Chromosomes must be accurately partitioned to daughter cells to prevent aneuploidy, a hallmark of many tumors and birth defects. Kinetochores are the macromolecular machines that segregate chromosomes by maintaining load-bearing attachments to the dynamic tips of microtubules. Here, we present the structure of isolated budding yeast kinetochore particles as visualized by electron microscopy (EM) and electron tomography of negatively stained preparations. The kinetochore appears as a ~126 nm particle containing a large central hub surrounded by multiple outer globular domains. In the presence of microtubules, some particles also have a ring that encircles the microtubule. Our data show that kinetochores bind to microtubules via multivalent attachments and lay the foundation to uncover the key mechanical and regulatory mechanisms by which kinetochores control chromosome segregation and cell division.

The kinetochore is the macromolecular complex that assembles onto centromeric DNA and orchestrates the segregation of duplicated chromosomes. More than 60 components make up the budding yeast kinetochore, including inner kinetochore proteins that bind to centromeric chromatin and outer proteins that directly interact with microtubules. However, little is known about how these components assemble into a functional kinetochore and whether there are quality control mechanisms that monitor kinetochore integrity. We previously developed a method to isolate kinetochore particles via purification of the conserved Dsn1 kinetochore protein. We find that the Mub1/Ubr2 ubiquitin ligase complex associates with kinetochore particles through the CENP-CMif2 protein. Although Mub1/Ubr2 are not stable kinetochore components in vivo, they regulate the levels of the conserved outer kinetochore protein Dsn1 via ubiquitylation. Strikingly, a deletion of Mub1/Ubr2 restores the levels and viability of a mutant Dsn1 protein, reminiscent of quality control systems that target aberrant proteins for degradation. Consistent with this, Mub1/Ubr2 help to maintain viability when kinetochores are defective. Together, our data identify a previously unknown regulatory mechanism for the conserved Dsn1 kinetochore protein. We propose that Mub1/Ubr2 are part of a quality control system that monitors kinetochore integrity, thus ensuring genomic stability.

Author Summary

The flawless execution of cell division is essential to the survival of all organisms. The loss or gain of a single chromosome, the state called aneuploidy, is a hallmark of cancer cells and is the leading cause of spontaneous miscarriages and hereditary birth defects. Segregation is mediated by the kinetochore, the macromolecular complex that assembles on each chromosome and attaches to spindle microtubules to pull chromosomes to opposite poles when cells divide. It is therefore critical to understand how kinetochores are assembled and maintained. Here, we find that the levels of a conserved kinetochore protein are regulated by proteolysis. We propose that cells have quality control systems that ensure kinetochore integrity and thus genome stability.

Non-coding transcription can trigger histone post-translational modifications forming specialized chromatin. In fission yeast, heterochromatin formation requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA production; it also displays E3-ubiquitin ligase activity in vitro. DCAFs act as substrate receptors for E3 ligases and may couple ubiquitination with histone methylation. Here, structural alignment and mutation of signature WDxR motifs in Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 methylation and siRNA amplification via two distinct, separable functions. The association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, but dispensable for processing of centromeric transcripts into siRNAs. Thus the association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone methylation and to allow RNAi to signal to chromatin.

Author Summary

Heterochromatin is a specialized form of chromatin which is frequently assembled on DNA sequences with little or no coding potential. Heterochromatin formation involves specific post-translational modifications of histone tails (e.g. methylation of histone H3 on lysine 9). In fission yeast, Schizosaccharomyces pombe, heterochromatin is found at centromeres, telomeres, and the mating type locus. Heterochromatin integrity at centromeres is important for normal chromosome segregation. The heterochromatin associated repeats at fission yeast centromeres are known to be transcribed, and these non-coding transcripts are processed into siRNAs. siRNA production is required for establishment and maintenance of H3K9 methylation. But H3K9 methylation itself is required for siRNA production. It is not known how these two processes are coupled. In this study we use structural modelling and genetic analyses to demonstrate that the heterochromatin component Raf1 plays an essential role in coupling H3K9 methylation and siRNA production. Our analyses show that the heterochromatin factors Rik1 and Raf1 can be structurally aligned with Cul4-E3 ubiquitin ligase components DDB1 and DDB2, respectively. We show that specific mutations impair the association of Raf1 with Rik1 and prevent H3K9 methylation but not siRNA production. These functional studies provide mechanistic insights into how siRNA production and chromatin modification are integrated.

We have recently established a system for purifying minichromosome in a native state from S. cerevisiae. This system is extremely efficient, and a single-step purification yields samples with sufficient purity and quantity for mass spectrometry (MS) analysis of histones and non-histone proteins tightly associated with the minichromosome. The templates can also be used in various biochemical assays in vitro, such as transcription and recombination, and might be applicable to allow EM or other studies to be performed.

Cells accumulate single-stranded DNA (ssDNA) when telomere capping, DNA replication, or DNA repair is impeded. This accumulation leads to cell cycle arrest through activating the DNA–damage checkpoints involved in cancer protection. Hence, ssDNA accumulation could be an anti-cancer mechanism. However, ssDNA has to accumulate above a certain threshold to activate checkpoints. What determines this checkpoint-activation threshold is an important, yet unanswered question. Here we identify Rif1 (Rap1-Interacting Factor 1) as a threshold-setter. Following telomere uncapping, we show that budding yeast Rif1 has unprecedented effects for a protein, inhibiting the recruitment of checkpoint proteins and RPA (Replication Protein A) to damaged chromosome regions, without significantly affecting the accumulation of ssDNA at those regions. Using chromatin immuno-precipitation, we provide evidence that Rif1 acts as a molecular “band-aid” for ssDNA lesions, associating with DNA damage independently of Rap1. In consequence, small or incipient lesions are protected from RPA and checkpoint proteins. When longer stretches of ssDNA are generated, they extend beyond the junction-proximal Rif1-protected regions. In consequence, the damage is detected and checkpoint signals are fired, resulting in cell cycle arrest. However, increased Rif1 expression raises the checkpoint-activation threshold to the point it simulates a checkpoint knockout and can also terminate a checkpoint arrest, despite persistent telomere deficiency. Our work has important implications for understanding the checkpoint and RPA–dependent DNA–damage responses in eukaryotic cells.

