1
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Yan H, Miranda EAD, Jin S, Wilson F, An K, Godbee B, Zheng X, Brau-Rodríguez AR, Lei L. Primary oocytes with cellular senescence features are involved in ovarian aging in mice. Sci Rep 2024; 14:13606. [PMID: 38871781 PMCID: PMC11176158 DOI: 10.1038/s41598-024-64441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
In mammalian females, quiescent primordial follicles serve as the ovarian reserve and sustain normal ovarian function and egg production via folliculogenesis. The loss of primordial follicles causes ovarian aging. Cellular senescence, characterized by cell cycle arrest and production of the senescence-associated secretory phenotype (SASP), is associated with tissue aging. In the present study, we report that some quiescent primary oocytes in primordial follicles become senescent in adult mouse ovaries. The senescent primary oocytes share senescence markers characterized in senescent somatic cells. The senescent primary oocytes were observed in young adult mouse ovaries, remained at approximately 15% of the total primary oocytes during ovarian aging from 6 to 12 months, and accumulated in aged ovaries. Administration of a senolytic drug ABT263 to 3-month-old mice reduced the percentage of senescent primary oocytes and the transcription of the SASP factors in the ovary, in addition, led to increased numbers of primordial and total follicles and a higher rate of oocyte maturation. Our study provides experimental evidence that primary oocytes, a germline cell type that is arrested in meiosis, become senescent in adult mouse ovaries and that senescent cell clearance reduced primordial follicle loss and mitigated ovarian aging phenotypes.
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Affiliation(s)
- Hao Yan
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Edgar Andres Diaz Miranda
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Shiying Jin
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Faith Wilson
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Kang An
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Brooke Godbee
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
- College of Health Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Astrid Roshealy Brau-Rodríguez
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Lei Lei
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA.
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, MO, 65211, USA.
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2
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Cullati SN, Akizuki K, Chen JS, Johnson JL, Yaron-Barir TM, Cantley LC, Gould KL. Substrate displacement of CK1 C-termini regulates kinase specificity. SCIENCE ADVANCES 2024; 10:eadj5185. [PMID: 38728403 PMCID: PMC11086627 DOI: 10.1126/sciadv.adj5185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
CK1 kinases participate in many signaling pathways, and their regulation is of meaningful biological consequence. CK1s autophosphorylate their C-terminal noncatalytic tails, and eliminating these tails increases substrate phosphorylation in vitro, suggesting that the autophosphorylated C-termini act as inhibitory pseudosubstrates. To test this prediction, we comprehensively identified the autophosphorylation sites on Schizosaccharomyces pombe Hhp1 and human CK1ε. Phosphoablating mutations increased Hhp1 and CK1ε activity toward substrates. Peptides corresponding to the C-termini interacted with the kinase domains only when phosphorylated, and substrates competitively inhibited binding of the autophosphorylated tails to the substrate binding grooves. Tail autophosphorylation influenced the catalytic efficiency with which CK1s targeted different substrates, and truncating the tail of CK1δ broadened its linear peptide substrate motif, indicating that tails contribute to substrate specificity as well. Considering autophosphorylation of both T220 in the catalytic domain and C-terminal sites, we propose a displacement specificity model to describe how autophosphorylation modulates substrate specificity for the CK1 family.
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Affiliation(s)
- Sierra N. Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kazutoshi Akizuki
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jared L. Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tomer M. Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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3
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Spangler RK, Ashley GE, Braun K, Wruck D, Ramos-Coronado A, Ragle JM, Iesmantavicius V, Hess D, Partch CL, Großhans H, Ward JD. A conserved chronobiological complex times C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593322. [PMID: 38766223 PMCID: PMC11100808 DOI: 10.1101/2024.05.09.593322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for the function of LIN-42 in timing rhythmic development. Here, using targeted deletions, we find that the LIN-42 PAS domains are dispensable for the protein's function in timing molts. Instead, we observe arrhythmic molts upon deletion of a distinct sequence element, conserved with PER. We show that this element mediates stable binding to KIN-20, the C. elegans CK1δ/ε orthologue. We demonstrate that CK1δ phosphorylates LIN-42 and define two conserved helical motifs, CK1δ-binding domain A (CK1BD-A) and CK1BD-B, that have distinct roles in controlling CK1δ-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molting timing in vivo. These interactions mirror the central role of a stable circadian PER-CK1 complex in setting a robust ~24-hour period. Hence, our results establish LIN-42/PER - KIN-20/CK1δ/ε as a functionally conserved signaling module of two distinct chronobiological systems.
