167:129–137
Leach DRF, Stahl FW (1983) Viability of λ phages carrying a perfect palindrome in the absence of recombination nuclease. Nature 305:448–451
Lockshon D, Morris DR (1985) Sites of reaction of Escherichia coli DNA gyrase on pBR322 in vivo as revealed by oxolinic acid-induced plasmid linearization. J Mol Biol 181:63–74
Lopez P, Espinosa M, Greenberg B, Lacks SA (1984) Generation of deletions in pneumococcal mal genes cloned in Bacillus subtilis. Proc Natl Acad Sci USA 81:5189–5193
Marvo SL, King SR, Jaskunas SR (1983) The role of short regions of homology in intermolecular illegitimate recombinations. Proc Natl Acad Sci USA 80:2452–2456
McCorkle GM, Altman S (1982) Large deletion mutants of Escherichia coli tRNA1 Tyr. J Mol Biol 155:83–103
Messing J, Vicira J (1982) A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene 19:269–276
Messing J (1983) New M13 vectors for cloning. Methods Enzymol 101:20–78
Miura A, Krueger JH, Itoh S, De Boer HA, Nomura M (1981) Growth-rate-dependent regulation of ribosome synthesis in E. coli: Expression of the lacZ and galK genes fused to ribosomal promoters. Cell 25:773–782
Nader WF, Isenberg G, Sauer HW (1986) Structure of Physarum actin gene locus ardA: A nonpalindromic sequence causes inviability of phage lambda and recA-independent deletions. Gene 48:133–144
Naito A, Naito S, Ikeda H (1984) Homology is not required for recombination mediated by DNA gyrase of Escherichia coli. Mol Gen Genet 193:238–243
Oka A, Nomura N, Morita M, Sugisaki H, Sugimoto K, Takanami M (1979) Nucleotide sequence of small colE1 derivatives: Structure of the regions essential for autonomous replication and colicin E1 immunity. Mol Gen Genet 172:151–159
Ross DG, Swan J, Kleckner N (1979) Nearly precise excision: A new type of DNA alteration associated with the translocatable element Tn10. Cell 16:733–738
Saing KM, Orii H, Tanaka Y, Yanagisawa K, Mirua A, Ikeda H (1988) Formation of deletion in Escherichia coli between direct repeats located in the long inverted repeats of a cellular slime mold plasmid: Participation of DNA gyrase. Mol Gen Genet 214:1–5
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Schaaper RM, Danforth BN, Glickman BW (1986) Mechanisms of spontaneous mutagenesis: An analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene. J Mol Biol 189:273–284
Steck TR, Pruss GJ, Manes SH, Burg L, Drlica K (1984) DNA supercoiling in gyrase mutants. J Bacteriol 158:397–403
Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, Terzaghi E, Inouye M (1966) Frameshift mutations and the genetic code. Cold Spring Harbor Symp Quant Biol 31:77–84
Streisinger G, Owen JM (1985) Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4. Genetics 109:633–659
Studier FW, Rosenberg AH, Simon MN, Dunn JJ (1979) Genetic and physical mapping in the early region of bacteriophage T7 DNA. J Mol Biol 135:917–937
Sugino A, Peebles CL, Kreuzer KN, Cozzarelli NR (1977) Mechanism of action of nalidixic acid: Purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc Natl Acad Sci USA 74:4767–4771
Author information
Authors and Affiliations
Additional information
Communicated by K. Isono
Rights and permissions
About this article
Cite this article
Miura-Masuda, A., Ikeda, H. The DNA gyrase of Escherichia coli participates in the formation of a spontaneous deletion by recA-independent recombination in vivo. Mol Gen Genet 220, 345–352 (1990). https://doi.org/10.1007/BF00391737
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF00391737