1
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Perez JD, Dieck ST, Alvarez-Castelao B, Tushev G, Chan IC, Schuman EM. Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons. eLife 2021; 10:63092. [PMID: 33404500 PMCID: PMC7819707 DOI: 10.7554/elife.63092] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
Although mRNAs are localized in the processes of excitatory neurons, it is still unclear whether interneurons also localize a large population of mRNAs. In addition, the variability in the localized mRNA population within and between cell types is unknown. Here we describe the unbiased transcriptomic characterization of the subcellular compartments of hundreds of single neurons. We separately profiled the dendritic and somatic transcriptomes of individual rat hippocampal neurons and investigated mRNA abundances in the soma and dendrites of single glutamatergic and GABAergic neurons. We found that, like their excitatory counterparts, interneurons contain a rich repertoire of ~4000 mRNAs. We observed more cell type-specific features among somatic transcriptomes than their associated dendritic transcriptomes. Finally, using celltype-specific metabolic labeling of isolated neurites, we demonstrated that the processes of glutamatergic and, notably, GABAergic neurons were capable of local translation, suggesting mRNA localization and local translation are general properties of neurons.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Ivy Cw Chan
- Department of Behavior and Brain Organization, Center of Advanced European Studies and Research, Bonn, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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2
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Navaratna T, Atangcho L, Mahajan M, Subramanian V, Case M, Min A, Tresnak D, Thurber GM. Directed Evolution Using Stabilized Bacterial Peptide Display. J Am Chem Soc 2020; 142:1882-1894. [PMID: 31880439 DOI: 10.1021/jacs.9b10716] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemically stabilized peptides have attracted intense interest by academics and pharmaceutical companies due to their potential to hit currently "undruggable" targets. However, engineering an optimal sequence, stabilizing linker location, and physicochemical properties is a slow and arduous process. By pairing non-natural amino acid incorporation and cell surface click chemistry in bacteria with high-throughput sorting, we developed a method to quantitatively select high affinity ligands and applied the Stabilized Peptide Evolution by E. coli Display technique to develop disrupters of the therapeutically relevant MDM2-p53 interface. Through in situ stabilization on the bacterial surface, we demonstrate rapid isolation of stabilized peptides with improved affinity and novel structures. Several peptides evolved a second loop including one sequence (Kd = 1.8 nM) containing an i, i+4 disulfide bond. NMR structural determination indicated a bent helix in solution and bound to MDM2. The bicyclic peptide had improved protease stability, and we demonstrated that protease resistance could be measured both on the bacterial surface and in solution, enabling the method to test and/or screen for additional drug-like properties critical for biologically active compounds.
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Affiliation(s)
- Tejas Navaratna
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lydia Atangcho
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mukesh Mahajan
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | | | - Marshall Case
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Andrew Min
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Daniel Tresnak
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Greg M Thurber
- Department of Chemical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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3
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A genetically encodable cell-type-specific protein synthesis inhibitor. Nat Methods 2019; 16:699-702. [DOI: 10.1038/s41592-019-0468-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/21/2019] [Indexed: 11/08/2022]
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4
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Altered steady state and activity-dependent de novo protein expression in fragile X syndrome. Nat Commun 2019; 10:1710. [PMID: 30979884 PMCID: PMC6461708 DOI: 10.1038/s41467-019-09553-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 03/15/2019] [Indexed: 12/22/2022] Open
Abstract
Whether fragile X mental retardation protein (FMRP) target mRNAs and neuronal activity contributing to elevated basal neuronal protein synthesis in fragile X syndrome (FXS) is unclear. Our proteomic experiments reveal that the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation, but the proteins expressed differ under these conditions. Several altered proteins, including Hexokinase 1 and Ras, also are expressed in the blood of FXS model mice and pharmacological treatments previously reported to ameliorate phenotypes modify their abundance in blood. In addition, plasma levels of Hexokinase 1 and Ras differ between FXS patients and healthy volunteers. Our data suggest that brain-based de novo proteomics in FXS model mice can be used to find altered expression of proteins in blood that could serve as disease-state biomarkers in individuals with FXS. Elevated protein synthesis, and dysregulated mGluR signalling, are documented in fragile X syndrome (FXS) Here the authors use proteomic analysis in a mouse model of FXS, and following mGluR5 stimulation, to identify potential biomarkers for the disease.
