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Bucher EA, Mészáros G, Gebre KT, Emmerling R, Sölkner J. Genome-wide association study for milking speed in Fleckvieh cattle. J Dairy Sci 2024:S0022-0302(24)00960-3. [PMID: 38908711 DOI: 10.3168/jds.2024-24854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/24/2024] [Indexed: 06/24/2024]
Abstract
Milking speed is an important trait influencing udder health of dairy cows as well as labor efficiency. Yet, it has received little attention in genomic association studies. The main objective of this study was to determine regions and genes on the genome with a potential effect on milking speed in Fleckvieh (dual purpose Simmental) cattle. Genome-wide association studies were conducted using de-regressed breeding values of bulls as phenotypes. Six SNP on 4 autosomes were significantly associated with milking speed for additive effects. Significant regions on BTA4 and BTA19 correspond with findings for other dairy cattle breeds. Based on the observation of Fleckvieh breed managers, variation of milking speed in batches of daughters of some bulls is much higher than in daughter groups of other bulls. This difference in within family variation may be caused by transmission of alternative alleles of bulls being heterozygous for a gene affecting milking speed. To check on this, we considered standard deviation of yield deviations in milking speed of half-sib daughters as a new trait and performed GWAS for dominance effects. One signal on BTA5 passed the genome wide Bonferroni threshold that corresponded to the significant signal from standard GWAS on de-regressed breeding values. The key conclusion of this study is that several strong genomic signals were found for milking speed in Fleckvieh cattle and that the strongest of them are supported by similar findings in Brown Swiss and Holstein Friesian cattle. Milking speed is a complex trait whose sub-processes have not yet been elucidated in detail. Hence, it remains a challenge to link the associated regions on the genome with causal genes and their functions.
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Affiliation(s)
- E A Bucher
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
| | - G Mészáros
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria.
| | - K T Gebre
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria; Mekelle University, Department of Animal, Rangeland and Wildlife Sciences (ARWS), Enda-Eyesus campus, P.O Box 231, Mekelle, Ethiopia
| | - R Emmerling
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586 Poing-Grub, Germany
| | - J Sölkner
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
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2
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Shen Y, Ori-McKenney KM. Microtubule-associated protein MAP7 promotes tubulin posttranslational modifications and cargo transport to enable osmotic adaptation. Dev Cell 2024; 59:1553-1570.e7. [PMID: 38574732 PMCID: PMC11187767 DOI: 10.1016/j.devcel.2024.03.022] [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: 06/23/2023] [Revised: 09/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live-cell imaging, ex vivo enzymatic assays, and in vitro reconstitution, we probe the impact of cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs). We find that human epithelial cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification and find that MAP7 promotes acetylation and inhibits detyrosination. Our data identify MAP7 in modulating the tubulin code, resulting in microtubule cytoskeleton remodeling and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
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Affiliation(s)
- Yusheng Shen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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3
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Rodrigues JS, Chenlo M, Bravo SB, Perez-Romero S, Suarez-Fariña M, Sobrino T, Sanz-Pamplona R, González-Prieto R, Blanco Freire MN, Nogueiras R, López M, Fugazzola L, Cameselle-Teijeiro JM, Alvarez CV. dsRNAi-mediated silencing of PIAS2beta specifically kills anaplastic carcinomas by mitotic catastrophe. Nat Commun 2024; 15:3736. [PMID: 38744818 PMCID: PMC11094195 DOI: 10.1038/s41467-024-47751-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
The E3 SUMO ligase PIAS2 is expressed at high levels in differentiated papillary thyroid carcinomas but at low levels in anaplastic thyroid carcinomas (ATC), an undifferentiated cancer with high mortality. We show here that depletion of the PIAS2 beta isoform with a transcribed double-stranded RNA-directed RNA interference (PIAS2b-dsRNAi) specifically inhibits growth of ATC cell lines and patient primary cultures in vitro and of orthotopic patient-derived xenografts (oPDX) in vivo. Critically, PIAS2b-dsRNAi does not affect growth of normal or non-anaplastic thyroid tumor cultures (differentiated carcinoma, benign lesions) or cell lines. PIAS2b-dsRNAi also has an anti-cancer effect on other anaplastic human cancers (pancreas, lung, and gastric). Mechanistically, PIAS2b is required for proper mitotic spindle and centrosome assembly, and it is a dosage-sensitive protein in ATC. PIAS2b depletion promotes mitotic catastrophe at prophase. High-throughput proteomics reveals the proteasome (PSMC5) and spindle cytoskeleton (TUBB3) to be direct targets of PIAS2b SUMOylation at mitotic initiation. These results identify PIAS2b-dsRNAi as a promising therapy for ATC and other aggressive anaplastic carcinomas.
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Affiliation(s)
- Joana S Rodrigues
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Miguel Chenlo
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Susana B Bravo
- Department of Proteomics, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Sihara Perez-Romero
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Maria Suarez-Fariña
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Tomas Sobrino
- Department of NeuroAging Group - Clinical Neurosciences Research Laboratory (LINC), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rebeca Sanz-Pamplona
- University Hospital Lozano Blesa, Institute for Health Research Aragon (IISA), ARAID Foundation, Aragon Government and CIBERESP, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Román González-Prieto
- Cell Dynamics and Signaling Department, Andalusian Center for Molecular Biology and Regenerative Medicine, Universidad de Sevilla - CSIC - Universidad Pablo de Olavide-Junta de Andalucía, 41092, Sevilla, Spain
- Department of Cell Biology, Faculty of Biology, University of Sevilla, 41012, Sevilla, Spain
| | - Manuel Narciso Blanco Freire
- Department of Surgery, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Ruben Nogueiras
- Molecular Metabolism, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Miguel López
- NeurObesity, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Laura Fugazzola
- Department of Endocrine and Metabolic Diseases and Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS); Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain.
| | - Clara V Alvarez
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain.
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4
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024:10.1038/s41589-024-01599-0. [PMID: 38658656 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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5
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Iuzzolino A, Pellegrini FR, Rotili D, Degrassi F, Trisciuoglio D. The α-tubulin acetyltransferase ATAT1: structure, cellular functions, and its emerging role in human diseases. Cell Mol Life Sci 2024; 81:193. [PMID: 38652325 PMCID: PMC11039541 DOI: 10.1007/s00018-024-05227-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: 12/30/2023] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
The acetylation of α-tubulin on lysine 40 is a well-studied post-translational modification which has been associated with the presence of long-lived stable microtubules that are more resistant to mechanical breakdown. The discovery of α-tubulin acetyltransferase 1 (ATAT1), the enzyme responsible for lysine 40 acetylation on α-tubulin in a wide range of species, including protists, nematodes, and mammals, dates to about a decade ago. However, the role of ATAT1 in different cellular activities and molecular pathways has been only recently disclosed. This review comprehensively summarizes the most recent knowledge on ATAT1 structure and substrate binding and analyses the involvement of ATAT1 in a variety of cellular processes such as cell motility, mitosis, cytoskeletal organization, and intracellular trafficking. Finally, the review highlights ATAT1 emerging roles in human diseases and discusses ATAT1 potential enzymatic and non-enzymatic roles and the current efforts in developing ATAT1 inhibitors.
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Affiliation(s)
- Angela Iuzzolino
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council of Italy, Via degli Apuli 4, Rome, 00185, Italy
| | - Francesca Romana Pellegrini
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council of Italy, Via degli Apuli 4, Rome, 00185, Italy
| | - Dante Rotili
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, 00185, Italy
| | - Francesca Degrassi
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council of Italy, Via degli Apuli 4, Rome, 00185, Italy.
| | - Daniela Trisciuoglio
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council of Italy, Via degli Apuli 4, Rome, 00185, Italy.
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6
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Wang Y, Li Y, Jing Y, Yang Y, Wang H, Ismtula D, Guo C. Tubulin alpha-1b chain was identified as a prognosis and immune biomarker in pan-cancer combing with experimental validation in breast cancer. Sci Rep 2024; 14:8201. [PMID: 38589634 PMCID: PMC11001892 DOI: 10.1038/s41598-024-58982-z] [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: 01/18/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024] Open
Abstract
The α-tubulin subtype, Tubulin α-1b chain (TUBA1B), has been shown to influence immune cell infiltration, cancer growth, and survival across various malignancies. However, a comprehensive study has not yet been undertaken examining the immunological and predictive effects of TUBA1B in a pan-carcinoma context. Using data from TCGA, GEO, and other databases, we analyzed TUBA1B expression across various carcinoma types using transcriptional profiling, prognostic implications, genetic and epigenetic alterations, methylation patterns, and immunological significance. To validate our findings, we conducted Western blot analysis to assess TUBA1B protein levels in matched breast cancer tissue samples and performed CCK-8 proliferation assay, flow cytometry, transwell invasion, and migration assays to comprehensively examine the functional impact of TUBA1B on breast cancer cells. Our pan-cancer analysis found TUBA1B upregulation across most tumor types, with varying expression patterns in distinct immune and molecular subtypes. High TUBA1B expression was an independent risk factor and associated with poor prognoses in several cancers, including BRCA, KICH, LGG, LUAD, and MESO. TUBA1B also demonstrates moderate to high diagnostic accuracy in most tumor types. Increased m6A methylation levels were observed in the TUBA1B gene, while its promoter region displayed low methylation levels. TUBA1B's expression impacted some cancers by elevating tumor mutation burden, microsatellite instability, neoantigen formation, immune cell infiltration, and the modulation of immune checkpoints. Functional enrichment analysis highlights TUBA1B's involvement in important cellular processes such as the cell cycle, p53 signaling, cell senescence, programmed cell death, and the regulation of immune-related pathways. Moreover, our study reveals higher TUBA1B protein expression in breast cancer tissues compared to adjacent tissues. In vitro experiments confirm that TUBA1B deletion reduces breast cancer cell proliferation, invasion, and migration while increasing apoptosis. In conclusion, our study suggests that TUBA1B could potentially serve as a diagnostic marker for predicting cancer immunological profiles and survival outcomes and shed light on the expression and role of TUBA1B in breast cancer, providing a solid foundation for considering it as a promising therapeutic target for breast cancer patient treatment.
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Affiliation(s)
- Yiyang Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yongxiang Li
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yubo Jing
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yuqi Yang
- The First Clinical Medical College of Xinjiang Medical University, Urumqi, 830054, China
| | - Haiyan Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Dilimulati Ismtula
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Chenming Guo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China.
