1
|
Cirri E, Knaudt H, Di Fraia D, Pömpner N, Rahnis N, Heinze I, Ori A, Dau T. Optimized Automated Workflow for BioID Improves Reproducibility and Identification of Protein-Protein Interactions. J Proteome Res 2024. [PMID: 39231529 DOI: 10.1021/acs.jproteome.4c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Proximity-dependent biotinylation is an important method to study protein-protein interactions in cells, for which an expanding number of applications has been proposed. The laborious and time-consuming sample processing has limited project sizes so far. Here, we introduce an automated workflow on a liquid handler to process up to 96 samples at a time. The automation not only allows higher sample numbers to be processed in parallel but also improves reproducibility and lowers the minimal sample input. Furthermore, we combined automated sample processing with shorter liquid chromatography gradients and data-independent acquisition to increase the analysis throughput and enable reproducible protein quantitation across a large number of samples. We successfully applied this workflow to optimize the detection of proteasome substrates by proximity-dependent labeling.
Collapse
Affiliation(s)
- Emilio Cirri
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Hannah Knaudt
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Domenico Di Fraia
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Nadine Pömpner
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Norman Rahnis
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Ivonne Heinze
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Therese Dau
- Leibniz Institute on Aging─Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| |
Collapse
|
2
|
Kutzner CE, Bauer KC, Lackmann JW, Acton RJ, Sarkar A, Pokrzywa W, Hoppe T. Optogenetic induction of mechanical muscle stress identifies myosin regulatory ubiquitin ligase NHL-1 in C. elegans. Nat Commun 2024; 15:6879. [PMID: 39128917 PMCID: PMC11317515 DOI: 10.1038/s41467-024-51069-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/26/2024] [Indexed: 08/13/2024] Open
Abstract
Mechanical stress during muscle contraction is a constant threat to proteome integrity. However, there is a lack of experimental systems to identify critical proteostasis regulators under mechanical stress conditions. Here, we present the transgenic Caenorhabditis elegans model OptIMMuS (Optogenetic Induction of Mechanical Muscle Stress) to study changes in the proteostasis network associated with mechanical forces. Repeated blue light exposure of a muscle-expressed Chlamydomonas rheinhardii channelrhodopsin-2 variant results in sustained muscle contraction and mechanical stress. Using OptIMMuS, combined with proximity labeling and mass spectrometry, we identify regulators that cooperate with the myosin-directed chaperone UNC-45 in muscle proteostasis. One of these is the TRIM E3 ligase NHL-1, which interacts with UNC-45 and muscle myosin in genetic epistasis and co-immunoprecipitation experiments. We provide evidence that the ubiquitylation activity of NHL-1 regulates myosin levels and functionality under mechanical stress. In the future, OptIMMuS will help to identify muscle-specific proteostasis regulators of therapeutic relevance.
Collapse
Affiliation(s)
- Carl Elias Kutzner
- Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Karen Carolyn Bauer
- Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jan-Wilm Lackmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Richard James Acton
- Human Developmental Biology Initiative (HDBI) at Babraham Institute, Cambridge, United Kingdom
| | - Anwesha Sarkar
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| |
Collapse
|
3
|
Tan CH, Wang TY, Park H, Lomenick B, Chou TF, Sternberg PW. Single-tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles. Proc Natl Acad Sci U S A 2024; 121:e2322588121. [PMID: 38861598 PMCID: PMC11194598 DOI: 10.1073/pnas.2322588121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of biomolecules; lysosome-related organelles known as gut granules are important for many of these functions. Aspects of intestine biology are not well understood, including the export of the nutrients it imports and the molecules it synthesizes, as well as the complete functions and protein content of the gut granules. Here, we report a mass spectrometry (MS)-based proteomic analysis of the intestine of the Caenorhabditis elegans and of its gut granules. Overall, we identified approximately 5,000 proteins each in the intestine and the gonad and showed that most of these proteins can be detected in samples extracted from a single worm, suggesting the feasibility of individual-level genetic analysis using proteomes. Comparing proteomes and published transcriptomes of the intestine and the gonad, we identified proteins that appear to be synthesized in the intestine and then transferred to the gonad. To identify gut granule proteins, we compared the proteome of individual intestines deficient in gut granules to the wild type. The identified gut granule proteome includes proteins known to be exclusively localized to the granules and additional putative gut granule proteins. We selected two of these putative gut granule proteins for validation via immunohistochemistry, and our successful confirmation of both suggests that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single-tissue MS-based proteomic analysis in small organisms and in its future utility.
Collapse
Affiliation(s)
- Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Ting-Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| |
Collapse
|
4
|
Huang S, Ran Q, Li XM, Bao X, Zheng C, Li XD. MACSPI enables tissue-selective proteomic and interactomic analyses in multicellular organisms. Proc Natl Acad Sci U S A 2024; 121:e2319060121. [PMID: 38753516 PMCID: PMC11126916 DOI: 10.1073/pnas.2319060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Multicellular organisms are composed of many tissue types that have distinct morphologies and functions, which are largely driven by specialized proteomes and interactomes. To define the proteome and interactome of a specific type of tissue in an intact animal, we developed a localized proteomics approach called Methionine Analog-based Cell-Specific Proteomics and Interactomics (MACSPI). This method uses the tissue-specific expression of an engineered methionyl-tRNA synthetase to label proteins with a bifunctional amino acid 2-amino-5-diazirinylnonynoic acid in selected cells. We applied MACSPI in Caenorhabditis elegans, a model multicellular organism, to selectively label, capture, and profile the proteomes of the body wall muscle and the nervous system, which led to the identification of tissue-specific proteins. Using the photo-cross-linker, we successfully profiled HSP90 interactors in muscles and neurons and identified tissue-specific interactors and stress-related interactors. Our study demonstrates that MACSPI can be used to profile tissue-specific proteomes and interactomes in intact multicellular organisms.
Collapse
Affiliation(s)
- Siyue Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Qiao Ran
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiucong Bao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chaogu Zheng
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
5
|
Wang Y, Qin W. Revealing protein trafficking by proximity labeling-based proteomics. Bioorg Chem 2024; 143:107041. [PMID: 38134520 DOI: 10.1016/j.bioorg.2023.107041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Protein trafficking is a fundamental process with profound implications for both intracellular and intercellular functions. Proximity labeling (PL) technology has emerged as a powerful tool for capturing precise snapshots of subcellular proteomes by directing promiscuous enzymes to specific cellular locations. These enzymes generate reactive species that tag endogenous proteins, enabling their identification through mass spectrometry-based proteomics. In this comprehensive review, we delve into recent advancements in PL-based methodologies, placing particular emphasis on the label-and-fractionation approach and TransitID, for mapping proteome trafficking. These methodologies not only facilitate the exploration of dynamic intracellular protein trafficking between organelles but also illuminate the intricate web of intercellular and inter-organ protein communications.
