1
|
Di Stefano LH, Saba LJ, Oghbaie M, Jiang H, McKerrow W, Benitez-Guijarro M, Taylor MS, LaCava J. Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. Methods Mol Biol 2023; 2607:215-256. [PMID: 36449166 DOI: 10.1007/978-1-0716-2883-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
During their proliferation and the host's concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.
Collapse
|
2
|
Spiniello M, Scalf M, Casamassimi A, Abbondanza C, Smith LM. Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. Int J Mol Sci 2022; 23:ijms23020942. [PMID: 35055128 PMCID: PMC8779001 DOI: 10.3390/ijms23020942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA–protein interactions is involved in many different pathological states. Several computational and experimental strategies have been developed to identify protein binders of selected RNA molecules. Amongst these, ‘in cell’ hybridization methods represent the gold standard in the field because they are designed to reveal the proteins bound to specific RNAs in a cellular context. Here, we compare the technical features of different ‘in cell’ hybridization approaches with a focus on their advantages, limitations, and current and potential future applications.
Collapse
Affiliation(s)
- Michele Spiniello
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, 80131 Naples, Italy
- Correspondence: (M.S.); (A.C.)
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.S.); (L.M.S.)
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
- Correspondence: (M.S.); (A.C.)
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.S.); (L.M.S.)
| |
Collapse
|
3
|
Trahan C, Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods Mol Biol 2022; 2477:195-223. [PMID: 35524119 DOI: 10.1007/978-1-0716-2257-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to get a comprehensive picture of cellular behavior and to understand biological systems. In the past two decades, affinity purification coupled to mass spectrometry has become a powerful tool to comprehensively study interaction networks and their assemblies. To overcome initial limitations of the approach, in particular, the effect of protein and RNA degradation, loss of transient interactors, and poor overall yield of intact complexes from cell lysates, various modifications to affinity purification protocols have been devised over the years. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol as described here has been optimized for the yeast S. cerevisiae.
Collapse
Affiliation(s)
- Christian Trahan
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada.
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada.
| |
Collapse
|
4
|
Shkel O, Kharkivska Y, Kim YK, Lee JS. Proximity Labeling Techniques: A Multi-Omics Toolbox. Chem Asian J 2021; 17:e202101240. [PMID: 34850572 DOI: 10.1002/asia.202101240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/29/2021] [Indexed: 01/17/2023]
Abstract
Proximity labeling techniques are emerging high-throughput methods for studying protein-protein, protein-RNA, and protein-DNA interactions with temporal and spatial precision. Proximity labeling methods take advantage of enzymes that can covalently label biomolecules with reactive substrates. These labeled biomolecules can be identified using mass spectrometry or next-generation sequencing. The main advantage of these methods is their ability to capture weak or transient interactions between biomolecules. Proximity labeling is indispensable for studying organelle interactomes. Additionally, it can be used to resolve spatial composition of macromolecular complexes. Many of these methods have only recently been introduced; nonetheless, they have already provided new and deep insights into the biological processes at the cellular, organ, and organism levels. In this paper, we review a broad range of proximity labeling techniques, their development, drawbacks and advantages, and implementations in recent studies.
Collapse
Affiliation(s)
- Olha Shkel
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yevheniia Kharkivska
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yun Kyung Kim
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
5
|
Henneberg F, Chari A. Chromatography-Free Purification Strategies for Large Biological Macromolecular Complexes Involving Fractionated PEG Precipitation and Density Gradients. Life (Basel) 2021; 11:1289. [PMID: 34947821 PMCID: PMC8707722 DOI: 10.3390/life11121289] [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: 10/09/2021] [Revised: 11/10/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
A complex interplay between several biological macromolecules maintains cellular homeostasis. Generally, the demanding chemical reactions which sustain life are not performed by individual macromolecules, but rather by several proteins that together form a macromolecular complex. Understanding the functional interactions amongst subunits of these macromolecular machines is fundamental to elucidate mechanisms by which they maintain homeostasis. As the faithful function of macromolecular complexes is essential for cell survival, their mis-function leads to the development of human diseases. Furthermore, detailed mechanistic interrogation of the function of macromolecular machines can be exploited to develop and optimize biotechnological processes. The purification of intact macromolecular complexes is an essential prerequisite for this; however, chromatographic purification schemes can induce the dissociation of subunits or the disintegration of the whole complex. Here, we discuss the development and application of chromatography-free purification strategies based on fractionated PEG precipitation and orthogonal density gradient centrifugation that overcomes existing limitations of established chromatographic purification protocols. The presented case studies illustrate the capabilities of these procedures for the purification of macromolecular complexes.
