Abstract
Eukaryotic structural maintenance of chromosomes (SMC)–kleisin complexes form large, ring-shaped assemblies that promote accurate chromosome segregation. Their asymmetric structural core comprises SMC heterodimers that associate with both ends of a kleisin subunit. However, prokaryotic condensin Smc–ScpAB is composed of symmetric Smc homodimers associated with the kleisin ScpA in a postulated symmetrical manner. Here, we demonstrate that Smc molecules have two distinct binding sites for ScpA. The N terminus of ScpA binds the Smc coiled coil, whereas the C terminus binds the Smc ATPase domain. We show that in Bacillus subtilis cells, an Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complexes. We define a molecular mechanism that ensures asymmetric assembly, and we conclude that the basic architecture of SMC–kleisin rings evolved before the emergence of eukaryotes.
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References
Hirano, T. At the heart of the chromosome: SMC proteins in action. Nat. Rev. Mol. Cell Biol. 7, 311–322 (2006).
Nasmyth, K. & Haering, C.H. Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009).
Cuylen, S. & Haering, C.H. Deciphering condensin action during chromosome segregation. Trends Cell Biol. 21, 552–559 (2011).
D'Ambrosio, C., Kelly, G., Shirahige, K. & Uhlmann, F. Condensin-dependent rDNA decatenation introduces a temporal pattern to chromosome segregation. Curr. Biol. 18, 1084–1089 (2008).
Fousteri, M.I. & Lehmann, A.R. A novel SMC protein complex in Schizosaccharomyces pombe contains the Rad18 DNA repair protein. EMBO J. 19, 1691–1702 (2000).
Kegel, A. et al. Chromosome length influences replication-induced topological stress. Nature 471, 392–396 (2011).
Mascarenhas, J., Soppa, J., Strunnikov, A.V. & Graumann, P.L. Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein. EMBO J. 21, 3108–3118 (2002).
Soppa, J. et al. Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol. Microbiol. 45, 59–71 (2002).
Britton, R.A., Lin, D.C. & Grossman, A.D. Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev. 12, 1254–1259 (1998).
Hirano, M. & Hirano, T. Positive and negative regulation of SMC-DNA interactions by ATP and accessory proteins. EMBO J. 23, 2664–2673 (2004).
Niki, H., Jaffe, A., Imamura, R., Ogura, T. & Hiraga, S. The new gene mukB codes for a 177 kd protein with coiled-coil domains involved in chromosome partitioning of E. coli. EMBO J. 10, 183–193 (1991).
Yamazoe, M. et al. Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli. EMBO J. 18, 5873–5884 (1999).
Gruber, S. & Errington, J. Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis. Cell 137, 685–696 (2009).
Minnen, A., Attaiech, L., Thon, M., Gruber, S. & Veening, J.W. SMC is recruited to oriC by ParB and promotes chromosome segregation in Streptococcus pneumoniae. Mol. Microbiol. 81, 676–688 (2011).
Sullivan, N.L., Marquis, K.A. & Rudner, D.Z. Recruitment of SMC by ParB-parS organizes the origin region and promotes efficient chromosome segregation. Cell 137, 697–707 (2009).
Danilova, O., Reyes-Lamothe, R., Pinskaya, M., Sherratt, D. & Possoz, C. MukB colocalizes with the oriC region and is required for organization of the two Escherichia coli chromosome arms into separate cell halves. Mol. Microbiol. 65, 1485–1492 (2007).
Griese, J.J., Witte, G. & Hopfner, K.P. Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins. Nucleic Acids Res. 38, 3454–3465 (2010).
Haering, C.H., Lowe, J., Hochwagen, A. & Nasmyth, K. Molecular architecture of SMC proteins and the yeast cohesin complex. Mol. Cell 9, 773–788 (2002).
Kurze, A. et al. A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion. EMBO J. 30, 364–378 (2011).
Haering, C.H. et al. Structure and stability of cohesin′s Smc1-kleisin interaction. Mol. Cell 15, 951–964 (2004).
Lammens, A., Schele, A. & Hopfner, K.P. Structural biochemistry of ATP-driven dimerization and DNA-stimulated activation of SMC ATPases. Curr. Biol. 14, 1778–1782 (2004).
Arumugam, P. et al. ATP hydrolysis is required for cohesin's association with chromosomes. Curr. Biol. 13, 1941–1953 (2003).
Weitzer, S., Lehane, C. & Uhlmann, F. A model for ATP hydrolysis-dependent binding of cohesin to DNA. Curr. Biol. 13, 1930–1940 (2003).
Hu, B. et al. ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4 loading complex. Curr. Biol. 21, 12–24 (2011).
Schleiffer, A. et al. Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. Mol. Cell 11, 571–575 (2003).
Gruber, S., Haering, C.H. & Nasmyth, K. Chromosomal cohesin forms a ring. Cell 112, 765–777 (2003).