Collapse
Affiliation(s)
- Yankun Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Qin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China; The State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
| |
Collapse
|
6
|
Shrestha HK, Sun H, Wang J, Peng J. Profiling Mouse Brain Single-Cell-Type Proteomes Via Adeno-Associated Virus-Mediated Proximity Labeling and Mass Spectrometry. Methods Mol Biol 2024; 2817:115-132. [PMID: 38907151 DOI: 10.1007/978-1-0716-3934-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Single-cell-type proteomics is an emerging field of research that combines cell-type specificity with the comprehensive proteome coverage offered by bulk proteomics. However, the extraction of single-cell-type proteomes remains a challenge, particularly for hard-to-isolate cells like neurons. In this chapter, we present an innovative technique for profiling single-cell-type proteomes using adeno-associated virus (AAV)-mediated proximity labeling (PL) and tandem-mass-tag (TMT) mass spectrometry. This technique eliminates the need for cell isolation and offers a streamlined workflow, including AAV delivery to express TurboID (an engineered biotin ligase) controlled by cell-type-specific promoters, biotinylated protein purification, on-bead digestion, TMT labeling, and liquid chromatography-mass spectrometry (LC-MS). We examined this method by analyzing distinct brain cell types in mice. Initially, recombinant AAVs were used to concurrently express TurboID and mCherry proteins driven by neuron- or astrocyte-specific promoters, which was validated through co-immunostaining with cellular markers. With biotin purification and TMT analysis, we successfully identified around 10,000 unique proteins from a few micrograms of protein samples with high reproducibility. Our statistical analyses revealed that these proteomes encompass cell-type-specific cellular pathways. By utilizing this technique, researchers can explore the proteomic landscape of specific cell types, paving the way for new insights into cellular processes, deciphering disease mechanisms, and identifying therapeutic targets in neuroscience and beyond.
Collapse
Affiliation(s)
- Him K Shrestha
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huan Sun
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ju Wang
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
7
|
Mishra PK, Park I, Sharma N, Yoo CM, Lee HY, Rhee HW. Enzymatic Recording of Local Hydrogen Peroxide Generation Using Genetically Encodable Enzyme. Anal Chem 2022; 94:14869-14877. [PMID: 36265183 DOI: 10.1021/acs.analchem.2c01966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive oxygen species (ROS) are endogenously generated in live cells and essential for cell signaling. However, excess ROS generation can cause oxidative damage to biomolecules, which are implicated in various human diseases, including aging. Here, we developed an in vivo hydrogen peroxide monitoring method using a genetically encodable peroxidase (APEX2)-based system. We confirmed that APEX2 is activated by endogenous H2O2 and generates phenoxyl radicals to produce biotinylated signals (i.e., biotin-phenol) and fluorescent signals (i.e., AmplexRed), which can be detected using a fluorescence microscope. We observed that all subcellular targeted APEX2s were activated by local H2O2 generation by menadione treatment. Among them, the endoplasmic reticulum lumen and lysosome-targeted APEX2 showed the highest response upon addition of menadione which implies that local H2O2 levels in those spaces are highly increased by menadione treatment. Using APEX2, we also found that a minimum amount of menadione (>10 μM) is required to generate detectable levels of H2O2 in all subcellular compartments. We also checked the local H2O2-quenching effect of N-acetylcysteine using our system. As APEX2 can be genetically expressed in diverse live organisms (e.g., cancer cell lines, mice, fly, worm, and yeast), our method can be effectively used to detect local generation of endogenously produced H2O2 in diverse live models.
Collapse
Affiliation(s)
- Pratyush Kumar Mishra
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44191, Korea
| | - Issac Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Nirmali Sharma
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44191, Korea
| | - Chang-Mo Yoo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hee Yong Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826 Korea
| |
Collapse
|
8
|
Dumrongprechachan V, Salisbury RB, Butler L, MacDonald ML, Kozorovitskiy Y. Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment. eLife 2022; 11:e78847. [PMID: 36239373 PMCID: PMC9629834 DOI: 10.7554/elife.78847] [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: 03/22/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type-specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.
Collapse
Affiliation(s)
- Vasin Dumrongprechachan
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
| | - Ryan B Salisbury
- Department of Psychiatry, University of PittsburghPittsburghUnited States
| | - Lindsey Butler
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | | | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
| |
Collapse
|
9
|
Higgins DP, Weisman CM, Lui DS, D'Agostino FA, Walker AK. Defining characteristics and conservation of poorly annotated genes in Caenorhabditis elegans using WormCat 2.0. Genetics 2022; 221:6588682. [PMID: 35587742 PMCID: PMC9339291 DOI: 10.1093/genetics/iyac085] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/04/2022] [Indexed: 12/03/2022] Open
Abstract
Omics tools provide broad datasets for biological discovery. However, the computational tools for identifying important genes or pathways in RNA-seq, proteomics, or GWAS (Genome-Wide Association Study) data depend on Gene Ontogeny annotations and are biased toward well-described pathways. This limits their utility as poorly annotated genes, which could have novel functions, are often passed over. Recently, we developed an annotation and category enrichment tool for Caenorhabditis elegans genomic data, WormCat, which provides an intuitive visualization output. Unlike Gene Ontogeny-based enrichment tools, which exclude genes with no annotation information, WormCat 2.0 retains these genes as a special UNASSIGNED category. Here, we show that the UNASSIGNED gene category enrichment exhibits tissue-specific expression patterns and can include genes with biological functions identified in published datasets. Poorly annotated genes are often considered to be potentially species-specific and thus, of reduced interest to the biomedical community. Instead, we find that around 3% of the UNASSIGNED genes have human orthologs, including some linked to human diseases. These human orthologs themselves have little annotation information. A recently developed method that incorporates lineage relationships (abSENSE) indicates that the failure of BLAST to detect homology explains the apparent lineage specificity for many UNASSIGNED genes. This suggests that a larger subset could be related to human genes. WormCat provides an annotation strategy that allows the association of UNASSIGNED genes with specific phenotypes and known pathways. Building these associations in C. elegans, with its robust genetic tools, provides a path to further functional study and insight into these understudied genes.
