1
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Roberts EL, Greenwood J, Kapadia N, Auchynnikava T, Basu S, Nurse P. CDK activity at the centrosome regulates the cell cycle. Cell Rep 2024; 43:114066. [PMID: 38578823 DOI: 10.1016/j.celrep.2024.114066] [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: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
In human cells and yeast, an intact "hydrophobic patch" substrate docking site is needed for mitotic cyclin centrosomal localization. A hydrophobic patch mutant (HPM) of the fission yeast mitotic cyclin Cdc13 cannot enter mitosis, but whether this is due to defective centrosomal localization or defective cyclin-substrate docking more widely is unknown. Here, we show that artificially restoring Cdc13-HPM centrosomal localization promotes mitotic entry and increases CDK (cyclin-dependent kinase) substrate phosphorylation at the centrosome and in the cytoplasm. We also show that the S-phase B-cyclin hydrophobic patch is required for centrosomal localization but not for S phase. We propose that the hydrophobic patch is essential for mitosis due to its requirement for the local concentration of cyclin-CDK with CDK substrates and regulators at the centrosome. Our findings emphasize the central importance of the centrosome as a hub coordinating cell-cycle control and explain why the cyclin hydrophobic patch is essential for mitosis.
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Affiliation(s)
- Emma L Roberts
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK.
| | - Jessica Greenwood
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Nitin Kapadia
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Tania Auchynnikava
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK; Protein Analysis and Proteomics Platform, The Francis Crick Institute, NW1 1AT London, UK
| | - Souradeep Basu
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, NW1 1AT London, UK; Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY 10065, USA
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2
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Ng HY, Adly AN, Whelpley DH, Suhandynata RT, Zhou H, Morgan DO. Phosphate-binding pocket on cyclin B governs CDK substrate phosphorylation and mitotic timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582599. [PMID: 38464173 PMCID: PMC10925351 DOI: 10.1101/2024.02.28.582599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Cell cycle progression is governed by complexes of the cyclin-dependent kinases (CDKs) and their regulatory subunits cyclin and Cks1. CDKs phosphorylate hundreds of substrates, often at multiple sites. Multisite phosphorylation depends on Cks1, which binds initial priming phosphorylation sites to promote secondary phosphorylation at other sites. Here, we describe a similar role for a recently discovered phosphate-binding pocket (PP) on B-type cyclins. Mutation of the PP in Clb2, the major mitotic cyclin of budding yeast, alters bud morphology and delays the onset of anaphase. Using phosphoproteomics in vivo and kinase reactions in vitro, we find that mutation of the PP reduces phosphorylation of several CDK substrates, including the Bud6 subunit of the polarisome and the Cdc16 and Cdc27 subunits of the anaphase-promoting complex/cyclosome. We conclude that the cyclin PP, like Cks1, controls the timing of multisite phosphorylation on CDK substrates, thereby helping to establish the robust timing of cell-cycle events.
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Affiliation(s)
- Henry Y. Ng
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Armin N. Adly
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Devon H. Whelpley
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Raymond T. Suhandynata
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla CA
- Department of Pathology, University of California San Diego, La Jolla CA
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA
| | - David O. Morgan
- Department of Physiology, University of California San Francisco, San Francisco CA
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3
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Valk E, Örd M, Faustova I, Loog M. CDK signaling via nonconventional CDK phosphorylation sites. Mol Biol Cell 2023; 34:pe5. [PMID: 37906435 PMCID: PMC10846619 DOI: 10.1091/mbc.e22-06-0196] [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: 03/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 11/02/2023] Open
Abstract
Since the discovery of cyclin-dependent kinases (CDKs), it has been perceived as a dogma that CDK signaling in the cell cycle is mediated via targeting the CDK consensus sites: the optimal and the minimal motifs S/T-P-x-K/R and S/T-P, respectively. However, more recent evidence suggests that often the CDK phosphorylation events of regulatory importance are mediated via nonconventional CDK sites that lack the required +1Pro of the consensus site motif. In these cases, the loss of specificity seems to be compensated via distant docking interactions facilitated by 1) phosphorylated priming sites binding to phospho-adaptor Cks1 and/or 2) cyclin-specific docking interactions via Short Linear Motifs (SLiMs) in substrates. This Perspective discusses the possible reasons why nonconventional CDK sites are used for CDK signaling. First, the nonconventional CDK sites can act as specificity filters to recognize and distinguish the CDK signal from many other proline-directed kinases in cells. Second, the nonconventional CDK sites in combination with the docking mechanisms provide a much wider range of phosphorylation rates, and thus, also a wider range of CDK thresholds during the accumulation and decline of CDK activity during the cell cycle. As a large number of Cks1-dependent nonconventional CDK sites have been discovered recently, past studies focusing on mutating only the consensus sites should likely be critically reexamined. It is also very likely that phosphorylation of nonconventional sites is crucial in many other kinase-signaling networks.
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Affiliation(s)
- Ervin Valk
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Ilona Faustova
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
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4
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Rojas J, Oz T, Jonak K, Lyzak O, Massaad V, Biriuk O, Zachariae W. Spo13/MEIKIN ensures a Two-Division meiosis by preventing the activation of APC/C Ama1 at meiosis I. EMBO J 2023; 42:e114288. [PMID: 37728253 PMCID: PMC10577557 DOI: 10.15252/embj.2023114288] [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: 04/14/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Genome haploidization at meiosis depends on two consecutive nuclear divisions, which are controlled by an oscillatory system consisting of Cdk1-cyclin B and the APC/C bound to the Cdc20 activator. How the oscillator generates exactly two divisions has been unclear. We have studied this question in yeast where exit from meiosis involves accumulation of the APC/C activator Ama1 at meiosis II. We show that inactivation of the meiosis I-specific protein Spo13/MEIKIN results in a single-division meiosis due to premature activation of APC/CAma1 . In the wild type, Spo13 bound to the polo-like kinase Cdc5 prevents Ama1 synthesis at meiosis I by stabilizing the translational repressor Rim4. In addition, Cdc5-Spo13 inhibits the activity of Ama1 by converting the B-type cyclin Clb1 from a substrate to an inhibitor of Ama1. Cdc20-dependent degradation of Spo13 at anaphase I unleashes a feedback loop that increases Ama1's synthesis and activity, leading to irreversible exit from meiosis at the second division. Thus, by repressing the exit machinery at meiosis I, Cdc5-Spo13 ensures that cells undergo two divisions to produce haploid gametes.
