7.06 Problem Set #4, Spring 2005

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1 7.06 Problem Set #4, Spring You re doing a mutant hunt in S. cerevisiae (budding yeast), looking for temperaturesensitive mutants that are defective in the cell cycle. You discover a mutant strain that cannot complete the cell cycle at the non-permissive temperature. You determine that the cells are blocked at the G1 to S transition. a. After treating the mutant strain with α-factor at the permissive temperature (25 C), you remove the α-factor and switch the cells to the non-permissive temperature (37 C). You then isolate different known cyclins via biochemical purification. Which cyclins should be present at high levels in these mutants at the non-permissive temperature? b. You determine that the temperature sensitive mutation is a recessive loss-of-function mutation. Outline an experiment to determine which gene is mutated in your strain. Through your experiment in part b, you determine that the mutation is in SCF, a ubiquitin ligase. To further characterize this mutant you perform the following experiment. You treat two cultures (one of wild-type cells, the other of scf-ts mutant cells) with alpha factor at 25 C. You treat two cultures (one of wild-type cells, the other of scf-ts mutant cells) with hydroxyurea at 25 C. Finally, you incubate one culture of scf-ts mutant cells at 25 C and then shift them up to 37 C for the length of one cell cycle. You make cell extracts from these five cell populations and run the extracts on SDS-PAGE gels. You then perform Western blot analyses using different antibodies against several cell cycle proteins. When blotting for Sic1, you see the following result: WT scf-ts WT scf-ts scf-ts alpha 25C alpha 25C HU 25C HU 25C 25C 37C Sic1 Sic1 1

2 c. Explain the results seen in the above gel, including why you see a shift in the migration of Sic1, and why a loss of function temperature sensitive mutation in SCF would give these results. Also include in your answer an explanation of how SCF normally interacts with Sic1 and why a loss of SCF function would cause a cell cycle block at the G1 to S transition. d. Briefly describe an experiment to prove that your explanation for the shift in the migration of Sic1 in the above blot is correct. 2. Your colleague identifies an interesting temperature sensitive (ts) mutant cdcx-ts in S. cerevisiae. He suspects that cdcx might be required for the entry into mitosis. a. In order to confirm his suspicion, he decides to perform an execution point study. He has never done one before and so you decide to help him design the experiment. How would you do an execution point study with this mutant, and what do you expect to see under the microscope and by FACS with the cdcx-ts mutant strain if cdcx really is required for entry into mitosis? b. Your colleague finds that cdcx is indeed important for entry into M phase in S. cerevisiae. You decide to study the homolog of cdcx in S. pombe (fission yeast). To this end, you isolate a cdcx-ts allele in S.pombe, and find that this allele also prevents entry into M phase at the non-permissive temperature. You suspect that your gene may function to promote M phase only when prior events in the cell cycle have been completed. Which major processes need to be complete before fission yeast cells will proceed into M phase? c. You perform a Western blot and find out that Cdc25 is present in the cdcx-ts mutant S. pombe cells at wild-type levels, even when grown at the non-permissive temperature. You conclude that that the regulation of mitotic cyclin/cdk complexes by Cdc25 must be normal in cdcx-ts mutants. Your colleague does not agree that such a conclusion can be made. Explain why the presence of Cdc25 in the cells does not guarantee that it performs its function normally. 2

3 d. You discover that CdcX is a kinase that phosphorylates and thereby activates Cdc25. You create a mutant form of the homolog of cdcx in S. pombe that encodes a constitutively active version of this kinase. What do you predict will be the phenotype of fission yeast that express this mutant form of cdcx? 3. In order to exit from mitosis, cells have to degrade the mitotic B-type cyclin/cdk complexes required to enter and proceed through mitosis. The APC (anaphase promoting complex) is responsible for destroying mitotic cyclin/cdk complex activity by ubiquitinating the B-type cyclins, leading to their proteasome-dependent degradation. This function of the APC requires association with a specificity factor termed Cdh1, and Cdh1 activity in turn is regulated by the protein phosphatase Cdc14. Cdh1 can only direct the APC towards the B-type cyclins when Cdh1 is dephosphorylated by Cdc14. a. You are interested in the dephosphorylation of Cdh1 by Cdc14 and want to know more about the regulation of Cdc14 at the end of mitosis. How would you show that Cdc14 could be regulated by sequestration in the nucleolus, and that Cdc14 is not regulated by a change in total protein levels of Cdc14 (e.g. by degradation)? b. Cdc14 is anchored in the nucleolus by a protein called Cfi1/Net1. To determine which part of Cdc14 is bound by Cfi1/Net1, you create a collection of DNA constructs containing the cdc14 gene using recombinant DNA technology. Each of these DNA constructs can be used to express a form of tagged Cdc14 that lacks a different short stretch of amino acids contained in wild-type Cdc14. How could you use these deletion constructs to figure out the region in Cdc14 to which Cfi1/Net1 binds inside yeast cells? c. From your experiments in part b, you find that a specific region ( X ) in Cdc14 is required for the interaction with Cfi1/Net1 (but is not required for any other function of Cdc14). Predict what might happen if you over-expressed a version of Cdc14 that lacked region X in yeast cells. d. What might happen if you over-expressed a short peptide containing just region X from Cdc14 in yeast cells? 3

