Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence

Genetics

Volumn 145, Issue 3, 1997, Pages 551-562

  Bachellier, Sophie ^a,b   Clément, Jean Marie ^a,c   Hofnung, Maurice ^a   Gilson, Eric ^a  

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

^c Department of Biochemistry   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA SEQUENCE; ESCHERICHIA COLI; GENE INSERTION SEQUENCE; GENETIC POLYMORPHISM; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SHIGELLA; SOUTHERN BLOTTING;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MOLECULAR SEQUENCE DATA; MOSAICISM; POLYMORPHISM, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SHIGELLA FLEXNERI; SHIGELLA SONNEI;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SHIGELLA;

EID: 1842406595     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (59)

1. BACHELLIER, S., 1995 Les BIMEs: un exemple de séquences répétées chez les entérobactéries. Bull. Inst. Pasteur 93: 97-152.
2. BACHELLIER, S., D. PERRIN, M. HOFNUNG and E. GII.SON', 1993 Bacterial Interspersed Mosaic Elements (BIMEs) are present in the genome of Klebsiella. Mol. Microbiol. 7: 537-544.
3. BACHELLIER, S., W. SAURIN, D. PERRIN, M. HOFNUNC, and E. GILSON, 1994 Stnictural and functional diversity among bacterial interspersed mosaic elements (BIMEs). Mol. Microbiol. 12: 61-70.
4. BACHELLIER, S., E. GILSON, M. HOFNUXG and C. W. HILL, 199G Repeated sequences, pp. 2012-2040 in Escherichia coli and Salmonella: Cellular and Molecular Biology, edited by F. C. NEIDIIARDT, R. CURTISS, III, J. L. IXGRAIIAM, E. C. C. Lix, K. B. Low et al. American Society for Microbiology, Washington, DC.
5. BIRKENBIHL, R. P., and W. VlELMETTER, 1989 Complete maps of 1S1, 152, IS3, IS4, IS5, IS30and IS 150 locations in Escherichia coliK.12. Mol. Gen. Genet. 220: 147-153.
6. BOCCARD, F., and P. PRENTKI, 1993 Specific interaction of IHF with RIBs, a class of bacterial repetitive DNTA elements located at the 3′ end of transcription units. EMBOJ. 12: 5019-5027.
7. CHANDLER, M., and O. FAYET, 1993 Translational frameshifting in the control of transposition in bacteria. Mol. Microbiol. 7: 497-503.
8. DAHI, M. K., E. FRANCOZ, W. SAURIN, W, Boos, M. D. MANSON et al., 1989 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. 218: 199-207.
9. DIMRI, G. P., K. E. RUDD, M. K. MORGAN, H. BAYAT and G. FERROLuzzi AMES, 1992 Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Eichenchia coli strains and other enteric bacteria. J. Bacteriol. 174: 4583-4593.
10. DODD, I. B., andj. B. EGAN, 1990 Improved detection of helix-turnhelix DN'A-binding motifs in protein sequences. Nucleic Acids Res. 18: 5019-5026.
11. GALAS, D. J., and M. CHANDLER, 1989 Bacterial insertion sequences, pp. 109-162 in Mobile DXA, edited by D.E. BERG and M. M. HOWE. American Society for Microbiology, Washington, DC.
12. GILSON, E., J.-M. CLÉMENT, D. BRUTIAG and M. HOFNUNG, 1984 A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBOJ. 3: 1417-1421.
13. GILSOX, E., J.-P. RoussET.J.-M. CLéMENT and M. HOFNUNG, 1986 A subfamily of E. coli palindromic units implicated in transcription termination? Ann. Inst. Pasteur/Microbiol. 137B: 259-270.
14. GILSON, E..J.-M. CLéMENT, D. PERRIN and M. HOFNUNG, 1987 Palindromic units: a case of highly repetitive DN'A sequences in bacteria. Trends Genet. 3: 226-230.
15. GILSON, E., D. PERRIN and M. HOFNUNG, 1990a DNA polymerase I and a protein complex bind specifically to E. coli palindromic units highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res. 18: 3941-3952.
16. GILSON, E., S. BACHELLIER, S. PERRIN, D. PERRIN, P.A.D. GRIMONT et al., 1990b Palindromic units highly repetitive DNA sequences exhibit species specificity within enterobacteriaceae. Res. Microbiol. 141: 1103-1116.
