Analysis of RNA sequence and structure in key genes of Mycobacterium ulcerans reveals conserved structural motifs and regions with apparent pressure to remain unstructured

Buruli Ulcer is a neglected tropical disease that results in disfiguring and potentially dangerous lesions in affected persons across a wide geographic area, which includes much of West Africa. The causative agent of Buruli Ulcer is Mycobacterium ulcerans, a relative of the bacterium that causes tuberculosis and leprosy. Few therapeutic options exist for the treatment of this disease beyond the main approach, surgical removal, which is frequently ineffective. In this study we analyze six genes in Mycobacterium ulcerans that have high potential of therapeutic targeting. We focus our analysis on a combined in silico and comparative sequence study of potential RNA secondary structure across these genes. The end result of this work was the comprehensive local RNA structural landscape across each of these significant genes. This revealed multiple sites of ordered and evolved RNA structure interspersed between sequences that either have no bias for structure or, indeed, appear to be ordered to be unstructured and (potentially) accessible. In addition to providing data that could be of interest to basic biology, our results provide guides for efforts aimed at targeting this pathogen at the RNA level. We explore this latter possibility through the in silico analysis of antisense oligonucleotides that could be used to target pathogen RNA. Author SummaryBuruli Ulcer is a neglected tropical necrotizing skin disease endemic to West Africa and several other developing countries. The disease is known to be caused by Mycobacterium ulcerans, but the mode of transmission is not well understood. Here, we present findings on the RNA secondary structural landscape of key genes found in its genome and virulence plasmid. We also suggest potential therapeutic strategies to treat this disease that leverage a better understanding of RNA secondary structure. In our analysis we have predicted regions within these genes that are potentially ordered by evolution to have unusual structural stability and likely functionality, as well as regions that lack stable structure and may be unordered for accessibility. These structured regions can act as potential targets of both antisense oligonucleotide and small molecule therapeutics, while the unstructured regions may be most advantageous for only antisense oligonucleotides. Both strategies have been proven to be effective in other bacterial and viral pathogens; therefore, adaptation to this neglected disease may prove beneficial to developing more effective and efficient treatment options. Through our analysis of the RNA secondary structure landscape of key genes in M. ulcerans, we hope to provide other researchers with new avenues for development of novel therapeutic strategies to treat this devastating and neglected disease.