Collapse
Affiliation(s)
- Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany;
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany;
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| |
Collapse
|
6
|
Siva Sankar D, Dengjel J. Protein complexes and neighborhoods driving autophagy. Autophagy 2021; 17:2689-2705. [PMID: 33183148 PMCID: PMC8526019 DOI: 10.1080/15548627.2020.1847461] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023] Open
Abstract
Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms.Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
Collapse
Affiliation(s)
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
7
|
Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021; 11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
Collapse
Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Etienne Coyaud
- Protéomique Réponse Inflammatoire Spectrométrie de Mass—PRISM, Inserm U1192, University Lille, CHU Lille, F-59000 Lille, France;
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8Z 7X8, Canada
- Genome BC Proteome Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada
| |
Collapse
|
8
|
Zhang Y, Natale R, Domingues AP, Toleco MR, Siemiatkowska B, Fàbregas N, Fernie AR. Rapid Identification of Protein-Protein Interactions in Plants. ACTA ACUST UNITED AC 2020; 4:e20099. [PMID: 31714676 DOI: 10.1002/cppb.20099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme-enzyme interactions can be discovered by affinity purification mass spectrometry (AP-MS) under in vivo conditions. Tagged enzymes can either be transiently transformed into plant leaves or stably transformed into plant cells prior to AP-MS. The success of AP-MS depends on the levels and stability of the bait protein, the stability of the protein-protein interactions, and the efficiency of trypsin digestion and recovery of tryptic peptides for MS analysis. Unlike in-gel-digestion AP-MS, in which the gel is cut into pieces for several independent trypsin digestions, we uses a proteomics-based in-solution digestion method to directly digest the proteins on the beads following affinity purification. Thus, a single replicate within an AP-MS experiment constitutes a single sample for LC-MS measurement. In subsequent data analysis, normalized signal intensities can be processed to determine fold-change abundance (FC-A) scores by use of the SAINT algorithm embedded within the CRAPome software. Following analysis of co-sublocalization of "bait" and "prey," we suggest considering only the protein pairs for which the intensities were more than 2% compared with the bait, corresponding to FC-A values of at least four within-biological replicates, which we recommend as minimum. If the procedure is faithfully followed, experimental assessment of enzyme-enzyme interactions can be carried out in Arabidopsis within 3 weeks (transient expression) or 5 weeks (stable expression). © 2019 The Authors. Basic Protocol 1: Gene cloning to the destination vectors Alternate Protocol: In-Fusion or Gibson gene cloning protocol Basic Protocol 2: Transformation of baits into the plant cell culture or plant leaf Basic Protocol 3: Affinity purification of protein complexes Basic Protocol 4: On-bead trypsin/LysC digestion and C18 column peptide desalting and concentration Basic Protocol 5: Data analysis and quality control.
Collapse
Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Roberto Natale
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.,Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Adilson Pereira Domingues
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.,Department of Crop Science, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Mitchell Rey Toleco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Beata Siemiatkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Norma Fàbregas
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| |
Collapse
|
9
|
Zhang H, Wei J, Qian W, Deng C. Analysis of HrpG regulons and HrpG-interacting proteins by ChIP-seq and affinity proteomics in Xanthomonas campestris. MOLECULAR PLANT PATHOLOGY 2020; 21:388-400. [PMID: 31916392 PMCID: PMC7036363 DOI: 10.1111/mpp.12903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/06/2019] [Accepted: 11/27/2019] [Indexed: 06/02/2023]
Abstract
Gamma-proteobacteria Xanthomonas spp. cause at least 350 different plant diseases among important agricultural crops, which result in serious yield losses. Xanthomonas spp. rely mainly on the type III secretion system (T3SS) to infect their hosts and induce a hypersensitive response in nonhosts. HrpG, the master regulator of the T3SS, plays the dominant role in bacterial virulence. In this study, we used chromatin immunoprecipitation followed by sequencing (ChIP-seq) and tandem affinity purification (TAP) to systematically characterize the HrpG regulon and HrpG interacting proteins in vivo. We obtained 186 candidate HrpG downstream genes from the ChIP-seq analysis, which represented the genomic-wide regulon spectrum. A consensus HrpG-binding motif was obtained and three T3SS genes, hpa2, hrcU, and hrpE, were confirmed to be directly transcriptionally activated by HrpG in the inducing medium. A total of 273 putative HrpG interacting proteins were identified from the TAP data and the DNA-binding histone-like HU protein of Xanthomonas campestris pv. campestris (HUxcc ) was proved to be involved in bacterial virulence by increasing the complexity and intelligence of the bacterial signalling pathways in the T3SS.
Collapse
Affiliation(s)
- Hong‐Yu Zhang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Jin‐Wei Wei
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Wei Qian
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Chao‐Ying Deng
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| |
Collapse
|
10
|
Yu S, Li F, Huang X, Dong C, Ren J. In Situ Study of Interactions between Endogenous c-myc mRNA with CRDBP in a Single Living Cell by Combining Fluorescence Cross-Correlation Spectroscopy with Molecular Beacons. Anal Chem 2020; 92:2988-2996. [DOI: 10.1021/acs.analchem.9b03934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shengrong Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Fucai Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| |
Collapse
|
11
|
Liu G, Fu T, Han Y, Hu S, Zhang X, Zheng M, Hao P, Pan L, Kang J. Probing Protein–Protein Interactions with Label-Free Mass Spectrometry Quantification in Combination with Affinity Purification by Spin-Tip Affinity Columns. Anal Chem 2020; 92:3913-3922. [DOI: 10.1021/acs.analchem.9b05355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guizhen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Fu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ying Han
- School of Life Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Shichen Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xuepei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Mengmeng Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| |
Collapse
|
12
|
Ren L, Ding S, Song Y, Li B, Ramanathan M, Co J, Amieva MR, Khavari PA, Greenberg HB. Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication. J Biol Chem 2019; 294:5993-6006. [PMID: 30770472 DOI: 10.1074/jbc.ra118.006004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 02/09/2019] [Indexed: 12/22/2022] Open
Abstract
Genome replication and virion assembly of segmented RNA viruses are highly coordinated events, tightly regulated by sequence and structural elements in the UTRs of viral RNA. This process is poorly defined and likely requires the participation of host proteins in concert with viral proteins. In this study, we employed a proteomics-based approach, named RNA-protein interaction detection (RaPID), to comprehensively screen for host proteins that bind to a conserved motif within the rotavirus (RV) 3' terminus. Using this assay, we identified ATP5B, a core subunit of the mitochondrial ATP synthase, as having high affinity to the RV 3'UTR consensus sequences. During RV infection, ATP5B bound to the RV 3'UTR and co-localized with viral RNA and viroplasm. Functionally, siRNA-mediated genetic depletion of ATP5B or other ATP synthase subunits such as ATP5A1 and ATP5O reduced the production of infectious viral progeny without significant alteration of intracellular viral RNA levels or RNA translation. Chemical inhibition of ATP synthase diminished RV yield in both conventional cell culture and in human intestinal enteroids, indicating that ATP5B positively regulates late-stage RV maturation in primary intestinal epithelial cells. Collectively, our results shed light on the role of host proteins in RV genome assembly and particle formation and identify ATP5B as a novel pro-RV RNA-binding protein, contributing to our understanding of how host ATP synthases may galvanize virus growth and pathogenesis.