Author Summary

Here we identified arguably the first anti-checkpoint protein in Rif1. The term anti-checkpoint was proposed by Ted Weinert, one of the parents of the checkpoint concept, to describe a factor that stops checkpoint proteins from responding to DNA damage by other means than repair, reduced amounts of ssDNA, or adaptation [1]. No such factor has been clearly identified; potential candidates (for example, shelterin or CST complexes at chromosome ends) may reduce the amount of damage, therefore exerting an indirect “anti-checkpoint” function. Interestingly, mammalian Rif1 was once thought to be a checkpoint protein [2]. Our study indicates that Rif1 out-competes checkpoint proteins for their substrate and sets a threshold for checkpoint activation in budding yeast. Rif1 can tune down the checkpoint responses, thus permitting cells to proliferate with DNA damage, a pre-requisite for chromosomal instability, the hallmark of cancer cells. Rif1 is an important link in understanding how eukaryotic cells balance the need to proliferate with the need to preserve their genetic heritage. Finding an anti-checkpoint is not of pure theoretical interest. In the future, Rif1 inhibitors could limit proliferation of chromosomally unstable cells. Conversely, Rif1 enhancers could tune down the over-blown checkpoint responses that lead to massive cell death following different insults.

Summary

Proper centromere function is critical to maintain genomic stability and to prevent aneuploidy, a hallmark of tumors and birth defects. A conserved feature of all eukaryotic centromeres is an essential histone H3 variant called CENP-A that requires a centromere targeting domain (CATD) for its localization. Although proteolysis prevents CENP-A from mislocalizing to euchromatin, regulatory factors have not been identified. Here, we identify an E3 ubiquitin ligase called Psh1 that leads to the degradation of Cse4, the budding yeast CENP-A homolog. Cse4 overexpression is toxic to psh1Δ cells and results in euchromatic localization. Strikingly, the Cse4 centromere targeting domain is a key regulator of its stability and helps Psh1 discriminate Cse4 from histone H3. Taken together, we propose that the CATD has a previously unknown role in maintaining the exclusive localization of Cse4 by preventing its mislocalization to euchromatin via Psh1-mediated degradation.

Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) in haploid cells is generally restricted to S/G2 cell cycle phases, when DNA has been replicated and a sister chromatid is available as a repair template. This cell cycle specificity depends on cyclin-dependent protein kinases (Cdk1 in Saccharomyces cerevisiae), which initiate HR by promoting 5′–3′ nucleolytic degradation of the DSB ends. Whether Cdk1 regulates other HR steps is unknown. Here we show that yku70Δ cells, which accumulate single-stranded DNA (ssDNA) at the DSB ends independently of Cdk1 activity, are able to repair a DSB by single-strand annealing (SSA) in the G1 cell cycle phase, when Cdk1 activity is low. This ability to perform SSA depends on DSB resection, because both resection and SSA are enhanced by the lack of Rad9 in yku70Δ G1 cells. Furthermore, we found that interchromosomal noncrossover recombinants are generated in yku70Δ and yku70Δ rad9Δ G1 cells, indicating that DSB resection bypasses Cdk1 requirement also for carrying out these recombination events. By contrast, yku70Δ and yku70Δ rad9Δ cells are specifically defective in interchromosomal crossover recombination when Cdk1 activity is low. Thus, Cdk1 promotes DSB repair by single-strand annealing and noncrossover recombination by acting mostly at the resection level, whereas additional events require Cdk1-dependent regulation in order to generate crossover outcomes.

Author Summary

Homologous recombination (HR) provides an important mechanism to eliminate deleterious lesions, such as DNA double-strand breaks (DSBs). DSB repair by HR uses homologous DNA sequences as a template to form recombinants that are either crossover or noncrossover with regard to flanking parental sequences. Furthermore, a DSB flanked by direct DNA repeats can be repaired by another HR pathway called single-strand annealing (SSA). HR is generally confined to the S and G2 phases of the cell cycle, when DNA has been replicated and a sister chromatid is available as repair template. This cell cycle specificity depends on the activity of cyclin-dependent kinases (Cdks), which regulate initiation of HR by promoting nucleolytic degradation (resection) of the DSB ends. Whether Cdks regulate other HR steps is unknown. Here, we show that Saccharomyces cerevisiae Cdk1 has a dual function in HR: it promotes SSA and noncrossover recombination by regulating primarily the resection step, whereas it plays additional functions in allowing recombination accompanied by crossovers. As crossovers during mitotic cell growth have the potential for deleterious genome rearrangements when the sister chromatid is not used as repair template, this additional function of Cdk1 in promoting crossovers can provide another safety mechanism to ensure genome stability.

