Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA

Zabrady, Katerina; Adamus, Marek; Vondrová, Lucie; Liao, Chunyan; Skoupilová, Hana; Nováková, Markéta; Jurčišinová, Lenka; Alt, Aaron; Oliver, Antony W.; Lehmann, Alan R.; Paleček, Jan

doi:10.1093/nar/gkv1021

Cited by 72 publications

(117 citation statements)

References 56 publications

Supporting

Mentioning

112

Contrasting

Order By: Relevance

“…To analyse the role of ATP binding to SMC5-SMC6 within the complex stabilized by KITE proteins, we added Nse1 and Nse3 to the p416ADH1-Nse4 plasmid (p416ADH1-Nse4+Nse3+Nse1 construct, 5Y2H; Fig. 3B; [30, 37]). Consistent with their Nse4-stabilizing roles (Fig.…”

Section: Resultsmentioning

confidence: 99%

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

Vondrová

Adamus

Nociar

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

1 0 1 1 Keywords: SMC5/6 complex; Nse4 klesin linker; Nse1/Nse3 KITE subunits; ATP binding; 1 2 protein-protein interaction, fission yeast 1 3 1 4 2 ABSTRACT 1 5 The SMC (Structural Maintenance of Chromosomes) complexes are composed of 1 6 SMC dimers, kleisin and kleisin-interacting subunits. Mutual interactions of these subunits 1 7 constitute the basal architecture of the SMC complexes. Particularly, terminal domains of the 1 8 kleisin subunit bridge the SMC head domains of the SMC molecules. Binding of ATP 1 9molecules to the heads and their hydrolysis alter the shape of long SMC molecules (from rod-2 0 3 1 upon ATP binding. This mechanism suggests an important role of the KITE subunits in the 3 2 dynamics of the SMC5/6 complexes. 3 3 3 4 AUTHOR SUMMARY 3 5The SMC5/6 complex is member of the Structural maintenance of chromosomes 3 6 (SMC) family, key organizers of both prokaryotic and eukaryotic genomes. Their architecture 3 7 and dynamics (driven by ATP binding and hydrolysis) are essential for cellular processes, like 3 8 3 chromatin segregation, condensation, replication and repair. In this paper, we described 3 9 conserved mode of the Nse4 kleisin subunit binding to the SMC6 (similar to cohesin and 4 0 condensin) and its bridging role. Furthermore, we showed different impact of the binding of 4 1 the Nse1-Nse3 KITE subunits to the Nse4 kleisin bridge. Our study suggested that the KITE 4 2 proteins modulate the stability of the SMC5/6 complex, depending on its binding and 4 3 hydrolysis of ATP. Our findings uncover molecular mechanisms underlying dynamics of the 4 4 SMC5/6 complexes.4 5 4 6 INTRODUCTION 4 7 The SMC (Structural Maintenance of Chromosomes) complexes are key organizers of 4 8 prokaryotic and eukaryotic genomes. They organize chromatin domains (cohesins; [1]), 4 9 condense mitotic chromosomes (condensins; [2]), assist in DNA repair (SMC5/6; [3, 4]) and 5 0 replication (SMC/ScpAB; [5]). These circular complexes use the energy of ATP hydrolysis to 5 1 drive DNA topology changes. In prokaryotes, SMC/ScpAB drives extrusion of loops forming 5 2 behind the replication fork. In eukaryotes, condensins extrude loops laterally and axially to 5 3 shape chromatin to the typical mitotic chromosomes. Cohesins assist in formation of 5 4 topologically associating domains during interphase. Cohesin rings can also hold newly 5 5 replicated sister chromatids together and release them in highly controlled manner. The 5 6 SMC5/6 complexes have been implicated in the repair of DNA damage by homologous 5 7 recombination, stabilization and restart of stressed replication forks. The SMC5/6 instability 5 8 leads to the chromosome breakage syndrome in human [6], however, the molecular 5 9mechanism of the SMC5/6 action is largely unclear. 6 0 All the SMC complexes are composed of three common categories of subunits: SMC, 6 1 kleisin and kleisin-interacting proteins [7, 8]. The SMC proteins are primarily build of long 6 2 anti-parallel coiled-coil arms, a globular hinge (situated in the middle of their peptide chain) 6 3 4...

show abstract

Section: Resultsmentioning

confidence: 99%

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

Vondrová

Adamus

Nociar

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Support for this alternative possibility stems from structural studies which suggest that in the SMC-like MRN complex, the DNA-binding site on Rad50 is within the globular head domains but outside of the central pore formed by the Rad50 coiled-coiled domains (Williams et al, 2008). Similarly, also in Smc5/6, the DNA binds to a sub-complex interacting with the head domains, outside of the coiled-coil pore (Zabrady et al, 2016). Future work mapping the precise path of DNA through cohesin will be necessary to test this alternative model.…”

Section: Discussionmentioning

confidence: 99%

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

et al. 2016

View full text Add to dashboard Cite

Cohesin is essential for the hierarchical organization of the eukaryotic genome and plays key roles in many aspects of chromosome biology. The conformation of cohesin bound to DNA remains poorly defined, leaving crucial gaps in our understanding of how cohesin fulfills its biological functions. Here we use single molecule microscopy to directly observe the dynamic and functional characteristics of cohesin bound to DNA. We show that cohesin can undergo rapid one-dimensional (1D) diffusion along DNA, but individual nucleosomes, nucleosome arrays, and other protein obstacles significantly restrict its mobility. We further demonstrate that DNA motor proteins can readily push cohesin along DNA, but they cannot pass through the interior of the cohesin ring. Together, our results reveal that DNA-bound cohesin has a central pore that is substantially smaller than anticipated. These findings have direct implications for understanding how cohesin and other SMC proteins interact with and distribute along chromatin.

show abstract

“…A variation of the single-translocator model might be one where a flanking DNA is bound to the exterior of the SMC protein complex through the entire reaction cycle (Fig. 7c), for example via the DNA binding sites located at the walls of the lower compartment in condensin and SMC5/6 [27][28][29]. If so, then translocation to the left would result in asymmetric loop extrusion, as has been observed for yeast condensin [23].…”

Section: Asymmetric Single-translocator Model With Permanently Bound Dnamentioning

confidence: 98%

“…4a, leftmost and rightmost states). A DNA segment is encircled by the lower compartment in bsSMC and yeast cohesin in the apo state [25,26], either sterically held, or possibly bound noncovalently to a DNA binding site as observed in eukaryotic SMC complexes [27][28][29][30]. The configuration of state 0 can be imagined to be the result of the type of 'loading' reaction associated with initiation of SMC complex activity.…”

Section: Reaction Cycle For Translocation Of Smc Along Dnamentioning

confidence: 99%

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Marko¹,

Rios

Barducci

et al. 2018

Preprint

View full text Add to dashboard Cite

Cells possess remarkable control of the folding and entanglement topology of very long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops.Recent experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a 'loop extrusion' process. We describe a Brownian loop-captureratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor 'track' -in this case DNA -are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity on tension in the DNA track that it is moving along.

show abstract

Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA

Cited by 72 publications

References 56 publications

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Contact Info

Product

Resources

About