1
|
Stage-Specific Genetic Interaction between FgYCK1 and FgBNI4 during Vegetative Growth and Conidiation in Fusarium graminearum. Int J Mol Sci 2022; 23:ijms23169106. [PMID: 36012372 PMCID: PMC9408904 DOI: 10.3390/ijms23169106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
CK1 casein kinases are well conserved in filamentous fungi. However, their functions are not well characterized in plant pathogens. In Fusarium graminearum, deletion of FgYCK1 caused severe growth defects and loss of conidiation, fertility, and pathogenicity. Interestingly, the Fgyck1 mutant was not stable and often produced fast-growing spontaneous suppressors. Suppressor mutations were frequently identified in the FgBNI4 gene by sequencing analyses. Deletion of the entire FgBNI4 or disruptions of its conserved C-terminal region could suppress the defects of Fgyck1 in hyphal growth and conidiation, indicating the genetic relationship between FgYCK1 and FgBNI4. Furthermore, the Fgyck1 mutant showed defects in polarized growth, cell wall integrity, internalization of FgRho1 and vacuole fusion, which were all partially suppressed by deletion of FgBNI4. Overall, our results indicate a stage-specific functional relationship between FgYCK1 and FgBNI4, possibly via FgRho1 signaling for regulating polarized hyphal growth and cell wall integrity.
Collapse
|
2
|
Wu Z, Wang J, Niu C, Liu C, Zheng F, Li Q. Transcriptomic and metabolomic analysis reveals genes related to stress tolerance in high gravity brewing. World J Microbiol Biotechnol 2022; 38:59. [DOI: 10.1007/s11274-021-03115-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
|
3
|
Kuzmin E, Taylor JS, Boone C. Retention of duplicated genes in evolution. Trends Genet 2022; 38:59-72. [PMID: 34294428 PMCID: PMC8678172 DOI: 10.1016/j.tig.2021.06.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Abstract
Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Duplicated genes may also be retained as a consequence of structural and functional entanglement. Advances in human gene editing have enabled the interrogation of duplicated genes in the human genome, providing new tools to evaluate the relative contributions of each of these factors to duplicate gene retention and the evolution of genome structure.
Collapse
Affiliation(s)
- Elena Kuzmin
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Ave des Pins Ouest, Montreal, QC, Canada H3A 1A3.
| | - John S Taylor
- Department of Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, Canada V8W 2Y2
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1; RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan, 351-0198
| |
Collapse
|
4
|
Roncero C, Celador R, Sánchez N, García P, Sánchez Y. The Role of the Cell Integrity Pathway in Septum Assembly in Yeast. J Fungi (Basel) 2021; 7:jof7090729. [PMID: 34575767 PMCID: PMC8471060 DOI: 10.3390/jof7090729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022] Open
Abstract
Cytokinesis divides a mother cell into two daughter cells at the end of each cell cycle and proceeds via the assembly and constriction of a contractile actomyosin ring (CAR). Ring constriction promotes division furrow ingression, after sister chromatids are segregated to opposing sides of the cleavage plane. Cytokinesis contributes to genome integrity because the cells that fail to complete cytokinesis often reduplicate their chromosomes. While in animal cells, the last steps of cytokinesis involve extracellular matrix remodelling and mid-body abscission, in yeast, CAR constriction is coupled to the synthesis of a polysaccharide septum. To preserve cell integrity during cytokinesis, fungal cells remodel their cell wall through signalling pathways that connect receptors to downstream effectors, initiating a cascade of biological signals. One of the best-studied signalling pathways is the cell wall integrity pathway (CWI) of the budding yeast Saccharomyces cerevisiae and its counterpart in the fission yeast Schizosaccharomyces pombe, the cell integrity pathway (CIP). Both are signal transduction pathways relying upon a cascade of MAP kinases. However, despite strong similarities in the assembly of the septa in both yeasts, there are significant mechanistic differences, including the relationship of this process with the cell integrity signalling pathways.
