Structural and mechanistic basis of σ-dependent transcriptional pausing

Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle S, Su, Min, Yin, Zhou, Winkelman, Jared T, Kinney, Justin B, Ebright, Richard H, Nickels, Bryce E (June 2022) Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences of USA, 119 (23). e2201301119. ISSN 0027-8424

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Abstract

SignificanceThe paradigmatic example of factor-dependent pausing in transcription elongation is σ-dependent pausing, in which sequence-specific σ-DNA interaction with a - 10 element-like sequence in a transcribed region results in pausing of a σ-containing transcription elongation complex. It has been proposed that σ-dependent pausing involves DNA scrunching, and that sequences downstream of the -10 element-like sequence modulate DNA scrunching. Here, using site-specific protein-DNA photocrosslinking, high-throughput sequencing, and cryoelectron microscopy structure determination, we show directly that σ-dependent pausing involves DNA scrunching, we define a consensus sequence for formation of a stable scrunched paused complex that is identical to the consensus sequence for pausing in initial transcription, and we identify positions of DNA scrunching on DNA nontemplate and template strands. Our results illuminate the structural and mechanistic basis of σ-dependent transcriptional pausing.

Item Type:	Paper
Subjects:	bioinformatics Investigative techniques and equipment > microscopy > Cryo-electron microscopy bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > RNA polymerase organism description > bacteria organism description > bacteria > escherichia coli Investigative techniques and equipment > microscopy
CSHL Authors:	Kooshkbaghi, Mahdi Tareen, Ammar Kinney, Justin B.
Communities:	CSHL labs > Kinney lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	7 June 2022
Date Deposited:	08 Jun 2022 19:18
Last Modified:	16 Jan 2024 21:20
PMCID:	PMC9191641
URI:	https://repository.cshl.edu/id/eprint/40652

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