Chapter 13 : Repetitive DNA in the Mycobacterium tuberculosis Complex

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Repetitive DNA is universally present in bacterial and eukaryotic genomes, with two major classes usually distinguished: interspersed repeats, such as mobile genetic elements, and tandem repeats (TRs). Although many repetitive-DNA sequences, especially mobile and extragenic elements, were thought to be primarily parasitic, recent work suggests that coadaptations between them and host genomes may occur. This chapter (i) describes different types of sequences, (ii) discusses their relative impacts on genetic variation and related functions, and finally (iii) addresses their exploitation for molecular epidemiology, evolution, and population genetics. It is therefore tempting to speculate that induction of REP13E12 in response to DNA damage may also induce the integrated prophage elements. A range of preferential integration loci for IS6110 have subsequently been identified, including the intergenic dnaA-dnaN region and the RvD2 locus. The genome contains at least four families of repetitive DNA, contributing approximately 2% to the total genome size. The LEPREP sequences are pseudogenes with similarity to transposases and the maturases of class II introns, enzymes that catalyze DNA transposition. It is also possible that mycobacterial interspersed repetitive units (MIRUs) exert no particular function and may therefore be considered as selfish DNA, as suggested for other repeated DNA sequences. Variation of repetitive DNA sequences is key to the molecular epidemiological tools that have had such a dramatic impact on the understanding of population structure and evolution.

Citation: Gordon S, Supply P. 2005. Repetitive DNA in the Mycobacterium tuberculosis Complex, p 191-202. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch13

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Restriction Fragment Length Polymorphism
Mobile Genetic Elements
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Image of Figure 1
Figure 1

Positions of 46 VNTR repeat loci on the H37Rv chromosome. Arabic numbers designate positions in kilobase pairs. Numbers in italics and in plain style correspond to microsatellites (repeat units with a length of 10 bp or less) and minisatellites (repeat units with a length of more than 10 bp), respectively. See the text for references.

Citation: Gordon S, Supply P. 2005. Repetitive DNA in the Mycobacterium tuberculosis Complex, p 191-202. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch13
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Image of Figure 2
Figure 2

IS-mediated deletion mechanism. Two IS elements are shown in the same orientation, flanked by 3-bp DRs. Homologous recombination between the IS elements leads to looping out and deletion of the intervening sequence. The remaining IS element now appears without direct repeats. Homologous recombination between proximal IS elements appears to be a major force in shaping the genomes of the complex.

Citation: Gordon S, Supply P. 2005. Repetitive DNA in the Mycobacterium tuberculosis Complex, p 191-202. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch13
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Image of Figure 3
Figure 3

DNA sequence alignment of orthologous intergenic regions in and H37Rv, indicating the position of the MIRU in the sequence. The sequences of the and genes (and in H37Rv, respectively) and their encoded products are shown. Duplicated nucleotides surrounding the MIRU insertion site are underlined. The stars correspond to stop codons. The “n” symbol indicates the presence of VNTRs in this locus. Translational coupling sites are apparent targets for MIRU insertion. This insertion predictably places the MIRU ORF under translational control of the upstream genes.

Citation: Gordon S, Supply P. 2005. Repetitive DNA in the Mycobacterium tuberculosis Complex, p 191-202. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch13
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Table 1

IS elements in H37Rv

Citation: Gordon S, Supply P. 2005. Repetitive DNA in the Mycobacterium tuberculosis Complex, p 191-202. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch13

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