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Journal of Clinical Microbiology, September 2001, p. 3423-3424, Vol. 39, No. 9
0095-1137/01/$04.00+0 DOI: 10.1128/JCM.39.9.3423-3424.2001
LETTERS TO THE EDITOR
IS6110 Insertions in Mycobacterium
tuberculosis: Predominantly into Coding Regions
 |
LETTER |
We read with interest the recent publication by Benjamin et al.
(2) regarding the characterization of IS6110
insertion sites in the direct repeat (DR) region of Mycobacterium
tuberculosis. This topical and relevant study described the
dissection of a single molecular event leading to an altered DNA
fingerprint pattern that was detected by two different strain
genotyping systems, namely, IS6110 DNA fingerprinting and
spoligotyping. It was shown that a single IS6110
transposition event in the DR region disrupted one of the spoligotyping
primer regions, thereby resulting in simultaneous changes in the
IS6110 fingerprint and spoligotype pattern. The authors
rightly recommended that some caution should be applied to the
interpretation of similar, but nonidentical, IS6110 DNA
fingerprint and spoligotype patterns. In addition, the results
corroborated the occurrence of IS6110 preferential integration loci, as previously identified by a number of investigators (3, 5, 7).
However, we would like to question the statement by the authors that
"nearly all IS6110 insertions are between open reading frames..." The assertion was not referenced, but we assume that this statement was occasioned by the original reporting of
IS6110 distribution in the reference strain M. tuberculosis H37Rv (4), which states that the
majority of insertions occur within noncoding regions. However, this
early conclusion was restricted to the analysis of a very limited
number of insertion sites in M. tuberculosis H37Rv. Since
this preliminary characterization, numerous investigators (ourselves
included) have characterized IS6110 integration loci in
clinical isolates (1, 3, 5, 7). Our analysis of insertion
locus sequence data collated from various sources demonstrated that 42 of 66 discrete IS6110 insertion sites (58%) occurred within coding regions of the M. tuberculosis genome (1, 5,
7). We performed an updated analysis (inclusive of data
published in the literature and DNA sequence databases since our
original report), the results of which demonstrated that of 95 discrete IS6110 integration loci identified (excluding multiple
insertions into the DR and ipl locus), 60% (57 of 95 sites)
occur within coding regions, 33% (31 of 95 sites) occur within
intergenic regions (Fig. 1), and 7% (7 of 95 sites) did not map to the M. tuberculosis H37Rv
genome. This strengthens our conclusion (5) that
IS6110 frequently disrupts coding regions. In addition, the
revised map (Fig. 1) of the genome distribution of
IS6110 insertions highlights the existence of numerous
preferential integration sites in addition to those previously
described (2, 3, 5, 7).
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FIG. 1.
Distribution of IS6110 insertion loci
relative to open reading frames (ORFs) of the Mycobacterium
tuberculosis H37Rv genome. The ORF numbers of the disrupted genes
are indicated in bold, while the intergenic insertions are represented
by two ORF numbers separated by a colon. The M. tuberculosis
H37Rv insertion sites are underlined. Multiple integration sites within
a single gene or intergenic region are denoted by multiple entries with
the same name. The relative positions of the DR region and the
ipl locus are shown, and the positions of regions deleted
from M. tuberculosis H37Rv relative to M. bovis
are indicated by their RvD numbers.
|
|
In the light of the limited structural gene diversity within M. tuberculosis strains, it has been suggested that IS6110
may be capable of driving genome evolution (6). Therefore,
while the biological significance of our finding remains to be
elucidated, it nonetheless deserves further attention, as it clearly
demonstrates the potential for the IS6110 element to impact
on strain phenotype by gene disruption. Finally, our approach
highlights the value of collation of data from various sources, and we
advocate the establishment of a web-based genome map of
IS6110 integration sites to facilitate this endeavor.
Authors' Reply
We acknowledge the extensive work by Drs. Sampson, Warren,
Richardson, van der Spuy, and van Helden to characterize the
IS6110 insertion sites within the M. tuberculosis
genome. The statement that "nearly all IS6110 insertions
are between open reading frames ..." was derived from the
original reporting of IS6110 distribution that focused
primarily on the H37Rv strain of M. tuberculosis. We
appreciate the letter correcting our error.
| |
FOOTNOTES |
*
Phone: (27) 21 9389401 Fax: (27) 21 9317810 E-mail: PVH{at}gerga.sun.ac.za
| |
REFERENCES |
| 1.
|
Beggs, M. L.,
K. D. Eisenach, and M. D. Cave.
2000.
Mapping of IS6110 insertion sites in two epidemic strains of Mycobacterium tuberculosis.
J. Clin. Microbiol.
38:2923-2928[Abstract/Free Full Text].
|
| 2.
|
Benjamin, W. H., Jr.,
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2001.
Identification of a contaminating Mycobacterium tuberculosis strain with a transposition of an IS6110 insertion element resulting in an altered spoligotype.
J. Clin. Microbiol.
39:1092-1096[Abstract/Free Full Text].
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| 3.
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Fang, Z., and K. J. Forbes.
1997.
A Mycobacterium tuberculosis IS6110 preferential locus (ipl) for insertion into the genome.
J. Clin. Microbiol.
35:479-481[Abstract].
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| 5.
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Sampson, S. L.,
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Tuberc. Lung Dis.
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| 6.
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Sreevatsan, S.,
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Proc. Natl. Acad. Sci. USA
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| 7.
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Warren, R. M.,
S. L. Sampson,
M. Richardson,
G. D. Van Der Spuy,
C. J. Lombard,
T. C. Victor, and P. D. van Helden.
2000.
Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity.
Mol. Microbiol.
37:1405-1416[CrossRef][Medline].
|
| | | | |
Samantha Sampson
Robin Warren
Madalene Richardson
Gian van der Spuy
Paul van Helden*
Department of Medical Biochemistry
P.O. Box 19063
University of Stellenbosch Faculty of
Health Sciences
Tygerberg, Cape Town, South Africa 7505
|
| | | | |
Nancy Dunlap
William H. Benjamin Jr.
The University of Alabama at Birmingham
Birmingham, Alabama
|
Journal of Clinical Microbiology, September 2001, p. 3423-3424, Vol. 39, No. 9
0095-1137/01/$04.00+0 DOI: 10.1128/JCM.39.9.3423-3424.2001
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