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Ceglowski J, Hoffman HK, Neumann AJ, Hoff KJ, McCurdy BL, Moore JK, Prekeris R. TTLL12 is required for primary ciliary axoneme formation in polarized epithelial cells. EMBO Rep 2024; 25:198-227. [PMID: 38177908 PMCID: PMC10883266 DOI: 10.1038/s44319-023-00005-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
The primary cilium is a critical sensory organelle that is built of axonemal microtubules ensheathed by a ciliary membrane. In polarized epithelial cells, primary cilia reside on the apical surface and must extend these microtubules directly into the extracellular space and remain a stable structure. However, the factors regulating cross-talk between ciliation and cell polarization, as well as axonemal microtubule growth and stabilization in polarized epithelia, are not fully understood. In this study, we find TTLL12, a previously uncharacterized member of the Tubulin Tyrosine Ligase-Like (TTLL) family, localizes to the base of primary cilia and is required for cilia formation in polarized renal epithelial cells. We also show that TTLL12 directly binds to the α/β-tubulin heterodimer in vitro and regulates microtubule dynamics, stability, and post-translational modifications (PTMs). While all other TTLLs catalyze the addition of glutamate or glycine to microtubule C-terminal tails, TTLL12 uniquely affects tubulin PTMs by promoting both microtubule lysine acetylation and arginine methylation. Together, this work identifies a novel microtubule regulator and provides insight into the requirements for apical extracellular axoneme formation.
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Affiliation(s)
- Julia Ceglowski
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Huxley K Hoffman
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Andrew J Neumann
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Katie J Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Bailey L McCurdy
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80015, USA.
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2
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Ceglowski J, Hoffman H, Hoff K, McCurdy B, Moore J, Prekeris R. TTLL12 is required for primary ciliary axoneme formation in polarized epithelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550533. [PMID: 37546873 PMCID: PMC10402096 DOI: 10.1101/2023.07.25.550533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The primary cilium is a critical sensory organelle that is built of axonemal microtubules ensheathed by a ciliary membrane. In polarized epithelial cells, primary cilia reside on the apical surface and must extend these microtubules directly into the extracellular space and remain a stable structure. However, the factors regulating cross-talk between ciliation and cell polarization, as well as, axonemal microtubule growth and stabilization in polarized epithelia are not fully understood. In this study, we find TTLL12, a previously uncharacterized member of the Tubulin Tyrosine Ligase-Like (TTLL) family, localizes to the base of primary cilia and is required for cilia formation in polarized renal epithelial cells. We also show that TTLL12 directly binds to the α/β-tubulin heterodimer in vitro and regulates microtubule dynamics, stability, and post-translational modifications (PTMs). While all other TTLLs catalyze the addition of glutamate or glycine to microtubule C-terminal tails, TTLL12 uniquely affects tubulin PTMs by promoting both microtubule lysine acetylation and arginine methylation. Together, this work identifies a novel microtubule regulator and provides insight into the requirements for apical extracellular axoneme formation.
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Affiliation(s)
- J. Ceglowski
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
| | - H.K. Hoffman
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
| | - K.J. Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
| | - B.L. McCurdy
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
| | - J.K. Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
| | - R. Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015
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3
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Carmona B, Marinho HS, Matos CL, Nolasco S, Soares H. Tubulin Post-Translational Modifications: The Elusive Roles of Acetylation. BIOLOGY 2023; 12:biology12040561. [PMID: 37106761 PMCID: PMC10136095 DOI: 10.3390/biology12040561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
Microtubules (MTs), dynamic polymers of α/β-tubulin heterodimers found in all eukaryotes, are involved in cytoplasm spatial organization, intracellular transport, cell polarity, migration and division, and in cilia biology. MTs functional diversity depends on the differential expression of distinct tubulin isotypes and is amplified by a vast number of different post-translational modifications (PTMs). The addition/removal of PTMs to α- or β-tubulins is catalyzed by specific enzymes and allows combinatory patterns largely enriching the distinct biochemical and biophysical properties of MTs, creating a code read by distinct proteins, including microtubule-associated proteins (MAPs), which allow cellular responses. This review is focused on tubulin-acetylation, whose cellular roles continue to generate debate. We travel through the experimental data pointing to α-tubulin Lys40 acetylation role as being a MT stabilizer and a typical PTM of long lived MTs, to the most recent data, suggesting that Lys40 acetylation enhances MT flexibility and alters the mechanical properties of MTs, preventing MTs from mechanical aging characterized by structural damage. Additionally, we discuss the regulation of tubulin acetyltransferases/desacetylases and their impacts on cell physiology. Finally, we analyze how changes in MT acetylation levels have been found to be a general response to stress and how they are associated with several human pathologies.