Collapse
Affiliation(s)
- Lili Ren
- From the Department of Medicine, Division of Gastroenterology and Hepatology, Stanford, California 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305; the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304; the School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, China
| | - Siyuan Ding
- From the Department of Medicine, Division of Gastroenterology and Hepatology, Stanford, California 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305; the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304.
| | - Yanhua Song
- From the Department of Medicine, Division of Gastroenterology and Hepatology, Stanford, California 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305; the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304; the Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Bin Li
- From the Department of Medicine, Division of Gastroenterology and Hepatology, Stanford, California 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305; the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304; the Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Muthukumar Ramanathan
- the Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Julia Co
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305
| | - Manuel R Amieva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305
| | - Paul A Khavari
- the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304; the Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Harry B Greenberg
- From the Department of Medicine, Division of Gastroenterology and Hepatology, Stanford, California 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305; the Palo Alto Veterans Institute of Research, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304.
| |
Collapse
|
13
|
Abstract
The systematic identification of all protein–protein interactions that take place in an organism (the ‘interactome’) is an important goal in modern biology. The nematode Caenorhabditis elegans was one of the first multicellular models for which a proteome-wide interactome mapping project was initiated. Most Caenorhabditis elegans interactome mapping efforts have utilized the yeast two-hybrid system, yielding an extensive binary interactome, while recent developments in mass spectrometry-based approaches hold great potential for further improving our understanding of protein interactome networks in a multicellular context. For example, methods like co-fractionation, proximity labeling, and tissue-specific protein purification not only identify protein–protein interactions, but have the potential to provide crucial insight into when and where interactions take place. Here we review current standards and recent improvements in protein interaction mapping in C. elegans. Protein interactome mapping is a key method to understanding biology. C. elegans was one of the first multicellular organisms whose interactome was mapped. Renewed efforts and improved technologies are needed to complete the interactome. Novel technologies are poised to provide spatial information to interactome networks.
Collapse
Affiliation(s)
- Sanne Remmelzwaal
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Mike Boxem
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| |
Collapse
|
14
|
Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
Collapse
Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
| |
Collapse
|
15
|
Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci 2018; 5:90. [PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.
Collapse
Affiliation(s)
| | | | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| |
Collapse
|
16
|
Kanellopoulos AH, Koenig J, Huang H, Pyrski M, Millet Q, Lolignier S, Morohashi T, Gossage SJ, Jay M, Linley JE, Baskozos G, Kessler BM, Cox JJ, Dolphin AC, Zufall F, Wood JN, Zhao J. Mapping protein interactions of sodium channel Na V1.7 using epitope-tagged gene-targeted mice. EMBO J 2018; 37:427-445. [PMID: 29335280 PMCID: PMC5793798 DOI: 10.15252/embj.201796692] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 11/24/2022] Open
Abstract
The voltage-gated sodium channel NaV1.7 plays a critical role in pain pathways. We generated an epitope-tagged NaV1.7 mouse that showed normal pain behaviours to identify channel-interacting proteins. Analysis of NaV1.7 complexes affinity-purified under native conditions by mass spectrometry revealed 267 proteins associated with Nav1.7 in vivo The sodium channel β3 (Scn3b), rather than the β1 subunit, complexes with Nav1.7, and we demonstrate an interaction between collapsing-response mediator protein (Crmp2) and Nav1.7, through which the analgesic drug lacosamide regulates Nav1.7 current density. Novel NaV1.7 protein interactors including membrane-trafficking protein synaptotagmin-2 (Syt2), L-type amino acid transporter 1 (Lat1) and transmembrane P24-trafficking protein 10 (Tmed10) together with Scn3b and Crmp2 were validated by co-immunoprecipitation (Co-IP) from sensory neuron extract. Nav1.7, known to regulate opioid receptor efficacy, interacts with the G protein-regulated inducer of neurite outgrowth (Gprin1), an opioid receptor-binding protein, demonstrating a physical and functional link between Nav1.7 and opioid signalling. Further information on physiological interactions provided with this normal epitope-tagged mouse should provide useful insights into the many functions now associated with the NaV1.7 channel.
Collapse
Affiliation(s)
| | - Jennifer Koenig
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Honglei Huang
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Martina Pyrski
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Queensta Millet
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Stéphane Lolignier
- Molecular Nociception Group, WIBR, University College London, London, UK
- Université Clermont Auvergne, Inserm U1107 Neuro-Dol, Pharmacologie Fondamentale et Clinique de la Douleur, Clermont-Ferrand, France
| | - Toru Morohashi
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Samuel J Gossage
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Maude Jay
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - John E Linley
- Molecular Nociception Group, WIBR, University College London, London, UK
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, Oxford, UK
| | - James J Cox
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Annette C Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Frank Zufall
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - John N Wood
- Molecular Nociception Group, WIBR, University College London, London, UK
| | - Jing Zhao
- Molecular Nociception Group, WIBR, University College London, London, UK
| |
Collapse
|
17
|
Abstract
Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.