Collapse
Affiliation(s)
- Daniel P Higgins
- Program in Molecular Medicine, UMASS Chan Medical School, Worcester MA 01605, USA
| | - Caroline M Weisman
- Lewis-Sigler Institute for Quantitative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Dominique S Lui
- Program in Molecular Medicine, UMASS Chan Medical School, Worcester MA 01605, USA
| | - Frank A D'Agostino
- Department of Applied Mathematics, Harvard University, Cambridge MA 02138, USA
| | - Amy K Walker
- Program in Molecular Medicine, UMASS Chan Medical School, Worcester MA 01605, USA
| |
Collapse
|
10
|
Abstract
![]()
Proximity
labeling can be defined as an enzymatic “in-cell”
chemical reaction that catalyzes the proximity-dependent modification
of biomolecules in live cells. Since the modified proteins can be
isolated and identified via mass spectrometry, this method has been
successfully utilized for the characterization of local proteomes
such as the sub-mitochondrial proteome and the proteome at membrane
contact sites, or spatiotemporal interactome information in live cells,
which are not “accessible” via conventional methods.
Currently, proximity labeling techniques can be applied not only for
local proteome mapping but also for profiling local RNA and DNA, in
addition to showing great potential for elucidating spatial cell–cell
interaction networks in live animal models. We believe that proximity
labeling has emerged as an essential tool in “spatiomics,”
that is, for the extraction of spatially distributed biological information
in a cell or organism. Proximity labeling is a multidisciplinary
chemical technique. For
a decade, we and other groups have engineered it for multiple applications
based on the modulation of enzyme chemistry, chemical probe design,
and mass analysis techniques that enable superior mapping results.
The technique has been adopted in biology and chemistry. This “in-cell”
reaction has been widely adopted by biologists who modified it into
an in vivo reaction in animal models. In our laboratory, we conducted
in vivo proximity labeling reactions in mouse models and could successfully
obtain the liver-specific secretome and muscle-specific mitochondrial
matrix proteome. We expect that proximity reaction can further contribute
to revealing tissue-specific localized molecular information in live
animal models. Simultaneously, chemists have also adopted the
concept and employed
chemical “photocatalysts” as artificial enzymes to develop
new proximity labeling reactions. Under light activation, photocatalysts
can convert the precursor molecules to the reactive species via electron
transfer or energy transfer and the reactive molecules can react with
proximal biomolecules within a definite lifetime in an aqueous solution.
To identify the modified biomolecules by proximity labeling, the modified
biomolecules should be enriched after lysis and sequenced using sequencing
tools. In this analysis step, the direct detection of modified residue(s)
on the modified proteins or nucleic acids can be the proof of their
labeling event by proximal enzymes or catalysts in the cell. In this
Account, we introduce the basic concept of proximity labeling and
the multidirectional advances in the development of this method. We
believe that this Account may facilitate further utilization and modification
of the method in both biological and chemical research communities,
thereby revealing unknown spatially distributed molecular or cellular
information or spatiome.
Collapse
Affiliation(s)
- Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
11
|
Buksh BF, Knutson SD, Oakley JV, Bissonnette NB, Oblinsky DG, Schwoerer MP, Seath CP, Geri JB, Rodriguez-Rivera FP, Parker DL, Scholes GD, Ploss A, MacMillan DWC. μMap-Red: Proximity Labeling by Red Light Photocatalysis. J Am Chem Soc 2022; 144:6154-6162. [PMID: 35363468 PMCID: PMC9843638 DOI: 10.1021/jacs.2c01384] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Modern proximity labeling techniques have enabled significant advances in understanding biomolecular interactions. However, current tools primarily utilize activation modes that are incompatible with complex biological environments, limiting our ability to interrogate cell- and tissue-level microenvironments in animal models. Here, we report μMap-Red, a proximity labeling platform that uses a red-light-excited SnIV chlorin e6 catalyst to activate a phenyl azide biotin probe. We validate μMap-Red by demonstrating photonically controlled protein labeling in vitro through several layers of tissue, and we then apply our platform in cellulo to label EGFR microenvironments and validate performance with STED microscopy and quantitative proteomics. Finally, to demonstrate labeling in a complex biological sample, we deploy μMap-Red in whole mouse blood to profile erythrocyte cell-surface proteins. This work represents a significant methodological advance toward light-based proximity labeling in complex tissue environments and animal models.
Collapse
Affiliation(s)
- Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - James V Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Noah B Bissonnette
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Michael P Schwoerer
- Department of Molecular Biology, Princeton University, Princeton, New Jersey08544, United States
| | - Ciaran P Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Jacob B Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | | | - Dann L Parker
- Discovery Chemistry, Merck & Co., Kenilworth, New Jersey07033, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey08544, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| |
Collapse
|
12
|
Sun X, Sun H, Han X, Chen PC, Jiao Y, Wu Z, Zhang X, Wang Z, Niu M, Yu K, Liu D, Dey KK, Mancieri A, Fu Y, Cho JH, Li Y, Poudel S, Branon TC, Ting AY, Peng J. Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling. Anal Chem 2022; 94:5325-5334. [PMID: 35315655 DOI: 10.1021/acs.analchem.1c05212] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.
Collapse
Affiliation(s)
- Xiaojun Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xian Han
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Ping-Chung Chen
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yun Jiao
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xue Zhang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Mingming Niu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Danting Liu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ariana Mancieri
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tess C Branon
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Alice Y Ting
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Junmin Peng
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| |
Collapse
|
13
|
Dionne U, Gingras AC. Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome. Front Mol Biosci 2022; 9:852911. [PMID: 35309513 PMCID: PMC8930824 DOI: 10.3389/fmolb.2022.852911] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.
Collapse
Affiliation(s)
- Ugo Dionne
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Anne-Claude Gingras,
| |
Collapse
|
14
|
Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| |
Collapse
|
15
|
Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods Cell Biol 2022; 169:237-266. [PMID: 35623704 PMCID: PMC10782847 DOI: 10.1016/bs.mcb.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study of protein complexes and protein-protein interactions is of great importance due to their fundamental roles in cellular function. Proximity labeling, often coupled with mass spectrometry, has become a powerful and versatile tool for studying protein-protein interactions by enriching and identifying proteins in the vicinity of a specified protein-of-interest. Here, we describe and compare traditional approaches to investigate protein-protein interactions to current day state-of-the-art proximity labeling methods. We focus on the wide array of proximity labeling strategies and underscore studies using diverse model systems to address numerous biological questions. In addition, we highlight current advances in mass spectrometry-based technology that exhibit promise in improving the depth and breadth of the data acquired in proximity labeling experiments. In all, we show the diversity of proximity labeling strategies and emphasize the broad range of applications and biological inquiries that can be addressed using this technology.
