Bacillus Calmette-Guérin ncBCG427 sRNA potentially enhances intracellular bacteria survival by inhibiting apoptosis and inflammatory responses

Bacterial small RNAs (sRNAs) are non-coding RNA types that regulate target mRNA expression. In our previous research, we identified a novel sRNA, ncBCG427, that reduced the invasion of Mycobacterium smegmatis (M. sm) and altered its single-colony morphology. This study examined whether ncBCG427 produces similar effects in Bacillus Calmette-Guérin (BCG) and investigated the underlying mechanisms of its action. Overexpressing ncBCG427 in BCG (BCG_ncBCG427) increased bacterial growth, adhesion, and invasion in A549 cells, improving intracellular survival in THP-1 cells. In THP-1 cells, IL-1β, IL-6, TNF-α, phosphorylated p38, ERK, and p65 levels decreased, while p65 nuclear entry was inhibited, indicating ncBCG427 suppresses inflammation through the MAPK and NF-κB pathways. Additionally, the overexpression strain showed reduced levels of apoptosis. Transcriptomic analysis revealed 121 differentially expressed genes, identifying rpmB and JTY_2977 as key targets. Mutant strains with low expression of these genes (BCG_M-rpmB and BCG_M-JTY2977) exhibited enhanced growth, adhesion, and invasion in A549 cells, along with improved intracellular survival in THP-1 cells. A dual-luciferase reporter assay validated these genes as targets of ncBCG427. Furthermore, BCG_M-rpmB and BCG_M-JTY2977 decreased the expression of inflammatory cytokines and apoptosis, which were restored in complementary strains (BCG_C-rpmB and BCG_C-JTY2977). Our study demonstrated that ncBCG427 improved BCG intracellular survival by targeting rpmB and JTY_2977, suppressing inflammation and apoptosis via the MAPK and NF-κB pathways.