Submitted to: Biomed Central (BMC) Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2003
Publication Date: 5/9/2003
Citation: Bannantine, J.P., Zhang, Q., Li, L., Kapur, V. 2003. Genomic hemogeneity between mycobacterium avium and mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. Biomed Central (BMC) Microbiology. Interpretive Summary: There are two species of bacteria, Mycobacterium avium and Mycobacterium paratuberculosis, that are highly similar in the sequence of their DNA, but are very different in terms of their characteristics. M. paratuberculosis is the cause of Johne's disease whereas M. avium is an organism in the environment that is also a pathogen of some birds. In this communication, we demonstrated conclusively the similarity of the DNA of the organisms through a careful analysis of a region in the DNA where replication begins. This region is termed the origin of replication. We amplified this region in M. paratuberculosis using primers designed from M. avium. We then analyzed the M. paratuberculosis region through a series of analyses. These analyses consisted of locating the genes, locating the start point for DNA replication, and comparing the sequence to that obtained for M. avium. In addition, we expanded our comparisons to regions of the DNA outside the origin of replication region. The findings from these analyses demonstrate why it is so difficult to develop a diagnostic test that is specific to only Mycobacterium paratuberculosis. Unfortunately, while a solid basis for genetic similarity was established, no conclusions could be drawn from the data regarding the diverse growth rates of these two species.
Technical Abstract: Background: Mycobacterium avium subspecies avium (M. avium) is frequently encountered in the environment, but also causes infections in animals and immunocompromised patients. In contrast, Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) is a slow-growing organism that is the causative agent of Johne's disease in cattle and chronic granulomatous infections in a variety of other ruminant hosts. Yet we show that despite their divergent phenotypes and the diseases they present, the genomes of M. avium and M. paratuberculosis share greater than 97% nucleotide identity. Results: To characterize genome similarity between these two subspecies as well as attempt to understand their different replication rates, we designed oligonucleotide primers from M. avium sequence to amplify 15 minimally overlapping fragments of M. paratuberculosis genomic DNA encompassing the chromosomal origin of replication. These strategies resulted in the successful amplification and sequencing of a contiguous 11-kb fragment containing the putative Mycobacterium paratuberculosis origin of replication (oriC). This fragment contains 11 predicted open reading frames, seven of which have significant homology with proteins involved in basic cellular processes such as replication, while the other four have significant homology with hypothetical proteins from Mycobacterium tuberculosis. The gene order in this region conforms to the conserved order in the oriC locus of several other Gram-positive bacteria. In addition, a GC skew analysis identified the origin of chromosomal replication which lies between the genes dnaA and dnaN. The presence of multiple DnaA boxes and the ATP-binding site in dnaA were also found in M. paratuberculosis. A comparison of this region of the M. paratuberculosis genome with M. avium shows a slightly higher level of nucleotide identity (98%) than that found in other regions of the genome. Conclusions: Collectively, these data suggest that genetic differences alone may not account for the diverse replication rates or phenotypes observed between M. avium and M. paratuberculosis subspecies.