RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes

• Type of Material: Article
• Authors: Yue Lu, Emory University; Zsuzsanna Voros, Emory University; Gustavo Borjas, Emory University; Cristin Hendrickson, Emory University; Keith Shearwin, University of Adelaide; David Dunlap, Emory University; Laura Finzi, Emory University
• Language: English
• Date: 2022-08-01
• Publisher: WILEY
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2022 Federation of European Biochemical Societies.
• Final Published Version (URL): http://dx.doi.org/10.1002/1873-3468.14447
• Title of Journal or Parent Work: FEBS LETTERS
• Volume: 596
• Issue: 16
• Start Page: 1994
• End Page: 2006
• Grant/Funding Information: This work was supported by the National Institutes of Health to L.F. (R01 GM084070) and Australian Research Council to KS (DP150103009).
• Keywords: RIGHT OPERATOR; Biophysics; atomic force microscopy; BINDING; Biochemistry & Molecular Biology; bacteriophage repressors; PURIFICATION; TRANSCRIPTIONAL INTERFERENCE; CI; roadblock efficiency; Life Sciences & Biomedicine; LAMBDA-REPRESSOR; Cell Biology; topology; PROTEINS; transcription; P-RM; Science & Technology; PHAGE-LAMBDA; GENE-REGULATION
• Research Categories: Chemistry, Biochemistry; Biology, Genetics; Biology, Cell; Biology, Molecular

Abstract

DNA can act as a scaffold for the cooperative binding of protein oligomers. For example, the phage 186 CI repressor forms a wheel of seven dimers wrapped in DNA with specific binding sites, while phage λ CI repressor dimers bind to two well-separated sets of operators, forming a DNA loop. Atomic force microscopy was used to measure transcription elongation by Escherichia coli RNA polymerase (RNAP) through these protein complexes. 186 CI, or λ CI, bound along unlooped DNA negligibly interfered with transcription by RNAP. Wrapped and looped topologies induced by these scaffolded, cooperatively bound repressor oligomers did not form significantly better roadblocks to transcription. Thus, despite binding with high affinity, these repressors are not effective roadblocks to transcription.