title: Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases.
abstract: Escherichia coli topoisomerase (Topo) IV is an essential type II Topo that removes DNA entanglements created during DNA replication. Topo IV relaxes (+) supercoils much faster than (-) supercoils, promoting replication while sparing the essential (-) supercoils. Here, we investigate the mechanism underlying this chiral preference. Using DNA binding assays and a single-molecule DNA braiding system, we show that Topo IV recognizes the chiral crossings imposed by the left-handed superhelix of a (+) supercoiled DNA, rather than global topology, twist deformation, or local writhe. Monte Carlo simulations of braid, supercoil, and catenane configurations demonstrate how a preference for a single-crossing geometry during strand passage can allow Topo IV to perform its physiological functions. Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Stone
authors.forename: Zev
authors.initials: Z
authors.lastname: Bryant
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Crisona
authors.forename: Steven B
authors.initials: SB
authors.lastname: Smith
authors.forename: Alexander
authors.initials: A
authors.lastname: Vologodskii
authors.forename: Carlos
authors.initials: C
authors.lastname: Bustamante
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Cozzarelli
mesh_terms: D004261:DNA Replication; D027101:DNA Topoisomerase IV / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology*; D008954:Models, Biological; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013237:Stereoisomerism; D013816:Thermodynamics
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical; D027101:DNA Topoisomerase IV