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Affiliation(s)
- Bruno Carmona
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
| | - H Susana Marinho
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Catarina Lopes Matos
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia Nolasco
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Helena Soares
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
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4
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Estève PO, Sen S, Vishnu US, Ruse C, Chin HG, Pradhan S. Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation in mammalian nuclear genome. Commun Biol 2022; 5:1292. [PMID: 36434141 PMCID: PMC9700808 DOI: 10.1038/s42003-022-04241-8] [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: 05/14/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised, and degradation via ubiquitylation pathway. Knockdown of PARP1 led to an increase of SET8 protein levels, leading to aberrant H4K20me1 and H4K20me3 domains in the genome. H4K20me1 is associated with higher gene transcription levels while the increase of H4K20me3 levels was predominant in DNA repeat elements. Hence, SET8 mediated chromatin remodeling in mammalian cells are modulated by poly ADP-ribosylation by PARP1.
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Affiliation(s)
- Pierre-Olivier Estève
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Sagnik Sen
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Udayakumar S. Vishnu
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Cristian Ruse
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139 USA
| | - Hang Gyeong Chin
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Sriharsa Pradhan
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
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5
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Hernandez‐Vicens R, Singh J, Pernicone N, Listovsky T, Gerlitz G. SETDB1 regulates microtubule dynamics. Cell Prolif 2022; 55:e13348. [DOI: 10.1111/cpr.13348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Jagreeti Singh
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Nomi Pernicone
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Tamar Listovsky
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
- Adelson School of Medicine Ariel University Ariel Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
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6
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Lotfollahzadeh S, Lo D, York EA, Napoleon MA, Yin W, Elzinad N, Le J, Zhang M, Yang X, Morrissey A, Elsadawi M, Zhao Q, Schaus SE, Hansen U, Chitalia VC. Pharmacologic Manipulation of Late SV40 Factor Suppresses Wnt Signaling and Inhibits Growth of Allogeneic and Syngeneic Colon Cancer Xenografts. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1167-1185. [PMID: 35710032 PMCID: PMC9379689 DOI: 10.1016/j.ajpath.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Aberrant hyperactivation of Wnt signaling, driven by nuclear β-catenin in the colonic epithelium, represents the seminal event in the initiation and progression of colorectal cancer (CRC). Despite its established role in CRC tumorigenesis, clinical translation of Wnt inhibitors remains unsuccessful. Late SV40 factor (LSF; encoded by TFCP2) is a transcription factor and a potent oncogene. The current study identified a chemotype, named factor quinolinone inhibitors (FQIs), that specifically inhibits LSF DNA-binding, partner protein-binding, and transactivation activities. The role of LSF and FQIs in CRC tumor growth was examined. Herein, the study showed that LSF and β-catenin interacted in several CRC cell lines irrespective of their mutational profile, which was disrupted by FQI2-34. FQI2-34 suppressed Wnt activity in CRC cells in a dose-dependent manner. Leveraging both allogeneic and syngeneic xenograft models showed that FQI2-34 suppressed CRC tumor growth, significantly reduced nuclear β-catenin, and down-regulated Wnt targets such as axis inhibition protein 2 (AXIN-2) and SRY-box transcription factor 9, in the xenograft cells. FQI2-34 suppressed the proliferation of xenograft cells. Adenocarcinomas from a series of stage IV CRC patients revealed a positive correlation between LSF expression and Wnt targets (AXIN-2 and SRY-box transcription factor 9) within the CRC cells. Collectively, this study uncovers the Wnt inhibitory and CRC growth-suppressive effects of these LSF inhibitors in CRC cells, revealing a novel target in CRC therapeutics.