4 e. Tem1 is a small protein GTPase involved in promoting the release of Cdc14 from the nucleolus. A temperature sensitive mutation in tem1 leads to the lethality of budding yeast cells at the non-permissive temperature, and the constitutive localization of Cdc14 to the nucleolus. Double mutant cells that contain a deletion in cfi1/net1 and the tem1- ts mutation are not temperature-sensitive lethal (although mitosis is severely impaired in these cells), and Cdc14 is constitutively released into the cytoplasm in these cells. What does this tell you about the relationship between Tem1 and Cfi1/Net1 in the signaling cascade that leads to the release of Cdc14? 4. In 2004, Marston et al. published a genetic screen carried out in Saccharomyces cerevisiae (budding yeast) for genes involved in meiotic chromosome segregation. In this screen, the authors tested each non-essential yeast gene in the genome for a potential role in meiotic chromosome segregation. They did this using the Saccharomyces Genome Deletion Collection, a collection of thousands of yeast strains, each of which carries one deletion in a different non-essential yeast gene. For the screen, each deletion strain was engineered to contain DNA binding sites for an altered form of GFP that was expressed in these strains. This form of GFP has been engineered to bind specifically to these DNA binding sites. These GFP binding sites were inserted into both chromosomes of one pair of homologous chromosomes (eg. both chromosome #3 s in a diploid cell) such that, under a fluorescent microscope, each homolog would be marked by a green GFP dot. The segregation of these GFP dots, and thus the segregation of the chromosomes that they were attached to, could then be followed during meiosis. In S. cerevisiae, one round of meiosis creates four haploid spores (together, these four spores are called a tetrad ) from one diploid cell. In a normal meiosis, each pair of homologous chromosomes in the original diploid cell will be replicated once and then will undergo two rounds of segregation as shown above, such that each of the four resulting haploid spores will contain one GFP dot (one copy of this chromosome). Aberrant chromosome segregation due to, for instance, mutations in genes that are involved in chromosome segregation, results in non-disjunction. If non-disjunction occurs in the system used in this screen, some spores end up without a dot (that is, no copy of this chromosome). Thus one can use this GFP dot system to screen for mutants that display aberrant meiotic chromosome segregation. 4

5 one tetrad = four haploid spores reproduced from Marston, et al. (2004) Science, 303: The light circles represent the bound GFP (the GFP dots ). The dark circles represent the centromeres. a. You decide to use this screen to find genes involved in meiosis in an organism related to S. cerevisiae. Luckily, this organism also has a genome deletion collection covering all non-essential genes in the genome. The first mutant you find in your screen is in a gene that is required for DNA recombination. Explain why you isolated a recombination mutant in a screen for genes required for proper meiotic chromosome segregation. b. When you analyze 100 of the tetrads that are defective in recombination, 50 of them contain two spores with zero dots each (that is, no copy of your labeled chromosome) and two spores with two dots each (that is, two copies of the labeled chromosome). The other 50 tetrads contain four spores with one dot each. In what stage of meiosis did non-disjunction occur in this mutant? Using the figure above as a guide, draw a schematic of the aberrant meioses that occur in this recombination mutant. 5

6 The second mutant you find in your screen contains a mutation in a gene that plays a role in sister chromatid cohesion. When you analyze the mutant tetrads, you find that each tetrad contains either 4, 3, or 2 spores with GFP dots, as shown in the figure below. This is because meiosis I occurred normally, but non-disjunction in meiosis II resulted in the random segregation of sister chromatids as shown in the figure below. c. What normally happens to cohesins throughout meiosis, and what type of cohesion defect may be present in this mutant to give this phenotype? d. Another student in your lab is studying point mutations in securin. She finds a particular mutant form of securin that cannot be ubiquitinated. Where in meiosis will yeast be arrested if you express this mutant form of securin during meiosis, and why? e. What would the meiotic phenotype be of a mutant strain that contains the mutation you found in part c (in the gene involved in sister chromatid cohesion) and is expressing the mutant form of securin from part d during meiosis? 6

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