title: New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv.
abstract: The genome sequence of Mycobacterium tuberculosis H37Rv was found to contain 56 loci with homology to insertion sequences (ISs). As well as the previously described IS6110, IS1081, IS1547 and IS-like elements, new ISs belonging to the IS3, IS5, IS21, IS30, IS110, IS256 and ISL3 families were identified. In addition, six ISs created a grouping of their own to form a new family (the IS1535 family). Elements with similarity to ISs in other actinomycetes were identified, suggesting the movement of ISs between related genera. The location of ISs on the chromosome revealed that an approximately 600 kb region close to the origin of replication lacks ISs, pointing to the possible detrimental effect of insertions in this area. Analysis of the distribution of ISs through the tubercle strains Mycobacterium africanum, M. microti, M. bovis, M. bovis BCG Pasteur, M. tuberculosis H37Ra, M. tuberculosis CSU#93 and 29 clinical isolates revealed that only IS1532, IS1533, 1S1534, and IS1561' were absent from some of the strains tested. A novel repeated sequence, the REP13E12 family, is described that is present in seven copies on the M. tuberculosis H37Rv chromosome and which contains a probable phage attachment site. This study therefore offers an insight into the possible role of ISs and repetitive elements in the evolution of the M. tuberculosis genome, as well as identifying genetic markers that may be useful for phylogenetic and epidemiological analysis of the tubercle complex.
authors.affiliation: Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue Dr Roux, 75724 Paris, Cedex 15, France.
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Gordon
authors.affiliation: Hópital Ambroise Paré, 9 Avenue Chalres-de-Gaulle, 92104 Boulogne Cedex, France.
authors.forename: Beate
authors.initials: B
authors.lastname: Heym
authors.affiliation: The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB 10 1SA, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB 10 1SA, UK.
authors.forename: Bart
authors.initials: B
authors.lastname: Barrell
authors.affiliation: Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue Dr Roux, 75724 Paris, Cedex 15, France.
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D008242:Lysogeny; D008969:Molecular Sequence Data; D009160:Mycobacteriophages / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D016133:Polymerase Chain Reaction / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012984:Software; D014376:Tuberculosis / Q000382:microbiology
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial