• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Dec 25, 1991; 19(24): 6823–6831.
PMCID: PMC329316

Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.

Abstract

Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.5M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Schmid CW, Jelinek WR. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. [PubMed]
  • Jelinek WR, Toomey TP, Leinwand L, Duncan CH, Biro PA, Choudary PV, Weissman SM, Rubin CM, Houck CM, Deininger PL, et al. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1398–1402. [PMC free article] [PubMed]
  • Houck CM, Rinehart FP, Schmid CW. A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol. 1979 Aug 15;132(3):289–306. [PubMed]
  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. [PubMed]
  • Nelson DL, Ledbetter SA, Corbo L, Victoria MF, Ramírez-Solis R, Webster TD, Ledbetter DH, Caskey CT. Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6686–6690. [PMC free article] [PubMed]
  • Rikke BA, Garvin LD, Hardies SC. Systematic identification of LINE-1 repetitive DNA sequence differences having species specificity between Mus spretus and Mus domesticus. J Mol Biol. 1991 Jun 20;219(4):635–643. [PubMed]
  • Bachmann BJ. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. [PMC free article] [PubMed]
  • Nesin M, Lupski JR, Svec P, Godson GN. Possible new genes as revealed by molecular analysis of a 5-kb Escherichia coli chromosomal region 5' to the rpsU-dnaG-rpoD macromolecular-synthesis operon. Gene. 1987;51(2-3):149–161. [PubMed]
  • Yanofsky C, Platt T, Crawford IP, Nichols BP, Christie GE, Horowitz H, VanCleemput M, Wu AM. The complete nucleotide sequence of the tryptophan operon of Escherichia coli. Nucleic Acids Res. 1981 Dec 21;9(24):6647–6668. [PMC free article] [PubMed]
  • Lawther RP, Wek RC, Lopes JM, Pereira R, Taillon BE, Hatfield GW. The complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli K-12. Nucleic Acids Res. 1987 Mar 11;15(5):2137–2155. [PMC free article] [PubMed]
  • Chu FK, Maley GF, Maley F, Belfort M. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc Natl Acad Sci U S A. 1984 May;81(10):3049–3053. [PMC free article] [PubMed]
  • Gott JM, Shub DA, Belfort M. Multiple self-splicing introns in bacteriophage T4: evidence from autocatalytic GTP labeling of RNA in vitro. Cell. 1986 Oct 10;47(1):81–87. [PubMed]
  • Kuhsel MG, Strickland R, Palmer JD. An ancient group I intron shared by eubacteria and chloroplasts. Science. 1990 Dec 14;250(4987):1570–1573. [PubMed]
  • Xu MQ, Kathe SD, Goodrich-Blair H, Nierzwicki-Bauer SA, Shub DA. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science. 1990 Dec 14;250(4987):1566–1570. [PubMed]
  • Stern MJ, Ames GF, Smith NH, Robinson EC, Higgins CF. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. [PubMed]
  • Gilson E, Clément JM, Brutlag D, Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. [PMC free article] [PubMed]
  • Sharples GJ, Lloyd RG. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 1990 Nov 25;18(22):6503–6508. [PMC free article] [PubMed]
  • Hulton CS, Higgins CF, Sharp PM. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol. 1991 Apr;5(4):825–834. [PubMed]
  • Higgins CF, Ames GF, Barnes WM, Clement JM, Hofnung M. A novel intercistronic regulatory element of prokaryotic operons. Nature. 1982 Aug 19;298(5876):760–762. [PubMed]
  • Yang Y, Ames GF. DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8850–8854. [PMC free article] [PubMed]
  • Gilson E, Rousset JP, Clément JM, Hofnung M. A subfamily of E. coli palindromic units implicated in transcription termination? Ann Inst Pasteur Microbiol. 1986 Nov-Dec;137B(3):259–270. [PubMed]
  • Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell. 1987 Jan 30;48(2):297–310. [PubMed]
  • Gilson E, Perrin D, Hofnung M. DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res. 1990 Jul 11;18(13):3941–3952. [PMC free article] [PubMed]
  • Loenen WA, Daniel AS, Braymer HD, Murray NE. Organization and sequence of the hsd genes of Escherichia coli K-12. J Mol Biol. 1987 Nov 20;198(2):159–170. [PubMed]
  • Martin FH, Castro MM, Aboul-ela F, Tinoco I., Jr Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res. 1985 Dec 20;13(24):8927–8938. [PMC free article] [PubMed]
  • Kawase Y, Iwai S, Inoue H, Miura K, Ohtsuka E. Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases. Nucleic Acids Res. 1986 Oct 10;14(19):7727–7736. [PMC free article] [PubMed]
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [PMC free article] [PubMed]
  • Noda A, Courtright JB, Denor PF, Webb G, Kohara Y, Ishihama A. Rapid identification of specific genes in E. coli by hybridization to membranes containing the ordered set of phage clones. Biotechniques. 1991 Apr;10(4):474–477. [PubMed]
