Supercoiling Effects on Short-Range DNA Looping in E. Coli

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Oct 27

PMID 27783696

Citations 9

Authors

Lauren S Mogil

Nicole A Becker

L James Maher 3rd

Affiliations

Soon will be listed here.

Abstract

DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E. coli strains characterized by different levels of global supercoiling: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10). DNA looping in each strain was measured by assaying repression of the endogenous lac operon, and repression of ten reporter constructs with DNA loop sizes between 70-85 base pairs. Our data are most simply interpreted as supporting the hypothesis that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.

Citing Articles

Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor.

Becker N, Peters J, Lewis E, Daby C, Clark K, Maher 3rd L Nucleic Acids Res. 2024; 52(16):9996-10004.

PMID: 39077947 PMC: 11381355. DOI: 10.1093/nar/gkae656.

High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria.

Becker N, Peters J, Maher 3rd L Methods Mol Biol. 2024; 2819:103-123.

PMID: 39028504 DOI: 10.1007/978-1-0716-3930-6_6.

Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.

Starr C, Bryant Z, Spakowitz A Biophys J. 2022; 121(10):1949-1962.

PMID: 35421389 PMC: 9199097. DOI: 10.1016/j.bpj.2022.04.009.

Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters.

Forquet R, Pineau M, Nasser W, Reverchon S, Meyer S mSystems. 2021; 6(4):e0097821.

PMID: 34427530 PMC: 8422995. DOI: 10.1128/mSystems.00978-21.

Dependence of DNA looping on culture density.

Peters J, Rao V, Becker N, Maher 3rd L Int J Biochem Mol Biol. 2019; 10(3):32-41.

PMID: 31523479 PMC: 6737385.

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