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Affiliation(s)
- Saran Lotfollahzadeh
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Dominic Lo
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Emily A York
- Center for Molecular Discovery, Department of Chemistry, Boston University, Boston, Massachusetts
| | - Marc A Napoleon
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Wenqing Yin
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Nagla Elzinad
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts; Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - John Le
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Mengwei Zhang
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Xiaosheng Yang
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Austin Morrissey
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Murad Elsadawi
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Qing Zhao
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Scott E Schaus
- Center for Molecular Discovery, Department of Chemistry, Boston University, Boston, Massachusetts
| | - Ulla Hansen
- Department of Biology, Boston University, Boston, Massachusetts
| | - Vipul C Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts; Veterans Affairs Boston Healthcare System, Boston, Massachusetts; Institute of Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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7
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Yunes SA, Willoughby JLS, Kwan JH, Biagi JM, Pokharel N, Chin HG, York EA, Su KC, George K, Shah JV, Emili A, Schaus SE, Hansen U. Factor quinolinone inhibitors disrupt spindles and multiple LSF (TFCP2)-protein interactions in mitosis, including with microtubule-associated proteins. PLoS One 2022; 17:e0268857. [PMID: 35704642 PMCID: PMC9200292 DOI: 10.1371/journal.pone.0268857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
Abstract
Factor quinolinone inhibitors (FQIs), a first-in-class set of small molecule inhibitors targeted to the transcription factor LSF (TFCP2), exhibit promising cancer chemotherapeutic properties. FQI1, the initial lead compound identified, unexpectedly induced a concentration-dependent delay in mitotic progression. Here, we show that FQI1 can rapidly and reversibly lead to mitotic arrest, even when added directly to mitotic cells, implying that FQI1-mediated mitotic defects are not transcriptionally based. Furthermore, treatment with FQIs resulted in a striking, concentration-dependent diminishment of spindle microtubules, accompanied by a concentration-dependent increase in multi-aster formation. Aberrant γ-tubulin localization was also observed. These phenotypes suggest that perturbation of spindle microtubules is the primary event leading to the mitotic delays upon FQI1 treatment. Previously, FQIs were shown to specifically inhibit not only LSF DNA-binding activity, which requires LSF oligomerization to tetramers, but also other specific LSF-protein interactions. Other transcription factors participate in mitosis through non-transcriptional means, and we recently reported that LSF directly binds α-tubulin and is present in purified cellular tubulin preparations. Consistent with a microtubule role for LSF, here we show that LSF enhanced the rate of tubulin polymerization in vitro, and FQI1 inhibited such polymerization. To probe whether the FQI1-mediated spindle abnormalities could result from inhibition of mitotic LSF-protein interactions, mass spectrometry was performed using as bait an inducible, tagged form of LSF that is biotinylated by endogenous enzymes. The global proteomics analysis yielded expected associations for a transcription factor, notably with RNA processing machinery, but also to nontranscriptional components. In particular, and consistent with spindle disruption due to FQI treatment, mitotic, FQI1-sensitive interactions were identified between the biotinylated LSF and microtubule-associated proteins that regulate spindle assembly, positioning, and dynamics, as well as centrosome-associated proteins. Probing the mitotic LSF interactome using small molecule inhibitors therefore supported a non-transcriptional role for LSF in mediating progression through mitosis.
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Affiliation(s)
- Sarah A. Yunes
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts, United States of America
| | - Jennifer L. S. Willoughby
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts, United States of America
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Julian H. Kwan
- Department of Biochemistry and Center for Network Systems Biology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Jessica M. Biagi
- Department of Chemistry and Center for Molecular Discovery, Boston University, Boston, Massachusetts, United States of America
| | - Niranjana Pokharel
- Department of Chemistry and Center for Molecular Discovery, Boston University, Boston, Massachusetts, United States of America
| | - Hang Gyeong Chin
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts, United States of America
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Emily A. York
- Department of Chemistry and Center for Molecular Discovery, Boston University, Boston, Massachusetts, United States of America
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Kelly George
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jagesh V. Shah
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew Emili
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Department of Biochemistry and Center for Network Systems Biology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Scott E. Schaus
- Department of Chemistry and Center for Molecular Discovery, Boston University, Boston, Massachusetts, United States of America
| | - Ulla Hansen
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts, United States of America
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Abstract
Polyglutamylation is a posttranslational modification (PTM) that adds several glutamates on glutamate residues in the form of conjugated peptide chains by a family of enzymes known as polyglutamylases. Polyglutamylation is well documented in microtubules. Polyglutamylated microtubules consist of different α- and β-tubulin subunits with varied number of added glutamate residues. Kinetic control and catalytic rates of tubulin modification by polyglutamylases influence the polyglutamylation pattern of functional microtubules. The recent studies uncovered catalytic mechanisms of the glutamylation enzymes family, particularly tubulin tyrosine ligase-like (TTLL). Variable length polyglutamylation of primary sequence glutamyl residues have been mapped with a multitude of protein chemistry and proteomics approaches. Although polyglutamylation was initially considered a tubulin-specific modification, the recent studies have uncovered a calmodulin-dependent glutamylase, SidJ. Nano-electrospray ionization (ESI) proteomic approaches have identified quantifiable polyglutamylated sites in specific substrates. Indeed, conjugated glutamylated peptides were used in nano-liquid chromatography gradient delivery due to their relative hydrophobicity for their tandem mass spectrometry (MS/MS) characterization. The recent polyglutamylation characterization has revealed three major sites: E445 in α-tubulin, E435 in β-tubulin, and E860 in SdeA. In this review, we have summarized the progress made using proteomic approaches for large-scale detection of polyglutamylated peptides, including biology and analysis.