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Affiliation(s)
- Julie Rojas
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Tugce Oz
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Katarzyna Jonak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Oleksii Lyzak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Vinal Massaad
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Olha Biriuk
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wolfgang Zachariae
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
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5
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Lara-Gonzalez P, Variyar S, Budrewicz J, Schlientz A, Varshney N, Bellaart A, Moghareh S, Nguyen ACN, Oegema K, Desai A. Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553011. [PMID: 37609212 PMCID: PMC10441424 DOI: 10.1101/2023.08.11.553011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
In many species, early embryonic mitoses proceed at a very rapid pace, but how this pace is achieved is not understood. Here we show that in the early C. elegans embryo, cyclin B3 is the dominant driver of rapid embryonic mitoses. Metazoans typically have three cyclin B isoforms that associate with and activate Cdk1 kinase to orchestrate mitotic events: the related cyclins B1 and B2 and the more divergent cyclin B3. We show that whereas embryos expressing cyclins B1 and B2 support slow mitosis (NEBD to Anaphase ~ 600s), the presence of cyclin B3 dominantly drives the ~3-fold faster mitosis observed in wildtype embryos. CYB-1/2-driven mitosis is longer than CYB-3-driven mitosis primarily because the progression of mitotic events itself is slower, rather than delayed anaphase onset due to activation of the spindle checkpoint or inhibitory phosphorylation of the anaphase activator CDC-20. Addition of cyclin B1 to cyclin B3-only mitosis introduces an ~60s delay between the completion of chromosome alignment and anaphase onset, which likely ensures segregation fidelity; this delay is mediated by inhibitory phosphorylation on CDC-20. Thus, the dominance of cyclin B3 in driving mitotic events, coupled to introduction of a short cyclin B1-dependent delay in anaphase onset, sets the rapid pace and ensures fidelity of mitoses in the early C. elegans embryo.
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Affiliation(s)
- Pablo Lara-Gonzalez
- Department of Developmental and Cell Biology, University of California Irvine, CA 92697
- Ludwig Institute for Cancer Research, La Jolla CA 92093
| | - Smriti Variyar
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
| | - Jacqueline Budrewicz
- Ludwig Institute for Cancer Research, La Jolla CA 92093
- Current address: Department of Molecular and Medical Genetics, Oregon Health & Science University (OHSU), OR 97239
- Current address: Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon
| | - Aleesa Schlientz
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
| | - Neha Varshney
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
| | - Andrew Bellaart
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
| | - Shabnam Moghareh
- Department of Developmental and Cell Biology, University of California Irvine, CA 92697
| | - Anh Cao Ngoc Nguyen
- Department of Developmental and Cell Biology, University of California Irvine, CA 92697
| | - Karen Oegema
- Ludwig Institute for Cancer Research, La Jolla CA 92093
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla CA 92093
- Department of Cell & Developmental Biology, University of California San Diego, CA 92093
- Department of Cellular & Molecular Medicine, University of California San Diego, CA 92093
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6
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El Dika M, Dudka D, Kloc M, Kubiak JZ. CDC6 as a Key Inhibitory Regulator of CDK1 Activation Dynamics and the Timing of Mitotic Entry and Progression. BIOLOGY 2023; 12:855. [PMID: 37372141 DOI: 10.3390/biology12060855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Timely mitosis is critically important for early embryo development. It is regulated by the activity of the conserved protein kinase CDK1. The dynamics of CDK1 activation must be precisely controlled to assure physiologic and timely entry into mitosis. Recently, a known S-phase regulator CDC6 emerged as a key player in mitotic CDK1 activation cascade in early embryonic divisions, operating together with Xic1 as a CDK1 inhibitor upstream of the Aurora A and PLK1, both CDK1 activators. Herein, we review the molecular mechanisms that underlie the control of mitotic timing, with special emphasis on how CDC6/Xic1 function impacts CDK1 regulatory network in the Xenopus system. We focus on the presence of two independent mechanisms inhibiting the dynamics of CDK1 activation, namely Wee1/Myt1- and CDC6/Xic1-dependent, and how they cooperate with CDK1-activating mechanisms. As a result, we propose a comprehensive model integrating CDC6/Xic1-dependent inhibition into the CDK1-activation cascade. The physiological dynamics of CDK1 activation appear to be controlled by the system of multiple inhibitors and activators, and their integrated modulation ensures concomitantly both the robustness and certain flexibility of the control of this process. Identification of multiple activators and inhibitors of CDK1 upon M-phase entry allows for a better understanding of why cells divide at a specific time and how the pathways involved in the timely regulation of cell division are all integrated to precisely tune the control of mitotic events.
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Affiliation(s)
- Mohammed El Dika
- Department of Biochemistry, Larner College of Medicine, UVM Cancer Center, University of Vermont, Burlington, VT 05405, USA
| | - Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malgorzata Kloc
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | - Jacek Z Kubiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine-National Research Institute (WIM-PIB), Szaserow 128, 04-141 Warsaw, Poland
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
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7
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Zhou K, Xiao J, Wang H, Ni B, Huang J, Long X. Estradiol regulates oxidative stress and angiogenesis of myocardial microvascular endothelial cells via the CDK1/CDK2 pathway. Heliyon 2023; 9:e14305. [PMID: 36942258 PMCID: PMC10023923 DOI: 10.1016/j.heliyon.2023.e14305] [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: 09/01/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Cardiovascular diseases remain the leading cause of death, morbidity, and disability. Recently, it has been reported that gonadal hormones such as estradiol can act on membrane receptors and activate intracellular signaling mechanisms, thereby altering cellular function. This study aims to explore the function and molecular mechanism of estradiol on cardiac microvascular endothelial cells (CMVECs). Estradiol had low toxicity to CMVECs. Hypoxia/reoxygenation (H/R) stimulation inhibited the proliferation and migration of CMVECs, while estradiol significantly promoted proliferation and migration. Estradiol inhibited il-1, IL6, and TNF-α secretion levels after H/R stimulation. Meanwhile, estradiol inhibits oxidative stress and promotes angiogenesis. Further, estradiol upregulated the gene and protein levels of cyclin-dependent kinases 1 (CDK1) and CDK2 after H/R stimulation. When knocking down CDK1 and CDK2 of CMVECs, estradiol did not affect the protein expression of Cyclin E1 and Cyclin D1. Meanwhile, the regulatory effect of estradiol on oxidative stress, angiogenesis, and inflammatory response was significantly weakened or even disappeared. In conclusion, estradiol mediates oxidative stress and angiogenesis of myocardial microvascular endothelial cells by regulating the CDK/cyclin signaling pathway.
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Affiliation(s)
- Ke Zhou
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Jun Xiao
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
- Corresponding author.
| | - Hao Wang
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Bing Ni
- Institute of Immunology of Army Medical University, Chongqing, 400014, China
| | - Jietao Huang
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Xueyuan Long
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
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8
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Al-Rawi A, Kaye E, Korolchuk S, Endicott JA, Ly T. Cyclin A and Cks1 promote kinase consensus switching to non-proline-directed CDK1 phosphorylation. Cell Rep 2023; 42:112139. [PMID: 36840943 DOI: 10.1016/j.celrep.2023.112139] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/17/2022] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of phosphorylation. Increases in CDK1 activity alter substrate choice, with intermediate- and low-sensitivity CDK1 substrates enriched in DNA replication and mitotic functions, respectively. This activity dependence is shared between Cyclin A- and Cyclin B-CDK1. Cks1 has a proteome-wide role as an enhancer of multisite CDK1 phosphorylation. Contrary to the model of CDK1 as an exclusively proline-directed kinase, we show that Cyclin A and Cks1 enhance non-proline-directed phosphorylation, preferably on sites with a +3 lysine residue. Indeed, 70% of cell-cycle-regulated phosphorylations, where the kinase carrying out this modification has not been identified, are non-proline-directed CDK1 sites.
