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Tang HW, Weng JH, Lee WX, Hu Y, Gu L, Cho S, Lee G, Binari R, Li C, Cheng ME, Kim AR, Xu J, Shen Z, Xu C, Asara JM, Blenis J, Perrimon N. mTORC1-chaperonin CCT signaling regulates m 6A RNA methylation to suppress autophagy. Proc Natl Acad Sci U S A 2021; 118:e2021945118. [PMID: 33649236 PMCID: PMC7958400 DOI: 10.1073/pnas.2021945118] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a central regulator of cell growth and metabolism that senses and integrates nutritional and environmental cues with cellular responses. Recent studies have revealed critical roles of mTORC1 in RNA biogenesis and processing. Here, we find that the m6A methyltransferase complex (MTC) is a downstream effector of mTORC1 during autophagy in Drosophila and human cells. Furthermore, we show that the Chaperonin Containing Tailless complex polypeptide 1 (CCT) complex, which facilitates protein folding, acts as a link between mTORC1 and MTC. The mTORC1 activates the chaperonin CCT complex to stabilize MTC, thereby increasing m6A levels on the messenger RNAs encoding autophagy-related genes, leading to their degradation and suppression of autophagy. Altogether, our study reveals an evolutionarily conserved mechanism linking mTORC1 signaling with m6A RNA methylation and demonstrates their roles in suppressing autophagy.
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Affiliation(s)
- Hong-Wen Tang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore;
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Jui-Hsia Weng
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Lei Gu
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Sungyun Cho
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065
| | - Gina Lee
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA 92697
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Cathleen Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Min En Cheng
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Ah-Ram Kim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Zhangfei Shen
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Chiwei Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - John Blenis
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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152
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STAU2 protein level is controlled by caspases and the CHK1 pathway and regulates cell cycle progression in the non-transformed hTERT-RPE1 cells. BMC Mol Cell Biol 2021; 22:16. [PMID: 33663378 PMCID: PMC7934504 DOI: 10.1186/s12860-021-00352-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Staufen2 (STAU2) is an RNA binding protein involved in the posttranscriptional regulation of gene expression. In neurons, STAU2 is required to maintain the balance between differentiation and proliferation of neural stem cells through asymmetric cell division. However, the importance of controlling STAU2 expression for cell cycle progression is not clear in non-neuronal dividing cells. We recently showed that STAU2 transcription is inhibited in response to DNA-damage due to E2F1 displacement from the STAU2 gene promoter. We now study the regulation of STAU2 steady-state levels in unstressed cells and its consequence for cell proliferation. Results CRISPR/Cas9-mediated and RNAi-dependent STAU2 depletion in the non-transformed hTERT-RPE1 cells both facilitate cell proliferation suggesting that STAU2 expression influences pathway(s) linked to cell cycle controls. Such effects are not observed in the CRISPR STAU2-KO cancer HCT116 cells nor in the STAU2-RNAi-depleted HeLa cells. Interestingly, a physiological decrease in the steady-state level of STAU2 is controlled by caspases. This effect of peptidases is counterbalanced by the activity of the CHK1 pathway suggesting that STAU2 partial degradation/stabilization fines tune cell cycle progression in unstressed cells. A large-scale proteomic analysis using STAU2/biotinylase fusion protein identifies known STAU2 interactors involved in RNA translation, localization, splicing, or decay confirming the role of STAU2 in the posttranscriptional regulation of gene expression. In addition, several proteins found in the nucleolus, including proteins of the ribosome biogenesis pathway and of the DNA damage response, are found in close proximity to STAU2. Strikingly, many of these proteins are linked to the kinase CHK1 pathway, reinforcing the link between STAU2 functions and the CHK1 pathway. Indeed, inhibition of the CHK1 pathway for 4 h dissociates STAU2 from proteins involved in translation and RNA metabolism. Conclusions These results indicate that STAU2 is involved in pathway(s) that control(s) cell proliferation, likely via mechanisms of posttranscriptional regulation, ribonucleoprotein complex assembly, genome integrity and/or checkpoint controls. The mechanism by which STAU2 regulates cell growth likely involves caspases and the kinase CHK1 pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00352-y.
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153
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Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo J. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res 2021; 49:1951-1971. [PMID: 33524141 PMCID: PMC7913686 DOI: 10.1093/nar/gkab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | | | - Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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154
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Vélot L, Lessard F, Bérubé-Simard FA, Tav C, Neveu B, Teyssier V, Boudaoud I, Dionne U, Lavoie N, Bilodeau S, Pouliot F, Bisson N. Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. Mol Cell Proteomics 2021; 20:100064. [PMID: 33640491 PMCID: PMC8050775 DOI: 10.1016/j.mcpro.2021.100064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer in men and the third cause of cancer mortality. PCa initiation and growth are driven by the androgen receptor (AR). The AR is activated by androgens such as testosterone and controls prostatic cell proliferation and survival. Here, we report an AR signaling network generated using BioID proximity labeling proteomics in androgen-dependent LAPC4 cells. We identified 31 AR-associated proteins in nonstimulated cells. Strikingly, the AR signaling network increased to 182 and 200 proteins, upon 24 h or 72 h of androgenic stimulation, respectively, for a total of 267 nonredundant AR-associated candidates. Among the latter group, we identified 213 proteins that were not previously reported in databases. Many of these new AR-associated proteins are involved in DNA metabolism, RNA processing, and RNA polymerase II transcription. Moreover, we identified 44 transcription factors, including the Kru¨ppel-like factor 4 (KLF4), which were found interacting in androgen-stimulated cells. Interestingly, KLF4 repressed the well-characterized AR-dependent transcription of the KLK3 (PSA) gene; AR and KLF4 also colocalized genome-wide. Taken together, our data report an expanded high-confidence proximity network for AR, which will be instrumental to further dissect the molecular mechanisms underlying androgen signaling in PCa cells. BioID proteomics identifies 267 androgen receptor (AR)-associated candidates Krüppel-like factor 4 (KLF4) is a new AR interaction partner AR and KLF4 colocalize genome-wide on >4000 genes, including KLK3 (PSA) KLF4 acts as a repressor for the AR target gene KLK3 (PSA)
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Affiliation(s)
- Lauriane Vélot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Christophe Tav
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada
| | - Bertrand Neveu
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Imène Boudaoud
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Ugo Dionne
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Steve Bilodeau
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Frédéric Pouliot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Department of Surgery, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
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155
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The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33655243 PMCID: PMC7924263 DOI: 10.1101/2021.02.23.432450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2. Author Summary SARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 is proximal to the EIF3 translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.
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156
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Bittremieux W, Adams C, Laukens K, Dorrestein PC, Bandeira N. Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. J Proteome Res 2021; 20:1464-1475. [PMID: 33605735 DOI: 10.1021/acs.jproteome.0c00929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research, including proteomics, is playing a role in determining the biology of this viral infection. Proteomics studies are starting to lead to an understanding of the roles of viral and host proteins during SARS-CoV-2 infection, their protein-protein interactions, and post-translational modifications. This is beginning to provide insights into potential therapeutic targets or diagnostic strategies that can be used to reduce the long-term burden of the pandemic. However, the extraordinary situation caused by the global pandemic is also highlighting the need to improve mass spectrometry data and workflow sharing. We therefore describe freely available data and computational resources that can facilitate and assist the mass spectrometry-based analysis of SARS-CoV-2. We exemplify this by reanalyzing a virus-host interactome data set to detect protein-protein interactions and identify host proteins that could potentially be used as targets for drug repurposing.
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Affiliation(s)
- Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science and Engineering, University of California San Diego, La Jolla 92093, California, United States
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157
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Drummond E, Pires G, MacMurray C, Askenazi M, Nayak S, Bourdon M, Safar J, Ueberheide B, Wisniewski T. Phosphorylated tau interactome in the human Alzheimer's disease brain. Brain 2021; 143:2803-2817. [PMID: 32812023 DOI: 10.1093/brain/awaa223] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/22/2020] [Indexed: 01/07/2023] Open
Abstract
Accumulation of phosphorylated tau is a key pathological feature of Alzheimer's disease. Phosphorylated tau accumulation causes synaptic impairment, neuronal dysfunction and formation of neurofibrillary tangles. The pathological actions of phosphorylated tau are mediated by surrounding neuronal proteins; however, a comprehensive understanding of the proteins that phosphorylated tau interacts with in Alzheimer's disease is surprisingly limited. Therefore, the aim of this study was to determine the phosphorylated tau interactome. To this end, we used two complementary proteomics approaches: (i) quantitative proteomics was performed on neurofibrillary tangles microdissected from patients with advanced Alzheimer's disease; and (ii) affinity purification-mass spectrometry was used to identify which of these proteins specifically bound to phosphorylated tau. We identified 542 proteins in neurofibrillary tangles. This included the abundant detection of many proteins known to be present in neurofibrillary tangles such as tau, ubiquitin, neurofilament proteins and apolipoprotein E. Affinity purification-mass spectrometry confirmed that 75 proteins present in neurofibrillary tangles interacted with PHF1-immunoreactive phosphorylated tau. Twenty-nine of these proteins have been previously associated with phosphorylated tau, therefore validating our proteomic approach. More importantly, 34 proteins had previously been associated with total tau, but not yet linked directly to phosphorylated tau (e.g. synaptic protein VAMP2, vacuolar-ATPase subunit ATP6V0D1); therefore, we provide new evidence that they directly interact with phosphorylated tau in Alzheimer's disease. In addition, we also identified 12 novel proteins, not previously known to be physiologically or pathologically associated with tau (e.g. RNA binding protein HNRNPA1). Network analysis showed that the phosphorylated tau interactome was enriched in proteins involved in the protein ubiquitination pathway and phagosome maturation. Importantly, we were able to pinpoint specific proteins that phosphorylated tau interacts with in these pathways for the first time, therefore providing novel potential pathogenic mechanisms that can be explored in future studies. Combined, our results reveal new potential drug targets for the treatment of tauopathies and provide insight into how phosphorylated tau mediates its toxicity in Alzheimer's disease.
