1
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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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2
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Cao R, Jones DTD, Pan L, Wang S, Rawson S, Aster JC, Blacklow SC. Molecular Mechanism of PP2A/B55α Inhibition by IER5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555174. [PMID: 37693604 PMCID: PMC10491241 DOI: 10.1101/2023.08.29.555174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
PP2A serine/threonine protein phosphatases are heterotrimeric complexes that have a wide range of essential physiologic functions. The B55α form of PP2A has critical roles in cell cycle regulation, mitotic exit, and the DNA damage response1-6. Its activity is modulated by additional regulatory proteins, such as ARPP197, FAM122A8, and IER59. However, the precise mechanisms underlying the modulation of PP2A activity by these proteins remain elusive. Here, we show that IER5 inhibits pTau dephosphorylation by PP2A/B55α in biochemical assays and report a cryoelectron microscopy structure of the PP2A/B55α-IER5 complex, which reveals that IER5 occludes a surface on B55α used for substrate recruitment10-12. Mutation of interface residues on IER5 interferes with recovery of B55α in co-immunoprecipitation assays and suppresses events in squamous carcinoma cells, such as KRT1 expression, that depend on inhibition of PP2A/B55α by IER59. These studies define the molecular basis for PP2A inhibition by IER5 and suggest a roadmap for selective pharmacologic modulation of PP2A/B55α complexes.
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Affiliation(s)
- Ruili Cao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Daniel TD Jones
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Li Pan
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Shumei Wang
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA USA
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3
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Nguyen H, Kettenbach AN. Substrate and phosphorylation site selection by phosphoprotein phosphatases. Trends Biochem Sci 2023; 48:713-725. [PMID: 37173206 PMCID: PMC10523993 DOI: 10.1016/j.tibs.2023.04.004] [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: 01/04/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Dynamic protein phosphorylation and dephosphorylation are essential regulatory mechanisms that ensure proper cellular signaling and biological functions. Deregulation of either reaction has been implicated in several human diseases. Here, we focus on the mechanisms that govern the specificity of the dephosphorylation reaction. Most cellular serine/threonine dephosphorylation is catalyzed by 13 highly conserved phosphoprotein phosphatase (PPP) catalytic subunits, which form hundreds of holoenzymes by binding to regulatory and scaffolding subunits. PPP holoenzymes recognize phosphorylation site consensus motifs and interact with short linear motifs (SLiMs) or structural elements distal to the phosphorylation site. We review recent advances in understanding the mechanisms of PPP site-specific dephosphorylation preference and substrate recruitment and highlight examples of their interplay in the regulation of cell division.
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Affiliation(s)
- Hieu Nguyen
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; Dartmouth Cancer Center, Lebanon, NH 03756, USA.
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4
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Camlin NJ, Venkatachalam I, Evans JP. Oscillations in PP1 activity are essential for accurate progression through mammalian oocyte meiosis. Cell Cycle 2023; 22:1614-1636. [PMID: 37340734 PMCID: PMC10361142 DOI: 10.1080/15384101.2023.2225924] [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: 08/25/2022] [Revised: 04/17/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Tightly controlled fluctuations in kinase and phosphatase activity play important roles in regulating M-phase transitions. Protein Phosphatase 1 (PP1) is one of these phosphatases, with oscillations in PP1 activity driving mitotic M-phase. Evidence from a variety of experimental systems also points to roles in meiosis. Here, we report that PP1 is important for M-phase transitions through mouse oocyte meiosis. We employed a unique small-molecule approach to inhibit or activate PP1 at distinct phases of mouse oocyte meiosis. These studies show that temporal control of PP1 activity is essential for the G2/M transition, metaphase I/anaphase I transition, and the formation of a normal metaphase II oocyte. Our data also reveal that inappropriate activation of PP1 is more deleterious at the G2/M transition than at prometaphase I-to-metaphase I, and that an active pool of PP1 during prometaphase is vital for metaphase I/anaphase I transition and metaphase II chromosome alignment. Taken together, these results establish that loss of oscillations in PP1 activity causes a range of severe meiotic defects, pointing to essential roles for PP1 in female fertility, and more broadly, M-phase regulation.
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Affiliation(s)
- Nicole J. Camlin
- Department of Biological Sciences, Purdue University, West Lafayette, INUnited States
| | - Ilakkiya Venkatachalam
- Department of Biological Sciences, Purdue University, West Lafayette, INUnited States
- Department of Human Genetics, University of Michigan, Ann Arbor, MIUnited States
| | - Janice P. Evans
- Department of Biological Sciences, Purdue University, West Lafayette, INUnited States
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5
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Mariano NC, Rusin SF, Nasa I, Kettenbach AN. Inducible protein degradation as a strategy to identify Phosphoprotein Phosphatase 6 substrates in RAS-mutant colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534211. [PMID: 36993243 PMCID: PMC10055397 DOI: 10.1101/2023.03.25.534211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation SITES and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent phosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation.
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6
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Kokot T, Köhn M. Emerging insights into serine/threonine-specific phosphoprotein phosphatase function and selectivity. J Cell Sci 2022; 135:277104. [DOI: 10.1242/jcs.259618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ABSTRACT
Protein phosphorylation on serine and threonine residues is a widely distributed post-translational modification on proteins that acts to regulate their function. Phosphoprotein phosphatases (PPPs) contribute significantly to a plethora of cellular functions through the accurate dephosphorylation of phosphorylated residues. Most PPPs accomplish their purpose through the formation of complex holoenzymes composed of a catalytic subunit with various regulatory subunits. PPP holoenzymes then bind and dephosphorylate substrates in a highly specific manner. Despite the high prevalence of PPPs and their important role for cellular function, their mechanisms of action in the cell are still not well understood. Nevertheless, substantial experimental advancements in (phospho-)proteomics, structural and computational biology have contributed significantly to a better understanding of PPP biology in recent years. This Review focuses on recent approaches and provides an overview of substantial new insights into the complex mechanism of PPP holoenzyme regulation and substrate selectivity.
