1
|
Kamal AHM, Chakrabarty JK, Chowdhury SM. Lipopolysaccharide and statin-mediated immune-responsive protein networks revealed in macrophages through affinity purification spacer-arm controlled cross-linking (AP-SPACC) proteomics. Mol Omics 2023; 19:48-59. [PMID: 36377691 DOI: 10.1039/d2mo00224h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Toll-like receptor 4 (TLR4), a pattern recognition receptor, is activated by lipopolysaccharides (LPS) and induces the MyD88 pathway, which subsequently produces pro-inflammatory cytokines through activation of transcriptional nuclear factor (NF)-κB. Statins have been widely prescribed to reduce cholesterol synthesis for patients with cardiovascular disease. Statins may have pleiotropic effects, which include anti- and pro-inflammatory effects on cells. The molecular mechanism of the sequential influence of LPS and statin on the innate immune system remains unknown. We employed affinity purification-spacer-arm controlled cross-linking (AP-SPACC) MS-based proteomics analysis to identify the LPS- and statin-LPS-responsive proteins and their networks. LPS-stimulated RAW 264.7 macrophage cells singly and combined with the drug statin used in this study. Two chemical cross-linkers with different spacer chain lengths were utilized to stabilize the weak and transient interactors. Proteomic analysis identified 1631 differentially expressed proteins. We identified 151 immune-response proteins through functional enrichment analysis and visualized their interaction networks. Selected candidate protein-coding genes were validated, specifically squamous cell carcinoma antigens recognized by T cells 3, sphingosine-1-phosphate lyase 1, Ras-related protein Rab-35, and tumor protein D52 protein-coding genes through transcript-level expression analysis. The expressions of those genes were significantly increased upon statin treatment and decreased in LPS-stimulated macrophage cells. Therefore, we presumed that the expression changes of genes occurred due to immune response during activation of inflammation. These results highlight the immune-responsive proteins network, providing a new platform for novel investigations and discovering future therapeutic targets for inflammatory diseases.
Collapse
Affiliation(s)
- Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA. .,Advanced Technology Cores, Dan L Duncan Comprehensive Cancer Center, Metabolomics Core, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA. .,Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, 10027, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA.
| |
Collapse
|
2
|
Sudarshan D, Avvakumov N, Lalonde ME, Alerasool N, Joly-Beauparlant C, Jacquet K, Mameri A, Lambert JP, Rousseau J, Lachance C, Paquet E, Herrmann L, Thonta Setty S, Loehr J, Bernardini MQ, Rouzbahman M, Gingras AC, Coulombe B, Droit A, Taipale M, Doyon Y, Côté J. Recurrent chromosomal translocations in sarcomas create a megacomplex that mislocalizes NuA4/TIP60 to Polycomb target loci. Genes Dev 2022; 36:664-683. [PMID: 35710139 DOI: 10.1101/gad.348982.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/31/2022] [Indexed: 11/25/2022]
Abstract
Chromosomal translocations frequently promote carcinogenesis by producing gain-of-function fusion proteins. Recent studies have identified highly recurrent chromosomal translocations in patients with endometrial stromal sarcomas (ESSs) and ossifying fibromyxoid tumors (OFMTs), leading to an in-frame fusion of PHF1 (PCL1) to six different subunits of the NuA4/TIP60 complex. While NuA4/TIP60 is a coactivator that acetylates chromatin and loads the H2A.Z histone variant, PHF1 is part of the Polycomb repressive complex 2 (PRC2) linked to transcriptional repression of key developmental genes through methylation of histone H3 on lysine 27. In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation. The chimeric protein assembles a megacomplex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically associating domain including part of the HOXD cluster. This is linked to aberrant gene expression-most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1-implicated with a PRC2 component in the most frequent translocation in ESSs, JAZF1-SUZ12-is a potent transcription activator that physically associates with NuA4/TIP60, its fusion creating outcomes similar to those of EPC1-PHF1 Importantly, the specific increased expression of PRC2 targets/HOX genes was also confirmed with ESS patient samples. Altogether, these results indicate that most chromosomal translocations linked to these sarcomas use the same molecular oncogenic mechanism through a physical merge of NuA4/TIP60 and PRC2 complexes, leading to mislocalization of histone marks and aberrant Polycomb target gene expression.