Collapse
Affiliation(s)
- Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
18
|
Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K. Protein complex analysis: From raw protein lists to protein interaction networks. MASS SPECTROMETRY REVIEWS 2017; 36:600-614. [PMID: 26709718 DOI: 10.1002/mas.21485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purification-mass spectrometry and other co-complex methods have become widely employed experimental techniques to identify protein complexes. These techniques typically suffer from a high number of false negatives and false positive contaminants due to technical shortcomings and purification biases. To support a diverse range of experimental designs and approaches, a large number of computational methods have been proposed to filter, infer and validate protein interaction networks from experimental pull-down MS data. Nevertheless, this expansion of available methods complicates the selection of the most optimal ones to support systems biology-driven knowledge extraction. In this review, we give an overview of the most commonly used computational methods to process and interpret co-complex results, and we discuss the issues and unsolved problems that still exist within the field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:600-614, 2017.
Collapse
Affiliation(s)
- Pieter Meysman
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Kevin Titeca
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Sven Eyckerman
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bart Goethals
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- IBioStat, Hasselt University, Hasselt, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| |
Collapse
|
19
|
Abstract
RNA-protein interactions are essential for proper gene expression regulation, particularly in neurons with unique spatial constraints. Currently, these interactions are defined biochemically, but a method is needed to evaluate them quantitatively within morphological context. Colocalization of two-color labels using wide-field microscopy is a method to infer these interactions. However, because of chromatic aberrations in the objective lens, this approach lacks the resolution to determine whether two molecules are physically in contact or simply nearby by chance. Here, we developed a robust super registration methodology that corrected the chromatic aberration across the entire image field to within 10 nm, which is capable of determining whether two molecules are physically interacting or simply in proximity by random chance. We applied this approach to image single-molecule FISH in combination with immunofluorescence (smFISH-IF) and determined whether the association between an mRNA and binding protein(s) within a neuron was significant or accidental. We evaluated several mRNA-binding proteins identified from RNA pulldown assays to determine which of these exhibit bona fide interactions. Surprisingly, many known mRNA-binding proteins did not bind the mRNA in situ, indicating that adventitious interactions are significant using existing technology. This method provides an ability to evaluate two-color registration compatible with the scale of molecular interactions.
Collapse
|
20
|
Di Tomasso G, Miller Jenkins LM, Legault P. ARiBo pull-down for riboproteomic studies based on label-free quantitative mass spectrometry. RNA (NEW YORK, N.Y.) 2016; 22:1760-1770. [PMID: 27659051 PMCID: PMC5066628 DOI: 10.1261/rna.057513.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
As part of their normal life cycle, most RNA molecules associate with several proteins that direct their fate and regulate their function. Here, we describe a novel method for identifying proteins that associate with a target RNA. The procedure is based on the ARiBo method for affinity purification of RNA, which was originally developed to quickly purify RNA with high yields and purity under native conditions. The ARiBo method was further optimized using in vitro transcribed RNA to capture RNA-associating proteins from cellular extracts with high yields and low background protein contamination. For these RNA pull-downs, stem-loops present in the immature forms of let-7 miRNAs (miRNA stem-loops) were used as the target RNAs. Label-free quantitative mass spectrometry analysis allowed for the reliable identification of proteins that are specific to the stem-loops present in the immature forms of two miRNAs, let-7a-1 and let-7g. Several proteins known to bind immature forms of these let-7 miRNAs were identified, but with an improved coverage compared to previous studies. In addition, several novel proteins were identified that better define the protein interactome of the let-7 miRNA stem-loops and further link let-7 biogenesis to important biological processes such as development and tumorigenesis. Thus, combining the ARiBo pull-down method with label-free quantitative mass spectrometry provides an effective proteomic approach for identification of proteins that associate with a target RNA.
Collapse
Affiliation(s)
- Geneviève Di Tomasso
- Département de biochimie et médecine moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
| |
Collapse
|
21
|
Baeyens A, Naessens E, Van Nuffel A, Weening KE, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B. HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome. Sci Rep 2016; 6:34573. [PMID: 27721439 PMCID: PMC5056386 DOI: 10.1038/srep34573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/12/2016] [Indexed: 01/11/2023] Open
Abstract
To facilitate studies on Vpr function in replicating HIV-1, we aimed to tag the protein in an infectious virus. First we showed that N-, but not C-terminal HA/FLAG tagging of Vpr protein preserves Vpr cytopathicity. Cloning the tags into proviral DNA however ablated viral production and replication. By construction of additional viral variants we could show this defect was not protein- but RNA-dependent and sequence specific, and characterized by oversplicing of the genomic RNA. Simulation of genomic RNA folding suggested that introduction of the tag sequence induced an alternative folding structure in a region enriched in splice sites and splicing regulatory sequences. In silico predictions identified the HA/His6-Vpr tagging in HIV-1 to affect mRNA folding less than HA/FLAG-Vpr tagging. In vitro infectivity and mRNA splice pattern improved but did not reach wild-type values. Thus, sequence-specific insertions may interfere with mRNA splicing, possibly due to altered RNA folding. Our results point to the complexity of viral RNA genome sequence interactions. This should be taken into consideration when designing viral manipulation strategies, for both research as for biological interventions.