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Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, Australia.,Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA.,Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Claire MacMurray
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | | | - Shruti Nayak
- Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, New York, NY, USA
| | - Marie Bourdon
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Jiri Safar
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Beatrix Ueberheide
- Biomedical Hosting LLC, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA.,Department of Psychiatry, New York University School of Medicine, New York, NY, USA
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158
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Basu A, Ash PEA, Wolozin B, Emili A. Protein Interaction Network Biology in Neuroscience. Proteomics 2021; 21:e1900311. [PMID: 33314619 PMCID: PMC7900949 DOI: 10.1002/pmic.201900311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/27/2020] [Indexed: 01/04/2023]
Abstract
Mapping the intricate networks of cellular proteins in the human brain has the potential to address unsolved questions in molecular neuroscience, including the molecular basis of cognition, synaptic plasticity, long-term potentiation, learning, and memory. Perturbations to the protein-protein interaction networks (PPIN) present in neurons, glia, and other cell-types have been linked to multifactorial neurological disorders. Yet while knowledge of brain PPINs is steadily improving, the complexity and dynamic nature of the heterogeneous central nervous system in normal and disease contexts poses a formidable experimental challenge. In this review, the recent applications of functional proteomics and systems biology approaches to study PPINs central to normal neuronal function, during neurodevelopment, and in neurodegenerative disorders are summarized. How systematic PPIN analysis offers a unique mechanistic framework to explore intra- and inter-cellular functional modules governing neuronal activity and brain function is also discussed. Finally, future technological advancements needed to address outstanding questions facing neuroscience are outlined.
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Affiliation(s)
- Avik Basu
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
| | - Peter EA Ash
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Andrew Emili
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
- Department of BiologyBoston UniversityBostonMA02215USA
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159
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Brunet MA, Jacques J, Nassari S, Tyzack GE, McGoldrick P, Zinman L, Jean S, Robertson J, Patani R, Roucou X. The FUS gene is dual-coding with both proteins contributing to FUS-mediated toxicity. EMBO Rep 2021; 22:e50640. [PMID: 33226175 PMCID: PMC7788448 DOI: 10.15252/embr.202050640] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Novel functional coding sequences (altORFs) are camouflaged within annotated ones (CDS) in a different reading frame. We show here that an altORF is nested in the FUS CDS, encoding a conserved 170 amino acid protein, altFUS. AltFUS is endogenously expressed in human tissues, notably in the motor cortex and motor neurons. Over-expression of wild-type FUS and/or amyotrophic lateral sclerosis-linked FUS mutants is known to trigger toxic mechanisms in different models. These include inhibition of autophagy, loss of mitochondrial potential and accumulation of cytoplasmic aggregates. We find that altFUS, not FUS, is responsible for the inhibition of autophagy, and pivotal in mitochondrial potential loss and accumulation of cytoplasmic aggregates. Suppression of altFUS expression in a Drosophila model of FUS-related toxicity protects against neurodegeneration. Some mutations found in ALS patients are overlooked because of their synonymous effect on the FUS protein. Yet, we show they exert a deleterious effect causing missense mutations in the overlapping altFUS protein. These findings demonstrate that FUS is a bicistronic gene and suggests that both proteins, FUS and altFUS, cooperate in toxic mechanisms.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry and Functional GenomicsUniversité de SherbrookeSherbrookeQCCanada
- PROTEOQuebec Network for Research on Protein Function, Structure, and EngineeringQuebecQCCanada
| | - Jean‐Francois Jacques
- Department of Biochemistry and Functional GenomicsUniversité de SherbrookeSherbrookeQCCanada
- PROTEOQuebec Network for Research on Protein Function, Structure, and EngineeringQuebecQCCanada
| | - Sonya Nassari
- Immunology and Cell Biology DepartmentUniversité de SherbrookeSherbrookeQCCanada
| | - Giulia E Tyzack
- The Francis Crick InstituteLondonUK
- Department of Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| | - Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Lorne Zinman
- Division of NeurologyDepartment of MedicineSunnybrook Health Sciences CentreUniversity of TorontoTorontoONCanada
| | - Steve Jean
- Immunology and Cell Biology DepartmentUniversité de SherbrookeSherbrookeQCCanada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Rickie Patani
- The Francis Crick InstituteLondonUK
- Department of Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| | - Xavier Roucou
- Department of Biochemistry and Functional GenomicsUniversité de SherbrookeSherbrookeQCCanada
- PROTEOQuebec Network for Research on Protein Function, Structure, and EngineeringQuebecQCCanada
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160
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Smejda M, Kądziołka D, Radczuk N, Krutyhołowa R, Chramiec-Głąbik A, Kędracka-Krok S, Jankowska U, Biela A, Glatt S. Same but different - Molecular comparison of human KTI12 and PSTK. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118945. [PMID: 33417976 DOI: 10.1016/j.bbamcr.2020.118945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Kti12 and PSTK are closely related and highly similar proteins implicated in different aspects of tRNA metabolism. Kti12 has been identified as an essential regulatory factor of the Elongator complex, involved in the modification of uridine bases in eukaryotic tRNAs. PSTK phosphorylates the tRNASec-bound amino acid serine, which is required to synthesize selenocysteine. Kti12 and PSTK have previously been studied independently in various organisms, but only appear simultaneously in some animalia, including humans. As Kti12- and PSTK-related pathways are clinically relevant, it is of prime importance to understand their biological functions and mutual relationship in humans. Here, we use different tRNA substrates to directly compare the enzymatic activities of purified human KTI12 and human PSTK proteins. Our complementary Co-IP and BioID2 approaches in human cells confirm that Elongator is the main interaction partner of KTI12 but additionally indicate potential links to proteins involved in vesicular transport, RNA metabolism and deubiquitination. Moreover, we identify and validate a yet uncharacterized interaction between PSTK and γ-taxilin. Foremost, we demonstrate that human KTI12 and PSTK do not share interactors or influence their respective biological functions. Our data provide a comprehensive analysis of the regulatory networks controlling the activity of the human Elongator complex and selenocysteine biosynthesis.
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Affiliation(s)
- Marta Smejda
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dominika Kądziołka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Natalia Radczuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Sylwia Kędracka-Krok
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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161
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Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol 2021; 17:e8792. [PMID: 33434350 PMCID: PMC7803364 DOI: 10.15252/msb.20188792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
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162
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Fossati A, Frommelt F, Uliana F, Martelli C, Vizovisek M, Gillet L, Collins B, Gstaiger M, Aebersold R. System-Wide Profiling of Protein Complexes Via Size Exclusion Chromatography-Mass Spectrometry (SEC-MS). Methods Mol Biol 2021; 2259:269-294. [PMID: 33687722 DOI: 10.1007/978-1-0716-1178-4_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In living cells, most proteins are organized in stable or transient functional assemblies, protein complexes, which control a multitude of vital cellular processes such as cell cycle progression, metabolism, and signal transduction. Over several decades, specific protein complexes have been analyzed by structural biology methods, initially X-ray crystallography and more recently single particle cryoEM. In parallel, mass spectrometry (MS)-based methods including in vitro affinity-purification coupled to MS or in vivo protein proximity-dependent labeling methods have proven particularly effective to detect complexes, thus nominating new assemblies for structural analysis. Those approaches, however, are either of limited in throughput or require specifically engineered protein systems.In this chapter, we present protocols for a workflow that supports the parallel analysis of multiple complexes from the same biological sample with respect to abundance, subunit composition, and stoichiometry. It consists of the separation of native complexes by size-exclusion chromatography (SEC) and the subsequent mass spectrometric analysis of the proteins in consecutive SEC fractions. In particular, we describe (1) optimized conditions to achieve native protein complex separation by SEC, (2) the preparation of the SEC fractions for MS analysis, (3) the acquisition of the MS data at high throughput via SWATH/DIA (data-independent analysis) mass spectrometry and short chromatographic gradients, and (4) a set of bioinformatic tools for the targeted analysis of protein complexes. Altogether, the parallel measurement of a high number of complexes from a single biological sample results in unprecedented system-level insights into the remodeling of cellular protein complexes in response to perturbations of a broad range of cellular systems.
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Affiliation(s)
- Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Matej Vizovisek
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ben Collins
- School of Biological Sciences, Queen's University of Belfast, Belfast, UK
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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163
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Tanneti NS, Federspiel JD, Cristea IM, Enquist LW. The axonal sorting activity of pseudorabies virus Us9 protein depends on the state of neuronal maturation. PLoS Pathog 2020; 16:e1008861. [PMID: 33370419 PMCID: PMC7794026 DOI: 10.1371/journal.ppat.1008861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/08/2021] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Alpha-herpesviruses establish a life-long infection in the nervous system of the affected host; while this infection is restricted to peripheral neurons in a healthy host, the reactivated virus can spread within the neuronal circuitry, such as to the brain, in compromised individuals and lead to adverse health outcomes. Pseudorabies virus (PRV), an alpha-herpesvirus, requires the viral protein Us9 to sort virus particles into axons and facilitate neuronal spread. Us9 sorts virus particles by mediating the interaction of virus particles with neuronal transport machinery. Here, we report that Us9-mediated regulation of axonal sorting also depends on the state of neuronal maturation. Specifically, the development of dendrites and axons is accompanied with proteomic changes that influence neuronal processes. Immature superior cervical ganglionic neurons (SCGs) have rudimentary neurites that lack markers of mature axons. Immature SCGs can be infected by PRV, but they show markedly reduced Us9-dependent regulation of sorting, and increased Us9-independent transport of particles into neurites. Mature SCGs have relatively higher abundances of proteins characteristic of vesicle-transport machinery. We also identify Us9-associated neuronal proteins that can contribute to axonal sorting and subsequent anterograde spread of virus particles in axons. We show that SMPD4/nsMase3, a sphingomyelinase abundant in lipid-rafts, associates with Us9 and is a negative regulator of PRV sorting into axons and neuronal spread, a potential antiviral function.
