1
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Tang Q, Chen X. Nascent Proteomics: Chemical Tools for Monitoring Newly Synthesized Proteins. Angew Chem Int Ed Engl 2023; 62:e202305866. [PMID: 37309018 DOI: 10.1002/anie.202305866] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Cellular proteins are dynamically regulated in response to environmental stimuli. Conventional proteomics compares the entire proteome in different cellular states to identify differentially expressed proteins, which suffers from limited sensitivity for analyzing acute and subtle changes. To address this challenge, nascent proteomics has been developed, which selectively analyzes the newly synthesized proteins, thus offering a more sensitive and timely insight into the dynamic changes of the proteome. In this Minireview, we discuss recent advancements in nascent proteomics, with an emphasis on methodological developments. Also, we delve into the current challenges and provide an outlook on the future prospects of this exciting field.
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Affiliation(s)
- Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Science, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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2
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Liu Y, Dong C, Ren J. In vivo monitoring of the ubiquitination of newly synthesized proteins in living cells by combining a click reaction with fluorescence cross-correlation spectroscopy (FCCS). Analyst 2023. [PMID: 37439656 DOI: 10.1039/d3an00890h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Newly synthesized proteins are closely related to a series of biological processes, including cell growth, differentiation, and signaling. The post-translational modifications (PTMs) of newly synthesized proteins help maintain normal cellular functions. Ubiquitination is one of the PTMs and plays a prominent role in regulating cellular functions. Although great progress has been made in studying the ubiquitination of newly synthesized proteins, the in vivo monitoring of the ubiquitination of newly synthesized proteins in living cells still remains challenging. In this study, we propose a new method for measuring the ubiquitination of newly synthesized proteins in living cells by combining a click reaction with fluorescence cross-correlation spectroscopy (FCCS). In this study, a puromycin derivative (Puro-TCO) and a fluorescence probe (Bodipy-TR-Tz) were synthesized, and then, the newly synthesized proteins in living cells were labelled with Bodipy-TR via the click reaction between Puro-TCO and Tz. Ubiquitin (Ub) in living cells was labelled with the enhanced green fluorescence protein (EGFP) by fusion using a gene engineering technique. FCCS was used to quantify the newly synthesized proteins with two labels (EGFP and Bodipy-TR) in living cells. After measurements, the cross-correlation (CC) value was used to evaluate the ubiquitination degree of proteins. Herein, we established a method for monitoring the ubiquitination of newly synthesized proteins with EGFP-Ub in living cells and studied the effects of the ubiquitin E1 enzyme inhibitor on newly synthesized proteins. Our preliminary results document that the combination of FCCS with a click reaction is an efficient strategy for studying the ubiquitination of newly synthesized proteins in vivo in living cells. This new method can be applied to basic research in protein ubiquitination and drug screening at the living-cell level.
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Affiliation(s)
- Yaoqi Liu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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3
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Hadidi K, Steinbuch KB, Dozier LE, Patrick GN, Tor Y. Inherently Emissive Puromycin Analogues for Live Cell Labelling. Angew Chem Int Ed Engl 2023; 62:e202216784. [PMID: 36973168 PMCID: PMC10213139 DOI: 10.1002/anie.202216784] [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: 11/14/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023]
Abstract
Puromycin derivatives containing an emissive thieno[3,4-d]-pyrimidine core, modified with azetidine and 3,3-difluoroazetidine as Me2 N surrogates, exhibit translation inhibition and bactericidal activity similar to the natural antibiotic. The analogues are capable of cellular puromycylation of nascent peptides, generating emissive products without any follow-up chemistry. The 3,3-difluoroazetidine-containing analogue is shown to fluorescently label newly translated peptides and be visualized in both live and fixed HEK293T cells and rat hippocampal neurons.
