1
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Zhang R, Feng W, Qian S, Li S, Wang F. Regulation of Rim4 distribution, function, and stability during meiosis by PKA, Cdc14, and 14-3-3 proteins. Cell Rep 2023; 42:113052. [PMID: 37659077 PMCID: PMC10591911 DOI: 10.1016/j.celrep.2023.113052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Meiotic gene expression in budding yeast is tightly controlled by RNA-binding proteins (RBPs), with the meiosis-specific RBP Rim4 playing a key role in sequestering mid-late meiotic transcripts to prevent premature translation. However, the mechanisms governing assembly and disassembly of the Rim4-mRNA complex, critical for Rim4's function and stability, remain poorly understood. In this study, we unveil regulation of the Rim4 ribonucleoprotein (RNP) complex by the yeast 14-3-3 proteins Bmh1 and Bmh2. These proteins form a Rim4-Bmh1-Bmh2 heterotrimeric complex that expels mRNAs from Rim4 binding. We identify four Bmh1/2 binding sites (BBSs) on Rim4, with two residing within the RNA recognition motifs (RRMs). Phosphorylation and dephosphorylation of serine/threonine (S/T) residues at these BBSs by PKA kinase and Cdc14 phosphatase activities primarily control formation of Rim4-Bmh1/2, regulating Rim4's subcellular distribution, function, and stability. These findings shed light on the intricate post-transcriptional regulatory mechanisms governing meiotic gene expression.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shunjin Li
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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2
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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3
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Shi G, Song C, Torres Robles J, Salichos L, Lou HJ, Lam TT, Gerstein M, Turk BE. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Sci Signal 2023; 16:eabm5518. [PMID: 36626580 PMCID: PMC9995140 DOI: 10.1126/scisignal.abm5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these "docking" interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform, we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. Our screen of a library consisting of ~12,000 sequences from the human proteome revealed multiple MAPK-selective interactors, including many that did not conform to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues that mediate selective binding. Last, we verified that docking sequences identified in the screen functioned in substrate recruitment in vitro and in cultured cells. Together, these studies establish an approach to characterize MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK.
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Affiliation(s)
- Guangda Shi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claire Song
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.,Keck MS and Proteomics Resource, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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4
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Milholland KL, AbdelKhalek A, Baker KM, Hoda S, DeMarco AG, Naughton NH, Koeberlein AN, Lorenz GR, Anandasothy K, Esperilla-Muñoz A, Narayanan SK, Correa-Bordes J, Briggs SD, Hall MC. Cdc14 phosphatase contributes to cell wall integrity and pathogenesis in Candida albicans. Front Microbiol 2023; 14:1129155. [PMID: 36876065 PMCID: PMC9977832 DOI: 10.3389/fmicb.2023.1129155] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
The Cdc14 phosphatase family is highly conserved in fungi. In Saccharomyces cerevisiae, Cdc14 is essential for down-regulation of cyclin-dependent kinase activity at mitotic exit. However, this essential function is not broadly conserved and requires only a small fraction of normal Cdc14 activity. Here, we identified an invariant motif in the disordered C-terminal tail of fungal Cdc14 enzymes that is required for full enzyme activity. Mutation of this motif reduced Cdc14 catalytic rate and provided a tool for studying the biological significance of high Cdc14 activity. A S. cerevisiae strain expressing the reduced-activity hypomorphic mutant allele (cdc14hm ) as the sole source of Cdc14 proliferated like the wild-type parent strain but exhibited an unexpected sensitivity to cell wall stresses, including chitin-binding compounds and echinocandin antifungal drugs. Sensitivity to echinocandins was also observed in Schizosaccharomyces pombe and Candida albicans strains lacking CDC14, suggesting this phenotype reflects a novel and conserved function of Cdc14 orthologs in mediating fungal cell wall integrity. In C. albicans, the orthologous cdc14hm allele was sufficient to elicit echinocandin hypersensitivity and perturb cell wall integrity signaling. It also caused striking abnormalities in septum structure and the same cell separation and hyphal differentiation defects previously observed with cdc14 gene deletions. Since hyphal differentiation is important for C. albicans pathogenesis, we assessed the effect of reduced Cdc14 activity on virulence in Galleria mellonella and mouse models of invasive candidiasis. Partial reduction in Cdc14 activity via cdc14hm mutation severely impaired C. albicans virulence in both assays. Our results reveal that high Cdc14 activity is important for C. albicans cell wall integrity and pathogenesis and suggest that Cdc14 may be worth future exploration as an antifungal drug target.