Haering, C.H., Farcas, A.M., Arumugam, P., Metson, J. & Nasmyth, K. The cohesin ring concatenates sister DNA molecules. Nature 454, 297–301 (2008).
Ivanov, D. & Nasmyth, K. A topological interaction between cohesin rings and a circular minichromosome. Cell 122, 849–860 (2005).
Woo, J.S. et al. Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions. Cell 136, 85–96 (2009).
Fennell-Fezzie, R., Gradia, S.D., Akey, D. & Berger, J.M. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. EMBO J. 24, 1921–1930 (2005).
Badrinarayanan, A., Reyes-Lamothe, R., Uphoff, S., Leake, M.C. & Sherratt, D.J. In vivo architecture and action of bacterial structural maintenance of chromosome proteins. Science 338, 528–531 (2012).
Fuentes-Perez, M.E., Gwynn, E.J., Dillingham, M.S. & Moreno-Herrero, F. Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope. Biophys. J. 102, 839–848 (2012).
Volkov, A., Mascarenhas, J., Andrei-Selmer, C., Ulrich, H.D. & Graumann, P.L. A prokaryotic condensin/cohesin-like complex can actively compact chromosomes from a single position on the nucleoid and binds to DNA as a ring-like structure. Mol. Cell. Biol. 23, 5638–5650 (2003).
Kim, J.S. et al. Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis. Proteins 71, 1553–1556 (2008).
Hirano, M. & Hirano, T. Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA. EMBO J. 21, 5733–5744 (2002).
Mascarenhas, J. et al. Dynamic assembly, localization and proteolysis of the Bacillus subtilis SMC complex. BMC Cell Biol. 6, 28 (2005).
Stephan, A.K., Kliszczak, M. & Morrison, C.G. The Nse2/Mms21 SUMO ligase of the Smc5/6 complex in the maintenance of genome stability. FEBS Lett. 585, 2907–2913 (2011).
Unal, E. et al. A molecular determinant for the establishment of sister chromatid cohesion. Science 321, 566–569 (2008).
Rolef Ben-Shahar, T. et al. Eco1-dependent cohesin acetylation during establishment of sister chromatid cohesion. Science 321, 563–566 (2008).
Gruber, S. MukBEF on the march: taking over chromosome organization in bacteria? Mol. Microbiol. 81, 855–859 (2011).
Gruber, S. et al. Evidence that loading of cohesin onto chromosomes involves opening of its SMC hinge. Cell 127, 523–537 (2006).
Chan, K.L. et al. Cohesin's DNA exit gate is distinct from its entrance gate and is regulated by acetylation. Cell 150, 961–974 (2012).
Carter, S.D. & Sjogren, C. The SMC complexes, DNA and chromosome topology: right or knot? Crit. Rev. Biochem. Mol. Biol. 47, 1–16 (2012).
Hamoen, L.W., Smits, W.K., de Jong, A., Holsappel, S. & Kuipers, O.P. Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res. 30, 5517–5528 (2002).
Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
Scholefield, G., Errington, J. & Murray, H. Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA. EMBO J. 31, 1542–1555 (2012).
Acknowledgements
We thank E. Conti and S. Jentsch for sharing resources and helpful advice and K. Nasmyth and W. Zachariae for critical reading of the manuscript. We are grateful to the MPI Crystallization Facility for HTP screening, to the MPI Core Facility and C. Eberl for help with MS analysis, to M. Blettinger, A.-L. Cost and P. Ringer for technical help and to H. Murray (Newcastle University, Newcastle upon Tyne, UK) for providing DnaA protein and antiserum. S. Uebel kindly performed and analyzed the analytical ultracentrifugation experiments. We thank A. Pauluhn, V. Olieric and the staff of the PX beamlines at the Swiss Light Source (SLS, Villigen, Zurich) for assistance during crystallographic data collection and E. Lorentzen and R. Prabu for helpful advice for twinning refinement. We also acknowledge the use of Beamline 5C at PAL and BL41XU at the SPring-8. This work was supported by funding from the Max Planck Society and a Starting Grant from the European Research Council ERC StG #260853 “DiseNtAngle” (S.G.) and by the National Research Foundation of Korea grant 2012-0005612 (B.-H.O.).
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F.B., B. subtilis strain constructions and cellular and biochemical experiments; H.-C.S., F.B., Y.-M.S. and V.G.-O., protein purification; H.-C.S. and Y.-M.S., structure determination and biochemical experiments; J.B. and Y.-G.K., X-ray data collection and structure determination; F.B., H.-C.S., S.G. and B.-H.O. conception of experiments and preparation of the manuscript.
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Bürmann, F., Shin, HC., Basquin, J. et al. An asymmetric SMC–kleisin bridge in prokaryotic condensin. Nat Struct Mol Biol 20, 371–379 (2013). https://doi.org/10.1038/nsmb.2488
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DOI: https://doi.org/10.1038/nsmb.2488
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