Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

Frank Bürmann,Louise F.H Funke,Jason W Chin,Jan Löwe

doi:10.1016/j.molcel.2021.10.011

Frank Bürmann, Louise F.H Funke + Show 2 more

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https://doi.org/10.1016/j.molcel.2021.10.011

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Journal: Molecular Cell	Publication Date: Nov 4, 2021
Citations: 55	License type: cc-by

Affiliation: MRC Laboratory of Molecular Biology

Abstract

SummaryThe ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.

Highlights

Associations between molecules due to their topology are known as mechanical bonds (Stoddart, 2009)
At the core of structural maintenance of chromosomes (SMC) complexes—such as cohesin, condensin, Smc5-6, Smc-ScpAB, MksBEF, and MukBEF—is a tripartite ring composed of two SMC proteins and a kleisin
Using electron cryomicroscopy single-particle analysis, we discovered that MukBEF entraps two distinct DNA double helices when bound to the unloader MatP

Summary

Introduction

Associations between molecules due to their topology are known as mechanical bonds (Stoddart, 2009). In eukaryotes as well as prokaryotes, ring-like structural maintenance of chromosomes (SMC) complexes are thought to structure chromosomes via mechanical bonds with DNA ( referred to as ‘‘DNA entrapment’’) and active DNA loop extrusion (Davidson and Peters, 2021; Hassler et al, 2018; Ma€kela€ and Sherratt, 2020a; Nasmyth, 2001; Yatskevich et al, 2019). These activities have been suggested to enable or facilitate processes such as lengthwise condensation of chromosomes, sister chromatid cohesion, regulation of interactions between enhancers and distant promoters, disentangling of replicated DNA by topoisomerases, DNA recombination, and DNA double-strand break repair. The neck-bound SMC is designated n-SMC (nu for neck), and the cap-bound subunit is designated k-SMC (kappa for cap)

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