Collapse
Affiliation(s)
- Conrad T Pfeiffer
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC, United States.
| |
Collapse
|
16
|
Tamim El Jarkass H, Mok C, Schertzberg MR, Fraser AG, Troemel ER, Reinke AW. An intestinally secreted host factor promotes microsporidia invasion of C. elegans. eLife 2022; 11:e72458. [PMID: 34994689 PMCID: PMC8806185 DOI: 10.7554/elife.72458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/06/2022] [Indexed: 12/11/2022] Open
Abstract
Microsporidia are ubiquitous obligate intracellular pathogens of animals. These parasites often infect hosts through an oral route, but little is known about the function of host intestinal proteins that facilitate microsporidia invasion. To identify such factors necessary for infection by Nematocida parisii, a natural microsporidian pathogen of Caenorhabditis elegans, we performed a forward genetic screen to identify mutant animals that have a Fitness Advantage with Nematocida (Fawn). We isolated four fawn mutants that are resistant to Nematocida infection and contain mutations in T14E8.4, which we renamed aaim-1 (Antibacterial and Aids invasion by Microsporidia). Expression of AAIM-1 in the intestine of aaim-1 animals restores N. parisii infectivity and this rescue of infectivity is dependent upon AAIM-1 secretion. N. parisii spores in aaim-1 animals are improperly oriented in the intestinal lumen, leading to reduced levels of parasite invasion. Conversely, aaim-1 mutants display both increased colonization and susceptibility to the bacterial pathogen Pseudomonas aeruginosa and overexpression ofaaim-1 reduces P. aeruginosa colonization. Competitive fitness assays show that aaim-1 mutants are favored in the presence of N. parisii but disadvantaged on P. aeruginosa compared to wild-type animals. Together, this work demonstrates how microsporidia exploits a secreted protein to promote host invasion. Our results also suggest evolutionary trade-offs may exist to optimizing host defense against multiple classes of pathogens.
Collapse
Affiliation(s)
| | - Calvin Mok
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | | | - Andrew G Fraser
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Emily R Troemel
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Aaron W Reinke
- Department of Molecular Genetics, University of TorontoTorontoCanada
| |
Collapse
|
17
|
Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. J Biol Chem 2021; 297:101094. [PMID: 34416233 PMCID: PMC8446793 DOI: 10.1016/j.jbc.2021.101094] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023] Open
Abstract
Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.
Collapse
Affiliation(s)
- Murat Artan
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Stephen Barratt
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Sean M Flynn
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Farida Begum
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mark Skehel
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Armel Nicolas
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Mario de Bono
- Institute of Science and Technology, Klosterneuburg, Austria.
| |
Collapse
|
18
|
Sanchez AD, Branon TC, Cote LE, Papagiannakis A, Liang X, Pickett MA, Shen K, Jacobs-Wagner C, Ting AY, Feldman JL. Proximity labeling reveals non-centrosomal microtubule-organizing center components required for microtubule growth and localization. Curr Biol 2021; 31:3586-3600.e11. [PMID: 34242576 PMCID: PMC8478408 DOI: 10.1016/j.cub.2021.06.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/13/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
Microtubules are polarized intracellular polymers that play key roles in the cell, including in transport, polarity, and cell division. Across eukaryotic cell types, microtubules adopt diverse intracellular organization to accommodate these distinct functions coordinated by specific cellular sites called microtubule-organizing centers (MTOCs). Over 50 years of research on MTOC biology has focused mainly on the centrosome; however, most differentiated cells employ non-centrosomal MTOCs (ncMTOCs) to organize their microtubules into diverse arrays, which are critical to cell function. To identify essential ncMTOC components, we developed the biotin ligase-based, proximity-labeling approach TurboID for use in C. elegans. We identified proteins proximal to the microtubule minus end protein PTRN-1/Patronin at the apical ncMTOC of intestinal epithelial cells, focusing on two conserved proteins: spectraplakin protein VAB-10B/MACF1 and WDR-62, a protein we identify as homologous to vertebrate primary microcephaly disease protein WDR62. VAB-10B and WDR-62 do not associate with the centrosome and instead specifically regulate non-centrosomal microtubules and the apical targeting of microtubule minus-end proteins. Depletion of VAB-10B resulted in microtubule mislocalization and delayed localization of a microtubule nucleation complex ɣ-tubulin ring complex (γ-TuRC), while loss of WDR-62 decreased the number of dynamic microtubules and abolished γ-TuRC localization. This regulation occurs downstream of cell polarity and in conjunction with actin. As this is the first report for non-centrosomal roles of WDR62 family proteins, we expand the basic cell biological roles of this important disease protein. Our studies identify essential ncMTOC components and suggest a division of labor where microtubule growth and localization are distinctly regulated.
Collapse
Affiliation(s)
- Ariana D Sanchez
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Tess C Branon
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Departments of Genetics and Chemistry, Stanford University, Stanford, CA, USA
| | - Lauren E Cote
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | | | - Xing Liang
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Melissa A Pickett
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Kang Shen
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Biology and ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Alice Y Ting
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Departments of Genetics and Chemistry, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jessica L Feldman
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA.
| |
Collapse
|
19
|
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis. Nat Methods 2021; 18:893-902. [PMID: 34312566 DOI: 10.1038/s41592-021-01216-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live imaging, we present a protein expression atlas of transcription factors (TFs) mapped onto developmental cell lineages during Caenorhabditis elegans embryogenesis, at single-cell resolution. This atlas reveals a spatiotemporal combinatorial code of TF expression, and a cascade of lineage-specific, tissue-specific and time-specific TFs that specify developmental states. The atlas uncovers regulators of embryogenesis, including an unexpected role of a skin specifier in neurogenesis and the critical function of an uncharacterized TF in convergent muscle differentiation. At the systems level, the atlas provides an opportunity to model cell state-fate relationships, revealing a lineage-dependent state diversity within functionally related cells and a winding trajectory of developmental state progression. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels.