  • Kogan SC, Doherty M, Gitschier J. An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. Application to hemophilia A. N Engl J Med. 1987 Oct 15;317(16):985–990. [PubMed]
  • Van Leuven F. The trouble with PCR machines: fill up the empty spaces! Trends Genet. 1991 May;7(5):142–142. [PubMed]
  • Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. [PMC free article] [PubMed]
  • Welsh J, McClelland M. Genomic fingerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Res. 1991 Feb 25;19(4):861–866. [PMC free article] [PubMed]
  • Gilson E, Bachellier S, Perrin S, Perrin D, Grimont PA, Grimont F, Hofnung M. Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriaceae. Res Microbiol. 1990 Nov-Dec;141(9):1103–1116. [PubMed]
  • Austin D, Larson TJ. Nucleotide sequence of the glpD gene encoding aerobic sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12. J Bacteriol. 1991 Jan;173(1):101–107. [PMC free article] [PubMed]
  • Kohara Y, Akiyama K, Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. [PubMed]
  • Versalovic J, Koeuth T, McCabe ER, Lupski JR. Use of the polymerase chain reaction for physical mapping of Escherichia coli genes. J Bacteriol. 1991 Sep;173(17):5253–5255. [PMC free article] [PubMed]
  • Owen RJ. Chromosomal DNA fingerprinting--a new method of species and strain identification applicable to microbial pathogens. J Med Microbiol. 1989 Oct;30(2):89–99. [PubMed]
  • Murray BE, Singh KV, Heath JD, Sharma BR, Weinstock GM. Comparison of genomic DNAs of different enterococcal isolates using restriction endonucleases with infrequent recognition sites. J Clin Microbiol. 1990 Sep;28(9):2059–2063. [PMC free article] [PubMed]
  • Carriere C, Allardet-Servent A, Bourg G, Audurier A, Ramuz M. DNA polymorphism in strains of Listeria monocytogenes. J Clin Microbiol. 1991 Jul;29(7):1351–1355. [PMC free article] [PubMed]
  • Litwin CM, Storm AL, Chipowsky S, Ryan KJ. Molecular epidemiology of Shigella infections: plasmid profiles, serotype correlation, and restriction endonuclease analysis. J Clin Microbiol. 1991 Jan;29(1):104–108. [PMC free article] [PubMed]
  • Lennon E, Gutman PD, Yao HL, Minton KW. A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK. J Bacteriol. 1991 Mar;173(6):2137–2140. [PMC free article] [PubMed]
  • Dahl MK, Francoz E, Saurin W, Boos W, Manson MD, Hofnung M. Comparison of sequences from the malB regions of Salmonella typhimurium and Enterobacter aerogenes with Escherichia coli K12: a potential new regulatory site in the interoperonic region. Mol Gen Genet. 1989 Aug;218(2):199–207. [PubMed]
  • Sapienza C, Doolittle WF. Unusual physical organization of the Halobacterium genome. Nature. 1982 Feb 4;295(5848):384–389. [PubMed]
  • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. [PMC free article] [PubMed]
  • Glare EM, Paton JC, Premier RR, Lawrence AJ, Nisbet IT. Analysis of a repetitive DNA sequence from Bordetella pertussis and its application to the diagnosis of pertussis using the polymerase chain reaction. J Clin Microbiol. 1990 Sep;28(9):1982–1987. [PMC free article] [PubMed]
  • Eisenach KD, Cave MD, Bates JH, Crawford JT. Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J Infect Dis. 1990 May;161(5):977–981. [PubMed]
  • Mazel D, Houmard J, Castets AM, Tandeau de Marsac N. Highly repetitive DNA sequences in cyanobacterial genomes. J Bacteriol. 1990 May;172(5):2755–2761. [PMC free article] [PubMed]
  • Scherer S, Stevens DA. A Candida albicans dispersed, repeated gene family and its epidemiologic applications. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1452–1456. [PMC free article] [PubMed]
  • Stringer SL, Hong ST, Giuntoli D, Stringer JR. Repeated DNA in Pneumocystis carinii. J Clin Microbiol. 1991 Jun;29(6):1194–1201. [PMC free article] [PubMed]
  • Higgins CF, McLaren RS, Newbury SF. Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. Gene. 1988 Dec 10;72(1-2):3–14. [PubMed]
  • Brosius J. Retroposons--seeds of evolution. Science. 1991 Feb 15;251(4995):753–753. [PubMed]
  • Inouye M, Inouye S. Retroelements in bacteria. Trends Biochem Sci. 1991 Jan;16(1):18–21. [PubMed]
  • Tabata S, Higashitani A, Takanami M, Akiyama K, Kohara Y, Nishimura Y, Nishimura A, Yasuda S, Hirota Y. Construction of an ordered cosmid collection of the Escherichia coli K-12 W3110 chromosome. J Bacteriol. 1989 Feb;171(2):1214–1218. [PMC free article] [PubMed]
  • Correia FF, Inouye S, Inouye M. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA. J Bacteriol. 1986 Sep;167(3):1009–1015. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...