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Affiliation(s)
- Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Wruck
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Ramos-Coronado
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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4
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Yan H, Miranda EAD, Jin S, Wilson F, An K, Godbee B, Zheng X, Brau-Rodríguez AR, Lei L. Primary oocytes with cellular senescence features are involved in ovarian aging in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574768. [PMID: 38260383 PMCID: PMC10802418 DOI: 10.1101/2024.01.08.574768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In mammalian females, quiescent primordial follicles serve as the ovarian reserve and sustain normal ovarian function and egg production via folliculogenesis. The loss of primordial follicles causes ovarian aging. Cellular senescence, characterized by cell cycle arrest and production of the senescence-associated secretory phenotype (SASP), is associated with tissue aging. In the present study, we report that some quiescent primary oocytes in primordial follicles become senescent in adult mouse ovaries. The senescent primary oocytes share senescence markers characterized in senescent somatic cells. The senescent primary oocytes were observed in young adult mouse ovaries, remained at approximately 15% of the total primary oocytes during ovarian aging from 6 months to 12 months, and accumulated in aged ovaries. Administration of a senolytic drug ABT263 to 3-month-old mice reduced the percentage of senescent primary oocytes and the transcription of the SASP cytokines in the ovary. In addition, led to increased numbers of primordial and total follicles and a higher rate of oocyte maturation and female fertility. Our study provides experimental evidence that primary oocytes, a germline cell type that is arrested in meiosis, become senescent in adult mouse ovaries and that senescent cell clearance reduced primordial follicle loss and mitigated ovarian aging phenotypes.
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Affiliation(s)
- Hao Yan
- Buck Institute for Research on Aging, Novato, California, 94945
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, 21218
| | - Edgar Andres Diaz Miranda
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
| | - Shiying Jin
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
| | - Faith Wilson
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, Missouri, 65211
| | - Kang An
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
| | - Brooke Godbee
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
- College of Health Sciences, University of Missouri, Columbia, Missouri, 65211
| | - Xiaobin Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, 21218
| | - Astrid Roshealy Brau-Rodríguez
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
| | - Lei Lei
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri School of Medicine, Columbia, Missouri, 65211
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, Missouri, 65211
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5
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Lambert M, Gebel J, Trejtnar C, Wesch N, Bozkurt S, Adrian-Allgood M, Löhr F, Münch C, Dötsch V. Fuzzy interactions between the auto-phosphorylated C-terminus and the kinase domain of CK1δ inhibits activation of TAp63α. Sci Rep 2023; 13:16423. [PMID: 37777570 PMCID: PMC10542812 DOI: 10.1038/s41598-023-43515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023] Open
Abstract
The p53 family member TAp63α plays an important role in maintaining the genetic integrity in oocytes. DNA damage, in particular DNA double strand breaks, lead to the transformation of the inhibited, only dimeric conformation into the active tetrameric one that results in the initiation of an apoptotic program. Activation requires phosphorylation by the kinase CK1 which phosphorylates TAp63α at four positions. The third phosphorylation event is the decisive step that transforms TAp63α into the active state. This third phosphorylation, however, is ~ 20 times slower than the first two phosphorylation events. This difference in the phosphorylation kinetics constitutes a safety mechanism that allows oocytes with a low degree of DNA damage to survive. So far these kinetic investigations of the phosphorylation steps have been performed with the isolated CK1 kinase domain. However, all CK1 enzymes contain C-terminal extensions that become auto-phosphorylated and inhibit the activity of the kinase. Here we have investigated the effect of auto-phosphorylation of the C-terminus in the kinase CK1δ and show that it slows down phosphorylation of the first two sites in TAp63α but basically inhibits the phosphorylation of the third site. We have identified up to ten auto-phosphorylation sites in the CK1δ C-terminal domain and show that all of them interact with the kinase domain in a "fuzzy" way in which not a single site is particularly important. Through mutation analysis we further show that hydrophobic amino acids following the phosphorylation site are important for a substrate to be able to successfully compete with the auto-inhibitory effect of the C-terminal domain. This auto-phosphorylation adds a new layer to the regulation of apoptosis in oocytes.
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Affiliation(s)
- Mahil Lambert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
| | - Jakob Gebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
| | - Charlotte Trejtnar
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany
| | - Martin Adrian-Allgood
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany
- Frankfurt Cancer Institute, Frankfurt/Main, Germany
- Cardio-Pulmonary Institute, Frankfurt/Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany.
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6
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Cullati SN, Akizuki K, Chen JS, Gould KL. Substrate displacement of CK1 C-termini regulates kinase specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547285. [PMID: 37425826 PMCID: PMC10327203 DOI: 10.1101/2023.06.30.547285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
CK1 kinases participate in many signaling pathways; how these enzymes are regulated is therefore of significant biological consequence. CK1s autophosphorylate their C-terminal non-catalytic tails, and eliminating these modifications increases substrate phosphorylation in vitro, suggesting that the autophosphorylated C-termini act as inhibitory pseudosubstrates. To test this prediction, we comprehensively identified the autophosphorylation sites on Schizosaccharomyces pombe Hhp1 and human CK1ε. Peptides corresponding to the C-termini interacted with the kinase domains only when phosphorylated, and phosphoablating mutations increased Hhp1 and CK1ε activity towards substrates. Interestingly, substrates competitively inhibited binding of the autophosphorylated tails to the substrate binding grooves. The presence or absence of tail autophosphorylation influenced the catalytic efficiency with which CK1s targeted different substrates, indicating that tails contribute to substrate specificity. Combining this mechanism with autophosphorylation of the T220 site in the catalytic domain, we propose a displacement specificity model to describe how autophosphorylation regulates substrate specificity for the CK1 family.