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Affiliation(s)
- Kaivin Hadidi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Kfir B Steinbuch
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Lara E Dozier
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0347, USA
| | - Gentry N Patrick
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0347, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
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4
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Liu H, Li H, Jiang Z, Jin S, Song R, Yang Y, Li J, Huang J, Zhang X, Dong X, Mori M, Fritzler MJ, He L, Cardoso WV, Lu J. A local translation program regulates centriole amplification in the airway epithelium. Sci Rep 2023; 13:7090. [PMID: 37127654 PMCID: PMC10151349 DOI: 10.1038/s41598-023-34365-8] [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: 01/10/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023] Open
Abstract
Biogenesis of organelles requires targeting of a subset of proteins to specific subcellular domains by signal peptides or mechanisms controlling mRNA localization and local translation. How local distribution and translation of specific mRNAs for organelle biogenesis is achieved remains elusive and likely to be dependent on the cellular context. Here we identify Trinucleotide repeat containing-6a (Tnrc6a), a component of the miRNA pathway, distinctively localized to apical granules of differentiating airway multiciliated cells (MCCs) adjacent to centrioles. In spite of being enriched in TNRC6A and the miRNA-binding protein AGO2, they lack enzymes for mRNA degradation. Instead, we found these apical granules enriched in components of the mRNA translation machinery and newly synthesized proteins suggesting that they are specific hubs for target mRNA localization and local translation in MCCs. Consistent with this, Tnrc6a loss of function prevented formation of these granules and led to a broad reduction, rather than stabilization of miRNA targets. These included downregulation of key genes involved in ciliogenesis and was associated with defective multicilia formation both in vivo and in primary airway epithelial cultures. Similar analysis of Tnrc6a disruption in yolk sac showed stabilization of miRNA targets, highlighting the potential diversity of these mechanisms across organs.
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Affiliation(s)
- Helu Liu
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Huijun Li
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Zhihua Jiang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Shibo Jin
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Rui Song
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Ying Yang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Jun Li
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Jingshu Huang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xiaoqing Zhang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xuesong Dong
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Munemasa Mori
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Marvin J Fritzler
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Wellington V Cardoso
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
| | - Jining Lu
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, 6705 Rockledge Drive, Room 407-J, MSC 7952, Bethesda, MD, 20892-7952, USA.
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5
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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6
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Chang B, Xu Q, Guo H, Zhong M, Shen R, Zhao L, Zhao J, Ma T, Chu Y, Zhang J, Fang J. Puromycin Prodrug Activation by Thioredoxin Reductase Overcomes Its Promiscuous Cytotoxicity. J Med Chem 2023; 66:3250-3261. [PMID: 36855911 DOI: 10.1021/acs.jmedchem.2c01509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Overexpression of the selenoprotein thioredoxin reductase (TrxR) has been documented in malignant tissues and is of pathological significance for many types of tumors. The antibiotic puromycin (Puro) is a protein synthesis inhibitor causing premature polypeptide chain termination during translation. The well-defined action mechanism of Puro makes it a useful tool in biomedical studies. However, the nonselective cytotoxicity of Puro limits its therapeutic applications. We report herein the construction and evaluation of two Puro prodrugs, that is, S1-Puro with a five-membered cyclic disulfide trigger and S2-Puro with a linear disulfide trigger. S1-Puro is selectively activated by TrxR and shows the TrxR-dependent cytotoxicity to cancer cells, while S2-Puro is readily activated by thiols. Furthermore, S1-Puro displays higher stability in plasma than S2-Puro. We expect that this prodrug strategy may promote the further development of Puro as a therapeutic agent.
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Affiliation(s)
- Bingbing Chang
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Qianhe Xu
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hairui Guo
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical College, Weihui, Henan 453100, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ruipeng Shen
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lanning Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Jintao Zhao
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Tao Ma
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yajun Chu
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Junmin Zhang
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China.,School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu 210094, China
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7
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Ko T, Oliveira MM, Alapin JM, Morstein J, Klann E, Trauner D. Optical Control of Translation with a Puromycin Photoswitch. J Am Chem Soc 2022; 144:21494-21501. [PMID: 36394560 PMCID: PMC11302736 DOI: 10.1021/jacs.2c07374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Translation is an elementary cellular process that involves a large number of factors interacting in a concerted fashion with the ribosome. Numerous natural products have emerged that interfere with the ribosomal function, such as puromycin, which mimics an aminoacyl tRNA and causes premature chain termination. Here, we introduce a photoswitchable version of puromycin that, in effect, puts translation under optical control. Our compound, termed puroswitch, features a diazocine that allows for reversible and nearly quantitative isomerization and pharmacological modulation. Its synthesis involves a new photoswitchable amino acid building block. Puroswitch shows little activity in the dark and becomes substantially more active and cytotoxic, in a graded fashion, upon irradiation with various wavelengths of visible light. In vitro translation assays confirm that puroswitch inhibits translation with a mechanism similar to that of puromycin itself. Once incorporated into nascent proteins, puroswitch reacts with standard puromycin antibodies, which allows for tracking de novo protein synthesis using western blots and immunohistochemistry. As a cell-permeable small molecule, puroswitch can be used for nascent proteome profiling in a variety of cell types, including primary mouse neurons. We envision puroswitch as a useful biochemical tool for the optical control of translation and for monitoring newly synthesized proteins in defined locations and at precise time points.
