Computational discovery of conserved RNA structures and functional characterization of a structured lncRNA in Leishmania braziliensis

<i>Leishmania</i> parasites alternate between hosts, facing environmental changes that demand rapid gene expression adaptation. Lacking canonical RNA polymerase II promoters, transcription in these eukaryotes is polycistronic, with gene regulation occurring post-transcriptionally. Although non-coding RNAs (ncRNAs) have been identified in <i>Leishmania</i> transcriptomes, their functions remain unclear. Recognizing RNA structure's importance, we performed a genome-wide alignment of <i>L. braziliensis</i> and related species, identifying conserved RNA structures, 38 of which overlap with known ncRNAs. One such ncRNA, <i>lncRNA45</i>, was functionally characterized. Using a knockout cell line, we demonstrated that <i>lncRNA45</i> is crucial for parasite fitness. Reintroducing the wild type <i>lncRNA45</i> restored fitness, while a version with a single nucleotide substitution in the structured region did not. This mutation also altered RNA-protein interactions. These findings suggest that <i>lncRNA45</i>'s regulatory role and protein interactions rely on its secondary structure. This study highlights the significance of structured lncRNAs in <i>Leishmania</i> biology and their potential as therapeutic targets. Further research into these ncRNAs could uncover new parasite regulation mechanisms and inspire novel treatment strategies.