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Affiliation(s)
- Sierra N. Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kazutoshi Akizuki
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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7
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Philpott JM, Freeberg AM, Park J, Lee K, Ricci CG, Hunt SR, Narasimamurthy R, Segal DH, Robles R, Cai Y, Tripathi S, McCammon JA, Virshup DM, Chiu JC, Lee C, Partch CL. PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period. Mol Cell 2023; 83:1677-1692.e8. [PMID: 37207626 DOI: 10.1016/j.molcel.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/16/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
PERIOD (PER) and Casein Kinase 1δ regulate circadian rhythms through a phosphoswitch that controls PER stability and repressive activity in the molecular clock. CK1δ phosphorylation of the familial advanced sleep phase (FASP) serine cluster embedded within the Casein Kinase 1 binding domain (CK1BD) of mammalian PER1/2 inhibits its activity on phosphodegrons to stabilize PER and extend circadian period. Here, we show that the phosphorylated FASP region (pFASP) of PER2 directly interacts with and inhibits CK1δ. Co-crystal structures in conjunction with molecular dynamics simulations reveal how pFASP phosphoserines dock into conserved anion binding sites near the active site of CK1δ. Limiting phosphorylation of the FASP serine cluster reduces product inhibition, decreasing PER2 stability and shortening circadian period in human cells. We found that Drosophila PER also regulates CK1δ via feedback inhibition through the phosphorylated PER-Short domain, revealing a conserved mechanism by which PER phosphorylation near the CK1BD regulates CK1 kinase activity.
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Affiliation(s)
- Jonathan M Philpott
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jiyoung Park
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Kwangjun Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sabrina R Hunt
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rajesh Narasimamurthy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - David H Segal
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rafael Robles
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yao Cai
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Choogon Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Huang C, Zhao S, Yang Y, Guo T, Ke H, Mi X, Qin Y, Chen ZJ, Zhao S. TP63 gain-of-function mutations cause premature ovarian insufficiency by inducing oocyte apoptosis. J Clin Invest 2023; 133:162315. [PMID: 36856110 PMCID: PMC9974095 DOI: 10.1172/jci162315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/10/2023] [Indexed: 03/02/2023] Open
Abstract
The transcription factor p63 guards genome integrity in the female germline, and its mutations have been reported in patients with premature ovarian insufficiency (POI). However, the precise contribution of the TP63 gene to the pathogenesis of POI needs to be further determined. Here, in 1,030 Chinese patients with POI, we identified 6 heterozygous mutations of the TP63 gene that impaired the C-terminal transactivation-inhibitory domain (TID) of the TAp63α protein and resulted in tetramer formation and constitutive activation of the mutant proteins. The mutant proteins induced cell apoptosis by increasing the expression of apoptosis-inducing factors in vitro. We next introduced a premature stop codon and selectively deleted the TID of TAp63α in mice and observed rapid depletion of the p63+/ΔTID mouse oocytes through apoptosis after birth. Finally, to further verify the pathogenicity of the mutation p.R647C in the TID that was present in 3 patients, we generated p63+/R647C mice and also found accelerated oocyte loss, but to a lesser degree than in the p63+/ΔTID mice. Together, these findings show that TID-related variants causing constitutive activation of TAp63α lead to POI by inducing oocyte apoptosis, which will facilitate the genetic diagnosis of POI in patients and provide a potential therapeutic target for extending female fertility.
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Affiliation(s)
- Chengzi Huang
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Simin Zhao
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Yajuan Yang
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Ting Guo
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Hanni Ke
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xin Mi
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Yingying Qin
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shidou Zhao
- Center for Reproductive Medicine and,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
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9
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Nicolaou ST, Kannan S, Warwicker J, Verma CS. Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ. Proteins 2022; 90:2009-2022. [PMID: 35752942 PMCID: PMC9796392 DOI: 10.1002/prot.26393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 01/01/2023]
Abstract
The N-terminal transactivation domain (TAD) of p53 is a disordered region with multiple phosphorylation sites. Phosphorylation at Thr18 is crucial for the release of p53 from its negative regulator, MDM2. In stressed cells, CK1δ is responsible for phosphorylating Thr18, but requires Ser15 to be phosphorylated. To understand the mechanistic underpinnings of this sequential phosphorylation, molecular modeling and molecular dynamics simulation studies of these phosphorylation events were carried out. Our models suggest that a positively charged region on CK1δ near the adenosine triphosphate (ATP) binding pocket, which is conserved across species, sequesters the negatively charged pSer15, thereby constraining the positioning of the rest of the peptide, such that the side chain of Thr18 is positioned close to the γ-phosphate of ATP. Furthermore, our studies show that the phosphorylated p53 TAD1 (p53pSer15) peptide binds more strongly to CK1δ than does p53. p53 adopts a helical structure when bound to CK1δ, which is lost upon phosphorylation at Ser15, thus gaining higher flexibility and ability to morph into the binding site. We propose that upon phosphorylation at Ser15 the p53 TAD1 peptide binds to CK1δ through an electrostatically driven induced fit mechanism resulting in a flanking fuzzy complex.