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9
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Stoiber P, Scribani Rossi P, Pokharel N, Germany JL, York EA, Schaus SE, Hansen U. Factor quinolinone inhibitors alter cell morphology and motility by destabilizing interphase microtubules. Sci Rep 2021; 11:23564. [PMID: 34876605 PMCID: PMC8651680 DOI: 10.1038/s41598-021-02962-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Factor quinolinone inhibitors are promising anti-cancer compounds, initially characterized as specific inhibitors of the oncogenic transcription factor LSF (TFCP2). These compounds exert anti-proliferative activity at least in part by disrupting mitotic spindles. Herein, we report additional interphase consequences of the initial lead compound, FQI1, in two telomerase immortalized cell lines. Within minutes of FQI1 addition, the microtubule network is disrupted, resulting in a substantial, although not complete, depletion of microtubules as evidenced both by microtubule sedimentation assays and microscopy. Surprisingly, this microtubule breakdown is quickly followed by an increase in tubulin acetylation in the remaining microtubules. The sudden breakdown and partial depolymerization of the microtubule network precedes FQI1-induced morphological changes. These involve rapid reduction of cell spreading of interphase fetal hepatocytes and increase in circularity of retinal pigment epithelial cells. Microtubule depolymerization gives rise to FH-B cell compaction, as pretreatment with taxol prevents this morphological change. Finally, FQI1 decreases the rate and range of locomotion of interphase cells, supporting an impact of FQI1-induced microtubule breakdown on cell motility. Taken together, our results show that FQI1 interferes with microtubule-associated functions in interphase, specifically cell morphology and motility.
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Affiliation(s)
- Patrick Stoiber
- grid.189504.10000 0004 1936 7558MCBB Graduate Program, Boston University, Boston, MA 02215 USA ,grid.189504.10000 0004 1936 7558Department of Biology, Boston University, Boston, MA 02215 USA
| | - Pietro Scribani Rossi
- grid.189504.10000 0004 1936 7558Department of Biology, Boston University, Boston, MA 02215 USA ,grid.7841.aPresent Address: Faculty of Medicine and Dentistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Niranjana Pokharel
- grid.189504.10000 0004 1936 7558Department of Chemistry, Boston University, Boston, MA 02215 USA ,grid.189504.10000 0004 1936 7558Center for Molecular Discovery, Boston University, Boston, MA 02215 USA
| | - Jean-Luc Germany
- grid.189504.10000 0004 1936 7558Department of Biology, Boston University, Boston, MA 02215 USA
| | - Emily A. York
- grid.189504.10000 0004 1936 7558Department of Chemistry, Boston University, Boston, MA 02215 USA ,grid.189504.10000 0004 1936 7558Center for Molecular Discovery, Boston University, Boston, MA 02215 USA
| | - Scott E. Schaus
- grid.189504.10000 0004 1936 7558Department of Chemistry, Boston University, Boston, MA 02215 USA ,grid.189504.10000 0004 1936 7558Center for Molecular Discovery, Boston University, Boston, MA 02215 USA
| | - Ulla Hansen
- MCBB Graduate Program, Boston University, Boston, MA, 02215, USA. .,Department of Biology, Boston University, Boston, MA, 02215, USA.
