title: Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences.
abstract: In the present study, we developed a method for detecting sequences whose similarity to a target sequence is statistically significant and we examined the distribution of these sequences in the E. coli K-12 genome. Target sequences examined are as follows: (i) short repeat: Crossover hot-spot instigator (Chi) sequence, replication termination (Ter) sequence, and DnaA binding sequence (DnaA box); (ii) potential stem-loop structure repeats: palindromic unit (PU), boxC sequences, and intergenic repeat unit (IRU); (iii) potential RNA coding repeats: rRNAs, PAIR, TRIP, and QUAD; and (iv) potential protein coding repeats: insertion elements (ISs) and Long Direct Repeats (LDRs). We also examined the distribution of these sequences on leading and lagging strands. We obtained another four statistically significant LDR sequences with more than 187 bp matched to LDR-A near the LDR loci, suggesting that these regions might be used as high recombination hot spots for LDR. Adaptation of individual LDRs to E. coli genome is also discussed on the basis of codon usage.
authors.affiliation: Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Ikoma, Japan.
authors.forename: Mitsuoki
authors.initials: M
authors.lastname: Kawano
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Masuda
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ara
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D004251:DNA Transposable Elements; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D012335:RNA, Ribosomal / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria; D012335:RNA, Ribosomal