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Affiliation(s)
- Sonia T. Nicolaou
- Faculty of Biology, Medicine and Health, School of Biological SciencesManchester Institute of Biotechnology, University of ManchesterManchesterUK,Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore
| | - Jim Warwicker
- Faculty of Biology, Medicine and Health, School of Biological SciencesManchester Institute of Biotechnology, University of ManchesterManchesterUK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore,School of Biological SciencesNanyang Technological UniversitySingaporeSingapore,Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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10
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Strubel A, Münick P, Chaikuad A, Dreier B, Schaefer J, Gebel J, Osterburg C, Tuppi M, Schäfer B, Knapp S, Plückthun A, Dötsch V. Designed Ankyrin Repeat Proteins as a tool box for analyzing p63. Cell Death Differ 2022; 29:2445-2458. [PMID: 35717504 PMCID: PMC9751120 DOI: 10.1038/s41418-022-01030-y] [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] [Received: 04/05/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/31/2023] Open
Abstract
The function of the p53 transcription factor family is dependent on several folded domains. In addition to a DNA-binding domain, members of this family contain an oligomerization domain. p63 and p73 also contain a C-terminal Sterile α-motif domain. Inhibition of most transcription factors is difficult as most of them lack deep pockets that can be targeted by small organic molecules. Genetic knock-out procedures are powerful in identifying the overall function of a protein, but they do not easily allow one to investigate roles of individual domains. Here we describe the characterization of Designed Ankyrin Repeat Proteins (DARPins) that were selected as tight binders against all folded domains of p63. We determine binding affinities as well as specificities within the p53 protein family and show that DARPins can be used as intracellular inhibitors for the modulation of transcriptional activity. By selectively inhibiting DNA binding of the ΔNp63α isoform that competes with p53 for the same promoter sites, we show that p53 can be reactivated. We further show that inhibiting the DNA binding activity stabilizes p63, thus providing evidence for a transcriptionally regulated negative feedback loop. Furthermore, the ability of DARPins to bind to the DNA-binding domain and the Sterile α-motif domain within the dimeric-only and DNA-binding incompetent conformation of TAp63α suggests a high structural plasticity within this special conformation. In addition, the developed DARPins can also be used to specifically detect p63 in cell culture and in primary tissue and thus constitute a very versatile research tool for studying the function of p63.
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Affiliation(s)
- Alexander Strubel
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Philipp Münick
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Apirat Chaikuad
- grid.7839.50000 0004 1936 9721Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany ,grid.7839.50000 0004 1936 9721Structural Genomics Consortium, Goethe University, 60438 Frankfurt, Germany
| | - Birgit Dreier
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jonas Schaefer
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jakob Gebel
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Christian Osterburg
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Marcel Tuppi
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Birgit Schäfer
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Stefan Knapp
- grid.7839.50000 0004 1936 9721Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany ,grid.7839.50000 0004 1936 9721Structural Genomics Consortium, Goethe University, 60438 Frankfurt, Germany
| | - Andreas Plückthun
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Volker Dötsch
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
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11
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Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4). Commun Biol 2022; 5:1257. [PMID: 36385162 PMCID: PMC9669019 DOI: 10.1038/s42003-022-04157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
AbstractIntegrin adhesion receptors provide links between extracellular ligands and cytoplasmic signaling. Multiple kinases have been found to directly engage with integrin β tails, but the molecular basis for these interactions remain unknown. Here, we assess the interaction between the kinase domain of p21-activated kinase 4 (PAK4) and the cytoplasmic tail of integrin β5. We determine three crystal structures of PAK4-β5 integrin complexes and identify the PAK-binding site. This is a region in the membrane-proximal half of the β5 tail and confirmed by site-directed mutagenesis. The β5 tail engages the kinase substrate-binding groove and positions the non-phosphorylatable integrin residue Glu767 at the phosphoacceptor site. Consistent with this, integrin β5 is poorly phosphorylated by PAK4, and in keeping with its ability to occlude the substrate-binding site, weakly inhibits kinase activity. These findings demonstrate the molecular basis for β5 integrin-PAK4 interactions but suggest modifications in understanding the potential cellular role of this interaction.
