title: Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome.
abstract: The naturally transformable, Gram-negative bacterium Haemophilus influenzae Rd preferentially takes up DNA of its own species by recognizing a 9-base pair sequence, 5'-AAGTGCGGT, carried in multiple copies in its chromosome. With the availability of the complete genome sequence, 1465 copies of the 9-base pair uptake site have been identified. Alignment of these sites unexpectedly reveals an extended consensus region of 29 base pairs containing the core 9-base pair region and two downstream 6-base pair A/T-rich regions, each spaced about one helix turn apart. Seventeen percent of the sites are in inverted repeat pairs, many of which are located downstream to gene termini and are capable of forming stem-loop structures in messenger RNA that might function as signals for transcription termination.
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: H O
authors.initials: HO
authors.lastname: Smith
authors.forename: J F
authors.initials: JF
authors.lastname: Tomb
authors.forename: B A
authors.initials: BA
authors.lastname: Dougherty
authors.forename: R D
authors.initials: RD
authors.lastname: Fleischmann
authors.forename: J C
authors.initials: JC
authors.lastname: Venter
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D016384:Consensus Sequence; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D006193:Haemophilus influenzae / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D014158:Transcription, Genetic; D014169:Transformation, Bacterial
chemical_list: D004269:DNA, Bacterial; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012333:RNA, Messenger