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Affiliation(s)
- Nikhila S. Tanneti
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Joel D. Federspiel
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Lynn W. Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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164
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Dziengelewski C, Rodrigue MA, Caillier A, Jacquet K, Boulanger MC, Bergeman J, Fuchs M, Lambert H, Laprise P, Richard DE, Bordeleau F, Huot MÉ, Lavoie JN. Adenoviral protein E4orf4 interacts with the polarity protein Par3 to induce nuclear rupture and tumor cell death. J Cell Biol 2020; 219:151580. [PMID: 32328642 PMCID: PMC7147092 DOI: 10.1083/jcb.201805122] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/12/2019] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
The tumor cell–selective killing activity of the adenovirus type 2 early region 4 ORF4 (E4orf4) protein is poorly defined at the molecular level. Here, we show that the tumoricidal effect of E4orf4 is typified by changes in nuclear dynamics that depend on its interaction with the polarity protein Par3 and actomyosin contractility. Mechanistically, E4orf4 induced a high incidence of nuclear bleb formation and repetitive nuclear ruptures, which promoted nuclear efflux of E4orf4 and loss of nuclear integrity. This process was regulated by nucleocytoskeletal connections, Par3 clustering proximal to nuclear lamina folds, and retrograde movement of actin bundles that correlated with nuclear ruptures. Significantly, Par3 also regulated the incidence of spontaneous nuclear ruptures facilitated by the downmodulation of lamins. This work uncovered a novel role for Par3 in controlling the actin-dependent forces acting on the nuclear envelope to remodel nuclear shape, which might be a defining feature of tumor cells that is harnessed by E4orf4.
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Affiliation(s)
- Claire Dziengelewski
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Marc-Antoine Rodrigue
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Alexia Caillier
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Kévin Jacquet
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Marie-Chloé Boulanger
- Department of Surgery, Quebec Heart and Lung Institute/Research Center, Université Laval, Québec, Canada
| | - Jonathan Bergeman
- Institut de Recherches Clinique de Montréal, Montréal, Québec, Canada
| | - Margit Fuchs
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Faculty of Management, Dalhousie University, Halifax, Canada
| | - Herman Lambert
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Patrick Laprise
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Québec City, Québec, Canada
| | - Darren E Richard
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Québec City, Québec, Canada.,Endocrinology and Nephrology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - François Bordeleau
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Québec City, Québec, Canada
| | - Marc-Étienne Huot
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Québec City, Québec, Canada
| | - Josée N Lavoie
- Centre de Recherche sur le Cancer de l'Université Laval, Québec City, Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Québec City, Québec, Canada
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165
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020; 11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex formation, which in turn constitutes the basis for protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes. In this study, we extend co-fractionation and mass spectrometric data analysis to perform quantitative, network-based studies of proteome organization, via the size-exclusion chromatography algorithmic toolkit (SECAT). This framework explicitly accounts for the dynamic nature and rewiring of protein complexes across multiple cell states and samples, thus, elucidating molecular mechanisms that are differentially implemented across different experimental settings. Systematic analysis of multiple datasets shows that SECAT represents a highly scalable and effective methodology to assess condition/state-specific protein-network state. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York NY, USA; Department of Biomedical Informatics, Columbia University, New York NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA.
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166
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Lacasse V, Beaudoin S, Jean S, Leyton JV. A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:99-119. [PMID: 33024794 PMCID: PMC7522293 DOI: 10.1016/j.omtm.2020.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 08/27/2020] [Indexed: 11/01/2022]
Abstract
The next breakthrough for protein therapeutics is effective intracellular delivery and accumulation within target cells. Nuclear localization signal (NLS)-tagged therapeutics have been hindered by the lack of efficient nuclear localization due to endosome entrapment. Although development of strategies for tagging therapeutics with technologies capable of increased membrane penetration has resulted in proportional increased potency, nonspecific membrane penetration limits target specificity and, hence, widespread clinical success. There is a long-standing idea that nuclear localization of NLS-tagged agents occurs exclusively via classical nuclear transport. In the present study, we modified the antibody-drug conjugate trastuzumab-emtansine (T-DM1) with a classical NLS linked to cholic acid (cell accumulator [Accum]) that enables modified antibodies to escape endosome entrapment and increase nuclear localization efficiency without abrogating receptor targeting. In parallel, we developed a proteomics-based method to evaluate nuclear transport. Accum-modified T-DM1 significantly enhanced cytotoxic efficacy in the human epidermal growth factor receptor 2 (HER2)-positive SKBR3 breast cancer system. We discovered that efficacy was dependent on the nonclassical importin-7. Our evaluation reveals that when multiple classical NLS tagging occurs, cationic charge build-up as opposed to sequence dominates and becomes a substrate for importin-7. This study results in an effective target cell-specific NLS therapeutic and a general approach to guide future NLS-based development initiatives.
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Affiliation(s)
- Vincent Lacasse
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Simon Beaudoin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Steve Jean
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
| | - Jeffrey V Leyton
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada.,Sherbrooke Molecular Imaging Centre (CIMS), Centre de Recherche du CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
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167
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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168
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Rogers CM, Sanders E, Nguyen PA, Smith-Kinnaman W, Mosley AL, Bochman ML. The Genetic and Physical Interactomes of the Saccharomyces cerevisiae Hrq1 Helicase. G3 (BETHESDA, MD.) 2020; 10:4347-4357. [PMID: 33115721 PMCID: PMC7718736 DOI: 10.1534/g3.120.401864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023]
Abstract
The human genome encodes five RecQ helicases (RECQL1, BLM, WRN, RECQL4, and RECQL5) that participate in various processes underpinning genomic stability. Of these enzymes, the disease-associated RECQL4 is comparatively understudied due to a variety of technical challenges. However, Saccharomyces cerevisiae encodes a functional homolog of RECQL4 called Hrq1, which is more amenable to experimentation and has recently been shown to be involved in DNA inter-strand crosslink (ICL) repair and telomere maintenance. To expand our understanding of Hrq1 and the RecQ4 subfamily of helicases in general, we took a multi-omics approach to define the Hrq1 interactome in yeast. Using synthetic genetic array analysis, we found that mutations of genes involved in processes such as DNA repair, chromosome segregation, and transcription synthetically interact with deletion of HRQ1 and the catalytically inactive hrq1-K318A allele. Pull-down of tagged Hrq1 and mass spectrometry identification of interacting partners similarly underscored links to these processes and others. Focusing on transcription, we found that hrq1 mutant cells are sensitive to caffeine and that mutation of HRQ1 alters the expression levels of hundreds of genes. In the case of hrq1-K318A, several of the most highly upregulated genes encode proteins of unknown function whose expression levels are also increased by DNA ICL damage. Together, our results suggest a heretofore unrecognized role for Hrq1 in transcription, as well as novel members of the Hrq1 ICL repair pathway. These data expand our understanding of RecQ4 subfamily helicase biology and help to explain why mutations in human RECQL4 cause diseases of genomic instability.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Elsbeth Sanders
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Phoebe A Nguyen
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Whitney Smith-Kinnaman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
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169
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A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. Proteomes 2020; 8:proteomes8040037. [PMID: 33276494 PMCID: PMC7709110 DOI: 10.3390/proteomes8040037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 01/08/2023] Open
Abstract
Proximity biotinylation was developed to detect physiologically relevant protein–protein interactions in living cells. In this method, the protein of interest is tagged with a promiscuous biotin ligase, such as BioID or BioID2, which produces activated biotin that reacts with nearby proteins; these proteins can subsequently be purified and identified by mass spectrometry. Here we report a novel modification of this technique by combining it with a self-associating split-GFP system in which we exploit the high-affinity interaction between GFP1–10 and GFP11 to recruit BioID2 to the protein of interest. As a test case, we fused GFP11 to clathrin light chain (CLTB) and BioID2 to GFP1–10. Co-expression of GFP11-CLTB and BioID2-GFP1–10 yielded a green fluorescent complex that co-localized with clathrin heavy chain. To facilitate removal of non-specifically biotinylated proteins, we generated an inducible cell line expressing BioID2-GFP1–10. Proximity biotinylation in this cell line with GFP11-CLTB yielded a higher percentage of biologically relevant interactions than direct fusion of BioID2 to CLTB. Thus, this system can be used to monitor expression and localization of BioID bait proteins and to identify protein–protein interactions.
