Skip to main content
Genetics logoLink to Genetics
. 1997 Nov;147(3):991–1001. doi: 10.1093/genetics/147.3.991

A Genetic Strategy to Demonstrate the Occurrence of Spontaneous Mutations in Nondividing Cells within Colonies of Escherichia Coli

M Reddy 1, J Gowrishankar 1
PMCID: PMC1208273  PMID: 9383047

Abstract

A genetic strategy was designed to examine the occurrence of mutations in stationary-phase populations. In this strategy, a parental population of cells is able to survive under both permissive and restrictive conditions whereas mutants at a particular target locus exhibit a conditional-lethal phenotype. Thus, by growing the population to stationary phase under restrictive conditions and then shifting it to permissive conditions, mutations that had arisen in stationary phase can be studied without confounding effects caused by the occurrence of similar mutations during growth of the population. In two different applications of this strategy, we have studied the reversion to Lac(+) in stationary phase of several Lac(-) mutations in Escherichia coli. Our results indicate that a variety of spontaneous point mutations and deletions, particularly those that are sensitive to the mechanisms of replication slippage (for their generation) and methyl-directed mismatch repair (for their correction), can arise in nondividing populations of cells within a colony. The frequency of their occurrence was also elevated in mutS strains, which are defective in such mismatch repair. These data have relevance to the ongoing debate on adaptive or directed mutations in bacteria.