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Affiliation(s)
- Tongil Ko
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Mauricio M. Oliveira
- Center for Neural Science, New York University, New York, New York, 10003, United States
| | - Jessica M. Alapin
- Center for Neural Science, New York University, New York, New York, 10003, United States
| | - Johannes Morstein
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Eric Klann
- Center for Neural Science, New York University, New York, New York, 10003, United States
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York, 10003, United States
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8
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Bagra N, Jain R. Synthesis of 4-(1,2,3-triazol-1-yl)-L-phenylalanines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2077114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitin Bagra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
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9
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Elamri I, Abdellaoui C, Bains JK, Hohmann KF, Gande SL, Stirnal E, Wachtveitl J, Schwalbe H. Wavelength-Selective Uncaging of Two Different Photoresponsive Groups on One Effector Molecule for Light-Controlled Activation and Deactivation. J Am Chem Soc 2021; 143:10596-10603. [PMID: 34236854 DOI: 10.1021/jacs.1c02817] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Photocleavable protecting groups (PPGs) play a pivotal role in numerous studies. They enable controlled release of small effector molecules to induce biochemical function. The number of PPGs attached to a variety of effector molecules has grown rapidly in recent years satisfying the high demand for new applications. However, until now molecules carrying PPGs have been designed to activate function only in a single direction, namely the release of the effector molecule. Herein, we present the new approach Two-PPGs-One-Molecule (TPOM) that exploits the orthogonal photolysis of two photoprotecting groups to first release the effector molecule and then to modify it to suppress its induced effect. The moiety resembling the tyrosyl side chain of the translation inhibitor puromycin was synthetically modified to the photosensitive ortho-nitrophenylalanine that cyclizes upon near UV-irradiation to an inactive puromycin cinnoline derivative. Additionally, the modified puromycin analog was protected by the thio-coumarylmethyl group as the second PPG. This TPOM strategy allows an initial wavelength-selective activation followed by a second light-induced deactivation. Both photolysis processes were spectroscopically studied in the UV/vis- and IR-region. In combination with quantum-chemical calculations and time-resolved NMR spectroscopy, the photoproducts of both activation and deactivation steps upon illumination were characterized. We further probed the translation inhibition effect of the new synthesized puromycin analog upon light activation/deactivation in a cell-free GFP translation assay. TPOM as a new method for precise triggering activation/deactivation of effector molecules represents a valuable addition for the control of biological processes with light.
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Affiliation(s)
- Isam Elamri
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Chahinez Abdellaoui
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Jasleen Kaur Bains
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Katharina Felicitas Hohmann
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Santosh Lakshmi Gande
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Elke Stirnal
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
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10
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The science of puromycin: From studies of ribosome function to applications in biotechnology. Comput Struct Biotechnol J 2020; 18:1074-1083. [PMID: 32435426 PMCID: PMC7229235 DOI: 10.1016/j.csbj.2020.04.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/19/2020] [Accepted: 04/19/2020] [Indexed: 11/20/2022] Open
Abstract
Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating nascent chains, blocking further extension and resulting in premature termination of translation. It is most commonly known as a selection marker for cell lines genetically engineered to express a resistance transgene, but its additional uses as a probe for protein synthesis have proven invaluable across a wide variety of model systems, ranging from purified ribosomes and cell-free translation to intact cultured cells and whole animals. Puromycin is comprised of a nucleoside covalently bound to an amino acid, mimicking the 3′ end of aminoacylated tRNAs that participate in delivery of amino acids to elongating ribosomes. Both moieties can tolerate some chemical substitutions and modifications without significant loss of activity, generating a diverse toolbox of puromycin-based reagents with added functionality, such as biotin for affinity purification or fluorophores for fluorescent microscopy detection. These reagents, as well as anti-puromycin antibodies, have played a pivotal role in advancing our understanding of the regulation and dysregulation of protein synthesis in normal and pathological processes, including immune response and neurological function. This manuscript reviews the current state of puromycin-based research, including structure and mechanism of action, relevant derivatives, use in advanced methodologies and some of the major insights generated using such techniques both in the lab and the clinic.
