Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis

Nucleic Acids Res. 2019 Jul 9;47(12):6488-6503. doi: 10.1093/nar/gkz290.


Ribosomal RNA synthesis in Escherichia coli involves a transcription complex, in which RNA polymerase is modified by a signal element on the transcript, Nus factors A, B, E and G, ribosomal protein S4 and inositol mono-phosphatase SuhB. This complex is resistant to ρ-dependent termination and facilitates ribosomal RNA folding, maturation and subunit assembly. The functional contributions of SuhB and their structural bases are presently unclear. We show that SuhB directly binds the RNA signal element and the C-terminal AR2 domain of NusA, and we delineate the atomic basis of the latter interaction by macromolecular crystallography. SuhB recruitment to a ribosomal RNA transcription complex depends on the RNA signal element but not on the NusA AR2 domain. SuhB in turn is required for stable integration of the NusB/E dimer into the complex. In vitro transcription assays revealed that SuhB is crucial for delaying or suppressing ρ-dependent termination, that SuhB also can reduce intrinsic termination, and that SuhB-AR2 contacts contribute to these effects. Together, our results reveal functions of SuhB during ribosomal RNA synthesis and delineate some of the underlying molecular interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Escherichia coli Proteins / physiology
  • Models, Molecular
  • Phosphoric Monoester Hydrolases / chemistry*
  • Phosphoric Monoester Hydrolases / metabolism
  • Phosphoric Monoester Hydrolases / physiology
  • RNA, Ribosomal / biosynthesis*
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism
  • RNA-Binding Proteins / metabolism
  • Ribosomal Proteins / metabolism
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism
  • Transcription Factors / physiology
  • Transcription, Genetic
  • Transcriptional Elongation Factors / chemistry*
  • Transcriptional Elongation Factors / metabolism
  • Transcriptional Elongation Factors / physiology


  • Bacterial Proteins
  • Escherichia coli Proteins
  • NusB protein, E coli
  • RNA, Ribosomal
  • RNA-Binding Proteins
  • Ribosomal Proteins
  • Transcription Factors
  • Transcriptional Elongation Factors
  • antiterminator proteins, Bacteria
  • nusA protein, E coli
  • ribosomal protein S10
  • ribosomal protein S4
  • Phosphoric Monoester Hydrolases
  • SuhB protein, E coli