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12
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Oocyte Casein kinase 1α deletion causes defects in primordial follicle formation and oocyte loss by impairing oocyte meiosis and enhancing autophagy in developing mouse ovary. Cell Death Dis 2022; 8:388. [PMID: 36115846 PMCID: PMC9482644 DOI: 10.1038/s41420-022-01184-1] [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: 07/07/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022]
Abstract
Casein kinase 1α is a member of CK1 family, which is ubiquitously expressed and plays multiple functions, including its potential roles in regulating cell division. But the functions of CK1α in mammalian oogenesis and folliculogenesis remain elusive. In this study, we assayed the cell type of CK1α expression in the developing mouse ovary and confirmed that CK1α was highly expressed in ovaries after birth. The oocyte-specific CK1α knockout (cKO) mouse model was then established by crossing Ddx4-Cre mice with Csnk1a1-floxp mice, and the effects of CK1α deletion on oogenesis and folliculogenesis were identified. The results showed that oocyte CK1α deletion impaired the progression of oocyte meiosis and primordial follicle formation during meiotic prophase I, which subsequently caused oocyte loss and mouse infertility. Further, the in vivo CK1α deletion and in vitro inhibition of CK1 activity resulted in the defects of DNA double-strand break (DSB) repair, whereas apoptosis and autophagy were enhanced in the developing ovary. These may contribute to oocyte loss and infertility in cKO mice. It is thus concluded that CK1α is essential for mouse oogenesis and folliculogenesis by involving in regulating the processes of oocyte meiosis and DNA DSB repair during meiotic prophase I of mouse oocytes. However, the related signaling pathway and molecular mechanisms need to be elucidated further.
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13
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Francisco JC, Virshup DM. Casein Kinase 1 and Human Disease: Insights From the Circadian Phosphoswitch. Front Mol Biosci 2022; 9:911764. [PMID: 35720131 PMCID: PMC9205208 DOI: 10.3389/fmolb.2022.911764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Biological systems operate in constant communication through shared components and feedback from changes in the environment. Casein kinase 1 (CK1) is a family of protein kinases that functions in diverse biological pathways and its regulation is beginning to be understood. The several isoforms of CK1 take part in key steps of processes including protein translation, cell-cell interactions, synaptic dopaminergic signaling and circadian rhythms. While CK1 mutations are rarely the primary drivers of disease, the kinases are often found to play an accessory role in metabolic disorders and cancers. In these settings, the dysregulation of CK1 coincides with increased disease severity. Among kinases, CK1 is unique in that its substrate specificity changes dramatically with its own phosphorylation state. Understanding the process that governs CK1 substrate selection is thus useful in identifying its role in various ailments. An illustrative example is the PERIOD2 (PER2) phosphoswitch, where CK1δ/ε kinase activity can be varied between three different substrate motifs to regulate the circadian clock.
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Affiliation(s)
- Joel C. Francisco
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M. Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: David M. Virshup,
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14
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Bibel B, Elkayam E, Silletti S, Komives EA, Joshua-Tor L. Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife 2022; 11:76908. [PMID: 35638597 PMCID: PMC9154749 DOI: 10.7554/elife.76908] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Argonaute (Ago) proteins play a central role in post-transcriptional gene regulation through RNA interference (RNAi). Agos bind small RNAs (sRNAs) including small interfering RNAs (siRNAs) and microRNAs (miRNAs) to form the functional core of the RNA-induced silencing complex (RISC). The sRNA is used as a guide to target mRNAs containing either partially or fully complementary sequences, ultimately leading to downregulation of the corresponding proteins. It was previously shown that the kinase CK1α phosphorylates a cluster of residues in the eukaryotic insertion (EI) of Ago, leading to the alleviation of miRNA-mediated repression through an undetermined mechanism. We show that binding of miRNA-loaded human Ago2 to target RNA with complementarity to the seed and 3’ supplementary regions of the miRNA primes the EI for hierarchical phosphorylation by CK1α. The added negative charges electrostatically promote target release, freeing Ago to seek out additional targets once it is dephosphorylated. The high conservation of potential phosphosites in the EI suggests that such a regulatory strategy may be a shared mechanism for regulating miRNA-mediated repression. Proteins are the chemical ‘workhorses’ of the cell: some help maintain a cell’s shape or structure, while others carry out the chemical reactions necessary for life. Organisms therefore need to keep tight control over the production of proteins in their cells, so that the right amount of each protein is made at the right time, in the right place. Instructions for making new proteins are encoded in a type of molecule called messenger RNA. Each messenger RNA contains the instructions for one protein, which are then ‘read’ and carried out by special cellular machinery called ribosomes. The cell can control how much protein it produces by regulating both the levels of different messenger RNA and the amount of protein ribosomes are allowed to make from those instructions. The main way to regulate the levels of messenger RNA is through their transcription from the genome. However, this needs fine tuning. Cells can do this in a highly specific way using molecules called microRNAs. A microRNA works by directing a protein called Argonaute to the messenger RNA that it targets. Once Argonaute arrives, it can call in additional ‘helper proteins’ to shut down, or reduce, protein production from that messenger RNA, or alternatively to break down the messenger RNA altogether. Cells can use an enzyme called CK1α to attach bulky chemical groups onto a specific part of the Argonaute protein, in a reaction termed phosphorylation. The ability to carry out this reaction (and to reverse it) also seems to be important for microRNAs to do their job properly, but why has remained unknown. Bibel et al. wanted to determine what triggers CK1α to phosphorylate Argonaute, and how this affects interactions between microRNAs, Argonaute and their target messenger RNAs. A series of ‘test tube’ experiments looked at the interaction between purified CK1α and Argonaute under different conditions. These demonstrated that CK1α could only carry out its phosphorylation reaction when Argonaute was already interacting with a microRNA and its corresponding messenger RNA. Further measurements revealed that phosphorylation of Argonaute made it detach from the messenger RNA more quickly. This suggests that phosphorylation might be a way to let Argonaute seek out new messenger RNAs after blocking protein production at its first ‘target’. These results shed new light on a fundamental mechanism that cells use to control protein production. Bibel et al. propose that this mechanism may be shared across many different species and could one day help guide the development of new medical therapies based on microRNAs.