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7
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Mostert D, Bubeneck WA, Rauh T, Kielkowski P, Itzen A, Jung K, Sieber SA. Pronucleotide Probes Reveal a Diverging Specificity for AMPylation vs UMPylation of Human and Bacterial Nucleotide Transferases. Biochemistry 2024; 63:651-659. [PMID: 38388156 PMCID: PMC10918828 DOI: 10.1021/acs.biochem.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
AMPylation is a post-translational modification utilized by human and bacterial cells to modulate the activity and function of specific proteins. Major AMPylators such as human FICD and bacterial VopS have been studied extensively for their substrate and target scope in vitro. Recently, an AMP pronucleotide probe also facilitated the in situ analysis of AMPylation in living cells. Based on this technology, we here introduce a novel UMP pronucleotide probe and utilize it to profile uninfected and Vibrio parahaemolyticus infected human cells. Mass spectrometric analysis of labeled protein targets reveals an unexpected promiscuity of human nucleotide transferases with an almost identical target set of AMP- and UMPylated proteins. Vice versa, studies in cells infected by V. parahaemolyticus and its effector VopS revealed solely AMPylation of host enzymes, highlighting a so far unknown specificity of this transferase for ATP. Taken together, pronucleotide probes provide an unprecedented insight into the in situ activity profile of crucial nucleotide transferases, which can largely differ from their in vitro activity.
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Affiliation(s)
- Dietrich Mostert
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Wilhelm Andrei Bubeneck
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Theresa Rauh
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Pavel Kielkowski
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, 81377 München, Germany
| | - Aymelt Itzen
- Department
of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Kirsten Jung
- Department
of Biology I, Microbiology, Ludwig-Maximilians-Universität
München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
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8
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Romeiro Motta M, Biswas S, Schaedel L. Beyond uniformity: Exploring the heterogeneous and dynamic nature of the microtubule lattice. Eur J Cell Biol 2023; 102:151370. [PMID: 37922811 DOI: 10.1016/j.ejcb.2023.151370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
A fair amount of research on microtubules since their discovery in 1963 has focused on their dynamic tips. In contrast, the microtubule lattice was long believed to be highly regular and static, and consequently received far less attention. Yet, as it turned out, the microtubule lattice is neither as regular, nor as static as previously believed: structural studies uncovered the remarkable wealth of different conformations the lattice can accommodate. In the last decade, the microtubule lattice was shown to be labile and to spontaneously undergo renovation, a phenomenon that is intimately linked to structural defects and was called "microtubule self-repair". Following this breakthrough discovery, further recent research provided a deeper understanding of the lattice self-repair mechanism, which we review here. Instrumental to these discoveries were in vitro microtubule reconstitution assays, in which microtubules are grown from the minimal components required for their dynamics. In this review, we propose a shift from the term "lattice self-repair" to "lattice dynamics", since this phenomenon is an inherent property of microtubules and can happen without microtubule damage. We focus on how in vitro microtubule reconstitution assays helped us learn (1) which types of structural variations microtubules display, (2) how these structural variations influence lattice dynamics and microtubule damage caused by mechanical stress, (3) how lattice dynamics impact tip dynamics, and (4) how microtubule-associated proteins (MAPs) can play a role in structuring the lattice. Finally, we discuss the unanswered questions about lattice dynamics and how technical advances will help us tackle these questions.
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Affiliation(s)
- Mariana Romeiro Motta
- Department of Physics, Center for Biophysics, Campus A2 4, Saarland University, 66123 Saarbrücken, Germany; Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École normale supérieure de Lyon, Lyon 69364, France
| | - Subham Biswas
- Department of Physics, Center for Biophysics, Campus A2 4, Saarland University, 66123 Saarbrücken, Germany
| | - Laura Schaedel
- Department of Physics, Center for Biophysics, Campus A2 4, Saarland University, 66123 Saarbrücken, Germany.
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9
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Liu W, Fu Y, Wang M, Zhao J, Chen J, Wang Y, Qin H. A preliminary study on the mechanism of VASH2 in childhood medulloblastoma. Sci Rep 2023; 13:17153. [PMID: 37821528 PMCID: PMC10567924 DOI: 10.1038/s41598-023-42869-6] [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: 12/31/2022] [Accepted: 09/15/2023] [Indexed: 10/13/2023] Open
Abstract
To study the differences in VASH2 expression in pediatric medulloblastoma (MB) tumor tissues of different molecular subtypes, to analyze the correlation between VASH2 and the molecular subtypes of medulloblastoma, clinicopathological data, and prognosis, and to explore the specific mechanism of VASH2's role in SHH medulloblastoma cell lines DAOY. We analyzed 47 pediatric medulloblastoma cases admitted to the Department of Pediatric Neurosurgery of the First Affiliated Hospital of Xinjiang Medical University from January 2011 to December 2019, and the expression levels of YAP1 and GAB1 in these tumor tissues were detected by immunohistochemistry (IHC) and molecularly typed (WNT-type, SHH-type, and non-WNT/SHH-type). The correlation between VASH2 and molecular typing of medulloblastoma was analyzed. We also analyzed the medulloblastoma dataset in the GEO database (GSE30074 and GSE202043) to explore the correlation between VASH2 and the prognosis of medulloblastoma patients, as well as performed a comprehensive GO enrichment analysis specifically for the VASH2 gene to reveal the underlying biological pathways of its complex molecular profile. We used vasopressin 2 (VASH2) as a research target and overexpressed and knocked down VASH2 in SHH medulloblastoma cell lines DAOY by lentiviral vectors in vitro, respectively, to investigate its role in SHH medulloblastoma cell lines DAOY cell proliferation, apoptosis, migration, invasion and biological roles in the cell cycle. (1) Among 47 pediatric medulloblastoma cases, 8 were WNT type, 29 were SHH type, and 10 were non-WNT/SHH type. the positive rate of VASH2 was highest in the SHH type with a 68.97% positive rate, followed by non-WNT/SHH and lowest in the WNT type. The results of the multifactorial analysis showed that positive expression of VASH2 was associated with medulloblastoma molecular subtype (SHH type), site of tumor development (four ventricles), and gender (male), P < 0.05. (2) The results of cellular experiments showed that overexpression of VASH2 increased the invasion and migration ability of medulloblast Daoy, while knockdown of VASH2 inhibited the invasion and Overexpression of VASH2 upregulated the expression of Smad2 + 3, Smad4, Mmp2 and the apoptotic indicators Bcl-2 and Caspase3, while knockdown of VASH2 suppressed the expression of Smad2 + 3 and Mmp2, and silenced the expression of Smad4 and the apoptotic indicators Bcl2, Caspase3 expression. Flow cytometric cycle analysis showed that VASH2 overexpression increased the S phase in the Daoy cell cycle, while VASH2 knockdown decreased the S phase in the SHH medulloblastoma cell lines DAOY cell cycle. Bioinformatics analysis showed that there was no statistically significant difference between the expression of VASH2 genes in the GSE30074 and GSE202043 datasets and the prognosis of the patients, but the results of this dataset analysis suggested that we need to continue to expand the sample size of the study in the future. The results of the GO enrichment analysis showed that the angiogenic pathway was the most significantly enriched, and the PPI interactions network of VASH2 was obtained from the STRING database. Using the STRING database, we obtained the PPI interaction network of VASH2, and the KEGG enrichment analysis of VASH2-related genes showed that VASH2-related genes were related to the apoptosis pathway, and therefore it was inferred that VASH2 also affects the development of tumors through apoptosis. We found for the first time that the positive expression rate of VASH2 was closely associated with SHH-type pediatric medulloblastoma and that VASH2 was involved in the invasion, migration, cell cycle, and apoptotic capacity of SHH medulloblastoma cell lines DAOY by affecting downstream indicators of the TGF-β pathway. This suggests that it is involved in the progression of pediatric medulloblastoma, and VASH2 is expected to be a diagnostic and therapeutic target for SHH-type pediatric medulloblastoma.
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Affiliation(s)
- Wen Liu
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yinan Fu
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Meng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Junhong Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Julin Chen
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yongxin Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
- Xinjiang Institute of Neurosurgery, Urumqi, China.
| | - Hu Qin
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
- Xinjiang Institute of Neurosurgery, Urumqi, China.
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10
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Amiri A, Dietz C, Rapp A, Cardoso MC, Stark RW. The cyto-linker and scaffolding protein "plectin" mis-localization leads to softening of cancer cells. NANOSCALE 2023; 15:15008-15026. [PMID: 37668423 DOI: 10.1039/d3nr02226a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Discovering tools to prevent cancer progression requires understanding the fundamental differences between normal and cancer cells. More than a decade ago, atomic force microscopy (AFM) revealed cancer cells' softer body compared to their healthy counterparts. Here, we investigated the mechanism underlying the softening of cancerous cells in comparison with their healthy counterparts based on AFM high resolution stiffness tomography and 3D confocal microscopy. We showed microtubules (MTs) network in invasive ductal carcinoma cell cytoskeleton is basally located and segmented for around 400 nm from the cell periphery. Additionally, the cytoskeleton scaffolding protein plectin exhibits a mis-localization from the cytoplasm to the surface of cells in the carcinoma which justifies the dissociation of the MT network from the cell's cortex. Furthermore, the assessment of MTs' persistence length using a worm-like-chain (WLC) model in high resolution AFM images showed lower persistence length of the single MTs in ductal carcinoma compared to that in the normal state. Overall, these tuned mechanics support the invasive cells to ascertain more flexibility under compressive forces in small deformations. These data provide new insights into the structural origins of cancer aids in progression.
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Affiliation(s)
- Anahid Amiri
- Physics of Surfaces, Institute of Materials Science, Technical University of Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany.
| | - Christian Dietz
- Physics of Surfaces, Institute of Materials Science, Technical University of Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany.
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Robert W Stark
- Physics of Surfaces, Institute of Materials Science, Technical University of Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany.
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11
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Cabrera-Rodríguez R, Pérez-Yanes S, Lorenzo-Sánchez I, Trujillo-González R, Estévez-Herrera J, García-Luis J, Valenzuela-Fernández A. HIV Infection: Shaping the Complex, Dynamic, and Interconnected Network of the Cytoskeleton. Int J Mol Sci 2023; 24:13104. [PMID: 37685911 PMCID: PMC10487602 DOI: 10.3390/ijms241713104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
HIV-1 has evolved a plethora of strategies to overcome the cytoskeletal barrier (i.e., actin and intermediate filaments (AFs and IFs) and microtubules (MTs)) to achieve the viral cycle. HIV-1 modifies cytoskeletal organization and dynamics by acting on associated adaptors and molecular motors to productively fuse, enter, and infect cells and then traffic to the cell surface, where virions assemble and are released to spread infection. The HIV-1 envelope (Env) initiates the cycle by binding to and signaling through its main cell surface receptors (CD4/CCR5/CXCR4) to shape the cytoskeleton for fusion pore formation, which permits viral core entry. Then, the HIV-1 capsid is transported to the nucleus associated with cytoskeleton tracks under the control of specific adaptors/molecular motors, as well as HIV-1 accessory proteins. Furthermore, HIV-1 drives the late stages of the viral cycle by regulating cytoskeleton dynamics to assure viral Pr55Gag expression and transport to the cell surface, where it assembles and buds to mature infectious virions. In this review, we therefore analyze how HIV-1 generates a cell-permissive state to infection by regulating the cytoskeleton and associated factors. Likewise, we discuss the relevance of this knowledge to understand HIV-1 infection and pathogenesis in patients and to develop therapeutic strategies to battle HIV-1.