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Affiliation(s)
- Thomas Kokot
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
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7
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Das D, Arur S. Regulation of oocyte maturation: Role of conserved ERK signaling. Mol Reprod Dev 2022; 89:353-374. [PMID: 35908193 PMCID: PMC9492652 DOI: 10.1002/mrd.23637] [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: 03/25/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 11/11/2022]
Abstract
During oogenesis, oocytes arrest at meiotic prophase I to acquire competencies for resuming meiosis, fertilization, and early embryonic development. Following this arrested period, oocytes resume meiosis in response to species-specific hormones, a process known as oocyte maturation, that precedes ovulation and fertilization. Involvement of endocrine and autocrine/paracrine factors and signaling events during maintenance of prophase I arrest, and resumption of meiosis is an area of active research. Studies in vertebrate and invertebrate model organisms have delineated the molecular determinants and signaling pathways that regulate oocyte maturation. Cell cycle regulators, such as cyclin-dependent kinase (CDK1), polo-like kinase (PLK1), Wee1/Myt1 kinase, and the phosphatase CDC25 play conserved roles during meiotic resumption. Extracellular signal-regulated kinase (ERK), on the other hand, while activated during oocyte maturation in all species, regulates both species-specific, as well as conserved events among different organisms. In this review, we synthesize the general signaling mechanisms and focus on conserved and distinct functions of ERK signaling pathway during oocyte maturation in mammals, non-mammalian vertebrates, and invertebrates such as Drosophila and Caenorhabditis elegans.
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Affiliation(s)
- Debabrata Das
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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Swartz SZ, Tan TH, Perillo M, Fakhri N, Wessel GM, Wikramanayake AH, Cheeseman IM. Polarized Dishevelled dissolution and reassembly drives embryonic axis specification in sea star oocytes. Curr Biol 2021; 31:5633-5641.e4. [PMID: 34739818 PMCID: PMC8692449 DOI: 10.1016/j.cub.2021.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/20/2021] [Accepted: 10/08/2021] [Indexed: 11/22/2022]
Abstract
The organismal body axes that are formed during embryogenesis are intimately linked to intrinsic asymmetries established at the cellular scale in oocytes.1 However, the mechanisms that generate cellular asymmetries within the oocyte and then transduce that polarity to organismal scale body axes are poorly understood outside of select model organisms. Here, we report an axis-defining event in meiotic oocytes of the sea star Patiria miniata. Dishevelled (Dvl) is a cytoplasmic Wnt pathway effector required for axis development in diverse species,2-4 but the mechanisms governing its function and distribution remain poorly defined. Using time-lapse imaging, we find that Dvl localizes uniformly to puncta throughout the cell cortex in Prophase I-arrested oocytes but becomes enriched at the vegetal pole following meiotic resumption through a dissolution-reassembly mechanism. This process is driven by an initial disassembly phase of Dvl puncta, followed by selective reformation of Dvl assemblies at the vegetal pole. Rather than being driven by Wnt signaling, this localization behavior is coupled to meiotic cell cycle progression and influenced by Lamp1+ endosome association and Frizzled receptors pre-localized within the oocyte cortex. Our results reveal a cell cycle-linked mechanism by which maternal cellular polarity is transduced to the embryo through spatially regulated Dvl dynamics.
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Affiliation(s)
- S Zachary Swartz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Embryology Course: Concepts and Techniques in Modern Developmental Biology, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Tzer Han Tan
- Massachusetts Institute of Technology, Department of Physics, Cambridge, MA 02142, USA
| | | | - Nikta Fakhri
- Massachusetts Institute of Technology, Department of Physics, Cambridge, MA 02142, USA
| | - Gary M Wessel
- MCB Department, Brown University, Providence, RI 02912, USA
| | - Athula H Wikramanayake
- Department of Biology, University of Miami, Coral Gables, FL 33134, USA; Embryology Course: Concepts and Techniques in Modern Developmental Biology, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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9
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Swartz SZ, Nguyen HT, McEwan BC, Adamo ME, Cheeseman IM, Kettenbach AN. Selective dephosphorylation by PP2A-B55 directs the meiosis I-meiosis II transition in oocytes. eLife 2021; 10:70588. [PMID: 34342579 PMCID: PMC8370769 DOI: 10.7554/elife.70588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Meiosis is a specialized cell cycle that requires sequential changes to the cell division machinery to facilitate changing functions. To define the mechanisms that enable the oocyte-to-embryo transition, we performed time-course proteomics in synchronized sea star oocytes from prophase I through the first embryonic cleavage. Although we found that protein levels were broadly stable, our analysis reveals that dynamic waves of phosphorylation underlie each meiotic stage. We found that the phosphatase PP2A-B55 is reactivated at the meiosis I/meiosis II (MI/MII) transition, resulting in the preferential dephosphorylation of threonine residues. Selective dephosphorylation is critical for directing the MI/MII transition as altering PP2A-B55 substrate preferences disrupts key cell cycle events after MI. In addition, threonine to serine substitution of a conserved phosphorylation site in the substrate INCENP prevents its relocalization at anaphase I. Thus, through its inherent phospho-threonine preference, PP2A-B55 imposes specific phosphoregulated behaviors that distinguish the two meiotic divisions.
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Affiliation(s)
- S Zachary Swartz
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Hieu T Nguyen
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Brennan C McEwan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Mark E Adamo
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, United States
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, United States
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