SMC5/6: Multifunctional Player in Replication

Abstract

The genome replication process is challenged at many levels. Replication must proceed through different problematic sites and obstacles, some of which can pause or even reverse the replication fork (RF). In addition, replication of DNA within chromosomes must deal with their topological constraints and spatial organization. One of the most important factors organizing DNA into higher-order structures are Structural Maintenance of Chromosome (SMC) complexes. In prokaryotes, SMC complexes ensure proper chromosomal partitioning during replication. In eukaryotes, cohesin and SMC5/6 complexes assist in replication. Interestingly, the SMC5/6 complexes seem to be involved in replication in many ways. They stabilize stalled RFs, restrain RF regression, participate in the restart of collapsed RFs, and buffer topological constraints during RF progression. In this (mini) review, I present an overview of these replication-related functions of SMC5/6.

Keywords: SMC complexes; SMC5/6; chromatin structure; collapsed replication fork; homologous recombination; loop extrusion; replication fork regression; stalled replication fork.

Figure 1

The structural maintenance of chromosome (SMC) complexes form rings. The long coiled-coil SMC proteins interact via their hinge domains at one pole and their heads are bridged at the other pole by the kleisin protein (violet; kleisin’s N- and C-terminal domains bind different SMC proteins). There are two types of kleisin-interacting subunits in different SMC complexes. In the prokaryotic SMC/ ScpAB (segregation and condensation protein) and eukaryotic SMC5/6 complexes, the kleisin molecules bind to the kleisin-interacting tandem winged-helix element (Kite) proteins (suggesting an evolutionary path from prokaryotes to eukaryotes via an ancestral SMC5/6-like complex; blue arrow). In the eukaryotic condensin and cohesin complexes, kleisins interact with the HEAT proteins associated with kleisin (Hawk) proteins (suggesting their later evolution; orange arrow). In addition, the SMC5/6 complex contains a unique conserved Nse2 subunit attached to the SMC5 coiled-coil arm, which possesses small ubiquitin-like modifier (SUMO)-ligase activity. The non-conserved Nse5 and Nse6 subunits are omitted for simplicity.

Figure 2

The SMC rings can topologically embrace two DNA strands. The circular shape and the size of the SMC rings enable them to encircle two DNA strands. Two DNA strands can originate from either two sister chromatids (a); (cohesin and SMC5/6 can interconnect two DNA strands [66,67]) or two segments of the same DNA molecule (b); (most SMC complexes are proposed to form intramolecular loops on DNA). (a) ATP binding and hydrolysis provide the SMC complexes with motor activity which allows their translocation along the DNA molecule. (b) SMC motor activity may also progressively enlarge loops of DNA in a process termed loop extrusion. Given the loop extrusion activity of the SMC/ScpAB and condensin complexes [64,65], it is very likely that SMC5/6 complexes can also form intramolecular loops on DNA.

Figure 3

Multiple roles of SMC5/6 in genome integrity maintenance and replication. (a) SMC5/6 (blue ring) is recruited to a double-stranded break (DSB) and promotes its repair via homologous recombination (HR) in several ways. It may assist cohesin (yellow ring) in holding sister chromatids and protects it via SUMOylation. In addition, SMC5/6-dependent SUMOylation of STR (Sgs1/Top3/Rmi1; pink circle) helicase promotes resolution of the Holliday junction (HJ). (b) SMC5/6 binds heterochromatin protein 1 (HP1; grey square) and blocks HR within the heterochromatin domain to prevent ectopic recombination. Nse2-mediated SUMOylation triggers the relocalization of repair sites to nuclear periphery, where Smc5/6 interacts with the SUMO-targeted ubiquitin-ligase (STUbL) complex (violet hexagon), which ubiquitylates SUMOylated proteins and enables HR progression (blue arrow) outside the heterochromatin domain. (c) SMC5/6 localizes to stalled replication fork (RF) and assists in its restart via HR when it collapses (blue arrow). SMC5/6 restricts RF regression (which would otherwise also lead to HR; blue arrow) promoted by Mph1/FANCM helicase (cyan triangle). Pausing sites (such as repetitive ribosomal DNA (rDNA)) are particularly prone to RF regression. The Rrm3 helicase (green triangle) facilitates replication through such pausing sites. (d) SMC5/6 promotes RF rotation to relax topological tensions (by topoisomerase II; black square) and remove sister chromatid intertwines (SCI) during replication.