1
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DeWitt JT, Chinwuba JC, Kellogg DR. Hyperactive Ras disrupts cell size control and a key step in cell cycle entry in budding yeast. Genetics 2023; 225:iyad144. [PMID: 37531631 PMCID: PMC10758756 DOI: 10.1093/genetics/iyad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/08/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023] Open
Abstract
Severe defects in cell size are a nearly universal feature of cancer cells. However, the underlying causes are unknown. A previous study suggested that a hyperactive mutant of yeast Ras (ras2G19V) that is analogous to the human Ras oncogene causes cell size defects, which could provide clues to how oncogenes influence cell size. However, the mechanisms by which ras2G19V influences cell size are unknown. Here, we found that ras2G19V inhibits a critical step in cell cycle entry, in which an early G1 phase cyclin induces transcription of late G1 phase cyclins. Thus, ras2G19V drives overexpression of the early G1 phase cyclin Cln3, yet Cln3 fails to induce normal transcription of late G1 phase cyclins, leading to delayed cell cycle entry and increased cell size. ras2G19V influences transcription of late G1 phase cyclins via a poorly understood step in which Cln3 inactivates the Whi5 transcriptional repressor. Previous studies found that yeast Ras relays signals via protein kinase A (PKA); however, ras2G19V appears to influence late G1 phase cyclin expression via novel PKA-independent signaling mechanisms. Together, the data define new mechanisms by which hyperactive Ras influences cell cycle entry and cell size in yeast. Hyperactive Ras also influences expression of G1 phase cyclins in mammalian cells, but the mechanisms remain unclear. Further analysis of Ras signaling in yeast could lead to discovery of new mechanisms by which Ras family members control expression of G1 phase cyclins.
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Affiliation(s)
- Jerry T DeWitt
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Jennifer C Chinwuba
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Douglas R Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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2
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Leite AC, Costa V, Pereira C. Mitochondria and the cell cycle in budding yeast. Int J Biochem Cell Biol 2023; 161:106444. [PMID: 37419443 DOI: 10.1016/j.biocel.2023.106444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
As centers for energy production and essential biosynthetic activities, mitochondria are vital for cell growth and proliferation. Accumulating evidence suggests an integrated regulation of these organelles and the nuclear cell cycle in distinct organisms. In budding yeast, a well-established example of this coregulation is the coordinated movement and positional control of mitochondria during the different phases of the cell cycle. The molecular determinants involved in the inheritance of the fittest mitochondria by the bud also seem to be cell cycle-regulated. In turn, loss of mtDNA or defects in mitochondrial structure or inheritance often lead to a cell cycle delay or arrest, indicating that mitochondrial function can also regulate cell cycle progression, possibly through the activation of cell cycle checkpoints. The up-regulation of mitochondrial respiration at G2/M, presumably to fulfil energetic requirements for progression at this phase, also supports a mitochondria-cell cycle interplay. Cell cycle-linked mitochondrial regulation is accomplished at the transcription level and through post-translational modifications, predominantly protein phosphorylation. Here, we address mitochondria-cell cycle interactions in the yeast Saccharomyces cerevisiae and discuss future challenges in the field.