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Affiliation(s)
- Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Kortany M Baker
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Noelle H Naughton
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Angela N Koeberlein
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Gabrielle R Lorenz
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kartikan Anandasothy
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sanjeev K Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D Briggs
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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5
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Feng W, Argüello-Miranda O, Qian S, Wang F. Cdc14 spatiotemporally dephosphorylates Atg13 to activate autophagy during meiotic divisions. J Cell Biol 2022; 221:213046. [PMID: 35238874 PMCID: PMC8919667 DOI: 10.1083/jcb.202107151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a conserved eukaryotic lysosomal degradation pathway that responds to environmental and cellular cues. Autophagy is essential for the meiotic exit and sporulation in budding yeast, but the underlying molecular mechanisms remain unknown. Here, we show that autophagy is maintained during meiosis and stimulated in anaphase I and II. Cells with higher levels of autophagy complete meiosis faster, and genetically enhanced autophagy increases meiotic kinetics and sporulation efficiency. Strikingly, our data reveal that the conserved phosphatase Cdc14 regulates meiosis-specific autophagy. Cdc14 is activated in anaphase I and II, accompanying its subcellular relocation from the nucleolus to the cytoplasm, where it dephosphorylates Atg13 to stimulate Atg1 kinase activity and thus autophagy. Together, our findings reveal a meiosis-tailored mechanism that spatiotemporally controls meiotic autophagy activity to ensure meiosis progression, exit, and sporulation.
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Affiliation(s)
- Wenzhi Feng
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Suhong Qian
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Fei Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX,Correspondence to Fei Wang:
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6
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Philip J, Örd M, Silva A, Singh S, Diffley JFX, Remus D, Loog M, Ikui AE. Cdc6 is sequentially regulated by PP2A-Cdc55, Cdc14, and Sic1 for origin licensing in S. cerevisiae. eLife 2022; 11:e74437. [PMID: 35142288 PMCID: PMC8830886 DOI: 10.7554/elife.74437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/15/2021] [Indexed: 01/31/2023] Open
Abstract
Cdc6, a subunit of the pre-replicative complex (pre-RC), contains multiple regulatory cyclin-dependent kinase (Cdk1) consensus sites, SP or TP motifs. In Saccharomyces cerevisiae, Cdk1 phosphorylates Cdc6-T7 to recruit Cks1, the Cdk1 phospho-adaptor in S phase, for subsequent multisite phosphorylation and protein degradation. Cdc6 accumulates in mitosis and is tightly bound by Clb2 through N-terminal phosphorylation in order to prevent premature origin licensing and degradation. It has been extensively studied how Cdc6 phosphorylation is regulated by the cyclin-Cdk1 complex. However, a detailed mechanism on how Cdc6 phosphorylation is reversed by phosphatases has not been elucidated. Here, we show that PP2ACdc55 dephosphorylates Cdc6 N-terminal sites to release Clb2. Cdc14 dephosphorylates the C-terminal phospho-degron, leading to Cdc6 stabilization in mitosis. In addition, Cdk1 inhibitor Sic1 releases Clb2·Cdk1·Cks1 from Cdc6 to load Mcm2-7 on the chromatin upon mitotic exit. Thus, pre-RC assembly and origin licensing are promoted by phosphatases through the attenuation of distinct Cdk1-dependent Cdc6 inhibitory mechanisms.