17. GILSON, E., W. SAURIN, D. PERRIN, S. BACIIEI.I.IF.R and M. HOFNUNG, 1991a Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 19: 1375-1383.
18. GILSON, E., W. SAURIN, D. PERRIN, S. BACIIELLIER and M. HOFNUNG, 1991b The BIME family of bacterial highly repetitive sequences. Res. Microbiol. 142: 217-222.
19. GUSTAFSON, C. E., S. CHU and T.J. TRUST, 1994 Mutagenesis of the paracrystalline surface protein array of Aeromonas salmonicida by endogenous insertion elements. J. Mol. Biol. 237: 452-463.
20. HERZER, P. J., S. INOUYE, M. INOUYE and T. S. WHITTAM, 1990 Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli.]. Bactcriol. 172: 6175-6181.
21. HIGGINS C. F., G. FERRO-Luzzi AMES, \V. M. BARNES, J.-M. CLéMENT and M. HOFNU.NG, 1982 A novel intercistronic regulator)- element of prokaryotic opérons. Nature 298: 760-762.
22. HIGGINS, D. G., A. J. BLEASBY and R. Fucus, 1991 CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8: 189-191.
23. HILL, C. W., C. H. SANDT and D. A. VLAZNY, 1994 Rlis elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein. Mol. Microbiol. 12: 865-871.
24. HILL, C. W., G. FEULNER, M. S. BRODY, S. ZIIAO, A. B. SADOSKY et al., 1995 Correlation of Rlis elements with Escherichia coli population structure. Genetics 141: 15-24.
25. HSIAO, K., 1991 A fast and simple procedure for sequencing double stranded DNA with Sequenase. Nucleic Acids Res. 19: 2787.
26. KULKOSKY, J., K. S.JONES, R. A. KATZ, J. P. G. MACK and A. M. SKALKA, 1992 Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12: 2331-2338.
27. LANDSCHULTZ, W. H., P. F. JOHNSON and S. L. MCKNIGIIT, 1988 The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240: 1759-1764.
28. LEE, N., W. GIELOW, R. MARTIN, E. HAMILTON and A. FOWLER, 1986 The organization of the araBAD operon of Escherichia coli. Gene 47: 231-244.
29. LIM, D., T.A. T. GOMES and W. K. MAAS, 1990 Distribution of msDN'A among serotypes of enteropathogenic Escherichia coli strains. Mol. Microbiol. 4: 1711-1714.
30. LIN, H.-C., S.-P. LEI, G. STUDNICKA and G. WILCOX, 1985 The araBAD operon of Salmonella typhimurium LT2. III. Nucleotide sequence of araD and its flanking regions, and primär)' structure of its product, L-ribulose-5-phophate 4-epimerase. Gene 34:129-134.
31. MACADAM, R. A., P. W. M. HERMANS, D. VAN SOOI.INGEN, Z. F. ZAINUDDIN, D. CATTY et al, 1990 Characterization of a Mycobacleiium tuberculosis insertion sequence belonging to the IS3 family. Mol. Microbiol. 4: 1607-1613.
32. MILLER, R. D., and D. L. HARTL, 1986 Biotyping confirms a nearly clonal population structure in Escherichia coli. Evolution 40: 1-12.
33. MUELLER, P. R., and B. WOLD, 1989 In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246: 780-786.
34. NEWBURY, S. F., N. H. SMITH and C. F. HIGGINS, 1987a Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51: 1131-1143.
35. NEWBURY, S. F., N. H. SMITH, E. C. ROBINSON, I. D. HII.ES and C. F. HICGINS, 1987b Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48: 297-310.
36. OCIIMAN, H., and R. K. SELANUER, 1984 Standard reference strains of Esclietichia coll from natural populations. J. Bacteriol. 157: 690-693.
37. OPPENHEIM, A. B., K. E. RUDD, I. MENDEi-SONand D.TEFF, 1993 Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coll. Mol. Microbiol. 10: 113-122.
38. POIARD, P., and M. CILXNDLER, 1995 Bacterial transposases and retroviral integrases. Mol. Microbiol. 15: 13-23.
39. POIARD, P., M. F. PRÈRE, M. CHANDLER and O. FAYET, 1991 Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911. J. Mol. Biol. 222: 465-477.
