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Comparative Genomics of the Escherichia coli Strains АВ1157, АВ2463, АВ2494, and АВ1885

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Abstract

Whole genome sequencing of the Escherichia coli strain АВ1157 and its mutants AB1885 uvrB5, AB2463 recA13, and AB2494 lexA1, which have deficient DNA repair, recombination, and mutagenesis systems, was performed. It was found that the genomes of the AB2463 recA13 and AB2494 lexA1 strains differ from the genome of ancestral strain in several hundred mutations which arose most probably in the course of a single treatment of AB1157 with N-methyl-N-nitro-N-nitrosoguanidine. At the same time, the genome of the strain AB1885 obtained after treatment with nitrous acid contained ten times fewer differences from its parent strain. Mutations in the AB2463 recA13 and AB2494 lexA1 genomes were predominantly represented by GC to AT transitions distributed randomly along the genomes, and their locations did not coincide in these strains. The effect of spontaneous mutations on the differences between the strains studied that appeared during the period from their isolation to the sequence experiments seems to be insignificant. Earlier known genetic and phenotypic traits are annotated on the molecular level.

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REFERENCES

  1. Adelberg, E.A. and Burns, S.N., Genetic variation in the sex factor of Escherichia coli, J. Bacteriol., 1960, vol. 79, pp. 321–330. https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC278688/pdf/jbacter00488-0027.pdf.

    Article  CAS  Google Scholar 

  2. DeWitt, S. and Adelberg, E., The occurrence of a genetic transposition in a strain of Escherichia coli, Gene-tics, 1962, vol. 47, pp. 577–685. https://www.ncbi.nlm. nih.gov/pmc/articles/PMC1210353/pdf/577.pd.

    CAS  Google Scholar 

  3. Howard-Flanders, P., Boyce, R.P., and Theriot, L., Three loci in Escherichia coli K-12 that control the excision of pyrimidine dimers and certain other mutagen products from DNA, Genetics, 1966, vol. 53, pp. 1119–1136.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Howard-Flanders, P. and Theriot, L., Mutants of Escherichia coli K-12 defective in DNA repair and in genetic recombination TL-53, Genetics, 1966, vol. 53, p. 1137. https://doi.org/10.2307/3583555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Howard-Flanders, P., Genes that control DNA repair and genetic recombination in Escherichia coli, Adv.  Biol. Med. Phys., 1968, vol. 12, pp. 299–317. http://www.ncbi.nlm.nih.gov/pubmed/4879502.

    Article  CAS  Google Scholar 

  6. Howard-Flanders, P., Theriot, L., and Stedeford, J.B., Some properties of excision-defective recombination-deficient mutants of Escherichia coli K-12, J. Bacteriol., 1969, vol. 97, pp. 1134–1141. https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC249825/pdf/jbacter00393-0184.pdf.

    Article  CAS  Google Scholar 

  7. Green, M.H.L., Greenberg, J., and Donch, J., Effect of a recA gene on cell division and capsular poly-saccharide production in a lon strain of Escherichia coli, Genetics Res., 1969, vol. 14, pp. 159–162. https://doi.org/10.1017/S0016672300001993

    Article  CAS  Google Scholar 

  8. Ganesan, A.K. and Smith, K.C., Dark-recovery processes in Escherichia coli irradiated with ultraviolet light. 3. Effect of rec mutations on recovery of excision-deficient mutants of Escherichia coli K-12, J. Bacteriol., 1970, vol. 102, pp. 404–410. https://pdfs.semanticscholar.org/ 3017/191fad191b9b4f7ff0735b567521e8750974.pdf.

    Article  CAS  Google Scholar 

  9. Sommer, S., Knezevic, J., Bailone, A., and Devoret, R., Induction of only one SOS operon, umuDC, is required for SOS mutagenesis in Escherichia coli, Mol. Genet. Genomics, 1993, vol. 239, pp. 137–144. https://doi.org/10.1007/BF00281612

    Article  CAS  Google Scholar 

  10. Bodoev, I.N., Ilina, E.N., and Smirnov, G.B., Characteristics of emergence of mutants resistant to nalidixic acid and novobiocin in E. coli strains with recA and lexA mutations, Mol. Genet., Microbiol. Virol., 2018, vol. 33, pp. 30–33. https://doi.org/10.3103/S0891416818010044

    Article  Google Scholar 

  11. Langmead, B. and Salzberg, S.L., Fast gapped-read alignment with Bowtie 2, Nat. Methods, 2012, vol. 9, pp. 357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Garrison, E. and Marth, G., Haplotype-based variant detection from short-read sequencing, 2012. https://arxiv.org/ pdf/1207.3907.pdf.

