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Azidane S, Gallego X, Durham L, Cáceres M, Guney E, Pérez-Cano L. Identification of novel driver risk genes in CNV loci associated with neurodevelopmental disorders. HGG ADVANCES 2024; 5:100316. [PMID: 38850022 PMCID: PMC11264174 DOI: 10.1016/j.xhgg.2024.100316] [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: 02/02/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
Copy-number variants (CNVs) are genome-wide structural variations involving the duplication or deletion of large nucleotide sequences. While these types of variations can be commonly found in humans, large and rare CNVs are known to contribute to the development of various neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). Nevertheless, given that these NDD-risk CNVs cover broad regions of the genome, it is particularly challenging to pinpoint the critical gene(s) responsible for the manifestation of the phenotype. In this study, we performed a meta-analysis of CNV data from 11,614 affected individuals with NDDs and 4,031 control individuals from SFARI database to identify 41 NDD-risk CNV loci, including 24 novel regions. We also found evidence for dosage-sensitive genes within these regions being significantly enriched for known NDD-risk genes and pathways. In addition, a significant proportion of these genes was found to (1) converge in protein-protein interaction networks, (2) be among most expressed genes in the brain across all developmental stages, and (3) be hit by deletions that are significantly over-transmitted to individuals with ASD within multiplex ASD families from the iHART cohort. Finally, we conducted a burden analysis using 4,281 NDD cases from Decipher and iHART cohorts, and 2,504 neurotypical control individuals from 1000 Genomes and iHART, which resulted in the validation of the association of 162 dosage-sensitive genes driving risk for NDDs, including 22 novel NDD-risk genes. Importantly, most NDD-risk CNV loci entail multiple NDD-risk genes in agreement with a polygenic model associated with the majority of NDD cases.
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Affiliation(s)
- Sara Azidane
- STALICLA Discovery and Data Science Unit, World Trade Center, Moll de Barcelona, Edif Este, 08039 Barcelona, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Xavier Gallego
- STALICLA Discovery and Data Science Unit, World Trade Center, Moll de Barcelona, Edif Este, 08039 Barcelona, Spain
| | - Lynn Durham
- STALICLA Discovery and Data Science Unit, World Trade Center, Moll de Barcelona, Edif Este, 08039 Barcelona, Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute, Barcelona, Spain
| | - Emre Guney
- STALICLA Discovery and Data Science Unit, World Trade Center, Moll de Barcelona, Edif Este, 08039 Barcelona, Spain
| | - Laura Pérez-Cano
- STALICLA Discovery and Data Science Unit, World Trade Center, Moll de Barcelona, Edif Este, 08039 Barcelona, Spain.
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2
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Palacios A, Acharya P, Peidl A, Beck M, Blanco E, Mishra A, Bawa-Khalfe T, Pakhrin S. SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model. NAR Genom Bioinform 2024; 6:lqae011. [PMID: 38327870 PMCID: PMC10849187 DOI: 10.1093/nargab/lqae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
SUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to fully expand and/or recognize the SUMOylated proteome. Herein, we present a novel, deep learning-based approach called SumoPred-PLM for human SUMOylation prediction with sensitivity, specificity, Matthew's correlation coefficient, and accuracy of 74.64%, 73.36%, 0.48% and 74.00%, respectively, on the CPLM 4.0 independent test dataset. In addition, this novel platform uses contextualized embeddings obtained from a pre-trained protein language model, ProtT5-XL-UniRef50 to identify SUMO2/3-specific conjugation sites. The results demonstrate that SumoPred-PLM is a powerful and unique computational tool to predict SUMOylation sites in proteins and accelerate discovery.
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Affiliation(s)
- Andrew Vargas Palacios
- Department of Computer Science and Engineering Technology, University of Houston-Downtown, 1 Main St., Houston, TX 77002, USA
| | - Pujan Acharya
- Department of Computer Science and Engineering Technology, University of Houston-Downtown, 1 Main St., Houston, TX 77002, USA
| | - Anthony Stephen Peidl
- Department of Biology and Biochemistry, Center for Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX 77204, USA
| | - Moriah Rene Beck
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount St., Wichita, KS 67260, USA
| | - Eduardo Blanco
- Department of Computer Science, University of Arizona, 1040 4th St., Tucson, AZ 85721, USA
| | - Avdesh Mishra
- Department of Electrical Engineering and Computer Science, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Tasneem Bawa-Khalfe
- Department of Biology and Biochemistry, Center for Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX 77204, USA
| | - Subash Chandra Pakhrin
- Department of Computer Science and Engineering Technology, University of Houston-Downtown, 1 Main St., Houston, TX 77002, USA
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3
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Karandikar P, Gerstl JVE, Kappel AD, Won SY, Dubinski D, Garcia-Segura ME, Gessler FA, See AP, Peruzzotti-Jametti L, Bernstock JD. SUMOtherapeutics for Ischemic Stroke. Pharmaceuticals (Basel) 2023; 16:ph16050673. [PMID: 37242456 DOI: 10.3390/ph16050673] [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: 03/28/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The small, ubiquitin-like modifier (SUMO) is a post-translational modifier with a profound influence on several key biological processes, including the mammalian stress response. Of particular interest are its neuroprotective effects, first recognized in the 13-lined ground squirrel (Ictidomys tridecemlineatus), in the context of hibernation torpor. Although the full scope of the SUMO pathway is yet to be elucidated, observations of its importance in managing neuronal responses to ischemia, maintaining ion gradients, and the preconditioning of neural stem cells make it a promising therapeutic target for acute cerebral ischemia. Recent advances in high-throughput screening have enabled the identification of small molecules that can upregulate SUMOylation, some of which have been validated in pertinent preclinical models of cerebral ischemia. Accordingly, the present review aims to summarize current knowledge and highlight the translational potential of the SUMOylation pathway in brain ischemia.