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Affiliation(s)
- Romina Cabrera-Rodríguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Silvia Pérez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Iria Lorenzo-Sánchez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
- Analysis Department, Faculty of Mathematics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain
| | - Judith Estévez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Jonay García-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
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12
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Mill P, Christensen ST, Pedersen LB. Primary cilia as dynamic and diverse signalling hubs in development and disease. Nat Rev Genet 2023; 24:421-441. [PMID: 37072495 PMCID: PMC7615029 DOI: 10.1038/s41576-023-00587-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/20/2023]
Abstract
Primary cilia, antenna-like sensory organelles protruding from the surface of most vertebrate cell types, are essential for regulating signalling pathways during development and adult homeostasis. Mutations in genes affecting cilia cause an overlapping spectrum of >30 human diseases and syndromes, the ciliopathies. Given the immense structural and functional diversity of the mammalian cilia repertoire, there is a growing disconnect between patient genotype and associated phenotypes, with variable severity and expressivity characteristic of the ciliopathies as a group. Recent technological developments are rapidly advancing our understanding of the complex mechanisms that control biogenesis and function of primary cilia across a range of cell types and are starting to tackle this diversity. Here, we examine the structural and functional diversity of primary cilia, their dynamic regulation in different cellular and developmental contexts and their disruption in disease.
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Affiliation(s)
- Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | | | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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13
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Shen Y, Ori-McKenney KM. Macromolecular Crowding Tailors the Microtubule Cytoskeleton Through Tubulin Modifications and Microtubule-Associated Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544846. [PMID: 37398431 PMCID: PMC10312695 DOI: 10.1101/2023.06.14.544846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live cell imaging, ex vivo enzymatic assays, and in vitro reconstitution, we probe the impact of acute perturbations in cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs), unraveling the molecular underpinnings of cellular adaptation via the microtubule cytoskeleton. We find that cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association, without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification, and find that MAP7 promotes acetylation by biasing the conformation of the microtubule lattice, and directly inhibits detyrosination. Acetylation and detyrosination can therefore be decoupled and utilized for distinct cellular purposes. Our data reveal that the MAP code dictates the tubulin code, resulting in remodeling of the microtubule cytoskeleton and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
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Affiliation(s)
- Yusheng Shen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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14
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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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15
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Akera T. Tubulin post-translational modifications in meiosis. Semin Cell Dev Biol 2023; 137:38-45. [PMID: 34836784 PMCID: PMC9124733 DOI: 10.1016/j.semcdb.2021.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/22/2021] [Accepted: 11/14/2021] [Indexed: 11/18/2022]
Abstract
Haploid gametes are produced from diploid parents through meiosis, a process inherent to all sexually reproducing eukaryotes. Faithful chromosome segregation in meiosis is essential for reproductive success, although it is less clear how the meiotic spindle achieves this compared to the mitotic spindle. It is becoming increasingly clear that tubulin post-translational modifications (PTMs) play critical roles in regulating microtubule functions in many biological processes, and meiosis is no exception. Here, I review recent advances in the understanding of tubulin PTMs in meiotic spindles, especially focusing on their roles in spindle integrity, oocyte aging, and non-Mendelian transmission.
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Affiliation(s)
- Takashi Akera
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, MD, USA.
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16
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Song DH, Song CW, Chung J, Jang EH, Kim H, Hur Y, Hur EM, Kim D, Chang JB. In situ silver nanoparticle development for molecular-specific biological imaging via highly accessible microscopies. NANOSCALE ADVANCES 2023; 5:1636-1650. [PMID: 36926569 PMCID: PMC10012848 DOI: 10.1039/d2na00449f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
In biological studies and diagnoses, brightfield (BF), fluorescence, and electron microscopy (EM) are used to image biomolecules inside cells. When compared, their relative advantages and disadvantages are obvious. BF microscopy is the most accessible of the three, but its resolution is limited to a few microns. EM provides a nanoscale resolution, but sample preparation is time-consuming. In this study, we present a new imaging technique, which we termed decoration microscopy (DecoM), and quantitative investigations to address the aforementioned issues in EM and BF microscopy. For molecular-specific EM imaging, DecoM labels proteins inside cells using antibodies bearing 1.4 nm gold nanoparticles (AuNPs) and grows silver layers on the AuNPs' surfaces. The cells are then dried without buffer exchange and imaged using scanning electron microscopy (SEM). Structures labeled with silver-grown AuNPs are clearly visible on SEM, even they are covered with lipid membranes. Using stochastic optical reconstruction microscopy, we show that the drying process causes negligible distortion of structures and that less structural deformation could be achieved through simple buffer exchange to hexamethyldisilazane. Using DecoM, we visualize the nanoscale alterations in microtubules by microtubule-severing proteins that cannot be observed with diffraction-limited fluorescence microscopy. We then combine DecoM with expansion microscopy to enable sub-micron resolution BF microscopy imaging. We first show that silver-grown AuNPs strongly absorb white light, and the structures labeled with them are clearly visible on BF microscopy. We then show that the application of AuNPs and silver development must follow expansion to visualize the labeled proteins clearly with sub-micron resolution.
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Affiliation(s)
- Dae-Hyeon Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Chang Woo Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | | | - Eun-Hae Jang
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Yongsuk Hur
- BioMedical Research Center, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Eun-Mi Hur
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
- BK21 Four Future Veterinary Medicine Leading Education & Research Center, Seoul National University Seoul Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University Seoul Korea
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
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17
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Niu X, Mao CX, Wang S, Wang X, Zhang Y, Hu J, Bi R, Liu Z, Shan J. α-Tubulin acetylation at lysine 40 regulates dendritic arborization and larval locomotion by promoting microtubule stability in Drosophila. PLoS One 2023; 18:e0280573. [PMID: 36827311 PMCID: PMC9955671 DOI: 10.1371/journal.pone.0280573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 01/03/2023] [Indexed: 02/25/2023] Open
Abstract
Posttranslational modification of tubulin increases the dynamic complexity and functional diversity of microtubules. Acetylation of α-tubulin at Lys-40 is a highly conserved posttranslational modification that has been shown to improve the flexibility and resilience of microtubules. Here we studied the in vivo functions of α-tubulin acetylation by knocking-out Atat, the Drosophila α-tubulin acetyltransferase, and by mutating Lys-40 to Arg in α1-tubulin. We found a reduction in the dendritic arborization of larval class I dendritic arborization (da) neurons in both mutants. The dendritic developmental defects in atat mutants could be reversed by enhancing the stability of microtubules either through knocking down the microtubule severing protein Katanin 60 or through overexpressing tubulin-specific chaperone E, suggesting that α-tubulin deacetylation impairsed dendritic morphology by decreasing the stability of microtubules. Using time-lapse recordings, we found that atat and α1-tubulinK40R mutations dramatically increased the number of dendritic protrusions that were likely to be immature dendritic precursors. Finally, we showed that both Atat and α-tubulin acetylation were required in class I da neurons to control larval locomotion. These findings add novel insight into the current knowledge of the role of α-tubulin acetylation in regulating neuronal development and functions.
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Affiliation(s)
- Xiaoxiao Niu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Chuan-Xi Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Shan Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Xiongxiong Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Youyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Juncheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Ran Bi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Zhihua Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
- * E-mail: (SJ); (ZL)
| | - Jin Shan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
- * E-mail: (SJ); (ZL)
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18
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van den Berg CM, Volkov VA, Schnorrenberg S, Huang Z, Stecker KE, Grigoriev I, Gilani S, Frikstad KAM, Patzke S, Zimmermann T, Dogterom M, Akhmanova A. CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side. J Cell Biol 2023; 222:213861. [PMID: 36752787 PMCID: PMC9948759 DOI: 10.1083/jcb.202208062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/14/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling the formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates the elongation and stability of ciliary axonemes and other microtubule-based structures.
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Affiliation(s)
- Cyntha M. van den Berg
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Vladimir A. Volkov
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands,https://ror.org/02e2c7k09Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Ziqiang Huang
- EMBL Imaging Centre, EMBL-Heidelberg, Heidelberg, Germany
| | - Kelly E. Stecker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Ilya Grigoriev
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Sania Gilani
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Department of Molecular Cell Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kari-Anne M. Frikstad
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sebastian Patzke
- https://ror.org/00j9c2840Department of Radiation Biology, Institute of Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Marileen Dogterom
- https://ror.org/02e2c7k09Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Anna Akhmanova
- https://ror.org/04pp8hn57Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands,Correspondence to Anna Akhmanova:
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19
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Lopes D, Seabra AL, Orr B, Maiato H. α-Tubulin detyrosination links the suppression of MCAK activity with taxol cytotoxicity. J Cell Biol 2023; 222:213730. [PMID: 36459065 PMCID: PMC9723805 DOI: 10.1083/jcb.202205092] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
α/β-Tubulin posttranslational modifications (PTMs) generate microtubule diversity, but whether they account for cancer cell resistance to microtubule-targeting drugs remains unknown. Here, we performed a pilot dissection of the "cancer tubulin code" using the NCI-60 cancer cell panel. We found that acetylated, detyrosinated, and ∆2-α-tubulin that typically accumulate on stable microtubules were uncoupled in many cancer cells. Acetylated α-tubulin did not affect microtubule dynamics, whereas its levels correlated with, but were not required for, taxol-induced cytotoxicity. In contrast, experimental increase of α-tubulin detyrosination, and/or depletion of the detyrosination-sensitive microtubule-depolymerizing enzyme MCAK, enhanced taxol-induced cytotoxicity by promoting cell death in mitosis and the subsequent interphase, without causing a cumulative effect. Interestingly, only increased detyrosinated α-tubulin aggravated taxol-induced spindle multipolarity. Overall, we identified high α-tubulin acetylation as a potential biomarker for cancer cell response to taxol and uncovered a mechanistic link between α-tubulin detyrosination and the suppression of MCAK activity in taxol-induced cytotoxicity, likely by promoting chromosome missegregation, regardless of spindle defects.
