Molecular structures and interactions in the yeast kinetochore

Abstract

Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes.

Figure 1

Hierarchical molecular organization of the S. cerevisiae kinetochore. Between the proteins that assemble directly on centromeric DNA (bottom, conserved subsites CDEI [red], CDEII [pink], and CDEIII [rose]) and those that interact with the spindle MT (top, in yellow) is a “layer” of intermediate linker complexes. Defined protein complexes (CBF3, MIND, etc.) are in colored boxes or ovals. The heterotetrameric Ndc80 complex is illustrated with an explicit representation of its extended structure, to emphasize that it is the one linker known to bind specifically to the MT. The numerals in parentheses after the name of each complex are the current best estimates of the number of the respective complexes in one kinetochore (Joglekar et al. 2006). The arrows indicate recruitment dependencies, as determined by genetic and imaging methods. Thus, the Bir1, Spc105, MIND, and Ndc80 complexes all require CBF3 for kinetochore localization, as does the Cse4p nucleosome. (The figure is adapted from Pagliuca et al. 2009 and reprinted with express permission from the Public Library of Science © 2009.)

Figure 2

Diagram of the budding yeast point centromere and its potential compaction by centromere-binding factors. (A) Conserved elements CDEI (red), CDEII (beige), and CDEIII (rose) and proteins known to bind them. The approximate lengths of these elements in S. cerevisiae are 8, 80, and 40 bp, respectively; CDEII in K. lactis is ~160 bp in length. There may be contacts with flanking, pericentromeric DNA (gray). (B) Proposed condensation of the centromere into a compact structure, established by interactions among the various binding components. Scm3p interacts with Ndc10p and the Cse4p nucleosome core (double-headed green arrow).

Figure 3

The Ndc80 complex. (A) Electron microscopy of rotary-shadowed, recombinant Ndc80 complexes. (Left) Field of molecules; (right) higher magnification of individual complexes (Wei et al. 2005). Bar, 1000 Å. (B) Diagram of molecular organization of the complex (Wei et al. 2005). (C) Ribbon representations of the Ndc80p/Nuf2p and Spc24p/Spc25p globular ends of the complex. The former is from the structure of the human homologs (Ciferri et al. 2008). The latter is from Wei et al. (2007). Colors as in B. The location of the amino-terminal extension of Ndc80p (the human homolog is Hec1), an unstructured region with Ipl1p/Aurora B phosphorylation sites, is indicated by a dotted line and labeled “N.” (Arrow) Likely surface for MT binding. Note that this surface is probably a composite of Ndc80p and Nuf2p and that the amino-terminal extension of Ndc80p projects from it. (A and B, Reprinted from Wei et al. 2005 with permission from the National Academy of Sciences © 2005; C [top], modified from Ciferri et al. 2008 and reprinted with permission from Cell Press © 2008; C [bottom], reprinted from Wei et al. [2007] with permission from Nature Publishing Group © 2007.)

Figure 4

DASH/Dam1 complex: formation of rings on microtubules (MTs). (A) Image of negatively stained MT “decorated” with DASH at high concentration. (B) Image of negatively stained MT decorated with DASH at lower concentration, followed by addition of gold-tagged antibody (against the His tag on the DASH components). The antibody clusters the rings in pairs; with no antibody added, the rings are randomly spaced (not shown). (C,D) Diagrams showing flexible connections between a DASH ring and an MT. The connections can adapt to different registers of the MT protofilaments. (A and B, Reprinted from Miranda et al. 2005 with permission from Nature Publishing Group © 2005; C and D, reprinted from Miranda et al. 2007 with permission from American Society for Cell Biology © 2007.)

Figure 5

Structure of the Csm1p/Lrs4p subcomplex of yeast monopolin. (A) Molecular organization of Csm1p. (B) Complex of Csm1p with Lrs4p. The amino-terminal 30 residues of Lrs4p form a dimerizing, α-helical segment; the dimeric segment, in turn, binds two Csm1p dimers, creating a V-shaped heterohexamer. The remaining residues of Lrs4p are disordered. (C) Superposition of the globular domains of Csm1p (blue) and Spc25p (magenta/gray). The arrow points to a lateral surface with somewhat divergent structures on the two proteins, as well as in Spc25p with respect to Spc24p (see Fig. 2C); this surface contains the hydrophobic patch, conserved among Csm1p orthologs, that binds Dsn1p (a component of the MIND complex) and Mif2p. (Figure from Corbett et al. 2010 and reprinted with permission from Cell Press © 2010.)

Figure 6

Electron microscopy of negatively stained, recombinant MIND complex (heterotetramer) from S. cerevisiae. Selected images from the field at the top are shown in the lower panels. Bars, 1000 Å. (Figure from Corbett et al. 2010 and reprinted with permission from Cell Press ©2010.)