MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

Zawadzka, Katarzyna; Zawadzki, Paweł; Baker, Richard; Rajasekar, Karthik V.; Wagner, Florence F.; Sherratt, David J.; Arciszewska, Lidia K.

doi:10.7554/elife.31522

Cited by 57 publications

(102 citation statements)

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“…Here we developed several systems to prove and analyse the interaction between Nse4 and SMC6. We mapped the Nse4-SMC6 interface in detail and found that the Nse4-SMC6 interaction mode is similar to the other νSMC-kleisin interactions [16–18, 26, 34]. Therefore, we assume that Nse4 bridges SMC5-SMC6 proteins in a way similar to kleisins in the other SMC complexes, except that the Nse4 bridge is specifically modulated by the Nse1-Nse3 KITE subunits in the SMC5/6 complex (see below).…”

Section: Discussionmentioning

confidence: 92%

“…Next, we took advantage of the crystal structures of the kleisin-νSMC complexes [16–18, 26, 34], which suggest a key role for the N-terminal HTH domain of the kleisin molecule in its binding to νSMC neck. We mutated residues within the third α-helix of the Nse4 HTH domain (aa62-68) and analysed their impact on the Nse4-SMC6 interaction using the SMC5-Nse4-SMC6 3Y2H system as above (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Kleisin binds to the cap side of one SMC (designated as κSMC) head domain via a winged-helix domain (WHD) at its carboxyl terminus. Kleisin’s α-helix located at its amino terminal helix-turn-helix (HTH) domain binds to the coiled-coil base region immediately adjacent to the other SMC head (called neck and designated as νSMC; [16–18]). This kleisin bridge mediated by protein-protein interactions seems to be more permanent than the ATP-mediated bridge (as the latter bridge dissolves upon ATP hydrolysis).…”

Section: Introductionmentioning

confidence: 99%

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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

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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...

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Section: Discussionmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

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“…Formation of such complexes could lead to effectively two-sided extrusion and gapless chromosome compaction. In prokaryotes, such as E. coli (which have MukBEF complexes, SMC complex homologs), experiments show that MukBEF forms dimers of complexes (Badrinarayanan et al, 2012) linked by the kleisin molecule, MukF (Zawadzka et al, 2018) . MukBEF complexes promote long-ranged contacts within E. coli chromosome arms (Lioy et al, 2018) , and they are proposed to function by two-sided loop extrusion.…”

Section: Oligomerization Of Smc Complexesmentioning

confidence: 99%

Chromosome organization by one-sided and two-sided loop extrusion

Banigan

Berg

Brandão

et al. 2019

Preprint

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AbstractSMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a “one-sided” manner. We therefore simulate one-sided loop extrusion to investigate whether “one-sided” complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by “two-sided” loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization.Impact statementWe reconcile seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization by computationally investigating mechanisms of loop extrusion that are consistent with both.

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“…MukBEF acts as a dimer of SMC dimers when it is loaded onto DNA, which are connected by an N‐terminal mediated dimerization of the kleisin MukF . Their proposed form of action is a “rock climbing” movement on two DNA strands to generate LEF activity (Figure c), where staggered topological entrapment, followed by extrusion of DNA through the kleisin interface of two SMC complexes in close proximity would generate loop extrusion …”

Section: Biophysical Models For Smc Complexes Acting As Lefsmentioning

confidence: 99%

Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact

2018

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The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome-wide contact frequency analyses indicate that intra-chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle. DNA loop extrusion has emerged as a unifying model for how chromosome loops are formed in cis in different genomic contexts and cell cycle stages. The highly conserved family of SMC complexes have been found to be required for DNA cis-looping and have been suggested to be the enzymatic core of loop extruding machines. Here, the current body of evidence available for the in vivo and in vitro action of SMC complexes is discussed and compared to the predictions made by the loop extrusion model. How SMC complexes may differentially act on chromatin to generate DNA loops and how they could work to generate the dynamic and functionally appropriate organization of DNA in cells is explored.

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MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

Cited by 57 publications

References 65 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

Chromosome organization by one-sided and two-sided loop extrusion

Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact

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