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5
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Chiminazzo A, Borsato G, Favero A, Fabbro C, McKenna CE, Dalle Carbonare LG, Valenti MT, Fabris F, Scarso A. Diketopyrrolopyrrole Bis‐Phosphonate Conjugate: A New Fluorescent Probe for In Vitro Bone Imaging. Chemistry 2019; 25:3617-3626. [PMID: 30600841 DOI: 10.1002/chem.201805436] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Andrea Chiminazzo
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari di Venezia via Torino 155 30172 Mestre (VE) Italy
| | - Giuseppe Borsato
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari di Venezia via Torino 155 30172 Mestre (VE) Italy
| | - Alessia Favero
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità AmbientaleUniversità di Parma Italy
| | - Chiara Fabbro
- Department of ChemistryImperial College London Wood Lane London W12 0BZ UK
| | - Charles E. McKenna
- Department of ChemistryUniversity of Southern California Los Angeles California 90089 USA
| | | | | | - Fabrizio Fabris
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari di Venezia via Torino 155 30172 Mestre (VE) Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari di Venezia via Torino 155 30172 Mestre (VE) Italy
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6
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Cell-type-specific metabolic labeling, detection and identification of nascent proteomes in vivo. Nat Protoc 2019; 14:556-575. [DOI: 10.1038/s41596-018-0106-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Huang LL, Liu K, Zhang Q, Xu J, Zhao D, Zhu H, Xie HY. Integrating Two Efficient and Specific Bioorthogonal Ligation Reactions with Natural Metabolic Incorporation in One Cell for Virus Dual Labeling. Anal Chem 2017; 89:11620-11627. [DOI: 10.1021/acs.analchem.7b03043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Li-Li Huang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Kejiang Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Qianmei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jin Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Dongxu Zhao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Houshun Zhu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hai-Yan Xie
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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8
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Kotapati HK, Robinson JD, Lawrence DR, Fortner KR, Stanford CW, Powell DR, Wardenga R, Bornscheuer UT, Masterson DS. Diastereoselective Hydrolysis of Branched Malonate Diesters by Porcine Liver Esterase: Synthesis of 5‐Benzyl‐Substituted C
α
‐Methyl‐β‐proline and Catalytic Evaluation. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hari Kiran Kotapati
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Jamarii D. Robinson
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Daniel R. Lawrence
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Kimberly R. Fortner
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Caleb W. Stanford
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway 73019‐5251 Norman Oklahoma USA
| | - Rainer Wardenga
- Enzymicals AG Walther‐Rathenau‐Str. 49a 17489 Greifswald Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis University of Greifswald Institute of Biochemistry Felix‐Hausdorff‐Str. 4 17487 Greifswald Germany
| | - Douglas S. Masterson
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
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9
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Nonradioactive quantification of autophagic protein degradation with L-azidohomoalanine labeling. Nat Protoc 2017; 12:279-288. [PMID: 28079880 DOI: 10.1038/nprot.2016.160] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
At present, several assays that use radioisotope labeling to quantify the degradation of long-lived proteins have been developed to measure autophagic flux. Here, we describe a nonradioactive pulse-chase protocol using L-azidohomoalanine (AHA) labeling to quantify long-lived protein degradation during autophagy. AHA is used as a surrogate for L-methionine, and, when added to cultured cells grown in methionine-free medium, AHA is incorporated into proteins during de novo protein synthesis. After a chase period to remove short-lived proteins, autophagy is induced by starvation or other stimuli. Cells then undergo a 'click' reaction between the azide group of AHA and a fluorescently tagged alkyne probe. The AHA-containing proteins can then be detected by flow cytometry. This protocol is nonradioactive, sensitive and quantitative, and it is easy to perform. It is also applicable to various cell culture systems. The whole protocol is estimated to take 4-5 d to complete.
