Affiliation:
1. National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa
2. Biomedical Genomics Center
3. Department of Medicine, University of Minnesota, Minneapolis, Minnesota
Abstract
ABSTRACT
The genetic similarity between
Mycobacterium avium
subsp.
paratuberculosis
and other mycobacterial species has confounded the development of
M. avium
subsp.
paratuberculosis
-specific diagnostic reagents. Random shotgun sequencing of the
M. avium
subsp.
paratuberculosis
genome in our laboratories has shown >98% sequence identity with
Mycobacterium avium
subsp.
avium
in some regions. However, an in silico comparison of the largest annotated
M. avium
subsp.
paratuberculosis
contigs, totaling 2,658,271 bp, with the unfinished
M. avium
subsp.
avium
genome has revealed 27 predicted
M. avium
subsp.
paratuberculosis
coding sequences that do not align with
M. avium
subsp.
avium
sequences. BLASTP analysis of the 27 predicted coding sequences (genes) shows that 24 do not match sequences in public sequence databases, such as GenBank. These novel sequences were examined by PCR amplification with genomic DNA from eight mycobacterial species and ten independent isolates of
M. avium
subsp.
paratuberculosis
. From these analyses, 21 genes were found to be present in all
M. avium
subsp.
paratuberculosis
isolates and absent from all other mycobacterial species tested. One region of the
M. avium
subsp.
paratuberculosis
genome contains a cluster of eight genes, arranged in tandem, that is absent in other mycobacterial species. This region spans 4.4 kb and is separated from other predicted coding regions by 1,408 bp upstream and 1,092 bp downstream. The gene upstream of this eight-gene cluster has strong similarity to mycobacteriophage integrase sequences. The GC content of this 4.4-kb region is 66%, which is similar to the rest of the genome, indicating that this region was not horizontally acquired recently. Southern hybridization analysis confirmed that this gene cluster is present only in
M. avium
subsp.
paratuberculosis
. Collectively, these studies suggest that a genomics approach will help in identifying novel
M. avium
subsp.
paratuberculosis
genes as candidate diagnostic sequences.
Publisher
American Society for Microbiology
Reference26 articles.
1. Comparative Genomics of BCG Vaccines by Whole-Genome DNA Microarray
2. Brosch, R., S. V. Gordon, C. Buchrieser, A. S. Pym, T. Garnier, and S. T. Cole. 2000. Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur. Yeast17:111-123.
3. Brosch, R., A. S. Pym, S. V. Gordon, and S. T. Cole. 2001. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol.9:452-458.
4. Bull, T. J., J. M. Sheridan, H. Martin, N. Sumar, M. Tizard, and J. Hermon-Taylor. 2000. Further studies on the GS element. A novel mycobacterial insertion sequence (IS1612), inserted into an acetylase gene (mpa) in Mycobacterium avium subsp. silvaticum but not in Mycobacterium avium subsp. paratuberculosis. Vet. Microbiol.77:453-463.
5. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
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