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Affiliation(s)
- Danilo Lopes
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandre L Seabra
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Bernardo Orr
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Helder Maiato
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Cell Division Group, Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
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20
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Zocchi R, Compagnucci C, Bertini E, Sferra A. Deciphering the Tubulin Language: Molecular Determinants and Readout Mechanisms of the Tubulin Code in Neurons. Int J Mol Sci 2023; 24:ijms24032781. [PMID: 36769099 PMCID: PMC9917122 DOI: 10.3390/ijms24032781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Microtubules (MTs) are dynamic components of the cell cytoskeleton involved in several cellular functions, such as structural support, migration and intracellular trafficking. Despite their high similarity, MTs have functional heterogeneity that is generated by the incorporation into the MT lattice of different tubulin gene products and by their post-translational modifications (PTMs). Such regulations, besides modulating the tubulin composition of MTs, create on their surface a "biochemical code" that is translated, through the action of protein effectors, into specific MT-based functions. This code, known as "tubulin code", plays an important role in neuronal cells, whose highly specialized morphologies and activities depend on the correct functioning of the MT cytoskeleton and on its interplay with a myriad of MT-interacting proteins. In recent years, a growing number of mutations in genes encoding for tubulins, MT-interacting proteins and enzymes that post-translationally modify MTs, which are the main players of the tubulin code, have been linked to neurodegenerative processes or abnormalities in neural migration, differentiation and connectivity. Nevertheless, the exact molecular mechanisms through which the cell writes and, downstream, MT-interacting proteins decipher the tubulin code are still largely uncharted. The purpose of this review is to describe the molecular determinants and the readout mechanisms of the tubulin code, and briefly elucidate how they coordinate MT behavior during critical neuronal events, such as neuron migration, maturation and axonal transport.
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Affiliation(s)
- Riccardo Zocchi
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Bambino Gesù Children’s Research Hospital, IRCCS, 00146 Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
| | - Antonella Sferra
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
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21
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Pero ME, Chowdhury F, Bartolini F. Role of tubulin post-translational modifications in peripheral neuropathy. Exp Neurol 2023; 360:114274. [PMID: 36379274 DOI: 10.1016/j.expneurol.2022.114274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
Abstract
Peripheral neuropathy is a common disorder that results from nerve damage in the periphery. The degeneration of sensory axon terminals leads to changes or loss of sensory functions, often manifesting as debilitating pain, weakness, numbness, tingling, and disability. The pathogenesis of most peripheral neuropathies remains to be fully elucidated. Cumulative evidence from both early and recent studies indicates that tubulin damage may provide a common underlying mechanism of axonal injury in various peripheral neuropathies. In particular, tubulin post-translational modifications have been recently implicated in both toxic and inherited forms of peripheral neuropathy through regulation of axonal transport and mitochondria dynamics. This knowledge forms a new area of investigation with the potential for developing therapeutic strategies to prevent or delay peripheral neuropathy by restoring tubulin homeostasis.
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Affiliation(s)
- Maria Elena Pero
- Department of Pathology and Cell Biology, Columbia University, New York, USA; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Italy
| | - Farihah Chowdhury
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, USA.
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22
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Altered Posttranslational Modification of Microtubules Contributes to Disturbed Enterocyte Morphology in Celiac Disease. Int J Mol Sci 2023; 24:ijms24032635. [PMID: 36768957 PMCID: PMC9917072 DOI: 10.3390/ijms24032635] [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: 10/11/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Celiac disease (CD) represents a frequent autoimmune disease triggered by the ingestion of gliadin in genetically predisposed individuals. The alteration of enterocytes and brush border membrane morphology have been repetitively demonstrated, but the underlying mechanisms remain unclear. Microtubules represent a major element of the cytoskeleton and exert multiple functions depending on their tyrosination status. The aim of our study was to investigate whether posttranslational modification of microtubules was altered in the context of CD and whether this mechanism contributed to morphological changes of CD enterocytes. We examined the expression of tubulin tyrosine ligase (TTL) and vasohibin-2 (VASH2) and the level of detyrosinated and acetylated tubulin in duodenal biopsies and Caco-2 cells by immunoblot and immunofluorescence microcopy. Electron microscopy was performed to investigate the subcellular distribution of detyrosinated tubulin and brush border membrane architecture in CD biopsies and Madin-Darby Canine Kidney type II (MDCK) cells lacking TTL. CD enterocytes and Caco-2 cells stimulated with digested gliadin or IFN-y displayed a flattened cell morphology. This disturbed cellular architecture was accompanied by an increased amount of detyrosinated and acetylated tubulin and corresponding high expression of VASH2 and low expression of TTL. The altered posttranslational modification of tubulin was reversible after the introduction of the gluten-free diet. CD enterocytes and MDCK cells deficient in TTL displayed a reduced cell height along with an increased cell width and a reduced number of apical microvilli. Our results provide a functional explanation for the observed morphological alterations of the enterocytes observed in CD and provide diagnostic potential of the tyrosination status of microtubules as an early marker of villous atrophy and CD inflammation.
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23
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Mehta V, Decan N, Ooi S, Gaudreau-Lapierre A, Copeland JW, Trinkle-Mulcahy L. SPECC1L binds the myosin phosphatase complex MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin. J Biol Chem 2023; 299:102893. [PMID: 36634848 PMCID: PMC9929477 DOI: 10.1016/j.jbc.2023.102893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
The subcellular localization, activity , and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit (PP1cat) is mediated through its dynamic association with regulatory subunits in holoenzyme complexes. While some functional overlap is observed for the three human PP1cat isoforms, they also show distinct targeting based on relative preferences for specific regulatory subunits. A well-known example is the preferential association of MYPT1 with PP1β in the myosin phosphatase complex. In smooth muscle, MYPT1/PP1β counteracts the muscle contraction induced by phosphorylation of the light chains of myosin by the myosin light chain kinase. This phosphatase complex is also found in nonmuscle cells, where it is targeted to both myosin and nonmyosin substrates and contributes to regulation of the balance of cytoskeletal structure and motility during cell migration and division. Although it remains unclear how MYPT1/PP1β traffics between microtubule- and actin-associated substrates, our identification of the microtubule- and actin-binding protein SPECC1L in both the PP1β and MYPT1 interactomes suggests that it is the missing link. Our validation of their association using coimmunoprecipitation and proximity biotinylation assays, together with the strong overlap that we observed for the SPECC1L and MYPT1 interactomes, confirmed that they exist in a stable complex in the cell. We further showed that SPECC1L binds MYPT1 directly and that it can impact the balance of the distribution of the MYPT1/PP1β complex between the microtubule and filamentous actin networks.
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Affiliation(s)
- Virja Mehta
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Nathalie Decan
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Sarah Ooi
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - John W. Copeland
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada.
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24
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Fang CT, Kuo HH, Amartuvshin O, Hsu HJ, Liu SL, Yao JS, Yih LH. Inhibition of acetyl-CoA carboxylase impaired tubulin palmitoylation and induced spindle abnormalities. Cell Death Dis 2023; 9:4. [PMID: 36617578 PMCID: PMC9826786 DOI: 10.1038/s41420-023-01301-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023]
Abstract
Tubulin s-palmitoylation involves the thioesterification of a cysteine residue in tubulin with palmitate. The palmitate moiety is produced by the fatty acid synthesis pathway, which is rate-limited by acetyl-CoA carboxylase (ACC). While it is known that ACC is phosphorylated at serine 79 (pSer79) by AMPK and accumulates at the spindle pole (SP) during mitosis, a functional role for tubulin palmitoylation during mitosis has not been identified. In this study, we found that modulating pSer79-ACC level at the SP using AMPK agonist and inhibitor induced spindle defects. Loss of ACC function induced spindle abnormalities in cell lines and in germ cells of the Drosophila germarium, and palmitic acid (PA) rescued the spindle defects in the cell line treated transiently with the ACC inhibitor, TOFA. Furthermore, inhibition of protein palmitoylating or depalmitoylating enzymes also induced spindle defects. Together, these data suggested that precisely regulated cellular palmitate level and protein palmitoylation may be required for accurate spindle assembly. We then showed that tubulin was largely palmitoylated in interphase cells but less palmitoylated in mitotic cells. TOFA treatment diminished tubulin palmitoylation at doses that disrupt microtubule (MT) instability and cause spindle defects. Moreover, spindle MTs comprised of α-tubulins mutated at the reported palmitoylation site exhibited disrupted dynamic instability. We also found that TOFA enhanced the MT-targeting drug-induced spindle abnormalities and cytotoxicity. Thus, our study reveals that precise regulation of ACC during mitosis impacts tubulin palmitoylation to delicately control MT dynamic instability and spindle assembly, thereby safeguarding nuclear and cell division.
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Affiliation(s)
- Chieh-Ting Fang
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Hui Kuo
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Oyundari Amartuvshin
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan ,grid.28665.3f0000 0001 2287 1366Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.260565.20000 0004 0634 0356Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
| | - Hwei-Jan Hsu
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan ,grid.28665.3f0000 0001 2287 1366Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.260565.20000 0004 0634 0356Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
| | - Sih-Long Liu
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jhong-Syuan Yao
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ling-Huei Yih
- grid.506933.a0000 0004 0633 7835Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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25
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Actin-microtubule cytoskeletal interplay mediated by MRTF-A/SRF signaling promotes dilated cardiomyopathy caused by LMNA mutations. Nat Commun 2022; 13:7886. [PMID: 36550158 PMCID: PMC9780334 DOI: 10.1038/s41467-022-35639-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in the lamin A/C gene (LMNA) cause dilated cardiomyopathy associated with increased activity of ERK1/2 in the heart. We recently showed that ERK1/2 phosphorylates cofilin-1 on threonine 25 (phospho(T25)-cofilin-1) that in turn disassembles the actin cytoskeleton. Here, we show that in muscle cells carrying a cardiomyopathy-causing LMNA mutation, phospho(T25)-cofilin-1 binds to myocardin-related transcription factor A (MRTF-A) in the cytoplasm, thus preventing the stimulation of serum response factor (SRF) in the nucleus. Inhibiting the MRTF-A/SRF axis leads to decreased α-tubulin acetylation by reducing the expression of ATAT1 gene encoding α-tubulin acetyltransferase 1. Hence, tubulin acetylation is decreased in cardiomyocytes derived from male patients with LMNA mutations and in heart and isolated cardiomyocytes from Lmnap.H222P/H222P male mice. In Atat1 knockout mice, deficient for acetylated α-tubulin, we observe left ventricular dilation and mislocalization of Connexin 43 (Cx43) in heart. Increasing α-tubulin acetylation levels in Lmnap.H222P/H222P mice with tubastatin A treatment restores the proper localization of Cx43 and improves cardiac function. In summary, we show for the first time an actin-microtubule cytoskeletal interplay mediated by cofilin-1 and MRTF-A/SRF, promoting the dilated cardiomyopathy caused by LMNA mutations. Our findings suggest that modulating α-tubulin acetylation levels is a feasible strategy for improving cardiac function.