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Affiliation(s)
- Jasmin Philip
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | | | - Andriele Silva
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | - Shaneen Singh
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | | | - Dirk Remus
- Memorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | | | - Amy E Ikui
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
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7
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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8
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Kumar M, Michael S, Alvarado-Valverde J, Mészáros B, Sámano‐Sánchez H, Zeke A, Dobson L, Lazar T, Örd M, Nagpal A, Farahi N, Käser M, Kraleti R, Davey N, Pancsa R, Chemes L, Gibson T. The Eukaryotic Linear Motif resource: 2022 release. Nucleic Acids Res 2022; 50:D497-D508. [PMID: 34718738 PMCID: PMC8728146 DOI: 10.1093/nar/gkab975] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023] Open
Abstract
Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano‐Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
- Biomedical Sciences, Edinburgh Medical School, The University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Laszlo Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Mihkel Örd
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Anurag Nagpal
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa 403726, India
| | - Nazanin Farahi
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Melanie Käser
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Ramya Kraleti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Justus Liebig University Giessen, Ludwigstraße 23, 35390 Gießen, Germany
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Rita Pancsa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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9
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Docking to a Basic Helix Promotes Specific Phosphorylation by G1-Cdk1. Int J Mol Sci 2021; 22:ijms22179514. [PMID: 34502421 PMCID: PMC8431026 DOI: 10.3390/ijms22179514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is coordinated by CDK both via general CDK activity thresholds and cyclin-specific substrate docking. Recently, it was found that the G1-cyclins of S. cerevisiae have a specific function in promoting polarization and growth of the buds, making the G1 cyclins essential for cell survival. Thus, while a uniform CDK specificity of a single cyclin can be sufficient to drive the cell cycle in some cells, such as in fission yeast, cyclin specificity can be essential in other organisms. However, the known G1-CDK specific LP docking motif, was not responsible for this essential function, indicating that G1-CDKs use yet other unknown docking mechanisms. Here we report a discovery of a G1 cyclin-specific (Cln1,2) lysine-arginine-rich helical docking motif (the K/R motif) in G1-CDK targets involved in the mating pathway (Ste7), transcription (Xbp1), bud morphogenesis (Bud2) and spindle pole body (Spc29, Spc42, Spc110, Sli15) function of S. cerevisiae. We also show that the docking efficiency of K/R motif can be regulated by basophilic kinases such as protein kinase A. Our results further widen the list of cyclin specificity mechanisms and may explain the recently demonstrated unique essential function of G1 cyclins in budding yeast.
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10
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Proline-Rich Motifs Control G2-CDK Target Phosphorylation and Priming an Anchoring Protein for Polo Kinase Localization. Cell Rep 2021; 31:107757. [PMID: 32553169 PMCID: PMC7301157 DOI: 10.1016/j.celrep.2020.107757] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/31/2020] [Accepted: 05/20/2020] [Indexed: 11/23/2022] Open
Abstract
The hydrophobic patch (hp), a docking pocket on cyclins of CDKs (cyclin-dependent kinases), has been thought to accommodate a single short linear motif (SLiM), the "RxL or Cy" docking motif. Here we show that hp can bind different motifs with high specificity. We identify a PxxPxF motif that is necessary for G2-cyclin Clb3 function in S. cerevisiae, and that mediates Clb3-Cdk1 phosphorylation of Ypr174c (proposed name: Cdc5 SPB anchor-Csa1) to regulate the localization of Polo kinase Cdc5. Similar motifs exist in other Clb3-Cdk1 targets. Our work completes the set of docking specificities for the four major cyclins: LP, RxL, PxxPxF, and LxF motifs for G1-, S-, G2-, and M-phase cyclins, respectively. Further, we show that variations in motifs can change their specificity for human cyclins. This diversity could provide complexity for the encoding of CDK thresholds to achieve ordered cell-cycle phosphorylation.
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11
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Ali M, Simonetti L, Ivarsson Y. Screening Intrinsically Disordered Regions for Short Linear Binding Motifs. Methods Mol Biol 2021; 2141:529-552. [PMID: 32696376 DOI: 10.1007/978-1-0716-0524-0_27] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The intrinsically disordered regions of the proteome are enriched in short linear motifs (SLiMs) that serve as binding sites for peptide binding proteins. These interactions are often of low-to-mid micromolar affinities and are challenging to screen for experimentally. However, a range of dedicated methods have been developed recently, which open for screening of SLiM-based interactions on large scale. A variant of phage display, termed proteomic peptide phage display (ProP-PD), has proven particularly useful for the purpose. Here, we describe a complete high-throughput ProP-PD protocol for screening intrinsically disordered regions for SLiMs. The protocol requires some basic bioinformatics skills for the design of the library and for data analysis but can be performed in a standard biochemistry lab. The protocol starts from the construction of a library, followed by the high-throughput expression and purification of bait proteins, the phage selection, and the analysis of the binding-enriched phage pools using next-generation sequencing. As the protocol generates rather large data sets, we also emphasize the importance of data management and storage.