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Affiliation(s)
- Paramesh Karandikar
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA 01655, USA
| | - Jakob V E Gerstl
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Ari D Kappel
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA 02215, USA
| | - Sae-Yeon Won
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Daniel Dubinski
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Monica Emili Garcia-Segura
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Florian A Gessler
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Alfred Pokmeng See
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Joshua D Bernstock
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
- Koch Institute for Integrated Cancer Research, MIT, Cambridge, MA 02142, USA
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4
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Kötter A, Mootz HD, Heuer A. Conformational and Interface Variability in Multivalent SIM-SUMO Interaction. J Phys Chem B 2023; 127:3806-3815. [PMID: 37079893 DOI: 10.1021/acs.jpcb.2c08760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
SUMO targeted ubiqutin ligases (STUbLs) like RNF4 or Arkadia/RNF111 recognize SUMO chains through multiple SUMO interacting motifs (SIMs). Typically, these are contained in disordered regions of these enzymes and also the individual SUMO domains of SUMO chains move relatively freely. It is assumed that binding the SIM region significantly restricts the conformational freedom of SUMO chains. Here, we present the results of extensive molecular dynamics simulations on the complex formed by the SIM2-SIM3 region of RNF4 and diSUMO3. Though our simulations highlight the importance of typical SIM-SUMO interfaces also in the multivalent situation, we observe that frequently other regions of the peptide than the canonical SIMs establish this interface. This variability regarding the individual interfaces leads to a conformationally highly flexible complex. Comparison with previous experimental measurements clearly supports our findings and indicates that our observations can be extended to other multivalent SIM-SUMO complexes.
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Affiliation(s)
- Alex Kötter
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
| | - Henning D Mootz
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 2, D-48149 Münster, Germany
| | - Andreas Heuer
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
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5
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García-Gutiérrez P, García-Domínguez M. SUMO control of nervous system development. Semin Cell Dev Biol 2022; 132:203-212. [PMID: 34848148 DOI: 10.1016/j.semcdb.2021.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
In the last decades, the post-translational modification system by covalent attachment of the SUMO polypeptide to proteins has emerged as an essential mechanism controlling virtually all the physiological processes in the eukaryotic cell. This includes vertebrate development. In the nervous system, SUMO plays crucial roles in synapse establishment and it has also been linked to a variety of neurodegenerative diseases. However, to date, the involvement of the modification of specific targets in key aspects of nervous system development, like patterning and differentiation, has remained largely elusive. A number of recent works confirm the participation of target-specific SUMO modification in critical aspects of nervous system development. Here, we review pioneering and new findings demonstrating the essential role SUMO plays in neurogenesis and other facets of neurodevelopment, which will help to precisely understand the variety of mechanisms SUMO utilizes to control most fundamental processes in the cell.
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Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
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6
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Ramazi S, Zahiri J. Posttranslational modifications in proteins: resources, tools and prediction methods. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6214407. [PMID: 33826699 DOI: 10.1093/database/baab012] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 02/20/2021] [Indexed: 12/21/2022]
Abstract
Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.
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Affiliation(s)
- Shahin Ramazi
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
- Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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7
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Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations. Biophys J 2020; 119:1558-1567. [PMID: 32976759 DOI: 10.1016/j.bpj.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Post-translational modification with one of the isoforms of the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome. The binding of SUMO to SUMO interacting motifs (SIMs) can translate the SUMOylation event into functional consequences. The E3 ubiquitin ligase RNF4 contains multiple SIMs and connects SUMOylation to the ubiquitin pathway. SIM2 and SIM3 of RNF4 were shown to be the most important motifs to recognize SUMO chains. However, the study of SIM-SUMO complexes is complicated by their typically low affinity and variable binding of the SIMs in parallel and antiparallel orientations. We investigated properties of complexes formed by SUMO3 with peptides containing either SIM2 or SIM3 using molecular dynamics simulations. The affinities of the complexes were determined using a state-of-the-art free energy protocol and were found to be in good agreement with experimental data, thus corroborating our method. Long unrestrained simulations allowed a new interpretation of experimental results regarding the structure of the SIM-SUMO interface. We show that both SIM2 and SIM3 bind SUMO3 in parallel and antiparallel orientations and identified main interaction sites for acidic residues flanking the SIM. We noticed unusual SIM-SUMO interfaces in a previously reported NMR structure (PDB: 2mp2) of a complex formed by a SUMO3 dimer with the bivalent SIM2-SIM3 peptide. Computational determination of the individual SIM-SUMO affinities based on these structural arrangements yielded significantly higher dissociation constants. To our knowledge, our approach adds new opportunities to characterize individual SIM-SUMO complexes and suggests that further studies will be necessary to understand these interactions when occurring in multivalent form.
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9
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Zárraga-Granados G, Muciño-Hernández G, Sánchez-Carbente MR, Villamizar-Gálvez W, Peñas-Rincón A, Arredondo C, Andrés ME, Wood C, Covarrubias L, Castro-Obregón S. The nuclear receptor NR4A1 is regulated by SUMO modification to induce autophagic cell death. PLoS One 2020; 15:e0222072. [PMID: 32210435 PMCID: PMC7094859 DOI: 10.1371/journal.pone.0222072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/08/2020] [Indexed: 12/31/2022] Open
Abstract
NR4A is a nuclear receptor protein family whose members act as sensors of cellular environment and regulate multiple processes such as metabolism, proliferation, migration, apoptosis, and autophagy. Since the ligand binding domains of these receptors have no cavity for ligand interaction, their function is most likely regulated by protein abundance and post-translational modifications. In particular, NR4A1 is regulated by protein abundance, phosphorylation, and subcellular distribution (nuclear-cytoplasmic translocation), and acts both as a transcription factor and as a regulator of other interacting proteins. SUMOylation is a post-translational modification that can affect protein stability, transcriptional activity, alter protein-protein interactions and modify intracellular localization of target proteins. In the present study we evaluated the role of SUMOylation as a posttranslational modification that can regulate the activity of NR4A1 to induce autophagy-dependent cell death. We focused on a model potentially relevant for neuronal cell death and demonstrated that NR4A1 needs to be SUMOylated to induce autophagic cell death. We observed that a triple mutant in SUMOylation sites has reduced SUMOylation, increased transcriptional activity, altered intracellular distribution, and more importantly, its ability to induce autophagic cell death is impaired.
