title: On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.
abstract: The majority of intrinsic rho-independent terminator signals, reported to consist of stable hairpin structures followed by T-rich regions, possess the potential to operate bi-directionally and to induce transcription terminations on both strands of the DNA duplex in Escherichia coli. By using RNAMotif software, we investigated the distributions of termination motifs around the 3'-ends of overlapping and non-overlapping genes at the genomic level. We suggest that the positions of compactly encoded E. coli genes and rho-independent terminators are optimized to terminate the adjoining genes on their antisense strands efficiently, and not to mis-terminate overlapping transcripts, due to their bi-directional properties.
authors.affiliation: Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa 252-8520, Kanagawa, Japan.
authors.forename: Nozomu
authors.initials: N
authors.lastname: Yachie
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Arakawa
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D023061:Gene Order / Q000235:genetics*; D009876:Operon / Q000235:genetics; D012234:Rho Factor / Q000235:genetics
chemical_list: D012234:Rho Factor