Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1988 Apr;170(4):1775–1782. doi: 10.1128/jb.170.4.1775-1782.1988

Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria.

A S Daniel 1, F V Fuller-Pace 1, D M Legge 1, N E Murray 1
PMCID: PMC211030  PMID: 2832380

Abstract

We screened Salmonella typhimurium, Citrobacter freundii, Klebsiella pneumoniae, Shigella boydii, and many isolates of Escherichia coli for DNA sequences homologous to those encoding each of two unrelated type I restriction and modification systems (EcoK and EcoA). Both K- and A-related hsd genes were identified, but never both in the same strain. S. typhimurium encodes three restriction and modification systems, but its DNA hybridized only to the K-specific probe which we know to identify the StySB system. No homology to either probe was detected in the majority of E. coli strains, but in C. freundii, we identified homology to the A-specific probe. We cloned this region of the C. freundii genome and showed that it encoded a functional, A-related restriction system whose specificity differs from those of known type I enzymes. Sequences immediately flanking the hsd K genes of E. coli K-12 and the hsd A genes of E. coli 15T- were shown to be homologous, indicating similar or even identical positions in their respective chromosomes. E. coli C has no known restriction system, and the organization of its chromosome is consistent with deletion of the three hsd genes and their neighbor, mcrB.

Full text

PDF
1778

Images in this article

1778Image
on p.1778

Selected References

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

  1. Appleyard R K. Segregation of New Lysogenic Types during Growth of a Doubly Lysogenic Strain Derived from Escherichia Coli K12. Genetics. 1954 Jul;39(4):440–452. doi: 10.1093/genetics/39.4.440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arber W. Host-controlled modification of bacteriophage. Annu Rev Microbiol. 1965;19:365–378. doi: 10.1146/annurev.mi.19.100165.002053. [DOI] [PubMed] [Google Scholar]
  3. Arber W., Wauters-Willems D. Host specificity of DNA produced by Escherichia coli. XII. The two restriction and modification systems of strain 15T-. Mol Gen Genet. 1970;108(3):203–217. doi: 10.1007/BF00283350. [DOI] [PubMed] [Google Scholar]
  4. Bertani L. E. Abortive induction of bacteriophage P2. Virology. 1968 Sep;36(1):87–103. doi: 10.1016/0042-6822(68)90119-0. [DOI] [PubMed] [Google Scholar]
  5. Borck K., Beggs J. D., Brammar W. J., Hopkins A. S., Murray N. E. The construction in vitro of transducing derivatives of phage lambda. Mol Gen Genet. 1976 Jul 23;146(2):199–207. doi: 10.1007/BF00268089. [DOI] [PubMed] [Google Scholar]
  6. Bouché J. P., Gélugne J. P., Louarn J., Louarn J. M., Kaiser K. Relationships between the physical and genetic maps of a 470 x 10(3) base-pair region around the terminus of Escherichia coli K12 DNA replication. J Mol Biol. 1982 Jan 5;154(1):21–32. doi: 10.1016/0022-2836(82)90414-4. [DOI] [PubMed] [Google Scholar]
  7. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  8. Bullas L. R., Colson C. DNA restriction and modification systems in Salmonella. III. SP, a Salmonella potsdam system allelic to the SB system in Salmonella typhimurium. Mol Gen Genet. 1975 Aug 27;139(3):177–188. [PubMed] [Google Scholar]
  9. Bullas L. R., Colson C., Neufeld B. Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes. J Bacteriol. 1980 Jan;141(1):275–292. doi: 10.1128/jb.141.1.275-292.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Caugant D. A., Levin B. R., Selander R. K. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics. 1981 Jul;98(3):467–490. doi: 10.1093/genetics/98.3.467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Clewell D. B., Helinski D. R. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an opern circular DNA form. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1159–1166. doi: 10.1073/pnas.62.4.1159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. DUGUID J. P., SMITH I. W., DEMPSTER G., EDMUNDS P. N. Non-flagellar filamentous appendages (fimbriae) and haemagglutinating activity in Bacterium coli. J Pathol Bacteriol. 1955 Oct;70(2):335–348. doi: 10.1002/path.1700700210. [DOI] [PubMed] [Google Scholar]
  13. Dixon R., Kennedy C., Kondorosi A., Krishnapillai V., Merrick M. Complementation analysis of Klebsiella pneumoniae mutants defective in nitrogen fixation. Mol Gen Genet. 1977 Nov 29;157(2):189–198. doi: 10.1007/BF00267397. [DOI] [PubMed] [Google Scholar]