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Affiliation(s)
- Gabriela Zárraga-Granados
- División de Neurociencias, Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Gabriel Muciño-Hernández
- División de Neurociencias, Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - María R. Sánchez-Carbente
- Biotechnology Research Center, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Wendy Villamizar-Gálvez
- División de Neurociencias, Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Ana Peñas-Rincón
- División de Neurociencias, Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Cristian Arredondo
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María E. Andrés
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, UNAM, Cuernavaca, Mexico
| | - Luis Covarrubias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, UNAM, Cuernavaca, Mexico
| | - Susana Castro-Obregón
- División de Neurociencias, Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
- * E-mail:
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Colnaghi L, Russo L, Natale C, Restelli E, Cagnotto A, Salmona M, Chiesa R, Fioriti L. Super Resolution Microscopy of SUMO Proteins in Neurons. Front Cell Neurosci 2019; 13:486. [PMID: 31749687 PMCID: PMC6844275 DOI: 10.3389/fncel.2019.00486] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022] Open
Abstract
The ubiquitously expressed SUMO proteins regulate a plethora of cellular pathways and processes. While they have a predominantly nuclear localization, extranuclear roles of SUMO isoforms at the synapse have also been described, making SUMOylation one of the major post-translational regulators of nerve functions. These findings have however recently been challenged, at least for SUMO1, by the analysis of knock-in mice expressing His6-HA-SUMO1, where the authors failed to detect the protein at the synapse. In the ongoing dispute, the subcellular distribution in neurons of SUMO2/3 and of the E2 SUMO ligase Ubc9 has not been examined. To investigate whether SUMO proteins do or do not localize at the synapse, we studied their localization in hippocampal primary neurons by super resolution microscopy. We found that SUMO1, SUMO2/3, and Ubc9 are primarily nuclear proteins, which also colocalize partially with pre- and post-synaptic markers such as synaptophysin and PSD95.
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Affiliation(s)
- Luca Colnaghi
- Department of Neuroscience, Dulbecco Telethon Institute, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Luca Russo
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carmina Natale
- Department of Neuroscience, Dulbecco Telethon Institute, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Elena Restelli
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Alfredo Cagnotto
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Mario Salmona
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Roberto Chiesa
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Luana Fioriti
- Department of Neuroscience, Dulbecco Telethon Institute, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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11
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Kumar R, Sabapathy K. RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination. Proteomics 2019; 19:e1900185. [DOI: 10.1002/pmic.201900185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Ramesh Kumar
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
| | - Kanaga Sabapathy
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
- Laboratory of Molecular Carcinogenesis Division of Cellular & Molecular Research Humphrey Oei Institute of Cancer Research National Cancer Centre Singapore 11 Hospital Drive Singapore 169610 Singapore
- Department of Biochemistry National University of Singapore 8 Medical Drive Singapore 117597 Singapore
- Institute of Molecular and Cellular Biology 61 Biopolis Drive Singapore 138673 Singapore
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12
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Kötter A, Mootz HD, Heuer A. Standard Binding Free Energy of a SIM–SUMO Complex. J Chem Theory Comput 2019; 15:6403-6410. [DOI: 10.1021/acs.jctc.9b00428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Alex Kötter
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
| | - Henning D. Mootz
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 2, D-48149 Münster, Germany
| | - Andreas Heuer
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
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13
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Eisenhardt N, Ilic D, Nagamalleswari E, Pichler A. Biochemical characterization of SUMO-conjugating enzymes by in vitro sumoylation assays. Methods Enzymol 2019; 618:167-185. [PMID: 30850051 DOI: 10.1016/bs.mie.2018.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The small ubiquitin-related modifier (SUMO) is a protein of ~10kDa that is covalently conjugated to its substrate proteins in an enzymatic process called sumoylation. This posttranslational modification is an essential regulatory mechanism that plays crucial roles in many cellular pathways. It allows rapid adaptation to environmental changes by switching protein functions due to alternate complex assemblies, changes in intracellular localization, enzymatic activity, or stability. SUMO conjugation is executed by the hierarchical action of E1, E2, and E3 enzymes. Both E2 and E3 enzymes contribute to substrate specificity but with E3 ligases being the more important for this. E1 and E2 activities are essential for all sumoylation reactions but usually-with a few exceptions-modify substrates only inefficiently. Hence, most substrates require the additional action of an E3 ligase or a cofactor. Here, we describe methods to distinguish a bona fide E3 ligase from a cofactor activity by using in vitro sumoylation assays.
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Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Dragana Ilic
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Easa Nagamalleswari
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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14
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Abstract
Protein regulation by reversible attachment of SUMO (small ubiquitin-related modifier) plays an important role in several cellular processes such as transcriptional regulation, nucleo-cytoplasmic transport, cell-cycle progression, meiosis, and DNA repair. However, most sumoylated proteins are of marginal abundance at steady state levels, which is due to strict regulation and/or rapid turnover of modification and de-modification. Consequently, analysis of protein sumoylation in vivo is very challenging. Nonetheless, a novel method was established that allows detection of sumoylated proteins at endogenous levels from vertebrate cells and tissues. This approach involves the enrichment of sumoylated proteins by immunoprecipitation followed by peptide elution. After endogenous substrate sumoylation is verified, addressing its functional consequences is the next logical step. This requires SUMO site mapping that benefits from larger quantities of modified protein. Here, we shortly describe strategies to achieve efficient in vitro sumoylation of many substrates.
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Affiliation(s)
- Jan Breucker
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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15
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Benlloch R, Lois LM. Sumoylation in plants: mechanistic insights and its role in drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4539-4554. [PMID: 29931319 DOI: 10.1093/jxb/ery233] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/11/2018] [Indexed: 05/20/2023]
Abstract
Post-translational modification by SUMO is an essential process that has a major role in the regulation of plant development and stress responses. Such diverse biological functions are accompanied by functional diversification among the SUMO conjugation machinery components and regulatory mechanisms that has just started to be identified in plants. In this review, we focus on the current knowledge of the SUMO conjugation system in plants in terms of components, substrate specificity, cognate interactions, enzyme activity, and subcellular localization. In addition, we analyze existing data on the role of SUMOylation in plant drought tolerance in model plants and crop species, paying attention to the genetic approaches used to stimulate or inhibit endogenous SUMO conjugation. The role in drought tolerance of potential SUMO targets identified in proteomic analyses is also discussed. Overall, the complexity of SUMOylation and the multiple genetic and environmental factors that are integrated to confer drought tolerance highlight the need for significant efforts to understand the interplay between SUMO and drought.
