The bacterial chromosome: architecture and action of bacterial SMC and SMC-like complexes

Abstract

Structural Maintenance of Chromosomes (SMC) protein complexes are found in all three domains of life. They are characterized by a distinctive and conserved architecture in which a globular ATPase 'head' domain is formed by the N- and C-terminal regions of the SMC protein coming together, with a c. 50-nm-long antiparallel coiled-coil separating the head from a dimerization 'hinge'. Dimerization gives both V- and O-shaped SMC dimers. The distinctive architecture points to a conserved biochemical mechanism of action. However, the details of this mechanism are incomplete, and the precise ways in which this mechanism leads to the biological functions of these complexes in chromosome organization and processing remain unclear. In this review, we introduce the properties of bacterial SMC complexes, compare them with eukaryotic complexes and discuss how their likely biochemical action relates to their roles in chromosome organization and segregation.

Keywords: SMC; chromosome; chromosome organization; chromosome segregation; cohesin; condensin.

Fig. 1

Architecture of SMC complexes. SMC proteins are composed of three distinctive parts, a head ATPase domain formed from the SMC N- and C-termini, a long intramolecular coiled-coil and a hinge dimerization domain. The complex is formed by an SMC dimer bridged by a kleisin (brown) associated with a second non-SMC subunit (orange). (a) The C-terminal domain of Escherichia coli MukF interacts with the ‘cap’ region of the MukB head, while the central region interacts with a homodimer of MukE. In the absence of ATP, two MukF and four MukE bind a dimer of MukB. ATP binding displaces one MukF giving a stoichiometry similar to other SMC complexes. However, a dimer of dimers can also be potentially formed via dimerization of the MukF N-terminal domain. (b) In Bacillus subtilis, the C-terminal domain of the kleisin ScpA interacts with the cap region of one Smc head, and the N-terminus binds the ‘neck’ region (interface between the coiled-coil domain and the head) of the other Smc monomer. In addition, a central ScpA domain wraps around a dimer of ScpB. ATP binding and head engagement prevent a second ScpA binding. (c) The core of eukaryotic SMC complexes is composed of an SMC heterodimer, a kleisin and at least one other non-SMC subunit. In addition, several other accessory proteins are required during SMC complex action. The cohesin complex is illustrated here. For clarity, an orange cloud represents non-SMC subunits. The C-terminal domain of the kleisin Scc1 interacts with the cap domain of Smc1, whereas the N-terminal domain interacts with the head domain of Smc3. A putative ‘neck’ interaction is shown, as in B. subtilis. (d) The Rad50-Mre11 complex is symmetrical in both ATP-bound and unbound forms. SMC-like protein Rad50 differs from true SMC proteins by having a zinc–hook dimerization domain. Dimerization is thought to be weak. The Mre11 C-terminal helix-loop-helix domain, represented by a hexagon, binds the Rad50 neck, while the central ‘capping’ domain interacts with the head. The N-terminal dimerization domain carries DNA binding and nuclease activities (yellow). ATP-dependent head engagement causes a dramatic rearrangement within the complex, suggesting a rotation of the coiled-coil domain. Structures of the complex were obtained with only a short part of the coiled-coil, and it is not clear whether this rearrangement would be possible in a full-length dimeric protein as drawn here or whether head engagement breaks the zinc–hook interaction. (e) RecN is an SMC-like protein that acts in DSB repair without known accessory proteins and possesses a short coiled-coil of about one quarter of the length of other SMC proteins. The dimerization interface is contained in the three apical α-helices. The rigidity of the coiled-coil is proposed to disfavour head engagement within a dimer, but to favour interactions between two dimers, potentially allowing ATP-dependent polymerization along the DNA.

Fig. 2

Conservation of ATPase head domains. (a) Head engagement in an SMC dimer forms two ATPase domains, indicated in yellow and orange. Appropriate letters specify the four conserved motifs. For each ATPase domain, the WalkerA and WalkerB motifs are carried, respectively, by the N-terminal (in dark green) and the C-terminal parts (in light green) of one SMC protein, whereas the C-motif and D-loop are found in the C-terminal domain of the second SMC monomer. ATP hydrolysis leads to head disengagement. (b) Alignment, using Clustal Omega (Goujon et al., 2010), showing the conservation of the four characteristic motifs among bacterial SMC proteins. ‘*’ indicates positions that have a single, fully conserved residue; ‘:’ and ‘.’ indicate conservation between groups of strongly and weakly similar properties, respectively. Consensus sequences are indicated. NCBI accession numbers are as follows: BAA06510.1, YP_249221.1, YP_003707593.1, CAD10418.1, AAF00713.1, NP_389476.2, NP_629712.1.

Fig. 3

DNA entrapment models. (a) Model for cohesion. The two sister chromatids are topologically entrapped within the cohesin ring. Release of cohesion can occur after kleisin cleavage by separase. (b and c) Models for action as a condensin and for ori positioning. Two DNA segments from the same chromosome are enclosed within the ring and can be topologically entrapped (c), or not (b). (d) A model for how bipolar ori segregation could be coordinated with sister ori decatenation. A cluster of MukBEF complexes (shown as a single complex for simplicity, overlaid on a grey ellipsoid representing the MukBEF cluster) is bound to sister ori regions that are catenated immediately after replication (only a single catenation link is shown). If the proposed MukBEF focus positioning system begins to separate to generate two sister MukBEF clusters, action of TopoIV (yellow; associated with the MukBEF clusters) will remove sister chromosome tension and allow sister ori separation.

Fig. 4

Localization of bacterial SMC. Escherichia coli MukB colocalized with the origin of replication and Bacillus subtilis SMC foci with Spo0J protein (Sullivan et al., 2009). Caulobacter crescentus bright foci are located at the cell pole, but colocalized only rarely with ParB proteins (Schwartz & Shapiro, 2011).