Kinetochores are macromolecular machines that couple chromosomes to dynamic microtubule tips during cell division, thereby generating force to segregate the chromosomes1,2. Accurate segregation depends on selective stabilization of correct ‘bi-oriented’ kinetochore-microtubule attachments, which come under tension due to opposing forces exerted by microtubules3. Tension is thought to stabilize these bi-oriented attachments indirectly, by suppressing the destabilizing activity of a kinase, Aurora B4,5. However, a complete mechanistic understanding of the role of tension requires reconstitution of kinetochore-microtubule attachments for biochemical and biophysical analyses in vitro. Here we show that native kinetochore particles retaining the majority of kinetochore proteins can be purified from budding yeast and used to reconstitute dynamic microtubule attachments. Individual kinetochore particles maintain load-bearing associations with assembling and disassembling ends of single microtubules for >30 min, providing a close match to the persistent coupling seen in vivo between budding yeast kinetochores and single microtubules6. Moreover, tension increases the lifetimes of the reconstituted attachments directly, via a catch bond-like mechanism that does not require Aurora B7-10. Based on these findings, we propose that tension selectively stabilizes proper kinetochore-microtubule attachments in vivo through a combination of direct mechanical stabilization and tension-dependent phosphoregulation.

Semi-conservative segregation of nucleosomes to sister chromatids during DNA replication creates gaps that must be filled by new nucleosome assembly. We analyzed the cell-cycle timing of centromeric chromatin assembly in Drosophila, which contains the H3 variant CID (CENP-A in humans), as well as CENP-C and CAL1, which are required for CID localization. Pulse-chase experiments show that CID and CENP-C levels decrease by 50% at each cell division, as predicted for semi-conservative segregation and inheritance, whereas CAL1 displays higher turnover. Quench-chase-pulse experiments demonstrate that there is a significant lag between replication and replenishment of centromeric chromatin. Surprisingly, new CID is recruited to centromeres in metaphase, by a mechanism that does not require an intact mitotic spindle, but does require proteasome activity. Interestingly, new CAL1 is recruited to centromeres before CID in prophase. Furthermore, CAL1, but not CENP-C, is found in complex with pre-nucleosomal CID. Finally, CENP-C displays yet a different pattern of incorporation, during both interphase and mitosis. The unusual timing of CID recruitment and unique dynamics of CAL1 identify a distinct centromere assembly pathway in Drosophila and suggest that CAL1 is a key regulator of centromere propagation.

Author Summary

The centromere is essential for kinetochore formation, chromosome attachment to spindle microtubules, and equal segregation of the genome to daughter cells. Centromeres are epigenetically inherited through a unique type of chromatin which contains centromere-specific proteins. At each round of DNA replication, centromeric proteins become diluted and must be replenished to ensure faithful maintenance of the centromere locus through cell division. Whether divergent eukaryotes share a common strategy for centromere identity and propagation remains an unanswered question. Here, we examine how Drosophila centromere proteins re-distribute after replication, and we determine the cell-cycle dynamics of their replenishment. We show that three chromatin components required for centromere maintenance display distinct dynamics during the cell cycle; surprisingly, two components are assembled at centromeres during mitosis. These results suggest a new model for regulation of centromere assembly in Drosophila, which emphasizes a key role for the Dipteran-specific protein CAL1.

Telomerase is a telomere dedicated reverse transcriptase that replicates the very ends of eukaryotic chromosomes. Saccharomyces cerevisiae telomerase consists of TLC1 (the RNA template), Est2 (the catalytic subunit), and two accessory proteins, Est1 and Est3, that are essential in vivo for telomerase activity but are dispensable for catalysis in vitro. Est1 functions in both recruitment and activation of telomerase. The association of Est3 with telomeres occurred largely in late S/G2 phase, the time when telomerase acts and Est1 telomere binding occurs. Est3 telomere binding was Est1-dependent. This dependence is likely due to a direct interaction between the two proteins, as purified recombinant Est1 and Est3 interacted in vitro. Est3 abundance was neither cell cycle–regulated nor Est1-dependent. Est3 was the most abundant of the three Est proteins (84.3±13.3 molecules per cell versus 71.1±19.2 for Est1 and 37.2±6.5 for Est2), so its telomere association and/or activity is unlikely to be limited by its relative abundance. Est2 and Est1 telomere binding was unaffected by the absence of Est3. Taken together, these data indicate that Est3 acts downstream of both Est2 and Est1 and that the putative activation function of Est1 can be explained by its role in recruiting Est3 to telomeres.

Author Summary

Owing to the biochemical properties of DNA polymerases, the free ends of linear chromosomes, called telomeres, cannot be replicated by the same mechanisms that suffice for the rest of the chromosome. Instead they are maintained by a telomere-dedicated reverse transcriptase called telomerase that uses its integral RNA component as the template to make more telomeric DNA. In baker's yeast, telomerase is composed of a catalytic subunit (Est2), the templating RNA (TLC1), and two accessory proteins, Est1 and Est3. Here we show that Est3 associates with telomeres late in the cell cycle, at the same time when telomerase is active, and this binding was Est1-dependent, even though Est3 abundance was neither cell cycle–regulated nor Est1-dependent. Since purified Est3 and Est1interacted in vitro, Est1-dependent recruitment of Est3 is probably due to direct protein–protein interaction. Neither Est1 nor Est2 telomere binding was Est3-dependent. Thus, Est3 acts downstream of telomerase recruitment to promote telomerase activity, and the telomerase activation functions of Est1 can be explained by its recruiting Est3 to telomeres.

To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene CDC13 (cdc13-1) or containing a null mutation in the DNA damage response and telomere capping gene YKU70 (yku70Δ). We performed Quantitative Fitness Analysis (QFA) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform QFA, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. QFA reveals that as many as 5% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with cdc13-1, yku70Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated RNA decay (NMD) pathway which, when disabled, suppress the conditional cdc13-1 mutation but enhance the null yku70Δ mutation. We show that the suppressing/enhancing role of the NMD pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to cdc13-1 and yku70Δ. QFA is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology.

