Mycobacterium tuberculosis produces small noncoding RNAs during infections to regulate mycobacterial and eukaryotic gene expression

Abstract

Abstract Mycobacterium tuberculosis (Mtb) presently infects 1/3 of the World’s population, causing both active and latent pulmonary tuberculosis (TB). The pathogenic mechanisms used by Mtb remain poorly defined. We used a small RNA sequencing strategy on RNA extracted from Mtb-infected THP-1 macrophages to characterize the changes in eukaryotic microRNAs (miRs) and identify any mycobacterially-encoded small RNAs. A large number of mammalian microRNAs were differentially regulated during the infection course. Target prediction programs indicated that the mRNAs regulated by the miRs were involved in immune processes, metabolic pathways, cell communication, and developmental events. In addition, 35 Mtb-encoded small RNAs (18–30 nucleotides, mRs) were discovered. Several of the Mtb-encoded mRs were detected in lung tissue biopsies from TB infected monkeys. The 100–150 nucleotides surrounding the 35 Mtb-encoded small RNAs had extensive secondary RNA folding capabilities, including hairpins and antisense stretches more characteristic of eukaryotic pre-microRNAs. Two such small RNAs, Mtb-mR-1 and Mtb-mR-6 were transcribed in Mycobacterium avium complex and Mtb in a hairpin loop and antisense sequence-dependent manner. These mRs were not expressed in Mycobacterium smegmatis, revealing a restricted expression to pathogenic strains. Mtb-encoded mR-1 and mR-6 modulated both prokaryotic and eukaryotic gene expression. Taken together, our findings reveal potentially novel pathogenic processes utilized by Mtb during infections.