Collapse
|
20
|
Li T, Xu C, Xu J, Luo J, Yu B, Meng X, Li C, Pan G, Zhou Z. Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB). Int J Mol Sci 2021; 22:ijms22095051. [PMID: 34068790 PMCID: PMC8126250 DOI: 10.3390/ijms22095051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Silkworm Bombyx mori is an economically important insect and a lepidopteran model. Organelle proteome is vital to understanding gene functions; however, it remains to be identified in silkworm. Here, using the engineered ascorbate peroxidase APEX, we constructed transgenic B. mori embryo cells (BmE) expressing APEX-NLS, COX4-APEX, APEX-Rev, and APEX-KDEL in nucleus, mitochondrial matrix (MM), cytosol, and endoplasmic reticulum (ER), and isolated the biotin-labeled proteins using streptavidin-affinity purification, respectively. The isolated proteins were determined using LC-MS/MS and annotated by searching B. mori genomes downloaded from GenBank, SilkBase, SilkDB 2.0, and SilkDB 3.0, resulting in 842, 495, 311, and 445 organelle proteins identified, respectively. We mapped the 296 MM proteins annotated in the GenBank data to mitochondrial protein databases of the fly, human, and mouse, and found that 140 (47%) proteins are homologous to 80 fly proteins, and 65 (22%) proteins match to 31 and 29 human and mouse proteins, respectively. Protein orthology was predicted in multiple insects using OrthoMCL, producing 460 families containing 839 proteins we identified. Out of 460 families, 363 were highly conserved and found in all insects, leaving only three proteins without orthology in other insects, indicating that the identified proteins are highly conserved and probably play important roles in insects. A gene ontology enrichment analysis by clusterProfiler revealed that the nucleus proteins significantly enriched in cellular component terms of nucleus and nucleolus, the MM proteins markedly enriched in molecular function terms of nucleotide binding, and the cytosol proteins mainly enriched in biological process terms of small molecule metabolism. To facilitate the usage and analysis of our data, we developed an open-access database, Silkworm Organelle Proteome Database (SilkOrganPDB), which provides multiple modules for searching, browsing, downloading, and analyzing these proteins, including BLAST, HMMER, Organelle Proteins, Protein Locations, Sequences, Gene Ontology, Homologs, and Phylogeny. In summary, our work revealed the protein composition of silkworm BmE organelles and provided a database resource helpful for understanding the functions and evolution of these proteins.
Collapse
Affiliation(s)
- Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- Correspondence: (T.L.); (Z.Z.)
| | - Chen Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jinzhi Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jian Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Bin Yu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Xianzhi Meng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Chunfeng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
- Correspondence: (T.L.); (Z.Z.)
| |
Collapse
|
21
|
mSphere of Influence: Where the Pathogen Proteins Are. mSphere 2021; 6:6/3/e00365-21. [PMID: 33952666 PMCID: PMC8103990 DOI: 10.1128/msphere.00365-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aaron Reinke studies microsporidian evolution and how microsporidia interact with their hosts. In this mSphere of Influence article, he reflects on how the papers “A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells” (K. Aaron Reinke studies microsporidian evolution and how microsporidia interact with their hosts. In this mSphere of Influence article, he reflects on how the papers “A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells” (K. J. Roux, D. I. Kim, M. Raida, and B. Burke, J Cell Biol 196:801–810, 2012, https://doi.org/10.1083/jcb.201112098) and “Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging” (H.-W. Rhee, P. Zou, N. D. Udeshi, J. D. Martell, et al., Science 339:1328–1331, 2013, https://doi.org/10.1126/science.1230593) impacted his thinking on how to determine where proteins from intracellular pathogens are located within host cells.
Collapse
|
22
|
Haskell D, Zinovyeva A. KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development. G3 (BETHESDA, MD.) 2021; 11:jkab013. [PMID: 33585875 PMCID: PMC8022929 DOI: 10.1093/g3journal/jkab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate their activities and the precise mechanisms of this coordination are not well understood. RBPs often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, whereas other KH domain genes showed genetic interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.
Collapse
Affiliation(s)
- Dustin Haskell
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
23
|
Van Damme S, De Fruyt N, Watteyne J, Kenis S, Peymen K, Schoofs L, Beets I. Neuromodulatory pathways in learning and memory: Lessons from invertebrates. J Neuroendocrinol 2021; 33:e12911. [PMID: 33350018 DOI: 10.1111/jne.12911] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022]
Abstract
In an ever-changing environment, animals have to continuously adapt their behaviour. The ability to learn from experience is crucial for animals to increase their chances of survival. It is therefore not surprising that learning and memory evolved early in evolution and are mediated by conserved molecular mechanisms. A broad range of neuromodulators, in particular monoamines and neuropeptides, have been found to influence learning and memory, although our knowledge on their modulatory functions in learning circuits remains fragmentary. Many neuromodulatory systems are evolutionarily ancient and well-conserved between vertebrates and invertebrates. Here, we highlight general principles and mechanistic insights concerning the actions of monoamines and neuropeptides in learning circuits that have emerged from invertebrate studies. Diverse neuromodulators have been shown to influence learning and memory in invertebrates, which can have divergent or convergent actions at different spatiotemporal scales. In addition, neuromodulators can regulate learning dependent on internal and external states, such as food and social context. The strong conservation of neuromodulatory systems, the extensive toolkit and the compact learning circuits in invertebrate models make these powerful systems to further deepen our understanding of neuromodulatory pathways involved in learning and memory.
Collapse
Affiliation(s)
- Sara Van Damme
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Nathan De Fruyt
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jan Watteyne
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Signe Kenis
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Katleen Peymen
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Isabel Beets
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| |
Collapse
|
24
|
Li Y, Liu K, Zhou Y, Yang J, Zou P. Protocol for Proximity-Dependent Proteomic Profiling in Yeast Cells by APEX and Alk-Ph Probe. STAR Protoc 2020; 1:100137. [PMID: 33377031 PMCID: PMC7757286 DOI: 10.1016/j.xpro.2020.100137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Alk-Ph is a clickable APEX2 substrate developed for spatially restricted protein/RNA labeling in intact yeast cells. Alk-Ph is more water soluble and cell wall permeable than biotin-phenol substrate, allowing more efficient profiling of the subcellular proteome in microorganisms. We describe the protocol for Alk-Ph probe synthesis, APEX2 expression, and protein/RNA labeling in yeast and the workflow for quantitative proteomic experiments and data analysis. Using the yeast mitochondria as an example, we provide guidelines to achieve high-resolution mapping of subcellular yeast proteome and transcriptome. For complete details on the use and execution of this protocol, please refer to Li et al. (2020). Synthesis of clickable APEX probe Alk-Ph Proximity-dependent proteomic profiling in yeast Spatially restricted RNA labeling in yeast
Collapse
Affiliation(s)
- Yi Li
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Keke Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ying Zhou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Jing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.,Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| |
Collapse
|
25
|
Lee HC, Carroll A, Crossett B, Connolly A, Batarseh A, Djordjevic MA. Improving the Identification and Coverage of Plant Transmembrane Proteins in Medicago Using Bottom-Up Proteomics. FRONTIERS IN PLANT SCIENCE 2020; 11:595726. [PMID: 33391307 PMCID: PMC7775423 DOI: 10.3389/fpls.2020.595726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Plant transmembrane proteins (TMPs) are essential for normal cellular homeostasis, nutrient exchange, and responses to environmental cues. Commonly used bottom-up proteomic approaches fail to identify a broad coverage of peptide fragments derived from TMPs. Here, we used mass spectrometry (MS) to compare the effectiveness of two solubilization and protein cleavage methods to identify shoot-derived TMPs from the legume Medicago. We compared a urea solubilization, trypsin Lys-C (UR-TLC) cleavage method to a formic acid solubilization, cyanogen bromide and trypsin Lys-C (FA-CTLC) cleavage method. We assessed the effectiveness of these methods by (i) comparing total protein identifications, (ii) determining how many TMPs were identified, and (iii) defining how many peptides incorporate all, or part, of transmembrane domains (TMD) sequences. The results show that the FA-CTLC method identified nine-fold more TMDs, and enriched more hydrophobic TMPs than the UR-TLC method. FA-CTLC identified more TMPs, particularly transporters, whereas UR-TLC preferentially identified TMPs with one TMD, particularly signaling proteins. The results suggest that combining plant membrane purification techniques with both the FA-CTLC and UR-TLC methods will achieve a more complete identification and coverage of TMPs.