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Affiliation(s)
- Ana Cláudia Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
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3
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Guerra P, Vuillemenot LAPE, van Oppen YB, Been M, Milias-Argeitis A. TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle. J Cell Sci 2022; 135:276358. [PMID: 35975715 DOI: 10.1242/jcs.260378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 10/15/2022] Open
Abstract
Recent studies have revealed that the growth rate of budding yeast and mammalian cells varies during the cell cycle. By linking a multitude of signals to cell growth, the highly conserved Target of Rapamycin Complex 1 (TORC1) and Protein Kinase A (PKA) pathways are prime candidates for mediating the dynamic coupling between growth and division. However, measurements of TORC1 and PKA activity during the cell cycle are still lacking. Following the localization dynamics of two TORC1 and PKA targets via time-lapse microscopy in hundreds of yeast cells, we found that the activity of these pathways towards ribosome biogenesis fluctuates in synchrony with the cell cycle even under constant external conditions. Mutations of upstream TORC1 and PKA regulators suggested that internal metabolic signals partially mediate these activity changes. Our study reveals a new aspect of TORC1 and PKA signaling, which will be important for understanding growth regulation during the cell cycle.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Luc-Alban P E Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Yulan B van Oppen
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Marije Been
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
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4
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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]
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5
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Jessulat M, Amin S, Hooshyar M, Malty R, Moutaoufik MT, Zilocchi M, Istace Z, Phanse S, Aoki H, Omidi K, Burnside D, Samanfar B, Aly KA, Golshani A, Babu M. The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF. Nucleic Acids Res 2021; 49:8145-8160. [PMID: 34244791 PMCID: PMC8373142 DOI: 10.1093/nar/gkab585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 06/13/2021] [Accepted: 06/24/2021] [Indexed: 02/03/2023] Open
Abstract
The yeast cyclic AMP-dependent protein kinase A (PKA) is a ubiquitous serine-threonine kinase, encompassing three catalytic (Tpk1-3) and one regulatory (Bcy1) subunits. Evidence suggests PKA involvement in DNA damage checkpoint response, but how DNA repair pathways are regulated by PKA subunits remains inconclusive. Here, we report that deleting the tpk1 catalytic subunit reduces non-homologous end joining (NHEJ) efficiency, whereas tpk2-3 and bcy1 deletion does not. Epistatic analyses revealed that tpk1, as well as the DNA damage checkpoint kinase (dun1) and NHEJ factor (nej1), co-function in the same pathway, and parallel to the NHEJ factor yku80. Chromatin immunoprecipitation and resection data suggest that tpk1 deletion influences repair protein recruitments and DNA resection. Further, we show that Tpk1 phosphorylation of Nej1 at S298 (a Dun1 phosphosite) is indispensable for NHEJ repair and nuclear targeting of Nej1 and its binding partner Lif1. In mammalian cells, loss of PRKACB (human homolog of Tpk1) also reduced NHEJ efficiency, and similarly, PRKACB was found to phosphorylate XLF (a Nej1 human homolog) at S263, a corresponding residue of the yeast Nej1 S298. Together, our results uncover a new and conserved mechanism for Tpk1 and PRKACB in phosphorylating Nej1 (or XLF), which is critically required for NHEJ repair.
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Affiliation(s)
- Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Shahreen Amin
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Ramy Malty
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | | | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zoe Istace
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Katayoun Omidi
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Daniel Burnside
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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6
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Gerbich TM, McLaughlin GA, Cassidy K, Gerber S, Adalsteinsson D, Gladfelter AS. Phosphoregulation provides specificity to biomolecular condensates in the cell cycle and cell polarity. J Cell Biol 2021; 219:151764. [PMID: 32399546 PMCID: PMC7337510 DOI: 10.1083/jcb.201910021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Biomolecular condensation is a way of organizing cytosol in which proteins and nucleic acids coassemble into compartments. In the multinucleate filamentous fungus Ashbya gossypii, the RNA-binding protein Whi3 regulates the cell cycle and cell polarity through forming macromolecular structures that behave like condensates. Whi3 has distinct spatial localizations and mRNA targets, making it a powerful model for how, when, and where specific identities are established for condensates. We identified residues on Whi3 that are differentially phosphorylated under specific conditions and generated mutants that ablate this regulation. This yielded separation of function alleles that were functional for either cell polarity or nuclear cycling but not both. This study shows that phosphorylation of individual residues on molecules in biomolecular condensates can provide specificity that gives rise to distinct functional identities in the same cell.
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Affiliation(s)
- Therese M Gerbich
- Department of Biological Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Grace A McLaughlin
- Department of Biological Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Katelyn Cassidy
- Department of Biochemistry, Geisel School of Medicine, Hanover, NH
| | - Scott Gerber
- Department of Biochemistry, Geisel School of Medicine, Hanover, NH
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amy S Gladfelter
- Department of Biological Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Marine Biological Laboratory, Woods Hole, MA
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7
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Martínez-Montañés F, Casanovas A, Sprenger RR, Topolska M, Marshall DL, Moreno-Torres M, Poad BL, Blanksby SJ, Hermansson M, Jensen ON, Ejsing CS. Phosphoproteomic Analysis across the Yeast Life Cycle Reveals Control of Fatty Acyl Chain Length by Phosphorylation of the Fatty Acid Synthase Complex. Cell Rep 2020; 32:108024. [DOI: 10.1016/j.celrep.2020.108024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
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8
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Mal3 is a multi-copy suppressor of the sensitivity to microtubule-depolymerizing drugs and chromosome mis-segregation in a fission yeast pka1 mutant. PLoS One 2019; 14:e0214803. [PMID: 30973898 PMCID: PMC6459531 DOI: 10.1371/journal.pone.0214803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/20/2019] [Indexed: 11/24/2022] Open
Abstract
The cAMP-dependent protein kinase Pka1 is known as a regulator of glycogenesis, transition into meiosis, chronological aging, and stress responses in the fission yeast, Schizosaccharomyces pombe. We demonstrated here that Pka1 is responsible for normal growth in the presence of the microtubule-destabilization drug TBZ and proper chromosome segregation. The deletion of the pka1 gene resulted in the TBZ-sensitive phenotype and chromosome mis-segregation. We isolated the mal3 gene as a multi-copy suppressor of the TBZ-sensitive phenotype in the pka1Δ strains. Overexpression of the CH domain (1–143) or the high-affinity microtubule binding mutant (1–143 Q89R) of Mal3 rescued the TBZ-sensitive phenotype in the pka1Δ and mal3Δ strains, while the EB1 domain (135–308) and the mutants defective in microtubule binding (1–143 Q89E) failed to do so in the same strains. Chromosome mis-segregation caused by TBZ in the pka1Δ or mal3Δ strains was suppressed by the overexpression of the Mal3 CH domain (1–143), Mal3 CH domain with the coiled-coil domain (1–197), or full-length Mal3. Overexpression of EB1 orthologs from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, or Homo sapiens suppressed the TBZ-sensitive phenotype in the pka1Δ strains, indicating their conserved functions. These findings suggest that Pka1 and the microtubule binding of the Mal3 CH domain play a role in the maintenance of proper chromosome segregation.
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9
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Tan XY, Wang X, Liu QS, Xie XQ, Li Y, Li BQ, Li ZQ, Xia QY, Zhao P. Inhibition of silkworm vacuolar-type ATPase activity by its inhibitor Bafilomycin A1 induces caspase-dependent apoptosis in an embryonic cell line of silkworm. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2018; 99:e21507. [PMID: 30246413 DOI: 10.1002/arch.21507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vacuolar-type ATPase (V-ATPase) is a type of hydrogen ion transporter located in the vesicular membrane-like system, which mediates active transport and intracellular acidification in various compartments. In mammals, V-ATPase has been reported to play a key role in cell proliferation and apoptosis. The studies of V-ATPase in silkworm mainly focus on the acidification regulation of midgut and silk gland and immune resistance. However, there are few reports about the function of silkworm V-ATPase on cell proliferation, autophagy, and apoptosis. Thus, the function of V-ATPase in a cell line of Bombyx mori (BmE) was investigated by treating the cell line with bafilomycin A1, a specific inhibitor of V-ATPase. Cell counting kit 8 (CCK8) and flow cytometry analysis showed that bafilomycin A1 treatment decreased the cell proliferation activity, affected the cell cycle progression and induced cell apoptosis. LysoTracker Red staining showed that the target of bafilomycin A1 is lysosome. The expression of all autophagy-related genes ( BmATG5, BmATG6, and BmATG8) decreased, indicating that cell autophagy was inhibited. The analysis of the apoptosis pathway demonstrated that inhibiting the activity of V-ATPase of BmE cells could promote mitochondria to release cytochrome C, inhibit the expression of BmIAP, and activate the caspase cascade to induce apoptosis. All these findings systematically illustrate the effects of V-ATPase on the proliferation, autophagy, and apoptosis in BmE cells, and provide new ideas and a theoretical basis for further study on the function of V-ATPase in BmE.
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Affiliation(s)
- Xiao-Yin Tan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Qing-Song Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xiao-Qian Xie
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Yi Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Bing-Qian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Zhi-Qing Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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10
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The Yeast Saccharomyces cerevisiae as a Model for Understanding RAS Proteins and their Role in Human Tumorigenesis. Cells 2018; 7:cells7020014. [PMID: 29463063 PMCID: PMC5850102 DOI: 10.3390/cells7020014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/05/2018] [Accepted: 02/12/2018] [Indexed: 12/16/2022] Open
Abstract
The exploitation of the yeast Saccharomyces cerevisiae as a biological model for the investigation of complex molecular processes conserved in multicellular organisms, such as humans, has allowed fundamental biological discoveries. When comparing yeast and human proteins, it is clear that both amino acid sequences and protein functions are often very well conserved. One example of the high degree of conservation between human and yeast proteins is highlighted by the members of the RAS family. Indeed, the study of the signaling pathways regulated by RAS in yeast cells led to the discovery of properties that were often found interchangeable with RAS proto-oncogenes in human pathways, and vice versa. In this work, we performed an updated critical literature review on human and yeast RAS pathways, specifically highlighting the similarities and differences between them. Moreover, we emphasized the contribution of studying yeast RAS pathways for the understanding of human RAS and how this model organism can contribute to unveil the roles of RAS oncoproteins in the regulation of mechanisms important in the tumorigenic process, like autophagy.
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11
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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12
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Weidberg H, Moretto F, Spedale G, Amon A, van Werven FJ. Nutrient Control of Yeast Gametogenesis Is Mediated by TORC1, PKA and Energy Availability. PLoS Genet 2016; 12:e1006075. [PMID: 27272508 PMCID: PMC4894626 DOI: 10.1371/journal.pgen.1006075] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/02/2016] [Indexed: 11/19/2022] Open
Abstract
Cell fate choices are tightly controlled by the interplay between intrinsic and extrinsic signals, and gene regulatory networks. In Saccharomyces cerevisiae, the decision to enter into gametogenesis or sporulation is dictated by mating type and nutrient availability. These signals regulate the expression of the master regulator of gametogenesis, IME1. Here we describe how nutrients control IME1 expression. We find that protein kinase A (PKA) and target of rapamycin complex I (TORC1) signalling mediate nutrient regulation of IME1 expression. Inhibiting both pathways is sufficient to induce IME1 expression and complete sporulation in nutrient-rich conditions. Our ability to induce sporulation under nutrient rich conditions allowed us to show that respiration and fermentation are interchangeable energy sources for IME1 transcription. Furthermore, we find that TORC1 can both promote and inhibit gametogenesis. Down-regulation of TORC1 is required to activate IME1. However, complete inactivation of TORC1 inhibits IME1 induction, indicating that an intermediate level of TORC1 signalling is required for entry into sporulation. Finally, we show that the transcriptional repressor Tup1 binds and represses the IME1 promoter when nutrients are ample, but is released from the IME1 promoter when both PKA and TORC1 are inhibited. Collectively our data demonstrate that nutrient control of entry into sporulation is mediated by a combination of energy availability, TORC1 and PKA activities that converge on the IME1 promoter.
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Affiliation(s)
- Hilla Weidberg
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gianpiero Spedale
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Folkert J. van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, United Kingdom
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13
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Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J. Experimental testing of a new integrated model of the budding yeast Start transition. Mol Biol Cell 2015; 26:3966-84. [PMID: 26310445 PMCID: PMC4710230 DOI: 10.1091/mbc.e15-06-0358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/19/2015] [Indexed: 01/29/2023] Open
Abstract
Mathematical modeling of the cell cycle has unveiled recurrent features and emergent behaviors of cellular networks. Constructing new mutants and performing experimental tests during development of a new model of the budding yeast cell cycle yields a more efficient modeling process and results in several testable hypotheses. The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1–S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1–S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model’s simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network.
