• 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. Apr 11, 1991; 19(7): 1375–1383.
PMCID: PMC333889

Palindromic units are part of a new bacterial interspersed mosaic element (BIME).

Abstract

Palindromic Units (PU or REP) were defined as DNA sequences of 40 nucleotides highly repeated on the genome of Escherichia coli and other Enterobacteriaceae. PU are found in clusters of up to six occurrences always localized in extragenic regions. By sorting the DNA sequences of the known PU containing regions into different classes, we show here for the first time that, besides the PU themselves, each PU clusters contains a number of other conserved sequence motifs. Seven such motifs were identified with the present list of PU regions. Remarkably, each PU cluster is exclusively composed of a mosaic combination of PU and of these other sequence motifs. We demonstrate directly by hybridization experiments that one of these motifs (called L) is indeed present at a large number of copies on the Escherichia coli chromosome and that its distribution follows the same species specificity as PU sequences themselves. We propose that the mosaic pattern of motif combination in PU clusters reveals a new type of bacterial genetic element which we propose to call BIME for Bacterial Interspersed Mosaic Element. The Escherichia coli genome contains about 500 BIME.

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 (1.7M), 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

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • 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]
  • 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]
  • Merino E, Bolivar F. The ribonucleoside diphosphate reductase gene (nrdA) of Escherichia coli carries a repetitive extragenic palindromic (REP) sequence in its 3' structural terminus. Mol Microbiol. 1989 Jun;3(6):839–841. [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]
  • 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]
  • 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]
  • 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]
  • Newbury SF, Smith NH, Higgins CF. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell. 1987 Dec 24;51(6):1131–1143. [PubMed]
  • Stern MJ, Prossnitz E, Ames GF. 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. 1988 Jan;2(1):141–152. [PubMed]
  • Shyamala V, Schneider E, Ames GF. Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point. EMBO J. 1990 Mar;9(3):939–946. [PMC free article] [PubMed]
  • Gilson E, Perrin D, Clement JM, Szmelcman S, Dassa E, Hofnung M. Palindromic units from E. coli as binding sites for a chromoid-associated protein. FEBS Lett. 1986 Oct 6;206(2):323–328. [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]
  • Claverie JM, Sauvaget I. Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput Appl Biosci. 1985;1(2):95–104. [PubMed]
  • Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. [PubMed]
  • Gribskov M, Lüthy R, Eisenberg D. Profile analysis. Methods Enzymol. 1990;183:146–159. [PubMed]
  • Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982 Dec 15;162(3):705–708. [PubMed]
  • Stark GR, Wahl GM. Gene amplification. Annu Rev Biochem. 1984;53:447–491. [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]
  • Otsuka AJ, Buoncristiani MR, Howard PK, Flamm J, Johnson C, Yamamoto R, Uchida K, Cook C, Ruppert J, Matsuzaki J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J Biol Chem. 1988 Dec 25;263(36):19577–19585. [PubMed]
  • Nohno T, Kasai Y, Saito T. Cloning and sequencing of the Escherichia coli chlEN operon involved in molybdopterin biosynthesis. J Bacteriol. 1988 Sep;170(9):4097–4102. [PMC free article] [PubMed]
  • Denk D, Böck A. L-cysteine biosynthesis in Escherichia coli: nucleotide sequence and expression of the serine acetyltransferase (cysE) gene from the wild-type and a cysteine-excreting mutant. J Gen Microbiol. 1987 Mar;133(3):515–525. [PubMed]