Collapse
Affiliation(s)
- Deepthi Sudarshan
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Nikita Avvakumov
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Marie-Eve Lalonde
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Joly-Beauparlant
- Computational Biology Laboratory, CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Karine Jacquet
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Amel Mameri
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jean-Philippe Lambert
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Justine Rousseau
- Institut de Recherches Cliniques de Montréal, Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Catherine Lachance
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Eric Paquet
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Lara Herrmann
- Computational Biology Laboratory, CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Samarth Thonta Setty
- Computational Biology Laboratory, CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Jeremy Loehr
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Marcus Q Bernardini
- Department of Gynecologic Oncology, Princess Margaret Cancer Center, University Health Network, Sinai Health System, Toronto, Ontario M5B 2M9, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Marjan Rouzbahman
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario M5G 2C4, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1V 4G2, Canada
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Yannick Doyon
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jacques Côté
- Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| |
Collapse
|
3
|
Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein. Curr Issues Mol Biol 2021; 43:767-781. [PMID: 34449532 PMCID: PMC8929021 DOI: 10.3390/cimb43020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein-protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Cloutier P, Poitras C, Faubert D, Bouchard A, Blanchette M, Gauthier MS, Coulombe B. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. J Proteome Res 2019; 19:18-27. [PMID: 31738558 DOI: 10.1021/acs.jproteome.9b00599] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PAQosome is an 11-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5' UTR of ASNSD1 mRNA, encodes the 12th subunit of the PAQosome. ASDURF displays significant structural homology to β-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provide an example of a eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.
Collapse
Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Mathieu Blanchette
- School of Computer Science , McGill University , 3480 University Street , Montréal , Quebec H3A 0E9 , Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine , Université de Montréal , 2900 Boulevard Édouart-Montpetit , Montréal , Quebec H3T 1J4 , Canada
| |
Collapse
|
6
|
Bhalla P, Vernekar DV, Gilquin B, Couté Y, Bhargava P. Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II. Gene 2018; 702:205-214. [PMID: 30593915 DOI: 10.1016/j.gene.2018.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic transcription is a highly regulated fundamental life process. A large number of regulatory proteins and complexes, many of them with sequence-specific DNA-binding activity are known to influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes genes encoding small, stable, non-translated RNAs. The pol III transcription is precisely regulated under various stress conditions. We used pol III transcription complex (TC) components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits and mass spectrometry to identify their potential interactors in vivo. A large interactome constituting chromatin modifiers, regulators and factors of transcription by pol I and pol II supports the possibility of a crosstalk between the three transcription machineries. The association of proteins and complexes involved in various basic life processes like ribogenesis, RNA processing, protein folding and degradation, DNA damage response, replication and transcription underscores the possibility of the pol III TC serving as a signaling hub for communication between the transcription and other cellular physiological activities under normal growth conditions. We also found an equally large number of proteins and complexes interacting with the TC under nutrient starvation condition, of which at least 25% were non-identical under the two conditions. The data reveal the possibility of a large number of signaling cues for pol III transcription against adverse conditions, necessary for an efficient co-ordination of various cellular functions.
Collapse
Affiliation(s)
- Pratibha Bhalla
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India
| | - Dipti Vinayak Vernekar
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India
| | - Benoit Gilquin
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India.