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26
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Kim ME, Kim DH, Lee JS. Transcription Factors as Targets of Natural Compounds in Age-Related Diseases and Cancer: Potential Therapeutic Applications. Int J Mol Sci 2022; 23:ijms232213882. [PMID: 36430361 PMCID: PMC9696520 DOI: 10.3390/ijms232213882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Inflammation exacerbates systemic pathophysiological conditions and chronic inflammation is a sustained and systemic phenomenon that aggravates aging that can lead to chronic age-related diseases. These inflammatory phenomena have recently been redefined and delineated at the molecular, cellular, and systemic levels. Many transcription factors that are activated in response to tumor metabolic state have been reported to be regulated by a class of histone deacetylase called sirtuins (SIRTs). Sirtuins play a pivotal role in the regulation of tumor cell metabolism, proliferation, and angiogenesis, including oxidative stress and inflammation. The SIRT1-mediated signaling pathway in diabetes and cancer is the SIRT1/forkhead-box class O (FoxO)/nuclear factor-kappa B (NF-κB) pathway. In this review, we describe the accumulation of SIRT1-, NF-κB-, and FoxO-mediated inflammatory processes and cellular proinflammatory signaling pathways. We also describe the proinflammatory mechanisms underlying metabolic molecular pathways in various diseases such as liver cancer and diabetes. Finally, the regulation of cancer and diabetes through the anti-inflammatory effects of natural compounds is highlighted. Evidence from inflammation studies strongly suggests that cells may be a major source of cytokines secreted during various diseases. A better understanding of the mechanisms that underpin the inflammatory response and palliative role of natural compounds will provide insights into the molecular mechanisms of inflammation and various diseases for potential intervention.
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Affiliation(s)
- Mi Eun Kim
- Department of Life Science, Immunology Research Lab, BK21-plus Research Team for Bioactive Control Technology, College of Natural Sciences, Chosun University, Dong-gu, Gwangju 61452, Korea
| | - Dae Hyun Kim
- Department of Life Science, Immunology Research Lab, BK21-plus Research Team for Bioactive Control Technology, College of Natural Sciences, Chosun University, Dong-gu, Gwangju 61452, Korea
- Correspondence: (D.H.K.); (J.S.L.); Tel.: +82-062-230-6651 (J.S.L.)
| | - Jun Sik Lee
- Department of Life Science, Immunology Research Lab, BK21-plus Research Team for Bioactive Control Technology, College of Natural Sciences, Chosun University, Dong-gu, Gwangju 61452, Korea
- LKBio Inc., Chosun University Business Incubator (CUBI) Building, Dong-gu, Gwangju 61452, Korea
- Correspondence: (D.H.K.); (J.S.L.); Tel.: +82-062-230-6651 (J.S.L.)
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27
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Sidorova-Darmos E, Fallah MS, Logan R, Lin CY, Eubanks JH. Mitochondrial brain proteome acetylation levels and behavioural responsiveness to amphetamine are altered in mice lacking Sirt3. Front Physiol 2022; 13:948387. [PMID: 36148309 PMCID: PMC9489219 DOI: 10.3389/fphys.2022.948387] [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: 05/19/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Post-translational modification of mitochondrial proteins represents one mechanism by which the functional activity of mitochondria can be regulated. In the brain, these modifications can influence the functional properties of different neural circuitries. Given that the sirtuin family member Sirt3 represents the primary protein deacetylase enzyme in mitochondria, we tested whether brain mitochondrial proteome acetylation would increase in male or female mice lacking Sirt3. Our results confirm that whole brain mitochondrial proteome acetylation levels are indeed elevated in both sexes of Sirt3-KO mice relative to controls. Consistently, we found the mitochondria of mouse embryonic fibroblast (MEF) cells derived from Sirt3-KO mice were smaller in size, and fewer in number than in wild-type MEFs, and that mitochondrial free calcium levels were elevated within the mitochondria of these cells. As protein acetylation can influence mitochondrial function, and changes in mitochondrial function have been linked to alterations in neural circuit function regulating motor activity and anxiety-like behavior, we tested whether Sirt3-deficient mice would display sensitized responsiveness to the stimulant amphetamine. Both male and female Sirt3-KO mice displayed hyper-locomotion and attenuated anxiety-like behavior in response to a dose of amphetamine that was insufficient to promote any behavioural responses in wild-type mice. Collectively, these results confirm that Sirt3 regulates mitochondrial proteome acetylation levels in brain tissue, and that the absence of Sirt3 increases the sensitivity of neural systems to amphetamine-induced behavioural responses.
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Affiliation(s)
- Elena Sidorova-Darmos
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Merrick S. Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Richard Logan
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
| | - Cheng Yu Lin
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
| | - James H. Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
- Department of Surgery (Neurosurgery), University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- *Correspondence: James H. Eubanks,
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28
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Samur MB, Ercan-Sencicek AG, Gümüş H, Ali GG, Baykan B, Caglayan AO, Per H. Childhood-Onset Neurodegeneration with Cerebellar Atrophy Syndrome: Severe Neuronal Degeneration and Cardiomyopathy with Loss of Tubulin Deglutamylase Cytosolic Carboxypeptidase 1. JOURNAL OF PEDIATRIC NEUROLOGY 2022. [DOI: 10.1055/s-0042-1749669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The cytoskeleton is a dynamic filamentous network with various cellular and developmental functions. The loss of cytosolic carboxypeptidase 1 (CCP1) causes neuronal death. Childhood-onset neurodegeneration with cerebellar atrophy (CONDCA, OMIM no.: 618276) is an extremely rare disease caused by ATP/GTP binding protein 1 (AGTPBP1) gene-related CCP1 dysfunction of microtubules affecting the cerebellum, spinal motor neurons, and peripheral nerves. Also, possible problems are expected in tissues where the cytoskeleton plays a dynamic role, such as cardiomyocytes. In the present study, we report a novel homozygous missense (NM_015239: c.2447A > C, p. Gln816Pro) variant in the AGTPBP1 gene that c.2447A > C variant has never been reported in a homozygous state in the Genome Aggregation (gnomAD; v2.1.1) database, identified by whole-exome sequencing in a patient with a seizure, dystonia, dilated cardiomyopathy (DCM)-accompanying atrophy of caudate nuclei, putamen, and cerebellum. Unlike other cases in the literature, we expand the phenotype associated with AGTPBP1 variants to include dysmorphic features, idiopathic DCM which could be reversed with supportive treatments, seizure patterns, and radiological findings. These findings expanded the spectrum of the AGTPBP1 gene mutations and associated possible manifestations. Our study may help establish appropriate genetic counseling and prenatal diagnosis for undiagnosed neurodegenerative patients.
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Affiliation(s)
- M B. Samur
- Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - A. Gulhan Ercan-Sencicek
- Masonic Medical Research Institute, Utica, New York, United States
- Department of Neurosurgery, Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Hakan Gümüş
- Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Gulsum Gumus Ali
- Division of Pediatric Radiology, Faculty of Medicine, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | - Baykan Baykan
- Division of Pediatric Cardiology, Faculty of Medicine, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | - Ahmet Okay Caglayan
- Department of Neurosurgery, Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Department of Neurosurgery, Yale School of Medicine, Connecticut, United States
- Department of Medical Genetics, School of Medicine, Dokuz Eylul University, Turkey
| | - Huseyin Per
- Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
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29
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Ahmed S, Mobashir M, Al-Keridis LA, Alshammari N, Adnan M, Abid M, Hassan MI. A Network-Guided Approach to Discover Phytochemical-Based Anticancer Therapy: Targeting MARK4 for Hepatocellular Carcinoma. Front Oncol 2022; 12:914032. [PMID: 35936719 PMCID: PMC9355243 DOI: 10.3389/fonc.2022.914032] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/15/2022] [Indexed: 12/15/2022] Open
Abstract
MAP/microtubule affinity-regulating kinase 4 (MARK4) is associated with various biological functions, including neuronal migration, cell polarity, microtubule dynamics, apoptosis, and cell cycle regulation, specifically in the G1/S checkpoint, cell signaling, and differentiation. It plays a critical role in different types of cancers. Hepatocellular carcinoma (HCC) is the one of the most common forms of liver cancer caused due to mutations, epigenetic aberrations, and altered gene expression patterns. Here, we have applied an integrated network biology approach to see the potential links of MARK4 in HCC, and subsequently identified potential herbal drugs. This work focuses on the naturally-derived compounds from medicinal plants and their properties, making them targets for potential anti-hepatocellular treatments. We further analyzed the HCC mutated genes from the TCGA database by using cBioPortal and mapped out the MARK4 targets among the mutated list. MARK4 and Mimosin, Quercetin, and Resveratrol could potentially interact with critical cancer-associated proteins. A set of the hepatocellular carcinoma altered genes is directly the part of infection, inflammation, immune systems, and cancer pathways. Finally, we conclude that among all these drugs, Gingerol and Fisetin appear to be the highly promising drugs against MARK4-based targets, followed by Quercetin, Resveratrol, and Apigenin.
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Affiliation(s)
- Sarfraz Ahmed
- Department of Biosciences, Faculty of Natural Science, Jamia Millia Islamia, New Delhi, India
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Mobashir
- Department of Biosciences, Faculty of Natural Science, Jamia Millia Islamia, New Delhi, India
| | - Lamya Ahmed Al-Keridis
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Mohammad Abid
- Department of Biosciences, Faculty of Natural Science, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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30
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Grignard J, Lamamy V, Vermersch E, Delagrange P, Stephan JP, Dorval T, Fages F. Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design. PLoS Comput Biol 2022; 18:e1010236. [PMID: 35759459 PMCID: PMC9236252 DOI: 10.1371/journal.pcbi.1010236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Microtubules and their post-translational modifications are involved in major cellular processes. In severe diseases such as neurodegenerative disorders, tyrosinated tubulin and tyrosinated microtubules are in lower concentration. We present here a mechanistic mathematical model of the microtubule tyrosination cycle combining computational modeling and high-content image analyses to understand the key kinetic parameters governing the tyrosination status in different cellular models. That mathematical model is parameterized, firstly, for neuronal cells using kinetic values taken from the literature, and, secondly, for proliferative cells, by a change of two parameter values obtained, and shown minimal, by a continuous optimization procedure based on temporal logic constraints to formalize experimental high-content imaging data. In both cases, the mathematical models explain the inability to increase the tyrosination status by activating the Tubulin Tyrosine Ligase enzyme. The tyrosinated tubulin is indeed the product of a chain of two reactions in the cycle: the detyrosinated microtubule depolymerization followed by its tyrosination. The tyrosination status at equilibrium is thus limited by both reaction rates and activating the tyrosination reaction alone is not effective. Our computational model also predicts the effect of inhibiting the Tubulin Carboxy Peptidase enzyme which we have experimentally validated in MEF cellular model. Furthermore, the model predicts that the activation of two particular kinetic parameters, the tyrosination and detyrosinated microtubule depolymerization rate constants, in synergy, should suffice to enable an increase of the tyrosination status in living cells.
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Affiliation(s)
- Jeremy Grignard
- Pole of Activity Data Sciences and Data Management, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
- * E-mail: (JG); (TD); (FF)
| | - Véronique Lamamy
- Pole of Activity Cellular Sciences, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
| | - Eva Vermersch
- Pole of Activity Cellular Sciences, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
| | - Philippe Delagrange
- Therapeutic Area Neuropsychiatry and Immunoinflammation, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
| | - Jean-Philippe Stephan
- In Vitro Pharmacology Unit, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
| | - Thierry Dorval
- Pole of Activity Data Sciences and Data Management, Institut de Recherches Servier (IdRS), Croissy-sur-Seine, France
- * E-mail: (JG); (TD); (FF)
| | - François Fages
- Team Project Lifeware, Institut National de Recherche en Informatique et Automatique, Inria Saclay, Palaiseau, France
- * E-mail: (JG); (TD); (FF)
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Dong Z, Wang J, Qiu T, Wu J, An Y, Shi X, Sun X, Jiang L, Liu X, Yang G, Cao J, Yao X. Perfluorooctane sulfonate induces mitochondrial calcium overload and early hepatic insulin resistance via autophagy/detyrosinated alpha-tubulin-regulated IP3R2-VDAC1-MICU1 interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153933. [PMID: 35192817 DOI: 10.1016/j.scitotenv.2022.153933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Perfluorooctane sulfonate (PFOS), one kind of persistent organic pollutants, is associated with insulin resistance (IR) in general population. However, the exact mechanism is still obscure. In this study, we found that 50 μM PFOS caused IR in L-02 hepatocytes after 1 h, and induced autophagy and mitochondrial calcium (Ca2+) accumulation as early as 0.5 h. Inhibiting autophagy relieved mitochondrial Ca2+ overload and then reversed IR. Mitochondria were aggregated at cell periphery, and extracellular Ca2+ from IP3R2 on the plasma membrane, rather than endoplasmic reticulum Ca2+, was the priority source of mitochondrial Ca2+ uptake at early stages of PFOS exposure. Furthermore, we discovered that the linkage connecting autophagy and mitochondrial Ca2+ response was detyrosinated α-tubulin, which autophagy-dependently ascended, interacted with VDAC1 and enhanced the formation of IP3R2-VDAC1-MICU1 complex. Consistently, PFOS caused IR, activated autophagy, induced mitochondrial Ca2+ overload, increased the level of detyrosinated α-tubulin, and promoted the formation of IP3R2-VDAC1-MICU1 complex in the liver of C57BL/6J mice exposed to 2.5 mg/kg/day PFOS for 6 weeks. This study clarified that autophagy and mitochondrial Ca2+ accumulation were the early and triggering event that caused PFOS-related IR, also unveiled a novel mechanism regulating mitochondrial Ca2+ homeostasis.
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Affiliation(s)
- Zhanchen Dong
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Jianyu Wang
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Tianming Qiu
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Jialu Wu
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Yu An
- Dalian Municipal Center for Disease Control and Prevention, 151 Yueling West Street, Ganjingzi District, Dalian 116037, PR China
| | - Xiaoxia Shi
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Xiance Sun
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Liping Jiang
- Department of Food Nutrition and Safety, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Xiaofang Liu
- Department of Food Nutrition and Safety, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Guang Yang
- Department of Food Nutrition and Safety, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Jun Cao
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China
| | - Xiaofeng Yao
- Department of Occupational and Environmental Health, Dalian Medical University, 9 W Lushun South Road, Dalian 116044, PR China.
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Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
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Transactive Response DNA-Binding Protein (TARDBP/TDP-43) Regulates Cell Permissivity to HIV-1 Infection by Acting on HDAC6. Int J Mol Sci 2022; 23:ijms23116180. [PMID: 35682862 PMCID: PMC9181786 DOI: 10.3390/ijms23116180] [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: 05/05/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
The transactive response DNA-binding protein (TARDBP/TDP-43) influences the processing of diverse transcripts, including that of histone deacetylase 6 (HDAC6). Here, we assessed TDP-43 activity in terms of regulating CD4+ T-cell permissivity to HIV-1 infection. We observed that overexpression of wt-TDP-43 increased both mRNA and protein levels of HDAC6, resulting in impaired HIV-1 infection independently of the viral envelope glycoprotein complex (Env) tropism. Consistently, using an HIV-1 Env-mediated cell-to-cell fusion model, the overexpression of TDP-43 levels negatively affected viral Env fusion capacity. Silencing of endogenous TDP-43 significantly decreased HDAC6 levels and increased the fusogenic and infection activities of the HIV-1 Env. Using pseudovirus bearing primary viral Envs from HIV-1 individuals, overexpression of wt-TDP-43 strongly reduced the infection activity of Envs from viremic non-progressors (VNP) and rapid progressors (RP) patients down to the levels of the inefficient HIV-1 Envs observed in long-term non-progressor elite controllers (LTNP-EC). On the contrary, silencing endogenous TDP-43 significantly favored the infectivity of primary Envs from VNP and RP individuals, and notably increased the infection of those from LTNP-EC. Taken together, our results indicate that TDP-43 shapes cell permissivity to HIV-1 infection, affecting viral Env fusion and infection capacities by altering the HDAC6 levels and associated tubulin-deacetylase anti-HIV-1 activity.
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Macrophage migration inhibitory factor (MIF) acetylation protects neurons from ischemic injury. Cell Death Dis 2022; 13:466. [PMID: 35585040 PMCID: PMC9117661 DOI: 10.1038/s41419-022-04918-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/14/2022]
Abstract
Ischemia-induced neuronal death leads to serious lifelong neurological deficits in ischemic stroke patients. Histone deacetylase 6 (HDAC6) is a promising target for neuroprotection in many neurological disorders, including ischemic stroke. However, the mechanism by which HDAC6 inhibition protects neurons after ischemic stroke remains unclear. Here, we discovered that genetic ablation or pharmacological inhibition of HDAC6 reduced brain injury after ischemic stroke by increasing macrophage migration inhibitory factor (MIF) acetylation. Mass spectrum analysis and biochemical results revealed that HDAC6 inhibitor or aspirin treatment promoted MIF acetylation on the K78 residue. MIF K78 acetylation suppressed the interaction between MIF and AIF, which impaired MIF translocation to the nucleus in ischemic cortical neurons. Moreover, neuronal DNA fragmentation and neuronal death were impaired in the cortex after ischemia in MIF K78Q mutant mice. Our results indicate that the neuroprotective effect of HDAC6 inhibition and aspirin treatment results from MIF K78 acetylation; thus, MIF K78 acetylation may be a therapeutic target for ischemic stroke and other neurological diseases.
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Akhmanova A, Kapitein LC. Mechanisms of microtubule organization in differentiated animal cells. Nat Rev Mol Cell Biol 2022; 23:541-558. [PMID: 35383336 DOI: 10.1038/s41580-022-00473-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 02/08/2023]
Abstract
Microtubules are polarized cytoskeletal filaments that serve as tracks for intracellular transport and form a scaffold that positions organelles and other cellular components and modulates cell shape and mechanics. In animal cells, the geometry, density and directionality of microtubule networks are major determinants of cellular architecture, polarity and proliferation. In dividing cells, microtubules form bipolar spindles that pull chromosomes apart, whereas in interphase cells, microtubules are organized in a cell type-specific fashion, which strongly correlates with cell physiology. In motile cells, such as fibroblasts and immune cells, microtubules are organized as radial asters, whereas in immotile epithelial and neuronal cells and in muscles, microtubules form parallel or antiparallel arrays and cortical meshworks. Here, we review recent work addressing how the formation of such microtubule networks is driven by the plethora of microtubule regulatory proteins. These include proteins that nucleate or anchor microtubule ends at different cellular structures and those that sever or move microtubules, as well as regulators of microtubule elongation, stability, bundling or modifications. The emerging picture, although still very incomplete, shows a remarkable diversity of cell-specific mechanisms that employ conserved building blocks to adjust microtubule organization in order to facilitate different cellular functions.
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Affiliation(s)
- Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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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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Mathias TJ, Ju JA, Lee RM, Thompson KN, Mull ML, Annis DA, Chang KT, Ory EC, Stemberger MB, Hotta T, Ohi R, Vitolo MI, Moutin MJ, Martin SS. Tubulin Carboxypeptidase Activity Promotes Focal Gelatin Degradation in Breast Tumor Cells and Induces Apoptosis in Breast Epithelial Cells That Is Overcome by Oncogenic Signaling. Cancers (Basel) 2022; 14:cancers14071707. [PMID: 35406479 PMCID: PMC8996877 DOI: 10.3390/cancers14071707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The recent discovery of the genetic identity of the tubulin carboxypeptidase (TCP) provides a unique opportunity to study the role of the detyrosination of α-tubulin (deTyr-Tub), as performed by the TCP, in breast epithelial cells and breast cancer cells. Previous research has shown that elevated deTyr-Tub conveys a poor prognosis in breast cancer and is upregulated in a coordinated manner at the invasive margin of patient tumor samples. Using TCP expression constructs, we have shown that increased deTyr-Tub promotes apoptosis in normal breast epithelial cells, that does not occur in the same cells with an oncogenic KRas mutation or Bcl-2/Bcl-xL overexpression. Furthermore, the addition of the TCP to the breast cancer cell lines MDA-MB-231 and Hs578t, also harboring Ras mutations, leads to increased focal gelatin degradation. Abstract Post-translational modifications (PTMs) of the microtubule network impart differential functions across normal cell types and their cancerous counterparts. The removal of the C-terminal tyrosine of α-tubulin (deTyr-Tub) as performed by the tubulin carboxypeptidase (TCP) is of particular interest in breast epithelial and breast cancer cells. The recent discovery of the genetic identity of the TCP to be a vasohibin (VASH1/2) coupled with a small vasohibin-binding protein (SVBP) allows for the functional effect of this tubulin PTM to be directly tested for the first time. Our studies revealed the immortalized breast epithelial cell line MCF10A undergoes apoptosis following transfection with TCP constructs, but the addition of oncogenic KRas or Bcl-2/Bcl-xL overexpression prevents subsequent apoptotic induction in the MCF10A background. Functionally, an increase in deTyr-Tub via TCP transfection in MDA-MB-231 and Hs578t breast cancer cells leads to enhanced focal gelatin degradation. Given the elevated deTyr-Tub at invasive tumor fronts and the correlation with poor breast cancer survival, these new discoveries help clarify how the TCP synergizes with oncogene activation, increases focal gelatin degradation, and may correspond to increased tumor cell invasion. These connections could inform more specific microtubule-directed therapies to target deTyr-tubulin.
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Affiliation(s)
- Trevor J. Mathias
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Graduate Program in Molecular Medicine, University of Maryland School of Medicine, 800 W. Baltimore St., Baltimore, MD 21201, USA
- Medical Scientist Training Program (MSTP), University of Maryland School of Medicine, 800 W. Baltimore St., Baltimore, MD 21201, USA
| | - Julia A. Ju
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
| | - Rachel M. Lee
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
| | - Keyata N. Thompson
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
| | - Makenzy L. Mull
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Graduate Program in Molecular Medicine, University of Maryland School of Medicine, 800 W. Baltimore St., Baltimore, MD 21201, USA
| | - David A. Annis
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, 800 W. Baltimore St., Baltimore, MD 21201, USA
| | - Katarina T. Chang
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Graduate Program in Molecular Medicine, University of Maryland School of Medicine, 800 W. Baltimore St., Baltimore, MD 21201, USA
| | - Eleanor C. Ory
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
| | - Megan B. Stemberger
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Graduate Program in Biochemistry & Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; (T.H.); (R.O.)