Full Text

The Full Text of this article is available as a PDF (6.2 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Albertini A. M., Hofer M., Calos M. P., Miller J. H. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell. 1982 Jun;29(2):319–328. doi: 10.1016/0092-8674(82)90148-9. [DOI] [PubMed] [Google Scholar]
  2. Boe L. Mechanism for induction of adaptive mutations in Escherichia coli. Mol Microbiol. 1990 Apr;4(4):597–601. doi: 10.1111/j.1365-2958.1990.tb00628.x. [DOI] [PubMed] [Google Scholar]
  3. Bridges B. A. Elevated mutation rate in mutT bacteria during starvation: evidence for DNA turnover? J Bacteriol. 1996 May;178(9):2709–2711. doi: 10.1128/jb.178.9.2709-2711.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bridges B. A. Microbial genetics. Hypermutation under stress. Nature. 1997 Jun 5;387(6633):557–558. doi: 10.1038/42370. [DOI] [PubMed] [Google Scholar]
  5. Bridges B. A., Sekiguchi M., Tajiri T. Effect of mutY and mutM/fpg-1 mutations on starvation-associated mutation in Escherichia coli: implications for the role of 7,8-dihydro-8-oxoguanine. Mol Gen Genet. 1996 Jun 12;251(3):352–357. doi: 10.1007/BF02172526. [DOI] [PubMed] [Google Scholar]
  6. Canceill D., Ehrlich S. D. Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli. Proc Natl Acad Sci U S A. 1996 Jun 25;93(13):6647–6652. doi: 10.1073/pnas.93.13.6647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chédin F., Dervyn E., Dervyn R., Ehrlich S. D., Noirot P. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol Microbiol. 1994 May;12(4):561–569. doi: 10.1111/j.1365-2958.1994.tb01042.x. [DOI] [PubMed] [Google Scholar]
  8. Cooper A. L., Dean A. C., Hinshelwood C. Factors affecting the growth of bacterial colonies on agar plates. Proc R Soc Lond B Biol Sci. 1968 Nov 5;171(1023):175–199. doi: 10.1098/rspb.1968.0063. [DOI] [PubMed] [Google Scholar]
  9. Cunningham-Rundles S., Maas W. K. Isolation, characterization, and mapping of Escherichia coli mutants blocked in the synthesis of ornithine decarboxylase. J Bacteriol. 1975 Nov;124(2):791–799. doi: 10.1128/jb.124.2.791-799.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Egner C., Berg D. E. Excision of transposon Tn5 is dependent on the inverted repeats but not on the transposase function of Tn5. Proc Natl Acad Sci U S A. 1981 Jan;78(1):459–463. doi: 10.1073/pnas.78.1.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Feng G., Tsui H. C., Winkler M. E. Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol. 1996 Apr;178(8):2388–2396. doi: 10.1128/jb.178.8.2388-2396.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Foster P. L. Adaptive mutation: the uses of adversity. Annu Rev Microbiol. 1993;47:467–504. doi: 10.1146/annurev.mi.47.100193.002343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Foster P. L., Cairns J. Mechanisms of directed mutation. Genetics. 1992 Aug;131(4):783–789. doi: 10.1093/genetics/131.4.783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Foster T. J., Lundblad V., Hanley-Way S., Halling S. M., Kleckner N. Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats. Cell. 1981 Jan;23(1):215–227. doi: 10.1016/0092-8674(81)90286-5. [DOI] [PubMed] [Google Scholar]
  15. Galitski T., Roth J. R. A search for a general phenomenon of adaptive mutability. Genetics. 1996 Jun;143(2):645–659. doi: 10.1093/genetics/143.2.645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hall B. G. On the specificity of adaptive mutations. Genetics. 1997 Jan;145(1):39–44. doi: 10.1093/genetics/145.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lenski R. E., Mittler J. E. The directed mutation controversy and neo-Darwinism. Science. 1993 Jan 8;259(5092):188–194. doi: 10.1126/science.7678468. [DOI] [PubMed] [Google Scholar]
  18. Lovett S. T., Feschenko V. V. Stabilization of diverged tandem repeats by mismatch repair: evidence for deletion formation via a misaligned replication intermediate. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7120–7124. doi: 10.1073/pnas.93.14.7120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. MacPhee D. G., Ambrose M. Spontaneous mutations in bacteria: chance or necessity? Genetica. 1996 Jan;97(1):87–101. doi: 10.1007/BF00132585. [DOI] [PubMed] [Google Scholar]
  20. Mackay W. J., Han S., Samson L. D. DNA alkylation repair limits spontaneous base substitution mutations in Escherichia coli. J Bacteriol. 1994 Jun;176(11):3224–3230. doi: 10.1128/jb.176.11.3224-3230.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Naas T., Blot M., Fitch W. M., Arber W. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics. 1994 Mar;136(3):721–730. doi: 10.1093/genetics/136.3.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nagelkerke F., Postma P. W. 2-deoxygalactose, a specific substrate of the Salmonella typhiimurium galactose permease: its use for the isolation of galP mutants. J Bacteriol. 1978 Feb;133(2):607–613. doi: 10.1128/jb.133.2.607-613.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Peters J. E., Bartoszyk I. M., Dheer S., Benson S. A. Redundant homosexual F transfer facilitates selection-induced reversion of plasmid mutations. J Bacteriol. 1996 Jun;178(11):3037–3043. doi: 10.1128/jb.178.11.3037-3043.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Pirt S. J. A kinetic study of the mode of growth of surface colonies of bacteria and fungi. J Gen Microbiol. 1967 May;47(2):181–197. doi: 10.1099/00221287-47-2-181. [DOI] [PubMed] [Google Scholar]
  25. Prival M. J., Cebula T. A. Adaptive mutation and slow-growing revertants of an Escherichia coli lacZ amber mutant. Genetics. 1996 Dec;144(4):1337–1341. doi: 10.1093/genetics/144.4.1337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Radicella J. P., Park P. U., Fox M. S. Adaptive mutation in Escherichia coli: a role for conjugation. Science. 1995 Apr 21;268(5209):418–420. doi: 10.1126/science.7716545. [DOI] [PubMed] [Google Scholar]
  27. Rosenberg S. M., Harris R. S., Torkelson J. Molecular handles on adaptive mutation. Mol Microbiol. 1995 Oct;18(2):185–189. doi: 10.1111/j.1365-2958.1995.mmi_18020185.x. [DOI] [PubMed] [Google Scholar]
  28. Ryan F. J. Spontaneous Mutation in Non-Dividing Bacteria. Genetics. 1955 Sep;40(5):726–738. doi: 10.1093/genetics/40.5.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Saroja G. N., Gowrishankar J. Roles of SpoT and FNR in NH4+ assimilation and osmoregulation in GOGAT (glutamate synthase)-deficient mutants of Escherichia coli. J Bacteriol. 1996 Jul;178(14):4105–4114. doi: 10.1128/jb.178.14.4105-4114.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Shapiro J. A. A role for the Clp protease in activating Mu-mediated DNA rearrangements. J Bacteriol. 1993 May;175(9):2625–2631. doi: 10.1128/jb.175.9.2625-2631.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Stahl F. W. Bacterial genetics. A unicorn in the garden. Nature. 1988 Sep 8;335(6186):112–113. doi: 10.1038/335112a0. [DOI] [PubMed] [Google Scholar]
  32. Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. doi: 10.1101/sqb.1966.031.01.014. [DOI] [PubMed] [Google Scholar]
  33. Taddei F., Matic I., Radman M. cAMP-dependent SOS induction and mutagenesis in resting bacterial populations. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11736–11740. doi: 10.1073/pnas.92.25.11736. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Trinh T. Q., Sinden R. R. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli. Genetics. 1993 Jun;134(2):409–422. doi: 10.1093/genetics/134.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wimpenny J. W. The growth and form of bacterial colonies. J Gen Microbiol. 1979 Oct;114(2):483–486. doi: 10.1099/00221287-114-2-483. [DOI] [PubMed] [Google Scholar]
  36. Zambrano M. M., Kolter R. GASPing for life in stationary phase. Cell. 1996 Jul 26;86(2):181–184. doi: 10.1016/s0092-8674(00)80089-6. [DOI] [PubMed] [Google Scholar]
  37. Zambrano M. M., Siegele D. A., Almirón M., Tormo A., Kolter R. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science. 1993 Mar 19;259(5102):1757–1760. doi: 10.1126/science.7681219. [DOI] [PubMed] [Google Scholar]
  38. d'Alençon E., Petranovic M., Michel B., Noirot P., Aucouturier A., Uzest M., Ehrlich S. D. Copy-choice illegitimate DNA recombination revisited. EMBO J. 1994 Jun 1;13(11):2725–2734. doi: 10.1002/j.1460-2075.1994.tb06563.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. de la Chapelle A., Peltomäki P. Genetics of hereditary colon cancer. Annu Rev Genet. 1995;29:329–348. doi: 10.1146/annurev.ge.29.120195.001553. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES