Identification and characterization of a new DNA secondary structure in the genome of Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis, is responsible for over 10 million new infections each year and remains the leading cause of death from a single infectious agent. The increasing prevalence of antibiotic-resistant strains has reinforced the need to identify new therapeutic targets. One promising line of research involves non-B DNA structures, such as G-quadruplexes, G-hairpins, and I-motifs, which are known to influence diverse biological processes in many species. This project began with a genome-wide investigation of the M. tuberculosis genome to identify sequences capable of adopting such secondary structures. Through this analysis, we discovered CORE-1, a G-rich nucleotide pattern highly repeated within the genome. Biophysical studies demonstrated that CORE-1 can fold into a stable G-hairpin. Notably, CORE-1 is predominantly associated with pe_pgrs genes and occurs abundantly in pathogenic mycobacteria, whereas it is rarely observed in non-pathogenic species or in humans. To further investigate the potential function of CORE-1, we searched for interacting proteins and identified Rv1488 as a specific binder of the CORE-1 G-hairpin. Given that Rv1488 had not been previously characterized, we initiated its functional analysis to explore its possible role both independently and in association with CORE-1. In summary, this work highlights CORE-1 as a novel, repetitive structural motif enriched in pathogenic M. tuberculosis and provides initial insights into one of its protein partners. While these findings represent a first step toward understanding its biological role, further functional characterisation of CORE-1 will be essential to shed light on its physiological and pathological significance for mycobacteria. Importantly, its selective abundance in pathogenic species, and absence in humans, underscores its potential as a promising target for the development of new therapeutic strategies.