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11
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Korotkovs V, Reichenbach LF, Pescheteau C, Burley GA, Liskamp RMJ. Molecular Construction of Sulfonamide Antisense Oligonucleotides. J Org Chem 2019; 84:10635-10648. [PMID: 31379169 DOI: 10.1021/acs.joc.9b00941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
An efficient and scalable synthesis of new oligonucleotide monomers was developed for replacement of the phosphodiester backbone of RNA by a sulfonamide-containing backbone to enable construction of sulfonamide antisense oligonucleotides (SaASOs). It was shown that by employing these sulfonamide RNA (SaRNA) monomers, it was possible to synthesize oligomers in solution. The properties of a sulfonamide moiety replacement were evaluated by incorporation of a SaRNA-monomer into a DNA strand and performing thermal stability tests of the resulting DNA and RNA-double-strand hybrids. Although sulfonamide modification caused a decrease in melting temperature (Tm) of both hybrids, it was lower for the sulfonamide-containing DNA-RNA hybrid than that for the sulfonamide-containing DNA-DNA hybrid.
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Affiliation(s)
- Valerijs Korotkovs
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K
| | - Linus F Reichenbach
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Clémentine Pescheteau
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K
| | - Glenn A Burley
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Rob M J Liskamp
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K.,Department of Pharmaceutical Sciences, Faculty of Science , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
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12
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Kandala D, Del Piano A, Minati L, Clamer M. Targeting Translation Activity at the Ribosome Interface with UV-Active Small Molecules. ACS OMEGA 2019; 4:10336-10345. [PMID: 31460127 PMCID: PMC6648492 DOI: 10.1021/acsomega.9b00366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Puromycin is a well-known antibiotic that is used to study the mechanism of protein synthesis and to monitor ribosome activity due to its incorporation into nascent peptide chains. However, puromycin effects outside the ribosome catalytic core remain unexplored. Here, we developed two analogues (3PB and 3PC) of the 3'-end of tyrosylated-tRNA that can efficiently interact with several proteins associated with ribosomes. We biochemically characterized the binding of these analogues and globally mapped the direct small molecule-protein interactions in living cells using clickable and photoreactive puromycin-like probes in combination with in-depth mass spectrometry. We identified a list of proteins targeted by the molecules during ribosome activity (e.g., GRP78), and we addressed possible uses of the probes to sense the activity of protein synthesis and to capture associated RNA. By coupling genome-wide RNA sequencing methods with these molecules, the characterization of unexplored translational control mechanisms will be feasible.
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13
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Dong J, Hong D, Lang W, Huang J, Qian L, Zhu Q, Li L, Ge J. Differently Tagged Probes for Protein Profiling of Mitochondria. Chembiochem 2019; 20:1155-1160. [PMID: 30600897 DOI: 10.1002/cbic.201800735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/10/2022]
Abstract
The mitochondrion is one of the most important organelles in the eukaryotic cell. Characterization of the mitochondrial proteome is a prerequisite for understanding its cellular functions at the molecular level. Here we report a proteomics method based on mitochondrion-targeting groups and click chemistry. In our strategy, three different mitochondrion-targeting moieties were each augmented with a clickable handle and a cysteine-reactive group. Fluorescence-based bioimaging and fractionation experiments clearly showed that most signals arising from the labels were localized in the mitochondria of cells, as a result of covalent attachment between probe and target proteins. The three probes had distinct profiling characteristics. Furthermore, we successfully identified more than two hundred mitochondrial proteins. The results showed that different mitochondrion-targeting groups targeted distinct proteins with partial overlap. Most of the labeled proteins were localized in the mitochondrial matrix and inner mitochondrial membrane. Our results provide a tool for chemoproteomic analysis of mitochondrion-related proteins.