Collapse
|
5
|
Herrero E, Stinus S, Bellows E, Berry LK, Wood H, Thorpe PH. Asymmetric Transcription Factor Partitioning During Yeast Cell Division Requires the FACT Chromatin Remodeler and Cell Cycle Progression. Genetics 2020; 216:701-716. [PMID: 32878900 PMCID: PMC7648576 DOI: 10.1534/genetics.120.303439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
The polarized partitioning of proteins in cells underlies asymmetric cell division, which is an important driver of development and cellular diversity. The budding yeast Saccharomyces cerevisiae divides asymmetrically, like many other cells, to generate two distinct progeny cells. A well-known example of an asymmetric protein is the transcription factor Ace2, which localizes specifically to the daughter nucleus, where it drives a daughter-specific transcriptional network. We screened a collection of essential genes to analyze the effects of core cellular processes in asymmetric cell division based on Ace2 localization. This screen identified mutations that affect progression through the cell cycle, suggesting that cell cycle delay is sufficient to disrupt Ace2 asymmetry. To test this model, we blocked cells from progressing through mitosis and found that prolonged metaphase delay is sufficient to disrupt Ace2 asymmetry after release, and that Ace2 asymmetry is restored after cytokinesis. We also demonstrate that members of the evolutionarily conserved facilitates chromatin transcription (FACT) chromatin-reorganizing complex are required for both asymmetric and cell cycle-regulated localization of Ace2, and for localization of the RAM network components.
Collapse
Affiliation(s)
- Eva Herrero
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Sonia Stinus
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UT3, 31062, France
| | - Eleanor Bellows
- School of Biosciences, The University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
| | - Lisa K Berry
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
| | - Henry Wood
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
| | - Peter H Thorpe
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
| |
Collapse
|
6
|
Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science 2020; 368:eaaz5667. [PMID: 32586993 PMCID: PMC7539174 DOI: 10.1126/science.aaz5667] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs: a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.
Collapse
Affiliation(s)
- Elena Kuzmin
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alex N Nguyen Ba
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | | | | | - Oren Kraus
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Amy Tresenrider
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael Pryszlak
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Ming-Che Hu
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Brenda Varriano
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alan Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
7
|
Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL. Systematic analysis of complex genetic interactions. Science 2018; 360:eaao1729. [PMID: 29674565 PMCID: PMC6215713 DOI: 10.1126/science.aao1729] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 02/23/2018] [Indexed: 12/11/2022]
Abstract
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance, including the genotype-to-phenotype relationship.
Collapse
Affiliation(s)
- Elena Kuzmin
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Yiqun Chen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Matej Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Attila Balint
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Biochemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Mojca Mattiazzi Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jolanda van Leeuwen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Andrius J Dagilis
- Department of Integrative Biology, 1 University Station C0990, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Pryszlak
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jason Zi Yang Wang
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Julia Hanchard
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Margot Riggi
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- iGE3 (Institute of Genetics and Genomics of Geneva), 1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, 1211 Geneva, Switzerland
| | - Kaicong Xu
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Hamed Heydari
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ermira Shuteriqi
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Hongwei Zhu
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Nydia Van Dyk
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Sara Sharifpoor
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
- iGE3 (Institute of Genetics and Genomics of Geneva), 1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, 1211 Geneva, Switzerland
| | - Amy Caudy
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Daniel Bolnick
- Department of Integrative Biology, 1 University Station C0990, University of Texas at Austin, Austin, TX 78712, USA
| | - Grant W Brown
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Biochemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
| |
Collapse
|
8
|
Pedraza N, Cemeli T, Monserrat MV, Garí E, Ferrezuelo F. Regulation of small GTPase activity by G1 cyclins. Small GTPases 2017; 10:47-53. [PMID: 28129038 DOI: 10.1080/21541248.2016.1268665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Together with a cyclin-dependent kinase (CDK) partner G1 cyclins control cell cycle entry by phosphorylating a number of nuclear targets and releasing a transcriptional program at the end of G1 phase. Yeast G1 cyclins also operate on cytoplasmic targets involved in the polarization of the cytoskeleton and vesicle trafficking. These processes are mainly controlled by the small GTPase Cdc42, and G1 cyclins regulate the activity of this and other small GTPases through the modulation of their regulators and effectors. This regulation is key for different developmental outcomes in unicellular organisms. In mammalian cells cytoplasmic G1 cyclin D1 has been shown to promote the activity of Rac1 and Ral GTPases and to block RhoA. Regulation of these small GTPases by G1 cyclins may constitute a mechanism to coordinate proliferation with cell migration and morphogenesis, important processes not only during normal development and organogenesis but also for tumor formation and metastasis. Here we briefly review the evidence supporting a role of G1 cyclins and CDKs as regulators of the activity of small GTPases, emphasizing their functional relevance both in budding yeast and in mammalian cells.