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10
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SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2016; 113:E597-605. [PMID: 26787849 DOI: 10.1073/pnas.1514412113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this issue, we used a time-selective proteome-labeling method [bioorthogonal noncanonical amino acid tagging (BONCAT)] to identify proteins synthesized preferentially, but at extremely low rates, under anaerobic survival conditions by the opportunistic pathogen Pseudomonas aeruginosa. One of these proteins is a transcriptional regulator that has no homology to any characterized protein domains and is posttranscriptionally up-regulated during survival and slow growth. This small, acidic protein associates with RNA polymerase, and chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing suggests that the protein associates with genomic DNA through this interaction. ChIP signal is found both in promoter regions and throughout the coding sequences of many genes and is particularly enriched at ribosomal protein genes and in the promoter regions of rRNA genes. Deletion of the gene encoding this protein affects expression of these and many other genes and impacts biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. On the basis of these observations, we have designated the protein SutA (survival under transitions A).
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11
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Bagert JD, van Kessel JC, Sweredoski MJ, Feng L, Hess S, Bassler BL, Tirrell DA. Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi. Chem Sci 2015; 7:1797-1806. [PMID: 26925210 PMCID: PMC4763989 DOI: 10.1039/c5sc03340c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacteria use a process of chemical communication called quorum sensing to assess their population density and to change their behavior in response to fluctuations in the cell number and species composition of the community. In this work, we identified the quorum-sensing-regulated proteome in the model organism Vibrio harveyi by bio-orthogonal non-canonical amino acid tagging (BONCAT). BONCAT enables measurement of proteome dynamics with temporal resolution on the order of minutes. We deployed BONCAT to characterize the time-dependent transition of V. harveyi from individual- to group-behaviors. We identified 176 quorum-sensing-regulated proteins at early, intermediate, and late stages of the transition, and we mapped the temporal changes in quorum-sensing proteins controlled by both transcriptional and post-transcriptional mechanisms. Analysis of the identified proteins revealed 86 known and 90 new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.
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Affiliation(s)
- John D Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Julia C van Kessel
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Lihui Feng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544; Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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12
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Erdmann I, Marter K, Kobler O, Niehues S, Abele J, Müller A, Bussmann J, Storkebaum E, Ziv T, Thomas U, Dieterich DC. Cell-selective labelling of proteomes in Drosophila melanogaster. Nat Commun 2015; 6:7521. [PMID: 26138272 PMCID: PMC4507001 DOI: 10.1038/ncomms8521] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 05/16/2015] [Indexed: 01/06/2023] Open
Abstract
The specification and adaptability of cells rely on changes in protein composition. Nonetheless, uncovering proteome dynamics with cell-type-specific resolution remains challenging. Here we introduce a strategy for cell-specific analysis of newly synthesized proteomes by combining targeted expression of a mutated methionyl-tRNA synthetase (MetRS) with bioorthogonal or fluorescent non-canonical amino-acid-tagging techniques (BONCAT or FUNCAT). Substituting leucine by glycine within the MetRS-binding pocket (MetRSLtoG) enables incorporation of the non-canonical amino acid azidonorleucine (ANL) instead of methionine during translation. Newly synthesized proteins can thus be labelled by coupling the azide group of ANL to alkyne-bearing tags through ‘click chemistry'. To test these methods for applicability in vivo, we expressed MetRSLtoG cell specifically in Drosophila. FUNCAT and BONCAT reveal ANL incorporation into proteins selectively in cells expressing the mutated enzyme. Cell-type-specific FUNCAT and BONCAT, thus, constitute eligible techniques to study protein synthesis-dependent processes in complex and behaving organisms. Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).
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Affiliation(s)
- Ines Erdmann
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Kathrin Marter
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Oliver Kobler
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Sven Niehues
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Julia Abele
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Anke Müller
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Julia Bussmann
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Erik Storkebaum
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ulrich Thomas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Daniela C Dieterich
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany [3] Center for Behavioral Brain Sciences, Magdeburg 39118, Germany
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13
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Direct visualization of newly synthesized target proteins in situ. Nat Methods 2015; 12:411-4. [PMID: 25775042 DOI: 10.1038/nmeth.3319] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 01/29/2015] [Indexed: 12/15/2022]
Abstract
Protein synthesis is a dynamic process that tunes the cellular proteome in response to internal and external demands. Metabolic labeling approaches identify the general proteomic response but cannot visualize specific newly synthesized proteins within cells. Here we describe a technique that couples noncanonical amino acid tagging or puromycylation with the proximity ligation assay to visualize specific newly synthesized proteins and monitor their origin, redistribution and turnover in situ.