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Affiliation(s)
- Aymen Al-Rawi
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Edward Kaye
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Jane A Endicott
- Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
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9
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DNA methylation-induced ablation of miR-133a accelerates cancer aggressiveness in glioma through upregulating peroxisome proliferator-activated receptor γ. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:19-28. [PMID: 36067936 DOI: 10.1016/j.slasd.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/31/2023]
Abstract
Emerging evidences suggest that miRNAs can be used as theranostic biomarkers for multiple cancers, including glioma. Thus, identification of novel miRNAs for glioma treatment and prognosis becomes necessary and urgent. Here, by analyzing miRNA expression profiles in the glioma and para-cancer tissues by miRNA microarray and verified by RT-PCR, we found that miR-133a was significantly downregulated in the cancerous tissues, and patients with low-expressed miR-133a levels predicted an unfavorable prognosis. The following functional experiments confirmed that overexpression of miR-133a restrained cell proliferation and colony formation abilities, and induced cell cycle arrest to restrain cancer progression in glioma cells. Then, the underlying mechanisms were uncovered, and the peroxisome proliferator-activated receptor γ (PPARγ, PPARG) was verified as the downstream target of miR-133a. Mechanistically, miR-133a negatively regulated PPARG expressions by binding to its 3' untranslated regions (3'UTR). The following rescuing experiments evidenced that miR-133a overexpression-induced anti-cancer effects in glioma cells were abrogated by upregulating PPARγ. Interestingly, we noticed that the promoter region of miR-133a was hypermethylated, and removal of DNA methylation by 5-Azacytidine (AZA) significantly increased the expression levels of miR-133a in glioma cells. Taken together, we concluded that DNA-methylation-induced miR-133a silence contributed to cancer progression in glioma through upregulating PPARγ, and firstly identified the DNA-methylation-regulated miR-133a/PPARG axis as the novel indicators for glioma treatment and prognosis.
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10
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Rathi S, Polat I, Pereira G. The budding yeast GSK-3 homologue Mck1 is an essential component of the spindle position checkpoint. Open Biol 2022; 12:220203. [PMID: 36321416 PMCID: PMC9627454 DOI: 10.1098/rsob.220203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The spindle position checkpoint (SPOC) is a mitotic surveillance mechanism in Saccharomyces cerevisiae that prevents cells from completing mitosis in response to spindle misalignment, thereby contributing to genomic integrity. The kinase Kin4, one of the most downstream SPOC components, is essential to stop the mitotic exit network (MEN), a signalling pathway that promotes the exit from mitosis and cell division. Previous work, however, suggested that a Kin4-independent pathway contributes to SPOC, yet the underlying mechanisms remain elusive. Here, we established the glycogen-synthase-kinase-3 (GSK-3) homologue Mck1, as a novel component that works independently of Kin4 to engage SPOC. Our data indicate that both Kin4 and Mck1 work in parallel to counteract MEN activation by the Cdc14 early anaphase release (FEAR) network. We show that Mck1's function in SPOC is mediated by the pre-replication complex protein and mitotic cyclin-dependent kinase (M-Cdk) inhibitor, Cdc6, which is degraded in a Mck1-dependent manner prior to mitosis. Moderate overproduction of Cdc6 phenocopies MCK1 deletion and causes SPOC deficiency via its N-terminal, M-Cdk inhibitory domain. Our data uncover an unprecedented role of GSK-3 kinases in coordinating spindle orientation with cell cycle progression.
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Affiliation(s)
- Siddhi Rathi
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany,Heidelberg Biosciences International Graduate School (HBIGS) and Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany,German Academic Exchange Service (DAAD), Bonn, Germany
| | - Irem Polat
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Gislene Pereira
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany,Centre for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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11
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Rathi S, Polat I, Pereira G. The budding yeast GSK-3 homologue Mck1 is an essential component of the spindle position checkpoint. Open Biol 2022. [PMID: 36321416 DOI: 10.6084/m9.figshare.c.6261880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The spindle position checkpoint (SPOC) is a mitotic surveillance mechanism in Saccharomyces cerevisiae that prevents cells from completing mitosis in response to spindle misalignment, thereby contributing to genomic integrity. The kinase Kin4, one of the most downstream SPOC components, is essential to stop the mitotic exit network (MEN), a signalling pathway that promotes the exit from mitosis and cell division. Previous work, however, suggested that a Kin4-independent pathway contributes to SPOC, yet the underlying mechanisms remain elusive. Here, we established the glycogen-synthase-kinase-3 (GSK-3) homologue Mck1, as a novel component that works independently of Kin4 to engage SPOC. Our data indicate that both Kin4 and Mck1 work in parallel to counteract MEN activation by the Cdc14 early anaphase release (FEAR) network. We show that Mck1's function in SPOC is mediated by the pre-replication complex protein and mitotic cyclin-dependent kinase (M-Cdk) inhibitor, Cdc6, which is degraded in a Mck1-dependent manner prior to mitosis. Moderate overproduction of Cdc6 phenocopies MCK1 deletion and causes SPOC deficiency via its N-terminal, M-Cdk inhibitory domain. Our data uncover an unprecedented role of GSK-3 kinases in coordinating spindle orientation with cell cycle progression.
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Affiliation(s)
- Siddhi Rathi
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS) and Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany.,German Academic Exchange Service (DAAD), Bonn, Germany
| | - Irem Polat
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Gislene Pereira
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany.,Centre for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany.,German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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12
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Faustova I, Örd M, Kiselev V, Fedorenko D, Borovko I, Macs D, Pääbo K, Lõoke M, Loog M. A synthetic biology approach reveals diverse and dynamic CDK response profiles via multisite phosphorylation of NLS-NES modules. SCIENCE ADVANCES 2022; 8:eabp8992. [PMID: 35977012 PMCID: PMC9385143 DOI: 10.1126/sciadv.abp8992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The complexity of multisite phosphorylation mechanisms in regulating nuclear localization signals (NLSs) and nuclear export signals (NESs) is not understood, and its potential has not been used in synthetic biology. The nucleocytoplasmic shuttling of many proteins is regulated by cyclin-dependent kinases (CDKs) that rely on multisite phosphorylation patterns and short linear motifs (SLiMs) to dynamically control proteins in the cell cycle. We studied the role of motif patterns in nucleocytoplasmic shuttling using sensors based on the CDK targets Dna2, Psy4, and Mcm2/3 of Saccharomyces cerevisiae. We designed multisite phosphorylation modules by rearranging phosphorylation sites, cyclin-specific SLiMs, phospho-priming, phosphatase specificity, and NLS/NES phospho-regulation and obtained very different substrate localization dynamics. These included ultrasensitive responses with and without a delay, graded responses, and different homeostatic plateaus. Thus, CDK can do much more than trigger sequential switches during the cell cycle as it can drive complex patterns of protein localization and activity by using multisite phosphorylation networks.
