The Smc5/6 complex is a DNA loop-extruding motor

Pradhan, Biswajit; Kanno, Takaharu; Igarashi, Miki Umeda; Loke, Mun Siong; Baaske, Martin D.; Wong, Jan Siu Kei; Jeppsson, Kristian; Sjögren, Camilla; Kim, Eugene

doi:10.1038/s41586-023-05963-3

Cited by 83 publications

(71 citation statements)

References 37 publications

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“…First, we tested whether the purified SMC5/6 used here is able to perform DNA loop extrusion, as reported previously 7 (Figure S2). Indeed, we confirmed that SMC5/6 exhibits loop extrusion of DNA with similar characteristics as reported (Figures S2B-S2E), although we found that yeast SMC5/6 -like human cohesin and yeast condensin -extrudes already as a monomer (Figures S2F-S2I), while Pradhan et al 7 S2G and S2I). While SMC5/6 exhibited dynamics comparable to cohesin, condensin exhibited only brief phases of diffusion (7 ± 4 s, median ± SD) while extrusion phases lasted 13 ± 9 s (median ± SD), and loop slipping was hardly ever observed (1/65 phases; Figure S1J).…”

Section: Phases Of Active Dna Loop Extrusion Are Interspersed By Loop...mentioning

confidence: 93%

“…S. cerevisiae SMC5/6 was expressed, purified, and fluorescently labelled from S. cerevisiae as described in Pradhan et al (ref. 7 ) with small modifications. The cells were lysed and bound to IgG Sepharose as described in Pradhan et al (ref.…”

Section: Experimental Model and Subject Details Protein Expression An...mentioning

confidence: 99%

“…The three major members of the SMC family in eukaryotes are condensin, cohesin, and SMC5/6. All three are capable of manipulating DNA via an ATP-dependent process called DNA loop extrusion [2][3][4][5][6][7][8][9][10] , where loops are created and enlarged stepwise by ATP-binding events to the SMC complex 9,11 . Condensin mainly extrudes DNA loops during mitosis to compact sister chromatids and facilitate chromosome segregation 12,13,13 .…”

Section: Introductionmentioning

confidence: 99%

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SMC motor proteins extrude DNA asymmetrically and contain a direction switch

Barth,

Davidson,

van der Torre

et al. 2023

Preprint

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SummaryStructural Maintenance of Chromosomes (SMC) complexes organize the genomeviaDNA loop extrusion. While some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perform loop extrusion asymmetrically toward one direction only. The mechanism underlying this variability remains unclear. Here, we examine the directionality of DNA loop extrusion by SMCs usingin vitrosingle-molecule experiments. We find that cohesin and SMC5/6 do not reel in DNA from both sides, as reported before, but instead extrude DNA asymmetrically, while the direction can switch over time. Asymmetric DNA loop extrusion thus is the shared mechanism across all eukaryotic SMC complexes. For cohesin, direction switches strongly correlate with the turnover of the subunit NIPBL, during which DNA strand switching may occur. STAG1 stabilizes NIPBL on cohesin, preventing NIPBL turnover and direction switches. The findings reveal that SMCs, surprisingly, contain a direction switch subunit.HighlightsAll eukaryotic SMC complexes extrude DNA asymmetrically.Apparent ‘symmetric’ loop extrusion is the result of frequent direction switches.n human cohesin, loop-extrusion direction changes require exchange of NIPBL.STAG1 stabilizes NIPBL on human cohesin.

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Section: Phases Of Active Dna Loop Extrusion Are Interspersed By Loop...mentioning

confidence: 93%

Section: Experimental Model and Subject Details Protein Expression An...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

SMC motor proteins extrude DNA asymmetrically and contain a direction switch

Barth,

Davidson,

van der Torre

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Smc5/6 also contributes to antiviral immunity (4)(5)(6)(7)(8), though the mechanisms of this activity are not known. For all three eukaryotic SMC complexes, DNA loop extrusion has been directly observed in vitro (9)(10)(11)(12)(13)(14)(15). In prokaryotes, widespread SMC-ScpAB and MukBEF complexes contribute to genome organization and chromosome segregation during cell division (16)(17)(18)(19).…”

Section: Introductionmentioning

confidence: 99%

Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex

Pradhan,

Deep,

Koenig

et al. 2024

Preprint

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Structural maintenance of chromosomes (SMC) protein complexes play pivotal roles in genome organization and maintenance across all domains of life. In prokaryotes, SMC family Wadjet complexes structurally resemble the widespread MukBEF genome-organizing complexes but serve a defensive role by inhibiting plasmid transformation. We previously showed that Wadjet specifically cleaves circular DNA; however, the molecular mechanism underlying DNA substrate recognition remains unclear. Here, we use in vitro single-molecule imaging to directly visualize DNA loop extrusion and plasmid cleavage by Wadjet. We find that Wadjet is a symmetric DNA loop extruder that simultaneously reels in DNA from both sides of a growing loop and that this activity requires a dimeric JetABC supercomplex containing two dimers of the JetC motor subunit. On surface-anchored plasmid DNAs, Wadjet extrudes the full length of a 44 kilobase pair plasmid, stalls, and then cleaves DNA. Our findings reveal the role of loop extrusion in the specific recognition and elimination of plasmids by Wadjet, and establish loop extrusion as an evolutionarily conserved mechanism among SMC complexes across kingdoms of life.

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“…Nevertheless, the role of loop extrusion in DNA immune sensing remains unclear 8,9 . The process of DNA loop extrusion by the eukaryotic SMC complexes has been observed directly by single-molecule experiments in vitro [12][13][14][15] .…”

Section: Introductionmentioning

confidence: 99%

Structural basis for plasmid restriction by SMC JET nuclease

Roisné-Hamelin,

Liu,

Taschner

et al. 2023

Preprint

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SummaryDNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of circular plasmids through DNA cleavage; yet the mechanisms for target recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage implying that residual unextruded DNA is cleaved. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as principle for non-self DNA recognition and molecular signature for plasmid cleavage. We elucidate key elements of SMC loop extrusion including motor directionality and the structure of a DNA-holding state.

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The Smc5/6 complex is a DNA loop-extruding motor

Cited by 83 publications

References 37 publications

SMC motor proteins extrude DNA asymmetrically and contain a direction switch

SMC motor proteins extrude DNA asymmetrically and contain a direction switch

Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex

Structural basis for plasmid restriction by SMC JET nuclease

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