Collapse
Affiliation(s)
- Han Chung Lee
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Adam Carroll
- ANU Joint Mass Spectrometry Facility, Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, Australia
| | - Angela Connolly
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, Australia
| | - Amani Batarseh
- BCAL Diagnostics, National Innovation Centre, Eveleigh, NSW, Australia
| | - Michael A. Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
26
|
Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
Collapse
Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
| |
Collapse
|
27
|
Busby KN, Fulzele A, Zhang D, Bennett EJ, Devaraj NK. Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-Protein Interactions. ACS Chem Biol 2020; 15:2247-2258. [PMID: 32706237 DOI: 10.1021/acschembio.0c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Throughout their cellular lifetime, RNA transcripts are bound to proteins, playing crucial roles in RNA metabolism, trafficking, and function. Despite the importance of these interactions, identifying the proteins that interact with an RNA of interest in mammalian cells represents a major challenge in RNA biology. Leveraging the ability to site-specifically and covalently label an RNA of interest using E. coli tRNA guanine transglycosylase and an unnatural nucleobase substrate, we establish the identification of RNA-protein interactions and the selective enrichment of cellular RNA in mammalian systems. We demonstrate the utility of this approach through the identification of known binding partners of 7SK snRNA via mass spectrometry. Through a minimal 4-nucleotide mutation of the long noncoding RNA HOTAIR, enzymatic biotinylation enables identification of putative HOTAIR binding partners in MCF7 breast cancer cells that suggest new potential pathways for oncogenic function. Furthermore, using RNA sequencing and qPCR, we establish that an engineered enzyme variant achieves high levels of labeling selectivity against the human transcriptome allowing for 145-fold enrichment of cellular RNA directly from mammalian cell lysates. The flexibility and breadth of this approach suggests that this system could be routinely applied to the functional characterization of RNA, greatly expanding the toolbox available for studying mammalian RNA biology.
Collapse
Affiliation(s)
- Kayla N Busby
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Amitkumar Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
28
|
Zhou Y, Zou P. The evolving capabilities of enzyme-mediated proximity labeling. Curr Opin Chem Biol 2020; 60:30-38. [PMID: 32801087 DOI: 10.1016/j.cbpa.2020.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
Abstract
The subcellular organization of proteins and RNA molecules is crucial for their proper functions. Over the past decade, both ligase-mediated and peroxidase-mediated proximity labeling (PL) techniques have been developed to map biomolecules at near-nanometer spatial resolution and subminute temporal resolution. These methods are shedding light on the spatial arrangement of proteome and transcriptome in their native context. Here, we review the recent evolution and applications of PL techniques, compare and contrast the two classes of methods, and highlight emerging trends and future opportunities.
Collapse
Affiliation(s)
- Ying Zhou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
| |
Collapse
|
29
|
Nguyen TMT, Kim J, Doan TT, Lee MW, Lee M. APEX Proximity Labeling as a Versatile Tool for Biological Research. Biochemistry 2019; 59:260-269. [PMID: 31718172 DOI: 10.1021/acs.biochem.9b00791] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most proteins are specifically localized in membrane-encapsulated organelles or non-membrane-bound compartments. The subcellular localization of proteins facilitates their functions and integration into functional networks; therefore, protein localization is tightly regulated in diverse biological contexts. However, protein localization has been mainly analyzed through immunohistochemistry or the fractionation of subcellular compartments, each of which has major drawbacks. Immunohistochemistry can examine only a handful of proteins at a time, and fractionation inevitably relies on the lysis of cells, which disrupts native cellular conditions. Recently, an engineered ascorbate peroxidase (APEX)-based proximity labeling technique combined with mass spectrometry was developed, which allows for temporally and spatially resolved proteomic mapping. In the presence of H2O2, engineered APEX oxidizes biotin-phenols into biotin-phenoxyl radicals, and these short-lived radicals biotinylate electron-rich amino acids within a radius of several nanometers. Biotinylated proteins are subsequently enriched by streptavidin and identified by mass spectrometry. This permits the sensitive and efficient labeling of proximal proteins around locally expressed APEX. Through the targeted expression of APEX in the subcellular region of interest, proteomic profiling of submitochondrial spaces, the outer mitochondrial membrane, the endoplasmic reticulum (ER)-mitochondrial contact, and the ER membrane has been performed. Furthermore, this method has been modified to define interaction networks in the vicinity of target proteins and has also been applied to analyze the spatial transcriptome. In this Perspective, we provide an outline of this newly developed technique and discuss its potential applications to address diverse biological questions.
