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    • Tutorial: Using TBDB to find the RD1 pathogenicity region

    Motivation

    The RD1 region is a locus on the M. tb. H37Rv genome that has been found to be conserved in all sequenced M. tb. strains so far, and is absent in the nonpathogenic strain, M. bovis BCG. The region is believed to contain genes involved in pathogenicity [1], including a PE/PPE pair, the secreted antigen ESAT-6, and its interacting partner CFP-10.

    1. To visualize that the RD1 region is indeed present in M. tb. H37Rv, and deleted from M. bovis BCG, go to the TBDB top page and select Tools & analysis -> Comparative analysis -> Synteny

    You will see the genome selection tool:


    2.     On the genome selection tool, select M. tuberculosis H37Rv as the reference genome, and M. bovis BCG as the query. The reference genome shows up as a two-tone vertical gray band. The query genome shows up as a colored (in this case blue) adjacent band. These two bands represent the whole-genome alignment of the H37Rv and BCG genomes. Notice that there are several gaps in the BCG genome relative to H37Rv, suggesting gene loss. The uppermost gap on the BCG genome is the RD1 region:


    3. Use the zoom tool (on the lower left) to enlarge this region and view it in more detail. You can drag and select with the mouse the region of the H37Rv genome that is deleted in BCG. It shows up in red. Click on this selected region and choose "View genes in selected region".


    4. A new tab will open up with the list of genes in the selected region. Click 'Locus' at the upper left of the table to sort the genes by chromosomal location. Note that, judging from the ORF numbers, this indeed appears to be a contiguous set of genes.


    Notice also, that the PE, PPE, ESAT-6, and CFP-10 mentioned in the review [1] genes are in the list.

    5. Select some other mycobacterial genomes to see whether they also contain the RD1 region. We would expect pathogenic mycobacteria, such as all M. tb. strains and M. bovis to contain the intact RD1 region, whereas, if this is indeed a pathogenicity-conferring region, we would expect less pathogenic strains to have all or some of the region deleted.

    Using the genome selection tool, select the other M. tb. strains, M. bovis, both M. avium strains, and M. ulcerans.


    As expected, all M. tb. genomes have the RD1 region intact. M. bovis, a cattle pathogen (turquoise band), which is also capable of infecting humans, has the region intact as well. M. ulcerans and two subspecies of M. avium, which are somewhat less problematic human pathogens, have some or all of RD1 region deleted, consistent with a possible dependence on the RD1 region for pathogenicity.

    Note also that the deletions from M. bovis BCG, M. avium and M. ulcerans are roughly the same as those shown in the figure from the review:

     

    References

    1. Abdallah AM, Gey van Pittius NC, Champion PA, Cox J, Luirink J, Vandenbroucke-Grauls CM, Appelmelk BJ, Bitter W. Nat. Rev. Microbiol. 2007 Nov; 5(11):883-91 [Journal] [PubMed]