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170
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Human VAPome Analysis Reveals MOSPD1 and MOSPD3 as Membrane Contact Site Proteins Interacting with FFAT-Related FFNT Motifs. Cell Rep 2020; 33:108475. [DOI: 10.1016/j.celrep.2020.108475] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/05/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
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171
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Khan MM, Välikangas T, Khan MH, Moulder R, Ullah U, Bhosale SD, Komsi E, Butt U, Qiao X, Westermarck J, Elo LL, Lahesmaa R. Protein interactome of the Cancerous Inhibitor of protein phosphatase 2A (CIP2A) in Th17 cells. CURRENT RESEARCH IN IMMUNOLOGY 2020; 1:10-22. [PMID: 33817627 PMCID: PMC8008788 DOI: 10.1016/j.crimmu.2020.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Cancerous inhibitor of protein phosphatase 2A (CIP2A) is involved in immune response, cancer progression, and Alzheimer's disease. However, an understanding of the mechanistic basis of its function in this wide spectrum of physiological and pathological processes is limited due to its poorly characterized interaction networks. Here we present the first systematic characterization of the CIP2A interactome by affinity-purification mass spectrometry combined with validation by selected reaction monitoring targeted mass spectrometry (SRM-MS) analysis in T helper (Th) 17 (Th17) cells. In addition to the known regulatory subunits of protein phosphatase 2A (PP2A), the catalytic subunits of protein PP2A were found to be interacting with CIP2A. Furthermore, the regulatory (PPP1R18, and PPP1R12A) and catalytic (PPP1CA) subunits of phosphatase PP1 were identified among the top novel CIP2A interactors. Evaluation of the ontologies associated with the proteins in this interactome revealed that they were linked with RNA metabolic processing and splicing, protein traffic, cytoskeleton regulation and ubiquitin-mediated protein degradation processes. Taken together, this network of protein-protein interactions will be important for understanding and further exploring the biological processes and mechanisms regulated by CIP2A both in physiological and pathological conditions. The first characterisation of the CIP2A interactome in Th17 cells. Key interactions validated by targeted SRM-MS proteomics, western blot and confocal microscopy. Pathway analysis of the interactome revealed interrelationships with proteins across a broad range of cellular processes. The study identifies for the first time the interaction of phosphatase PP1 with CIP2A.
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Affiliation(s)
- Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM), Medical Faculty, University of Turku, Turku, Finland
| | - Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Doctoral Programme in Mathematics and Computer Sciences (MATTI), University of Turku, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ubaid Ullah
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh Dilip Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM), Medical Faculty, University of Turku, Turku, Finland
| | - Elina Komsi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Umar Butt
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Xi Qiao
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Corresponding author. Turku Bioscience Centre, Tykistökatu 6A, Turku, 20520, Finland.
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172
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Béganton B, Coyaud E, Laurent EMN, Mangé A, Jacquemetton J, Le Romancer M, Raught B, Solassol J. Proximal Protein Interaction Landscape of RAS Paralogs. Cancers (Basel) 2020; 12:cancers12113326. [PMID: 33187149 PMCID: PMC7696408 DOI: 10.3390/cancers12113326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/01/2020] [Accepted: 11/07/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary RAS paralogs (HRAS, NRAS and KRAS) are of major interest in biology because they are involved in developmental disorders (e.g., Costello and Noonan syndromes) and in a broad variety of human neoplasia. Many research groups have devoted tremendous efforts to deepen our understanding of the RAS proteins functions and regulations, notably through identifying their functional protein partners. However, while most of these studies were focused on pathogenic RAS mutants, much less research has been dedicated to deciphering the normal activities of RAS paralogs. However, such characterization appears as a prerequisite to clearly identify pathogenic features. We delineated and compared the wild type RAS paralogs proximal interactomes. We detected more than 800 RAS high confident proximal interactors, either shared between paralogs or unique, and validated a subset of data through proximity ligation assays-based validation. Our results describe differential interactors enrichment between RAS paralogs and uncover novel ties between RAS signaling and cellular metabolism. We believe that our findings will support further studies aiming at better understanding how RAS paralogs could be differentially involved in discrete cellular processes and could serve as a basis to template oncogenic mechanism investigations. Abstract RAS proteins (KRAS, NRAS and HRAS) are frequently activated in different cancer types (e.g., non-small cell lung cancer, colorectal cancer, melanoma and bladder cancer). For many years, their activities were considered redundant due to their high degree of sequence homology (80% identity) and their shared upstream and downstream protein partners. However, the high conservation of the Hyper-Variable-Region across mammalian species, the preferential activation of different RAS proteins in specific tumor types and the specific post-translational modifications and plasma membrane-localization of each paralog suggest they could ensure discrete functions. To gain insights into RAS proteins specificities, we explored their proximal protein–protein interaction landscapes using the proximity-dependent biotin identification technology (BioID) in Flp-In T-REx 293 cell lines stably transfected and inducibly expressing wild type KRAS4B, NRAS or HRAS. We identified more than 800 high-confidence proximal interactors, allowing us to propose an unprecedented comparative analysis of wild type RAS paralogs protein networks. These data bring novel information on poorly characterized RAS functions, e.g., its putative involvement in metabolic pathways, and on shared as well as paralog-specific protein networks that could partially explain the complexity of RAS functions. These networks of protein interactions open numerous avenues to better understand RAS paralogs biological activities.
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Affiliation(s)
- Benoît Béganton
- CHU Montpellier, Department of Pathology and Onco-Biology, Univ Montpellier, 34295 Montpellier, France;
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
- Correspondence: ; Tel.: +33-467-33-58-71
| | - Etienne Coyaud
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Estelle M. N. Laurent
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Alain Mangé
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
| | - Julien Jacquemetton
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286, Université Lyon 1, 69008 Lyon, France; (J.J.); (M.L.R.)
| | - Muriel Le Romancer
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286, Université Lyon 1, 69008 Lyon, France; (J.J.); (M.L.R.)
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Jérôme Solassol
- CHU Montpellier, Department of Pathology and Onco-Biology, Univ Montpellier, 34295 Montpellier, France;
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
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173
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Nadeau R, Shahryari Fard S, Scheer A, Hashimoto-Roth E, Nygard D, Abramchuk I, Chung YE, Bennett SAL, Lavallée-Adam M. Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. J Proteome Res 2020; 19:4553-4566. [PMID: 33103435 PMCID: PMC7640966 DOI: 10.1021/acs.jproteome.0c00422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 12/13/2022]
Abstract
While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK 293 cells published by Gordon et al. (Nature2020, 583, 459-468) to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on PPI networks generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in PPI networks. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in PPI networks. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
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Affiliation(s)
- Rachel Nadeau
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Soroush Shahryari Fard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Amit Scheer
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Emily Hashimoto-Roth
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Dallas Nygard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Iryna Abramchuk
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Yun-En Chung
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Steffany A. L. Bennett
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre
for Catalysis and Research Innovation, University
of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, Ontario K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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174
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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175
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Preuss F, Chatterjee D, Mathea S, Shrestha S, St-Germain J, Saha M, Kannan N, Raught B, Rottapel R, Knapp S. Nucleotide Binding, Evolutionary Insights, and Interaction Partners of the Pseudokinase Unc-51-like Kinase 4. Structure 2020; 28:1184-1196.e6. [PMID: 32814032 DOI: 10.1016/j.str.2020.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/17/2020] [Accepted: 07/29/2020] [Indexed: 01/11/2023]
Abstract
Unc-51-like kinase 4 (ULK4) is a pseudokinase that has been linked to the development of several diseases. Even though sequence motifs required for ATP binding in kinases are lacking, ULK4 still tightly binds ATP and the presence of the co-factor is required for structural stability of ULK4. Here, we present a high-resolution structure of a ULK4-ATPγS complex revealing a highly unusual ATP binding mode in which the lack of the canonical VAIK motif lysine is compensated by K39, located N-terminal to αC. Evolutionary analysis suggests that degradation of active site motifs in metazoan ULK4 has co-occurred with an ULK4-specific activation loop, which stabilizes the C helix. In addition, cellular interaction studies using BioID and biochemical validation data revealed high confidence interactors of the pseudokinase and armadillo repeat domains. Many of the identified ULK4 interaction partners were centrosomal and tubulin-associated proteins and several active kinases suggesting interesting regulatory roles for ULK4.
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Affiliation(s)
- Franziska Preuss
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Safal Shrestha
- Institute of Bioinformatics & Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA 30602-7229, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Manipa Saha
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Natarajan Kannan
- Institute of Bioinformatics & Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA 30602-7229, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada; Departments of Medicine, Immunology and Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada; Division of Rheumatology, St. Michael's Hospital, Toronto M5B 1W8, Canada
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) and Frankfurt Cancer Institute (FCI), 60596 Frankfurt am Main, Germany.
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176
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Jacquet K, Rodrigue MA, Richard DE, Lavoie JN. The adenoviral protein E4orf4: a probing tool to decipher mechanical stress-induced nuclear envelope remodeling in tumor cells. Cell Cycle 2020; 19:2963-2981. [PMID: 33103553 DOI: 10.1080/15384101.2020.1836441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The human adenovirus (Ad) type 2/5 early region 4 (E4) ORF4 protein (E4orf4) exerts a remarkable tumor cell-selective killing activity in mammalian cells. This indicates that E4orf4 can target tumor cell-defining features and is a unique tool to probe cancer cell vulnerabilities. Recently, we found that E4orf4, through an interaction with the polarity protein PAR3, subverts nuclear envelope (NE) remodeling processes in a tumor cell-selective manner. In this Perspective, we outline mechanical signals that modify nuclear dynamics and tumor cell behavior to highlight potential mechanisms for E4orf4's tumoricidal activity. Through an analysis of E4orf4's cellular targets, we define a protein subnetwork that comprises phosphatase systems interconnected to polarity protein hubs, which could contribute to enhanced NE plasticity. We infer that elucidating E4orf4's protein network at a functional level could uncover key mechanisms of NE remodeling that define the tumor cell phenotype.