Author Summary

Telomeres, specialized structures at the end of linear chromosomes, ensure that chromosome ends are not mistakenly treated as DNA double-strand breaks. Defects in the telomere cap contribute to ageing and cancer. In yeast, defects in telomere capping proteins can cause telomeres to behave like double-strand breaks. To better understand the telomere and responses to capping failure, we have combined a systematic yeast gene deletion library with mutations affecting important yeast telomere capping proteins, Cdc13 or Yku70. Quantitative Fitness Analysis (QFA) was used to accurately measure the fitness of thousands of different yeast strains containing telomere capping defects and additional deletion mutations. Interestingly, we find that many gene deletions suppress one type of telomere capping defect while enhancing another. Through QFA, we can begin to define the roles of different gene products in contributing to different aspects of the telomere cap. Strikingly, mutations in nonsense-mediated mRNA decay pathways, which degrade many RNA molecules, suppress the cdc13-1 defect while enhancing the yku70Δ defect. QFA is widely applicable and will be useful for understanding other aspects of yeast cell biology.

Coordination of the cell cycle with developmental events is crucial for generation of tissues during development and their maintenance in adults. Defects in that coordination can shift the balance of cell fates with devastating clinical effects. Yet our understanding of the molecular mechanisms integrating core cell cycle regulators with developmental regulators remains in its infancy. This work focuses on the interplay between cell cycle and developmental regulators in the Caenorhabditis elegans germline. Key developmental regulators control germline stem cells (GSCs) to self-renew or begin differentiation: FBF RNA–binding proteins promote self-renewal, while GLD RNA regulatory proteins promote meiotic entry. We first discovered that many but not all germ cells switch from the mitotic into the meiotic cell cycle after RNAi depletion of CYE-1 (C. elegans cyclin E) or CDK-2 (C. elegans Cdk2) in wild-type adults. Therefore, CYE-1/CDK-2 influences the mitosis/meiosis balance. We next found that GLD-1 is expressed ectopically in GSCs after CYE-1 or CDK-2 depletion and that GLD-1 removal can rescue cye-1/cdk-2 defects. Therefore, GLD-1 is crucial for the CYE-1/CDK-2 mitosis/meiosis control. Indeed, GLD-1 appears to be a direct substrate of CYE-1/CDK-2: GLD-1 is a phosphoprotein; CYE-1/CDK-2 regulates its phosphorylation in vivo; and human cyclin E/Cdk2 phosphorylates GLD-1 in vitro. Transgenic GLD-1(AAA) harbors alanine substitutions at three consensus CDK phosphorylation sites. GLD-1(AAA) is expressed ectopically in GSCs, and GLD-1(AAA) transgenic germlines have a smaller than normal mitotic zone. Together these findings forge a regulatory link between CYE-1/CDK-2 and GLD-1. Finally, we find that CYE-1/CDK-2 works with FBF-1 to maintain GSCs and prevent their meiotic entry, at least in part, by lowering GLD-1 abundance. Therefore, CYE-1/CDK-2 emerges as a critical regulator of stem cell maintenance. We suggest that cyclin E and Cdk-2 may be used broadly to control developmental regulators.

Author Summary

How are cell cycle regulators coordinated with cell fate and patterning regulators during development? Several studies suggest that core cell cycle regulators can influence development, but molecular mechanisms remain unknown for the most part. We have tackled this question in the nematode Caenorhabditis elegans. Specifically, we have investigated how cell cycle regulators affect germline stem cells. Previous work had identified conserved developmental regulators that control the choice between self-renewal and differentiation in this tissue. In this work, we focus on cyclin E/Cdk-2, which is a core cell cycle kinase, and GLD-1, a key regulator of stem cell differentiation. Our work shows that cyclin E/Cdk-2 phosphorylates GLD-1 and lowers its abundance in stem cells via a post-translational mechanism. We also find that a post-transcriptional GLD-1 regulator, called FBF-1, works synergistically with cyclin E/Cdk-2 to ensure that GLD-1 is off in germline stem cells. When both FBF-1 and cyclin E/Cdk-2 are removed, the stem cells are no longer maintained and instead differentiate. Our findings reveal that cyclin E/Cdk-2 kinase is a critical stem cell regulator and provide a paradigm for how cell cycle regulators interface with developmental regulators.

Telomere integrity in budding yeast depends on the CST (Cdc13-Stn1-Ten1) and shelterin-like (Rap1-Rif1-Rif2) complexes, which are thought to act independently from each other. Here we show that a specific functional interaction indeed exists among components of the two complexes. In particular, unlike RIF2 deletion, the lack of Rif1 is lethal for stn1ΔC cells and causes a dramatic reduction in viability of cdc13-1 and cdc13-5 mutants. This synthetic interaction between Rif1 and the CST complex occurs independently of rif1Δ-induced alterations in telomere length. Both cdc13-1 rif1Δ and cdc13-5 rif1Δ cells display very high amounts of telomeric single-stranded DNA and DNA damage checkpoint activation, indicating that severe defects in telomere integrity cause their loss of viability. In agreement with this hypothesis, both DNA damage checkpoint activation and lethality in cdc13 rif1Δ cells are partially counteracted by the lack of the Exo1 nuclease, which is involved in telomeric single-stranded DNA generation. The functional interaction between Rif1 and the CST complex is specific, because RIF1 deletion does not enhance checkpoint activation in case of CST-independent telomere capping deficiencies, such as those caused by the absence of Yku or telomerase. Thus, these data highlight a novel role for Rif1 in assisting the essential telomere protection function of the CST complex.

