A direct link between sister chromatid cohesion and chromosome condensation revealed through the analysis of MCD1 in S. cerevisiae

Abstract

The S. cerevisiae MCD1 (mitotic chromosome determinant) gene was identified in genetic screens for genes important for chromosome structure. MCD1 is essential for viability and homologs are found from yeast to humans. Analysis of the mcd1 mutant and cell cycle-dependent expression pattern of Mcd1p suggest that this protein functions in chromosome morphogenesis from S phase through mitosis. The mcd1 mutant is defective in sister chromatid cohesion and chromosome condensation. The physical association between Mcd1p and Smc1p, one of the SMC family of chromosomal proteins, further suggests that Mcd1p functions directly on chromosomes. These data implicate Mcd1p as a nexus between cohesion and condensation. We present a model for mitotic chromosome structure that incorporates this previously unsuspected link.

Figure 1. Characterization of the mcd1–1 Mutant and the MCD1 Gene

(A) Ts⁻ phenotype of mcd1–1 cells. Wild-type (VG906–1A) and mcd1 (VG955–7D) cells grown at 23°C in YPD liquid were plated in 10-fold serial dilutions on YPD and incubated at 23°C, 30°C, and 37°C. (B) Cell cycle–dependent lethality of mcd1–1 cells. Strains in (A) were arrested at 23°C in either G1 (αF), S (HU), or M (Nz) phase, incubated at 37°C while arrested, then plated on YPD at 23°C to determine percent viability. Data from two independent experiments was used to generate error bars. (C) Suppression of smc1–2 Ts⁻ phenotype by multiple copies of MCD1. smc1–2 (3aAS273) cells bearing either plasmid pAS140 (SMC1, CEN vector), pRS426 (2μ vector), pAS271/3 (MCD1, 2μ vector), or pAS333 (mcd1::TRP1, 2μ vector) were grown at 23°C, then plated at 23°C and 37°C as described in (A). (D) Coimmunoprecipitation of Mcd1p and Smc1p. Mcd1p was overexpressed in strain BS334/pAS339, and cells either left untreated (Async), arrested in S (HU), or M (NZ) phase, then processed for immunoprecipitation. Proteins were immunoprecipitated (IP) using either anti-T7 Ab, anti-Smc1p Ab, or anti-Smc1p depleted Ab. IP proteins were Western blotted using anti-Smc1p Ab to detect Smc1p and anti-T7 Ab to detect T7 tagged Mcd1p. (E) MCD1 is a member of a conserved gene family. Multiple sequence alignment of Mcd1p, S. pombe Rad21 protein (S.p. Rad21p) (Birkenbihl and Subramani, 1992), C. elegans ORF F10G7.4, accession U40029 (C.el. F10G7.4); mouse protein PW29 (M.m. PW29) (Yu et al., 1995), human ORF from KIAA0078 cDNA (H.s. KIAA0078) (Nomura et al., 1994) using the Pileup program of the GCG package. Boxes I, II, and III are the regions of highest shared similarity. Black bars are PESTsequences with PEST-FIND scores in parentheses.

Figure 2. Cell Cycle Progression in Wild-Type and mcd1–1 Cells

(A) DNA content of wild-type (VG906–1A) and mcd1 (VG955–7D) cells grown asynchronously at 23°C or shifted to 37°C for 3 hr. (B) Micrographs showing the mitotic spindle in cells 1 hr after release at 37°C from S phase. Wild-type (VG982–6A) and mcd1 (VG985–7C) cells were synchronously released at 37°C from S phase arrest, and after 1 hr cells were processed for immunofluorescence. Chromosomal DNA (top) and microtubules (bottom). (C) Quantitation of cell and DNA morphologies after release at 37°C from S phase. Strains in B were scored for cell and DNA morphologies in S phase–arrested cells at 37°C [S (HU)] and in cells 2 hr after release (2 hr after S). Data from 200–300 cells from two independent experiments were scored to generate error bars.