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10
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Huang Y, Zhang W, Zhao S, Xie Z, Chen S, Yi G. Ultra-sensitive detection of DNA N6-adenine methyltransferase based on a 3D tetrahedral fluorescence scaffold assisted by symmetrical double-ring dumbbells. Anal Chim Acta 2021; 1184:339018. [PMID: 34625260 DOI: 10.1016/j.aca.2021.339018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/13/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic modification that plays a vital role in X chromosome inactivation, genome imprinting, and gene expression. DNA methyltransferase establishes and maintains a stable methylation state in genomic DNA. Efficient and specific DNA methyltransferase testing is essential for the early diagnosis and treatment of cancer. In this study, we designed an ultra-sensitive fluorescent biosensor, based on a 3D tetrahedral fluorescent scaffold assisted by symmetrical double-ring dumbbells, for the detection of DNA-[N 6-adenine]-methyltransferase (Dam MTase). Double-stranded DNA was methylated by Dam MTase and then digested by DpnI to form two identical dumbbell rings. The 3D tetrahedral fluorescent scaffold was synthesized from four oligonucleotide chains containing hairpins. When the sheared dumbbells reacted with the 3D tetrahedral fluorescent scaffold, the hairpins opened and a fluorescence signal could be detected. The strategy was successful over a wide detection range, from 0.002 to 100 U mL-1 Dam MTase, and the lowest detection limit was 0.00036 U mL-1. Control experiments with M.SssI methyltransferase and HpaII methylation restriction endonuclease confirmed the specificity of the method. Experiments with spiked human serum and the 5-fluorouracil inhibitor proved the suitability of the method for early cancer diagnosis.
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Affiliation(s)
- Yuqi Huang
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wenxiu Zhang
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shuhui Zhao
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zuowei Xie
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyi Chen
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Gang Yi
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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11
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Koenning M, Wang X, Karki M, Jangid RK, Kearns S, Tripathi DN, Cianfrocco M, Verhey KJ, Jung SY, Coarfa C, Ward CS, Kalish BT, Grimm SL, Rathmell WK, Mostany R, Dere R, Rasband MN, Walker CL, Park IY. Neuronal SETD2 activity links microtubule methylation to an anxiety-like phenotype in mice. Brain 2021; 144:2527-2540. [PMID: 34014281 PMCID: PMC8418347 DOI: 10.1093/brain/awab200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Gene discovery efforts in autism spectrum disorder have identified heterozygous defects in chromatin remodeller genes, the 'readers, writers and erasers' of methyl marks on chromatin, as major contributors to this disease. Despite this advance, a convergent aetiology between these defects and aberrant chromatin architecture or gene expression has remained elusive. Recently, data have begun to emerge that chromatin remodellers also function directly on the cytoskeleton. Strongly associated with autism spectrum disorder, the SETD2 histone methyltransferase for example, has now been shown to directly methylate microtubules of the mitotic spindle. However, whether microtubule methylation occurs in post-mitotic cells, for example on the neuronal cytoskeleton, is not known. We found the SETD2 α-tubulin lysine 40 trimethyl mark occurs on microtubules in the brain and in primary neurons in culture, and that the SETD2 C-terminal SRI domain is required for binding and methylation of α-tubulin. A CRISPR knock-in of a pathogenic SRI domain mutation (Setd2SRI) that disables microtubule methylation revealed at least one wild-type allele was required in mice for survival, and while viable, heterozygous Setd2SRI/wtmice exhibited an anxiety-like phenotype. Finally, whereas RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) showed no concomitant changes in chromatin methylation or gene expression in Setd2SRI/wtmice, primary neurons exhibited structural deficits in axon length and dendritic arborization. These data provide the first demonstration that microtubules of neurons are methylated, and reveals a heterozygous chromatin remodeller defect that specifically disables microtubule methylation is sufficient to drive an autism-associated phenotype.