Author Summary

Protection of chromosome ends is crucial for maintaining chromosome stability and genome integrity, and its failure leads to genome rearrangements that may facilitate carcinogenesis. This protection is achieved by the packaging of chromosome ends into protective structures called telomeres that prevent DNA repair/recombination activities. Telomeric DNA is bound and stabilized by two protein complexes named CST and shelterin, which are present in a wide range of multicellular organisms. Whether structural and functional connections exist between these two capping complexes is an important issue in telomere biology. Here, we investigate this topic by analyzing the consequences of disabling the two Saccharomyces cerevisiae shelterin-like components, Rif1 and Rif2, in different hypomorphic mutants defective in CST components. We demonstrate that Rif1 plays a previously unanticipated role in assisting the essential telomere protection function of the CST complex, indicating a tight coupling between CST and Rif1. As CST complexes have been recently identified also in other organisms, including humans, which all rely on shelterin for telomere protection, this functional link between CST and shelterin might be an evolutionarily conserved common feature to ensure telomere integrity.

The yeast prion [SWI+], formed of heritable amyloid aggregates of the Swi1 protein, results in a partial loss of function of the SWI/SNF chromatin-remodeling complex, required for the regulation of a diverse set of genes. Our genetic analysis revealed that [SWI+] propagation is highly dependent upon the action of members of the Hsp70 molecular chaperone system, specifically the Hsp70 Ssa, two of its J-protein co-chaperones, Sis1 and Ydj1, and the nucleotide exchange factors of the Hsp110 family (Sse1/2). Notably, while all yeast prions tested thus far require Sis1, [SWI+] is the only one known to require the activity of Ydj1, the most abundant J-protein in yeast. The C-terminal region of Ydj1, which contains the client protein interaction domain, is required for [SWI+] propagation. However, Ydj1 is not unique in this regard, as another, closely related J-protein, Apj1, can substitute for it when expressed at a level approaching that of Ydj1. While dependent upon Ydj1 and Sis1 for propagation, [SWI+] is also highly sensitive to overexpression of both J-proteins. However, this increased prion-loss requires only the highly conserved 70 amino acid J-domain, which serves to stimulate the ATPase activity of Hsp70 and thus to stabilize its interaction with client protein. Overexpression of the J-domain from Sis1, Ydj1, or Apj1 is sufficient to destabilize [SWI+]. In addition, [SWI+] is lost upon overexpression of Sse nucleotide exchange factors, which act to destabilize Hsp70's interaction with client proteins. Given the plethora of genes affected by the activity of the SWI/SNF chromatin-remodeling complex, it is possible that this sensitivity of [SWI+] to the activity of Hsp70 chaperone machinery may serve a regulatory role, keeping this prion in an easily-lost, meta-stable state. Such sensitivity may provide a means to reach an optimal balance of phenotypic diversity within a cell population to better adapt to stressful environments.

Author Summary

Yeast prions are heritable genetic elements, formed spontaneously by aggregation of a single protein. Prions can thus generate diverse phenotypes in a dominant, non-Mendelian fashion, without a corresponding change in chromosomal gene structure. Since the phenotypes caused by the presence of a prion are thought to affect the ability of cells to survive under different environmental conditions, those that have global effects on cell physiology are of particular interest. Here we report the results of a study of one such prion, [SWI+], formed by a component of the SWI/SNF chromatin-remodeling complex, which is required for the regulation of a diverse set of genes. We found that, compared to previously well-studied prions, [SWI+] is highly sensitive to changes in the activities of molecular chaperones, particularly components of the Hsp70 machinery. Both under- and over-expression of components of this system initiated rapid loss of the prion from the cell population. Since expression of molecular chaperones, often known as heat shock proteins, are known to vary under diverse environmental conditions, such “chaperone sensitivity” may allow alteration of traits that under particular environmental conditions convey a selective advantage and may be a common characteristic of prions formed from proteins involved in global gene regulation.

During cell division, the spindle checkpoint ensures accurate chromosome segregation by monitoring the kinetochore–microtubule interaction and delaying the onset of anaphase until each pair of sister chromosomes is properly attached to microtubules. The spindle checkpoint is deactivated as chromosomes start moving toward the spindles in anaphase, but the mechanisms by which this deactivation and adaptation to prolonged mitotic arrest occur remain obscure. Our results strongly suggest that Cdc28-mediated phosphorylation of Bub1 at T566 plays an important role for the degradation of Bub1 in anaphase, and the phosphorylation is required for adaptation of the spindle checkpoint to prolonged mitotic arrest.

Author Summary

The spindle checkpoint protects cells from aneuploidy by monitoring the status of the kinetochore-microtubule attachment. Defects in this checkpoint pathway and in kinetochore-microtubule attachment can cause substantial aneuploidy in cells. The duration of the mitotic arrest induced by the spindle checkpoint is not indefinite: cells eventually exit from mitosis and re-enter interphase. Because continued activation of the spindle checkpoint is lethal, adaptation to the spindle checkpoint arrest is essential so that cells have a chance for survival as opposed to certain death. However, adaptation of the spindle checkpoint has a flip side—adapted cells could have an increased chance of aneuploidy due to premature mitotic exit. Thus, it is essential that this mechanism be regulated appropriately. Despite the importance of understanding the adaptation of the spindle checkpoint, little is known to date about this mechanism. We found that Cdc28-mediated phosphorylation of Bub1 at T566 plays an important role for adaptation of the spindle checkpoint, a finding providing the molecular insight on how adaptation to prolonged mitotic arrest induced by the spindle checkpoint occurs.

Summary

Accurate chromosome segregation depends on sister kinetochores coming under tension when they make bioriented attachments to microtubules from opposite poles. The spindle checkpoint halts the cell cycle in response to defects in generating proper attachments or tension on kinetochores [1, 2], although the precise signal that triggers the checkpoint is unclear because tension and attachment are coupled [3]. The target of the checkpoint is the Cdc20 protein that initiates the anaphase promoting complex (APC)-dependent degradation of the anaphase inhibitor Pds1/securin [4]. Although the molecular details of spindle checkpoint activation are still being elucidated, phosphorylation by at least four kinases is a crucial requirement [5]. However, less is known about the mechanisms that silence the checkpoint once kinetochores biorient. Here, we show that the catalytic subunit of the budding yeast protein phosphatase I, Glc7, regulates exit from the checkpoint. Glc7 overexpression prevents spindle checkpoint activation in response to both tension and attachment defects. Although glc7 mutant cells are able to efficiently release from a non-checkpoint-mediated metaphase arrest, they are uniquely sensitive to transient spindle checkpoint activation due to a failure in spindle checkpoint exit. We therefore propose that PP1 activity silences the checkpoint by reversing key phosphorylation events.