Figure 3. Analysis of Sister Chromatid Cohesion in Mid-M Phase Wild-Type and mcd1–1 Cells

(A) Micrographs of mid-M cells subjected to FISH using a chromosome XVI CEN-distal probe. Wild-type (VG906–1A) and mcd1 (VG955–7D) cells arrested in G1 phase [G1 (αF) 23°C] were released from G1 and arrested in mid-M phase [M (Nz) 37°C]. Mid-M cells were processed for FISH. Chromosomal DNA (red) and hybridized probe (green). Bar is 5 μm. (B) Quantitation of FISH for G1 and mid-M cells. Cells described in (A) were hybridized with either a chromosome XVI CEN-proximal (23 kb from CEN16) or distal (295 kb from CEN16) probe. The number of FISH signals in each DNA mass was determined and plotted as a percentage of total nuclei. For each probe, 200 nuclei from two independent experiments were scored to generate data and error bars. (C) Quantitation of FISH for cells arrested in mid-M phase at 23°C then incubated at 37°C. Strains described in (A) were arrested in G1 phase at 23°C, released from G1, and arrested in mid-M phase at 23°C [M (Nz) 23°C] then transferred to 37°C [M (Nz) 23°C to 37°C]. For each probe, at least three hundred nuclei from three independent experiments were scored and data plotted as described in (B).

Figure 4. Analysis of Chromosome Condensation in Wild-Type and mcd1–1 Cells in Mid-M Phase

(A) Micrographs showing FISH of the rDNA. Wild-type (VG906–1A) and mcd1 (VG955–7D) cells were synchronously arrested in mid-M at 23°C then incubated 37°C while arrested as described in the legend to Figure 3C. Mid-M phase cells at 37°C were subjected to FISH using rDNA as probe. Chromosomal DNA (DAP) and hybridized probe (FIT) are shown. Bar is 5 μm. (B) Micrographs showing FISH of regions of chromosomes VIII and XVI in mid-M cells. Strains in (A) were synchronously arrested in mid-M at 37°C then subjected to FISH using a mixture of chromosome VIII or chromosome XVI probes. Chromosomal DNA (red) and hybridized probes (green) are shown. Bar is 5 μm.

Figure 5. In Vivo Localization of Mcd1p

(A) Specificity of affinity-purified anti-Mcd1 Ab. Strain YPH499b/pAS339 was grown under conditions to induce MCD1 overexpression (Induction +) or to repress MCD1 expression (Induction −). Cells were processed for Western blot and probed with anti-Mcd1p Ab. The protein equivalent of 10⁷ cells was loaded per lane. (B) Redistribution of Mcd1p in mitosis. Mcd1p was overexpressed in asynchronously growing cells (YPH499b/pAS339) then subjected to indirect immunofluorescence using anti-Mcd1p Ab. Arrow indicates an anaphase cell. (C) Cell cycle–dependent changes in Mcd1p levels by Western blot. Wild-type strain YPH499b was arrested in either G1 [G1 (αF)], S [S (HU)] or mid-M [M (Nz)] phase and Mcd1p levels monitored using anti-Mcd1p Ab. (D) Cell cycle–dependent changes in Mcd1p levels in vivo. Cells in (C) were processed for indirect immunofluorescence using anti-Mcd1p Ab. Bar is 5 μm.

Figure 6. Cell Cycle–Dependent Expression of Mcd1p

(A) Mcd1p levels in synchronized cycling cells. Wild-type strain YPH499b was arrested in G1 phase (T = 0) then released from G1 and aliquots taken every 20 min for Western analysis and flow cytometry. Mcd1p was detected using anti-Mcd1p Ab whereas protein loading was shown by monitoring α tubulin levels using YOL1/34 Ab. (B) Relative levels of Pds1p and Mcd1p in synchronized cycling cells. Strain OCF1522 was grown as described in (A). For each time point, Mcd1p and Pds1p levels were determined by Western analysis using anti-Mcd1p Ab and anti-HA Ab, respectively, then normalized to tubulin levels as detected in (A). Relative protein amounts were calculated by comparing the normalized value for G1 cells (T = 0), arbitrarily set at 1, to that at each time point and the results plotted. Arrows indicate the distinct curve minima for Mcd1p and Pds1p-HA levels. (C) MCD1 mRNA levels are cell cycle regulated. Cells in B were subjected to Northern analysis using MCD1 probe to monitor mRNA levels. mRNA levels were normalized to ACT1 mRNA levels.

Figure 7. Model for Mitotic Chromosome Structure

Sister chromatid cohesion is established during S phase by assembly of chromosomal core components (open circles) like Mcd1p and cohesion-specific factors (hatched circles) at DNA cohesion sites (rectangles). Condensation is achieved by coalescence of the cohesion complexes by condensation-specific factors (closed circles). It should be noted that the model does not account for additional putative folds that lead to higher order compaction of the loops and axis (reviewed in Koshland and Strunnikov, 1996). The model does not demand DNA replication for condensation, assuming that these factors can associate with cohesion sites of unreplicated chromosomes. At the metaphase-to-anaphase transition, cohesion-specific factors are either degraded or modified to allow sister chromatid separation. At telophase, condensation factors are inactivated to allow decondensation (not shown).