Collapse
Affiliation(s)
- Thanh My Thi Nguyen
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Thi Tram Doan
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| |
Collapse
|
30
|
Qin W, Xie Z, Wang J, Ou G, Wang C, Chen X. Chemoproteomic Profiling of O-GlcNAcylation in Caenorhabditis elegans. Biochemistry 2019; 59:3129-3134. [DOI: 10.1021/acs.biochem.9b00622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Zhongyun Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | | | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | | | | |
Collapse
|
31
|
Li L, Veksler-Lublinsky I, Zinovyeva A. HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008067. [PMID: 31584932 PMCID: PMC6795461 DOI: 10.1371/journal.pgen.1008067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/16/2019] [Accepted: 09/11/2019] [Indexed: 01/14/2023] Open
Abstract
microRNAs (miRNAs) are potent regulators of gene expression that function in diverse developmental and physiological processes. Argonaute proteins loaded with miRNAs form the miRNA Induced Silencing Complexes (miRISCs) that repress gene expression at the post-transcriptional level. miRISCs target genes through partial sequence complementarity between the miRNA and the target mRNA’s 3’ UTR. In addition to being targeted by miRNAs, these mRNAs are also extensively regulated by RNA-binding proteins (RBPs) through RNA processing, transport, stability, and translation regulation. While the degree to which RBPs and miRISCs interact to regulate gene expression is likely extensive, we have only begun to unravel the mechanisms of this functional cooperation. An RNAi-based screen of putative ALG-1 Argonaute interactors has identified a role for a conserved RNA binding protein, HRPK-1, in modulating miRNA activity during C. elegans development. Here, we report the physical and genetic interaction between HRPK-1 and ALG-1/miRNAs. Specifically, we report the genetic and molecular characterizations of hrpk-1 and its role in C. elegans development and miRNA-mediated target repression. We show that loss of hrpk-1 causes numerous developmental defects and enhances the mutant phenotypes associated with reduction of miRNA activity, including those of lsy-6, mir-35-family, and let-7-family miRNAs. In addition to hrpk-1 genetic interaction with these miRNA families, hrpk-1 is required for efficient regulation of lsy-6 target cog-1. We report that hrpk-1 plays a role in processing of some but not all miRNAs and is not required for ALG-1/AIN-1 miRISC assembly. We suggest that HRPK-1 may functionally interact with miRNAs by both affecting miRNA processing and by enhancing miRNA/miRISC gene regulatory activity and present models for its activity. microRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. The core microRNA Induced Silencing Complex (miRISC), composed of Argonaute, mature microRNA, and GW182 protein effector, assembles on the target messenger RNA and inhibits translation or leads to messenger RNA degradation. RNA binding proteins interface with miRNA pathways on multiple levels to coordinate gene expression regulation. Here, we report identification and characterization of HRPK-1, a conserved RNA binding protein, as a physical and functional interactor of miRNAs. We confirm the physical interaction between HRPK-1, an hnRNPK homolog, and Argonaute ALG-1. We report characterizations of hrpk-1 role in development and its functional interactions with multiple miRNA families. We suggest that HRPK-1 promotes miRNA activity on multiple levels in part by contributing to miRNA processing and by coordinating with miRISC at the level of target RNAs. This work contributes to our understanding of how RNA binding proteins and auxiliary miRNA cofactors may interface with miRNA pathways to modulate miRNA gene regulatory activity.
Collapse
Affiliation(s)
- Li Li
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-sheva, Israel
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
| |
Collapse
|
32
|
Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
Collapse
Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
33
|
Mannix KM, Starble RM, Kaufman RS, Cooley L. Proximity labeling reveals novel interactomes in live Drosophila tissue. Development 2019; 146:dev.176644. [PMID: 31208963 DOI: 10.1242/dev.176644] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022]
Abstract
Gametogenesis is dependent on intercellular communication facilitated by stable intercellular bridges connecting developing germ cells. During Drosophila oogenesis, intercellular bridges (referred to as ring canals; RCs) have a dynamic actin cytoskeleton that drives their expansion to a diameter of 10 μm. Although multiple proteins have been identified as components of RCs, we lack a basic understanding of how RC proteins interact together to form and regulate the RC cytoskeleton. Thus, here, we optimized a procedure for proximity-dependent biotinylation in live tissue using the APEX enzyme to interrogate the RC interactome. APEX was fused to four different RC components (RC-APEX baits) and 55 unique high-confidence prey were identified. The RC-APEX baits produced almost entirely distinct interactomes that included both known RC proteins and uncharacterized proteins. A proximity ligation assay was used to validate close-proximity interactions between the RC-APEX baits and their respective prey. Furthermore, an RNA interference screen revealed functional roles for several high-confidence prey genes in RC biology. These findings highlight the utility of enzyme-catalyzed proximity labeling for protein interactome analysis in live tissue and expand our understanding of RC biology.
Collapse
Affiliation(s)
- Katelynn M Mannix
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rebecca M Starble
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ronit S Kaufman
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lynn Cooley
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
34
|
Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell 2019; 178:473-490.e26. [PMID: 31230715 PMCID: PMC6786773 DOI: 10.1016/j.cell.2019.05.027] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 05/14/2019] [Indexed: 01/25/2023]
Abstract
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
Collapse
Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alice Y Ting
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
35
|
Abstract
Lipid droplets (LDs) are ubiquitous lipid storage organelles composed of a neutral lipid core surrounded by a phospholipid monolayer that is decorated with integral and peripheral proteins. Accurate identification of LD proteins using biochemical fractionation methods has been challenging due to the presence of contaminant proteins from co-fractionating organelles. Here, we describe a method to identify high-confidence LD proteomes that employs an engineered ascorbate peroxidase (APEX2) to induce spatially and temporally restricted biotinylation of LD proteins. This proximity labeling method can be broadly applied to define the composition of the LD proteome in any cultured cell line and can be utilized to examine LD proteome dynamics.
Collapse
|
36
|
Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
Collapse
Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
| |
Collapse
|
37
|
Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Proteomes 2018; 6:proteomes6040048. [PMID: 30487426 PMCID: PMC6313906 DOI: 10.3390/proteomes6040048] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022] Open
Abstract
Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons. This reporter marked excitatory synapses as measured by confocal microcopy and was targeted to the edge zone of the synaptic cleft as determined using 3D dSTORM super-resolution imaging. Proximity labeling with a membrane-impermeant biotin-phenol compound restricted labeling to the cell surface, and Label-Free Quantitation (LFQ) mass spectrometry combined with ratiometric HRP tagging of membrane vs. synaptic surface proteins was used to identify the proteomic content of excitatory clefts. Novel cleft candidates were identified, and Receptor-type tyrosine-protein phosphatase zeta was selected and successfully validated. This study supports the robust applicability of peroxidase-mediated proximity labeling for synaptic cleft proteomics and its potential for understanding synapse heterogeneity in health and changes in diseases such as psychiatric disorders and addiction.
Collapse
Affiliation(s)
- Tony Cijsouw
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Austin M Ramsey
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M. Keck Biotechnology Resource Laboratory, Yale University School of Medicine, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Beatrice E Carbone
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Thomas A Blanpied
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| |
Collapse
|
38
|
Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol 2018; 36:880-887. [PMID: 30125270 PMCID: PMC6126969 DOI: 10.1038/nbt.4201] [Citation(s) in RCA: 969] [Impact Index Per Article: 161.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 h of labeling time or utilize chemicals with limited cell permeability or high toxicity. We used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, TurboID and miniTurbo, which catalyze PL with much greater efficiency than BioID or BioID2, and enable 10-min PL in cells with non-toxic and easily deliverable biotin. Furthermore, TurboID extends biotin-based PL to flies and worms.
