DNA supercoiling: A regulatory signal for the lambda repressor

• Type of Material: Article
• Authors: Yue Ding, Emory University; Carlo Manzo, Emory University; Geraldine Fulcrand, Florida International University; Fenfei Leng, Florida International University; David Dunlap, Emory University; Laura Finzi, Emory University
• Language: English
• Date: 2014-10-28
• Publisher: National Academy of Sciences
• Publication Version: Final Published Version
• Copyright Statement: © 2014, National Academy of Sciences. All rights reserved.
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.1320644111
• Title of Journal or Parent Work: Proceedings of the National Academy of Sciences
• Volume: 111
• Issue: 43
• Start Page: 15402
• End Page: 15407
• Grant/Funding Information: This work was supported by Human Frontier Science Program Grant RGP0051/2009 (to D.D.) and NIH Grants RGM084070A (to L.F.) and 5SC1HD063059-02 (to F.L.).
• Keywords: CHROMATIN STRUCTURES; Multidisciplinary Sciences; DNA supercoiling; MOLECULE; TRANSCRIPTION; DNA looping; Science & Technology; BINDING; BACTERIOPHAGE-LAMBDA; GENE-REGULATION; transcription; COOPERATIVITY; magnetic tweezer; DYNAMICS; Science & Technology - Other Topics; bacteriophage lambda repressor; CHROMOSOME; ELASTICITY
• Research Categories: Biology, Genetics

Abstract

Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling between them. Furthermore, in single DNA molecules stretched and twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops ranged from -15% or +11%. Finally, in DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation and was essential for DNA looping. Supercoiling-enhanced looping can influence the maintenance of lysogeny in the λ repressor system; it can encode sensitivity to the energy level of the cell and creates independent topological domains of distinct superhelical density.