title: H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.
abstract: Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Higashi
authors.affiliation: Department of Biomedical Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Tobe
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kanai
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Ebru
authors.initials: E
authors.lastname: Uyar
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Shu
authors.initials: S
authors.lastname: Ishikawa
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Naotake
authors.initials: N
authors.lastname: Ogasawara
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.|Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D002876:Chromosomes, Bacterial; D004268:DNA-Binding Proteins / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D036781:Fimbriae Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C529458:FimG protein, E coli; D014157:Transcription Factors; C000607313:ybdO protein, E coli; D036781:Fimbriae Proteins