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

• Published in: PloS one Vol. 11; no. 10; p. e0165306
• Main Authors: Mogil, Lauren S, Becker, Nicole A, Maher, 3rd, L James
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26-10-2016; Public Library of Science (PLoS)
• Subjects: Analysis; Antibiotics; Base pairs; Biochemistry; Biology and Life Sciences; Cell division; Deoxyribonucleic acid; DNA; DNA Gyrase - genetics; DNA Gyrase - metabolism; DNA Topoisomerases, Type I - genetics; DNA Topoisomerases, Type I - metabolism; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA, Superhelical - chemistry; DNA, Superhelical - genetics; DNA, Superhelical - metabolism; E coli; Electrophoresis, Agar Gel; Enzymes; Escherichia coli; Escherichia coli - genetics; Gene expression; Gene regulation; Genes; Genes, Reporter; Genetic aspects; Genetic research; Hypotheses; Lac Operon - genetics; Lactose; Lactose operon; Medicine; Medicine and Health Sciences; Model testing; Molecular biology; Mutation; Nucleic Acid Conformation; Proteins; Research and Analysis Methods; RNA polymerase; Supercoiling; Superhelical DNA; United States > US; Minnesota
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0165306

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.