| |
Collapse
|
7
|
Mendes MI, Gutierrez Salazar M, Guerrero K, Thiffault I, Salomons GS, Gauquelin L, Tran LT, Forget D, Gauthier MS, Waisfisz Q, Smith DE, Simons C, van der Knaap MS, Marquardt I, Lemes A, Mierzewska H, Weschke B, Koehler W, Coulombe B, Wolf NI, Bernard G. Bi-allelic Mutations in EPRS, Encoding the Glutamyl-Prolyl-Aminoacyl-tRNA Synthetase, Cause a Hypomyelinating Leukodystrophy. Am J Hum Genet 2018; 102:676-684. [PMID: 29576217 DOI: 10.1016/j.ajhg.2018.02.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Hypomyelinating leukodystrophies are genetic disorders characterized by insufficient myelin deposition during development. They are diagnosed on the basis of both clinical and MRI features followed by genetic confirmation. Here, we report on four unrelated affected individuals with hypomyelination and bi-allelic pathogenic variants in EPRS, the gene encoding cytoplasmic glutamyl-prolyl-aminoacyl-tRNA synthetase. EPRS is a bifunctional aminoacyl-tRNA synthetase that catalyzes the aminoacylation of glutamic acid and proline tRNA species. It is a subunit of a large multisynthetase complex composed of eight aminoacyl-tRNA synthetases and its three interacting proteins. In total, five different EPRS mutations were identified. The p.Pro1115Arg variation did not affect the assembly of the multisynthetase complex (MSC) as monitored by affinity purification-mass spectrometry. However, immunoblot analyses on protein extracts from fibroblasts of the two affected individuals sharing the p.Pro1115Arg variant showed reduced EPRS amounts. EPRS activity was reduced in one affected individual's lymphoblasts and in a purified recombinant protein model. Interestingly, two other cytoplasmic aminoacyl-tRNA synthetases have previously been implicated in hypomyelinating leukodystrophies bearing clinical and radiological similarities to those in the individuals we studied. We therefore hypothesized that leukodystrophies caused by mutations in genes encoding cytoplasmic aminoacyl-tRNA synthetases share a common underlying mechanism, such as reduced protein availability, abnormal assembly of the multisynthetase complex, and/or abnormal aminoacylation, all resulting in reduced translation capacity and insufficient myelin deposition in the developing brain.
Collapse
|
8
|
Hesketh GG, Youn JY, Samavarchi-Tehrani P, Raught B, Gingras AC. Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry. Methods Mol Biol 2018; 1550:115-136. [PMID: 28188527 DOI: 10.1007/978-1-4939-6747-6_10] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein-protein interactions, but the requirement to maintain protein-protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.
Collapse
Affiliation(s)
- Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | | | - Brian Raught
- Princess Margaret Cancer Centre, Princess Margaret Research Institute, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave., Rm 992A (9th floor), Toronto, ON, Canada, M5G 1X5.
| |
Collapse
|
9
|
Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome. Proc Natl Acad Sci U S A 2018; 115:E620-E629. [PMID: 29311329 DOI: 10.1073/pnas.1715378115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined. Here, we report the characterization of a mouse model for CHD7 mutation-negative cases of CHARGE syndrome generated by insertional mutagenesis of Fam172a (family with sequence similarity 172, member A). We show that Fam172a plays a key role in the regulation of cotranscriptional alternative splicing, notably by interacting with Ago2 (Argonaute-2) and Chd7. Validation studies in a human cohort allow us to propose that dysregulation of cotranscriptional alternative splicing is a unifying pathogenic mechanism for both CHD7 mutation-positive and CHD7 mutation-negative cases. We also present evidence that such splicing defects can be corrected in vitro by acute rapamycin treatment.
Collapse
|
10
|
Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell 2017; 169:350-360.e12. [PMID: 28388416 DOI: 10.1016/j.cell.2017.03.022] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/02/2017] [Accepted: 03/15/2017] [Indexed: 11/25/2022]
Abstract
Cells operate through protein interaction networks organized in space and time. Here, we describe an approach to resolve both dimensions simultaneously by using proximity labeling mediated by engineered ascorbic acid peroxidase (APEX). APEX has been used to capture entire organelle proteomes with high temporal resolution, but its breadth of labeling is generally thought to preclude the higher spatial resolution necessary to interrogate specific protein networks. We provide a solution to this problem by combining quantitative proteomics with a system of spatial references. As proof of principle, we apply this approach to interrogate proteins engaged by G-protein-coupled receptors as they dynamically signal and traffic in response to ligand-induced activation. The method resolves known binding partners, as well as previously unidentified network components. Validating its utility as a discovery pipeline, we establish that two of these proteins promote ubiquitin-linked receptor downregulation after prolonged activation.
