Dynamic architecture of the Escherichia coli Structural Maintenance of Chromosomes (SMC) complex, MukBEF

Abstract

Structural Maintenance of Chromosomes (SMC) complexes use a proteinaceous ring-shaped architecture to organise chromosomes, thereby facilitating chromosome segregation. They utilise cycles of ATP binding and hydrolysis to transport themselves rapidly with respect to DNA, a process requiring protein conformational changes and multiple DNA contacts. We have analysed changes in the architecture of the Escherichia coli SMC complex, MukBEF, as a function of nucleotide binding to MukB and subsequent ATP hydrolysis. This builds upon previous work showing that MukF kleisin directs formation of a MukBEF tripartite ring as a consequence of functional interactions between the C-and N-terminal domains of MukF with the MukB head and neck, respectively (Zawadzka et al., 2018). Using both model truncated substrates and complexesAlthough the Escherichia coli SMC complex, MukBEF, shares many aspects of the distinctive SMC complex architecture, its kleisin, MukF, is dimeric, which could potentially facilitate the formation and action of higher order complexes (Fennell-Fezzie et al., 2005; Badrinaryananan et al., 2012;Nolivos and Sherratt, 2014). MukBEF homologs are only found in a fraction of γproteobacteria, where they have co-evolved with a group of other proteins, including MatP, Dam and SeqA (Brézellec et al., 2006). MukBEF also coordinates the localization and action of TopoIV

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

“…This is consistent with an earlier study that relied on over-expression of tagged mammalian cohesin subunits (Zhang et al, 2008). Along these lines, the related bacterial SMC complex, MukBEF, also forms a dimer or and even ‘dimers of dimers’ (Arciszewska et al, 2019; Badrinarayanan et al, 2012; Fennell-Fezzie et al, 2005; Matoba et al, 2005; Woo et al, 2009). Moreover, the B. subtilis SMC condensin complex has been proposed to extrude DNA loops at a speed of ~50 kb/min as a dimeric handcuff complex (Wang et al, 2017).…”

SMC complexes organize the bacterial chromosome by lengthwise compaction

“…The mechanistic and functional differences between Muk-BEF and SMC-ScpAB complexes remain elusive, but in our opinion, it is likely that they both act through ATP hydrolysis-driven loop extrusion. The requirement of MukBEF dimers of dimers for function (Badrinarayanan et al 2012;Rajasekar et al 2019) provides a conceptually straightforward way of having a symmetrical loop extrusion mechanism, which in our model is essential for efficient lengthwise compaction (Mäkelä and Sherratt 2020). Whether other SMC complexes form dimers of dimers, or other-higher order cooperative structures, is hotly debated, although the apparent coordination of putative loop extrusion on the two B. subtilis arms could be explained by higher order SMC action.…”

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

“…MukF binds the dimeric KITE protein MukE, which is structurally related to ScpB of prokaryotic Smc-ScpAB and Nse1-3 of the Smc5-6 complex (Palecek and Gruber, 2015). MukB2E2F assemblies (hereafter 'MukBEF monomers') dimerize via MukF (Fennell-Fezzie et al, 2005;Woo et al, 2009) into MukB4E4F2 complexes (also called 'MukB dimers of dimers', hereafter simply 'MukBEF dimers'), which are the functional form (Badrinarayanan et al, 2012;Rajasekar et al, 2019).…”