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13
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Evening Primrose Extracts Inhibit PDGF-BB-Induced Vascular Smooth Muscle Cell Proliferation and Migration by Regulating Cell-Cycle-Related Proteins. Curr Issues Mol Biol 2022; 44:1928-1940. [PMID: 35678660 PMCID: PMC9164085 DOI: 10.3390/cimb44050131] [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: 04/02/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
The proliferation and migration of vascular smooth muscle cells (VSMCs) are important factors in the occurrence of cardiovascular diseases, such as blood flow abnormalities, stroke and atherosclerosis. Evening primrose, known as Oenothera biennis, is a plant native to Korea that exerts physiological activities, such as antioxidant effects, the inhibition of lipid accumulation and the prevention of muscle atrophy. However, the function of evening primrose stem (EVP) in the regulation of VSMC proliferation and migration and the underlying mechanisms have not been identified. In this study, the effect of EVP on the platelet-derived growth factor (PDGF)-induced proliferation and migration of VSMCs was investigated. The results show that PDGF-BB-induced proliferation of VSMCs was inhibited by EVP at concentrations of 25, 50 or 100 μg/mL in a concentration-dependent manner, and a migration assay showed that EVP inhibited cell migration. Cell cycle analysis was performed to confirm the mechanism by which cell proliferation and migration was inhibited. The results indicate that proteins involved in the cell cycle, such as cyclin, CDK and phosphorylated Rb, were downregulated by EVP at concentrations of 100 μg/mL, thereby increasing the proportion of cells in the G0/G1 phase and inhibiting cell cycle progression. In the PDGF receptor (PDGFR) signaling pathway, phosphorylation of the PDGFR was inhibited by EVP at concentrations of 100 μg/mL, and PLCγ phosphorylation was also decreased. The PDGF-BB-induced effect of EVP on the proliferation of VSMCs involved the inhibition of Akt phosphorylation and the reduction in the phosphorylation of MAPK proteins such as ERK, P38 and JNK. In conclusion, the results demonstrate that EVP inhibited PDGF-BB-induced VSMC proliferation and migration by regulating cell-cycle-related proteins.
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14
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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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15
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Ma X, Øvrebø JI, Thompson EM. Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos. Front Cell Dev Biol 2022; 9:770939. [PMID: 35155443 PMCID: PMC8832800 DOI: 10.3389/fcell.2021.770939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/27/2021] [Indexed: 12/03/2022] Open
Abstract
The active site of the essential CDK1 kinase is generated by core structural elements, among which the PSTAIRE motif in the critical αC-helix, is universally conserved in the single CDK1 ortholog of all metazoans. We report serial CDK1 duplications in the chordate, Oikopleura. Paralog diversifications in the PSTAIRE, activation loop substrate binding platform, ATP entrance site, hinge region, and main Cyclin binding interface, have undergone positive selection to subdivide ancestral CDK1 functions along the S-M phase cell cycle axis. Apparent coevolution of an exclusive CDK1d:Cyclin Ba/b pairing is required for oogenic meiosis and early embryogenesis, a period during which, unusually, CDK1d, rather than Cyclin Ba/b levels, oscillate, to drive very rapid cell cycles. Strikingly, the modified PSTAIRE of odCDK1d shows convergence over great evolutionary distance with plant CDKB, and in both cases, these variants exhibit increased specialization to M-phase.
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Affiliation(s)
- Xiaofei Ma
- College of Life Sciences, Northwest Normal University, Lanzhou, China
- Sars International Centre, University of Bergen, Bergen, Norway
- *Correspondence: Xiaofei Ma, , ; Eric M. Thompson,
| | - Jan Inge Øvrebø
- Sars International Centre, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Eric M. Thompson
- Sars International Centre, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Xiaofei Ma, , ; Eric M. Thompson,
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16
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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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17
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Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription. Curr Biol 2022; 32:256-263.e4. [PMID: 34818519 PMCID: PMC8752490 DOI: 10.1016/j.cub.2021.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 01/12/2023]
Abstract
Cell-cycle progression is driven by the phosphorylation of cyclin-dependent kinase (Cdk) substrates.1-3 The order of substrate phosphorylation depends in part on the general rise in Cdk activity during the cell cycle,4-7 together with variations in substrate docking to sites on associated cyclin and Cks subunits.3,6,8-10 Many substrates are modified at multiple sites to provide more complex regulation.10-14 Here, we describe an elegant regulatory circuit based on multisite phosphorylation of Ndd1, a transcriptional co-activator of budding yeast genes required for mitotic progression.11,12 As cells enter mitosis, Ndd1 phosphorylation by Cdk1 is known to promote mitotic cyclin (CLB2) gene transcription, resulting in positive feedback.13-16 Consistent with these findings, we show that low Cdk1 activity promotes CLB2 expression at mitotic entry. We also find, however, that when high Cdk1 activity accumulates in a mitotic arrest, CLB2 expression is inhibited. Inhibition is accompanied by Ndd1 degradation, and we present evidence that degradation is triggered by multisite Ndd1 phosphorylation by high mitotic Cdk1-Clb2 activity. Complete Ndd1 phosphorylation by Clb2-Cdk1-Cks1 requires the phosphothreonine-binding site of Cks1, as well as a recently identified phosphate-binding pocket on the cyclin Clb2.17 We therefore propose that initial phosphorylation by Cdk1 primes Ndd1 for delayed secondary phosphorylation at suboptimal sites that promote degradation. Together, our results suggest that rising levels of mitotic Cdk1 activity act at multiple phosphorylation sites on Ndd1, first triggering rapid positive feedback and then promoting delayed negative feedback, resulting in a pulse of mitotic gene expression.
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18
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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: 115] [Impact Index Per Article: 57.5] [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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19
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Zhou S, Qu KL, Li JA, Chen SL, Zhang YG, Zhu C, Jin H, Wang Y, Pang Q, Liu HC. YY1 activates EMI2 and promotes the progression of cholangiocarcinoma through the PI3K/Akt signaling axis. Cancer Cell Int 2021; 21:699. [PMID: 34933678 PMCID: PMC8693494 DOI: 10.1186/s12935-021-02328-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is one of the deadliest cancers of the digestive tract. The prognosis of CCA is poor and the 5-year survival rate is low. Bioinformatic analysis showed that early mitotic inhibitor 2 (EMI2) was overexpressed in CCA but the underlying mechanism is not known. METHODS The data on bile duct carcinoma from TCGA and GEO databases were used to detect the expression of EMI2. The transcription factors of EMI2 were predicted using JASPAR and PROMO databases. Among the predicted transcription factors, YY1 has been rarely reported in cholangiocarcinoma, and was verified using the luciferase reporter gene assay. RT-PCR was performed to predict the downstream pathway of EMI2, and PI3K/Akt was suspected to be associated with it. Subsequently, in vivo and in vitro experiments were conducted to verify the effects of silencing and overexpressing EMI2 and YY1 on the proliferation, invasion, and metastasis of the bile duct cancer cells. RESULTS EMI2 was highly expressed in CCA. Silencing EMI2 inhibited the proliferation, invasion, and migration of CCA cells, arrested cell cycle in the G1 phase, and promoted of apoptosis. The luciferase reporter gene assay showed that YY1 bound to the promoter region of EMI2, and after silencing YY1, the expression of EMI2 decreased and the progression of CCA was inhibited. Moreover, key proteins in the PI3K/Akt signaling pathway decreased after silencing EMI2. CONCLUSION EMI2 may be one of the direct targets of YY1 and promotes the progression of CCA through the PI3K/Akt signaling pathway.
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Affiliation(s)
- Shuai Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Kang Lin Qu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Jin Ang Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Shi Lei Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Yi Gang Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Chao Zhu
- The Fourth Department of General Surgery, Second People's Hospital of Anhui Province, No. 1868 Dangshan Road, North Second Ring, Hefei, 230041, Anhui, China
| | - Hao Jin
- The Fourth Department of General Surgery, Second People's Hospital of Anhui Province, No. 1868 Dangshan Road, North Second Ring, Hefei, 230041, Anhui, China
| | - Yong Wang
- The Fourth Department of General Surgery, Second People's Hospital of Anhui Province, No. 1868 Dangshan Road, North Second Ring, Hefei, 230041, Anhui, China
| | - Qing Pang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China.
| | - Hui Chun Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China. .,The Fourth Department of General Surgery, Second People's Hospital of Anhui Province, No. 1868 Dangshan Road, North Second Ring, Hefei, 230041, Anhui, China.
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20
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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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21
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Böhm M, Killinger K, Dudziak A, Pant P, Jänen K, Hohoff S, Mechtler K, Örd M, Loog M, Sanchez-Garcia E, Westermann S. Cdc4 phospho-degrons allow differential regulation of Ame1 CENP-U protein stability across the cell cycle. eLife 2021; 10:67390. [PMID: 34308839 PMCID: PMC8341979 DOI: 10.7554/elife.67390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/24/2021] [Indexed: 02/05/2023] Open
Abstract
Kinetochores are multi-subunit protein assemblies that link chromosomes to microtubules of the mitotic and meiotic spindle. It is still poorly understood how efficient, centromere-dependent kinetochore assembly is accomplished from hundreds of individual protein building blocks in a cell cycle-dependent manner. Here, by combining comprehensive phosphorylation analysis of native Ctf19CCAN subunits with biochemical and functional assays in the model system budding yeast, we demonstrate that Cdk1 phosphorylation activates phospho-degrons on the essential subunit Ame1CENP-U, which are recognized by the E3 ubiquitin ligase complex SCF-Cdc4. Gradual phosphorylation of degron motifs culminates in M-phase and targets the protein for degradation. Binding of the Mtw1Mis12 complex shields the proximal phospho-degron, protecting kinetochore-bound Ame1 from the degradation machinery. Artificially increasing degron strength partially suppresses the temperature sensitivity of a cdc4 mutant, while overexpression of Ame1-Okp1 is toxic in SCF mutants, demonstrating the physiological importance of this mechanism. We propose that phospho-regulated clearance of excess CCAN subunits facilitates efficient centromere-dependent kinetochore assembly. Our results suggest a novel strategy for how phospho-degrons can be used to regulate the assembly of multi-subunit complexes.
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Affiliation(s)
- Miriam Böhm
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Kerstin Killinger
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Alexander Dudziak
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Pradeep Pant
- Department of Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karolin Jänen
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Simone Hohoff
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karl Mechtler
- IMP - Research Institute of Molecular Pathology, Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Stefan Westermann
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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22
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Claude KL, Bureik D, Chatzitheodoridou D, Adarska P, Singh A, Schmoller KM. Transcription coordinates histone amounts and genome content. Nat Commun 2021; 12:4202. [PMID: 34244507 PMCID: PMC8270936 DOI: 10.1038/s41467-021-24451-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Biochemical reactions typically depend on the concentrations of the molecules involved, and cell survival therefore critically depends on the concentration of proteins. To maintain constant protein concentrations during cell growth, global mRNA and protein synthesis rates are tightly linked to cell volume. While such regulation is appropriate for most proteins, certain cellular structures do not scale with cell volume. The most striking example of this is the genomic DNA, which doubles during the cell cycle and increases with ploidy, but is independent of cell volume. Here, we show that the amount of histone proteins is coupled to the DNA content, even though mRNA and protein synthesis globally increase with cell volume. As a consequence, and in contrast to the global trend, histone concentrations decrease with cell volume but increase with ploidy. We find that this distinct coordination of histone homeostasis and genome content is already achieved at the transcript level, and is an intrinsic property of histone promoters that does not require direct feedback mechanisms. Mathematical modeling and histone promoter truncations reveal a simple and generalizable mechanism to control the cell volume- and ploidy-dependence of a given gene through the balance of the initiation and elongation rates.
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Affiliation(s)
- Kora-Lee Claude
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Bureik
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Petia Adarska
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Abhyudai Singh
- Department of Electrical & Computer Engineering, University of Delaware, Newark, DE, USA
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
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23
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Koliopoulos MG, Alfieri C. Cell cycle regulation by complex nanomachines. FEBS J 2021; 289:5100-5120. [PMID: 34143558 DOI: 10.1111/febs.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The cell cycle is the essential biological process where one cell replicates its genome and segregates the resulting two copies into the daughter cells during mitosis. Several aspects of this process have fascinated humans since the nineteenth century. Today, the cell cycle is exhaustively investigated because of its profound connections with human diseases and cancer. At the heart of the molecular network controlling the cell cycle, we find the cyclin-dependent kinases (CDKs) acting as an oscillator to impose an orderly and highly regulated progression through the different cell cycle phases. This oscillator integrates both internal and external signals via a multitude of signalling pathways involving posttranslational modifications including phosphorylation, protein ubiquitination and mechanisms of transcriptional regulation. These tasks are specifically performed by multi-subunit complexes, which are intensively studied both biochemically and structurally with the aim to unveil mechanistic insights into their molecular function. The scope of this review is to summarise the structural biology of the cell cycle machinery, with specific focus on the core cell cycle machinery involving the CDK-cyclin oscillator. We highlight the contribution of cryo-electron microscopy, which has started to revolutionise our understanding of the molecular function and dynamics of the key players of the cell cycle.