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12
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Faustova I, Bulatovic L, Matiyevskaya F, Valk E, Örd M, Loog M. A new linear cyclin docking motif that mediates exclusively S-phase CDK-specific signaling. EMBO J 2020; 40:e105839. [PMID: 33210757 PMCID: PMC7809796 DOI: 10.15252/embj.2020105839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/23/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Cyclin‐dependent kinases (CDKs), the master regulators of cell division, are activated by different cyclins at different cell cycle stages. In addition to being activators of CDKs, cyclins recognize various linear motifs to target CDK activity to specific proteins. We uncovered a cyclin docking motif, NLxxxL, that contributes to phosphorylation‐dependent degradation of the CDK inhibitor Far1 at the G1/S stage in the yeast Saccharomyces cerevisiae. This motif is recognized exclusively by S‐phase CDK (S‐CDK) Clb5/6‐Cdc28 and is considerably more potent than the conventional RxL docking motif. The NLxxxL and RxL motifs were found to overlap in some target proteins, suggesting that cyclin docking motifs can evolve to switch from one to another for fine‐tuning of cell cycle events. Using time‐lapse fluorescence microscopy, we show how different docking connections temporally control phosphorylation‐driven target degradation. This also revealed a differential function of the phosphoadaptor protein Cks1, as Cks1 docking potentiated degron phosphorylation of RxL‐containing but not of NLxxxL‐containing substrates. The NLxxxL motif was found to govern S‐cyclin‐specificity in multiple yeast CDK targets including Fin1, Lif1, and Slx4, suggesting its wider importance.
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Affiliation(s)
- Ilona Faustova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Luka Bulatovic
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
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13
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Bandyopadhyay S, Bhaduri S, Örd M, Davey NE, Loog M, Pryciak PM. Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo. Curr Biol 2020; 30:4454-4466.e5. [PMID: 32976810 PMCID: PMC8009629 DOI: 10.1016/j.cub.2020.08.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022]
Abstract
Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phosphorylate different substrates at different stages, thus enforcing a temporally ordered series of events. In budding yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late G1 phase, yet the key sequence features of these motifs were unknown. Here, we comprehensively analyze LP motif requirements in vivo by combining a competitive growth assay with deep mutational scanning. We quantified the effect of all single-residue replacements in five different LP motifs by using six distinct G1 cyclins from diverse fungi including medical and agricultural pathogens. The results uncover substantial tolerance for deviations from the consensus sequence, plus requirements at some positions that are contingent on the favorability of other motif residues. They also reveal the basis for variations in functional potency among wild-type motifs, and allow derivation of a quantitative matrix that predicts the strength of other candidate motif sequences. Finally, we find that variation in docking motif potency can advance or delay the time at which CDK substrate phosphorylation occurs, and thereby control the temporal ordering of cell cycle regulation. The overall results provide a general method for surveying viable docking motif sequences and quantifying their potency in vivo, and they reveal how variations in docking strength can tune the degree and timing of regulatory modifications.
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Affiliation(s)
- Sushobhana Bandyopadhyay
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Samyabrata Bhaduri
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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14
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Touati SA, Hofbauer L, Jones AW, Snijders AP, Kelly G, Uhlmann F. Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit. Cell Rep 2020; 29:2105-2119.e4. [PMID: 31722221 PMCID: PMC6857435 DOI: 10.1016/j.celrep.2019.10.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/27/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022] Open
Abstract
Temporal control over protein phosphorylation and dephosphorylation is crucial for accurate chromosome segregation and for completion of the cell division cycle during exit from mitosis. In budding yeast, the Cdc14 phosphatase is thought to be a major regulator at this time, while in higher eukaryotes PP2A phosphatases take a dominant role. Here, we use time-resolved phosphoproteome analysis in budding yeast to evaluate the respective contributions of Cdc14, PP2ACdc55, and PP2ARts1. This reveals an overlapping requirement for all three phosphatases during mitotic progression. Our time-resolved phosphoproteome resource reveals how Cdc14 instructs the sequential pattern of phosphorylation changes, in part through preferential recognition of serine-based cyclin-dependent kinase (Cdk) substrates. PP2ACdc55 and PP2ARts1 in turn exhibit a broad substrate spectrum with some selectivity for phosphothreonines and a role for PP2ARts1 in sustaining Aurora kinase activity. These results illustrate synergy and coordination between phosphatases as they orchestrate phosphoproteome dynamics during mitotic progression. Cdc14, PP2ACdc55, and PP2ARts1 phosphatases cooperate during budding yeast mitosis Cdc14 targets serine Cdk motifs for rapid dephosphorylation PP2ACdc55 dephosphorylates Cdk and Plk substrates on threonine residues PP2ARts1 displays regulatory crosstalk with Aurora kinase