Collapse
Affiliation(s)
- Ann Baeyens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anouk Van Nuffel
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Karin E Weening
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anne-Marie Reilly
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Eva Claeys
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Wim Trypsteen
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| |
Collapse
|
22
|
Samra N, Arava Y. Novel RNA-Binding Proteins Isolation by the RaPID Methodology. J Vis Exp 2016. [PMID: 27768054 DOI: 10.3791/54467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
RNA-binding proteins (RBPs) play important roles in every aspect of RNA metabolism and regulation. Their identification is a major challenge in modern biology. Only a few in vitro and in vivo methods enable the identification of RBPs associated with a particular target mRNA. However, their main limitations are the identification of RBPs in a non-cellular environment (in vitro) or the low efficiency isolation of RNA of interest (in vivo). An RNA-binding protein purification and identification (RaPID) methodology was designed to overcome these limitations in yeast and enable efficient isolation of proteins that are associated in vivo. To achieve this, the RNA of interest is tagged with MS2 loops, and co-expressed with a fusion protein of an MS2-binding protein and a streptavidin-binding protein (SBP). Cells are then subjected to crosslinking and lysed, and complexes are isolated through streptavidin beads. The proteins that co-purify with the tagged RNA can then be determined by mass spectrometry. We recently used this protocol to identify novel proteins associated with the ER-associated PMP1 mRNA. Here, we provide a detailed protocol of RaPID, and discuss some of its limitations and advantages.
Collapse
Affiliation(s)
- Nitzan Samra
- Faculty of Biology, Technion - Israel Institute of Technology; Department of Biomolecular Sciences, Weizmann Institute of Science
| | - Yoav Arava
- Faculty of Biology, Technion - Israel Institute of Technology;
| |
Collapse
|
23
|
Eyckerman S, Impens F, Van Quickelberghe E, Samyn N, Vandemoortele G, De Sutter D, Tavernier J, Gevaert K. Intelligent Mixing of Proteomes for Elimination of False Positives in Affinity Purification-Mass Spectrometry. J Proteome Res 2016; 15:3929-3937. [PMID: 27640904 DOI: 10.1021/acs.jproteome.6b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein complexes are essential in all organizational and functional aspects of the cell. Different strategies currently exist for analyzing such protein complexes by mass spectrometry, including affinity purification (AP-MS) and proximal labeling-based strategies. However, the high sensitivity of current mass spectrometers typically results in extensive protein lists mainly consisting of nonspecifically copurified proteins. Finding the true positive interactors in these lists remains highly challenging. Here, we report a powerful design based on differential labeling with stable isotopes combined with nonequal mixing of control and experimental samples to discover bona fide interaction partners in AP-MS experiments. We apply this intelligent mixing of proteomes (iMixPro) concept to overexpression experiments for RAF1, RNF41, and TANK and also to engineered cell lines expressing epitope-tagged endogenous PTPN14, JIP3, and IQGAP1. For all baits, we confirmed known interactions and found a number of novel interactions. The results for RNF41 and TANK were compared to a classical affinity purification experiment, which demonstrated the efficiency and specificity of the iMixPro approach.
Collapse
Affiliation(s)
- Sven Eyckerman
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Francis Impens
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,VIB Proteomics Expertise Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Emmy Van Quickelberghe
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Noortje Samyn
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Giel Vandemoortele
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Delphine De Sutter
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Jan Tavernier
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| |
Collapse
|
24
|
Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
Collapse
Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
25
|
LaCava J, Fernandez-Martinez J, Hakhverdyan Z, Rout MP. Protein Complex Purification by Affinity Capture. Cold Spring Harb Protoc 2016; 2016:2016/7/pdb.top077545. [PMID: 27371601 DOI: 10.1101/pdb.top077545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Affinity capture has become a powerful technique for consistently purifying endogenous protein complexes, facilitating biochemical and biophysical assays on otherwise inaccessible biological assemblies, and enabling broader interactomic exploration. For this procedure, cells are broken and their contents separated and extracted into a solvent, permitting access to target macromolecular complexes thus released in solution. The complexes are specifically enriched from the extract onto a solid medium coupled with an affinity reagent-usually an antibody-that recognizes the target either directly or through an appended affinity tag, allowing subsequent characterization of the complex. Here, we discuss approaches and considerations for purifying endogenous yeast protein complexes by affinity capture.
Collapse
Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| | | | - Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| |
Collapse
|
26
|
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
|
27
|
Trahan C, Aguilar LC, Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods Mol Biol 2016; 1361:265-287. [PMID: 26483027 DOI: 10.1007/978-1-4939-3079-1_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems. In the last decade, affinity purification coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their assemblies. However, the study of these interactomes has been hampered by severe methodological limitations. In particular, the affinity purification of intact complexes from cell lysates suffers from protein and RNA degradation, loss of transient interactors, and poor overall yields. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol described here has been optimized for the yeast S. cerevisiae.
Collapse
Affiliation(s)
- Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada, H3T 1J4
| | - Lisbeth-Carolina Aguilar
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7.
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada, H3T 1J4.
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada, H3A 1A3.
| |
Collapse
|
28
|
Abstract
The LINE-1 retrotransposon (L1) encodes two proteins, ORF1p and ORF2p, which bind to the L1 RNA in cis, forming a ribonucleoprotein (RNP) complex that is critical for retrotransposition. Interactions with both permissive and repressive host factors pervade every step of the L1 life cycle. Until recently, limitations in detection and production precluded in-depth characterization of L1 RNPs. Inducible expression and recombinant engineering of epitope tags have made detection of both L1 ORFs routine. Here, we describe large-scale production of L1-expressing HEK-293T cells in suspension cell culture, cryomilling and affinity capture of L1 RNP complexes, sample preparation for analysis by mass spectrometry, and assay using the L1 element amplification protocol (LEAP) and qRT-PCR.
