Ms1 is a sRNA recently found in mycobacteria and several other actinobacterial species. Ms1 interacts with the RNA polymerase (RNAP) core devoid of sigma factors, which differs from 6S RNA that binds to RNAP holoenzymes containing the primary sigma factor. Here we show that Ms1 is the most abundant non-rRNA transcript in stationary phase in Mycobacterium smegmatis. The accumulation of Ms1 stems from its high-level synthesis combined with decreased degradation. We identify the Ms1 promoter, PMs1 , and cis-acting elements important for its activity. Furthermore, we demonstrate that PNPase (an RNase) contributes to the differential accumulation of Ms1 during growth. Then, by comparing the transcriptomes of wt and ΔMs1 strains from stationary phase, we reveal that Ms1 affects the intracellular level of RNAP. The absence of Ms1 results in decreased levels of the mRNAs encoding β and β' subunits of RNAP, which is also reflected at the protein level. Thus, the ΔMs1 strain has a smaller pool of RNAPs available when the transcriptional demand increases. This contributes to the inability of the ΔMs1 strain to rapidly react to environmental changes during outgrowth from stationary phase.

Department of Genomics and Bioinformatics Institute of Molecular Genetics Czech Academy of Sciences Prague Czech Republic

Faculty of Nuclear Science and Physical Engineering Department of Nuclear Chemistry Czech Technical University Prague Prague Czech Republic

Faculty of Science Department of Cell Biology Charles University Prague Czech Republic

Laboratory of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences Prague Czech Republic

Laboratory of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences Prague Czech Republic Faculty of Science Department of Genetics and Microbiology Charles University Prague Czech Republic

Military Health Institute Military Medical Agency Prague Czech Republic

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