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Affiliation(s)
- Marios G Koliopoulos
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
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24
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Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER. NPJ Syst Biol Appl 2021; 7:28. [PMID: 34117265 PMCID: PMC8196193 DOI: 10.1038/s41540-021-00187-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
In budding yeast, synchronization of waves of mitotic cyclins that activate the Cdk1 kinase occur through Forkhead transcription factors. These molecules act as controllers of their sequential order and may account for the separation in time of incompatible processes. Here, a Forkhead-mediated design principle underlying the quantitative model of Cdk control is proposed for budding yeast. This design rationalizes timing of cell division, through progressive and coordinated cyclin/Cdk-mediated phosphorylation of Forkhead, and autonomous cyclin/Cdk oscillations. A “clock unit” incorporating this design that regulates timing of cell division is proposed for both yeast and mammals, and has a DRIVER operating the incompatible processes that is instructed by multiple CLOCKS. TIMERS determine whether the clocks are active, whereas CONTROLLERS determine how quickly the clocks shall function depending on external MODULATORS. This “clock unit” may coordinate temporal waves of cyclin/Cdk concentration/activity in the eukaryotic cell cycle making the driver operate the incompatible processes, at separate times.
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Faustova I, Loog M. SLiMs in intrinsically disordered protein regions regulate the cell cycle dynamics of ORC1-CDC6 interaction and pre-replicative complex assembly. Mol Cell 2021; 81:1861-1862. [PMID: 33961774 DOI: 10.1016/j.molcel.2021.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hossain et al. (2021) show that human origin recognition complex subunit ORC1 and licensing factor CDC6 interact when the pre-replicative complex forms in G1. Short linear motifs (SLiMs) in intrinsically disordered regions (IDRs) mediate this interaction and its regulation by CDKs.
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Affiliation(s)
- Ilona Faustova
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu 50411, Estonia.
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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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27
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Pirincci Ercan D, Chrétien F, Chakravarty P, Flynn HR, Snijders AP, Uhlmann F. Budding yeast relies on G 1 cyclin specificity to couple cell cycle progression with morphogenetic development. SCIENCE ADVANCES 2021; 7:eabg0007. [PMID: 34088668 PMCID: PMC8177710 DOI: 10.1126/sciadv.abg0007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
Two models have been put forward for cyclin-dependent kinase (Cdk) control of the cell cycle. In the qualitative model, cell cycle events are ordered by distinct substrate specificities of successive cyclin waves. Alternatively, in the quantitative model, the gradual rise of Cdk activity from G1 phase to mitosis leads to ordered substrate phosphorylation at sequential thresholds. Here, we study the relative contributions of qualitative and quantitative Cdk control in Saccharomyces cerevisiae All S phase and mitotic cyclins can be replaced by a single mitotic cyclin, albeit at the cost of reduced fitness. A single cyclin can also replace all G1 cyclins to support ordered cell cycle progression, fulfilling key predictions of the quantitative model. However, single-cyclin cells fail to polarize or grow buds and thus cannot survive. Our results suggest that budding yeast has become dependent on G1 cyclin specificity to couple cell cycle progression to essential morphogenetic events.
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Affiliation(s)
| | - Florine Chrétien
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Probir Chakravarty
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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28
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Zhang Y, Zhang JQ, Zhang T, Xue H, Zuo WB, Li YN, Zhao Y, Sun G, Fu ZR, Zhang Q, Zhao X, Teng Y, Wang AQ, Li JZ, Wang Y, Jin CH. Calycosin Induces Gastric Cancer Cell Apoptosis via the ROS-Mediated MAPK/STAT3/NF-κB Pathway. Onco Targets Ther 2021; 14:2505-2517. [PMID: 33883905 PMCID: PMC8053610 DOI: 10.2147/ott.s292388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/05/2021] [Indexed: 11/23/2022] Open
Abstract
Background Calycosin, an active compound in plants, can promote the apoptosis of various cancer cells; however, the mechanism by which it regulates reactive oxygen species (ROS) in gastric cancer (GC) cells remains unclear. Purpose In this study, we investigated the effects of calycosin on apoptosis, the cell cycle, and migration in GC cells under ROS regulation. Results The results of the Cell Counting Kit-8 assay suggested that calycosin had significant cytotoxic effects on 12 gastric cancer cells, but no significant cytotoxic effects on normal cells. Hoechst 33342/propidium iodide (PI) double staining and flow cytometry showed that calycosin had clear pro-apoptotic effects on AGS cells. Western blotting revealed that the expression of cytochrome C and pro-apoptotic proteins B-cell lymphoma 2 (Bcl-2)-associated agonist of cell death (Bad), cleaved (cle)-caspase-3, and cle-poly (ADP-ribose) polymerase gradually increased, and the expression of anti-apoptotic protein Bcl-2 gradually decreased. Calycosin also decreased the expression of extracellular signal-regulated kinase, nuclear factor kappa B (NF-κB), and signal transducer and activator of transcription 3 (STAT3), and increased the phosphorylation levels of p38, c-Jun N-terminal kinase, and inhibitor of NF-κB. In addition, calycosin markedly increased ROS accumulation, and pretreatment with active oxygen scavenger n-acetyl-l-cysteine (NAC) clearly inhibited apoptosis. Calycosin downregulated the cell cycle proteins cyclin-dependent kinase 2 (CDK2), CDK4, CDK6, cyclin D1, and cyclin E; upregulated p21 and p27; and arrested cells in the G0/G1 phase. Similarly, calycosin also downregulated Snail family transcriptional repressor 1, E-cadherin, and β-catenin and inhibited cell migration. However, pretreatment with NAC inhibited the calycosin-induced effects of cycle arrest and migration. Conclusion In summary, calycosin induces apoptosis via ROS-mediated MAPK/STAT3/NF-κB pathways, thereby exerting its anti-carcinogenic functions in GC cells.
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Affiliation(s)
- Yu Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Jian-Qiang Zhang
- Department of Food Science and Technology, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Heyi Dairy Technology Co. Ltd., Daqing, People's Republic of China
| | - Tong Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Hui Xue
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Wen-Bo Zuo
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Yan-Nan Li
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Yue Zhao
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Geng Sun
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Zhong-Ren Fu
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Qing Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Xue Zhao
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Yue Teng
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - An-Qi Wang
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Jia-Zhu Li
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China
| | - Ying Wang
- Department of Food Science and Engineering, College of Food Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China.,National Coarse Cereals Engineering Research Center, Daqing, People's Republic of China
| | - Cheng-Hao Jin
- Department of Biochemistry and Molecular Biology, College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China.,Department of Food Science and Engineering, College of Food Science & Technology, Heilongjiang Bayi Agricultural University, Daqing, People's Republic of China.,National Coarse Cereals Engineering Research Center, Daqing, People's Republic of China
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29
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Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Mol Cell 2021; 81:1951-1969.e6. [PMID: 33761311 DOI: 10.1016/j.molcel.2021.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/18/2021] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
The initiation of DNA replication involves cell cycle-dependent assembly and disassembly of protein complexes, including the origin recognition complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short linear protein motifs (SLiMs) within intrinsically disordered regions (IDRs) in ORC1 and CDC6 mediate cyclin-CDK-dependent and independent protein-protein interactions, conditional on the cell cycle phase. A domain within the ORC1 IDR is required for interaction between the ORC1 and CDC6 AAA+ domains in G1, whereas the same domain prevents CDC6-ORC1 interaction during mitosis. Then, during late G1, this domain facilitates ORC1 destruction by a SKP2-cyclin A-CDK2-dependent mechanism. During G1, the CDC6 Cy motif cooperates with cyclin E-CDK2 to promote ORC1-CDC6 interactions. The CDC6 IDR regulates self-interaction by ORC1, thereby controlling ORC1 protein levels. Protein phosphatase 1 binds directly to a SLiM in the ORC1 IDR, causing ORC1 de-phosphorylation upon mitotic exit, increasing ORC1 protein, and promoting pre-RC assembly.
