Mutation analysis of the latency-associated gene Rv2660c in Mycobacterium tuberculosis clinical isolates from South Sulawesi, Indonesia: In-silico prediction of implications for antigenicity.

BACKGROUND: The Rv2660c gene, associated with Mycobacterium tuberculosis (Mtb) latency and survival, is considered highly conserved. However, genetic variations may influence pathogenicity and drug resistance. This study investigates mutations in the Rv2660c gene and their potential impact on protein structure and function.

MATERIALS AND METHODS: The Rv2660c gene from 40 clinical isolates was analysed using PCR amplification and sequencing. Structural and immunological analyses were conducted using I-TASSER, B-cell epitope prediction tools, T-cell epitope prediction, and molecular docking simulations to evaluate the effects of mutations on protein structure and immune interactions.

RESULTS: A T>C mutation at position 139 was identified in one isolate (MDR094R, NCBI GenBank Accession PV544294), resulting in a phenylalanine-to-leucine substitution at position 47 (Phe47Leu). This variation was also found in several other strains, M. tuberculosis strain SEA14117P6C4 (CP.041797.1.), M. tuberculosis strain 24 (CP136191.1), and M. tuberculosis strain 4 (CP136200.1). Phylogenetic analysis showed that proteins with the Phe47Leu mutation formed a separate cluster, indicating a unique evolutionary trajectory. Structural predictions indicated minimal changes in the protein structure, with slight alterations near the mutation site. Immunological analysis revealed that the mutation affected both continuous and discontinuous B-cell epitopes, altering their conformation and length. T-cell epitope predictions showed reduced binding affinity for certain HLA alleles, while some epitopes gained higher affinity. Docking studies confirmed minor changes in binding energy and hydrogen bond interactions.

CONCLUSION: The Phe47Leu mutation in the Rv2660c gene underscores the genetic diversity of M. tuberculosis and may influence antigenicity and immune recognition. These findings highlight the importance of further functional validation to assess the implications of this variation, particularly in the context of vaccine design and host-pathogen interactions.