Collapse
Affiliation(s)
- Braden T Lobingier
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, QBI, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelsie Eichel
- Program in Biochemistry and Molecular Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Mark von Zastrow
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, QBI, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
| |
Collapse
|
11
|
Cloutier P, Poitras C, Durand M, Hekmat O, Fiola-Masson É, Bouchard A, Faubert D, Chabot B, Coulombe B. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. Nat Commun 2017; 8:15615. [PMID: 28561026 PMCID: PMC5460035 DOI: 10.1038/ncomms15615] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/12/2017] [Indexed: 01/11/2023] Open
Abstract
The R2TP/Prefoldin-like (R2TP/PFDL) complex has emerged as a cochaperone complex involved in the assembly of a number of critical protein complexes including snoRNPs, nuclear RNA polymerases and PIKK-containing complexes. Here we report on the use of multiple target affinity purification coupled to mass spectrometry to identify two additional complexes that interact with R2TP/PFDL: the TSC1–TSC2 complex and the U5 small nuclear ribonucleoprotein (snRNP). The interaction between R2TP/PFDL and the U5 snRNP is mostly mediated by the previously uncharacterized factor ZNHIT2. A more general function for the zinc-finger HIT domain in binding RUVBL2 is exposed. Disruption of ZNHIT2 and RUVBL2 expression impacts the protein composition of the U5 snRNP suggesting a function for these proteins in promoting the assembly of the ribonucleoprotein. A possible implication of R2TP/PFDL as a major effector of stress-, energy- and nutrient-sensing pathways that regulate anabolic processes through the regulation of its chaperoning activity is discussed. The R2TP/Prefoldin-like cochaperone complex is involved in the assembly of a number of protein complexes. Here the authors provide evidence that RUVBL1/RUVBL2, subunits of that cochaperone complex, directly interact with ZNHIT2 to regulate assembly of U5 small ribonucleoprotein.
Collapse
Affiliation(s)
- Philippe Cloutier
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Mathieu Durand
- Laboratory of Functional Genomics, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Omid Hekmat
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Émilie Fiola-Masson
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Annie Bouchard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Denis Faubert
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7
| | - Benoit Chabot
- Laboratory of Functional Genomics, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8.,Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada H2W 1R7.,Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada H3T 1J4
| |
Collapse
|
12
|
Choquet K, Yang S, Moir RD, Forget D, Larivière R, Bouchard A, Poitras C, Sgarioto N, Dicaire MJ, Noohi F, Kennedy TE, Rochford J, Bernard G, Teichmann M, Coulombe B, Willis IM, Kleinman CL, Brais B. Absence of neurological abnormalities in mice homozygous for the Polr3a G672E hypomyelinating leukodystrophy mutation. Mol Brain 2017; 10:13. [PMID: 28407788 PMCID: PMC5391615 DOI: 10.1186/s13041-017-0294-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/04/2017] [Indexed: 01/08/2023] Open
Abstract
Recessive mutations in the ubiquitously expressed POLR3A gene cause one of the most frequent forms of childhood-onset hypomyelinating leukodystrophy (HLD): POLR3-HLD. POLR3A encodes the largest subunit of RNA Polymerase III (Pol III), which is responsible for the transcription of transfer RNAs (tRNAs) and a large array of other small non-coding RNAs. In order to study the central nervous system pathophysiology of the disease, we introduced the French Canadian founder Polr3a mutation c.2015G > A (p.G672E) in mice, generating homozygous knock-in (KI/KI) as well as compound heterozygous mice for one Polr3a KI and one null allele (KI/KO). Both KI/KI and KI/KO mice are viable and are able to reproduce. To establish if they manifest a motor phenotype, WT, KI/KI and KI/KO mice were submitted to a battery of behavioral tests over one year. The KI/KI and KI/KO mice have overall normal balance, muscle strength and general locomotion. Cerebral and cerebellar Luxol Fast Blue staining and measurement of levels of myelin proteins showed no significant differences between the three groups, suggesting that myelination is not overtly impaired in Polr3a KI/KI and KI/KO mice. Finally, expression levels of several Pol III transcripts in the brain showed no statistically significant differences. We conclude that the first transgenic mice with a leukodystrophy-causing Polr3a mutation do not recapitulate the childhood-onset HLD observed in the majority of human patients with POLR3A mutations, and provide essential information to guide selection of Polr3a mutations for developing future mouse models of the disease.