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30
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Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins Using Quantitative Mass-Spectrometry. Methods Mol Biol 2021; 2141:819-833. [PMID: 32696391 DOI: 10.1007/978-1-0716-0524-0_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) within proteins have attracted considerable attention in recent years. Several important biological signaling mechanisms including protein-protein interactions and post-translational modifications can be easily mediated by IDPs and IDRs due to their flexible structure. These regions can encode linear sequences that are indispensable in cell-signaling networks and circuits. For example, the linear multisite phosphorylation networks encoded in disordered protein sequences play a key role in cell-cycle regulation where the phosphorylation of proteins controls the orchestration of all major mechanisms. While elucidating a systems-level understanding of this process and other multisite phosphorylation processes, we extensively used mass-spectrometry and found it to be an ideal tool to identify, characterize, and quantify phosphorylation dynamics within IDPs. Here, we describe a quantitative proteomics method, together with a detailed protocol to analyze dynamic multisite phosphorylation processes within IDPs using an in vitro protein phosphorylation assay with "light" gamma-16O ATP and "heavy" gamma-18O ATP, combined with liquid chromatography mass spectrometry.
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31
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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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32
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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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33
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Roy J, Cyert MS. Cell Biology: Deciphering the ABCs of SLiMs in G1-CDK Signaling. Curr Biol 2020; 30:R1382-R1385. [PMID: 33202241 PMCID: PMC10763628 DOI: 10.1016/j.cub.2020.09.026] [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] [Indexed: 10/23/2022]
Abstract
A new study uses an elegant in vivo assay to comprehensively characterize the LP docking motif, which determines G1-CDK substrate specificity in fungi. The authors show that LP-cyclin docking strength determines the timing of Sic1 degradation, a key cell cycle event.
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Affiliation(s)
- Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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34
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Tatum NJ, Endicott JA. Chatterboxes: the structural and functional diversity of cyclins. Semin Cell Dev Biol 2020; 107:4-20. [PMID: 32414682 DOI: 10.1016/j.semcdb.2020.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Proteins of the cyclin family have divergent sequences and execute diverse roles within the cell while sharing a common fold: the cyclin box domain. Structural studies of cyclins have played a key role in our characterization and understanding of cellular processes that they control, though to date only ten of the 29 CDK-activating cyclins have been structurally characterized by X-ray crystallography or cryo-electron microscopy with or without their cognate kinases. In this review, we survey the available structures of human cyclins, highlighting their molecular features in the context of their cellular roles. We pay particular attention to how cyclin activity is regulated through fine control of degradation motif recognition and ubiquitination. Finally, we discuss the emergent roles of cyclins independent of their roles as cyclin-dependent protein kinase activators, demonstrating the cyclin box domain to be a versatile and generalized scaffolding domain for protein-protein interactions across the cellular machinery.
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Affiliation(s)
- Natalie J Tatum
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
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35
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Petty EL, Pillus L. Cell cycle roles for GCN5 revealed through genetic suppression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194625. [PMID: 32798737 DOI: 10.1016/j.bbagrm.2020.194625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022]
Abstract
The conserved acetyltransferase Gcn5 is a member of several complexes in eukaryotic cells, playing roles in regulating chromatin organization, gene expression, metabolism, and cell growth and differentiation via acetylation of both nuclear and cytoplasmic proteins. Distinct functions of Gcn5 have been revealed through a combination of biochemical and genetic approaches in many in vitro studies and model organisms. In this review, we focus on the unique insights that have been gleaned from suppressor studies of gcn5 phenotypes in the budding yeast Saccharomyces cerevisiae. Such studies were fundamental in the early understanding of the balance of counteracting chromatin activities in regulating transcription. Most recently, suppressor screens have revealed roles for Gcn5 in early cell cycle (G1 to S) gene expression and regulation of chromosome segregation during mitosis. Much has been learned, but many questions remain which will be informed by focused analysis of additional genetic and physical interactions.
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Affiliation(s)
- Emily L Petty
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
| | - Lorraine Pillus
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
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36
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A processive phosphorylation circuit with multiple kinase inputs and mutually diversional routes controls G1/S decision. Nat Commun 2020; 11:1836. [PMID: 32296067 PMCID: PMC7160111 DOI: 10.1038/s41467-020-15685-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
Studies on multisite phosphorylation networks of cyclin-dependent kinase (CDK) targets have opened a new level of signaling complexity by revealing signal processing routes encoded into disordered proteins. A model target, the CDK inhibitor Sic1, contains linear phosphorylation motifs, docking sites, and phosphodegrons to empower an N-to-C terminally directed phosphorylation process. Here, we uncover a signal processing mechanism involving multi-step competition between mutually diversional phosphorylation routes within the S-CDK-Sic1 inhibitory complex. Intracomplex phosphorylation plays a direct role in controlling Sic1 degradation, and provides a mechanism to sequentially integrate both the G1- and S-CDK activities while keeping S-CDK inhibited towards other targets. The competing phosphorylation routes prevent premature Sic1 degradation and demonstrate how integration of MAPK from the pheromone pathway allows one to tune the competition of alternative phosphorylation paths. The mutually diversional phosphorylation circuits may be a general way for processing multiple kinase signals to coordinate cellular decisions in eukaryotes. The decision of whether and when a cell divides is tightly controlled. Here, the authors show in yeast that there is a multi-step competition between different phosphorylation states and sites in the S phase CDK-Sic1 complex, which controls Sic1 degradation and coordinates the precise timing of the G1/S transition.