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Affiliation(s)
- Jia Dong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Danqi Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Jintao Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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14
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Qian L, Pan S, Lee JS, Ge J, Li L, Yao SQ. Live-cell imaging and profiling of c-Jun N-terminal kinases using covalent inhibitor-derived probes. Chem Commun (Camb) 2019; 55:1092-1095. [PMID: 30620026 DOI: 10.1039/c8cc09558b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
c-Jun N-terminal kinases (JNKs) are involved in critical cellular functions. Herein, small-molecule JNK-targeting probes are reported based on a covalent inhibitor. Together with newly developed two-photon fluorescence Turn-ON reporters and chemoproteomic studies, we showed that some probes may be suitable for live-cell imaging and profiling of JNKs.
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Affiliation(s)
- Linghui Qian
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore. and Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, South Korea
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211800, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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15
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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.
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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.
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16
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Abbas M, Elshahawi SI, Wang X, Ponomareva LV, Sajid I, Shaaban KA, Thorson JS. Puromycins B-E, Naturally Occurring Amino-Nucleosides Produced by the Himalayan Isolate Streptomyces sp. PU-14G. JOURNAL OF NATURAL PRODUCTS 2018; 81:2560-2566. [PMID: 30418763 PMCID: PMC6393767 DOI: 10.1021/acs.jnatprod.8b00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The isolation and structure elucidation of four new naturally occurring amino-nucleoside [puromycins B-E (1-4)] metabolites from a Himalayan isolate ( Streptomyces sp. PU-14-G, isolated from the Bara Gali region of northern Pakistan) is reported. Consistent with prior reports, comparative antimicrobial assays revealed the need for the free 2″-amine for anti-Gram-positive bacteria and antimycobacterial activity. Similarly, comparative cancer cell line cytotoxicity assays highlighted the importance of the puromycin-free 2″-amine and the impact of 3'-nucleoside substitution. These studies extend the repertoire of known naturally occurring puromycins and their corresponding SAR. Notably, 1 represents the first reported naturally occurring bacterial puromycin-related metabolite with a 3'- N-amino acid substitution that differs from the 3'- N-tyrosinyl of classical puromycin-type natural products. This discovery suggests the biosynthesis of 1 in Streptomyces sp. PU-14G may invoke a uniquely permissive amino-nucleoside synthetase and/or multiple synthetases and sets the stage for further studies to elucidate, and potentially exploit, new biocatalysts for puromycin chemoenzymatic diversification.
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Affiliation(s)
- Muhammad Abbas
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Sherif I. Elshahawi
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Imran Sajid
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Corresponding Authors.,
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Corresponding Authors.,
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17
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Elamri I, Heumüller M, Herzig L, Stirnal E, Wachtveitl J, Schuman EM, Schwalbe H. A New Photocaged Puromycin for an Efficient Labeling of Newly Translated Proteins in Living Neurons. Chembiochem 2018; 19:2458-2464. [DOI: 10.1002/cbic.201800408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/11/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Isam Elamri
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Maximilian Heumüller
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Lisa‐M. Herzig
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elke Stirnal
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Erin M. Schuman
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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18
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Active Ribosome Profiling with RiboLace. Cell Rep 2018; 25:1097-1108.e5. [DOI: 10.1016/j.celrep.2018.09.084] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/20/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
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19
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Stefanik MT, Milovanovic M, Werner CT, Spainhour JCG, Wolf ME. Withdrawal From Cocaine Self-administration Alters the Regulation of Protein Translation in the Nucleus Accumbens. Biol Psychiatry 2018; 84:223-232. [PMID: 29622268 PMCID: PMC6054574 DOI: 10.1016/j.biopsych.2018.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/26/2018] [Accepted: 02/12/2018] [Indexed: 10/18/2022]
Abstract
BACKGROUND Cue-induced cocaine craving incubates during abstinence from cocaine self-administration. Expression of incubation ultimately depends on elevation of homomeric GluA1 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors in the nucleus accumbens (NAc). This adaptation requires ongoing protein translation for its maintenance. Aberrant translation is implicated in central nervous system diseases, but nothing is known about glutamatergic regulation of translation in the drug-naïve NAc or after incubation. METHODS NAc tissue was obtained from drug-naïve rats and from rats after 1 or >40 days of abstinence from extended-access cocaine or saline self-administration. Newly translated proteins were labeled using 35S-Met/Cys or puromycin. We compared basal overall translation and its regulation by metabotropic glutamate receptor 1 (mGlu1), mGlu5, and N-methyl-D-aspartate receptors (NMDARs) in drug-naïve, saline control, and cocaine rats, and we compared GluA1 and GluA2 translation by immunoprecipitating puromycin-labeled proteins. RESULTS In all groups, overall translation was unaltered by mGlu1 blockade (LY367385) but increased by mGlu5 blockade (MTEP). NMDAR blockade (AVP) increased overall translation in drug-naïve and saline control rats but not in cocaine/late withdrawal rats. Cocaine/late withdrawal rats exhibited greater translation of GluA1 (but not GluA2), which was not further affected by NMDAR blockade. CONCLUSIONS Our results suggest that increased GluA1 translation contributes to the elevated homomeric GluA1 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor levels in the NAc that mediate incubation. Additional contributions to incubation-related plasticity may result from loss of the braking influence on translation normally exerted by NMDARs. Apart from elucidating incubation-related adaptations, we found a suppressive effect of mGlu5 on NAc translation regardless of drug exposure, which is opposite to results obtained in the hippocampus and points to heterogeneity of translational regulation between brain regions.