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Affiliation(s)
- Kévin Jacquet
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Marc-Antoine Rodrigue
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Darren E Richard
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval , Québec, Canada.,Endocrinology and Nephrology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Josée N Lavoie
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval , Québec, Canada
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177
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Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT. RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acids Res 2020; 48:e90. [PMID: 32609809 PMCID: PMC7470977 DOI: 10.1093/nar/gkaa542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/03/2020] [Accepted: 06/27/2020] [Indexed: 12/25/2022] Open
Abstract
Specific genomic functions are dictated by macromolecular complexes (MCs) containing multiple proteins. Affinity purification of these complexes, often using antibodies, followed by mass spectrometry (MS) has revolutionized our ability to identify the composition of MCs. However, conventional immunoprecipitations suffer from contaminating antibody/serum-derived peptides that limit the sensitivity of detection for low-abundant interacting partners using MS. Here, we present AptA-MS (aptamer affinity-mass spectrometry), a robust strategy primarily using a specific, high-affinity RNA aptamer against Green Fluorescent Protein (GFP) to identify interactors of a GFP-tagged protein of interest by high-resolution MS. Utilizing this approach, we have identified the known molecular chaperones that interact with human Heat Shock Factor 1 (HSF1), and observed an increased association with several proteins upon heat shock, including translation elongation factors and histones. HSF1 is known to be regulated by multiple post-translational modifications (PTMs), and we observe both known and new sites of modifications on HSF1. We show that AptA-MS provides a dramatic target enrichment and detection sensitivity in evolutionarily diverse organisms and allows identification of PTMs without the need for modification-specific enrichments. In combination with the expanding libraries of GFP-tagged cell lines, this strategy offers a general, inexpensive, and high-resolution alternative to conventional approaches for studying MCs.
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Affiliation(s)
- Judhajeet Ray
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Angela Kruse
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Takuya Kajitani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Heck
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture Agricultural Research Service (USDA ARS), Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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178
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Park SS, Ponce-Balbuena D, Kuick R, Guerrero-Serna G, Yoon J, Mellacheruvu D, Conlon KP, Basrur V, Nesvizhskii AI, Jalife J, Rual JF. Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. Mol Cell Proteomics 2020; 19:1436-1449. [PMID: 32541000 PMCID: PMC8143648 DOI: 10.1074/mcp.ra120.002071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 12/27/2022] Open
Abstract
Kir2.1, a strong inward rectifier potassium channel encoded by the KCNJ2 gene, is a key regulator of the resting membrane potential of the cardiomyocyte and plays an important role in controlling ventricular excitation and action potential duration in the human heart. Mutations in KCNJ2 result in inheritable cardiac diseases in humans, e.g. the type-1 Andersen-Tawil syndrome (ATS1). Understanding the molecular mechanisms that govern the regulation of inward rectifier potassium currents by Kir2.1 in both normal and disease contexts should help uncover novel targets for therapeutic intervention in ATS1 and other Kir2.1-associated channelopathies. The information available to date on protein-protein interactions involving Kir2.1 channels remains limited. Additional efforts are necessary to provide a comprehensive map of the Kir2.1 interactome. Here we describe the generation of a comprehensive map of the Kir2.1 interactome using the proximity-labeling approach BioID. Most of the 218 high-confidence Kir2.1 channel interactions we identified are novel and encompass various molecular mechanisms of Kir2.1 function, ranging from intracellular trafficking to cross-talk with the insulin-like growth factor receptor signaling pathway, as well as lysosomal degradation. Our map also explores the variations in the interactome profiles of Kir2.1WTversus Kir2.1Δ314-315, a trafficking deficient ATS1 mutant, thus uncovering molecular mechanisms whose malfunctions may underlie ATS1 disease. Finally, using patch-clamp analysis, we validate the functional relevance of PKP4, one of our top BioID interactors, to the modulation of Kir2.1-controlled inward rectifier potassium currents. Our results validate the power of our BioID approach in identifying functionally relevant Kir2.1 interactors and underline the value of our Kir2.1 interactome as a repository for numerous novel biological hypotheses on Kir2.1 and Kir2.1-associated diseases.
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Affiliation(s)
- Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Daniela Ponce-Balbuena
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Guadalupe Guerrero-Serna
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin Yoon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - José Jalife
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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179
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Chastney MR, Lawless C, Humphries MJ. Multiplexed Proximity Biotinylation Coupled to Mass Spectrometry for Defining Integrin Adhesion Complexes. CURRENT PROTOCOLS IN CELL BIOLOGY 2020; 88:e113. [PMID: 32833344 DOI: 10.1002/cpcb.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BioID, a proximity biotinylation technique, offers a valuable approach to examine the interactions occurring within protein complexes that complements traditional protein biochemical methods. BioID has various advantages that are beneficial to the study of complexes, including an ability to detect insoluble and transient proteins. We have applied BioID to the study of integrin adhesion complexes (IACs), which are located at the junction between the plasma membrane and actin cytoskeleton. The use of multiple BioID baits enables a complex-wide, spatial annotation of IACs, which in turn facilitates the detection of novel proximal interactors and provides insights into IAC architecture. This article describes the labeling and affinity purification of IAC-proximal proteins and their analysis by label-free quantitative mass spectrometry. The article also outlines steps to identify high-confidence proximity interactors, and to interrogate the topology and functional relevance of proximity interaction networks through bioinformatic analyses. © 2020 The Authors. Basic Protocol 1: Proximity biotinylation of integrin adhesion complex components Basic Protocol 2: Mass spectrometry data processing by MaxQuant and detection of high-confidence proximal interactors Basic Protocol 3: Bioinformatic analysis and data visualization.
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Affiliation(s)
- Megan R Chastney
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
| | - Craig Lawless
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
| | - Martin J Humphries
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
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180
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Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Mol Cell Proteomics 2020; 19:1575-1585. [PMID: 32616513 PMCID: PMC7996969 DOI: 10.1074/mcp.tir120.002048] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/21/2020] [Indexed: 01/01/2023] Open
Abstract
Ion mobility brings an additional dimension of separation to LC-MS, improving identification of peptides and proteins in complex mixtures. A recently introduced timsTOF mass spectrometer (Bruker) couples trapped ion mobility separation to TOF mass analysis. With the parallel accumulation serial fragmentation (PASEF) method, the timsTOF platform achieves promising results, yet analysis of the data generated on this platform represents a major bottleneck. Currently, MaxQuant and PEAKS are most used to analyze these data. However, because of the high complexity of timsTOF PASEF data, both require substantial time to perform even standard tryptic searches. Advanced searches (e.g. with many variable modifications, semi- or non-enzymatic searches, or open searches for post-translational modification discovery) are practically impossible. We have extended our fast peptide identification tool MSFragger to support timsTOF PASEF data, and developed a label-free quantification tool, IonQuant, for fast and accurate 4-D feature extraction and quantification. Using a HeLa data set published by Meier et al. (2018), we demonstrate that MSFragger identifies significantly (∼30%) more unique peptides than MaxQuant (1.6.10.43), and performs comparably or better than PEAKS X+ (∼10% more peptides). IonQuant outperforms both in terms of number of quantified proteins while maintaining good quantification precision and accuracy. Runtime tests show that MSFragger and IonQuant can fully process a typical two-hour PASEF run in under 70 min on a typical desktop (6 CPU cores, 32 GB RAM), significantly faster than other tools. Finally, through semi-enzymatic searching, we significantly increase the number of identified peptides. Within these semi-tryptic identifications, we report evidence of gas-phase fragmentation before MS/MS analysis.
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Affiliation(s)
- Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dmitry M Avtonomov
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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181
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Abstract
M. tuberculosis infections are responsible for more than 1 million deaths per year. Developing effective strategies to combat this disease requires a greater understanding of M. tuberculosis biology. As in all cells, protein quality control is essential for the viability of M. tuberculosis, which likely faces proteotoxic stress within a host. Here, we identify an M. tuberculosis protein, Ruc, that gains chaperone activity upon oxidation. Ruc represents a previously unrecognized family of redox-regulated chaperones found throughout the bacterial superkingdom. Additionally, we found that oxidized Ruc promotes the protein-folding activity of the essential M. tuberculosis Hsp70 chaperone system. This work contributes to a growing body of evidence that oxidative stress provides a particular strain on cellular protein stability. The bacterial pathogen Mycobacterium tuberculosis is the leading cause of death by an infectious disease among humans. Here, we describe a previously uncharacterized M. tuberculosis protein, Rv0991c, as a molecular chaperone that is activated by oxidation. Rv0991c has homologs in most bacterial lineages and appears to function analogously to the well-characterized Escherichia coli redox-regulated chaperone Hsp33, despite a dissimilar protein sequence. Rv0991c is transcriptionally coregulated with hsp60 and hsp70 chaperone genes in M. tuberculosis, suggesting that Rv0991c functions with these chaperones in maintaining protein quality control. Supporting this hypothesis, we found that, like oxidized Hsp33, oxidized Rv0991c prevents the aggregation of a model unfolded protein in vitro and promotes its refolding by the M. tuberculosis Hsp70 chaperone system. Furthermore, Rv0991c interacts with DnaK and can associate with many other M. tuberculosis proteins. We therefore propose that Rv0991c, which we named “Ruc” (redox-regulated protein with unstructured C terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress.
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182
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Clairfeuille T, Buchholz KR, Li Q, Verschueren E, Liu P, Sangaraju D, Park S, Noland CL, Storek KM, Nickerson NN, Martin L, Dela Vega T, Miu A, Reeder J, Ruiz-Gonzalez M, Swem D, Han G, DePonte DP, Hunter MS, Gati C, Shahidi-Latham S, Xu M, Skelton N, Sellers BD, Skippington E, Sandoval W, Hanan EJ, Payandeh J, Rutherford ST. Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Nature 2020; 584:479-483. [PMID: 32788728 DOI: 10.1038/s41586-020-2597-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Lipopolysaccharide (LPS) resides in the outer membrane of Gram-negative bacteria where it is responsible for barrier function1,2. LPS can cause death as a result of septic shock, and its lipid A core is the target of polymyxin antibiotics3,4. Despite the clinical importance of polymyxins and the emergence of multidrug resistant strains5, our understanding of the bacterial factors that regulate LPS biogenesis is incomplete. Here we characterize the inner membrane protein PbgA and report that its depletion attenuates the virulence of Escherichia coli by reducing levels of LPS and outer membrane integrity. In contrast to previous claims that PbgA functions as a cardiolipin transporter6-9, our structural analyses and physiological studies identify a lipid A-binding motif along the periplasmic leaflet of the inner membrane. Synthetic PbgA-derived peptides selectively bind to LPS in vitro and inhibit the growth of diverse Gram-negative bacteria, including polymyxin-resistant strains. Proteomic, genetic and pharmacological experiments uncover a model in which direct periplasmic sensing of LPS by PbgA coordinates the biosynthesis of lipid A by regulating the stability of LpxC, a key cytoplasmic biosynthetic enzyme10-12. In summary, we find that PbgA has an unexpected but essential role in the regulation of LPS biogenesis, presents a new structural basis for the selective recognition of lipids, and provides opportunities for future antibiotic discovery.