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Affiliation(s)
- Reyes Benlloch
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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16
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An overview of the possible therapeutic role of SUMOylation in the treatment of Alzheimer’s disease. Pharmacol Res 2018; 130:420-437. [DOI: 10.1016/j.phrs.2017.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
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17
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Zhang Z, Chen H, Lu Y, Feng T, Sun W. LncRNA BC032020 suppresses the survival of human pancreatic ductal adenocarcinoma cells by targeting ZNF451. Int J Oncol 2018. [PMID: 29532883 PMCID: PMC5843399 DOI: 10.3892/ijo.2018.4289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This study examined the effects of long non‑coding RNA (lncRNA) BC032020 on the development of human pancreatic ductal adenocarcinoma (PDAC), and the potential molecular mechanisms responsible for these effects. The expression of BC032020 was assessed in 20 pairs of PDAC tumor tissues and adjacent normal tissues. The overexpression of BC032020 was enforced in the AsPC‑1 and PANC‑1 cells, and the effects on cell proliferation, cell cycle distribution, cell migration and apoptosis were determined. We also analyzed the functions of zinc finger protein 451 (ZNF451), which shares a gene sequence with two exons of BC032020 and a non‑coding region with another two exons, in PDAC cells. The AsPC‑1 and PANC‑1 cells that overexpressed BC032020 were used to establish a subcutaneous tumor xenograft model in order to examine the effects of BC032020 on tumor growth in vivo. The results revealed that the BC032020 levels in the PDAC tumor tissues were lower than those in the adjacent normal tissues, and ZNF451 expression inversely correlated with the BC032020 levels in the PDAC tumor tissues and cell lines. BC032020 overexpression led to a decrease in ZNF451 expression; it also suppressed the proliferation and migration of the AsPC‑1 and PANC‑1 cells, and induced G1 phase arrest and cell apoptosis. The results of in vivo experiments revealed that BC032020 suppressed tumor growth in a xenograft model by inhibiting ZNF451 expression. Taken together, the findings of this study indicate that BC032020 suppresses the survival of PDAC cells by inhibiting ZNF451 expression.
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Affiliation(s)
- Zhipeng Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hongxi Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yebin Lu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Tiecheng Feng
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Weijia Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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18
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Horita H, Law A, Middleton K. Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins. J Vis Exp 2018. [PMID: 29364248 PMCID: PMC5908451 DOI: 10.3791/56912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is now well-appreciated that post-translational modifications (PTMs) play an integral role in regulating a protein's structure and function, which may be essential for a given protein's role both physiologically and pathologically. Enrichment of PTMs is often necessary when investigating the PTM status of a target protein, because PTMs are often transient and relatively low in abundance. Many pitfalls are encountered when enriching for a PTM of a target protein, such as buffer incompatibility, the target protein antibody is not IP-compatible, loss of PTM signal, and others. The degree of difficulty is magnified when investigating multiple PTMs like acetylation, ubiquitination, SUMOylation 2/3, and tyrosine phosphorylation for a given target protein. Studying a combination of these PTMs may be necessary, as crosstalk between PTMs is prevalent and critical for protein regulation. Often, these PTMs are studied in different lysis buffers and with unique inhibitor compositions. To simplify the process, a unique denaturing lysis system was developed that effectively isolates and preserves these four PTMs; thus, enabling investigation of potential crosstalk in a single lysis system. A unique filter system was engineered to remove contaminating genomic DNA from the lysate, which is a problematic by-product of denaturing buffers. Robust affinity matrices targeting each of the four PTMs were developed in concert with the buffer system to maximize the enrichment and detection of the endogenous states of these four PTMs. This comprehensive PTM detection toolset streamlines the process of obtaining critical information about whether a protein is modified by one or more of these PTMs.
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Affiliation(s)
| | - Andy Law
- R&D Department, Cytoskeleton Inc
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19
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Ficulle E, Sufian MDS, Tinelli C, Corbo M, Feligioni M. Aging-related SUMOylation pattern in the cortex and blood plasma of wild type mice. Neurosci Lett 2018; 668:48-54. [PMID: 29325714 DOI: 10.1016/j.neulet.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022]
Abstract
Protein activities and mechanisms related to aging has become a growing interest nowadays. Since SUMOylation is implicated in several cellular processes, its investigation related to senescence, aging and frailty is of high interest. In our study, wild type mice cortical lysates, synaptosomes and plasma have been processed to evaluate SUMOylation and SUMO machinery expression (Ubc9 and SENP1 enzymes) profile at different ages. In cortical lysates, SUMO-1ylation reached a peak at 6 months followed by a decrease; while in synaptosomes, it progressively increased till 18 months. Regarding SUMO-2/3ylation, it was observed a similar trend in both lysate and synaptosomes where the protein conjugation was the highest at 6 months but interestingly decreased afterwards. In addition, Ubc9 and SENP1 enzymes showed a linear increased expression level in both brain preparations. Since SUMOylation process is ubiquitously expressed, we were interested to identify SUMO conjugation at peripheral level too. Thus, SUMO-1ylation and SUMO-2/3ylation expression level has been detected in mouse plasma that revealed an inverted U-shaped curve trend during mice lifespan. Surprisingly, SENP1 enzyme was not present in the plasma while Ubc9 enzyme reached a plateau at 6 months and was highly expressed till 18 months. In conclusion, our data indicates that SUMOylation is highly correlated with age-related processes which indisputably need to be considered for further investigation.
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Affiliation(s)
- E Ficulle
- Laboratory of Neurobiology in Translational Medicine, Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | - M D Shah Sufian
- Laboratory of Neurobiology in Translational Medicine, Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | - C Tinelli
- Laboratory of Neuronal Cell Signaling, EBRI Rita Levi-Montalcini Foundation, Rome, Italy
| | - M Corbo
- Laboratory of Neurobiology in Translational Medicine, Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | - M Feligioni
- Laboratory of Neurobiology in Translational Medicine, Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy; Laboratory of Neuronal Cell Signaling, EBRI Rita Levi-Montalcini Foundation, Rome, Italy.