The FACT complex participates in chromatin assembly and disassembly during transcription elongation. The yeast mutants affected in the SPT16 gene, which encodes one of the FACT subunits, alter the expression of G1 cyclins and exhibit defects in the G1/S transition. Here we show that the dysfunction of chromatin reassembly factors, like FACT or Spt6, down-regulates the expression of the gene encoding the cyclin that modulates the G1 length (CLN3) in START by specifically triggering the repression of its promoter. The G1 delay undergone by spt16 mutants is not mediated by the DNA–damage checkpoint, although the mutation of RAD53, which is otherwise involved in histone degradation, enhances the cell-cycle defects of spt16-197. We reveal how FACT dysfunction triggers an accumulation of free histones evicted from transcribed chromatin. This accumulation is enhanced in a rad53 background and leads to a delay in G1. Consistently, we show that the overexpression of histones in wild-type cells down-regulates CLN3 in START and causes a delay in G1. Our work shows that chromatin reassembly factors are essential players in controlling the free histones potentially released from transcribed chromatin and describes a new cell cycle phenomenon that allows cells to respond to excess histones before starting DNA replication.

Author Summary

Lengthy genomic DNA is packed in a highly organized nucleoprotein structure called chromatin, whose basic subunit is the nucleosome which is formed by DNA wrapped around an octamer of proteins called histones. Nucleosomes need to be disassembled to allow DNA transcription by RNA polymerases. An essential factor for the disassembly/reassembly process during DNA transcription is the FACT complex. We investigated a phenotype of yeast FACT mutants, a delay in a specific step of the cell cycle division process immediately prior to starting DNA replication. The dysfunction caused by the FACT mutation causes a downregulation of a gene, CLN3, which controls the length of that specific step of the cell cycle. FACT dysfunction also increases the level of the free histones released from chromatin during transcription, and the phenotype of the Spt16 mutant is enhanced by a second mutation affecting a protein that regulates DNA repair and excess histone degradation. Moreover, we show that the overexpression of histones causes a cell cycle delay before DNA replication in wild-type cells. Our results point out a so-far unknown connection between chromatin dynamics and the regulation of the cell cycle.

Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes, kinesin-5 motors, and the SCFCdc4 ubiquitin ligase are required for the separation of spindle poles and assembly of a bipolar spindle. It has been suggested that, in budding yeast, B-type cyclin/CDK (Clb/Cdc28) complexes promote spindle pole separation by inhibiting the degradation of the kinesins-5 Kip1 and Cin8 by the anaphase-promoting complex (APCCdh1). We have determined, however, that the Kip1 and Cin8 proteins are present at wild-type levels in the absence of Clb/Cdc28 kinase activity. Here, we show that Kip1 and Cin8 are in vitro targets of Clb2/Cdc28 and that the mutation of conserved CDK phosphorylation sites on Kip1 inhibits spindle pole separation without affecting the protein's in vivo localization or abundance. Mass spectrometry analysis confirms that two CDK sites in the tail domain of Kip1 are phosphorylated in vivo. In addition, we have determined that Sic1, a Clb/Cdc28-specific inhibitor, is the SCFCdc4 target that inhibits spindle pole separation in cells lacking functional Cdc4. Based on these findings, we propose that Clb/Cdc28 drives spindle pole separation by direct phosphorylation of kinesin-5 motors.

Author Summary

The assembly of a bipolar mitotic spindle is essential for the accurate segregation of sister chromatids during mitosis and, hence, for successful cell division. Spindle assembly depends on the successful duplication of the spindle poles, followed by their separation to opposing ends of the cell. Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle, the relevant CDK targets have not been identified. Motor proteins of the kinesin-5 family generate movement on the microtubules that make up the spindle and are believed to power spindle pole separation. By employing the budding yeast Saccharomyces cerevisiae as a model, we have found evidence that cyclin/CDKs control spindle assembly by phosphorylating the kinesins-5 Kip1 and Cin8. When phosphorylation at a conserved CDK site in the motor domain of Kip1 is blocked, spindle pole separation is greatly diminished but neither protein abundance nor localization is affected. We have also obtained direct evidence by mass spectrometry that Kip1 and Cin8 are phosphorylated in vivo at consensus CDK sites in their tail domains. Our findings suggest that B-cyclin/CDKs regulate spindle assembly by regulating kinesin-5 motor activity.

The activation of phase-specific cyclin-dependent kinases (Cdks) is associated with ordered cell cycle transitions. Among the mammalian Cdks, only Cdk1 is essential for somatic cell proliferation. Cdk1 can apparently substitute for Cdk2, Cdk4, and Cdk6, which are individually dispensable in mice. It is unclear if all functions of non-essential Cdks are fully redundant with Cdk1. Using a genetic approach, we show that Cdk2, the S-phase Cdk, uniquely controls the G2/M checkpoint that prevents cells with damaged DNA from initiating mitosis. CDK2-nullizygous human cells exposed to ionizing radiation failed to exclude Cdk1 from the nucleus and exhibited a marked defect in G2/M arrest that was unmasked by the disruption of P53. The DNA replication licensing protein Cdc6, which is normally stabilized by Cdk2, was physically associated with the checkpoint regulator ATR and was required for efficient ATR-Chk1-Cdc25A signaling. These findings demonstrate that Cdk2 maintains a balance of S-phase regulatory proteins and thereby coordinates subsequent p53-independent G2/M checkpoint activation.