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Affiliation(s)
- Brianna Bibel
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Elad Elkayam
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
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15
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Osterburg C, Dötsch V. Structural diversity of p63 and p73 isoforms. Cell Death Differ 2022; 29:921-937. [PMID: 35314772 PMCID: PMC9091270 DOI: 10.1038/s41418-022-00975-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/25/2023] Open
Abstract
Abstract
The p53 protein family is the most studied protein family of all. Sequence analysis and structure determination have revealed a high similarity of crucial domains between p53, p63 and p73. Functional studies, however, have shown a wide variety of different tasks in tumor suppression, quality control and development. Here we review the structure and organization of the individual domains of p63 and p73, the interaction of these domains in the context of full-length proteins and discuss the evolutionary origin of this protein family.
Facts
Distinct physiological roles/functions are performed by specific isoforms.
The non-divided transactivation domain of p63 has a constitutively high activity while the transactivation domains of p53/p73 are divided into two subdomains that are regulated by phosphorylation.
Mdm2 binds to all three family members but ubiquitinates only p53.
TAp63α forms an autoinhibited dimeric state while all other vertebrate p53 family isoforms are constitutively tetrameric.
The oligomerization domain of p63 and p73 contain an additional helix that is necessary for stabilizing the tetrameric states. During evolution this helix got lost independently in different phylogenetic branches, while the DNA binding domain became destabilized and the transactivation domain split into two subdomains.
Open questions
Is the autoinhibitory mechanism of mammalian TAp63α conserved in p53 proteins of invertebrates that have the same function of genomic quality control in germ cells?
What is the physiological function of the p63/p73 SAM domains?
Do the short isoforms of p63 and p73 have physiological functions?
What are the roles of the N-terminal elongated TAp63 isoforms, TA* and GTA?
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16
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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17
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The process of ovarian aging: it is not just about oocytes and granulosa cells. J Assist Reprod Genet 2022; 39:783-792. [PMID: 35352316 PMCID: PMC9051003 DOI: 10.1007/s10815-022-02478-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ovarian age is classically considered the main cause of female reproductive infertility. In women, the process proceeds as an ongoing decline in the primordial follicle stockpile and it is associated with reduced fertility in the mid-thirties, irregular menstruation from the mid-forties, cessation of fertility, and, eventually, menopause in the early fifties. Reproductive aging is historically associated with changes in oocyte quantity and quality. However, besides the oocyte, other cellular as well as environmental factors have been the focus of more recent investigations suggesting that ovarian decay is a complex and multifaceted process. Among these factors, we will consider mitochondria and oxidative stress as related to nutrition, changes in extracellular matrix molecules, and the associated ovarian stromal compartment where immune cells of both the native and adaptive systems seem to play an important role. Understanding such processes is crucial to design treatment strategies to slow down ovarian aging and consequently prolong reproductive lifespan and, more to this, alleviaingt side effects of menopause on the musculoskeletal, cardiovascular, and nervous systems.
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18
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Enhanced pro-apoptosis gene signature following the activation of TAp63α in oocytes upon γ irradiation. Cell Death Dis 2022; 13:204. [PMID: 35246516 PMCID: PMC8897389 DOI: 10.1038/s41419-022-04659-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore, not only detrimental for the individual but affect the entire species. In oocytes, the surveillance of the structural integrity of the DNA is maintained by the p53 family member TAp63α. The TAp63α protein is highly expressed in a closed and inactive state and gets activated to the open conformation upon the detection of DNA damage, in particular DNA double-strand breaks. To understand the cellular response to DNA damage that leads to the TAp63α triggered oocyte death we have investigated the RNA transcriptome of oocytes following irradiation at different time points. The analysis shows enhanced expression of pro-apoptotic and typical p53 target genes such as CDKn1a or Mdm2, concomitant with the activation of TAp63α. While DNA repair genes are not upregulated, inflammation-related genes become transcribed when apoptosis is initiated by activation of STAT transcription factors. Furthermore, comparison with the transcriptional profile of the ΔNp63α isoform from other studies shows only a minimal overlap, suggesting distinct regulatory programs of different p63 isoforms.