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20
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Antila CJM, Rraklli V, Blomster HA, Dahlström KM, Salminen TA, Holmberg J, Sistonen L, Sahlgren C. Sumoylation of Notch1 represses its target gene expression during cell stress. Cell Death Differ 2018; 25:600-615. [PMID: 29305585 PMCID: PMC5864205 DOI: 10.1038/s41418-017-0002-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The Notch signaling pathway is a key regulator of stem cells during development, and its deregulated activity is linked to developmental defects and cancer. Transcriptional activation of Notch target genes requires cleavage of the Notch receptor in response to ligand binding, production of the Notch intracellular domain (NICD1), NICD1 migration into the nucleus, and assembly of a transcriptional complex. Post-translational modifications of Notch regulate its trafficking, turnover, and transcriptional activity. Here, we show that NICD1 is modified by small ubiquitin-like modifier (SUMO) in a stress-inducible manner. Sumoylation occurs in the nucleus where NICD1 is sumoylated in the RBPJ-associated molecule (RAM) domain. Although stress and sumoylation enhance nuclear localization of NICD1, its transcriptional activity is attenuated. Molecular modeling indicates that sumoylation can occur within the DNA-bound ternary transcriptional complex, consisting of NICD1, the transcription factor Suppressor of Hairless (CSL), and the co-activator Mastermind-like (MAML) without its disruption. Mechanistically, sumoylation of NICD1 facilitates the recruitment of histone deacetylase 4 (HDAC4) to the Notch transcriptional complex to suppress Notch target gene expression. Stress-induced sumoylation decreases the NICD1-mediated induction of Notch target genes, which was abrogated by expressing a sumoylation-defected mutant in cells and in the developing central nervous system of the chick in vivo. Our findings of the stress-inducible sumoylation of NICD1 reveal a novel context-dependent regulatory mechanism of Notch target gene expression.
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Affiliation(s)
- Christian J M Antila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, 285 SE-171 77, Stockholm, Sweden
| | - Henri A Blomster
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Käthe M Dahlström
- Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 285 SE-171 77, Stockholm, Sweden
| | - Lea Sistonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Cecilia Sahlgren
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland. .,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland. .,Department of Biomedical Engineering, Technical University of Eindhoven, 5613 DR, Eindhoven, The Netherlands.
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21
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A simple toolset to identify endogenous post-translational modifications for a target protein: a snapshot of the EGFR signaling pathway. Biosci Rep 2017; 37:BSR20170919. [PMID: 28724604 PMCID: PMC6192658 DOI: 10.1042/bsr20170919] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 06/22/2017] [Accepted: 07/18/2017] [Indexed: 12/17/2022] Open
Abstract
Identification of a novel post-translational modification (PTM) for a target protein, defining its physiologic role, and studying its potential crosstalk with other PTMs is a challenging process. A set of highly sensitive tools termed Signal-Seeker kits was developed, which enables rapid and simple detection of post-translational modifications on any target protein. The methodology for these tools utilizes affinity purification of modified proteins from a cell or tissue lysate and immunoblot analysis. These tools utilize a single lysis system that is effective at identifying endogenous, dynamic PTM changes, as well as the potential crosstalk between PTMs. As a proof-of-concept experiment, the acetylation, tyrosine phosphorylation, SUMOylation 2/3, and ubiquitination profiles of the EGFR - Ras - c-Fos axis were examined in response to EGF stimulation. All 10 previously identified PTMs of this signaling axis were confirmed using these tools, and it also identified acetylation as a novel modification of c-Fos. This axis in the EGF/EGFR signaling pathway was chosen because it is a well-established signaling pathway with proteins localized in the membrane, cytoplasmic, and nuclear compartments that ranged in abundance from 4.18x108 (EGFR) to 1.35x104 (c-Fos) molecules per A431 cell. These tools enabled the identification of low abundance PTMs, such as c-Fos Ac, at 17 molecules per cell. These studies highlight how pervasive PTMs are, and how stimulants like EGF induce multiple PTM changes on downstream signaling axis. Identification of endogenous changes and potential crosstalk between multiple PTMs for a target protein or signaling axis will provide regulatory mechanistic insight to investigators.
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22
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Li G, Liu X, Su Z, Zhang D. Hypothermia exerts early neuroprotective effects involving protein conjugation of SUMO‑2/3 in a rat model of middle cerebral artery occlusion. Mol Med Rep 2017; 16:3217-3223. [PMID: 28713891 PMCID: PMC5548067 DOI: 10.3892/mmr.2017.6994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 03/23/2017] [Indexed: 11/23/2022] Open
Abstract
How hypothermia serves an early protective role against cerebral ischemia remains to be determined. The small ubiquitin-related modifier protein (SUMO) functions as a post-translational modification system and SUMO-2/3 subtypes are often activated in early stress. The present study investigated changes in the protein level of SUMO using western blotting and immunocytochemistry when neurons were exposed to oxygen-glucose deprivation (OGD) in vitro, as well as in a rat model of middle cerebral artery occlusion (MCAO) in vivo. The results demonstrated that a large number of proteins were conjugated to SUMO-2/3 in OGD-injured neurons (within 10 min, peaking at 12 h), and was markedly enhanced under conditions of hypothermia (33°C). Concordantly, lactate dehydrogenase (LDH) release and the apoptosis rate, as determined by LDH and TUNEL assays, respectively, were lower in hypothermia-treated neurons. Similar results were obtained in a rat model of MCAO. Neurological deficit scores were lower in the hypothermia group than in the sham group in the early stage of cerebral ischemia (P<0.05). However, no significant differences in neurological deficit scores were detected between the hypothermia group and the sham group in the late stage of ischemia (21 days; P>0.05). This study implicates a role for SUMO-2/3 in early hypothermia-induced neuroprotection against stroke. The development of small molecule therapeutics based on SUMO-2/3 may benefit patients with cerebral ischemia.
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Affiliation(s)
- Gang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Xiaozhi Liu
- Department of Neurosurgery, Tianjin 5th Central Hospital, Tianjin 300450, P.R. China
| | - Zhiguo Su
- Department of Neurosurgery, Tianjin 5th Central Hospital, Tianjin 300450, P.R. China
| | - Dong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
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23
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Yoo DY, Kim DW, Kwon HJ, Jung HY, Nam SM, Kim JW, Chung JY, Won MH, Yoon YS, Choi SY, Hwang IK. Chronic administration of SUMO‑1 has negative effects on novel object recognition memory as well as cell proliferation and neuroblast differentiation in the mouse dentate gyrus. Mol Med Rep 2017; 16:3427-3432. [PMID: 28713906 DOI: 10.3892/mmr.2017.6946] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/09/2017] [Indexed: 11/05/2022] Open
Abstract
Post‑translational modifications have been associated with developmental and aging processes, as well as in the pathogenesis of certain diseases. The present study aimed to investigate the effects of small ubiquitin‑like modifier 1 (SUMO‑1) on hippocampal dependent memory function, cell proliferation and neuroblast differentiation. To facilitate the delivery of SUMO‑1 into hippocampal neurons, a transactivator of transcription (Tat)‑SUMO‑1 fusion protein was constructed and mice were divided into two groups: A vehicle (Tat peptide)‑treated group and a Tat‑SUMO‑1‑treated group. The vehicle or Tat‑SUMO‑1 was administered intraperitoneally to 7‑week‑old mice once daily for 3 weeks, and a novel object recognition test was conducted following the final treatment; the animals were sacrificed 2 h following the test for further analysis. Administration of Tat‑SUMO‑1 significantly decreased exploration of a new object in a novel object recognition test compared with mice in the vehicle‑treated group. In addition, cell proliferation and neuroblast differentiation analyses (based on Ki67 and doublecortin immunohistochemistry, respectively) revealed that the administration of Tat‑SUMO‑1 significantly reduced cell proliferation and neuroblast differentiation in the dentate gyrus. These results suggested that chronic supplementation of Tat‑SUMO‑1 affects hippocampal functions by decreasing cell proliferation and neuroblast differentiation in the mouse dentate gyrus.