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14
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Zhang G, Bowling H, Hom N, Kirshenbaum K, Klann E, Chao MV, Neubert TA. In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor. J Proteome Res 2014; 13:5707-14. [PMID: 25271054 PMCID: PMC4261974 DOI: 10.1021/pr5006982] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Measuring the synthesis of new proteins
in the context of a much
greater number of pre-existing proteins can be difficult. To overcome
this obstacle, bioorthogonal noncanonical amino acid tagging (BONCAT)
can be combined with stable isotope labeling by amino acid in cell
culture (SILAC) for comparative proteomic analysis of de novo protein
synthesis (BONLAC). In the present study, we show that alkyne resin-based
isolation of l-azidohomoalanine (AHA)-labeled proteins using
azide/alkyne cycloaddition minimizes contamination from pre-existing
proteins. Using this approach, we isolated and identified 7414 BONCAT-labeled
proteins. The nascent proteome isolated by BONCAT was very similar
to the steady-state proteome, although transcription factors were
highly enriched by BONCAT. About 30% of the methionine residues were
replaced by AHA in our BONCAT samples, which allowed for identification
of methionine-containing peptides. There was no bias against low-methionine
proteins by BONCAT at the proteome level. When we applied the BONLAC
approach to screen for brain-derived neurotrophic factor (BDNF)-induced
protein synthesis, 53 proteins were found to be significantly changed
2 h after BDNF stimulation. Our study demonstrated that the newly
synthesized proteome, even after a short period of stimulation, can
be efficiently isolated by BONCAT and analyzed to a depth that is
similar to that of the steady-state proteome.
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Affiliation(s)
- Guoan Zhang
- Department of Biochemistry and Molecular Pharmacology, ‡Departments of Cell Biology, Physiology, and Neuroscience and Psychiatry, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine , New York, New York 10016, United States
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15
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Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol 2014; 16:2568-90. [PMID: 24571640 PMCID: PMC4122687 DOI: 10.1111/1462-2920.12436] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/14/2014] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
Abstract
Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry ((15)NH(3) assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and (15)N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level.
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Affiliation(s)
- Roland Hatzenpichler
- Divisions of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
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16
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Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol 2014. [PMID: 24571640 DOI: 10.1111/1462‐2920.12436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry ((15)NH(3) assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and (15)N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level.
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Affiliation(s)
- Roland Hatzenpichler
- Divisions of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
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17
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Coupling bioorthogonal chemistries with artificial metabolism: intracellular biosynthesis of azidohomoalanine and its incorporation into recombinant proteins. Molecules 2014; 19:1004-22. [PMID: 24434673 PMCID: PMC6271081 DOI: 10.3390/molecules19011004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/17/2022] Open
Abstract
In this paper, we present a novel, “single experiment” methodology based on genetic engineering of metabolic pathways for direct intracellular production of non-canonical amino acids from simple precursors, coupled with expanded genetic code. In particular, we engineered the intracellular biosynthesis of l-azidohomoalanine from O-acetyl-l-homoserine and NaN3, and achieved its direct incorporation into recombinant target proteins by AUG codon reassignment in a methionine-auxotroph E. coli strain. In our system, the host’s methionine biosynthetic pathway was first diverted towards the production of the desired non-canonical amino acid by exploiting the broad reaction specificity of recombinant pyridoxal phosphate-dependent O-acetylhomoserine sulfhydrylase from Corynebacterium glutamicum. Then, the expression of the target protein barstar, accompanied with efficient l-azidohomoalanine incorporation in place of l-methionine, was accomplished. This work stands as proof-of-principle and paves the way for additional work towards intracellular production and site-specific incorporation of biotechnologically relevant non-canonical amino acids directly from common fermentable sources.