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Affiliation(s)
| | - Kerry R Buchholz
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Qingling Li
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Erik Verschueren
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Peter Liu
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Dewakar Sangaraju
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA, USA
| | - Summer Park
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Cameron L Noland
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | | | - Lynn Martin
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Trisha Dela Vega
- BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Anh Miu
- Biochemical & Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Janina Reeder
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Maria Ruiz-Gonzalez
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Danielle Swem
- Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford University, Department of Structural Biology, Stanford, CA, USA
| | | | - Min Xu
- Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Emily J Hanan
- Discovery Chemistry Departments, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Structural Biology, Genentech Inc., South San Francisco, CA, USA. .,Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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183
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Combined proximity labeling and affinity purification-mass spectrometry workflow for mapping and visualizing protein interaction networks. Nat Protoc 2020; 15:3182-3211. [PMID: 32778839 DOI: 10.1038/s41596-020-0365-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022]
Abstract
Affinity purification coupled with mass spectrometry (AP-MS) and proximity-dependent biotinylation identification (BioID) methods have made substantial contributions to interaction proteomics studies. Whereas AP-MS results in the identification of proteins that are in a stable complex, BioID labels and identifies proteins that are in close proximity to the bait, resulting in overlapping yet distinct protein identifications. Integration of AP-MS and BioID data has been shown to comprehensively characterize a protein's molecular context, but interactome analysis using both methods in parallel is still labor and resource intense with respect to cell line generation and protein purification. Therefore, we developed the Multiple Approaches Combined (MAC)-tag workflow, which allows for both AP-MS and BioID analysis with a single construct and with almost identical protein purification and mass spectrometry (MS) identification procedures. We have applied the MAC-tag workflow to a selection of subcellular markers to provide a global view of the cellular protein interactome landscape. This localization database is accessible via our online platform ( http://proteomics.fi ) to predict the cellular localization of a protein of interest (POI) depending on its identified interactors. In this protocol, we present the detailed three-stage procedure for the MAC-tag workflow: (1) cell line generation for the MAC-tagged POI; (2) parallel AP-MS and BioID protein purification followed by MS analysis; and (3) protein interaction data analysis, data filtration and visualization with our localization visualization platform. The entire procedure can be completed within 25 d.
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184
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Zeng J, Dong S, Luo Z, Xie X, Fu B, Li P, Liu C, Yang X, Chen Y, Wang X, Liu Z, Wu J, Yan Y, Wang F, Chen JF, Zhang J, Long G, Goldman SA, Li S, Zhao Z, Liang Q. The Zika Virus Capsid Disrupts Corticogenesis by Suppressing Dicer Activity and miRNA Biogenesis. Cell Stem Cell 2020; 27:618-632.e9. [PMID: 32763144 DOI: 10.1016/j.stem.2020.07.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/08/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022]
Abstract
Zika virus (ZIKV) causes microcephaly and disrupts neurogenesis. Dicer-mediated miRNA biogenesis is required for embryonic brain development and has been suggested to be disrupted upon ZIKV infection. Here we mapped the ZIKV-host interactome in neural stem cells (NSCs) and found that Dicer is specifically targeted by the capsid from ZIKV, but not other flaviviruses, to facilitate ZIKV infection. We identified a capsid mutant (H41R) that loses this interaction and does not suppress Dicer activity. Consistently, ZIKV-H41R is less virulent and does not inhibit neurogenesis in vitro or corticogenesis in utero. Epidemic ZIKV strains contain capsid mutations that increase Dicer binding affinity and enhance pathogenicity. ZIKV-infected NSCs show global dampening of miRNA production, including key miRNAs linked to neurogenesis, which is not observed after ZIKV-H41R infection. Together these findings show that capsid-dependent suppression of Dicer is a major determinant of ZIKV immune evasion and pathogenesis and may underlie ZIKV-related microcephaly.
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Affiliation(s)
- Jianxiong Zeng
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shupeng Dong
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifei Luo
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaochun Xie
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bishi Fu
- Department of Paediatrics, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, China; State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Chengrong Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Yang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yujie Chen
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenshan Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Wu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Youzhen Yan
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Feng Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester, Rochester, NY, USA; Department of Neurology, University of Rochester, Rochester, NY, USA; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shitao Li
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.
| | - Zhen Zhao
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Qiming Liang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.
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185
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St-Germain JR, Samavarchi Tehrani P, Wong C, Larsen B, Gingras AC, Raught B. Variability in Streptavidin-Sepharose Matrix Quality Can Significantly Affect Proximity-Dependent Biotinylation (BioID) Data. J Proteome Res 2020; 19:3554-3561. [PMID: 32628020 DOI: 10.1021/acs.jproteome.0c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to their ease of use and high binding affinity, streptavidin-based purification tools have become widely used for isolating biotinylated compounds from complex mixtures. We and others routinely use streptavidin-sepharose matrices to isolate biotinylated polypeptides generated in proximity-dependent biotinylation approaches, such as BioID or APEX. However, we noted sporadic, substantial variation in the quality of BioID experiments performed in the same laboratories over time, using seemingly identical protocols. Identifying the source of this problem, here, we highlight considerable variability in streptavidin contamination derived from different production lots of streptavidin-sepharose beads from the same manufacturer and demonstrate that high levels of streptavidin peptide contamination can have detrimental effects on BioID data. We also describe two simple, rapid approaches to assess the degree of streptavidin "shedding" from individual lots of the sepharose matrix before use to avoid the use of lower quality reagent.
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Affiliation(s)
- Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Payman Samavarchi Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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186
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Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell 2020; 182:297-316.e27. [PMID: 32619424 DOI: 10.1016/j.cell.2020.05.049] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
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Affiliation(s)
- Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Andrew Zhai
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leena Babiker
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Daleum Kim
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Tak C Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Youngjun Kim
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael D Nissen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, and Princess Margaret Cancer Centre, Toronto, ON M5S 1A8, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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187
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Botham A, Coyaud E, Nirmalanandhan VS, Gronda M, Hurren R, Maclean N, St-Germain J, Mirali S, Laurent E, Raught B, Schimmer A. Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2. Proteomics 2020; 19:e1900139. [PMID: 31617661 DOI: 10.1002/pmic.201900139] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/30/2019] [Indexed: 12/20/2022]
Abstract
A number of unique proteases localize to specific sub-compartments of the mitochondria, but the functions of these enzymes are poorly defined. Here, in vivo proximity-dependent biotinylation (BioID) is used to map the interactomes of seven proteases localized to the mitochondrial intermembrane space (IMS). In total, 802 high confidence proximity interactions with 342 unique proteins are identified. While all seven proteases co-localized with the IMS markers OPA1 and CLPB, 230 of the interacting partners are unique to just one or two protease bait proteins, highlighting the ability of BioID to differentiate unique interactomes within the confined space of the IMS. Notably, high-temperature requirement peptidase 2 (HTRA2) interacts with eight of 13 components of the mitochondrial intermembrane space bridging (MIB) complex, a multiprotein assembly essential for the maintenance of mitochondrial cristae structure. Knockdown of HTRA2 disrupts cristae in HEK 293 and OCI-AML2 cells, and leads to increased intracellular levels of the MIB subunit IMMT. Using a cell-free assay it is demonstrated that HTRA2 can degrade recombinant IMMT but not two other core MIB complex subunits, SAMM50 and CHCHD3. The IMS protease interactome thus represents a rich dataset that can be mined to uncover novel IMS protease biology.
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Affiliation(s)
- Aaron Botham
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | | | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Neil Maclean
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Sara Mirali
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5G 1L7, ON, Canada
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188
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Hao W, Wang L, Li S. FKBP5 Regulates RIG-I-Mediated NF-κB Activation and Influenza A Virus Infection. Viruses 2020; 12:E672. [PMID: 32580383 PMCID: PMC7354574 DOI: 10.3390/v12060672] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 01/19/2023] Open
Abstract
Influenza A virus (IAV) is a highly transmissible respiratory pathogen and is a constant threat to global health with considerable economic and social impact. Influenza viral RNA is sensed by host pattern recognition receptors (PRRs), such as the Toll-like receptor 7 (TLR7) and retinoic acid-inducible gene I (RIG-I). The activation of these PRRs instigates the interferon regulatory factor (IRF) and nuclear factor kappa B (NF-κB) signaling pathways that induce the expression of interferon-stimulated genes (ISGs) and inflammatory genes. FK506-binding protein 5 (FKBP5) has been implied in the IκBα kinase (IKK) complex. However, the role of FKBP5 in the RIG-I signaling and IAV infection is not well elucidated. Here, we demonstrate that the knockout of FKBP5 increases IAV infection. Furthermore, FKBP5 binds IKKα, which is critical for RIG-I-induced innate immune responses and ISG expression. Taken together, FKBP5 is a novel anti-influenza host factor that restricts IAV infection by the activation of RIG-I-mediated NF-κB signaling.
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Affiliation(s)
| | | | - Shitao Li
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (W.H.); (L.W.)