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Affiliation(s)
- Dae Young Yoo
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Dae Won Kim
- Department of Biochemistry and Molecular Biology, Research Institute of Oral Sciences, College of Dentistry, Kangneung‑Wonju National University, Gangneung 25457, Republic of Korea
| | - Hyun Jung Kwon
- Department of Biochemistry and Molecular Biology, Research Institute of Oral Sciences, College of Dentistry, Kangneung‑Wonju National University, Gangneung 25457, Republic of Korea
| | - Hyo Young Jung
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Min Nam
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong Whi Kim
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin Young Chung
- Department of Veterinary Internal Medicine and Geriatrics, College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Moo-Ho Won
- Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yeo Sung Yoon
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo Young Choi
- Department of Biomedical Sciences, Research Institute for Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Republic of Korea
| | - In Koo Hwang
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
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24
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Pichler A, Fatouros C, Lee H, Eisenhardt N. SUMO conjugation - a mechanistic view. Biomol Concepts 2017; 8:13-36. [PMID: 28284030 DOI: 10.1515/bmc-2016-0030] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 02/08/2023] Open
Abstract
The regulation of protein fate by modification with the small ubiquitin-related modifier (SUMO) plays an essential and crucial role in most cellular pathways. Sumoylation is highly dynamic due to the opposing activities of SUMO conjugation and SUMO deconjugation. SUMO conjugation is performed by the hierarchical action of E1, E2 and E3 enzymes, while its deconjugation involves SUMO-specific proteases. In this review, we summarize and compare the mechanistic principles of how SUMO gets conjugated to its substrate. We focus on the interplay of the E1, E2 and E3 enzymes and discuss how specificity could be achieved given the limited number of conjugating enzymes and the thousands of substrates.
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Affiliation(s)
- Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Chronis Fatouros
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Heekyoung Lee
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Nathalie Eisenhardt
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
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25
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Abstract
Small ubiquitin-like modifier (SUMO) is a posttranslational protein modifier that binds target proteins covalently (protein sumoylation) and remarkably alters their functions. Protein sumoylation has been linked to various cellular functions such as cell division, DNA repair, and import of nuclear proteins. Thus, its dysregulation is implicated in diverse human diseases such as neurodegenerative disorders and cancers. We recently found that the kinase activity of MEK proteins, which function as central components of the ERK-MAPK cascade and amplify an extracellular proliferation signal, is negatively regulated by sumoylation. Moreover, the oncogenic activity of Ras is enhanced by the abrogation of MEK-sumoylation in cancer cells. Here, we describe several tools and techniques utilized for the elucidation of the properties of SUMO-MEK in our previous reports. We believe that these methods can be used as robust tools for investigating and understanding the biological roles of various SUMO-modified (sumoylated) proteins.
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Affiliation(s)
- Yuji Kubota
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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26
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Targeting SUMO-1ylation Contrasts Synaptic Dysfunction in a Mouse Model of Alzheimer's Disease. Mol Neurobiol 2016; 54:6609-6623. [PMID: 27738871 DOI: 10.1007/s12035-016-0176-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022]
Abstract
Synaptic dysfunction has been recognized as an early feature occurring at the onset of Alzheimer's disease (AD). Compromised neurotransmission leads over time to synaptic loss and these events correlate with the cognitive decline that progressively affects AD patients.Protein SUMOylation (Small Ubiquitin-like MOdifier) is a post-translational modification (PTM) involved in several cellular processes including synaptic transmission.We here demonstrate that cortical synaptosomes prepared from Tg2576 mice of 6 months of age show an increased SUMO-1ylation, which returns back to normal levels at 20 months although synaptic SUMOylation, at this age, resulted more sensible to KCl stimulus. Our previous findings have shown that increased SUMOylation at presynaptic level reduces the KCl-induced glutamate release. Accordingly, Tg2576 mice of 6 and 20 months show a reduced KCl-evoked neurotransmitter (NT) release. In order to target SUMOylation, we developed two cell penetrating HIV Tat-linked peptides, namely TU-1 and TS-1. This strategy allowed us to modulate the SUMO machinery either positively (TU-1) or negatively (TS-1). As expected, Tg2576 synaptosomes treated with TU-1 exhibited a reduced NT release evoked by KCl. On the contrary, TS-1 treatment, which decreased SUMOylation, was able to normalize impaired glutamate release. Notably, an analysis of autopsy human AD brains has shown an increased SUMOylation in both cortical tissue and synaptosomal lysate. Our data indicate that SUMOylation level changes contribute to the development of synaptic alterations typically occurring at the AD onset and that SUMOylation could be a pharmacological target in AD synaptic dysfunction.