Collapse
Affiliation(s)
- Karine Choquet
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Sharon Yang
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Diane Forget
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Roxanne Larivière
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Annie Bouchard
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Nicolas Sgarioto
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Marie-Josée Dicaire
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Forough Noohi
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Timothy E Kennedy
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | | | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, and Pediatrics, McGill University, Montreal, Canada.,Department of Medical Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Martin Teichmann
- INSERM U1212 - CNRS UMR5320, Université de Bordeaux, Bordeaux, France
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada.,Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada. .,Department of Human Genetics, McGill University, Montréal, Québec, Canada.
| |
Collapse
|
13
|
Havis S, Moree WJ, Mali S, Bark SJ. Solid support resins and affinity purification mass spectrometry. MOLECULAR BIOSYSTEMS 2017; 13:456-462. [DOI: 10.1039/c6mb00735j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-support resins are critical components of AP-MS experiments, but their interactions with experimental conditions are underappreciated.
Collapse
Affiliation(s)
- Spencer Havis
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Wilna J. Moree
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Sujina Mali
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Steven J. Bark
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| |
Collapse
|
14
|
Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
Collapse
Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
15
|
Lavallée-Adam M, Park SKR, Martínez-Bartolomé S, He L, Yates JR. From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1820-1826. [PMID: 26002791 PMCID: PMC4607643 DOI: 10.1007/s13361-015-1161-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 06/04/2023]
Abstract
In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Mathieu Lavallée-Adam
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Sung Kyu Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Salvador Martínez-Bartolomé
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Lin He
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology and Molecular and Cellular Neurobiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
| |
Collapse
|
16
|
Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Nat Commun 2015; 6:7623. [PMID: 26151409 PMCID: PMC4506509 DOI: 10.1038/ncomms8623] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/26/2015] [Indexed: 12/20/2022] Open
Abstract
A small proportion of 4H (Hypomyelination, Hypodontia and Hypogonadotropic Hypogonadism) or RNA polymerase III (POLR3)-related leukodystrophy cases are negative for mutations in the previously identified causative genes POLR3A and POLR3B. Here we report eight of these cases carrying recessive mutations in POLR1C, a gene encoding a shared POLR1 and POLR3 subunit, also mutated in some Treacher Collins syndrome (TCS) cases. Using shotgun proteomics and ChIP sequencing, we demonstrate that leukodystrophy-causative mutations, but not TCS mutations, in POLR1C impair assembly and nuclear import of POLR3, but not POLR1, leading to decreased binding to POLR3 target genes. This study is the first to show that distinct mutations in a gene coding for a shared subunit of two RNA polymerases lead to selective modification of the enzymes' availability leading to two different clinical conditions and to shed some light on the pathophysiological mechanism of one of the most common hypomyelinating leukodystrophies, POLR3-related leukodystrophy.
Collapse
|
17
|
Dedecker M, Van Leene J, De Jaeger G. Unravelling plant molecular machineries through affinity purification coupled to mass spectrometry. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:1-9. [PMID: 25603557 DOI: 10.1016/j.pbi.2015.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/30/2014] [Accepted: 01/04/2015] [Indexed: 05/23/2023]
Abstract
Rather than functioning independently, proteins tend to work in concert with each other and with other macromolecules to form macromolecular complexes. Affinity purification coupled to mass spectrometry (AP-MS) can lead to a better understanding of the cellular functions of these complexes. With the development of easy purification protocols and ultra-sensitive MS, AP-MS is currently widely used for screening co-complex membership in plants. Studying complexes in their developmental context through the isolation of specific organs and tissues has now become feasible. Besides, the tagged protein can be employed for probing other interactions like protein-DNA and protein-RNA interactions. With the tools at hand, protein-centred interaction studies will greatly improve our knowledge of how plant cells wire their functional components in relation to their function.
Collapse
Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; CropDesign N.V., Technologiepark 21, B-9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| |
Collapse
|
18
|
Feng S, Zhou L, Huang C, Xie K, Nice EC. Interactomics: toward protein function and regulation. Expert Rev Proteomics 2015; 12:37-60. [DOI: 10.1586/14789450.2015.1000870] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
19
|
Tandem affinity purification to identify cytosolic and nuclear gβγ-interacting proteins. Methods Mol Biol 2015; 1234:161-84. [PMID: 25304356 DOI: 10.1007/978-1-4939-1755-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
It has become clear in recent years that the Gβγ subunits of heterotrimeric proteins serve broad roles in the regulation of cellular activity and interact with many proteins in different subcellular locations including the nucleus. Protein affinity purification is a common method to identify and confirm protein interactions. When used in conjugation with mass spectrometry it can be used to identify novel protein interactions with a given bait protein. The tandem affinity purification (TAP) technique identifies partner proteins bound to tagged protein bait. Combined with protocols to enrich the nuclear fraction of whole cell lysate through sucrose cushions, TAP allows for purification of interacting proteins found specifically in the nucleus. Here we describe the use of the TAP technique on cytosolic and nuclear lysates to identify candidate proteins, through mass spectrometry, that bind to Gβ1 subunits.