Collapse
|
29
|
Sinz A, Arlt C, Chorev D, Sharon M. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology. Protein Sci 2015; 24:1193-209. [PMID: 25970732 PMCID: PMC4534171 DOI: 10.1002/pro.2696] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/14/2015] [Accepted: 04/29/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.
Collapse
Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Dror Chorev
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| |
Collapse
|
30
|
Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J. Rapid, optimized interactomic screening. Nat Methods 2015; 12:553-60. [PMID: 25938370 PMCID: PMC4449307 DOI: 10.1038/nmeth.3395] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 03/03/2015] [Indexed: 12/25/2022]
Abstract
We must reliably map the interactomes of cellular macromolecular
complexes in order to fully explore and understand biological systems. However,
there are no methods to accurately predict how to capture a given macromolecular
complex with its physiological binding partners. Here, we present a screen that
comprehensively explores the parameters affecting the stability of interactions
in affinity-captured complexes, enabling the discovery of physiological binding
partners and the elucidation of their functional interactions in unparalleled
detail. We have implemented this screen on several macromolecular complexes from
a variety of organisms, revealing novel profiles even for well-studied proteins.
Our approach is robust, economical and automatable, providing an inroad to the
rigorous, systematic dissection of cellular interactomes.
Collapse
Affiliation(s)
- Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Michal Domanski
- 1] Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA. [2] Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Loren E Hough
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | | | | | - Sarah Keegan
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - David J Dilworth
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Vadim Sherman
- High Energy Physics Instrument Shop, The Rockefeller University, New York, New York, USA
| | - John D Aitchison
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - David Fenyö
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
31
|
Bernaudo F, Monteleone F, Mesuraca M, Krishnan S, Chiarella E, Scicchitano S, Cuda G, Morrone G, Bond HM, Gaspari M. Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521. J Proteome Res 2015; 14:1888-99. [PMID: 25774781 DOI: 10.1021/pr501288h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The study of protein-protein interactions is increasingly relying on mass spectrometry (MS). The classical approach of separating immunoprecipitated proteins by SDS-PAGE followed by in-gel digestion is long and labor-intensive. Besides, it is difficult to integrate it with most quantitative MS-based workflows, except for stable isotopic labeling of amino acids in cell culture (SILAC). This work describes a fast, flexible and quantitative workflow for the discovery of novel protein-protein interactions. A cleavable cross-linker, dithiobis[succinimidyl propionate] (DSP), is utilized to stabilize protein complexes before immunoprecipitation. Protein complex detachment from the antibody is achieved by limited proteolysis. Finally, protein quantitation is performed via (18)O labeling. The workflow has been optimized concerning (i) DSP concentration and (ii) incubation times for limited proteolysis, using the stem cell-associated transcription cofactor ZNF521 as a model target. The interaction of ZNF521 with the core components of the nuclear remodelling and histone deacetylase (NuRD) complex, already reported in the literature, was confirmed. Additionally, interactions with newly discovered molecular partners of potentially relevant functional role, such as ZNF423, Spt16, Spt5, were discovered and validated by Western blotting.
Collapse
Affiliation(s)
- Francesca Bernaudo
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Francesca Monteleone
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Maria Mesuraca
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Shibu Krishnan
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Emanuela Chiarella
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Stefania Scicchitano
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Giovanni Cuda
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Giovanni Morrone
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Heather M Bond
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Marco Gaspari
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| |
Collapse
|
32
|
LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
Collapse
Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
| |
Collapse
|
33
|
Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
Collapse
Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | | | | |
Collapse
|
34
|
Keilhauer EC, Hein MY, Mann M. Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics 2014; 14:120-35. [PMID: 25363814 PMCID: PMC4288248 DOI: 10.1074/mcp.m114.041012] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein–protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein–protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers.
Collapse
Affiliation(s)
- Eva C Keilhauer
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- From the ‡Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
35
|
Mehta A, Sonam S, Gouri I, Loharch S, Sharma DK, Parkesh R. SMMRNA: a database of small molecule modulators of RNA. Nucleic Acids Res 2014; 42:D132-41. [PMID: 24163098 PMCID: PMC3965028 DOI: 10.1093/nar/gkt976] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/13/2013] [Accepted: 10/01/2013] [Indexed: 02/05/2023] Open
Abstract
We have developed SMMRNA, an interactive database, available at http://www.smmrna.org, with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ∼770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, ΔTm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.
Collapse
Affiliation(s)
- Ankita Mehta
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Surabhi Sonam
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Isha Gouri
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Saurabh Loharch
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Deepak K. Sharma
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Raman Parkesh
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| |
Collapse
|
36
|
Kim K, Park SJ, Na S, Kim JS, Choi H, Kim YK, Paek E, Lee C. Reinvestigation of aminoacyl-tRNA synthetase core complex by affinity purification-mass spectrometry reveals TARSL2 as a potential member of the complex. PLoS One 2013; 8:e81734. [PMID: 24312579 PMCID: PMC3846882 DOI: 10.1371/journal.pone.0081734] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/18/2013] [Indexed: 11/26/2022] Open
Abstract
Twenty different aminoacyl-tRNA synthetases (ARSs) link each amino acid to their cognate tRNAs. Individual ARSs are also associated with various non-canonical activities involved in neuronal diseases, cancer and autoimmune diseases. Among them, eight ARSs (D, EP, I, K, L, M, Q and RARS), together with three ARS-interacting multifunctional proteins (AIMPs), are currently known to assemble the multi-synthetase complex (MSC). However, the cellular function and global topology of MSC remain unclear. In order to understand the complex interaction within MSC, we conducted affinity purification-mass spectrometry (AP-MS) using each of AIMP1, AIMP2 and KARS as a bait protein. Mass spectrometric data were funneled into SAINT software to distinguish true interactions from background contaminants. A total of 40, 134, 101 proteins in each bait scored over 0.9 of SAINT probability in HEK 293T cells. Complex-forming ARSs, such as DARS, EPRS, IARS, Kars, LARS, MARS, QARS and RARS, were constantly found to interact with each bait. Variants such as, AIMP2-DX2 and AIMP1 isoform 2 were found with specific peptides in KARS precipitates. Relative enrichment analysis of the mass spectrometric data demonstrated that TARSL2 (threonyl-tRNA synthetase like-2) was highly enriched with the ARS-core complex. The interaction was further confirmed by coimmunoprecipitation of TARSL2 with other ARS core-complex components. We suggest TARSL2 as a new component of ARS core-complex.