Author Summary

Metazoan cells contain multiple Cdks that regulate cell cycle progression. Recent studies have shown that mouse cells can grow normally with just Cdk1. The roles of the non-essential Cdks remain a fundamental question. In this study, we describe the generation and detailed characterization of CDK2-knockout human somatic cells. Our study demonstrates that Cdk2 is required for robust DNA damage checkpoint signaling. Loss of Cdk2 caused a marked deficiency in the G2/M arrest—a basic response to DNA damage—in cells that were also nullizygous for P53. We propose that the multiple Cdks present in metazoan cells provide a mechanism by which the cell cycle can be efficiently halted after DNA damage. Significantly, this study reveals a heretofore unrecognized dependence for Cdk2 in p53-deficient cancer cells.

Checkpoints are surveillance mechanisms that constitute a barrier to oncogenesis by preserving genome integrity. Loss of checkpoint function is an early event in tumorigenesis. Polo kinases (Plks) are fundamental regulators of cell cycle progression in all eukaryotes and are frequently overexpressed in tumors. Through their polo box domain, Plks target multiple substrates previously phosphorylated by CDKs and MAPKs. In response to DNA damage, Plks are temporally inhibited in order to maintain the checkpoint-dependent cell cycle block while their activity is required to silence the checkpoint response and resume cell cycle progression. Here, we report that, in budding yeast, overproduction of the Cdc5 polo kinase overrides the checkpoint signaling induced by double strand DNA breaks (DSBs), preventing the phosphorylation of several Mec1/ATR targets, including Ddc2/ATRIP, the checkpoint mediator Rad9, and the transducer kinase Rad53/CHK2. We also show that high levels of Cdc5 slow down DSB processing in a Rad9-dependent manner, but do not prevent the binding of checkpoint factors to a single DSB. Finally, we provide evidence that Sae2, the functional ortholog of human CtIP, which regulates DSB processing and inhibits checkpoint signaling, is regulated by Cdc5. We propose that Cdc5 interferes with the checkpoint response to DSBs acting at multiple levels in the signal transduction pathway and at an early step required to resect DSB ends.

Author Summary

Double strand DNA breaks (DSBs) are dangerous chromosomal lesions that can lead to genome rearrangements, genetic instability, and cancer if not accurately repaired. Eukaryotes activate a surveillance mechanism, called DNA damage checkpoint, to arrest cell cycle progression and facilitate DNA repair. Several factors are physically recruited to DSBs, and specific kinases phosphorylate multiple targets leading to checkpoint activation. Budding yeast is a good model system to study checkpoint, and most of the factors involved in the DSBs response were originally characterized in this organism. Using the yeast Saccharomyces cerevisiae, we explored the functional role of polo kinase Cdc5 in regulating the DSB–induced checkpoint. Polo kinases have been previously involved in checkpoint inactivation in all the eukaryotes, and they are frequently overexpressed in cancer cells. We found that elevated levels of Cdc5 affect the cellular response to a DSB at different steps, altering DNA processing and overriding the signal triggered by checkpoint kinases. Our findings suggest that Cdc5 likely regulates multiple factors in response to a DSB and provide a rationale for a proteome-wide screening to identify targets of polo kinases in yeast and human cells. Such information may have a practical application to design specific molecular tools for cancer therapy. Two related papers published in PLoS Biology—by Vidanes et al., doi:10.1371/journal.pbio.1000286, and van Vugt et al., doi:10.1371/journal.pbio.1000287—similarly investigate the phenomenon of checkpoint adaptation/overriding.

Accurate chromosome segregation depends on sister kinetochores making bioriented attachments to microtubules from opposite poles. An essential regulator of biorientation is the Ipl1/Aurora B protein kinase that destabilizes improper microtubule–kinetochore attachments. To identify additional biorientation pathways, we performed a systematic genetic analysis between the ipl1-321 allele and all nonessential budding yeast genes. One of the mutants, mcm21Δ, precociously separates pericentromeres and this is associated with a defect in the binding of the Scc2 cohesin-loading factor at the centromere. Strikingly, Mcm21 becomes essential for biorientation when Ipl1 function is reduced, and this appears to be related to its role in pericentromeric cohesion. When pericentromeres are artificially tethered, Mcm21 is no longer needed for biorientation despite decreased Ipl1 activity. Taken together, these data reveal a specific role for pericentromeric linkage in ensuring kinetochore biorientation.

Localization of specific mRNAs is an important mechanism through which cells achieve polarity and direct asymmetric growth. Based on a framework established in Saccharomyces cerevisiae, we describe a She3-dependent RNA transport system in Candida albicans, a fungal pathogen of humans that grows as both budding (yeast) and filamentous (hyphal and pseudohyphal) forms. We identify a set of 40 mRNAs that are selectively transported to the buds of yeast-form cells and to the tips of hyphae, and we show that many of the genes encoded by these mRNAs contribute to hyphal development, as does the transport system itself. Although the basic system of mRNA transport is conserved between S. cerevisiae and C. albicans, we find that the cargo mRNAs have diverged considerably, implying that specific mRNAs can easily move in and out of transport control over evolutionary timescales. The differences in mRNA cargos likely reflect the distinct selective pressures acting on the two species.