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; (T.H.); (R.O.)
| | - Michele I. Vitolo
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
| | - Marie-Jo Moutin
- Grenoble Institut Neurosciences, University Grenoble Alpes, Inserm, U1216, CEA, CNRS, 38000 Grenoble, France;
| | - Stuart S. Martin
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA; (T.J.M.); (J.A.J.); (R.M.L.); (K.N.T.); (M.L.M.); (D.A.A.); (K.T.C.); (E.C.O.); (M.B.S.); (M.I.V.)
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201, USA
- United States Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD 21201, USA
- Correspondence: ; Tel.: +1-410-706-6601
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Wang L, Paudyal SC, Kang Y, Owa M, Liang FX, Spektor A, Knaut H, Sánchez I, Dynlacht BD. Regulators of tubulin polyglutamylation control nuclear shape and cilium disassembly by balancing microtubule and actin assembly. Cell Res 2022; 32:190-209. [PMID: 34782749 PMCID: PMC8807603 DOI: 10.1038/s41422-021-00584-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/05/2021] [Indexed: 02/03/2023] Open
Abstract
Cytoskeletal networks play an important role in regulating nuclear morphology and ciliogenesis. However, the role of microtubule (MT) post-translational modifications in nuclear shape regulation and cilium disassembly has not been explored. Here we identified a novel regulator of the tubulin polyglutamylase complex (TPGC), C11ORF49/CSTPP1, that regulates cytoskeletal organization, nuclear shape, and cilium disassembly. Mechanistically, loss of C11ORF49/CSTPP1 impacts the assembly and stability of the TPGC, which modulates long-chain polyglutamylation levels on microtubules (MTs) and thereby balances the binding of MT-associated proteins and actin nucleators. As a result, loss of TPGC leads to aberrant, enhanced assembly of MTs that penetrate the nucleus, which in turn leads to defects in nuclear shape, and disorganization of cytoplasmic actin that disrupts the YAP/TAZ pathway and cilium disassembly. Further, we showed that C11ORF49/CSTPP1-TPGC plays mechanistically distinct roles in the regulation of nuclear shape and cilium disassembly. Remarkably, disruption of C11ORF49/CSTPP1-TPGC also leads to developmental defects in vivo. Our findings point to an unanticipated nexus that links tubulin polyglutamylation with nuclear shape and ciliogenesis.
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Affiliation(s)
- Lei Wang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
| | - Sharad C Paudyal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuchen Kang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Mikito Owa
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, NYU Langone Health, New York, NY, USA
| | - Alexander Spektor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Irma Sánchez
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
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Gadadhar S, Hirschmugl T, Janke C. The tubulin code in mammalian sperm development and function. Semin Cell Dev Biol 2022; 137:26-37. [PMID: 35067438 DOI: 10.1016/j.semcdb.2021.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 01/11/2023]
Abstract
Microtubules are cytoskeletal elements that play key roles throughout the different steps of sperm development. As an integral part of the sperm flagellum, the molecular machine that generates sperm motility, microtubules are also essential for the progressive swimming of sperm to the oocyte, which is a prerequisite for fertilisation. Given the central role of microtubules in all steps of spermatogenesis, their functions need to be tightly controlled. Recent work has showcased tubulin posttranslational modifications as key players in sperm development and function, with aberrations often leading to male infertility with a broad spectrum of sperm defects. Posttranslational modifications are part of the tubulin code, a mechanism that can control microtubule functions by modulating the properties of their molecular building blocks, the tubulin proteins. Here we review the current knowledge on the implications of the tubulin code in sperm development and functions and its importance for male fertility.
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Affiliation(s)
- Sudarshan Gadadhar
- Institut Curie, Université PSL, CNRS UMR3348, F-91401 Orsay, France; Université Paris-Saclay, CNRS UMR3348, F-91401 Orsay, France.
| | | | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, F-91401 Orsay, France; Université Paris-Saclay, CNRS UMR3348, F-91401 Orsay, France.
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Zhang K, Zhang J, Ding N, Zellmer L, Zhao Y, Liu S, Liao DJ. ACTB and GAPDH appear at multiple SDS-PAGE positions, thus not suitable as reference genes for determining protein loading in techniques like Western blotting. Open Life Sci 2021; 16:1278-1292. [PMID: 34966852 PMCID: PMC8669867 DOI: 10.1515/biol-2021-0130] [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: 08/02/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.
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Affiliation(s)
- Keyin Zhang
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Ju Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Nan Ding
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center , 730 South 8th St. , Minneapolis , MN 55415 , United States of America
| | - Yan Zhao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Siqi Liu
- Beijing Genomic Institute, Building 11 of Beishan Industrial Zone, Tantian District , Shengzhen 518083 , Guangdong Province , People’s Republic of China
| | - Dezhong Joshua Liao
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Department of Clinical Biochemistry, Guizhou Medical University Hospital , Guiyang 550004 , Guizhou Province , People’s Republic of China
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41
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Smith BJ, Silva-Costa LC, Martins-de-Souza D. Human disease biomarker panels through systems biology. Biophys Rev 2021; 13:1179-1190. [PMID: 35059036 PMCID: PMC8724340 DOI: 10.1007/s12551-021-00849-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
As more uses for biomarkers are sought after for an increasing number of disease targets, single-target biomarkers are slowly giving way for biomarker panels. These panels incorporate various sources of biomolecular and clinical data to guarantee a higher robustness and power of separation for a clinical test. Multifactorial diseases such as psychiatric disorders show great potential for clinical use, assisting medical professionals during the analysis of risk and predisposition, disease diagnosis and prognosis, and treatment applicability and efficacy. More specific tests are also being developed to assist in ruling out, distinguishing between, and confirming suspicions of multifactorial diseases, as well as to predict which therapy option may be the best option for a given patient's biochemical profile. As more complex datasets are entering the field, involving multi-omic approaches, systems biology has stepped in to facilitate the discovery and validation steps during biomarker panel generation. Filtering biomolecules and clinical data, pre-validating and cross-validating potential biomarkers, generating final biomarker panels, and testing the robustness and applicability of those panels are all beginning to rely on machine learning and systems biology and research in this area will only benefit from advances in these approaches.
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Affiliation(s)
- Bradley J. Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Licia C. Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico E Tecnológico, Sao Paulo, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
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42
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Wareham LK, Echevarria FD, Sousa JL, Konlian DO, Dallas G, Formichella CR, Sankaran P, Goralski PJ, Gustafson JR, Sappington RM. Interleukin-6 promotes microtubule stability in axons via Stat3 protein-protein interactions. iScience 2021; 24:103141. [PMID: 34646984 PMCID: PMC8496173 DOI: 10.1016/j.isci.2021.103141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/02/2021] [Accepted: 09/14/2021] [Indexed: 10/25/2022] Open
Abstract
The interleukin-6 (IL-6) family of cytokines and its downstream effector, STAT3, are important mediators of neuronal health, repair, and disease throughout the CNS, including the visual system. Here, we elucidate a transcription-independent mechanism for the neuropoietic activities of IL-6 related to axon development, regeneration, and repair. We examined the outcome of IL-6 deficiency on structure and function of retinal ganglion cell (RGC) axons, which form the optic projection. We found that IL-6 deficiency substantially delays anterograde axon transport in vivo. The reduced rate of axon transport is accompanied by changes in morphology, structure, and post-translational modification of microtubules. In vivo and in vitro studies in mice and swine revealed that IL-6-dependent microtubule phenotypes arise from protein-protein interactions between STAT3 and stathmin. As in tumor cells and T cells, this STAT3-stathmin interaction stabilizes microtubules in RGCs. Thus, this IL-6-STAT3-dependent mechanism for axon architecture is likely a fundamental mechanism for microtubule stability systemically.
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Affiliation(s)
- Lauren K Wareham
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Jennifer L Sousa
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Atrium Health Wake Forest Baptist Medical Center, 1 Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Danielle O Konlian
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Atrium Health Wake Forest Baptist Medical Center, 1 Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Gabrielle Dallas
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Cathryn R Formichella
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Priya Sankaran
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Peter J Goralski
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Atrium Health Wake Forest Baptist Medical Center, 1 Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Jenna R Gustafson
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Atrium Health Wake Forest Baptist Medical Center, 1 Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Rebecca M Sappington
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Atrium Health Wake Forest Baptist Medical Center, 1 Medical Center Boulevard, Winston-Salem, NC 27157, USA.,Department of Ophthalmology, Wake Forest School of Medicine, Winston-Salem, NC 27106, USA
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43
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Post-translational modifications of tubulin: their role in cancers and the regulation of signaling molecules. Cancer Gene Ther 2021; 30:521-528. [PMID: 34671113 DOI: 10.1038/s41417-021-00396-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022]
Abstract
Microtubules play an important role in regulating several vital cellular activities, including cell division and tissue organization, through their dynamic protofilament network. In addition to forming the cytoskeleton, microtubules regulate the intracellular trafficking of cytoplasmic components and various signaling molecules, depending on the presence of post-transitional modifications (PTMs) and binding proteins. Accumulating evidence indicates the significant role of microtubule PTMs on cancer behavior. The PTMs that frequently occur on microtubules include acetylation, detyrosination, tyrosination, polyglutamylation, and polyglycylation. Alterations in these PTMs cause global effects on intracellular signal transduction, strongly linked to cancer pathogenesis. This review provides an update on the role of microtubule PTMs in cancer aggressiveness, particularly regarding cell death, sensitivity to chemotherapy, cell migration, and invasion. Additionally, it provides a mechanistic explanation of the molecular signaling pathways involved. This information might prove useful for predictive or therapeutic purposes.
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44
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Du J, Li Y, Song D, Liu J, Huang Q, Li J, Li B, Li L. Protective effects of crocin against endogenous Aβ-induced neurotoxicity in N2a/APP695swe cells. Psychopharmacology (Berl) 2021; 238:2839-2847. [PMID: 34191112 DOI: 10.1007/s00213-021-05899-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD) is a most common neurodegenerative disorder worldwide. Because of its complex pathogenesis, the prevention and therapies of AD still are a severe challenge. Evidence suggested that crocin, the major component of saffron, exhibited neuroprotective effects in AD. As such, in this study, N2a/APP695swe cells were enrolled to investigate the effects of crocin on endogenous Aβ-induced neurotoxicity. Crocin (100 and 200 μM) could ameliorate cytotoxicity according to CCK-8 assay and reduce apoptosis in line with Hoechst 33,342 staining and Annexin V-FITC/PI double staining in N2a/APP695swe cells. Reduced ROS generation and elevated MMP were found in N2a/APP695swe cells treated with crocin (100 and 200 μM). Additionally, crocin at concentrations of 100 and 200 μM inhibited the release of cytochrome and attenuated caspases-3 activity in N2a/APP695swe cells. Furthermore, succinylation, crotonylation, 2-hydroxyisobutyrylation, malonylation, and phosphorylation were significantly reduced, while a slight increase of acetylation was found in 100-μM crocin treated N2a/APP695swe cells. Taken together, crocin may be a promising natural product candidate for the effective cure of AD.
