Evidence for a compact σ70 conformation in vitro and in vivo
Khalil Joron,
Joanna Zamel,
Nir Kalisman,
Eitan Lerner
Affiliations
Khalil Joron
Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
Joanna Zamel
Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
Nir Kalisman
Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
Eitan Lerner
Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Corresponding author
Summary: The initiation of transcription in Escherichia coli (E. coli) is facilitated by promoter specificity factors, also known as σ factors, which may bind a promoter only as part of a complex with RNA polymerase (RNAP). By performing in vitro cross-linking mass spectrometry (CL-MS) of apo-σ70, we reveal structural features suggesting a compact conformation compared to the known RNAP-bound extended conformation. Then, we validate the existence of the compact conformation using in vivo CL-MS by identifying cross-links similar to those found in vitro, which deviate from the extended conformation only during the stationary phase of bacterial growth. Conclusively, we provide information in support of a compact conformation of apo-σ70 that exists in live cells, which might represent a transcriptionally inactive form that can be activated upon binding to RNAP.