Collapse
Affiliation(s)
- Neus Pedraza
- a Cell Cycle Lab, Institut de Recerca Biomèdica de Lleida (IRBLleida) , and Departament de Ciències Mèdiques Bàsiques , Facultat de Medicina, Universitat de Lleida , Lleida , Catalonia , Spain
| | - Tània Cemeli
- a Cell Cycle Lab, Institut de Recerca Biomèdica de Lleida (IRBLleida) , and Departament de Ciències Mèdiques Bàsiques , Facultat de Medicina, Universitat de Lleida , Lleida , Catalonia , Spain
| | - Ma Ventura Monserrat
- a Cell Cycle Lab, Institut de Recerca Biomèdica de Lleida (IRBLleida) , and Departament de Ciències Mèdiques Bàsiques , Facultat de Medicina, Universitat de Lleida , Lleida , Catalonia , Spain
| | - Eloi Garí
- a Cell Cycle Lab, Institut de Recerca Biomèdica de Lleida (IRBLleida) , and Departament de Ciències Mèdiques Bàsiques , Facultat de Medicina, Universitat de Lleida , Lleida , Catalonia , Spain
| | - Francisco Ferrezuelo
- a Cell Cycle Lab, Institut de Recerca Biomèdica de Lleida (IRBLleida) , and Departament de Ciències Mèdiques Bàsiques , Facultat de Medicina, Universitat de Lleida , Lleida , Catalonia , Spain
| |
Collapse
|
9
|
Pérez J, Arcones I, Gómez A, Casquero V, Roncero C. Phosphorylation of Bni4 by MAP kinases contributes to septum assembly during yeast cytokinesis. FEMS Yeast Res 2016; 16:fow060. [DOI: 10.1093/femsyr/fow060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2016] [Indexed: 02/05/2023] Open
|
10
|
Kuzmin E, Costanzo M, Andrews B, Boone C. Synthetic Genetic Arrays: Automation of Yeast Genetics. Cold Spring Harb Protoc 2016; 2016:pdb.top086652. [PMID: 27037078 DOI: 10.1101/pdb.top086652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype.
Collapse
Affiliation(s)
- Elena Kuzmin
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
11
|
Abstract
Genetic interactions occur when mutant alleles of two or more genes collaborate to generate an unusual composite phenotype, one that would not be predicted based on the expected combined effects of the individual mutant alleles. Synthetic Genetic Array (SGA) methodology was developed to automate yeast genetic analysis and enable systematic genetic interaction studies. In its simplest form, SGA consists of a series of replica pinning steps, which enable the construction of haploid double mutants through mating and meiotic recombination. For example, a strain carrying a query mutation, such as a deletion allele of a nonessential gene or a conditional temperature sensitive allele of an essential gene, could be crossed to an input array of yeast mutants, such as the complete set of ~5,000 viable deletion mutants, to generate an output array of double mutants, that can be scored for genetic interactions based on estimates of cellular fitness derived from colony-size measurements. A simple quantitative measure of genetic interactions can be derived from colony size, which serves as a proxy for fitness. Furthermore, SGA can be applied in a variety of other contexts, such as Synthetic Dosage Lethality (SDL), in which a query mutation is crossed into an array of yeast strains, each of which overexpresses a different gene, thus making use of SGA to probe for gain-of-function phenotypes in specific genetic backgrounds. High-Content Screening (HCS) also integrates SGA to perform genome-wide screens for quantitative analysis of morphological phenotypes or pathway activity based upon fluorescent markers, extending genetic interaction analysis beyond fitness-based measurements. Genetic interaction studies offer insight into gene function, pathway structure, and buffering, and thus a complete genetic interaction network of yeast will generate a global functional wiring diagram for a eukaryotic cell.
