Structural insights into DNA loop extrusion by SMC protein complexes

https://doi.org/10.1016/j.sbi.2020.06.009Get rights and content

Highlights

  • Protein complexes of the SMC family organize chromosomes by extruding large DNA loops.

  • SMC-mediated loop extrusion presumably requires DNA anchor and motor elements.

  • Changes in coiled-coil conformations might appose distant DNA binding sites during DNA translocation.

Structural Maintenance of Chromosomes (SMC) protein complexes play key roles in the three-dimensional organization of genomes in all kingdoms of life. Recent insights from chromosome contact mapping experiments and single-molecule imaging assays suggest that these complexes achieve distinct cellular functions by extruding large loops of DNA while they move along the chromatin fiber. In this short review, we summarize recent insights into the molecular architecture of these unconventional DNA motor complexes, their interaction with their DNA substrates, and the remarkable dynamic changes they can undergo during their ATPase reaction cycle.

Introduction

A multitude of genomic functions — ranging from the control of gene expression and the repair of DNA damage to the compaction of individual chromatin fibers into mitotic chromosomes — require a series of complex rearrangements in the spatial organization of the chromatin fiber. These structural changes in chromosome architecture are governed by ubiquitous multi-subunit protein complexes of the SMC family, which can be subdivided into three major categories both in prokaryotes (Smc–ScpAB, MukBEF, MksBEF) and eukaryotes (cohesin, condensin and Smc5/6) [1]. The eukaryotic SMC complexes fulfill specific functions during different stages of the cell cycle: cohesin maintains chromatin domains during interphase and holds together sister chromatids once they emerge from the DNA replication fork [2]; condensin organizes mitotic and meiotic chromosomes into the iconic cylindrical structures described decades ago [3]; Smc5/6 controls DNA superhelicity and plays a role in DNA damage repair [4].

Despite their discrete roles, SMC complexes share a common three-dimensional architecture. At their core is a pair of ∼50-nm-long intra-molecular coiled-coil SMC subunits that dimerize via a globular ‘hinge’ domain at one end of the coils. The amino and carboxy termini brought together at the other ends of the coils fold into ATP-Binding-Cassette (ABC) ATPase ‘head’ domains (Figure 1). The two ATPase heads of an SMC dimer are able to engage with each other upon binding a pair of ATP molecules between the Walker A/B motifs of one head and the conserved ABC signature motifs of the opposite head, whereas nucleotide hydrolysis and release are thought to again drive the heads apart. The SMC heads are furthermore connected by a subunit of the kleisin protein family, which binds via a helical domain located at its amino terminus to the coiled-coil ‘neck’ region immediately adjacent to one head and via a winged-helix domain located at its carboxy terminus to the opposite ‘cap’ surface of the second head. The kleisin recruits additional subunits to the complex that are either composed of tandem winged-helix domains (in Smc–ScpAB, MukBEF, MksBEF and Smc5/6) or of helical HEAT (Huntingtin, EF3, PP2A, TOR1) repeats (in cohesin and condensin) [5].

Although the structures of most of their subunits have now been resolved to near-atomic detail, it still remains mysterious how SMC protein complexes engage with their chromatin substrates and carry out their functions. In this brief review, we focus our discussion on the current understanding of the physical interactions between SMC complexes and DNA and speculate how these interactions might mediate diverse biological functions.

Section snippets

Chromosome organization by DNA loop extrusion

A unifying mechanism for the seemingly different functions of SMC protein complexes might be their ability to generate large DNA loops. The idea that SMC complexes act as a pair of bidirectional DNA motors that move into opposite directions on the same DNA and thereby extrude a DNA loop elegantly explains several features of chromosome contact frequency maps that were obtained from high-throughput sequencing techniques in vertebrate cells. These features include the co-localization of cohesin

DNA anchor elements in SMC complexes

Whereas the identity of the DNA motor element(s) in condensin and other SMC complexes remains unknown (see below), it is likely that a positively charged groove, which is formed when the Ycg1/CAP-G HEAT-repeat subunit of condensin engages the Brn1/CAP-H kleisin subunit (Figure 2a), serves as an anchor element [18, 19, 20]. Co-crystal structures revealed that DNA is bound in the groove exclusively via backbone contacts with residues from both the kleisin subunit and the HEAT-repeat subunit, and

Potential DNA motor elements in SMC complexes

It seems reasonable to assume that any DNA motor element must require the presence of at least two distinct DNA binding sites that alternate in their contact with the DNA double helix in a manner that is controlled by cycles of ATP binding and hydrolysis by the SMC heads. Where might such DNA binding sites be located?

The SMC ATPase heads themselves are excellent candidates for creating a transient DNA binding site. Crystal and cryo-electron microscopy (cryo-EM) structures of the SMC-related

Conformational changes that could drive DNA loop extrusion

Comparison of ATP hydrolysis rates measured in ensemble assays and DNA-loop extrusion speeds measured in single-molecule experiments suggests that cohesin and condensin might be able to take steps that are in the range of the entire length of these complexes — 50 nm or more — in a single reaction cycle [12••,13••]. If this comparison were accurate, SMC complexes must be able to undergo extensive conformational changes that allow them to move in such large steps along DNA and, more importantly,

Conclusions

SMC protein complexes have emerged as the universal key players in the functional organization of genomes. Their common working principle presumably depends on the extrusion of large chromatin loops by their processive movement along the DNA double helix, but the molecular basis of their DNA motor activity has remained largely mysterious. Uncovering how these exceptional machines move DNA and entire chromatin fibers will require the unambiguous identification of the parts of the complexes that

Conflict of interest statement

Nothing declared.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We are grateful to Markus Hassler and Indra Shaltiel for comments on the manuscript. S.D. acknowledges support from a Darwin Trust Fellowship. Work in the Haering group is funded by the European Research Council (ERC, grant number 681365), the German Research Foundation (DFG, grant number HA5853/4-1), the European Molecular Biology Laboratory (EMBL) and the University of Würzburg.

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