PT  - JOURNAL ARTICLE
AU  - Chirangini Pukhrambam
AU  - Vadim Molodtsov
AU  - Mahdi Kooshbaghi
AU  - Ammar Tareen
AU  - Hoa Vu
AU  - Kyle S. Skalenko
AU  - Min Su
AU  - Yin Zhou
AU  - Jared T. Winkelman
AU  - Justin B. Kinney
AU  - Richard H. Ebright
AU  - Bryce E. Nickels
TI  - Structural and mechanistic basis of σ-dependent transcriptional pausing
AID  - 10.1101/2022.01.24.477500
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.24.477500
4099  - http://biorxiv.org/content/early/2022/01/25/2022.01.24.477500.short
4100  - http://biorxiv.org/content/early/2022/01/25/2022.01.24.477500.full
AB  - In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family, and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR’ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and that σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2-3 bp--and only that state--is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3’ end), which is identical to the consensus for pausing in initial transcription, and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryo-EM structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.Competing Interest StatementThe authors have declared no competing interest.