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Affiliation(s)
- Matthias Koenning
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xianlong Wang
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul Kumar Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kearns
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Durga Nand Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Scott Ward
- Molecular Physiology and Biophysics, Mouse Metabolic and Phenotyping Core, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ricardo Mostany
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Kearns S, Mason FM, Rathmell WK, Park IY, Walker C, Verhey KJ, Cianfrocco MA. Molecular determinants for α-tubulin methylation by SETD2. J Biol Chem 2021; 297:100898. [PMID: 34157286 PMCID: PMC8294582 DOI: 10.1016/j.jbc.2021.100898] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications to tubulin are important for many microtubule-based functions inside cells. It was recently shown that methylation of tubulin by the histone methyltransferase SETD2 occurs on mitotic spindle microtubules during cell division, with its absence resulting in mitotic defects. However, the catalytic mechanism of methyl addition to tubulin is unclear. We used a truncated version of human wild type SETD2 (tSETD2) containing the catalytic SET and C-terminal Set2-Rpb1-interacting (SRI) domains to investigate the biochemical mechanism of tubulin methylation. We found that recombinant tSETD2 had a higher activity toward tubulin dimers than polymerized microtubules. Using recombinant single-isotype tubulin, we demonstrated that methylation was restricted to lysine 40 of α-tubulin. We then introduced pathogenic mutations into tSETD2 to probe the recognition of histone and tubulin substrates. A mutation in the catalytic domain (R1625C) allowed tSETD2 to bind to tubulin but not methylate it, whereas a mutation in the SRI domain (R2510H) caused loss of both tubulin binding and methylation. Further investigation of the role of the SRI domain in substrate binding found that mutations within this region had differential effects on the ability of tSETD2 to bind to tubulin versus the binding partner RNA polymerase II for methylating histones in vivo, suggesting distinct mechanisms for tubulin and histone methylation by SETD2. Finally, we found that substrate recognition also requires the negatively charged C-terminal tail of α-tubulin. Together, this study provides a framework for understanding how SETD2 serves as a dual methyltransferase for both histone and tubulin methylation.
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Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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13
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Histone lysine methyltransferase SET8 is a novel therapeutic target for cancer treatment. Drug Discov Today 2021; 26:2423-2430. [PMID: 34022460 DOI: 10.1016/j.drudis.2021.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 12/24/2022]
Abstract
SET8 is the only lysine methyltransferase that can specifically monomethylate the histone H4K20. SET8-mediated protein modifications are largely involved in the regulation of cell cycle, DNA repair, gene transcription, cell apoptosis, and other vital physiological processes. The aberrant expression of SET8 is closely linked to the proliferation, invasion, metastasis, and prognosis of a variety of cancers. As a consequence, targeting SET8 could be an appealing strategy for cancer therapy. In this article, we introduce the molecular structure of SET8, followed by summarizing its roles in various biological pathways. Crucially, we highlight the potential functions of SET8 in tumors, as well as progress in the development of SET inhibitors for cancer treatment.
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14
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Ugai K, Matsuda S, Mikami H, Shimada A, Misawa T, Nakamura H, Tatsumi K, Hatano M, Murayama T, Kasuya Y. Inhibition of the SET8 Pathway Ameliorates Lung Fibrosis Even Through Fibroblast Dedifferentiation. Front Mol Biosci 2020; 7:192. [PMID: 32850975 PMCID: PMC7419601 DOI: 10.3389/fmolb.2020.00192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease of unknown etiopathogenesis. The activation of extracellular matrix (ECM)-producing myofibroblasts plays a key role in fibrotic tissue remodeling. The dedifferentiation of myofibroblasts has attracted considerable attention as a promising target for the development of effective therapeutic interventions against IPF. Here, we screened a small library of epigenetics-related inhibitors using dedifferentiation assay of lung myofibroblasts prepared from a patient at the terminal stages of IPF and chose UNC0379. The inhibition of SET8, a histone H4 lysine 20 (H4K20) monomethyltransferase, by UNC0379 markedly suppressed the expression of α-smooth muscle actin (SMA) and ED-A-fibronectin in myofibroblasts. In IPF myofibroblasts, SET8 expression and H4K20 monomethylation (H4K20me1) levels, which were significantly higher than those in normal human lung fibroblasts, were reduced upon treatment with UNC0379. Hence, the changes in the expression of the two fibrotic markers clearly correlated with those in SET8 expression and H4K20me1 level. Furthermore, in a mouse model of bleomycin (BLM)-induced lung fibrosis, the intratracheal administration of UNC0379 at an early fibrotic stage markedly ameliorated the histopathological changes associated with collagen deposition in the lungs. However, treatment with UNC0379 did not significantly affect the number of proinflammatory cells or cytokine production in the bronchoalveolar lavage fluids from mice treated with BLM. In the BLM-injured lung, SET8 was predominantly localized to the nuclei of α-SMA-positive cells, which colocalized with H4K20me1. Taken together, our results indicate that the inhibition of SET8 resulting in myofibroblast dedifferentiation may partly mitigate lung fibrosis without affecting the inflammatory responses.
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Affiliation(s)
- Keita Ugai
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Shuichi Matsuda
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideki Mikami
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ayako Shimada
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoko Misawa
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Nakamura
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiko Hatano
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshihiko Murayama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Yoshitoshi Kasuya
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Biochemistry and Molecular Pharmacology, Graduate School of Medicine, Chiba University, Chiba, Japan
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