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18
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McGouran JF, Gaertner SR, Altun M, Kramer HB, Kessler BM. Deubiquitinating enzyme specificity for ubiquitin chain topology profiled by di-ubiquitin activity probes. ACTA ACUST UNITED AC 2013; 20:1447-55. [PMID: 24290882 PMCID: PMC3899023 DOI: 10.1016/j.chembiol.2013.10.012] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/22/2013] [Accepted: 10/15/2013] [Indexed: 11/16/2022]
Abstract
Posttranslational modification with ubiquitin (Ub) controls many cellular processes, and aberrant ubiquitination can contribute to cancer, immunopathology, and neurodegeneration. The versatility arises from the ability of Ub to form polymer chains with eight distinct linkages via lysine side chains and the N terminus. In this study, we engineered Di-Ub probes mimicking all eight different poly-Ub linkages and profiled the deubiquitinating enzyme (DUB) selectivity for recognizing Di-Ub moieties in cellular extracts. Mass spectrometric profiling revealed that most DUBs examined have broad selectivity, whereas a subset displays a clear preference for recognizing noncanonical over K48/K63 Ub linkages. Our results expand knowledge of Ub processing enzyme functions in cellular contexts that currently depends largely on using recombinant enzymes and substrates. Synthesis of Di-ubiquitin-based active site probes representing all eight linkages Mass spectrometric profiling of DUB-Ub linkage preference in whole cell extracts Activity-based Di-Ub probe screen for DUB specificity toward poly-Ub linkages DUBs detected with a preference for noncanonical linkages over K48/K63-linked Ub
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Affiliation(s)
- Joanna F McGouran
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Selina R Gaertner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Mikael Altun
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Holger B Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
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19
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Hodas JJL, Nehring A, Höche N, Sweredoski MJ, Pielot R, Hess S, Tirrell DA, Dieterich DC, Schuman EM. Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT). Proteomics 2012; 12:2464-76. [PMID: 22744909 DOI: 10.1002/pmic.201200112] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Local protein synthesis and its activity-dependent modulation via dopamine receptor stimulation play an important role in synaptic plasticity - allowing synapses to respond dynamically to changes in their activity patterns. We describe here the metabolic labeling, enrichment, and MS-based identification of candidate proteins specifically translated in intact hippocampal neuropil sections upon treatment with the selective D1/D5 receptor agonist SKF81297. Using the noncanonical amino acid azidohomoalanine and click chemistry, we identified over 300 newly synthesized proteins specific to dendrites and axons. Candidates specific for the SKF81297-treated samples were predominantly involved in protein synthesis and synapse-specific functions. Furthermore, we demonstrate a dendrite-specific increase in proteins synthesis upon application of SKF81297. This study provides the first snapshot in the dynamics of the dopaminergic hippocampal neuropil proteome.
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Affiliation(s)
- Jennifer J L Hodas
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
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20
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Tom Dieck S, Müller A, Nehring A, Hinz FI, Bartnik I, Schuman EM, Dieterich DC. Metabolic labeling with noncanonical amino acids and visualization by chemoselective fluorescent tagging. CURRENT PROTOCOLS IN CELL BIOLOGY 2012; Chapter 7:7.11.1-7.11.29. [PMID: 22968844 PMCID: PMC3736104 DOI: 10.1002/0471143030.cb0711s56] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fluorescent labeling of proteins by genetically encoded fluorescent protein tags has enabled an enhanced understanding of cell biological processes but is restricted to the analysis of a limited number of identified proteins. This approach does not permit, e.g., the unbiased visualization of a full proteome in situ. We describe here a fluorescence-based method to follow proteome-wide patterns of newly synthesized proteins in cultured cells, tissue slices, and a whole organism. This technique is compatible with immunohistochemistry and in situ hybridization. Key to this method is the introduction of a small bio-orthogonal reactive group by metabolic labeling. This is accomplished by replacing the amino acid methionine by the azide-bearing methionine surrogate azidohomoalanine (AHA) in a step very similar to classical radioisotope labeling. Subsequently, an alkyne-bearing fluorophore is covalently attached to the group by "click chemistry"--a copper(I)-catalyzed [3+2]azide-alkyne cycloaddition. By similar means, metabolic labeling can also be performed with the alkyne-bearing homopropargylglycine (HPG) and clicked to an azide-functionalized fluorophore.