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Affiliation(s)
- Jikun Du
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, The Second People's Hospital of Bao'an Shenzhen (Group) Shajing People's Hospital of Bao'an Shenzhen, Shenzhen, China
| | - Yuanhua Li
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Daibo Song
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Jierong Liu
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Qunfa Huang
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Jinwen Li
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Baohong Li
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China.
| | - Li Li
- School of Pharmacy, Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China.
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45
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Dong Z, Qiu T, Zhang J, Sha S, Han X, Kang J, Shi X, Sun X, Jiang L, Yang G, Yao X, Ma Y. Perfluorooctane sulfonate induces autophagy-dependent lysosomal membrane permeabilization by weakened interaction between tyrosinated alpha-tubulin and spinster 1. Food Chem Toxicol 2021; 157:112540. [PMID: 34500008 DOI: 10.1016/j.fct.2021.112540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/15/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Perfluorooctane sulfonate (PFOS) is one kind of persistent organic pollutants. In previous study, we found that PFOS induced autophagy-dependent lysosomal membrane permeabilization (LMP) in hepatocytes, and siRNA against lysosomal permease spinster 1 (SPNS1) relieved PFOS-induced LMP. However, whether and how SPNS1 functioned as the link between autophagy and LMP was still not defined. In this study, we constructed a stable cell line expressing high levels of SPNS1. We found that SPNS1 interacted specifically with α-tubulin of tyrosinated isotype by pull-down assay. After treatment with PFOS, the level of tyrosinated α-tubulin was autophagy-dependently decreased. SPNS1-tyrosinated α-tubulin interaction was disrupted subsequently, which led to LMP eventually. We also found that stable high-expression of SPNS1 in hepatocytes accelerated lysosomal acidification, and deteriorated PFOS-induced LMP. This study pointed out that SPNS1-tyrosinated α-tubulin interaction mediated the cross-talk between autophagy and LMP induced by PFOS, shedding new light on the mechanism of PFOS hepatotoxicity.
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Affiliation(s)
- Zhanchen Dong
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
| | - Tianming Qiu
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Jingyuan Zhang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiuyan Han
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Jian Kang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiaoxia Shi
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiance Sun
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Liping Jiang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Guang Yang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiaofeng Yao
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
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46
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Kassab S, Albalawi Z, Daghistani H, Kitmitto A. Mitochondrial Arrest on the Microtubule Highway-A Feature of Heart Failure and Diabetic Cardiomyopathy? Front Cardiovasc Med 2021; 8:689101. [PMID: 34277734 PMCID: PMC8282893 DOI: 10.3389/fcvm.2021.689101] [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: 03/31/2021] [Accepted: 06/08/2021] [Indexed: 01/16/2023] Open
Abstract
A pathophysiological consequence of both type 1 and 2 diabetes is remodelling of the myocardium leading to the loss of left ventricular pump function and ultimately heart failure (HF). Abnormal cardiac bioenergetics associated with mitochondrial dysfunction occurs in the early stages of HF. Key factors influencing mitochondrial function are the shape, size and organisation of mitochondria within cardiomyocytes, with reports identifying small, fragmented mitochondria in the myocardium of diabetic patients. Cardiac mitochondria are now known to be dynamic organelles (with various functions beyond energy production); however, the mechanisms that underpin their dynamism are complex and links to motility are yet to be fully understood, particularly within the context of HF. This review will consider how the outer mitochondrial membrane protein Miro1 (Rhot1) mediates mitochondrial movement along microtubules via crosstalk with kinesin motors and explore the evidence for molecular level changes in the setting of diabetic cardiomyopathy. As HF and diabetes are recognised inflammatory conditions, with reports of enhanced activation of the NLRP3 inflammasome, we will also consider evidence linking microtubule organisation, inflammation and the association to mitochondrial motility. Diabetes is a global pandemic but with limited treatment options for diabetic cardiomyopathy, therefore we also discuss potential therapeutic approaches to target the mitochondrial-microtubule-inflammatory axis.
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Affiliation(s)
- Sarah Kassab
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Zainab Albalawi
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Hussam Daghistani
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Ashraf Kitmitto
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
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47
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A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol Cell 2021; 81:2669-2681.e9. [PMID: 33894155 DOI: 10.1016/j.molcel.2021.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Posttranslational modification (PTM), through the recruitment of effector proteins (i.e., "readers") that signal downstream events, plays key roles in regulating a variety of cellular processes. To understand how a PTM is recognized, it is necessary to find its readers and, importantly, the location of the binding pockets responsible for PTM recognition. Although various methods have been developed to identify PTM readers, it remains a challenge to directly map the PTM-binding regions, especially for intrinsically disordered domains. Here, we demonstrate a photo-crosslinkable, clickable, and cleavable tri-functional amino acid, ADdis-Cys, that when coupled with mass spectrometry (ADdis-Cys-MS) can not only identify PTM readers from complex proteomes but also simultaneously map their PTM-recognition modules. Using ADdis-Cys-MS, we successfully identify the binding sites of several reader-PTM interactions, among which we discover human C1QBP as a histone chaperone. This robust method should find wide applications in examining other histone or non-histone PTM-mediated protein-protein interactions.
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48
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Waites C, Qu X, Bartolini F. The synaptic life of microtubules. Curr Opin Neurobiol 2021; 69:113-123. [PMID: 33873059 DOI: 10.1016/j.conb.2021.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
In neurons, control of microtubule dynamics is required for multiple homeostatic and regulated activities. Over the past few decades, a great deal has been learned about the role of the microtubule cytoskeleton in axonal and dendritic transport, with a broad impact on neuronal health and disease. However, significantly less attention has been paid to the importance of microtubule dynamics in directly regulating synaptic function. Here, we review emerging literature demonstrating that microtubules enter synapses and control central aspects of synaptic activity, including neurotransmitter release and synaptic plasticity. The pleiotropic effects caused by a dysfunctional synaptic microtubule cytoskeleton may thus represent a key point of vulnerability for neurons and a primary driver of neurological disease.
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Affiliation(s)
- Clarissa Waites
- Department of Neuroscience, Columbia University, 3227 Broadway, New York, NY 10027, USA
| | - Xiaoyi Qu
- Department of Pathology & Cell Biology, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Francesca Bartolini
- Department of Pathology & Cell Biology, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032, USA.
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49
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Bigman LS, Levy Y. Modulating Microtubules: A Molecular Perspective on the Effects of Tail Modifications. J Mol Biol 2021; 433:166988. [PMID: 33865866 DOI: 10.1016/j.jmb.2021.166988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Microtubules (MTs), an essential component of the eukaryotic cytoskeleton, are a lattice of polymerized tubulin dimers and are crucial for various cellular processes. The genetic and chemical diversity of tubulin and their disordered tails gives rise to a "tubulin code". The functional role of tubulin post-translational modifications (PTMs), which contribute to the chemical diversity of the tubulin code, is gradually being unraveled. However, variation in the length and spatial organization of tubulin poly-modifications leads to an enormous combinatorial PTM space, which is difficult to study experimentally. Hence, the impact of the combinatorial tubulin PTM space on the biophysical properties of tubulin tails and their interactions with other proteins remains elusive. Here, we combine all-atom and coarse-grained molecular dynamics simulations to elucidate the biophysical implications of the large combinatorial tubulin PTM space in the context of an MT lattice. We find that tail-body interactions are more dominant in the tubulin dimer than in an MT lattice, and are more significant for the tails of α compared with β tubulin. In addition, polyglutamylation, but not polyglycylation, expands the dimensions of the tubulin tails. Polyglutamylation also leads to a decrease in the diffusion rate of MT-associated protein EB1 on MTs, while polyglycylation often increases diffusion rate. These observations are generally not sensitive to the organization of the polymodifications. The effect of PTMs on MT charge density and tail dynamics are also discussed. Overall, this study presents a molecular quantification of the biophysical properties of tubulin tails and their polymodifications, and provides predictions on the functional importance of tubulin PTMs.
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Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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50
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Kesarwani S, Lama P, Chandra A, Reddy PP, Jijumon AS, Bodakuntla S, Rao BM, Janke C, Das R, Sirajuddin M. Genetically encoded live-cell sensor for tyrosinated microtubules. J Cell Biol 2021; 219:152071. [PMID: 32886100 PMCID: PMC7659708 DOI: 10.1083/jcb.201912107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
Microtubule cytoskeleton exists in various biochemical forms in different cells due to tubulin posttranslational modifications (PTMs). Tubulin PTMs are known to affect microtubule stability, dynamics, and interaction with MAPs and motors in a specific manner, widely known as tubulin code hypothesis. At present, there exists no tool that can specifically mark tubulin PTMs in living cells, thus severely limiting our understanding of their dynamics and cellular functions. Using a yeast display library, we identified a binder against terminal tyrosine of α-tubulin, a unique PTM site. Extensive characterization validates the robustness and nonperturbing nature of our binder as tyrosination sensor, a live-cell tubulin nanobody specific towards tyrosinated microtubules. Using this sensor, we followed nocodazole-, colchicine-, and vincristine-induced depolymerization events of tyrosinated microtubules in real time and found each distinctly perturbs the microtubule polymer. Together, our work describes a novel tyrosination sensor and its potential applications to study the dynamics of microtubule and their PTM processes in living cells.
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Affiliation(s)
- Shubham Kesarwani
- Centre for Cardiovascular Biology and Diseases, Institute for Stem Cell Science and Regenerative Medicine, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prakash Lama
- Centre for Cardiovascular Biology and Diseases, Institute for Stem Cell Science and Regenerative Medicine, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anchal Chandra
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India
| | - P Purushotam Reddy
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India
| | - A S Jijumon
- Institut Curie, Paris Sciences et Lettres University, Centre National de la Recherche Scientifique UMR3348, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique UMR3348, Orsay, France
| | - Satish Bodakuntla
- Institut Curie, Paris Sciences et Lettres University, Centre National de la Recherche Scientifique UMR3348, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique UMR3348, Orsay, France
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC
| | - Carsten Janke
- Institut Curie, Paris Sciences et Lettres University, Centre National de la Recherche Scientifique UMR3348, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique UMR3348, Orsay, France
| | - Ranabir Das
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India
| | - Minhajuddin Sirajuddin
- Centre for Cardiovascular Biology and Diseases, Institute for Stem Cell Science and Regenerative Medicine, Gandhi Krishi Vigyan Kendra Campus, Bangalore, India
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