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189
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Abstract
De novo identification of chromatin interactors can reveal unexpected pathways relevant to physiology and human disease. Inspired by the DNA mediated chromatin pull-down (Dm-ChP) technology (also known as iPOND [isolation of proteins on nascent DNA]) for the proteomic characterization of nascent DNA, we have recently reported a new experimental protocol that allows for the identification of proteins on total DNA (iPOTD) for bulk chromatome profiling and de novo identification of chromatin-bound proteins. Here, we detail a step-by-step protocol to survey the cellular chromatin-bound proteome in a simple, robust, and unbiased manner. For complete details on the use and execution of this protocol, please refer to Aranda et al. (2019).
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author
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190
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Khodadadi E, Zeinalzadeh E, Taghizadeh S, Mehramouz B, Kamounah FS, Khodadadi E, Ganbarov K, Yousefi B, Bastami M, Kafil HS. Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies. Infect Drug Resist 2020; 13:1785-1806. [PMID: 32606829 PMCID: PMC7305820 DOI: 10.2147/idr.s238446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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191
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MacLeod G, Bozek DA, Rajakulendran N, Monteiro V, Ahmadi M, Steinhart Z, Kushida MM, Yu H, Coutinho FJ, Cavalli FMG, Restall I, Hao X, Hart T, Luchman HA, Weiss S, Dirks PB, Angers S. Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells. Cell Rep 2020; 27:971-986.e9. [PMID: 30995489 DOI: 10.1016/j.celrep.2019.03.047] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/19/2018] [Accepted: 03/13/2019] [Indexed: 01/14/2023] Open
Abstract
Glioblastoma therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells (GSCs) to interrogate function of the coding genome, we identify actionable pathways responsible for growth, which reveal the gene-essential circuitry of GBM stemness and proliferation. In particular, we characterize members of the SOX transcription factor family, SOCS3, USP8, and DOT1L, and protein ufmylation as important for GSC growth. Additionally, we reveal mechanisms of temozolomide resistance that could lead to combination strategies. By reaching beyond static genome analysis of bulk tumors, with a genome-wide functional approach, we reveal genetic dependencies within a broad range of biological processes to provide increased understanding of GBM growth and treatment resistance.
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Affiliation(s)
- Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Danielle A Bozek
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Vernon Monteiro
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Moloud Ahmadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Zachary Steinhart
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Yu
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian Restall
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Xiaoguang Hao
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - H Artee Luchman
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, Department of Laboratory Medicine and Pathobiology, Division of Neurosurgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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192
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Postic G, Marcoux J, Reys V, Andreani J, Vandenbrouck Y, Bousquet MP, Mouton-Barbosa E, Cianférani S, Burlet-Schiltz O, Guerois R, Labesse G, Tufféry P. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. J Proteome Res 2020; 19:2807-2820. [PMID: 32338910 DOI: 10.1021/acs.jproteome.0c00066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hierarchical view of the interactions between the members of the flat list becomes highly tedious for large data sets when done by hand. To help hierarchize this data, we introduce a new bioinformatics protocol that integrates information of the multimeric protein 3D structures available in the Protein Data Bank using remote homology detection, as well as information related to Short Linear Motifs and interaction data from the BioGRID. We illustrate on two unrelated use-cases of different complexity how our approach can be useful to decipher the network of interactions hidden in the list of input proteins, and how it provides added value compared to state-of-the-art resources such as Interactome3D or STRING. Particularly, we show the added value of using homology detection to distinguish between orthologs and paralogs, and to distinguish between core obligate and more facultative interactions. We also demonstrate the potential of considering interactions occurring through Short Linear Motifs.
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Affiliation(s)
- Guillaume Postic
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, 75013 Paris, France.,Institut Français de Bioinformatique (IFB), UMS 3601-CNRS, Universite Paris-Saclay, 91400 Orsay, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Victor Reys
- CBS, Univ. Montpellier, CNRS, INSERM, 34095 Montpellier, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes, INSERM, CEA, IRIG-BGE, U1038, 38000 Grenoble, France
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Gilles Labesse
- CBS, Univ. Montpellier, CNRS, INSERM, 34095 Montpellier, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, 75013 Paris, France
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193
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Zhao M, Song K, Hao W, Wang L, Patil G, Li Q, Xu L, Hua F, Fu B, Schwamborn JC, Dorf ME, Li S. Non-proteolytic ubiquitination of OTULIN regulates NF-κB signaling pathway. J Mol Cell Biol 2020; 12:163-175. [PMID: 31504727 PMCID: PMC7181720 DOI: 10.1093/jmcb/mjz081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/23/2019] [Accepted: 06/12/2019] [Indexed: 12/25/2022] Open
Abstract
NF-κB signaling regulates diverse processes such as cell death, inflammation, immunity, and cancer. The activity of NF-κB is controlled by methionine 1-linked linear polyubiquitin, which is assembled by the linear ubiquitin chain assembly complex (LUBAC) and the ubiquitin-conjugating enzyme UBE2L3. Recent studies found that the deubiquitinase OTULIN breaks the linear ubiquitin chain, thus inhibiting NF-κB signaling. Despite the essential role of OTULIN in NF-κB signaling has been established, the regulatory mechanism for OTULIN is not well elucidated. To discover the potential regulators of OTULIN, we analyzed the OTULIN protein complex by proteomics and revealed several OTULIN-binding proteins, including LUBAC and tripartite motif-containing protein 32 (TRIM32). TRIM32 is known to activate NF-κB signaling, but the mechanism is not clear. Genetic complement experiments found that TRIM32 is upstream of OTULIN and TRIM32-mediated NF-κB activation is dependent on OTULIN. Mutagenesis of the E3 ligase domain showed that the E3 ligase activity is essential for TRIM32-mediated NF-κB activation. Further experiments found that TRIM32 conjugates polyubiquitin onto OTULIN and the polyubiquitin blocks the interaction between HOIP and OTULIN, thereby activating NF-κB signaling. Taken together, we report a novel regulatory mechanism by which TRIM32-mediated non-proteolytic ubiquitination of OTULIN impedes the access of OTULIN to the LUBAC and promotes NF-κB activation.
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Affiliation(s)
- Mengmeng Zhao
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kun Song
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Wenzhuo Hao
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lingyan Wang
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Girish Patil
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Qingmei Li
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lingling Xu
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fang Hua
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Bishi Fu
- State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg City, Luxembourg
| | - Martin E Dorf
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Shitao Li
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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194
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Murtaza N, Uy J, Singh KK. Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders. Mol Autism 2020; 11:27. [PMID: 32317014 PMCID: PMC7171839 DOI: 10.1186/s13229-020-00334-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Proteomics is the large-scale study of the total protein content and their overall function within a cell through multiple facets of research. Advancements in proteomic methods have moved past the simple quantification of proteins to the identification of post-translational modifications (PTMs) and the ability to probe interactions between these proteins, spatially and temporally. Increased sensitivity and resolution of mass spectrometers and sample preparation protocols have drastically reduced the large amount of cells required and the experimental variability that had previously hindered its use in studying human neurological disorders. Proteomics offers a new perspective to study the altered molecular pathways and networks that are associated with autism spectrum disorders (ASD). The differences between the transcriptome and proteome, combined with the various types of post-translation modifications that regulate protein function and localization, highlight a novel level of research that has not been appropriately investigated. In this review, we will discuss strategies using proteomics to study ASD and other neurological disorders, with a focus on how these approaches can be combined with induced pluripotent stem cell (iPSC) studies. Proteomic analysis of iPSC-derived neurons have already been used to measure changes in the proteome caused by patient mutations, analyze changes in PTMs that resulted in altered biological pathways, and identify potential biomarkers. Further advancements in both proteomic techniques and human iPSC differentiation protocols will continue to push the field towards better understanding ASD disease pathophysiology. Proteomics using iPSC-derived neurons from individuals with ASD offers a window for observing the altered proteome, which is necessary in the future development of therapeutics against specific targets.
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Affiliation(s)
- Nadeem Murtaza
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Jarryll Uy
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada.
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195
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Kiepas A, Voorand E, Senecal J, Ahn R, Annis MG, Jacquet K, Tali G, Bisson N, Ursini-Siegel J, Siegel PM, Brown CM. The SHCA adapter protein cooperates with lipoma-preferred partner in the regulation of adhesion dynamics and invadopodia formation. J Biol Chem 2020; 295:10535-10559. [PMID: 32299913 DOI: 10.1074/jbc.ra119.011903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
SHC adaptor protein (SHCA) and lipoma-preferred partner (LPP) mediate transforming growth factor β (TGFβ)-induced breast cancer cell migration and invasion. Reduced expression of either protein diminishes breast cancer lung metastasis, but the reason for this effect is unclear. Here, using total internal reflection fluorescence (TIRF) microscopy, we found that TGFβ enhanced the assembly and disassembly rates of paxillin-containing adhesions in an SHCA-dependent manner through the phosphorylation of the specific SHCA tyrosine residues Tyr-239, Tyr-240, and Tyr-313. Using a BioID proximity labeling approach, we show that SHCA exists in a complex with a variety of actin cytoskeletal proteins, including paxillin and LPP. Consistent with a functional interaction between SHCA and LPP, TGFβ-induced LPP localization to cellular adhesions depended on SHCA. Once localized to the adhesions, LPP was required for TGFβ-induced increases in cell migration and adhesion dynamics. Mutations that impaired LPP localization to adhesions (mLIM1) or impeded interactions with the actin cytoskeleton via α-actinin (ΔABD) abrogated migratory responses to TGFβ. Live-cell TIRF microscopy revealed that SHCA clustering at the cell membrane preceded LPP recruitment. We therefore hypothesize that, in the presence of TGFβ, SHCA promotes the formation of small, dynamic adhesions by acting as a nucleator of focal complex formation. Finally, we defined a previously unknown function for SHCA in the formation of invadopodia, a process that also required LPP. Our results reveal that SHCA controls the formation and function of adhesions and invadopodia, two key cellular structures required for breast cancer metastasis.
