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Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences.

Authors :
Kawano M
Kanaya S
Oshima T
Masuda Y
Ara T
Mori H
Source :
DNA research : an international journal for rapid publication of reports on genes and genomes [DNA Res] 2002 Feb 28; Vol. 9 (1), pp. 1-10.
Publication Year :
2002

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.

Details

Language :
English
ISSN :
1340-2838
Volume :
9
Issue :
1
Database :
MEDLINE
Journal :
DNA research : an international journal for rapid publication of reports on genes and genomes
Publication Type :
Academic Journal
Accession number :
11939563
Full Text :
https://doi.org/10.1093/dnares/9.1.1