Collapse
|
20
|
Lavallée-Adam M, Rauniyar N, McClatchy DB, Yates JR. PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. J Proteome Res 2014; 13:5496-509. [PMID: 25177766 PMCID: PMC4258137 DOI: 10.1021/pr500473n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The majority of large-scale proteomics quantification methods yield long lists of quantified proteins that are often difficult to interpret and poorly reproduced. Computational approaches are required to analyze such intricate quantitative proteomics data sets. We propose a statistical approach to computationally identify protein sets (e.g., Gene Ontology (GO) terms) that are significantly enriched with abundant proteins with reproducible quantification measurements across a set of replicates. To this end, we developed PSEA-Quant, a protein set enrichment analysis algorithm for label-free and label-based protein quantification data sets. It offers an alternative approach to classic GO analyses, models protein annotation biases, and allows the analysis of samples originating from a single condition, unlike analogous approaches such as GSEA and PSEA. We demonstrate that PSEA-Quant produces results complementary to GO analyses. We also show that PSEA-Quant provides valuable information about the biological processes involved in cystic fibrosis using label-free protein quantification of a cell line expressing a CFTR mutant. Finally, PSEA-Quant highlights the differences in the mechanisms taking place in the human, rat, and mouse brain frontal cortices based on tandem mass tag quantification. Our approach, which is available online, will thus improve the analysis of proteomics quantification data sets by providing meaningful biological insights.
Collapse
Affiliation(s)
- Mathieu Lavallée-Adam
- Department of Chemical Physiology, The Scripps Research Institute , 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | | | | | | |
Collapse
|
21
|
Gpn1 and Gpn3 associate tightly and their protein levels are mutually dependent in mammalian cells. FEBS Lett 2014; 588:3823-9. [DOI: 10.1016/j.febslet.2014.08.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/03/2014] [Accepted: 08/28/2014] [Indexed: 11/24/2022]
|
22
|
Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin. J Proteomics 2013; 100:115-24. [PMID: 24140279 DOI: 10.1016/j.jprot.2013.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/25/2013] [Accepted: 10/07/2013] [Indexed: 02/06/2023]
Abstract
UNLABELLED Kin17 is a protein that was discovered through its immunoreactivity towards an antibody directed against prokaryotic RecA. Further study of Kin17 revealed a function in DNA replication and repair, as well as in pre-mRNA processing. Recently, it was found that Kin17 is methylated on lysine 135 by the newly discovered methyltransferase METTL22. To better understand the function of Kin17 and its regulation by methylation, we used multiple cell compartment protein affinity purification coupled with mass spectrometry (MCC-AP-MS) to identify novel interaction partners of Kin17 and to assess whether these interactions can take place on chromatin. Our results confirm that Kin17 interacts with METTL22 both in the soluble and chromatin fractions. We also show that many RNA-binding proteins, including the previously identified interactor BUD13 as well as spliceosomal and ribosomal subunits, associate with Kin17 in the soluble fraction. Interestingly, overexpression of METTL22 in HEK 293 cells displaces Kin17 from the chromatin to the cytoplasmic fraction, suggesting a role for methylation of lysine 135, a residue that lies within a winged helix domain of Kin17, in regulating association with chromatin. These results are discussed in view of the putative cellular function of Kin17. BIOLOGICAL SIGNIFICANCE The results shown here broaden our understanding of METTL22, a member of a family of newly-discovered non-histone lysine methyltransferases and its substrate, Kin17, a DNA/RNA-binding protein with reported roles in DNA repair and replication and mRNA processing. An innovative method to study protein-protein interactions in multiple cell compartments is employed to outline the interaction network of both proteins. Functional experiments uncover a correlative role between Kin17 lysine methylation and its association with chromatin. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
Collapse
Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mathieu Lavallée-Adam
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Biochemistry, Université de Montréal, Montréal, Québec H3T 1J4, Canada.
| |
Collapse
|