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Affiliation(s)
- Alex Kiepas
- Department of Physiology, McGill University, Montréal H3G 1Y6, Québec, Canada.,Goodman Cancer Research Centre, McGill University, Montréal H3A 1A3, Québec, Canada
| | - Elena Voorand
- Goodman Cancer Research Centre, McGill University, Montréal H3A 1A3, Québec, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Québec, Canada
| | - Julien Senecal
- Goodman Cancer Research Centre, McGill University, Montréal H3A 1A3, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal H4A 3J1, Québec, Canada
| | - Ryuhjin Ahn
- Division of Experimental Medicine, McGill University, Montréal H4A 3J1, Québec, Canada.,Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada
| | - Matthew G Annis
- Goodman Cancer Research Centre, McGill University, Montréal H3A 1A3, Québec, Canada.,Department of Medicine, McGill University, Montréal H3G 1Y6, Québec, Canada
| | - Kévin Jacquet
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Québec, Québec G1R 2J6, Canada
| | - George Tali
- Department of Physiology, McGill University, Montréal H3G 1Y6, Québec, Canada
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Québec, Québec G1R 2J6, Canada.,PROTEO Network and Cancer Research Centre, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Josie Ursini-Siegel
- Department of Biochemistry, McGill University, Montréal H3G 1Y6, Québec, Canada.,Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Oncology, McGill University, Montréal H4A 3T2, Québec, Canada
| | - Peter M Siegel
- Goodman Cancer Research Centre, McGill University, Montréal H3A 1A3, Québec, Canada .,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Québec, Canada.,Department of Medicine, McGill University, Montréal H3G 1Y6, Québec, Canada
| | - Claire M Brown
- Department of Physiology, McGill University, Montréal H3G 1Y6, Québec, Canada .,Advanced BioImaging Facility (ABIF), McGill University, Montréal H3G 0B1, Québec, Canada
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196
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Xu G, Fromholt SE, Chakrabarty P, Zhu F, Liu X, Pace MC, Koh J, Golde TE, Levites Y, Lewis J, Borchelt DR. Diversity in Aβ deposit morphology and secondary proteome insolubility across models of Alzheimer-type amyloidosis. Acta Neuropathol Commun 2020; 8:43. [PMID: 32252825 PMCID: PMC7137436 DOI: 10.1186/s40478-020-00911-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/30/2022] Open
Abstract
A hallmark pathology of Alzheimer's disease (AD) is the formation of amyloid β (Aβ) deposits that exhibit diverse localization and morphologies, ranging from diffuse to cored-neuritic deposits in brain parenchyma, with cerebral vascular deposition in leptomeningeal and parenchymal compartments. Most AD brains exhibit the full spectrum of pathologic Aβ morphologies. In the course of studies to model AD amyloidosis, we have generated multiple transgenic mouse models that vary in the nature of the transgene constructs that are expressed; including the species origin of Aβ peptides, the levels and length of Aβ that is deposited, and whether mutant presenilin 1 (PS1) is co-expressed. These models recapitulate features of human AD amyloidosis, but interestingly some models can produce pathology in which one type of Aβ morphology dominates. In prior studies of mice that primarily develop cored-neuritic deposits, we determined that Aβ deposition is associated with changes in cytosolic protein solubility in which a subset of proteins become detergent-insoluble, indicative of secondary proteome instability. Here, we survey changes in cytosolic protein solubility across seven different transgenic mouse models that exhibit a range of Aβ deposit morphologies. We find a surprisingly diverse range of changes in proteome solubility across these models. Mice that deposit human Aβ40 and Aβ42 in cored-neuritic plaques had the most robust changes in proteome solubility. Insoluble cytosolic proteins were also detected in the brains of mice that develop diffuse Aβ42 deposits but to a lesser extent. Notably, mice with cored deposits containing only Aβ42 had relatively few proteins that became detergent-insoluble. Our data provide new insight into the diversity of biological effects that can be attributed to different types of Aβ pathology and support the view that fibrillar cored-neuritic plaque pathology is the more disruptive Aβ pathology in the Alzheimer's cascade.
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Affiliation(s)
- Guilian Xu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Susan E Fromholt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Fanchao Zhu
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Xuefei Liu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Michael C Pace
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Yona Levites
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jada Lewis
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - David R Borchelt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- SantaFe Healthcare Alzheimer's Disease Research Center, Gainesville, FL, USA.
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197
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Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020; 85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.
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Affiliation(s)
| | - O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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198
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Müller PM, Rademacher J, Bagshaw RD, Wortmann C, Barth C, van Unen J, Alp KM, Giudice G, Eccles RL, Heinrich LE, Pascual-Vargas P, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Gingras AC, Roth FP, Colwill K, Bakal C, Pertz O, Pawson T, Petsalaki E, Rocks O. Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nat Cell Biol 2020; 22:498-511. [PMID: 32203420 DOI: 10.1038/s41556-020-0488-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Rho GTPases are central regulators of the cytoskeleton and, in humans, are controlled by 145 multidomain guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating proteins (RhoGAPs). How Rho signalling patterns are established in dynamic cell spaces to control cellular morphogenesis is unclear. Through a family-wide characterization of substrate specificities, interactomes and localization, we reveal at the systems level how RhoGEFs and RhoGAPs contextualize and spatiotemporally control Rho signalling. These proteins are widely autoinhibited to allow local regulation, form complexes to jointly coordinate their networks and provide positional information for signalling. RhoGAPs are more promiscuous than RhoGEFs to confine Rho activity gradients. Our resource enabled us to uncover a multi-RhoGEF complex downstream of G-protein-coupled receptors controlling CDC42-RHOA crosstalk. Moreover, we show that integrin adhesions spatially segregate GEFs and GAPs to shape RAC1 activity zones in response to mechanical cues. This mechanism controls the protrusion and contraction dynamics fundamental to cell motility. Our systems analysis of Rho regulators is key to revealing emergent organization principles of Rho signalling.
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Affiliation(s)
- Paul M Müller
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Richard D Bagshaw
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Carolin Barth
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jakobus van Unen
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Keziban M Alp
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Louise E Heinrich
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | | | - Marta Sanchez-Castro
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Geraldine Mbamalu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Monika Tucholska
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Lisa Spatt
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Maciej T Czajkowski
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Sunqu Zhang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Vivian Nguyen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Philipp Trnka
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Kiara Freitag
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Oliver Popp
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Philipp Mertins
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, Ontario, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Chris Bakal
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Evangelia Petsalaki
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Oliver Rocks
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
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199
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Kaplan A, Andrei SA, van Regteren Altena A, Simas T, Banerjee SL, Kato N, Bisson N, Higuchi Y, Ottmann C, Fournier AE. Polypharmacological Perturbation of the 14-3-3 Adaptor Protein Interactome Stimulates Neurite Outgrowth. Cell Chem Biol 2020; 27:657-667.e6. [PMID: 32220335 DOI: 10.1016/j.chembiol.2020.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/05/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
Targeting protein-protein interactions (PPIs) is a promising approach in the development of drugs for many indications. 14-3-3 proteins are a family of phosphoprotein-binding molecules with critical functions in dozens of cell signaling networks. 14-3-3s are abundant in the central nervous system, and the small molecule fusicoccin-A (FC-A), a tool compound that can be used to manipulate 14-3-3 PPIs, enhances neurite outgrowth in cultured neurons. New semisynthetic FC-A derivatives with improved binding affinity for 14-3-3 complexes have recently been developed. Here, we use a series of screens that identify these compounds as potent inducers of neurite outgrowth through a polypharmacological mechanism. Using proteomics and X-ray crystallography, we discover that these compounds extensively regulate the 14-3-3 interactome by stabilizing specific PPIs, while disrupting others. These results provide new insights into the development of drugs to target 14-3-3 PPIs, a potential therapeutic strategy for CNS diseases.
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Affiliation(s)
- Andrew Kaplan
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Sebastian A Andrei
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anna van Regteren Altena
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Tristan Simas
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Sara L Banerjee
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Centre de Recherche sur le Cancer, Université Laval, Québec, QC, Canada
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Nicolas Bisson
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Centre de Recherche sur le Cancer, Université Laval, Québec, QC, Canada
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alyson E Fournier
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada.
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200
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Mei L, Montoya MR, Quanrud GM, Tran M, Villa-Sharma A, Huang M, Genereux JC. Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. J Proteome Res 2020; 19:1565-1573. [PMID: 32138514 DOI: 10.1021/acs.jproteome.9b00825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantitative multiplexing capacity of isobaric tandem mass tags (TMT) has increased the throughput of affinity purification mass spectrometry (AP-MS) to characterize protein interaction networks of immunoprecipitated bait proteins. However, variable bait levels between replicates can convolute interactor identification. We compared the Student's t-test and Pearson's R correlation as methods to generate t-statistics and assessed the significance of interactors following TMT-AP-MS. Using a simple linear model of protein recovery in immunoprecipitates to simulate reporter ion ratio distributions, we found that correlation-derived t-statistics protect against bait variance while robustly controlling type I errors (false positives). We experimentally determined the performance of these two approaches for determining t-statistics under two experimental conditions: irreversible prey association to the Hsp40 mutant DNAJB8H31Q followed by stringent washing, and reversible association to 14-3-3ζ with gentle washing. Correlation-derived t-statistics performed at least as well as Student's t-statistics for each sample and with substantial improvement in performance for experiments with high bait-level variance. Deliberately varying bait levels over a large range fails to improve selectivity but does increase the robustness between runs. The use of correlation-derived t-statistics should improve identification of interactors using TMT-AP-MS. Data are available via ProteomeXchange with identifier PXD016613.
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Affiliation(s)
- Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Guy M Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Minh Tran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Athena Villa-Sharma
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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