Collapse
|
12
|
Styles E, Youn JY, Mattiazzi Usaj M, Andrews B. Functional genomics in the study of yeast cell polarity: moving in the right direction. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130118. [PMID: 24062589 PMCID: PMC3785969 DOI: 10.1098/rstb.2013.0118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.
Collapse
Affiliation(s)
- Erin Styles
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
- Department of Molecular Genetics, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
| | - Ji-Young Youn
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
| | - Mojca Mattiazzi Usaj
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
| | - Brenda Andrews
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
- Department of Molecular Genetics, University of Toronto, 160 College St., Toronto, Ontario, CanadaM5S 3E1
| |
Collapse
|
13
|
Jiménez J, Ricco N, Grijota-Martínez C, Fadó R, Clotet J. Redundancy or specificity? The role of the CDK Pho85 in cell cycle control. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 4:140-149. [PMID: 24049669 PMCID: PMC3776146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 08/31/2013] [Indexed: 06/02/2023]
Abstract
It is generally accepted that progression through the eukaryotic cell cycle is driven by cyclin-dependent kinases (CDKs), which are regulated by interaction with oscillatory expressed proteins called cyclins. CDKs may be separated into 2 categories: essential and non-essential. Understandably, more attention has been focused on essential CDKs because they are shown to control cell cycle progression to a greater degree. After clearly determining the basic and "core" mechanisms of essential CDKs, several questions arise. What role do non-essential CDKs play? Are these CDKs functionally redundant and do they serve as a mere backup? Or might they be responsible for some accessory tasks in cell cycle progression or control? In the present review we will try to answer these questions based on recent findings on the involvement of non-essential CDKs in cell cycle progression. We will analyse the most recent information with regard to these questions in the yeast Saccharomyces cerevisiae, a well-established eukaryotic model, and in its unique non-essential CDK involved in the cell cycle, Pho85. We will also briefly extend our discussion to higher eukaryotic systems.
Collapse
Affiliation(s)
- Javier Jiménez
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, International University of Catalonia Barcelona, Catalonia
| | | | | | | | | |
Collapse
|
14
|
Simon E, Gildor T, Kornitzer D. Phosphorylation of the cyclin CaPcl5 modulates both cyclin stability and specific recognition of the substrate. J Mol Biol 2013; 425:3151-65. [PMID: 23763991 DOI: 10.1016/j.jmb.2013.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/16/2013] [Accepted: 06/03/2013] [Indexed: 12/01/2022]
Abstract
The Candida albicans cyclin CaPcl5 activates the cyclin-dependent kinase Pho85 and induces phosphorylation of the transcription factor CaGcn4, leading to its degradation. The high substrate specificity of the CaPcl5/Pho85 complex provides the opportunity to study the determinants of substrate selectivity of cyclins. Mutational analysis of CaPcl5 suggests that residues in a predicted α-helix at the N-terminal end of the cyclin box, as well as in helix I of the cyclin box, play a role in specific substrate recognition. Similar to Saccharomyces cerevisiae Pcl5, we show here that CaPcl5 induces its own phosphorylation at two adjacent sites in the N-terminal region of the protein and that this phosphorylation causes degradation of the cyclin in vivo via the SCF(CDC4) ubiquitin ligase. Remarkably, however, in vitro studies reveal that this phosphorylation also results in a loss of specific substrate recognition, thereby providing an additional novel mechanism for limiting cyclin activity.
