Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli

Authors

  • Mikhail Bubunenko,

    1. Frederick National Laboratory for Cancer Research, Basic Research Program, SAIC-Frederick, Inc., Frederick, MD, USA
    2. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
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    • These authors contributed equally to this work.
  • Donald L. Court,

    Corresponding author
    1. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
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  • Abdalla Al Refaii,

    1. CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, Paris, France
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    • These authors contributed equally to this work.
  • Shivalika Saxena,

    1. Departments of Microbiology and Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
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  • Alexey Korepanov,

    1. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
    Current affiliation:
    1. Institute of Protein Research, Moscow Region, Russia
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  • David I. Friedman,

    1. Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
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  • Max E. Gottesman,

    1. Departments of Microbiology and Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
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  • Jean-Hervé Alix

    Corresponding author
    1. CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, Paris, France
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Summary

Escherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho-dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus-modified transcription complex in rrn operons is as an RNA chaperone insuring co-ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold-sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5′ RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.

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