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Kushner JS, Liu G, Eisert RJ, Bradshaw GA, Pitt GS, Hinson JT, Kalocsay M, Marx SO. Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics. Circ Res 2022; 130:273-287. [PMID: 35050691 PMCID: PMC8852690 DOI: 10.1161/circresaha.121.319810] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity purification and mass spectrometry, have revealed many macromolecular complexes in cardiomyocytes and the vasculature. Yet these methods often fail to identify in vivo or transient protein-protein interactions. To capture these interactions in living cells and animals with subsequent mass spectrometry identification, enzyme-catalyzed proximity labeling techniques have been developed in the past decade. Although the application of this methodology to cardiovascular research is still in its infancy, the field is developing rapidly, and the promise is substantial. In this review, we outline important concepts and discuss how proximity proteomics has been applied to study physiological and pathophysiological processes relevant to the cardiovascular system.
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Affiliation(s)
- Jared S. Kushner
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Guoxia Liu
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Robyn J. Eisert
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Gary A. Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Geoffrey S. Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College
| | - J. Travis Hinson
- Cardiology Center, UConn Health, Farmington, CT
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Marian Kalocsay
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Steven O. Marx
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
- Department of Molecular Pharmacology and Therapeutics, Columbia University, Vagelos College of Physicians and Surgeons
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Santos HJ, Nozaki T. The mitosome of the anaerobic parasitic protist Entamoeba histolytica: A peculiar and minimalist mitochondrion-related organelle. J Eukaryot Microbiol 2022; 69:e12923. [PMID: 35588086 PMCID: PMC9796589 DOI: 10.1111/jeu.12923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The simplest class of mitochondrion-related organelles (MROs) is the mitosome, an organelle present in a few anaerobic protozoan parasites such as Entamoeba histolytica, Giardia intestinalis, and Cryptosporidium parvum. E. histolytica causes amoebiasis in humans, deemed as one of the important, yet neglected tropical infections in the world. Much of the enigma of the E. histolytica mitosome circles around the obvious lack of a majority of known mitochondrial components and functions exhibited in other organisms. The identification of enzymes responsible for sulfate activation (AS, IPP, and APSK) and a number of lineage-specific proteins such as the outer membrane beta-barrel protein (MBOMP30), and transmembrane domain-containing proteins that bind to various organellar proteins (ETMP1, ETMP30, EHI_170120, and EHI_099350) showcased the remarkable divergence of this organelle compared to the other MROs of anaerobic protozoa. Here, we summarize the findings regarding the biology of the mitosomes in E. histolytica, from their discovery up to the present understanding of its roles and interactions. We also include current advances and future perspectives on the biology, biochemistry, and evolution of the mitosomes of E. histolytica.
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Affiliation(s)
- Herbert J. Santos
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. SUBCELLULAR TRANSCRIPTOMICS & PROTEOMICS: A COMPARATIVE METHODS REVIEW. Mol Cell Proteomics 2021; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics. Subcellular information of protein and RNA give insights into molecular function. This review discusses strategies available to measure subcellular information. Hybridization of methods shows promise for exploring the composition of organelles. Advances are aiding understanding of the organisation and dynamics of cells.
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Affiliation(s)
- Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
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Dolgalev G, Poverennaya E. Applications of CRISPR-Cas Technologies to Proteomics. Genes (Basel) 2021; 12:1790. [PMID: 34828396 PMCID: PMC8625504 DOI: 10.3390/genes12111790] [Citation(s) in RCA: 1] [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: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics.
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Huang Z, Liu Z, Xie X, Zeng R, Chen Z, Kong L, Fan X, Chen PR. Bioorthogonal Photocatalytic Decaging-Enabled Mitochondrial Proteomics. J Am Chem Soc 2021; 143:18714-18720. [PMID: 34709827 DOI: 10.1021/jacs.1c09171] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spatiotemporally resolved dissection of subcellular proteome is crucial to our understanding of cellular functions in health and disease. We herein report a bioorthogonal and photocatalytic decaging-enabled proximity labeling strategy (CAT-Prox) for spatiotemporally resolved mitochondrial proteome profiling in living cells. Our systematic survey of the photocatalysts has led to the identification of Ir(ppy)2bpy as a bioorthogonal and mitochondria-targeting catalyst that allowed photocontrolled, rapid rescue of azidobenzyl-caged quinone methide as a highly reactive Michael acceptor for proximity-based protein labeling in mitochondria of live cells. Upon careful validation through in vitro labeling, mitochondria-targeting specificity, in situ catalytic activity as well as protein tagging, we applied CAT-Prox for mitochondria proteome profiling in living Hela cells as well as hard-to-transfect macrophage RAW264.7 cells with approximately 70% mitochondria specificity observed from up to 300 proteins enriched. Finally, CAT-Prox was further applied to the dynamic dissection of mitochondria proteome of macrophage cells upon lipopolysaccharide stimulation. By integrating photocatalytic decaging chemistry with proximity-based protein labeling, CAT-Prox offers a general, catalytic, and nongenetic alternative to the enzyme-based proximity labeling strategies for diverse live cell settings.
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Affiliation(s)
- Zongyu Huang
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ruxin Zeng
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zujie Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Linghao Kong
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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Khoury L, Slavov N. Comprehensive Identification of Regulatory Protein Networks. J Proteome Res 2021; 20:4913-4914. [PMID: 34736325 PMCID: PMC8608403 DOI: 10.1021/acs.jproteome.1c00813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luke Khoury
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
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