Collapse
Affiliation(s)
- Tess C. Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
| | - Justin A. Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ariana D. Sanchez
- Department of Biology, Stanford University, Stanford, California, USA
| | | | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| |
Collapse
|
39
|
Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet 2018; 14:e1007559. [PMID: 30096138 PMCID: PMC6105014 DOI: 10.1371/journal.pgen.1007559] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/22/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022] Open
Abstract
The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are critical for understanding molecular mechanisms that control their phenotypes. We used adult cell-specific isolation to identify the transcriptomes of C. elegans' four major tissues (or "tissue-ome"), identifying ubiquitously expressed and tissue-specific "enriched" genes. These data newly reveal the hypodermis' metabolic character, suggest potential worm-human tissue orthologies, and identify tissue-specific changes in the Insulin/IGF-1 signaling pathway. Tissue-specific alternative splicing analysis identified a large set of collagen isoforms. Finally, we developed a machine learning-based prediction tool for 76 sub-tissue cell types, which we used to predict cellular expression differences in IIS/FOXO signaling, stage-specific TGF-β activity, and basal vs. memory-induced CREB transcription. Together, these data provide a rich resource for understanding the biology governing multicellular adult animals.
Collapse
Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Victoria Yao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - April Williams
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alexi M. Runnels
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Coleen T. Murphy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
40
|
Uncovering Discrete Synaptic Proteomes to Understand Neurological Disorders. Proteomes 2018; 6:proteomes6030030. [PMID: 30029459 PMCID: PMC6161107 DOI: 10.3390/proteomes6030030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
The mammalian nervous system is an immensely heterogeneous organ composed of a diverse collection of neuronal types that interconnect in complex patterns. Synapses are highly specialized neuronal cell-cell junctions with common and distinct functional characteristics that are governed by their protein composition or synaptic proteomes. Even a single neuron can possess a wide-range of different synapse types and each synapse contains hundreds or even thousands of proteins. Many neurological disorders and diseases are caused by synaptic dysfunction within discrete neuronal populations. Mass spectrometry (MS)-based proteomic analysis has emerged as a powerful strategy to characterize synaptic proteomes and potentially identify disease driving synaptic alterations. However, most traditional synaptic proteomic analyses have been limited by molecular averaging of proteins from multiple types of neurons and synapses. Recently, several new strategies have emerged to tackle the ‘averaging problem’. In this review, we summarize recent advancements in our ability to characterize neuron-type specific and synapse-type specific proteomes and discuss strengths and limitations of these emerging analysis strategies.
Collapse
|
41
|
Zuzow N, Ghosh A, Leonard M, Liao J, Yang B, Bennett EJ. Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. Mol Biol Cell 2018. [PMID: 29540532 PMCID: PMC5935074 DOI: 10.1091/mbc.e17-12-0714] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Previous genetic and biochemical studies from Saccharomyces cerevisiae have identified a critical ribosome-associated quality control complex (RQC) that facilitates resolution of stalled ribosomal complexes. While components of the mammalian RQC have been examined in vitro, a systematic characterization of RQC protein interactions in mammalian cells has yet to be described. Here we utilize both proximity-labeling proteomic approaches, BioID and APEX, and traditional affinity-based strategies to both identify interacting proteins of mammalian RQC members and putative substrates for the RQC resident E3 ligase, Ltn1. Surprisingly, validation studies revealed that a subset of substrates are ubiquitylated by Ltn1 in a regulatory manner that does not result in subsequent substrate degradation. We demonstrate that Ltn1 catalyzes the regulatory ubiquitylation of ribosomal protein S6 kinase 1 and 2 (RPS6KA1, RPS6KA3). Further, loss of Ltn1 function results in hyperactivation of RSK1/2 signaling without impacting RSK1/2 protein turnover. These results suggest that Ltn1-mediated RSK1/2 ubiquitylation is inhibitory and establishes a new role for Ltn1 in regulating mitogen-activated kinase signaling via regulatory RSK1/2 ubiquitylation. Taken together, our results suggest that mammalian RQC interactions are difficult to observe and may be more transient than the homologous complex in S. cerevisiae and that Ltn1 has RQC-independent functions.
Collapse
Affiliation(s)
- Nathan Zuzow
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Arit Ghosh
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Marilyn Leonard
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Jeffrey Liao
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Bing Yang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| |
Collapse
|
42
|
Han S, Li J, Ting AY. Proximity labeling: spatially resolved proteomic mapping for neurobiology. Curr Opin Neurobiol 2017; 50:17-23. [PMID: 29125959 DOI: 10.1016/j.conb.2017.10.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 01/18/2023]
Abstract
Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.
Collapse
Affiliation(s)
- Shuo Han
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Jiefu Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alice Y Ting
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
43
|
Ramberger E, Dittmar G. Tissue Specific Labeling in Proteomics. Proteomes 2017; 5:proteomes5030017. [PMID: 28718811 PMCID: PMC5620534 DOI: 10.3390/proteomes5030017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
Collapse
Affiliation(s)
- Evelyn Ramberger
- Mass-Spectrometry Core Unit, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
- Berlin School of Integrative Oncology (BSIO), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1272 Strassen, Luxembourg.
| |
Collapse
|
44
|
Reinke AW, Balla KM, Bennett EJ, Troemel ER. Identification of microsporidia host-exposed proteins reveals a repertoire of rapidly evolving proteins. Nat Commun 2017; 8:14023. [PMID: 28067236 PMCID: PMC5423893 DOI: 10.1038/ncomms14023] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/22/2016] [Indexed: 01/19/2023] Open
Abstract
Pathogens use a variety of secreted and surface proteins to interact with and manipulate their hosts, but a systematic approach for identifying such proteins has been lacking. To identify these ‘host-exposed' proteins, we used spatially restricted enzymatic tagging followed by mass spectrometry analysis of Caenorhabditis elegans infected with two species of Nematocida microsporidia. We identified 82 microsporidia proteins inside of intestinal cells, including several pathogen proteins in the nucleus. These microsporidia proteins are enriched in targeting signals, are rapidly evolving and belong to large Nematocida-specific gene families. We also find that large, species-specific families are common throughout microsporidia species. Our data suggest that the use of a large number of rapidly evolving species-specific proteins represents a common strategy for microsporidia to interact with their hosts. The unbiased method described here for identifying potential pathogen effectors represents a powerful approach to study a broad range of pathogens. Unbiased identification of proteins from pathogens that are exposed to a host can provide insight into host–pathogen interaction. Here, the authors use an enzymatic tagging method and mass spectrometry to identify rapidly evolving Nematocida microsporidia proteins when infecting C. elegans.
Collapse
Affiliation(s)
- Aaron W Reinke
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Keir M Balla
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Eric J Bennett
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Emily R Troemel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| |
Collapse
|