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19
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Cullati SN, Chaikuad A, Chen JS, Gebel J, Tesmer L, Zhubi R, Navarrete-Perea J, Guillen RX, Gygi SP, Hummer G, Dötsch V, Knapp S, Gould KL. Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Mol Cell 2022; 82:2006-2020.e8. [DOI: 10.1016/j.molcel.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/27/2022] [Accepted: 03/01/2022] [Indexed: 12/01/2022]
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20
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Schirmer B, Giehl K, Kubatzky KF. Report of the 24th Meeting on Signal Transduction 2021. Int J Mol Sci 2022; 23:ijms23042015. [PMID: 35216127 PMCID: PMC8877372 DOI: 10.3390/ijms23042015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
The annual meeting “Signal Transduction—Receptors, Mediators and Genes” of the Signal Transduction Society (STS) is an interdisciplinary conference which is open to all scientists sharing a common interest in the elucidation of the signaling pathways mediating physiological or pathological processes in the health and disease of humans, animals, plants, fungi, prokaryotes, and protists. The 24th meeting on signal transduction was held from 15 to 17 November 2021 in Weimar, Germany. As usual, keynote presentations by invited scientists introduced the respective workshops, and were followed by speakers chosen from the submitted abstracts. A special workshop focused on “Target Identification and Interaction”. Ample time was reserved for the discussion of the presented data during the workshops. Unfortunately, due to restrictions owing to the SARS-CoV-2 pandemic, the poster sessions—and thus intensive scientific discussions at the posters—were not possible. In this report, we provide a concise summary of the various workshops and further aspects of the scientific program.
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Affiliation(s)
- Bastian Schirmer
- Institut für Pharmakologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany;
| | - Klaudia Giehl
- Signaltransduktion Zellulärer Motilität, Innere Medizin V, Justus-Liebig-Universität Giessen, Aulweg 128, 35392 Giessen, Germany;
| | - Katharina F. Kubatzky
- Zentrum für Infektiologie, Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-56-38361
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21
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The Role of Mutant p63 in Female Fertility. Int J Mol Sci 2021; 22:ijms22168968. [PMID: 34445673 PMCID: PMC8396438 DOI: 10.3390/ijms22168968] [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: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
The transcription factor p63, one of the p53 family members, plays an essential role in regulating maternal reproduction and genomic integrity as well as epidermal development. TP63 (human)/Trp63 (mouse) produces multiple isoforms: TAp63 and ΔNp63, which possess a different N-terminus depending on two different promoters, and p63a, p63b, p63g, p63δ, and p63ε as products of alternative splicing at the C-terminus. TAp63 expression turns on in the nuclei of primordial germ cells in females and is maintained mainly in the oocyte nuclei of immature follicles. It has been established that TAp63 is the genomic guardian in oocytes of the female ovaries and plays a central role in determining the oocyte fate upon oocyte damage. Lately, there is increasing evidence that TP63 mutations are connected with female infertility, including isolated premature ovarian insufficiency (POI) and syndromic POI. Here, we review the biological functions of p63 in females and discuss the consequences of p63 mutations, which result in infertility in human patients.
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22
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Panatta E, Zampieri C, Melino G, Amelio I. Understanding p53 tumour suppressor network. Biol Direct 2021; 16:14. [PMID: 34362419 PMCID: PMC8348811 DOI: 10.1186/s13062-021-00298-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/04/2021] [Indexed: 12/17/2022] Open
Abstract
The mutation of TP53 gene affects half of all human cancers, resulting in impairment of the regulation of several cellular functions, including cell cycle progression and cell death in response to genotoxic stress. In the recent years additional p53-mediated tumour suppression mechanisms have been described, questioning the contribution of its canonical pathway for tumour suppression. These include regulation of alternative cell death modalities (i.e. ferroptosis), cell metabolism and the emerging role in RNA stability. Here we briefly summarize our knowledge on p53 “canonical DNA damage response” and discuss the most relevant recent findings describing potential mechanistic explanation of p53-mediated tumour suppression.
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Affiliation(s)
- Emanuele Panatta
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Carlotta Zampieri
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy. .,School of Life Sciences, University of Nottingham, Nottingham, UK.
