The condensin complex is a mechanochemical motor that translocates along DNA

Abstract

One Sentence Summary: Single-molecule imaging reveals that eukaryotic condensin is a highly processive DNA-translocating motor complex. Abstract:Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. Here, we use single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of ATP hydrolysis-dependent translocation along double-stranded DNA. Condensin's translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ~60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil subunits, suggestive of a translocation mechanism that is distinct from any reported DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.Main Text: Structural maintenance of chromosomes (SMC) complexes are the major organizers of chromosomes in all living organisms (1, 2). These protein complexes play essential roles in sister chromatid cohesion, chromosome condensation and segregation, DNA replication, DNA damage repair, and gene expression. A distinguishing feature of SMC complexes is their large ring-like architecture, the circumference of which is made up of two SMC protein coiled-coil proteins and a single kleisin subunit (Fig.1A) (1-4). The ~50-nm long antiparallel coiled-coils are connected at one end by a stable dimerization interface, referred to as the hinge domain, and at the other end by globular ATP-binding cassette (ABC) family ATPase domains (5). The ATPase domains are bound by a protein of the kleisin family, along with additional accessory subunits, which vary for different types of SMC complexes (Fig. 1A). The relationship between SMC peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/137711 doi: bioRxiv preprint first posted online May. 13, 2017; 2 structures and their functions in chromosome organization is not completely understood (6), but many models envision that the coiled-coil domains allow the complexes to topologically embrace DNA (1-4). Given the general resemblance to myosin and kinesin, some early models postulated that SMC proteins might be mechanochemical motors (7-10).SMC complexes are thought to regulate genome architecture by physically linking distal chromosomal loci, but how these bridging interactions might be formed remains unknown (1, 2, 11). An early model suggested that many three-dimensional (3D) features of eukaryotic chromosomes might be explained by DNA loop extrusion (Fig. 1B) (12), and recent polymer dynamics simulations have shown that loop extrusion can recapitulate the formation of topologically associating domains (TADs), chromatin compaction, and sister chromatid segr...

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

“…More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al 2017).Condensin is composed of five subunits, two coiledcoils SMC2 and 4, a kleisin (Brn1), and two heat-repeatcontaining proteins (Ycs4 and Ycg1). The heat-repeat proteins are likely to be sites of DNA-binding within the condensin complex.…”

“…More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al 2017).…”

“…Here, we introduce a new model, RotoStep, as a first-principles statistical mechanics approach to simulate condensin dynamics. Terekawa et al (2017) have recently examined the behavior of single condensin molecules on DNA sheets. Terekawa et al (2017) provides critical experimental metrics for evaluating results from simulation.…”

“…Terekawa et al (2017) have recently examined the behavior of single condensin molecules on DNA sheets. Terekawa et al (2017) provides critical experimental metrics for evaluating results from simulation. Using RotoStep to simulate hand-over-hand motion (e.g., microtubule-based kinesin motor [Kull et al 1996]), our simulations indicate that condensin can translocate along taut linear DNA and compact singly tethered DNA chains.…”

“…The heat-repeat proteins are likely to be sites of DNA-binding within the condensin complex. Terekawa et al (2017) showed the ability of condensin to move processively along linear DNA sheets (Fazio et al 2008). The challenge ahead is to understand, first, how local motion and topological constraints of the DNA exerted by condensin will be dissipated along the length of a long-chain polymer and, second, how the fluctuating, loopy genome feeds back to the ability of condensin to translocate processively.…”