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Affiliation(s)
- Susanne Tom Dieck
- Max Planck Institute for Brain Research, Department of Synaptic Plasticity, Frankfurt, Germany
| | - Anke Müller
- Leibniz Institute for Neurobiology, Research Group Neuralomics, Magdeburg, Germany
- Otto-von-Guericke-University Magdeburg, Medical Faculty, Institute for Pharmacology and Toxicology, Magdeburg, Germany
| | - Anne Nehring
- Max Planck Institute for Brain Research, Department of Synaptic Plasticity, Frankfurt, Germany
| | - Flora I Hinz
- Max Planck Institute for Brain Research, Department of Synaptic Plasticity, Frankfurt, Germany
| | - Ina Bartnik
- Max Planck Institute for Brain Research, Department of Synaptic Plasticity, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Department of Synaptic Plasticity, Frankfurt, Germany
| | - Daniela C Dieterich
- Leibniz Institute for Neurobiology, Research Group Neuralomics, Magdeburg, Germany
- Otto-von-Guericke-University Magdeburg, Medical Faculty, Institute for Pharmacology and Toxicology, Magdeburg, Germany
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21
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Rubino FA, Oum YH, Rajaram L, Chu Y, Carrico IS. Chemoselective modification of viral surfaces via bioorthogonal click chemistry. J Vis Exp 2012:e4246. [PMID: 22929552 DOI: 10.3791/4246] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The modification of virus particles has received a significant amount of attention for its tremendous potential for impacting gene therapy, oncolytic applications and vaccine development. Current approaches to modifying viral surfaces, which are mostly genetics-based, often suffer from attenuation of virus production, infectivity and cellular transduction. Using chemoselective click chemistry, we have developed a straightforward alternative approach which sidesteps these issues while remaining both highly flexible and accessible. The goal of this protocol is to demonstrate the effectiveness of using bioorthogonal click chemistry to modify the surface of adenovirus type 5 particles. This two-step process can be used both therapeutically or analytically, as it allows for chemoselective ligation of targeting molecules, dyes or other molecules of interest onto proteins pre-labeled with azide tags. The three major advantages of this method are that (1) metabolic labeling demonstrates little to no impact on viral fitness, (2) a wide array of effector ligands can be utilized, and (3) it is remarkably fast, reliable and easy to access. In the first step of this procedure, adenovirus particles are produced bearing either azidohomoalanine (Aha, a methionine surrogate) or the unnatural sugar O-linked N-azidoacetylglucosamine (O-GlcNAz), both of which contain the azide (-N3) functional group. After purification of the azide-modified virus particles, an alkyne probe containing the fluorescent TAMRA moiety is ligated in a chemoselective manner to the pre-labeled proteins or glycoproteins. Finally, an SDS-PAGE analysis is performed to demonstrate the successful ligation of the probe onto the viral capsid proteins. Aha incorporation is shown to label all viral capsid proteins (Hexon, Penton and Fiber), while O-GlcNAz incorporation results in labeling of Fiber only. In this evolving field, multiple methods for azide-alkyne ligation have been successfully developed; however only the two we have found to be most convenient are demonstrated herein - strain-promoted azide-alkyne cycloaddition (SPAAC) and copper-catalyzed azide-alkyne cycloaddition (CuAAC) under deoxygenated atmosphere.
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22
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Ngo JT, Babin BM, Champion JA, Schuman EM, Tirrell DA. State-selective metabolic labeling of cellular proteins. ACS Chem Biol 2012; 7:1326-30. [PMID: 22692961 DOI: 10.1021/cb300238w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcriptional activity from a specified promoter can provide a useful marker for the physiological state of a cell. Here we introduce a method for selective tagging of proteins made in cells in which specified promoters are active. Tagged proteins can be modified with affinity reagents for enrichment or with fluorescent dyes for visualization. The method allows state-selective analysis of the proteome, whereby proteins synthesized in predetermined physiological states can be identified. The approach is demonstrated by proteome-wide labeling of bacterial proteins upon activation of the P(BAD) promoter and the SoxRS regulon and provides a basis for analysis of more complex systems including spatially heterogeneous microbial cultures and biofilms.