  • Sirko A, Hryniewicz M, Hulanicka D, Böck A. Sulfate and thiosulfate transport in Escherichia coli K-12: nucleotide sequence and expression of the cysTWAM gene cluster. J Bacteriol. 1990 Jun;172(6):3351–3357. [PMC free article] [PubMed]
  • Yang SY, Yang XY, Healy-Louie G, Schulz H, Elzinga M. Nucleotide sequence of the fadA gene. Primary structure of 3-ketoacyl-coenzyme A thiolase from Escherichia coli and the structural organization of the fadAB operon. J Biol Chem. 1990 Jun 25;265(18):10424–10429. [PubMed]
  • Cleton-Jansen AM, Goosen N, Fayet O, van de Putte P. Cloning, mapping, and sequencing of the gene encoding Escherichia coli quinoprotein glucose dehydrogenase. J Bacteriol. 1990 Nov;172(11):6308–6315. [PMC free article] [PubMed]
  • Wallace B, Yang YJ, Hong JS, Lum D. Cloning and sequencing of a gene encoding a glutamate and aspartate carrier of Escherichia coli K-12. J Bacteriol. 1990 Jun;172(6):3214–3220. [PMC free article] [PubMed]
  • Hussain K, Elliott EJ, Salmond GP. The parD- mutant of Escherichia coli also carries a gyrAam mutation. The complete sequence of gyrA. Mol Microbiol. 1987 Nov;1(3):259–273. [PubMed]
  • Wek RC, Hatfield GW. Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. J Biol Chem. 1986 Feb 15;261(5):2441–2450. [PubMed]
  • Adams MD, Wagner LM, Graddis TJ, Landick R, Antonucci TK, Gibson AL, Oxender DL. Nucleotide sequence and genetic characterization reveal six essential genes for the LIV-I and LS transport systems of Escherichia coli. J Biol Chem. 1990 Jul 15;265(20):11436–11443. [PubMed]
  • Stephens PE, Lewis HM, Darlison MG, Guest JR. Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K12. Eur J Biochem. 1983 Oct 3;135(3):519–527. [PubMed]
  • Pugsley AP, Dubreuil C. Molecular characterization of malQ, the structural gene for the Escherichia coli enzyme amylomaltase. Mol Microbiol. 1988 Jul;2(4):473–479. [PubMed]
  • Saint-Girons I, Duchange N, Zakin MM, Park I, Margarita D, Ferrara P, Cohen GN. Nucleotide sequence of metF, the E. coli structural gene for 5-10 methylene tetrahydrofolate reductase and of its control region. Nucleic Acids Res. 1983 Oct 11;11(19):6723–6732. [PMC free article] [PubMed]
  • Reed RE, Altman S. Repeated sequences and open reading frames in the 3' flanking region of the gene for the RNA subunit of Escherichia coli ribonuclease P. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5359–5363. [PMC free article] [PubMed]
  • Plumbridge JA. Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon. Mol Microbiol. 1989 Apr;3(4):505–515. [PubMed]
  • Hudson GS, Davidson BE. Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12. J Mol Biol. 1984 Dec 25;180(4):1023–1051. [PubMed]
  • Tiedeman AA, DeMarini DJ, Parker J, Smith JM. DNA sequence of the purC gene encoding 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide synthetase and organization of the dapA-purC region of Escherichia coli K-12. J Bacteriol. 1990 Oct;172(10):6035–6041. [PMC free article] [PubMed]
  • Lundberg LG, Thoresson HO, Karlström OH, Nyman PO. Nucleotide sequence of the structural gene for dUTPase of Escherichia coli K-12. EMBO J. 1983;2(6):967–971. [PMC free article] [PubMed]
  • Shinagawa H, Makino K, Amemura M, Kimura S, Iwasaki H, Nakata A. Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination. J Bacteriol. 1988 Sep;170(9):4322–4329. [PMC free article] [PubMed]
  • Szumanski MB, Boyle SM. Analysis and sequence of the speB gene encoding agmatine ureohydrolase, a putrescine biosynthetic enzyme in Escherichia coli. J Bacteriol. 1990 Feb;172(2):538–547. [PMC free article] [PubMed]
  • Schwartz I, Klotsky RA, Elseviers D, Gallagher PJ, Krauskopf M, Siddiqui MA, Wong JF, Roe BA. Molecular cloning and sequencing of pheU, a gene for Escherichia coli tRNAPhe. Nucleic Acids Res. 1983 Jul 11;11(13):4379–4389. [PMC free article] [PubMed]
  • McCorkle GM, Altman S. Large deletion mutants of Escherichia coli tRNATyr1. J Mol Biol. 1982 Feb 25;155(2):83–103. [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

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...