  14. Endlich B., Linn S. The DNA restriction endonuclease of Escherichia coli B. II. Further studies of the structure of DNA intermediates and products. J Biol Chem. 1985 May 10;260(9):5729–5738. [PubMed] [Google Scholar]
  15. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  16. Fuller-Pace F. V., Bullas L. R., Delius H., Murray N. E. Genetic recombination can generate altered restriction specificity. Proc Natl Acad Sci U S A. 1984 Oct;81(19):6095–6099. doi: 10.1073/pnas.81.19.6095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fuller-Pace F. V., Cowan G. M., Murray N. E. EcoA and EcoE: alternatives to the EcoK family of type I restriction and modification systems of Escherichia coli. J Mol Biol. 1985 Nov 5;186(1):65–75. doi: 10.1016/0022-2836(85)90257-8. [DOI] [PubMed] [Google Scholar]
  18. Fuller-Pace F. V., Murray N. E. Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9368–9372. doi: 10.1073/pnas.83.24.9368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gann A. A., Campbell A. J., Collins J. F., Coulson A. F., Murray N. E. Reassortment of DNA recognition domains and the evolution of new specificities. Mol Microbiol. 1987 Jul;1(1):13–22. doi: 10.1111/j.1365-2958.1987.tb00521.x. [DOI] [PubMed] [Google Scholar]
  20. Gough J. A., Murray N. E. Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol. 1983 May 5;166(1):1–19. doi: 10.1016/s0022-2836(83)80047-3. [DOI] [PubMed] [Google Scholar]
  21. Kaiser K., Murray N. E. Physical characterisation of the "Rac prophage" in E. coli K12. Mol Gen Genet. 1979 Sep;175(2):159–174. doi: 10.1007/BF00425532. [DOI] [PubMed] [Google Scholar]
  22. Murray N. E., Brammar W. J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet. 1977 Jan 7;150(1):53–61. doi: 10.1007/BF02425325. [DOI] [PubMed] [Google Scholar]
  23. Murray N. E., Gough J. A., Suri B., Bickle T. A. Structural homologies among type I restriction-modification systems. EMBO J. 1982;1(5):535–539. doi: 10.1002/j.1460-2075.1982.tb01205.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nagaraja V., Stieger M., Nager C., Hadi S. M., Bickle T. A. The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme. Nucleic Acids Res. 1985 Jan 25;13(2):389–399. doi: 10.1093/nar/13.2.389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Price C., Bickle T. A. A possible role for DNA restriction in bacterial evolution. Microbiol Sci. 1986 Oct;3(10):296–299. [PubMed] [Google Scholar]
  26. Price C., Pripfl T., Bickle T. A. EcoR124 and EcoR124/3: the first members of a new family of type I restriction and modification systems. Eur J Biochem. 1987 Aug 17;167(1):111–115. doi: 10.1111/j.1432-1033.1987.tb13310.x. [DOI] [PubMed] [Google Scholar]
  27. Radding C. M. Molecular mechanisms in genetic recombination. Annu Rev Genet. 1973;7:87–111. doi: 10.1146/annurev.ge.07.120173.000511. [DOI] [PubMed] [Google Scholar]
  28. Raleigh E. A., Wilson G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A. 1986 Dec;83(23):9070–9074. doi: 10.1073/pnas.83.23.9070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  30. Ross T. K., Braymer H. D. Localization of a genetic region involved in McrB restriction by Escherichia coli K-12. J Bacteriol. 1987 Apr;169(4):1757–1759. doi: 10.1128/jb.169.4.1757-1759.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sain B., Murray N. E. The hsd (host specificity) genes of E. coli K 12. Mol Gen Genet. 1980;180(1):35–46. doi: 10.1007/BF00267350. [DOI] [PubMed] [Google Scholar]
  32. Selander R. K., Levin B. R. Genetic diversity and structure in Escherichia coli populations. Science. 1980 Oct 31;210(4469):545–547. doi: 10.1126/science.6999623. [DOI] [PubMed] [Google Scholar]
  33. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  34. Studier F. W. The genetics and physiology of bacteriophage T7. Virology. 1969 Nov;39(3):562–574. doi: 10.1016/0042-6822(69)90104-4. [DOI] [PubMed] [Google Scholar]
  35. Suri B., Bickle T. A. EcoA: the first member of a new family of type I restriction modification systems. Gene organization and enzymatic activities. J Mol Biol. 1985 Nov 5;186(1):77–85. doi: 10.1016/0022-2836(85)90258-x. [DOI] [PubMed] [Google Scholar]
  36. Wilson G. G., Tanyashin V. I., Murray N. E. Molecular cloning of fragments of bacteriophage T4 DNA. Mol Gen Genet. 1977 Nov 14;156(2):203–214. doi: 10.1007/BF00283493. [DOI] [PubMed] [Google Scholar]
  37. Yuan R. Structure and mechanism of multifunctional restriction endonucleases. Annu Rev Biochem. 1981;50:285–319. doi: 10.1146/annurev.bi.50.070181.001441. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES