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Talavera RA, Prichard BE, Sommer RA, Leitao RM, Sarabia CJ, Hazir S, Paulo JA, Gygi SP, Kellogg DR. Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast. J Cell Biol 2024; 223:e202305008. [PMID: 38722822 PMCID: PMC11082370 DOI: 10.1083/jcb.202305008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 01/03/2024] [Accepted: 04/04/2024] [Indexed: 05/13/2024] Open
Abstract
Cell growth is required for cell cycle progression. The amount of growth required for cell cycle progression is reduced in poor nutrients, which leads to a reduction in cell size. In budding yeast, nutrients can influence cell size by modulating the extent of bud growth, which occurs predominantly in mitosis. However, the mechanisms are unknown. Here, we used mass spectrometry to identify proteins that modulate bud growth in response to nutrient availability. This led to the discovery that nutrients regulate numerous components of the mitotic exit network (MEN), which controls exit from mitosis. A key component of the MEN undergoes gradual multisite phosphorylation during bud growth that is dependent upon bud growth and correlated with the extent of growth. Furthermore, activation of the MEN is sufficient to override a growth requirement for mitotic exit. The data suggest a model in which the MEN ensures that mitotic exit occurs only when an appropriate amount of bud growth has occurred.
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Affiliation(s)
- Rafael A. Talavera
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Beth E. Prichard
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Robert A. Sommer
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Ricardo M. Leitao
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Christopher J. Sarabia
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Semin Hazir
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Douglas R. Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Zhou X, Weng SY, Bell SP, Amon A. A noncanonical GTPase signaling mechanism controls exit from mitosis in budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594582. [PMID: 38798491 PMCID: PMC11118470 DOI: 10.1101/2024.05.16.594582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In the budding yeast Saccharomyces cerevisiae , exit from mitosis is coupled to spindle position to ensure successful genome partitioning between mother and daughter cell. This coupling occurs through a GTPase signaling cascade known as the mitotic exit network (MEN). The MEN senses spindle position via a Ras-like GTPase Tem1 which localizes to the spindle pole bodies (SPBs, yeast equivalent of centrosomes) during anaphase and signals to its effector protein kinase Cdc15. How Tem1 couples the status of spindle position to MEN activation is not fully understood. Here, we show that Cdc15 has a relatively weak preference for Tem1 GTP and Tem1's nucleotide state does not change upon MEN activation. Instead, we find that Tem1's nucleotide cycle establishes a localization-based concentration difference in the cell where only Tem1 GTP is recruited to the SPB, and spindle position regulates the MEN by controlling Tem1 localization. SPB localization of Tem1 primarily functions to promote Tem1-Cdc15 interaction for MEN activation by increasing the effective concentration of Tem1. Consistent with this model, we demonstrate that artificially tethering Tem1 to the SPB or concentrating Tem1 in the cytoplasm with genetically encoded multimeric nanoparticles could bypass the requirement of Tem1 GTP and correct spindle position for MEN activation. This localization/concentration-based GTPase signaling mechanism for Tem1 differs from the canonical Ras-like GTPase signaling paradigm and is likely relevant to other localization-based signaling scenarios.
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Papouskova K, Zimmermannova O, Sychrova H. Distinct regions of its first intracellular loop contribute to the proper localization, transport activity and substrate-affinity adjustment of the main yeast K + importer Trk1. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184369. [PMID: 38969203 DOI: 10.1016/j.bbamem.2024.184369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 06/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Trk1 is the main K+ importer of Saccharomyces cerevisiae. Its proper functioning enables yeast cells to grow in environments with micromolar amounts of K+. Although the structure of Trk1 has not been experimentally determined, the transporter is predicted to be composed of four MPM (transmembrane segment - pore loop - transmembrane segment) motifs which are connected by intracellular loops. Of those, in particular the first loop (IL1) is unique in its length; it forms more than half of the entire protein. The deletion of the majority of IL1 does not abolish the transport activity of Trk1. However IL1 is thought to be involved in the modulation of the transporter's functioning. In this work, we prepared a series of internally shortened versions of Trk1 that lacked various parts of IL1, and we studied their properties in S. cerevisiae cells without chromosomal copies of TRK genes. Using this approach, we were able to determine that both N- and C-border regions of IL1 are necessary for the proper localization of Trk1. Moreover, the N-border part of IL1 is also important for the functioning of Trk1, as its absence resulted in a decrease in the transporter's substrate affinity. In addition, in the internal part of IL1, we newly identified a stretch of amino-acid residues that are indispensable for retaining the transporter's maximum velocity, and another region whose deletion affected the ability of Trk1 to adjust its affinity in response to external levels of K+.
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Affiliation(s)
- Klara Papouskova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
| | - Olga Zimmermannova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
| | - Hana Sychrova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague 4, Czech Republic.
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4
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Masanta S, Wiesyk A, Panja C, Pilch S, Ciesla J, Sipko M, De A, Enkhbaatar T, Maslanka R, Skoneczna A, Kucharczyk R. Fmp40 ampylase regulates cell survival upon oxidative stress by controlling Prx1 and Trx3 oxidation. Redox Biol 2024; 73:103201. [PMID: 38795545 PMCID: PMC11140801 DOI: 10.1016/j.redox.2024.103201] [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: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Reactive oxygen species (ROS), play important roles in cellular signaling, nonetheless are toxic at higher concentrations. Cells have many interconnected, overlapped or backup systems to neutralize ROS, but their regulatory mechanisms remain poorly understood. Here, we reveal an essential role for mitochondrial AMPylase Fmp40 from budding yeast in regulating the redox states of the mitochondrial 1-Cys peroxiredoxin Prx1, which is the only protein shown to neutralize H2O2 with the oxidation of the mitochondrial glutathione and the thioredoxin Trx3, directly involved in the reduction of Prx1. Deletion of FMP40 impacts a cellular response to H2O2 treatment that leads to programmed cell death (PCD) induction and an adaptive response involving up or down regulation of genes encoding, among others the catalase Cta1, PCD inducing factor Aif1, and mitochondrial redoxins Trx3 and Grx2. This ultimately perturbs the reduced glutathione and NADPH cellular pools. We further demonstrated that Fmp40 AMPylates Prx1, Trx3, and Grx2 in vitro and interacts with Trx3 in vivo. AMPylation of the threonine residue 66 in Trx3 is essential for this protein's proper endogenous level and its precursor forms' maturation under oxidative stress conditions. Additionally, we showed the Grx2 involvement in the reduction of Trx3 in vivo. Taken together, Fmp40, through control of the reduction of mitochondrial redoxins, regulates the hydrogen peroxide, GSH and NADPH signaling influencing the yeast cell survival.
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Affiliation(s)
- Suchismita Masanta
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Sylwia Pilch
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Jaroslaw Ciesla
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Marta Sipko
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Abhipsita De
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland.
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5
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Pujari AN, Cullen PJ. Modulators of MAPK pathway activity during filamentous growth in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2024; 14:jkae072. [PMID: 38560781 PMCID: PMC11152069 DOI: 10.1093/g3journal/jkae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Mitogen-activated protein kinase (MAPK) pathways control the response to intrinsic and extrinsic stimuli. In the budding yeast Saccharomyces cerevisiae, cells undergo filamentous growth, which is regulated by the fMAPK pathway. To better understand the regulation of the fMAPK pathway, a genetic screen was performed to identify spontaneous mutants with elevated activity of an fMAPK pathway-dependent growth reporter (ste4 FUS1-HIS3). In total, 159 mutants were isolated and analyzed by secondary screens for invasive growth by the plate-washing assay and filament formation by microscopy. Thirty-two mutants were selected for whole-genome sequencing, which identified new alleles in genes encoding known regulators of the fMAPK pathway. These included gain-of-function alleles in STE11, which encodes the MAPKKK, as well as loss-of-function alleles in KSS1, which encodes the MAP kinase, and loss-of-function alleles in RGA1, which encodes a GTPase-activating protein (GAP) for CDC42. New alleles in previously identified pathway modulators were also uncovered in ALY1, AIM44, RCK2, IRA2, REG1, and in genes that regulate protein folding (KAR2), glycosylation (MNN4), and turnover (BLM10). Mutations leading to C-terminal truncations in the transcription factor Ste12p were also uncovered that resulted in elevated reporter activity, identifying an inhibitory domain of the protein from residues 491 to 688. We also find that a diversity of filamentous growth phenotypes can result from combinatorial effects of multiple mutations and by loss of different regulators of the response. The alleles identified here expand the connections surrounding MAPK pathway regulation and reveal new features of proteins that function in the signaling cascade.
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Affiliation(s)
- Atindra N Pujari
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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6
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [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: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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7
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Koch LB, Spanos C, Kelly V, Ly T, Marston AL. Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast. EMBO J 2024; 43:1351-1383. [PMID: 38413836 PMCID: PMC10987667 DOI: 10.1038/s44318-024-00059-8] [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: 09/13/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade.
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Affiliation(s)
- Lori B Koch
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Van Kelly
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Tony Ly
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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8
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Diep DTV, Collado J, Hugenroth M, Fausten RM, Percifull L, Wälte M, Schuberth C, Schmidt O, Fernández-Busnadiego R, Bohnert M. A metabolically controlled contact site between vacuoles and lipid droplets in yeast. Dev Cell 2024; 59:740-758.e10. [PMID: 38367622 DOI: 10.1016/j.devcel.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
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Affiliation(s)
- Duy Trong Vien Diep
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Javier Collado
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Marie Hugenroth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Louis Percifull
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany
| | - Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Imaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Faculty of Physics, University of Göttingen, Göttingen 37077, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany.
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9
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Jiang L, Li Y, Gu Y, Zheng J, Wei L, Wei M, Zou J, Wei C, Mo B, Pan L, Zhao L, Wang D. Identification of the Beta Subunit Fas1p of Fatty Acid Synthetase as an Interacting Partner of Yeast Calcium/Calmodulin-Dependent Protein Kinase Cmk2p Through Mass Spectrometry Analysis. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04891-w. [PMID: 38411936 DOI: 10.1007/s12010-024-04891-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
The calcium/calmodulin-dependent protein kinase II (CaMKII) is a mediator of calcium signals and regulates fatty acid metabolism in mammalian cells. Cmk2p is a yeast homolog of CaMKII and functions as a negative regulator of calcium signaling. However, its substrates remain to be identified. Combination of immunoprecipitation (IP) and mass spectrometry has been proven to be very useful for identification of interacting partner proteins and interactome. In this study, through these approaches, we have identified 65 and 110 potential Cmk2p-interacting proteins in yeast cells in the absence or presence of calcium stress, respectively. In yeast cells expressing both CMK2-HA and FAS1-GFP fusion proteins, in the absence or presence of calcium stress, less amounts of FAS1-GFP proteins are present in cell lysates after IP with anti-HA antibody than cell lysates before IP, while FAS1-GFP proteins are detected on both types of IP beads. However, as an internal control, similar amounts of Pgk1p proteins were detected in both after-IP and before-IP cell lysates but not on the IP beads. Therefore, our biochemical analysis demonstrates that the β subunit Fas1p of fatty acid synthetase interacts with Cmk2p in yeast cells independent of calcium stress. It is also interesting to note that, in addition to the expected 52-kDa CMK2-HA band, a faster-moving 48-kDa CMK2-HA band is present in the calcium-stressed cell lysate but not in the cell lysate without calcium stress. Our data would provide important clues for understanding the functions of CaMKII in the regulation of fatty acid metabolism as well as related diseases such as cancers, diabetes, and obesity.
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Affiliation(s)
- Linghuo Jiang
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China.
| | - Yiwu Li
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Yiying Gu
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Jiashi Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Liudan Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Jie Zou
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Chunyu Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Bei Mo
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lingxin Pan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lijiao Zhao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
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10
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Durant M, Mucelli X, Huang LS. Meiotic Cytokinesis in Saccharomyces cerevisiae: Spores That Just Need Closure. J Fungi (Basel) 2024; 10:132. [PMID: 38392804 PMCID: PMC10890087 DOI: 10.3390/jof10020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, sporulation occurs during starvation of a diploid cell and results in the formation of four haploid spores forming within the mother cell ascus. Meiosis divides the genetic material that is encapsulated by the prospore membrane that grows to surround the haploid nuclei; this membrane will eventually become the plasma membrane of the haploid spore. Cellularization of the spores occurs when the prospore membrane closes to capture the haploid nucleus along with some cytoplasmic material from the mother cell, and thus, closure of the prospore membrane is the meiotic cytokinetic event. This cytokinetic event involves the removal of the leading-edge protein complex, a complex of proteins that localizes to the leading edge of the growing prospore membrane. The development and closure of the prospore membrane must be coordinated with other meiotic exit events such as spindle disassembly. Timing of the closure of the prospore membrane depends on the meiotic exit pathway, which utilizes Cdc15, a Hippo-like kinase, and Sps1, an STE20 family GCKIII kinase, acting in parallel to the E3 ligase Ama1-APC/C. This review describes the sporulation process and focuses on the development of the prospore membrane and the regulation of prospore membrane closure.
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Affiliation(s)
- Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Linda S Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
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11
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Sunder S, Bauman JS, Decker SJ, Lifton AR, Kumar A. The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1. J Biol Chem 2024; 300:105657. [PMID: 38224949 PMCID: PMC10851228 DOI: 10.1016/j.jbc.2024.105657] [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: 11/03/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
The yeast Snf1/AMP-activated kinase (AMPK) maintains energy homeostasis, controlling metabolic processes and glucose derepression in response to nutrient levels and environmental cues. Under conditions of nitrogen or glucose limitation, Snf1 regulates pseudohyphal growth, a morphological transition characterized by the formation of extended multicellular filaments. During pseudohyphal growth, Snf1 is required for wild-type levels of inositol polyphosphate (InsP), soluble phosphorylated species of the six-carbon cyclitol inositol that function as conserved metabolic second messengers. InsP levels are established through the activity of a family of inositol kinases, including the yeast inositol polyphosphate kinase Kcs1, which principally generates pyrophosphorylated InsP7. Here, we report that Snf1 regulates Kcs1, affecting Kcs1 phosphorylation and inositol kinase activity. A snf1 kinase-defective mutant exhibits decreased Kcs1 phosphorylation, and Kcs1 is phosphorylated in vivo at Ser residues 537 and 646 during pseudohyphal growth. By in vitro analysis, Snf1 directly phosphorylates Kcs1, predominantly at amino acids 537 and 646. A yeast strain carrying kcs1 encoding Ser-to-Ala point mutations at these residues (kcs1-S537A,S646A) shows elevated levels of pyrophosphorylated InsP7, comparable to InsP7 levels observed upon deletion of SNF1. The kcs1-S537A,S646A mutant exhibits decreased pseudohyphal growth, invasive growth, and cell elongation. Transcriptional profiling indicates extensive perturbation of metabolic pathways in kcs1-S537A,S646A. Growth of kcs1-S537A,S646A is affected on medium containing sucrose and antimycin A, consistent with decreased Snf1p signaling. This work identifies Snf1 phosphorylation of Kcs1, collectively highlighting the interconnectedness of AMPK activity and InsP signaling in coordinating nutrient availability, energy homoeostasis, and cell growth.
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Affiliation(s)
- Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S Bauman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stuart J Decker
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandra R Lifton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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12
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [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: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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13
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Blank HM, Griffith WP, Polymenis M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol Biol Cell 2023; 34:br20. [PMID: 37792491 PMCID: PMC10848943 DOI: 10.1091/mbc.e23-05-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of FAS1, encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the FAS1 transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target FAS1 and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the FAS1 mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.
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Affiliation(s)
- Heidi M. Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Wendell P. Griffith
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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14
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Abeliovich H. Mitophagy in yeast: known unknowns and unknown unknowns. Biochem J 2023; 480:1639-1657. [PMID: 37850532 PMCID: PMC10586778 DOI: 10.1042/bcj20230279] [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: 07/12/2023] [Revised: 09/06/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Mitophagy, the autophagic breakdown of mitochondria, is observed in eukaryotic cells under various different physiological circumstances. These can be broadly categorized into two types: mitophagy related to quality control events and mitophagy induced during developmental transitions. Quality control mitophagy involves the lysosomal or vacuolar degradation of malfunctioning or superfluous mitochondria within lysosomes or vacuoles, and this is thought to serve as a vital maintenance function in respiring eukaryotic cells. It plays a crucial role in maintaining physiological balance, and its disruption has been associated with the progression of late-onset diseases. Developmentally induced mitophagy has been reported in the differentiation of metazoan tissues which undergo metabolic shifts upon developmental transitions, such as in the differentiation of red blood cells and muscle cells. Although the mechanistic studies of mitophagy in mammalian cells were initiated after the initial mechanistic findings in Saccharomyces cerevisiae, our current understanding of the physiological role of mitophagy in yeast remains more limited, despite the presence of better-defined assays and tools. In this review, I present my perspective on our present knowledge of mitophagy in yeast, focusing on physiological and mechanistic aspects. I aim to focus on areas where our understanding is still incomplete, such as the role of mitochondrial dynamics and the phenomenon of protein-level selectivity.
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Affiliation(s)
- Hagai Abeliovich
- Institute of Biochemistry, Food Science and Nutrition, Hebrew University of Jerusalem, 1 Hankin St, Rehovot 7610001, Israel
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15
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Lai CC, Chiu WY, Chen YT, Wu CL, Lee FJS. The SNARE-associated protein Sft2 functions in Imh1-mediated SNARE recycling transport upon ER stress. Mol Biol Cell 2023; 34:ar112. [PMID: 37610835 PMCID: PMC10559307 DOI: 10.1091/mbc.e23-01-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Vesicular trafficking involving SNARE proteins play a crucial role in the delivery of cargo to the target membrane. Arf-like protein 1 (Arl1) is an important regulator of the endosomal trans-Golgi network (TGN) and secretory trafficking. In yeast, ER stress-enhances Arl1 activation and Golgin Imh1 recruitment to the late-Golgi. Although Arl1 and Imh1 are critical for GARP-mediated endosomal SNARE-recycling transport in response to ER stress, their downstream effectors are unknown. Here, we report that the SNARE-associated protein Sft2 acts downstream of the Arl1-Imh1 axis to regulate SNARE recycling upon ER stress. We first demonstrated that Sft2 is required for Tlg1/Snc1 SNARE-recycling transport under tunicamycin-induced ER stress. Interestingly, we found that Imh1 regulates Tlg2 retrograde transport to the late-Golgi under ER stress, which in turn is required for Sft2 targeting to the late-Golgi. We further showed that Sft2 with 40 amino acids deleted from the N-terminus exhibits defective mediation of SNARE recycling and decreased association with Tlg1 under ER stress. Finally, we demonstrated that Sft2 is required for GARP-dependent endosome-to-Golgi transport in the absence of Rab protein Ypt6. This study highlights Sft2 as a critical downstream effector of the Arl1-Imh1 axis, mediating the endosome-to-Golgi transport of SNAREs.
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Affiliation(s)
- Chun-Chi Lai
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Wan-Yun Chiu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Yan-Ting Chen
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Chia-Lu Wu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
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16
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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17
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Yates LA, Zhang X. Phosphoregulation of the checkpoint kinase Mec1 ATR. DNA Repair (Amst) 2023; 129:103543. [PMID: 37480741 DOI: 10.1016/j.dnarep.2023.103543] [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: 07/05/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Yeast Mec1, and its mammalian ortholog, Ataxia-Telangiectasia and Rad3-related, are giant protein kinases central to replication stress and double strand DNA break repair. Mec1ATR, in complex with Ddc2ATRIP, is a 'sensor' of single stranded DNA, and phosphorylates numerous cell cycle and DNA repair factors to enforce cell cycle arrest and facilitate repair. Over the last several years, new techniques - particularly in structural biology - have provided molecular mechanisms for Mec1ATR function. It is becoming increasingly clear how post-translational modification of Mec1ATR and its interaction partners modulates the DNA damage checkpoint. In this review, we summarise the most recent work unravelling Mec1ATR function in the DNA damage checkpoint and provide a molecular context for its regulation by phosphorylation.
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Affiliation(s)
- Luke A Yates
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
| | - Xiaodong Zhang
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
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18
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Seitz BC, Mucelli X, Majano M, Wallis Z, Dodge AC, Carmona C, Durant M, Maynard S, Huang LS. Meiosis II spindle disassembly requires two distinct pathways. Mol Biol Cell 2023; 34:ar98. [PMID: 37436806 PMCID: PMC10551701 DOI: 10.1091/mbc.e23-03-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
During exit from meiosis II, cells undergo several structural rearrangements, including disassembly of the meiosis II spindles and cytokinesis. Each of these changes is regulated to ensure that they occur at the proper time. Previous studies have demonstrated that both SPS1, which encodes a STE20-family GCKIII kinase, and AMA1, which encodes a meiosis-specific activator of the Anaphase Promoting Complex, are required for both meiosis II spindle disassembly and cytokinesis in the budding yeast Saccharomyces cerevisiae. We examine the relationship between meiosis II spindle disassembly and cytokinesis and find that the meiosis II spindle disassembly failure in sps1Δ and ama1∆ cells is not the cause of the cytokinesis defect. We also see that the spindle disassembly defects in sps1Δ and ama1∆ cells are phenotypically distinct. We examined known microtubule-associated proteins Ase1, Cin8, and Bim1, and found that AMA1 is required for the proper loss of Ase1 and Cin8 on meiosis II spindles while SPS1 is required for Bim1 loss in meiosis II. Taken together, these data indicate that SPS1 and AMA1 promote distinct aspects of meiosis II spindle disassembly, and that both pathways are required for the successful completion of meiosis.
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Affiliation(s)
- Brian C. Seitz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Maira Majano
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Zoey Wallis
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Ashley C. Dodge
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Catherine Carmona
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Sharra Maynard
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Linda S. Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
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19
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Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability. Int J Mol Sci 2022; 23:ijms232213888. [PMID: 36430366 PMCID: PMC9697909 DOI: 10.3390/ijms232213888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
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20
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The N-Terminal Domain of Bfa1 Coordinates Mitotic Exit Independent of GAP Activity in Saccharomyces cerevisiae. Cells 2022; 11:cells11142179. [PMID: 35883622 PMCID: PMC9316867 DOI: 10.3390/cells11142179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/10/2022] Open
Abstract
The spindle position checkpoint (SPOC) of budding yeast delays mitotic exit in response to misaligned spindles to ensure cell survival and the maintenance of genomic stability. The GTPase-activating protein (GAP) complex Bfa1–Bub2, a key SPOC component, inhibits the GTPase Tem1 to induce mitotic arrest in response to DNA and spindle damage, as well as spindle misorientation. However, previous results strongly suggest that Bfa1 exerts a GAP-independent function in blocking mitotic exit in response to misaligned spindles. Thus, the molecular mechanism by which Bfa1 controls mitotic exit in response to misaligned spindles remains unclear. Here, we observed that overexpression of the N-terminal domain of Bfa1 (Bfa1-D16), which lacks GAP activity and cannot localize to the spindle pole body (SPB), induced cell cycle arrest along with hyper-elongation of astral microtubules (aMTs) as Bfa1 overexpression in Δbub2. We found that Δbub2 cells overexpressing Bfa1 or Bfa1-D16 inhibited activation of Mob1, which is responsible for mitotic exit. In anaphase-arrested cells, Bfa1-D16 overexpression inhibited Tem1 binding to the SPB as well as Bfa1 overexpression. Additionally, endogenous levels of Bfa1-D16 showed minor SPOC activity that was not regulated by Kin4. These results suggested that Bfa1-D16 may block mitotic exit through inhibiting Tem1 activity outside of SPBs. Alternatively, Bfa1-D16 dispersed out of SPBs may block Tem1 binding to SPBs by physically interacting with Tem1 as previously reported. Moreover, we observed hyper-elongated aMTs in tem1-3, cdc15-2, and dbf2-2 mutants that induce anaphase arrest and cannot undergo mitotic exit at restrictive temperatures, suggesting that aMT dynamics are closely related to the regulation of mitotic exit. Altogether, these observations suggest that Bfa1 can control the SPOC independent of its GAP activity and SPB localization.
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21
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Vannini M, Mingione VR, Meyer A, Sniffen C, Whalen J, Seshan A. A Novel Hyperactive Nud1 Mitotic Exit Network Scaffold Causes Spindle Position Checkpoint Bypass in Budding Yeast. Cells 2021; 11:46. [PMID: 35011608 PMCID: PMC8750578 DOI: 10.3390/cells11010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mitotic exit is a critical cell cycle transition that requires the careful coordination of nuclear positioning and cyclin B destruction in budding yeast for the maintenance of genome integrity. The mitotic exit network (MEN) is a Ras-like signal transduction pathway that promotes this process during anaphase. A crucial step in MEN activation occurs when the Dbf2-Mob1 protein kinase complex associates with the Nud1 scaffold protein at the yeast spindle pole bodies (SPBs; centrosome equivalents) and thereby becomes activated. This requires prior priming phosphorylation of Nud1 by Cdc15 at SPBs. Cdc15 activation, in turn, requires both the Tem1 GTPase and the Polo kinase Cdc5, but how Cdc15 associates with SPBs is not well understood. We have identified a hyperactive allele of NUD1, nud1-A308T, that recruits Cdc15 to SPBs in all stages of the cell cycle in a CDC5-independent manner. This allele leads to early recruitment of Dbf2-Mob1 during metaphase and requires known Cdc15 phospho-sites on Nud1. The presence of nud1-A308T leads to loss of coupling between nuclear position and mitotic exit in cells with mispositioned spindles. Our findings highlight the importance of scaffold regulation in signaling pathways to prevent improper activation.
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Affiliation(s)
- Michael Vannini
- Boston University School of Medicine, Boston, MA 02118, USA;
| | - Victoria R. Mingione
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA;
| | | | - Courtney Sniffen
- Renaissance School of Medicine, Stony Brook University Hospital, Stony Brook, NY 11794, USA;
| | - Jenna Whalen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA;
| | - Anupama Seshan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
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22
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Alonso-Ramos P, Álvarez-Melo D, Strouhalova K, Pascual-Silva C, Garside GB, Arter M, Bermejo T, Grigaitis R, Wettstein R, Fernández-Díaz M, Matos J, Geymonat M, San-Segundo PA, Carballo JA. The Cdc14 Phosphatase Controls Resolution of Recombination Intermediates and Crossover Formation during Meiosis. Int J Mol Sci 2021; 22:ijms22189811. [PMID: 34575966 PMCID: PMC8470964 DOI: 10.3390/ijms22189811] [Citation(s) in RCA: 4] [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: 08/20/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. The coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for the accurate completion of both rounds of chromosome segregation. Numerous master kinases orchestrate the correct assembly and activity of the repair machinery. Although much less is known, the reversal of phosphorylation events in meiosis must also be key to coordinate the timing and functionality of repair enzymes. Cdc14 is a crucial phosphatase required for the dephosphorylation of multiple CDK1 targets in many eukaryotes. Mutations that inactivate this phosphatase lead to meiotic failure, but until now it was unknown if Cdc14 plays a direct role in meiotic recombination. Here, we show that the elimination of Cdc14 leads to severe defects in the processing and resolution of recombination intermediates, causing a drastic depletion in crossovers when other repair pathways are compromised. We also show that Cdc14 is required for the correct activity and localization of the Holliday Junction resolvase Yen1/GEN1. We reveal that Cdc14 regulates Yen1 activity from meiosis I onwards, and this function is essential for crossover resolution in the absence of other repair pathways. We also demonstrate that Cdc14 and Yen1 are required to safeguard sister chromatid segregation during the second meiotic division, a late action that is independent of the earlier role in crossover formation. Thus, this work uncovers previously undescribed functions of the evolutionary conserved Cdc14 phosphatase in the regulation of meiotic recombination.
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Affiliation(s)
- Paula Alonso-Ramos
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - David Álvarez-Melo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Katerina Strouhalova
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic
| | - Carolina Pascual-Silva
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - George B. Garside
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 4DY, UK;
- Leibniz Institute for Age Research/Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Teresa Bermejo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Rokas Grigaitis
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Rahel Wettstein
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marta Fernández-Díaz
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marco Geymonat
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK;
| | - Pedro A. San-Segundo
- Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC) and University of Salamanca, 37007 Salamanca, Spain;
| | - Jesús A. Carballo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Correspondence:
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