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Affiliation(s)
- John T. Ngo
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Brett M. Babin
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Julie A. Champion
- School of Chemical and Biomolecular
Engineering, Georgia Institute of Technology, 311 Ferst Drive, N.W., Atlanta, Georgia 30332, United States
| | - Erin M. Schuman
- Max Planck Institute for Brain Research, Max von Laue Strasse 3, Frankfurt,
Germany 60438
| | - David A. Tirrell
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
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23
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24
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Truong F, Yoo TH, Lampo TJ, Tirrell DA. Two-strain, cell-selective protein labeling in mixed bacterial cultures. J Am Chem Soc 2012; 134:8551-6. [PMID: 22575034 DOI: 10.1021/ja3004667] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell-selective metabolic labeling of proteins with noncanonical amino acids enables the study of proteomic changes in specified subpopulations of complex multicellular systems. For example, azidonorleucine (Anl) and 2-aminooctynoic acid, both of which are activated by an engineered methionyl-tRNA synthetase (designated NLL-MetRS), are excluded from proteins made in wild-type cells but incorporated readily into proteins made in cells that carry NLL-MetRS. To expand the set of tools available for cell-selective metabolic labeling, we sought a MetRS variant capable of activating propargylglycine (Pra). Pra was chosen as the target amino acid because its alkynyl side chain can be selectively and efficiently conjugated to azide-functionalized fluorescence probes and affinity tags. Directed evolution, using active-site randomization and error-prone PCR, yielded a MetRS variant (designated PraRS) capable of incorporating Pra at near-quantitative levels into proteins made in a Met-auxotrophic strain of Escherichia coli cultured in Met-depleted media. Proteins made in E. coli strains expressing PraRS were labeled with Pra in Met-supplemented media as shown by in-gel fluorescence after conjugation to Cy5-azide. The combined use of NLL-MetRS and PraRS enabled differential, cell-selective labeling of marker proteins derived from two bacterial strains cocultured in media supplemented with Met, Anl, and Pra. Treatment of the mixed marker proteins by sequential strain-promoted and copper(I)-catalyzed cycloadditions allowed straightforward identification of the cellular origin of each protein.
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Affiliation(s)
- Frank Truong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, 91125, United States
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25
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Hinz FI, Dieterich DC, Tirrell DA, Schuman EM. Non-canonical amino acid labeling in vivo to visualize and affinity purify newly synthesized proteins in larval zebrafish. ACS Chem Neurosci 2012; 3:40-49. [PMID: 22347535 DOI: 10.1021/cn2000876] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Protein expression in the nervous system undergoes regulated changes in response to changes in behavioral states, in particular long-term memory formation. Recently, methods have been developed (BONCAT and FUNCAT), which introduce non-canonical amino acids bearing small bio-orthogonal functional groups into proteins using the cells' own translational machinery. Using the selective 'click reaction', this allows for the identification and visualization of newly synthesized proteins in vitro. Here we demonstrate that non-canonical amino acid labeling can be achieved in vivo in an intact organism capable of simple learning behavior, the larval zebrafish. We show that azidohomoalanine is metabolically incorporated into newly synthesized proteins, in a time- and concentration-dependent manner, but has no apparent toxic effect and does not influence simple behaviors such as spontaneous swimming and escape responses. This enables fluorescent labeling of newly synthesized proteins in whole mount larval zebrafish. Furthermore, stimulation with a GABA antagonist that elicits seizures in the larval zebrafish causes an increase in protein synthesis throughout the proteome, which can also be visualized in intact larvae.
