Structural and functional diversity among bacterial interspersed mosaic elements (BIMEs)

Palindromic units (PU or REP) were defined as 40‐nucleotide DNA sequences which are highly repeated in the genome of several members of the Enterobacteriaceae. They were shown to be a constituent of the bacterial interspersed mosaic element (BIME), in which they are associated with other repetitive sequences. We report here that Escherichia coli PU sequences contain three motifs (Y, Z1 and Z2), leading to the definition of two BIME families. The BIME‐1 family, highly conserved over 145 nucleotides, contains two PUs (motifs Y and Z1). The BIME‐2 family contains a variable number of PUs (motifs Y and Z2). We present evidence, using band shift experiments, that each PU motif binds DNA gyrase with a different affinity. This suggests that the two families are functionally distinct.

[1]  F. Boccard,et al.  Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units. , 1993, The EMBO journal.

[2]  K. Rudd,et al.  Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli , 1993, Molecular microbiology.

[3]  F. Blattner,et al.  DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. , 1993, Genomics.

[4]  K. Makino,et al.  Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli , 1993, Journal of bacteriology.

[5]  S Karlin,et al.  Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups. , 1993, Journal of molecular biology.

[6]  H. Buc,et al.  E. coli DNA polymerase I as a reverse transcriptase. , 1993, The EMBO journal.

[7]  E. Gilson,et al.  Bacterial interspersed mosaic elements (BIMEs) are present in the genome of Klebsiella , 1993, Molecular microbiology.

[8]  H. Bergler,et al.  Sequences of the envM gene and of two mutated alleles in Escherichia coli. , 1992, Journal of general microbiology.

[9]  P. Alifano,et al.  Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella typhimurium: protein homology and functional complementation , 1992, Journal of bacteriology.

[10]  John Walker,et al.  A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae , 1992, Nucleic Acids Res..

[11]  K. Rudd,et al.  Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria , 1992, Journal of bacteriology.

[12]  J. Lupski,et al.  Short, interspersed repetitive DNA sequences in prokaryotic genomes , 1992, Journal of bacteriology.

[13]  J. Slonczewski,et al.  pH dependence and gene structure of inaA in Escherichia coli , 1992, Journal of bacteriology.

[14]  S. Inouye,et al.  In vivo duplication of genetic elements by the formation of stem-loop DNA without an RNA intermediate. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  E. Gilson,et al.  Palindromic units are part of a new bacterial interspersed mosaic element (BIME). , 1991, Nucleic acids research.

[16]  P. Sharp,et al.  ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria , 1991, Molecular microbiology.

[17]  J. Griffith,et al.  Drosophila topoisomerase II-DNA interactions are affected by DNA structure. , 1991, Journal of molecular biology.

[18]  R. G. Lloyd,et al.  A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. , 1990, Nucleic acids research.

[19]  E. Gilson,et al.  Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriaceae. , 1990, Research in microbiology.

[20]  Eric Gilson,et al.  DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization , 1990, Nucleic Acids Res..

[21]  G. Ames,et al.  Tandem chromosomal duplications: role of REP sequences in the recombination event at the join‐point. , 1990, The EMBO journal.

[22]  C. Higgins,et al.  Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. , 1988, Gene.

[23]  G. Ames,et al.  DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[24]  E. Zuckerkandl,et al.  Generation of high specificity of effect through low‐specificity binding of proteins to DNA , 1988, FEBS letters.

[25]  G. Ames,et al.  Role of the intercistronic region in post‐transcriptional control of gene expression in the histidine transport operon of Salmonella typhimurium: involvement of REP sequences , 1988, Molecular microbiology.

[26]  Sarah F. Newbury,et al.  Differential mRNA stability controls relative gene expression within a polycistronic operon , 1987, Cell.

[27]  Sarah F. Newbury,et al.  Stabilization of translationally active mRNA by prokaryotic REP sequences , 1987, Cell.

[28]  E. Gilson,et al.  A subfamily of E. coli palindromic units implicated in transcription termination? , 1986, Annales de l'Institut Pasteur. Microbiology.

[29]  M. Gellert,et al.  Cloning and simplified purification of Escherichia coli DNA gyrase A and B proteins. , 1984, The Journal of biological chemistry.

[30]  G. Ames,et al.  Repetitive extragenic palindromic sequences: A major component of the bacterial genome , 1984, Cell.

[31]  E. Gilson,et al.  A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. , 1984, The EMBO journal.

[32]  J. Clément,et al.  A novel intercistronic regulatory element of prokaryotic operons , 1982, Nature.

[33]  W. Staudenbauer,et al.  DNA gyrase: affinity chromatography on novobiocin-Sepharose and catalytic properties. , 1981, Nucleic acids research.

[34]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[35]  E. Gilson,et al.  The BIME family of bacterial highly repetitive sequences. , 1991, Research in microbiology.

[36]  Eric Gilson,et al.  Palindromic units: a case of highly repetitive DNA sequences in bacteria , 1987 .