Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex
Jin Young Kang,
Paul Dominic B Olinares,
James Chen,
Elizabeth A Campbell,
Arkady Mustaev,
Brian T Chait,
Max E Gottesman,
Seth A Darst
Affiliations
Jin Young Kang
Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
Paul Dominic B Olinares
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York City, United States
James Chen
Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
Elizabeth A Campbell
Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
Arkady Mustaev
Public Health Research Institute, Newark, United States; Department of Microbiology and Molecular Genetics, Rutgers Biomedical and Health Sciences, Newark, United States; Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, United States
Brian T Chait
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York City, United States
Max E Gottesman
Department of Microbiology and Immunology, Columbia University Medical Center, New York City, United States
Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β’ subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.