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Affiliation(s)
- Sandra A Touati
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Lorena Hofbauer
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew W Jones
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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15
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DeMarco AG, Milholland KL, Pendleton AL, Whitney JJ, Zhu P, Wesenberg DT, Nambiar M, Pepe A, Paula S, Chmielewski J, Wisecaver JH, Tao WA, Hall MC. Conservation of Cdc14 phosphatase specificity in plant fungal pathogens: implications for antifungal development. Sci Rep 2020; 10:12073. [PMID: 32694511 PMCID: PMC7374715 DOI: 10.1038/s41598-020-68921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/24/2020] [Indexed: 11/08/2022] Open
Abstract
Cdc14 protein phosphatases play an important role in plant infection by several fungal pathogens. This and other properties of Cdc14 enzymes make them an intriguing target for development of new antifungal crop treatments. Active site architecture and substrate specificity of Cdc14 from the model fungus Saccharomyces cerevisiae (ScCdc14) are well-defined and unique among characterized phosphatases. Cdc14 appears absent from some model plants. However, the extent of conservation of Cdc14 sequence, structure, and specificity in fungal plant pathogens is unknown. We addressed this by performing a comprehensive phylogenetic analysis of the Cdc14 family and comparing the conservation of active site structure and specificity among a sampling of plant pathogen Cdc14 homologs. We show that Cdc14 was lost in the common ancestor of angiosperm plants but is ubiquitous in ascomycete and basidiomycete fungi. The unique substrate specificity of ScCdc14 was invariant in homologs from eight diverse species of dikarya, suggesting it is conserved across the lineage. A synthetic substrate mimetic inhibited diverse fungal Cdc14 homologs with similar low µM Ki values, but had little effect on related phosphatases. Our results justify future exploration of Cdc14 as a broad spectrum antifungal target for plant protection.
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Affiliation(s)
- Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - John J Whitney
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Peipei Zhu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Daniel T Wesenberg
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Monessha Nambiar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Antonella Pepe
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stefan Paula
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, California State University, 6000 J Street, Sacramento, CA, 95819, USA
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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16
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Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Bradburn DA, Tsekitsidou E, Hong SH, Kaderali MA, Xu SL, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE, Cyert MS. Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. Mol Cell 2020; 79:342-358.e12. [PMID: 32645368 DOI: 10.1016/j.molcel.2020.06.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 03/24/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins-structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.
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Affiliation(s)
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Nikhil P Damle
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vikash K Yadav
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Cecilia Blikstad
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Eduard Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | - Su Hyun Hong
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Malika Amyn Kaderali
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3H7 ON, Canada
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fullham Road, London SW3 6JB, UK
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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17
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The Multiple Roles of the Cdc14 Phosphatase in Cell Cycle Control. Int J Mol Sci 2020; 21:ijms21030709. [PMID: 31973188 PMCID: PMC7038166 DOI: 10.3390/ijms21030709] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdc14 phosphatase is a key regulator of mitosis in the budding yeast Saccharomyces cerevisiae. Cdc14 was initially described as playing an essential role in the control of cell cycle progression by promoting mitotic exit on the basis of its capacity to counteract the activity of the cyclin-dependent kinase Cdc28/Cdk1. A compiling body of evidence, however, has later demonstrated that this phosphatase plays other multiple roles in the regulation of mitosis at different cell cycle stages. Here, we summarize our current knowledge about the pivotal role of Cdc14 in cell cycle control, with a special focus in the most recently uncovered functions of the phosphatase.
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18
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Gong Q, Qin W, Xiao P, Wu X, Li L, Zhang G, Zhang R, Sun J, Yao SQ, Huang W. Internal standard fluorogenic probe based on vibration-induced emission for visualizing PTP1B in living cells. Chem Commun (Camb) 2020; 56:58-61. [DOI: 10.1039/c9cc07680h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, as a proof of concept, we developed the first enzymatic VIE fluorogenic probe for protein tyrosine phosphatase 1B (PTP1B).