Collapse
Affiliation(s)
- Einav Simon
- Department of Molecular Microbiology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | | | | |
Collapse
|
15
|
Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FCP, Johnson JR, Bloom K, Krogan NJ. Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Cell Rep 2013; 3:2168-78. [PMID: 23746449 DOI: 10.1016/j.celrep.2013.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/27/2013] [Accepted: 05/06/2013] [Indexed: 01/08/2023] Open
Abstract
Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA). We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.
Collapse
Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Waltham, MA 02454, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Kaluarachchi Duffy S, Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D, Andrews B. Exploring the yeast acetylome using functional genomics. Cell 2012; 149:936-48. [PMID: 22579291 DOI: 10.1016/j.cell.2012.02.064] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 01/24/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
Lysine acetylation is a dynamic posttranslational modification with a well-defined role in regulating histones. The impact of acetylation on other cellular functions remains relatively uncharacterized. We explored the budding yeast acetylome with a functional genomics approach, assessing the effects of gene overexpression in the absence of lysine deacetylases (KDACs). We generated a network of 463 synthetic dosage lethal (SDL) interactions involving class I and II KDACs, revealing many cellular pathways regulated by different KDACs. A biochemical survey of genes interacting with the KDAC RPD3 identified 72 proteins acetylated in vivo. In-depth analysis of one of these proteins, Swi4, revealed a role for acetylation in G1-specific gene expression. Acetylation of Swi4 regulates interaction with its partner Swi6, both components of the SBF transcription factor. This study expands our view of the yeast acetylome, demonstrates the utility of functional genomic screens for exploring enzymatic pathways, and provides functional information that can be mined for future studies.
Collapse
Affiliation(s)
- Supipi Kaluarachchi Duffy
- Department of Molecular Genetics, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | | | | | | | | | | | | |
Collapse
|
17
|
García-Rodríguez N, Díaz de la Loza MDC, Andreson B, Monje-Casas F, Rothstein R, Wellinger RE. Impaired manganese metabolism causes mitotic misregulation. J Biol Chem 2012; 287:18717-29. [PMID: 22493290 DOI: 10.1074/jbc.m112.358309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Manganese is an essential trace element, whose intracellular levels need to be carefully regulated. Mn(2+) acts as a cofactor for many enzymes and excess of Mn(2+) is toxic. Alterations in Mn(2+) homeostasis affect metabolic functions and mutations in the human Mn(2+)/Ca(2+) transporter ATP2C1 have been linked to Hailey-Hailey disease. By deletion of the yeast orthologue PMR1 we have studied the impact of Mn(2+) on cell cycle progression and show that an excess of cytosolic Mn(2+) alters S-phase transit, induces transcriptional up-regulation of cell cycle regulators, bypasses the need for S-phase cell cycle checkpoints and predisposes to genomic instability. On the other hand, we find that depletion of the Golgi Mn(2+) pool requires a functional morphology checkpoint to avoid the formation of polyploid cells.
Collapse
Affiliation(s)
- Néstor García-Rodríguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Sevilla, Spain
| | | | | | | | | | | |
Collapse
|
18
|
Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, VanderSluis B, Myers CL, Papp B, Boone C, Andrews BJ. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res 2012; 22:791-801. [PMID: 22282571 DOI: 10.1101/gr.129213.111] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of synthetic dosage lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function GIs, and literature-curated kinase-substrate interactions revealed kinase-dependent regulatory motifs predictive of novel gene-specific phenotypes. Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks.
