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An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3

Author

Listed:
  • Jason M. Schifano

    (Rutgers University, Robert Wood Johnson Medical School)

  • Irina O. Vvedenskaya

    (Waksman Institute, Rutgers University
    Rutgers University)

  • Jared G. Knoblauch

    (Waksman Institute, Rutgers University
    Rutgers University)

  • Ming Ouyang

    (University of Massachusetts Boston)

  • Bryce E. Nickels

    (Waksman Institute, Rutgers University
    Rutgers University)

  • Nancy A Woychik

    (Rutgers University, Robert Wood Johnson Medical School)

Abstract

Toxin–antitoxin (TA) systems are widespread in prokaryotes. Among these, the mazEF TA system encodes an endoribonucleolytic toxin, MazF, that inhibits growth by sequence-specific cleavage of single-stranded RNA. Defining the physiological targets of a MazF toxin first requires the identification of its cleavage specificity, yet the current toolkit is antiquated and limited. We describe a rapid genome-scale approach, MORE (mapping by overexpression of an RNase in Escherichia coli) RNA-seq, for defining the cleavage specificity of endoribonucleolytic toxins. Application of MORE RNA-seq to MazF-mt3 from Mycobacterium tuberculosis reveals two critical ribosomal targets—the essential, evolutionarily conserved helix/loop 70 of 23S rRNA and the anti-Shine-Dalgarno (aSD) sequence of 16S rRNA. Our findings support an emerging model where both ribosomal and messenger RNAs are principal targets of MazF toxins and suggest that, as in E. coli, removal of the aSD sequence by a MazF toxin modifies ribosomes to selectively translate leaderless mRNAs in M. tuberculosis.

Suggested Citation

  • Jason M. Schifano & Irina O. Vvedenskaya & Jared G. Knoblauch & Ming Ouyang & Bryce E. Nickels & Nancy A Woychik, 2014. "An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3," Nature Communications, Nature, vol. 5(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4538
    DOI: 10.1038/ncomms4538
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