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Affiliation(s)
- Qiuyu Gong
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
- Department of Chemistry
| | - Wenjing Qin
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education
- Department of Biochemistry and Molecular Biology
- Shandong University School of Medicine
- Jinan
- P. R. China
| | - Xiang Wu
- Key Laboratory Experimental Teratology of the Ministry of Education
- Department of Biochemistry and Molecular Biology
- Shandong University School of Medicine
- Jinan
- P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
| | - Gaobin Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
| | - Renshuai Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
| | - Jinpeng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education
- Department of Biochemistry and Molecular Biology
- Shandong University School of Medicine
- Jinan
- P. R. China
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)
- Nanjing Tech University (Nanjing Tech)
- Nanjing
- P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE)
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19
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Zhang L, Winkler S, Schlottmann FP, Kohlbacher O, Elias JE, Skotheim JM, Ewald JC. Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast. Front Cell Dev Biol 2019; 7:338. [PMID: 31921850 PMCID: PMC6927922 DOI: 10.3389/fcell.2019.00338] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/29/2019] [Indexed: 01/20/2023] Open
Abstract
The coordination of metabolism and growth with cell division is crucial for proliferation. While it has long been known that cell metabolism regulates the cell division cycle, it is becoming increasingly clear that the cell division cycle also regulates metabolism. In budding yeast, we previously showed that over half of all measured metabolites change concentration through the cell cycle indicating that metabolic fluxes are extensively regulated during cell cycle progression. However, how this regulation is achieved still remains poorly understood. Since both the cell cycle and metabolism are regulated to a large extent by protein phosphorylation, we here decided to measure the phosphoproteome through the budding yeast cell cycle. Specifically, we chose a cell cycle synchronization strategy that avoids stress and nutrient-related perturbations of metabolism, and we grew the yeast on ethanol minimal medium to force cells to utilize their full biosynthetic repertoire. Using a tandem-mass-tagging approach, we found over 200 sites on metabolic enzymes and transporters to be phospho-regulated. These sites were distributed among many pathways including carbohydrate catabolism, lipid metabolism, and amino acid synthesis and therefore likely contribute to changing metabolic fluxes through the cell cycle. Among all one thousand sites whose phosphorylation increases through the cell cycle, the CDK consensus motif and an arginine-directed motif were highly enriched. This arginine-directed R-R-x-S motif is associated with protein-kinase A, which regulates metabolism and promotes growth. Finally, we also found over one thousand sites that are dephosphorylated through the G1/S transition. We speculate that the phosphatase Glc7/PP1, known to regulate both the cell cycle and carbon metabolism, may play an important role because its regulatory subunits are phospho-regulated in our data. In summary, our results identify extensive cell cycle dependent phosphorylation and dephosphorylation of metabolic enzymes and suggest multiple mechanisms through which the cell division cycle regulates metabolic signaling pathways to temporally coordinate biosynthesis with distinct phases of the cell division cycle.
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Affiliation(s)
- Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States
| | - Sebastian Winkler
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Fabian P. Schlottmann
- Molecular Cell Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josh E. Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States
| | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Jennifer C. Ewald
- Molecular Cell Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
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20
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Liu Y, Wang M, Marcora EM, Zhang B, Goate AM. Promoter DNA hypermethylation - Implications for Alzheimer's disease. Neurosci Lett 2019; 711:134403. [PMID: 31351091 PMCID: PMC6759378 DOI: 10.1016/j.neulet.2019.134403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 12/31/2022]
Abstract
Recent methylome-wide association studies (MWAS) in humans have solidified the concept that aberrant DNA methylation is associated with Alzheimer's disease (AD). We summarize these findings to improve the understanding of mechanisms governing DNA methylation pertinent to transcriptional regulation, with an emphasis of AD-associated promoter DNA hypermethylation, which establishes an epigenetic barrier for transcriptional activation. By considering brain cell type specific expression profiles that have been published only for non-demented individuals, we detail functional activities of selected neuron, microglia, and astrocyte-enriched genes (AGAP2, DUSP6 and GPR37L1, respectively), which are DNA hypermethylated at promoters in AD. We highlight future directions in MWAS including experimental confirmation, functional relevance to AD, cell type-specific temporal characterization, and mechanism investigation.