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27
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Koidl S, Eisenhardt N, Fatouros C, Droescher M, Chaugule VK, Pichler A. The SUMO2/3 specific E3 ligase ZNF451-1 regulates PML stability. Int J Biochem Cell Biol 2016; 79:478-487. [PMID: 27343429 DOI: 10.1016/j.biocel.2016.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/01/2023]
Abstract
The small ubiquitin related modifier SUMO regulates protein functions to maintain cell homeostasis. SUMO attachment is executed by the hierarchical action of E1, E2 and E3 enzymes of which E3 ligases ensure substrate specificity. We recently identified the ZNF451 family as novel class of SUMO2/3 specific E3 ligases and characterized their function in SUMO chain formation. The founding member, ZNF451isoform1 (ZNF451-1) partially resides in PML bodies, nuclear structures organized by the promyelocytic leukemia gene product PML. As PML and diverse PML components are well known SUMO substrates the question arises whether ZNF451-1 is involved in their sumoylation. Here, we show that ZNF451-1 indeed functions as SUMO2/3 specific E3 ligase for PML and selected PML components in vitro. Mutational analysis indicates that substrate sumoylation employs an identical biochemical mechanism as we described for SUMO chain formation. In vivo, ZNF451-1 RNAi depletion leads to PML stabilization and an increased number of PML bodies. By contrast, PML degradation upon arsenic trioxide treatment is not ZNF451-1 dependent. Our data suggest a regulatory role of ZNF451-1 in fine-tuning physiological PML levels in a RNF4 cooperative manner in the mouse neuroblastoma N2a cell-line.
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Affiliation(s)
- Stefanie Koidl
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany
| | - Nathalie Eisenhardt
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany
| | - Chronis Fatouros
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany
| | - Mathias Droescher
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany
| | - Viduth K Chaugule
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany
| | - Andrea Pichler
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, 79108 Freiburg, Stübeweg 51, Germany.
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28
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Eisenhardt N, Chaugule VK, Pichler A. A Fluorescent In Vitro Assay to Investigate Paralog-Specific SUMO Conjugation. Methods Mol Biol 2016; 1475:67-78. [PMID: 27631798 DOI: 10.1007/978-1-4939-6358-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein modification with the small ubiquitin-related modifier SUMO is a potent regulatory mechanism implicated in a variety of biological pathways. In vitro sumoylation reactions have emerged as a versatile tool to identify and characterize novel SUMO enzymes as well as their substrates. Here, we present detailed protocols for the purification and fluorescent labeling of mammalian SUMO paralogs for their application in sumoylation assays. These assays provide a fast readout for in vitro SUMO chain formation activity of E3 ligases in a paralog-specific manner. Finally, we critically analyze the application of fluorescent SUMO proteins to study substrate modification in vitro revealing also the drawbacks of the system.
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Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Viduth K Chaugule
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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Eisenhardt N, Chaugule VK, Koidl S, Droescher M, Dogan E, Rettich J, Sutinen P, Imanishi SY, Hofmann K, Palvimo JJ, Pichler A. A new vertebrate SUMO enzyme family reveals insights into SUMO-chain assembly. Nat Struct Mol Biol 2015; 22:959-67. [PMID: 26524493 DOI: 10.1038/nsmb.3114] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/22/2015] [Indexed: 12/25/2022]
Abstract
SUMO chains act as stress-induced degradation tags or repair factor-recruiting signals at DNA lesions. Although E1 activating, E2 conjugating and E3 ligating enzymes efficiently assemble SUMO chains, specific chain-elongation mechanisms are unknown. E4 elongases are specialized E3 ligases that extend a chain but are inefficient in the initial conjugation of the modifier. We identified ZNF451, a representative member of a new class of SUMO2 and SUMO3 (SUMO2/3)-specific enzymes that execute catalysis via a tandem SUMO-interaction motif (SIM) region. One SIM positions the donor SUMO while a second SIM binds SUMO on the back side of the E2 enzyme. This tandem-SIM region is sufficient to extend a back side-anchored SUMO chain (E4 elongase activity), whereas efficient chain initiation also requires a zinc-finger region to recruit the initial acceptor SUMO (E3 ligase activity). Finally, we describe four human proteins sharing E4 elongase activities and their function in stress-induced SUMO2/3 conjugation.
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Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Viduth K Chaugule
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Stefanie Koidl
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Mathias Droescher
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jan Rettich
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Päivi Sutinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Susumu Y Imanishi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Eifler K, Vertegaal ACO. Mapping the SUMOylated landscape. FEBS J 2015; 282:3669-80. [PMID: 26185901 PMCID: PMC4869838 DOI: 10.1111/febs.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/15/2015] [Accepted: 07/14/2015] [Indexed: 12/26/2022]
Abstract
SUMOylation is a post‐translational modification that regulates a multitude of cellular processes, including replication, cell‐cycle progression, protein transport and the DNA damage response. Similar to ubiquitin, SUMO (small ubiquitin‐like modifier) is covalently attached to target proteins in a reversible process via an enzymatic cascade. SUMOylation is essential for nearly all eukaryotic organisms, and deregulation of the SUMO system is associated with human diseases such as cancer and neurodegenerative diseases. Therefore, it is of great interest to understand the regulation and dynamics of this post‐translational modification. Within the last decade, mass spectrometry analyses of SUMO proteomes have overcome several obstacles, greatly expanding the number of known SUMO target proteins. In this review, we briefly outline the basic concepts of the SUMO system, and discuss the potential of proteomic approaches to decipher SUMOylation patterns in order to understand the role of SUMO in health and disease.
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Affiliation(s)
- Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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Abstract
α-Synuclein inclusion bodies are a pathological hallmark of several neurodegenerative diseases, including Parkinson’s disease, and contain aggregated α-synuclein and a variety of recruited factors, including protein chaperones, proteasome components, ubiquitin and the small ubiquitin-like modifier, SUMO-1. Cell culture and animal model studies suggest that misfolded, aggregated α-synuclein is actively translocated via the cytoskeletal system to a region of the cell where other factors that help to lessen the toxic effects can also be recruited. SUMO-1 covalently conjugates to various intracellular target proteins in a way analogous to ubiquitination to alter cellular distribution, function and metabolism and also plays an important role in a growing list of cellular pathways, including exosome secretion and apoptosis. Furthermore, SUMO-1 modified proteins have recently been linked to cell stress responses, such as oxidative stress response and heat shock response, with increased SUMOylation being neuroprotective in some cases. Several recent studies have linked SUMOylation to the ubiquitin-proteasome system, while other evidence implicates the lysosomal pathway. Other reports depict a direct mechanism whereby sumoylation reduced the aggregation tendency of α-synuclein, and reduced the toxicity. However, the precise role of SUMO-1 in neurodegeneration remains unclear. In this review, we explore the potential direct or indirect role(s) of SUMO-1 in the cellular response to misfolded α-synuclein in neurodegenerative disorders.