  13. Garrison, E. and Marth, G., Haplotype-based variant detection from short-read sequencing, 2016. https://www.cs. umd.edu/class/spring2016/cmsc702/public/FreeBayesDraft2015Jan12.pdf.

  14. Lucchesi, P., Carraway, M., and Marinus, M.G., Analysis of forward mutations induced by N-methyl-N'-nitro-N-nitrosoguanidine in the bacteriophage P22 mnt repressor gene, J. Bacteriol., 1986, vol. 166, pp. 34–37. http://www.ncbi.nlm.nih.gov/pubmed/3957871.

    Article  CAS  Google Scholar 

  15. Wright, B.E. and Minnick, M.F., Reversion rates in a leuB auxotroph of Escherichia coli K-12 correlate with ppGpp levels during exponential growth, Microbiology, 1997, vol. 143, pp. 847–854. https://doi.org/10.1099/00221287-143-3-847

    Article  CAS  PubMed  Google Scholar 

  16. Serebrijski, I., Reyes, O., and Leblon, G., Corrected gene assignments of Escherichia coli Pro-mutations, J. Bacteriol., 1995, vol. 177, pp. 7261–7264. https://doi.org/10.1128/jb.177.24.7261-7264.1995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Song, Y., Lee, B.R., Cho, S., Cho, Y.B., Kim, S.W., Kang, T.J., et al., Determination of single nucleotide variants in Escherichia coli DH5α by using short-read sequencing, FEMS Microbiol. Lett., 2015, vol. 362, pp. 1–7. https://doi.org/10.1093/femsle/fnv073

    Article  CAS  PubMed  Google Scholar 

  18. Lange, R. and Hengge-Aronis, R., The cellular concentration of the s subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability, Genes Dev., 1994, vol. 8, pp. 1600–1612. https://doi.org/10.1101/gad.8.13.1600

    Article  CAS  PubMed  Google Scholar 

  19. Sun, H., Zeng, J., Li, S., Liang, P., Zheng, C., Liu, Y., et al., Interaction between rpsL and gyrA mutations affects the fitness and dual resistance of mycobacterium tuberculosis clinical isolates against streptomycin and fluoroquinolones, Infect. Drug Resist., 2018, vol. 11, pp. 431–440. https://doi.org/10.2147/IDR.S152335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lin, L.L. and Little, J.W., Isolation and characterization of noncleavable (Ind-) mutants of the LexA repressor of Escherichia coli K-12, J. Bacteriol., 1988, vol. 170, pp. 2163–2173. https://doi.org/10.1128/jb.170.5.2163-2173.1988

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lin, L.L. and Little, J.W., Autodigestion and RecA-dependent cleavage of Ind-mutant LexA proteins, J. Mol. Biol., 1989, vol. 210, pp. 439–452. https://doi.org/10.1016/0022-2836(89)90121-6

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Molecular Genetics of Microorganisms, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical Biological Agency, 119435, Moscow, Russia

    G. B. Smirnov, I. N. Bodoev, A. P. Makarova, T. B. Butusova, V. A. Veselovsky, A. S. Gulyaev, E. A. Shitikov & E. N. Ilina

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  1. G. B. Smirnov
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  2. I. N. Bodoev
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  3. A. P. Makarova
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  4. T. B. Butusova
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  5. V. A. Veselovsky
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  6. A. S. Gulyaev
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  7. E. A. Shitikov
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  8. E. N. Ilina
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Correspondence to G. B. Smirnov, I. N. Bodoev, A. P. Makarova, T. B. Butusova, V. A. Veselovsky, A. S. Gulyaev, E. A. Shitikov or E. N. Ilina.

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Smirnov, G.B., Bodoev, I.N., Makarova, A.P. et al. Comparative Genomics of the Escherichia coli Strains АВ1157, АВ2463, АВ2494, and АВ1885. Mol. Genet. Microbiol. Virol. 34, 182–187 (2019). https://doi.org/10.3103/S0891416819030054

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