Translation Inhibiting Antibiotics Induce an asRNA Regulating Purine Metabolism in S. pneumoniae TIGR4 via an ISL3 Insertion Derived Hybrid Promoter

Abstract

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 Streptococcus 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 (ISL3) immediately downstream. A survey of S. pneumoniae genomes shows the promoter is present in several phylogenetically distinct strain clusters. However, other common laboratory strains of S. pneumoniae lack the promoter, 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.