Translation Inhibiting Antibiotics Induce a Strain Specific asRNA Regulating Purine Metabolism in S. pneumoniae TIGR4

Translation inhibiting antibiotics (TIA) are an important class of antibiotics that elicit a wide variety of transcriptional responses. In this work we characterize the transcriptional responses of S. pneumoniae TIGR4, via RNA-seq, 5’-, and 3’-end mapping, to sub-MIC levels of three TIA, chloramphenicol, tetracycline, and kasugamycin. We find that kasugamycin (initiation inhibitor) displays a distinct transcriptomic profile compared to chloramphenicol and tetracycline (elongation inhibitors). However, genes in nucleotide metabolism were consistently downregulated. We also detected a TIA induced antisense transcript complementary to downregulated genes for purine metabolism, which we term SP_0835as. Mutating the promoter for SP_0835as eliminates both induction of SP_0835as, and repression of the complementary genes in response to chloramphenicol. The mutated strain also displays slower growth rates than control strains in conditions that strongly induce SP_0835as, implying biologically relevant activity. Furthermore, the SP_0835as promoter straddles the boundary between SP_0835 and an insertion sequence (IS3) immediately downstream. A survey of diverse S. pneumoniae genomes shows that the promoter is identified in another clinical strain. However, other laboratory strains of S. pneumoniae lack this insertion sequence, SP_0835as expression, and TIA repression of the complementary genes. Thus, SP_0835as represents a nascent RNA regulator that significantly remodels the metabolic response to TIA.