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Beauclair G, Bridier-Nahmias A, Zagury JF, Saïb A, Zamborlini A. JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs. Bioinformatics 2015; 31:3483-91. [PMID: 26142185 DOI: 10.1093/bioinformatics/btv403] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/25/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs. RESULTS JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files. AVAILABILITY AND IMPLEMENTATION JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported. CONTACT guillaume.beauclair@inserm.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guillaume Beauclair
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis
| | - Antoine Bridier-Nahmias
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de bioinformatique, Conservatoire national des arts et métiers (Cnam), Paris, France
| | - Ali Saïb
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and
| | - Alessia Zamborlini
- CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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Stastna M, Van Eyk JE. Posttranslational modifications of lysine and evolving role in heart pathologies-recent developments. Proteomics 2015; 15:1164-80. [PMID: 25430483 DOI: 10.1002/pmic.201400312] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 02/06/2023]
Abstract
The alteration in proteome composition induced by environmental changes and various pathologies is accompanied by the modifications of proteins by specific cotranslational and PTMs. The type and site stoichiometry of PTMs can affect protein functions, alter cell signaling, and can have acute and chronic effects. The particular interest is drawn to those amino acid residues that can undergo several different PTMs. We hypothesize that these selected amino acid residues are biologically rare and act within the cell as molecular switches. There are, at least, 12 various lysine modifications currently known, several of them have been shown to be competitive and they influence the ability of a particular lysine to be modified by a different PTM. In this review, we discuss the PTMs that occur on lysine, specifically neddylation and sumoylation, and the proteomic approaches that can be applied for the identification and quantification of these PTMs. Of interest are the emerging roles for these modifications in heart disease and what can be inferred from work in other cell types and organs.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic, v. v. i, Brno, Czech Republic
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Yuan Y, Isom LL. SUMOylation of Neuronal K⁺ channels: a potential therapeutic pathway for epilepsy and SUDEP? Neuron 2014; 83:996-8. [PMID: 25189206 DOI: 10.1016/j.neuron.2014.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Critical unmet clinical needs are the treatment of epilepsy without side effects and prevention of sudden unexpected death in epilepsy, or SUDEP. In this issue of Neuron, Qi et al. (2014), define how hyper-SUMOylation impacts K(+) channel activity in vivo and could serve as a potential pathway for development of novel epilepsy therapeutics.
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Affiliation(s)
- Yukun Yuan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lori L Isom
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Henley JM, Craig TJ, Wilkinson KA. Neuronal SUMOylation: mechanisms, physiology, and roles in neuronal dysfunction. Physiol Rev 2014; 94:1249-85. [PMID: 25287864 PMCID: PMC4187031 DOI: 10.1152/physrev.00008.2014] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein SUMOylation is a critically important posttranslational protein modification that participates in nearly all aspects of cellular physiology. In the nearly 20 years since its discovery, SUMOylation has emerged as a major regulator of nuclear function, and more recently, it has become clear that SUMOylation has key roles in the regulation of protein trafficking and function outside of the nucleus. In neurons, SUMOylation participates in cellular processes ranging from neuronal differentiation and control of synapse formation to regulation of synaptic transmission and cell survival. It is a highly dynamic and usually transient modification that enhances or hinders interactions between proteins, and its consequences are extremely diverse. Hundreds of different proteins are SUMO substrates, and dysfunction of protein SUMOylation is implicated in a many different diseases. Here we briefly outline core aspects of the SUMO system and provide a detailed overview of the current understanding of the roles of SUMOylation in healthy and diseased neurons.
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Affiliation(s)
- Jeremy M Henley
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Tim J Craig
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Kevin A Wilkinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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Feligioni M, Mattson MP, Nisticò R. SUMOylation in neuroplasticity and neurological disorders. Neuromolecular Med 2014; 15:637-8. [PMID: 24354012 DOI: 10.1007/s12017-013-8267-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Nisticò R, Ferraina C, Marconi V, Blandini F, Negri L, Egebjerg J, Feligioni M. Age-related changes of protein SUMOylation balance in the AβPP Tg2576 mouse model of Alzheimer's disease. Front Pharmacol 2014; 5:63. [PMID: 24778618 PMCID: PMC3985012 DOI: 10.3389/fphar.2014.00063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/19/2014] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD) is a complex disorder that affects the central nervous system causing a severe neurodegeneration. This pathology affects an increasing number of people worldwide due to the overall aging of the human population. In recent years SUMO protein modification has emerged as a possible cellular mechanism involved in AD. Some of the proteins engaged in the physiopathological process of AD, like BACE1, GSK3-β tau, AβPP, and JNK, are in fact subject to protein SUMO modifications or interactions. Here, we have investigated the SUMO/deSUMOylation balance and SUMO-related proteins during the onset and progression of the pathology in the Tg2576 mouse model of AD. We examined four age-stages (1.5, 3, 6, 17 months old) and observed shows an increase in SUMO-1 protein conjugation at 3 and 6 months in transgenic mice with respect to WT in both cortex and hippocampus. Interestingly this is paralleled by increased expression levels of Ubc9 and SENP1 in both brain regions. At 6 months of age also the SUMO-1 mRNA resulted augmented. SUMO-2-ylation was surprisingly decreased in old transgenic mice and was unaltered in the other time windows. The fact that alterations in SUMO/deSUMOylation equilibrium occur from the early phases of AD suggests that global posttranslational modifications may play an important role in the mechanisms underlying disease pathogenesis, thus providing potential targets for pharmacological interventions.
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Affiliation(s)
- Robert Nisticò
- IRCCS Fondazione Santa Lucia Rome, Italy ; Department of Physiology and Pharmacology, Sapienza University of Rome Rome, Italy
| | - Caterina Ferraina
- Laboratory of Pharmacology of Synaptic Plasticity, EBRI "Rita Levi-Montalcini" Foundation Rome, Italy
| | - Veronica Marconi
- Department of Physiology and Pharmacology, Sapienza University of Rome Rome, Italy
| | - Fabio Blandini
- Center for Research in Neurodegenerative Diseases, C. Mondino National Neurological Institute Pavia, Italy
| | - Lucia Negri
- Department of Physiology and Pharmacology, Sapienza University of Rome Rome, Italy
| | - Jan Egebjerg
- Neuroscience Drug Discovery DK H. Lundbeck A/S, Valby, Denmark
| | - Marco Feligioni
- Laboratory of Pharmacology of Synaptic Plasticity, EBRI "Rita Levi-Montalcini" Foundation Rome, Italy
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