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37
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Basu S, Roberts EL, Jones AW, Swaffer MP, Snijders AP, Nurse P. The Hydrophobic Patch Directs Cyclin B to Centrosomes to Promote Global CDK Phosphorylation at Mitosis. Curr Biol 2020; 30:883-892.e4. [PMID: 32084401 PMCID: PMC7063568 DOI: 10.1016/j.cub.2019.12.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 11/15/2022]
Abstract
The cyclin-dependent kinases (CDKs) are the major cell-cycle regulators that phosphorylate hundreds of substrates, controlling the onset of S phase and M phase [1, 2, 3]. However, the patterns of substrate phosphorylation increase are not uniform, as different substrates become phosphorylated at different times as cells proceed through the cell cycle [4, 5]. In fission yeast, the correct ordering of CDK substrate phosphorylation can be established by the activity of a single mitotic cyclin-CDK complex [6, 7]. Here, we investigate the substrate-docking region, the hydrophobic patch, on the fission yeast mitotic cyclin Cdc13 as a potential mechanism to correctly order CDK substrate phosphorylation. We show that the hydrophobic patch targets Cdc13 to the yeast centrosome equivalent, the spindle pole body (SPB), and disruption of this motif prevents both centrosomal localization of Cdc13 and the onset of mitosis but does not prevent S phase. CDK phosphorylation in mitosis is compromised for approximately half of all mitotic CDK substrates, with substrates affected generally being those that require the highest levels of CDK activity to become phosphorylated and those that are located at the SPB. Our experiments suggest that the hydrophobic patch of mitotic cyclins contributes to CDK substrate selection by directing the localization of Cdc13-CDK to centrosomes and that this localization of CDK contributes to the CDK substrate phosphorylation necessary to ensure proper entry into mitosis. Finally, we show that mutation of the hydrophobic patch prevents cyclin B1 localization to centrosomes in human cells, suggesting that this mechanism of cyclin-CDK spatial regulation may be conserved across eukaryotes. The hydrophobic patch of human and yeast cyclin B directs it to the centrosome Loss of the yeast cyclin B hydrophobic patch allows S phase but prevents mitosis Compartmentalized mitotic CDK phosphorylation relies on the hydrophobic patch
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Affiliation(s)
- Souradeep Basu
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Emma L Roberts
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew W Jones
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Protein Analysis and Proteomics Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Matthew P Swaffer
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY 10065, USA
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38
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ZNF143 Suppresses Cell Apoptosis and Promotes Proliferation in Gastric Cancer via ROS/p53 Axis. DISEASE MARKERS 2020; 2020:5863178. [PMID: 32076462 PMCID: PMC7017572 DOI: 10.1155/2020/5863178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022]
Abstract
Aim This study was aimed at identifying the role of zinc finger protein 143 (ZNF143) in gastric cancer (GC) progression. Methods The impact of ZNF143 on the proliferation ability and apoptosis of GC cells was detected. The expression of ZNF143 and related targeted genes was determined using Western blot analysis. The reactive oxygen species (ROS) level of GC cells was examined using the ROS generation assay. The role of ZNF143 in the proliferation of GC cells in vivo was examined using tumor xenograft assay. Results The ectopic overexpression of ZNF143 promoted the proliferation of GC cells, while its knockdown reduced the effect in vitro. The downregulation of ZNF143 facilitated cell apoptosis. ZNF143 decreased the ROS level in GC cells, resulting in the reduction of cell apoptosis. Transfection with p53 reversed the antiapoptotic effect of ZNF143, while pifithrin-α, a specific inhibitor of p53, reduced the apoptosis in ZNF143-knockdown GC cells. However, p53 had no influence on the ROS level in GC cells. p53 played a key role in inhibiting ROS generation in GC cells, thereby inhibiting apoptosis. The transplanted tumor weight and volume were higher in the ZNF143-overexpressed group than in the ZNF143-knockdown group in vivo was examined using tumor xenograft assay. Conclusion ZNF143, as a tumor oncogene, promoted the proliferation of GC cells both in vitro and in vivo, indicating that ZNF143 might function as a novel target for GC therapy.in vitro. The downregulation of ZNF143 facilitated cell apoptosis. ZNF143 decreased the ROS level in GC cells, resulting in the reduction of cell apoptosis. Transfection with p53 reversed the antiapoptotic effect of ZNF143, while pifithrin-in vivo was examined using tumor xenograft assay.
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Örd M, Loog M. Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins Using Phos-tag SDS-PAGE. Methods Mol Biol 2020; 2141:779-792. [PMID: 32696389 DOI: 10.1007/978-1-0716-0524-0_40] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phos-tagTM SDS-PAGE is a method that enables electrophoretic separation of proteins based on their phosphorylation status. With Phos-tagTM SDS-PAGE, it is possible to discriminate between different phosphoforms of proteins based on their phosphorylation level and the number of phosphorylated sites, and to determine the stoichiometry of different phosphorylation products. Phos-tagTM SDS-PAGE is useful for analyzing disordered proteins with multiple phosphorylation sites and can be used for any of the downstream applications used in combination with conventional SDS-PAGE, for example, Western blotting and mass-spectrometry. To obtain the best results with Phos-tagTM SDS-PAGE, however, it is often necessary to optimize the gel composition. Depending on the molecular weight and number of phosphoryl groups added to the protein, different gel composition or running conditions should be used. Here, we provide protocols for Mn2+- and Zn2+-Phos-tagTM SDS-PAGE and give examples of how disordered proteins with different characteristics behave in gels with various Phos-tag concentrations.
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Affiliation(s)
- Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia.
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Crncec A, Hochegger H. Triggering mitosis. FEBS Lett 2019; 593:2868-2888. [PMID: 31602636 DOI: 10.1002/1873-3468.13635] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
Abstract
Entry into mitosis is triggered by the activation of cyclin-dependent kinase 1 (Cdk1). This simple reaction rapidly and irreversibly sets the cell up for division. Even though the core step in triggering mitosis is so simple, the regulation of this cellular switch is highly complex, involving a large number of interconnected signalling cascades. We do have a detailed knowledge of most of the components of this network, but only a poor understanding of how they work together to create a precise and robust system that ensures that mitosis is triggered at the right time and in an orderly fashion. In this review, we will give an overview of the literature that describes the Cdk1 activation network and then address questions relating to the systems biology of this switch. How is the timing of the trigger controlled? How is mitosis insulated from interphase? What determines the sequence of events, following the initial trigger of Cdk1 activation? Which elements ensure robustness in the timing and execution of the switch? How has this system been adapted to the high levels of replication stress in cancer cells?
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Affiliation(s)
- Adrijana Crncec
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
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Abstract
The quantitative model of cyclin-dependent kinase (CDK) function states that cyclins temporally order cell cycle events at different CDK activity levels, or thresholds. The model lacks a mechanistic explanation, as it is not understood how different thresholds are encoded into substrates. We show that a multisite phosphorylation code governs the phosphorylation of CDK targets and that phosphorylation clusters act as timing tags that trigger specific events at different CDK thresholds. Using phospho-degradable CDK threshold sensors with rationally encoded phosphorylation patterns, we were able to predictably program thresholds over the entire range of the Saccharomyces cerevisiae cell cycle. We defined three levels of CDK multisite phosphorylation encoding: (i) Ser-Thr swapping in phosphorylation sites, (ii) patterning of phosphorylation sites, and (iii) cyclin-specific docking combined with modulation of CDK activity. Thus, CDK can signal via hundreds of differentially encoded targets at precise times to provide a temporally ordered phosphorylation pattern required for cell division.
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