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Affiliation(s)
- Yiyuan Liu
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
| | - Edoardo M Marcora
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Alison M Goate
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
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21
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Interplay between Phosphatases and the Anaphase-Promoting Complex/Cyclosome in Mitosis. Cells 2019; 8:cells8080814. [PMID: 31382469 PMCID: PMC6721574 DOI: 10.3390/cells8080814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Accurate division of cells into two daughters is a process that is vital to propagation of life. Protein phosphorylation and selective degradation have emerged as two important mechanisms safeguarding the delicate choreography of mitosis. Protein phosphatases catalyze dephosphorylation of thousands of sites on proteins, steering the cells through establishment of the mitotic phase and exit from it. A large E3 ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C) becomes active during latter stages of mitosis through G1 and marks hundreds of proteins for destruction. Recent studies have revealed the complex interregulation between these two classes of enzymes. In this review, we highlight the direct and indirect mechanisms by which phosphatases and the APC/C mutually influence each other to ensure accurate spatiotemporal and orderly progression through mitosis, with a particular focus on recent insights and conceptual advances.
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22
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Örd M, Venta R, Möll K, Valk E, Loog M. Cyclin-Specific Docking Mechanisms Reveal the Complexity of M-CDK Function in the Cell Cycle. Mol Cell 2019; 75:76-89.e3. [PMID: 31101497 PMCID: PMC6620034 DOI: 10.1016/j.molcel.2019.04.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/28/2019] [Accepted: 04/19/2019] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinases (CDKs) coordinate hundreds of molecular events during the cell cycle. Multiple cyclins are involved, but the global role of cyclin-specific phosphorylation has remained unsolved. We uncovered a cyclin docking motif, LxF, that mediates binding of replication factor Cdc6 to mitotic cyclin. This interaction leads to phospho-adaptor Cks1-mediated inhibition of M-CDK to facilitate Cdc6 accumulation and sequestration in mitosis. The LxF motif and Cks1 also mediate the mutual inhibition between M-CDK and the tyrosine kinase Swe1. Additionally, the LxF motif is critical for targeting M-CDK to phosphorylate several mitotic regulators; for example, Spo12 is targeted via LxF to release the phosphatase Cdc14. The results complete the full set of G1, S, and M-CDK docking mechanisms and outline the unified role of cyclin specificity and CDK activity thresholds. Cooperation of cyclin and Cks1 docking creates a variety of CDK thresholds and switching orders, including combinations of last in, first out (LIFO) and first in, first out (FIFO) ordering. Mitotic cyclin Clb2 binds a specific linear motif, LxF, in targets or inhibitors LxF interaction enhances mitotic CDK substrate phosphorylation Phospho-adaptor Cks1 and the LxF docking mediate CDK inhibition by Cdc6 and Swe1 Cyclin-specific targeting enables finetuning of CDK function
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Affiliation(s)
- Mihkel Örd
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Rainis Venta
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Kaidi Möll
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu 50411, Estonia.
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23
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Proteins that physically interact with the phosphatase Cdc14 in Candida albicans have diverse roles in the cell cycle. Sci Rep 2019; 9:6258. [PMID: 31000734 PMCID: PMC6472416 DOI: 10.1038/s41598-019-42530-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
The chromosome complement of the human fungal pathogen Candida albicans is unusually unstable, suggesting that the process of nuclear division is error prone. The Cdc14 phosphatase plays a key role in organising the intricate choreography of mitosis and cell division. In order to understand the role of Cdc14 in C. albicans we used quantitative proteomics to identify proteins that physically interact with Cdc14. To distinguish genuine Cdc14-interactors from proteins that bound non-specifically to the affinity matrix, we used a substrate trapping mutant combined with mass spectrometry analysis using Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC). The results identified 126 proteins that interact with Cdc14 of which 80% have not previously been identified as Cdc14 interactors in C. albicans or S. cerevisiae. In this set, 55 proteins are known from previous research in S. cerevisiae and S. pombe to play roles in the cell cycle, regulating the attachment of the mitotic spindle to kinetochores, mitotic exit, cytokinesis, licensing of DNA replication by re-activating pre-replication complexes, and DNA repair. Five Cdc14-interacting proteins with previously unknown functions localised to the Spindle Pole Bodies (SPBs). Thus, we have greatly increased the number of proteins that physically interact with Cdc14 in C. albicans.
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