Collapse
Affiliation(s)
- Sara Sharifpoor
- Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Studies of the processes leading to the construction of a bud and its separation from the mother cell in Saccharomyces cerevisiae have provided foundational paradigms for the mechanisms of polarity establishment, cytoskeletal organization, and cytokinesis. Here we review our current understanding of how these morphogenetic events occur and how they are controlled by the cell-cycle-regulatory cyclin-CDK system. In addition, defects in morphogenesis provide signals that feed back on the cyclin-CDK system, and we review what is known regarding regulation of cell-cycle progression in response to such defects, primarily acting through the kinase Swe1p. The bidirectional communication between morphogenesis and the cell cycle is crucial for successful proliferation, and its study has illuminated many elegant and often unexpected regulatory mechanisms. Despite considerable progress, however, many of the most puzzling mysteries in this field remain to be resolved.
Collapse
Affiliation(s)
- Audrey S. Howell
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Daniel J. Lew
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| |
Collapse
|
20
|
A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proc Natl Acad Sci U S A 2011; 108:18748-53. [PMID: 22042866 DOI: 10.1073/pnas.1115885108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) control the eukaryotic cell cycle, and a single CDK, Cdc28 (also known as Cdk1), is necessary and sufficient for cell cycle regulation in the budding yeast Saccharomyces cerevisiae. Cdc28 regulates cell cycle-dependent processes such as transcription, DNA replication and repair, and chromosome segregation. To gain further insight into the functions of Cdc28, we performed a high-throughput chemical-genetic array (CGA) screen aimed at unraveling the genetic network of CDC28. We identified 107 genes that strongly genetically interact with CDC28. Although these genes serve multiple cellular functions, genes involved in cell cycle regulation, transcription, and chromosome metabolism were overrepresented. DOA1, which is involved in maintaining free ubiquitin levels, as well as the RAD6-BRE1 pathway, which is involved in transcription, displayed particularly strong genetic interactions with CDC28. We discovered that DOA1 is important for cell cycle entry by supplying ubiquitin. Furthermore, we found that the RAD6-BRE1 pathway functions downstream of DOA1/ubiquitin but upstream of CDC28, by promoting transcription of cyclins. These results link cellular ubiquitin levels and the Rad6-Bre1 pathway to cell cycle progression.
Collapse
|
21
|
Mitchell L, Lau A, Lambert JP, Zhou H, Fong Y, Couture JF, Figeys D, Baetz K. Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4. PLoS One 2011; 6:e25336. [PMID: 21984913 PMCID: PMC3184947 DOI: 10.1371/journal.pone.0025336] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/01/2011] [Indexed: 01/08/2023] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, the lysine acetyltransferase NuA4 has been linked to a host of cellular processes through the acetylation of histone and non-histone targets. To discover proteins regulated by NuA4-dependent acetylation, we performed genome-wide synthetic dosage lethal screens to identify genes whose overexpression is toxic to non-essential NuA4 deletion mutants. The resulting genetic network identified a novel link between NuA4 and septin proteins, a group of highly conserved GTP-binding proteins that function in cytokinesis. We show that acetyltransferase-deficient NuA4 mutants have defects in septin collar formation resulting in the development of elongated buds through the Swe1-dependent morphogenesis checkpoint. We have discovered multiple sites of acetylation on four of the five yeast mitotic septins, Cdc3, Cdc10, Cdc12 and Shs1, and determined that NuA4 can acetylate three of the four in vitro. In vivo we find that acetylation levels of both Shs1 and Cdc10 are reduced in a catalytically inactive esa1 mutant. Finally, we determine that cells expressing a Shs1 protein with decreased acetylation in vivo have defects in septin localization that are similar to those observed in NuA4 mutants. These findings provide the first evidence that yeast septin proteins are acetylated and that NuA4 impacts septin dynamics.