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Affiliation(s)
- Neil R Adames
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061
| | - P Logan Schuck
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061
| | - Katherine C Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, VA 24061
| | - John J Tyson
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061 Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Jean Peccoud
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061 ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, VA 24061
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14
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Braun KA, Vaga S, Dombek KM, Fang F, Palmisano S, Aebersold R, Young ET. Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling. Sci Signal 2014; 7:ra64. [PMID: 25005228 DOI: 10.1126/scisignal.2005000] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stresses, such as glucose depletion, activate Snf1, the Saccharomyces cerevisiae ortholog of adenosine monophosphate-activated protein kinase (AMPK), enabling adaptive cellular responses. In addition to affecting transcription, Snf1 may also promote mRNA stability in a gene-specific manner. To understand Snf1-mediated signaling, we used quantitative mass spectrometry to identify proteins that were phosphorylated in a Snf1-dependent manner. We identified 210 Snf1-dependent phosphopeptides in 145 proteins. Thirteen of these proteins are involved in mRNA metabolism. Of these, we found that Ccr4 (the major cytoplasmic deadenylase), Dhh1 (an RNA helicase), and Xrn1 (an exoribonuclease) were required for the glucose-induced decay of Snf1-dependent mRNAs that were activated by glucose depletion. Unexpectedly, deletion of XRN1 reduced the accumulation of Snf1-dependent transcripts that were synthesized during glucose depletion. Deletion of SNF1 rescued the synthetic lethality of simultaneous deletion of XRN1 and REG1, which encodes a regulatory subunit of a phosphatase that inhibits Snf1. Mutation of three Snf1-dependent phosphorylation sites in Xrn1 reduced glucose-induced mRNA decay. Thus, Xrn1 is required for Snf1-dependent mRNA homeostasis in response to nutrient availability.
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Affiliation(s)
- Katherine A Braun
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8057 Zurich, Switzerland
| | - Kenneth M Dombek
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA
| | - Fang Fang
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA
| | - Salvator Palmisano
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8057 Zurich, Switzerland. Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
| | - Elton T Young
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA.
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Cai Y, Futcher B. Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. PLoS One 2013; 8:e84630. [PMID: 24386402 PMCID: PMC3875557 DOI: 10.1371/journal.pone.0084630] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/15/2013] [Indexed: 11/20/2022] Open
Abstract
Whi3 is an RNA binding protein known to bind the mRNA of the yeast G1 cyclin gene CLN3. It inhibits CLN3 function, but the mechanism of this inhibition is unclear; in previous studies, Whi3 made no observable difference to CLN3 mRNA levels, translation, or protein abundance. Here, we re-approach this issue using microarrays, RNA-Seq, ribosome profiling, and other methods. By multiple methods, we find that the whi3 mutation causes a small but consistent increase in the abundance of hundreds of mRNAs, including the CLN3 mRNA. The effect on various mRNAs is roughly in proportion to the density of GCAU or UGCAU motifs carried by these mRNAs, which may be a binding site for Whi3. mRNA instability of Whi3 targets may in part depend on a 3′ AU rich element (ARE), AUUUUA. In addition, the whi3 mutation causes a small increase in the translational efficiency of CLN3 mRNA. The increase in CLN3 mRNA half-life and abundance together with the increase in translational efficiency is fully sufficient to explain the small-cell phenotype of whi3 mutants. Under stress conditions, Whi3 becomes a component of P-bodies or stress granules, but Whi3 also acts under non-stress condition, when no P-bodies are visible. We suggest that Whi3 may be a very broadly-acting, but mild, modulator of mRNA stability. In CLN3, Whi3 may bind to the 3′ GCAU motifs to attract the Ccr4-Not complex to promote RNA deadenylation and turnover, and Whi3 may bind to the 5′ GCAU motifs to inhibit translation.
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Affiliation(s)
- Ying Cai
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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16
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Evidence of antagonistic regulation of restart from G(1) delay in response to osmotic stress by the Hog1 and Whi3 in budding yeast. Biosci Biotechnol Biochem 2013; 77:2002-7. [PMID: 24096659 DOI: 10.1271/bbb.130260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hog1 of Saccharomyces cerevisiae is activated by hyperosmotic stress, and this leads to cell-cycle delay in G1, but the mechanism by which cells restart from G1 delay remains elusive. We found that Whi3, a negative regulator of G1 cyclin, counteracted Hog1 in the restart from G1 delay caused by osmotic stress. We have found that phosphorylation of Ser-568 in Whi3 by RAS/cAMP-dependent protein kinase (PKA) plays an inhibitory role in Whi3 function. In this study we found that the phosphomimetic Whi3 S568D mutant, like the Δwhi3 strain, slightly suppressed G1 delay of Δhog1 cells under osmotic stress conditions, whereas the non-phosphorylatable S568A mutation of Whi3 caused prolonged G1 arrest of Δhog1 cells. These results indicate that Hog1 activity is required for restart from G1 arrest under osmotic stress conditions, whereas Whi3 acts as a negative regulator for this restart mechanism.
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