Collapse
Affiliation(s)
- Kyutae Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, Korea
| | - Seong-Jun Park
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
| | - Seungjin Na
- Division of Computer Science and Engineering, Hanyang University, Seongdong-gu, Seoul, Korea
| | - Jun Seok Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yoon Ki Kim
- School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, Korea
| | - Eunok Paek
- Division of Computer Science and Engineering, Hanyang University, Seongdong-gu, Seoul, Korea
| | - Cheolju Lee
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon, Korea
- * E-mail:
| |
Collapse
|
37
|
Han Y, Garcia BA. Combining genomic and proteomic approaches for epigenetics research. Epigenomics 2013; 5:439-52. [PMID: 23895656 DOI: 10.2217/epi.13.37] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromatin immunoprecipitation (ChIP) followed by sequencing and other ChIP-based techniques are powerful techniques for genome-wide profiling of DNA-binding proteins, histone post-translational modifications or nucleosome positions. However, mass spectrometry-based proteomics is increasingly being used in functional biological studies and has proved to be an indispensable tool to characterize histone modifications, as well as DNA-protein and protein-protein interactions. With the development of genomic and proteomic approaches, combination of ChIP and mass spectrometry has the potential to expand our knowledge of epigenetics research to a higher level.
Collapse
Affiliation(s)
- Yumiao Han
- Epigenetics Program, Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 1009C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA
| | | |
Collapse
|
38
|
Poly(A) tail-mediated gene regulation by opposing roles of Nab2 and Pab2 nuclear poly(A)-binding proteins in pre-mRNA decay. Mol Cell Biol 2013; 33:4718-31. [PMID: 24081329 DOI: 10.1128/mcb.00887-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The 3' end of most eukaryotic transcripts is decorated by poly(A)-binding proteins (PABPs), which influence the fate of mRNAs throughout gene expression. However, despite the fact that multiple PABPs coexist in the nuclei of most eukaryotes, how functional interplay between these nuclear PABPs controls gene expression remains unclear. By characterizing the ortholog of the Nab2/ZC3H14 zinc finger PABP in Schizosaccharomyces pombe, we show here that the two major fission yeast nuclear PABPs, Pab2 and Nab2, have opposing roles in posttranscriptional gene regulation. Notably, we find that Nab2 functions in gene-specific regulation in a manner opposite to that of Pab2. By studying the ribosomal-protein-coding gene rpl30-2, which is negatively regulated by Pab2 via a nuclear pre-mRNA decay pathway that depends on the nuclear exosome subunit Rrp6, we show that Nab2 promotes rpl30-2 expression by acting at the level of the unspliced pre-mRNA. Our data support a model in which Nab2 impedes Pab2/Rrp6-mediated decay by competing with Pab2 for polyadenylated transcripts in the nucleus. The opposing roles of Pab2 and Nab2 reveal that interplay between nuclear PABPs can influence gene regulation.
Collapse
|
39
|
Abstract
Macromolecular complexes are involved in a broad spectrum of cellular processes including protein biosynthesis, protein secretion and degradation, metabolism, DNA replication and repair, and signal transduction along with other important biological processes. The analysis of protein complexes in health and disease is important to gain insights into cellular physiology and pathophysiology. In the last few decades, research has focused on the identification and the dynamics of macromolecular complexes. Several techniques have been developed to isolate native protein complexes from cells and tissues to allow further characterization by microscopic and proteomic analysis. In the present paper, we provide a brief overview of proteomic methods that can be used to identify protein–protein interactions, focusing on recent developments to study the entire complexome of a biological sample.