Author Summary

Generation of cellular polarity – asymmetry in shape, protein distribution, and/or sub-cellular function – is an essential feature of most eukaryotic cells and underlies such diverse processes as differentiation, mating, nutrient acquisition, and growth. Localization of specific mRNAs is one mechanism through which cells achieve polarity. We describe an RNA transport system in Candida albicans, a fungal pathogen of humans, that grows in both single cell (budding yeast) and filamentous (hyphal and pseudohyphal) forms. Hyphae are chains of elongated cells that remain attached after cell division and exhibit highly polarized growth at their tips. We show that the C. albicans She3-dependent RNA transport system binds to 40 mRNAs and transports these mRNAs to yeast buds and to the tips of hyphae. Both the transport system itself and many of the genes encoded by transported mRNAs are required for normal growth and function of hyphae. Although the basic transport mechanism appears conserved with that of the model yeast, Saccharomyces cerevisiae, the cargo mRNAs are largely distinct. The apparently rapid evolution of the transported mRNAs probably reflects distinct selective pressures acting on the two organisms.

Telomeres are nucleoprotein structures located at the linear ends of eukaryotic chromosomes. Telomere integrity is required for cell proliferation and survival. Although the vast majority of eukaryotic species use telomerase as a primary means for telomere maintenance, a few species can use recombination or retrotransposon-mediated maintenance pathways. Since Saccharomyces cerevisiae can use both telomerase and recombination to replicate telomeres, budding yeast provides a useful system with which to examine the evolutionary advantages of telomerase and recombination in preserving an organism or cell under natural selection. In this study, we examined the life span in telomerase-null, post-senescent type II survivors that have employed homologous recombination to replicate their telomeres. Type II recombination survivors stably maintained chromosomal integrity but exhibited a significantly reduced replicative life span. Normal patterns of cell morphology at the end of a replicative life span and aging-dependent sterility were observed in telomerase-null type II survivors, suggesting the type II survivors aged prematurely in a manner that is phenotypically consistent with that of wild-type senescent cells. The shortened life span of type II survivors was extended by calorie restriction or TOR1 deletion, but not by Fob1p inactivation or Sir2p over-expression. Intriguingly, rDNA recombination was decreased in type II survivors, indicating that the premature aging of type II survivors was not caused by an increase in extra-chromosomal rDNA circle accumulation. Reintroduction of telomerase activity immediately restored the replicative life span of type II survivors despite their heterogeneous telomeres. These results suggest that telomere recombination accelerates cellular aging in telomerase-null type II survivors and that telomerase is likely a superior telomere maintenance pathway in sustaining yeast replicative life span.

Author Summary

Telomeres are the specialized structures at the ends of eukaryotic linear chromosomes. The simple guanine-rich DNA repeats at telomeres and their associated proteins are important for chromosome stability. Most eukaryotic species have evolved an enzyme named telomerase to replicate their telomeric DNA. Telomerase usually contains a protein catalytic subunit and a RNA template subunit. A few eukaryotic species can use either telomere recombination or retrotransposon-mediated transposition to accomplish telomere elongation. Interestingly, the baker's yeast Saccharomyces cerevisiae can use both telomerase and recombination to replicate telomeres. In this study, we utilize this unique eukaryotic model system to compare the efficiency of these two mechanisms in the maintenance of cellular function and life span. Telomerase-null cells that used recombination to elongate telomeres were able to maintain relatively stable chromosomes; however, they exhibited a shortened replicative life span which may represent a novel aging pathway. Reintroduction of telomerase inhibited telomere recombination and restored the replicative life span of these cells, implying that telomerase is superior to telomere recombination in the regulation of yeast replicative life span.

TORC1 is a central regulator of cell growth in response to amino acid availability, yet little is known about how it is regulated. Here, we performed a reverse genetic screen in yeast for genes necessary to inactivate TORC1. The screen consisted of monitoring the expression of a TORC1 sensitive GFP-based transcriptional reporter in all yeast deletion strains using flow cytometry. We find that in response to amino acid starvation, but not to carbon starvation or rapamycin treatment, cells lacking NPR2 and NPR3 fail to fully (1) activate transcription factors Gln3/Gat1, (2) dephosphorylate TORC1 effector Npr1, and (3) repress ribosomal protein gene expression. Both mutants show proliferation defects only in media containing a low quality nitrogen source, such as proline or ammonia, whereas no defects are evident when cells are grown in the presence of glutamine or peptone mixture. Proliferation defects in npr2Δ and npr3Δ cells can be completely rescued by artificially inhibiting TORC1 by rapamycin, demonstrating that overactive TORC1 in both strains prevents their ability to adapt to an environment containing a low quality nitrogen source. A biochemical purification of each demonstrates that Npr2 and Npr3 form a heterodimer, and this interaction is evolutionarily conserved since the human homologs of NPR2 and NPR3 (NPRL2 and NPRL3, respectively) also co-immunoprecipitate. We conclude that, in yeast, the Npr2/3 complex mediates an amino acid starvation signal to TORC1.

Author Summary

Before a eukaryotic cell commits to cell division it must be large enough so that both daughter cells would be of viable size. The control of cell size is largely mediated by nutritional input signals via an evolutionarily conserved protein complex termed TORC1. In particular, TORC1 has been shown to sense the level of amino acids and its activity correlates with the level of amino acids present in the media. Yet, it is largely unknown how TORC1 senses amino acids. Here we demonstrate that the evolutionarily conserved Npr2/3 complex mediates the amino acid scarcity signal to TORC1. Cells lacking NPR2 and NPR3 genes fail to inactivate TORC1 when amino acids are scarce. Overactive TORC1 prevents these cells from adapting to an amino acid scarce environment, and, as a result, these cells are unable to proliferate in media that is not rich in amino acids. Artificially inhibiting TORC1 with rapamycin can completely rescue these defects. These results provide insight into how cells sense amino acid deficiency. Moreover, as deletions of NPR2 have been implicated in tumor growth, these results offer a fertile ground to study the role overactive TORC1 might play in those cancers.