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Affiliation(s)
- Flora I. Hinz
- Division of Biology, California Institute of Technology, Pasadena, California
91125, United States
- Max Planck Institute for Brain Research, D-60528 Frankfurt am Main, Germany
| | - Daniela C. Dieterich
- Emmy Noether Research Group Neuralomics, Leibniz Institute for Neurobiology, D-39118 Magdeburg,
Germany
| | - David A. Tirrell
- Division of Chemistry
and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Erin M. Schuman
- Division of Biology, California Institute of Technology, Pasadena, California
91125, United States
- Max Planck Institute for Brain Research, D-60528 Frankfurt am Main, Germany
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26
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Eger S, Scheffner M, Marx A, Rubini M. Formation of ubiquitin dimers via azide-alkyne click reaction. Methods Mol Biol 2012; 832:589-596. [PMID: 22350914 DOI: 10.1007/978-1-61779-474-2_41] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The conjugation of poly-ubiquitin chains is a widespread post-translational modification of proteins that plays a role in many different cellular processes. Notably, the biological function of the attached ubiquitin chain depends on which lysine residue is used for chain formation. Here, we report a method for the modular synthesis of site-specifically linked ubiquitin dimers, which is based on click reaction between two artificial amino acids. In this way, it is possible to synthesize all seven naturally occurring ubiquitin connectivities, thus giving access to all ubiquitin dimers. Furthermore, this method can be generally applied to link ubiquitin to any substrate protein or even to link any two proteins site specifically.
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Affiliation(s)
- Silvia Eger
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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27
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Eger S, Castrec B, Hübscher U, Scheffner M, Rubini M, Marx A. Corrigendum: Generation of a Mono-ubiquitinated PCNA Mimic by Click Chemistry. Chembiochem 2011. [DOI: 10.1002/cbic.201100736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Szychowski J, Mahdavi A, Hodas JJL, Bagert JD, Ngo JT, Landgraf P, Dieterich DC, Schuman EM, Tirrell DA. Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition. J Am Chem Soc 2010; 132:18351-60. [PMID: 21141861 PMCID: PMC3016050 DOI: 10.1021/ja1083909] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.
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Affiliation(s)
- Janek Szychowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Alborz Mahdavi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Jennifer J. L. Hodas
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
| | - John D. Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - John T. Ngo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Peter Landgraf
- Leibniz-Institute for Neurobiology, Research Group Neuralomics, Brenneckestraße 6, 39118 Magdeburg, Germany
| | - Daniela C. Dieterich
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
- Leibniz-Institute for Neurobiology, Research Group Neuralomics, Brenneckestraße 6, 39118 Magdeburg, Germany
| | - Erin M. Schuman
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
- Max Planck Institute for Brain Research, Deutschordenstraße 46, 60528 Frankfurt, Germany
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
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29
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Abstract
A concise and highly efficient synthetic route to L-azidohomoalanine (L-Aha) and its homologues is presented here. These chemically modified amino acids are used for the introduction of bioorthogonal handles into proteins. The described route avoids major problems of previously reported methods including expensive starting materials, low efficiency, and lack of scalability. Starting from inexpensive N-Boc-O-Bn-L-aspartic acid, gram quantities of L-Aha hydrochloride can be prepared with high purity. The reactions can be completed within 1 week and the products can be incorporated into proteins using L-methionine auxotrophs.
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30
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Strable E, Prasuhn DE, Udit AK, Brown S, Link AJ, Ngo JT, Lander G, Quispe J, Potter CS, Carragher B, Tirrell DA, Finn MG. Unnatural amino acid incorporation into virus-like particles. Bioconjug Chem 2008; 19:866-75. [PMID: 18318461 PMCID: PMC2713011 DOI: 10.1021/bc700390r] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.
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31
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Link AJ, Vink MKS, Tirrell DA. Synthesis of the functionalizable methionine surrogate azidohomoalanine using Boc-homoserine as precursor. Nat Protoc 2007; 2:1884-7. [PMID: 17703199 DOI: 10.1038/nprot.2007.269] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes a synthetic route to the non-canonical amino acid azidohomoalanine (AHA) using protected homoserine as a starting material. An alternative route to AHA is presented in a companion paper. This synthesis can be completed in 5 days.
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Affiliation(s)
- A James Link
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106, USA.
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