Collapse
|
40
|
Yoshigi M, Pronovost SM, Kadrmas JL. Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes. Proteome Sci 2013; 11:21. [PMID: 23663728 PMCID: PMC3688448 DOI: 10.1186/1477-5956-11-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/08/2013] [Indexed: 01/29/2023] Open
Abstract
Background Here we describe a novel approach used to identify the constituents of protein complexes with high fidelity, using the integrin-associated scaffolding protein PINCH as a test case. PINCH is comprised of five LIM domains, zinc-finger protein interaction modules. In Drosophila melanogaster, PINCH has two known high-affinity binding partners—Integrin-linked kinase (ILK) that binds to LIM1 and Ras Suppressor 1 (RSU1) that binds to LIM5—but has been postulated to bind additional proteins as well. Results To purify PINCH complexes, in parallel we fused different affinity tags (Protein A and Flag) to different locations within the PINCH sequence (N- and C-terminus). We expressed these tagged versions of PINCH both in cell culture (overexpressed in Drosophila S2 cell culture in the presence of endogenous PINCH) and in vivo (at native levels in Drosophila lacking endogenous PINCH). After affinity purification, we analyzed PINCH complexes by a novel 2D-gel electrophoresis analysis, iGEO (interactions by 2D Gel Electrophoresis Overlap), with mass spectrometric identification of individual spots of interest. iGEO allowed the identification of protein partners that associate with PINCH under two independent purification strategies, providing confidence in the significance of the interaction. Proteins identified by iGEO were validated against a highly inclusive list of candidate PINCH interacting proteins identified in previous analyses by MuDPIT mass spectrometry. Conclusions The iGEO strategy confirmed a core complex comprised of PINCH, RSU1, ILK, and ILK binding partner Parvin. Our iGEO method also identified five novel protein partners that specifically interacted with PINCH in Drosophila S2 cell culture. Because of the improved reproducibility of 2D-GE methodology and the increasing affordability of the required labeling reagents, iGEO is a method that is accessible to most moderately well-equipped biological laboratories. The biochemical co-purifications inherent in iGEO allow for rapid and unambiguous identification of the constituents of protein complexes, without the need for extensive follow-up experiments.
Collapse
Affiliation(s)
- Masaaki Yoshigi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
| | | | | |
Collapse
|
41
|
Piazzi M, Blalock WL, Bavelloni A, Faenza I, D'Angelo A, Maraldi NM, Cocco L. Phosphoinositide-specific phospholipase C β 1b (PI-PLCβ1b) interactome: affinity purification-mass spectrometry analysis of PI-PLCβ1b with nuclear protein. Mol Cell Proteomics 2013; 12:2220-35. [PMID: 23665500 DOI: 10.1074/mcp.m113.029686] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two isoforms of inositide-dependent phospholipase C β1 (PI-PLCβ1) are generated by alternative splicing (PLCβ1a and PLCβ1b). Both isoforms are present within the nucleus, but in contrast to PLCβ1a, the vast majority of PLCβ1b is nuclear. In mouse erythroid leukemia cells, PI-PLCβ1 is involved in the regulation of cell division and the balance between cell proliferation and differentiation. It has been demonstrated that nuclear localization is crucial for the enzymatic function of PI-PLCβ1, although the mechanism by which this nuclear import occurs has never been fully characterized. The aim of this study was to characterize both the mechanism of nuclear localization and the molecular function of nuclear PI-PLCβ1 by identifying its interactome in Friend's erythroleukemia isolated nuclei, utilizing a procedure that coupled immuno-affinity purification with tandem mass spectrometry analysis. Using this procedure, 160 proteins were demonstrated to be in association with PI-PLCβ1b, some of which have been previously characterized, such as the splicing factor SRp20 (Srsf3) and Lamin B (Lmnb1). Co-immunoprecipitation analysis of selected proteins confirmed the data obtained via mass spectrometry. Of particular interest was the identification of the nuclear import proteins Kpna2, Kpna4, Kpnb1, Ran, and Rangap1, as well as factors involved in hematological malignancies and several anti-apoptotic proteins. These data give new insight into possible mechanisms of nuclear trafficking and functioning of this critical signaling molecule.
Collapse
Affiliation(s)
- Manuela Piazzi
- Cell Signaling Laboratory, Department of Biomedical Science DIBINEM, University of Bologna, 40126 Bologna, Italy
| | | | | | | | | | | | | |
Collapse
|
42
|
Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE. Protein interactions, post-translational modifications and topologies in human cells. Mol Cell Proteomics 2013; 12:1451-67. [PMID: 23354917 PMCID: PMC3650351 DOI: 10.1074/mcp.m112.024497] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/12/2012] [Indexed: 12/22/2022] Open
Abstract
The unique and remarkable physicochemical properties of protein surface topologies give rise to highly specific biomolecular interactions, which form the framework through which living systems are able to carry out their vast array of functions. Technological limitations undermine efforts to probe protein structures and interactions within unperturbed living systems on a large scale. Rapid chemical stabilization of proteins and protein complexes through chemical cross-linking offers the alluring possibility to study details of the protein structure to function relationships as they exist within living cells. Here we apply the latest technological advances in chemical cross-linking combined with mass spectrometry to study protein topologies and interactions from living human cells identifying a total of 368 cross-links. These include cross-links from all major cellular compartments including membrane, cytosolic and nuclear proteins. Intraprotein and interprotein cross-links were also observed for core histone proteins, including several cross-links containing post-translational modifications which are known histone marks conferring distinct epigenetic functions. Excitingly, these results demonstrate the applicability of cross-linking to make direct topological measurements on post-translationally modified proteins. The results presented here provide new details on the structures of known multi-protein complexes as well as evidence for new protein-protein interactions.
Collapse
Affiliation(s)
- Juan D. Chavez
- From the ‡Department of Genome Science, University of Washington, Seattle, Washington 98109
| | - Chad R. Weisbrod
- From the ‡Department of Genome Science, University of Washington, Seattle, Washington 98109
| | - Chunxiang Zheng
- From the ‡Department of Genome Science, University of Washington, Seattle, Washington 98109
| | - Jimmy K. Eng
- From the ‡Department of Genome Science, University of Washington, Seattle, Washington 98109
| | - James E. Bruce
- From the ‡Department of Genome Science, University of Washington, Seattle, Washington 98109
| |
Collapse
|
43
|
Dunham WH, Mullin M, Gingras AC. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 2012; 12:1576-90. [PMID: 22611051 DOI: 10.1002/pmic.201100523] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.
Collapse
Affiliation(s)
- Wade H Dunham
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | | | | |
Collapse
|