Evidence for a compact σ 70 conformation in vitro and in vivo

The initiation of transcription in Escherichia 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 cross-linking mass spectrometry (CL-MS) of apo-σ , 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 CL-MS by identifying cross-links similar to those found , 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-σ that exists in live cells, which might represent a transcriptionally inactive form that can be activated upon binding to RNAP.