Proteins mediating DNA loops effectively block transcription

• Type of Material: Article
• Authors: Zsuzsanna Voros, Emory University; Yan Yan, Emory University; Daniel T. Kovari, Emory University; Laura Finzi, Emory University; David Dunlap, Emory University
• Language: English
• Date: 2017-01-01
• Publisher: Wiley
• Publication Version: Final Published Version
• Copyright Statement: © 2017 The Protein Society.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1002/pro.3156
• Title of Journal or Parent Work: Protein Science
• ISSN: 0961-8368
• Volume: 26
• Issue: 7
• Start Page: 1427
• End Page: 1438
• Keywords: transcription elongation; scanning force microscopy; RNAP; DNA looping; magnetic tweezers; lac repressor protein
• Research Categories: Physics, Molecular; Biology, Genetics

Abstract

Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.