Collapse
Affiliation(s)
- Leslie Mitchell
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrea Lau
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-Philippe Lambert
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ying Fong
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
22
|
Cryptococcal titan cell formation is regulated by G-protein signaling in response to multiple stimuli. EUKARYOTIC CELL 2011; 10:1306-16. [PMID: 21821718 DOI: 10.1128/ec.05179-11] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The titan cell is a recently described morphological form of the pathogenic fungus Cryptococcus neoformans. Occurring during the earliest stages of lung infection, titan cells are 5 to 10 times larger than the normal yeast-like cells, thereby resisting engulfment by lung phagocytes and favoring the persistence of infection. These enlarged cells exhibit an altered capsule structure, a thickened cell wall, increased ploidy, and resistance to nitrosative and oxidative stresses. We demonstrate that two G-protein-coupled receptors are important for induction of the titan cell phenotype: the Ste3a pheromone receptor (in mating type a cells) and the Gpr5 protein. Both receptors control titan cell formation through elements of the cyclic AMP (cAMP)/protein kinase A (PKA) pathway. This conserved signaling pathway, in turn, mediates its effect on titan cells through the PKA-regulated Rim101 transcription factor. Additional downstream effectors required for titan cell formation include the G(1) cyclin Pcl103, the Rho104 GTPase, and two GTPase-activating proteins, Gap1 and Cnc1560. These observations support developing models in which the PKA signaling pathway coordinately regulates many virulence-associated phenotypes in diverse human pathogens.
Collapse
|
23
|
Sambuk EV, Fizikova AY, Savinov VA, Padkina MV. Acid phosphatases of budding yeast as a model of choice for transcription regulation research. Enzyme Res 2011; 2011:356093. [PMID: 21785706 PMCID: PMC3137970 DOI: 10.4061/2011/356093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Acid phosphatases of budding yeast have been studied for more than forty years. This paper covers biochemical characteristics of acid phosphatases and different aspects in expression regulation of eukaryotic genes, which were researched using acid phosphatases model. A special focus is devoted to cyclin-dependent kinase Pho85p, a negative transcriptional regulator, and its role in maintaining mitochondrial genome stability and to pleiotropic effects of pho85 mutations.
Collapse
Affiliation(s)
- Elena V Sambuk
- Genetics and Breeding Department, Biology and Soil Sciences Faculty, Saint Petersburg State University, Universitetskaya emb. 7-9, Saint Petersburg 199034, Russia
| | | | | | | |
Collapse
|
24
|
Cannon JF. Function of protein phosphatase-1, Glc7, in Saccharomyces cerevisiae. ADVANCES IN APPLIED MICROBIOLOGY 2010; 73:27-59. [PMID: 20800758 DOI: 10.1016/s0065-2164(10)73002-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Budding yeast, Saccharomyces cerevisiae, and its close relatives are unique among eukaryotes in having a single gene, GLC7, encoding protein phosphatase-1 (PP1). This enzyme with a highly conserved amino acid sequence controls many processes in all eukaryotic cells. Therefore, the study of Glc7 function offers a unique opportunity to gain a comprehensive understanding of this critical regulatory enzyme. This review summarizes our current knowledge of how Glc7 function modulates processes in the cytoplasm and nucleus. Additionally, global Glc7 regulation is described.
Collapse
Affiliation(s)
- John F Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA.