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23
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Mechanisms of quality control differ in male and female germ cells. Cell Death Differ 2021; 28:2300-2302. [PMID: 34131311 PMCID: PMC8257794 DOI: 10.1038/s41418-021-00818-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022] Open
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24
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Narasimamurthy R, Virshup DM. The phosphorylation switch that regulates ticking of the circadian clock. Mol Cell 2021; 81:1133-1146. [PMID: 33545069 DOI: 10.1016/j.molcel.2021.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
In our 24/7 well-lit world, it's easy to skip or delay sleep to work, study, and play. However, our circadian rhythms are not easily fooled; the consequences of jet lag and shift work are many and severe, including metabolic, mood, and malignant disorders. The internal clock that keeps track of time has at its heart the reversible phosphorylation of the PERIOD proteins, regulated by isoforms of casein kinase 1 (CK1). In-depth biochemical, genetic, and structural studies of these kinases, their mutants, and their splice variants have combined over the past several years to provide a robust understanding of how the core clock is regulated by a phosphoswitch whereby phosphorylation of a stabilizing site on PER blocks phosphorylation of a distant phosphodegron. The recent structure of a circadian mutant form of CK1 implicates an internal activation loop switch that regulates this phosphoswitch and points to new approaches to regulation of the clock.
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Affiliation(s)
- Rajesh Narasimamurthy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
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Isoform-Specific Roles of Mutant p63 in Human Diseases. Cancers (Basel) 2021; 13:cancers13030536. [PMID: 33572532 PMCID: PMC7866788 DOI: 10.3390/cancers13030536] [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: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary The protein p63 belongs to the family of the p53 tumor suppressor. Mouse models have, however, shown that it is not a classical tumor suppressor but instead involved in developmental processes. Mutations in the p63 gene cause several developmental defects in human patients characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia due to p63’s role as a master regulator of epidermal development. In addition, p63 plays a key role as a quality control factor in oocytes and p63 mutations can result either in compromised genetic quality control or premature cell death of all oocytes. Abstract The p63 gene encodes a master regulator of epidermal commitment, development, and differentiation. Heterozygous mutations in the DNA binding domain cause Ectrodactyly, Ectodermal Dysplasia, characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia while mutations in in the C-terminal domain of the α-isoform cause Ankyloblepharon-Ectodermal defects-Cleft lip/palate (AEC) syndrome, a life-threatening disorder characterized by skin fragility, severe, long-lasting skin erosions, and cleft lip/palate. The molecular disease mechanisms of these syndromes have recently become elucidated and have enhanced our understanding of the role of p63 in epidermal development. Here we review the molecular cause and functional consequences of these p63-mutations for skin development and discuss the consequences of p63 mutations for female fertility.
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Achieving effective and selective CK1 inhibitors through structure modification. Future Med Chem 2021; 13:505-528. [PMID: 33438471 DOI: 10.4155/fmc-2020-0215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Casein kinase 1 (CK1) is an extensively expressed serine/threonine kinase family, with six highly conserved isoforms of human CK1. Due to its involvement in many biological processes, CK1 is a promising target for several pathological states, including circadian sleep disorder, neurodegenerative diseases, cancer and inflammation. However, due to the structural similarities between the six CK1 members, the design of CK1 inhibitors is intricate. So far, no effective CK1 inhibitors are reported to reach clinical trials; thus, approaches to obtaining both selective and effective CK1 inhibitors are in great demand. Here we analyze several CK1 inhibitors that provide successful experience for structure-based drug design and rational structure modification, which could provide references for further drug design.
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Gebel J, Tuppi M, Sänger N, Schumacher B, Dötsch V. DNA Damaged Induced Cell Death in Oocytes. Molecules 2020; 25:molecules25235714. [PMID: 33287328 PMCID: PMC7730327 DOI: 10.3390/molecules25235714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
The production of haploid gametes through meiosis is central to the principle of sexual reproduction. The genetic diversity is further enhanced by exchange of genetic material between homologous chromosomes by the crossover mechanism. This mechanism not only requires correct pairing of homologous chromosomes but also efficient repair of the induced DNA double-strand breaks. Oocytes have evolved a unique quality control system that eliminates cells if chromosomes do not correctly align or if DNA repair is not possible. Central to this monitoring system that is conserved from nematodes and fruit fly to humans is the p53 protein family, and in vertebrates in particular p63. In mammals, oocytes are stored for a long time in the prophase of meiosis I which, in humans, can last more than 50 years. During the entire time of this arrest phase, the DNA damage checkpoint remains active. The treatment of female cancer patients with DNA damaging irradiation or chemotherapeutics activates this checkpoint and results in elimination of the oocyte pool causing premature menopause and infertility. Here, we review the molecular mechanisms of this quality control system and discuss potential therapeutic intervention for the preservation of the oocyte pool during chemotherapy.
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Affiliation(s)
- Jakob Gebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany; (J.G.); (M.T.)
| | - Marcel Tuppi
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany; (J.G.); (M.T.)
| | - Nicole Sänger
- Department for Gynecological Endocrinology and Reproductive Medicine, University Hospital of Bonn, Venusberg-Campus 1, 53217 Bonn, Germany;
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, and Center for Molecular Medicine, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany;
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany; (J.G.); (M.T.)
- Correspondence: ; Tel.: +49-69-798-29631
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