40. PRèRE, M.-F., M. CHANDLER and O. FAYET, 1990 Transposition in Shigella dysenteriae: isolation and analysis of IS9/7, a new member of the IS group of insertion sequences. J. Bacteriol. 172: 4094-4099.
41. SADOSKY, A. B., A. DAVIDSON, R.-J. LIN and C. W. HILL, 19S9 rhs gene family of Esclieiicliia coli K-12.J. Bacteriol. 171: 636-642.
42. SAMBROOK,J., E. F. FRISCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, New York.
43. SANSONETTI, P. J., and J. ARONDEL, 1989 Construction and evaluation of a double mutant of Shigella flexneri as a candidate for oral vaccination against shigellosis. Vaccine 7: 443-450.
44. SAWYER, S. A., D. E. DYKHUISEN, R. F. DUBOSE, L. GREEN, T. MLTANGADURA-MIUANGA et al, 1987 Distribution and abundance of insertion sequences among natural isolates of Esclieiicliia coli. Genetics 115: 51-63.
45. SEKINE, Y., N. EISAKI and E. OHTSUBO, 1994 Translational control in production of transposase and in transposition of insertion sequence 153. J. Mol. Biol. 235: 1406-1420.
46. SELANDER, R. K., D. A. CUJGANT and T. S. WHITTAM, 1987 Genetic structure and variation in natural populations of Esclieiicliia coli, pp. 1625-1648 in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, edited by J. L. I.VGRAllAM, K. B. Low, B. MAGASANIK, M. SCHAECHTER and H. E. UMBARGER. American Society for Microbiology, Washington, DC.
47. SHYAMALA, V., E. SCHNEIDER and G. FERRO-LUZZI AMES, 1990 Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point. EMBO J. 9: 939-946.
48. SILILYAY, T.J., M. L. HERMAN and L. W. ENQUIST, 1984 Experiments Willi Gene Fusions. ColiI Spring Harbor Laboratory, Cold Spring Harbor, NY.
49. SKAUGEN, M., and I. F. NES, 1994 Transposition in Lactobacillus sake and its abolition of lactocin S production by insertion of IS1163, a new member of the IS5 family. Appl. Environ. Microbiol. 60: 2818-2825.
50. STERN, M. J., G. FERRO-LUZZI AMES, N. H. SMITH, E. C. ROBINSON and C. F. HIGGINS, 1984 Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37: 1015-1026.
51. STERN, M.J., E. PROSSNTTZ and G. FERRO-LUZZI AMES, 1988 Role of the intercistronic region in post-transcriptional control of gene expression in the histidine transport operon of Salmonella typhimurium: involvement of REP sequences. Mol. Microbiol. 2: 141-152.
52. THOMPSON-STEWART, D., G. H. KARTEN and A. C. SPARDLING, 1994 A transposable element can drive the concerted evolution of tandemly repetitious DN'A. Proc. Natl. Acad. Sei. USA 91: 9042-9046.
53. VÖGELE, K., E. SCHWARTZ, C. WELZ, E. SCIIILTZ and B. RAK, 1991 High-level ribosomal frameshifting directs the synthesis if IS/50 gene products. Nucleic Acids Res. 19: 4377-4385.
54. WALKER, J. E., M. SARASTE, M.J. RUNSWICK and N.J. GAY, 1982 Distantly related sequences in the α- and β- subunits of ATP synthase, myosin, kinases and other ATP-rcquiring enzymes and a common nucleotide binding fold. EMBO J. 1: 945-951.
55. XIANG, S.-H., M. HOBBS and P. R. REEVES, 1994 Molecular analysis of the ijb gene cluster of a group D2 Salmonella enterica strain: evidence for its origin from an insertion sequence-mediated recombination event between group E and Dl strains. J. Bacteriol. 176: 4357-4365.
56. YANG, Y., and G. FERRO-LUZZI AMES, 1988 DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc. Natl. Acad. Sei. USA 85: 8850-8854.
57. ZHAO, S., and C. W. HILI., 1995 Reshuffling of Khs components to create a new element. J. Bacteriol. 177: 1393-1398.
58. ZHAO, S., C. H. SANDT, G. FEULNER, D. A. VIAZNY, J. A. GRAY et al. 1993 Rhs elements of Escherichia coli K-12: complex composites of shared and unique components that have different evolutionary histories. J. Bacteriol. 175: 2799-2808.
59. Zou, S., N. KE, J. M. KIM and D. F. VOYTAS, 1996 The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10: 634-644.