| |
Collapse
|
25
|
Haworth J, Alver RC, Anderson M, Bielinsky AK. Ubc4 and Not4 regulate steady-state levels of DNA polymerase-α to promote efficient and accurate DNA replication. Mol Biol Cell 2010; 21:3205-19. [PMID: 20660159 PMCID: PMC2938386 DOI: 10.1091/mbc.e09-06-0452] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
DNA polymerase-alpha (pol-alpha) is essential for eukaryotic replication but lacks proofreading activity. Its turnover is regulated by the E2 Ubc4 and the E3 Not4, which are known transcriptional regulators. This pathway likely prevents accumulation of the potential mutator pol-alpha to promote genome stability. The accurate duplication of chromosomal DNA is required to maintain genomic integrity. However, from an evolutionary point of view, a low mutation rate during DNA replication is desirable. One way to strike the right balance between accuracy and limited mutagenesis is to use a DNA polymerase that lacks proofreading activity but contributes to DNA replication in a very restricted manner. DNA polymerase-α fits this purpose exactly, but little is known about its regulation at the replication fork. Minichromosome maintenance protein (Mcm) 10 regulates the stability of the catalytic subunit of pol-α in budding yeast and human cells. Cdc17, the catalytic subunit of pol-α in yeast, is rapidly degraded after depletion of Mcm10. Here we show that Ubc4 and Not4 are required for Cdc17 destabilization. Disruption of Cdc17 turnover resulted in sensitivity to hydroxyurea, suggesting that this pathway is important for DNA replication. Furthermore, overexpression of Cdc17 in ubc4 and not4 mutants caused slow growth and synthetic dosage lethality, respectively. Our data suggest that Cdc17 levels are very tightly regulated through the opposing forces of Ubc4 and Not4 (destabilization) and Mcm10 (stabilization). We conclude that regular turnover of Cdc17 via Ubc4 and Not4 is required for proper cell proliferation.
Collapse
Affiliation(s)
- Justin Haworth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | |
Collapse
|
26
|
Roncero C, Sánchez Y. Cell separation and the maintenance of cell integrity during cytokinesis in yeast: the assembly of a septum. Yeast 2010; 27:521-30. [DOI: 10.1002/yea.1779] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
27
|
Larson JR, Kozubowski L, Tatchell K. Changes in Bni4 localization induced by cell stress in Saccharomyces cerevisiae. J Cell Sci 2010; 123:1050-9. [PMID: 20197406 DOI: 10.1242/jcs.066258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Septin complexes at the bud neck in Saccharomyces cerevisiae serve as a scaffold for proteins involved in signaling, cell cycle control, and cell wall synthesis. Many of these bind asymmetrically, associating with either the mother- or daughter-side of the neck. Septin structures are inherently apolar so the basis for the asymmetric binding remains unknown. Bni4, a regulatory subunit of yeast protein phosphatase type 1, Glc7, binds to the outside of the septin ring prior to bud formation and remains restricted to the mother-side of the bud neck after bud emergence. Bni4 is responsible for targeting Glc7 to the mother-side of the bud neck for proper deposition of the chitin ring. We show here that Bni4 localizes symmetrically, as two distinct rings on both sides of the bud neck following energy depletion or activation of cell cycle checkpoints. Our data indicate that loss of Bni4 asymmetry can occur via at least two different mechanisms. Furthermore, we show that Bni4 has a Swe1-dependent role in regulating the cell morphogenesis checkpoint in response to hydroxyurea, which suggests that the change in localization of Bni4 following checkpoint activation may help stabilize the cell cycle regulator Swe1 during cell cycle arrest.
Collapse
Affiliation(s)
- Jennifer R Larson
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | | | | |
Collapse
|
28
|
Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
29
|
McMurray MA, Thorner J. Septins: molecular partitioning and the generation of cellular asymmetry. Cell Div 2009; 4:18. [PMID: 19709431 PMCID: PMC2749018 DOI: 10.1186/1747-1028-4-18] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 08/26/2009] [Indexed: 11/10/2022] Open
Abstract
During division, certain cellular contents can be distributed unequally; daughter cells with different fates have different needs. Septins are proteins that participate in the establishment and maintenance of asymmetry during cell morphogenesis, thereby contributing to the unequal partitioning of cellular contents during division. The septins themselves provide a paradigm for studying how elaborate multi-component structures are assembled, dynamically modified, and segregated through each cell division cycle and during development. Here we review our current understanding of the supramolecular organization of septins, the function of septins in cellular compartmentalization, and the mechanisms that control assembly, dynamics, and inheritance of higher-order septin structures, with particular emphasis on recent findings made in budding yeast (Saccharomyces cerevisiae).
Collapse
Affiliation(s)
- Michael A McMurray
- Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, Room 16, Barker Hall, University of California at Berkeley, Berkeley, CA 94720-3202 USA.
| | | |
Collapse
|