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Affiliation(s)
- Michael T Stefanik
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin School of Medicine and Science, North Chicago, Illinois
| | - Mike Milovanovic
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin School of Medicine and Science, North Chicago, Illinois
| | - Craig T Werner
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin School of Medicine and Science, North Chicago, Illinois
| | - John C G Spainhour
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia
| | - Marina E Wolf
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin School of Medicine and Science, North Chicago, Illinois.
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20
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Chung CYS, Timblin GA, Saijo K, Chang CJ. Versatile Histochemical Approach to Detection of Hydrogen Peroxide in Cells and Tissues Based on Puromycin Staining. J Am Chem Soc 2018; 140:6109-6121. [PMID: 29722974 PMCID: PMC6069982 DOI: 10.1021/jacs.8b02279] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrogen peroxide (H2O2) is a central reactive oxygen species (ROS) that contributes to diseases from obesity to cancer to neurodegeneration but is also emerging as an important signaling molecule. We now report a versatile histochemical approach for detection of H2O2 that can be employed across a broad range of cell and tissue specimens in both healthy and disease states. We have developed a first-generation H2O2-responsive analogue named Peroxymycin-1, which is based on the classic cell-staining molecule puromycin and enables covalent staining of biological samples and retains its signal after fixation. H2O2-mediated boronate cleavage uncages the puromycin aminonucleoside, which leaves a permanent and dose-dependent mark on treated biological specimens that can be detected with high sensitivity and precision through a standard immunofluorescence assay. Peroxymycin-1 is selective and sensitive enough to image both exogenous and endogenous changes in cellular H2O2 levels and can be exploited to profile resting H2O2 levels across a panel of cell lines to distinguish metastatic, invasive cancer cells from less invasive cancer and nontumorigenic counterparts, based on correlations with ROS status. Moreover, we establish that Peroxymycin-1 is an effective histochemical probe for in vivo H2O2 analysis, as shown through identification of aberrant elevations in H2O2 levels in liver tissues in a murine model of nonalcoholic fatty liver disease, thus demonstrating the potential of this approach for studying disease states and progression associated with H2O2. This work provides design principles that should enable development of a broader range of histochemical probes for biological use that operate via activity-based sensing.
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Affiliation(s)
- Clive Yik-Sham Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Greg A. Timblin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kaoru Saijo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, United States
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21
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Du S, Wang D, Lee JS, Peng B, Ge J, Yao SQ. Cell type-selective imaging and profiling of newly synthesized proteomes by using puromycin analogues. Chem Commun (Camb) 2018; 53:8443-8446. [PMID: 28702584 DOI: 10.1039/c7cc04536k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have developed a versatile antibody-assisted strategy for the imaging and profiling of newly synthesized proteomes in a cell-specific manner. This strategy remained highly selective even in heterogeneous co-cultured cells, thus enabling labeling and enrichment of nascent proteomes from targeted cells without the need for physical separation.
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Affiliation(s)
- Shubo Du
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jun-Seok Lee
- Molecular Recognition Research Center & Department of Biological Chemistry, KIST-School Korea Institute of Science & Technology, South Korea
| | - Bo Peng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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22
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Nagelreiter F, Coats MT, Klanert G, Gludovacz E, Borth N, Grillari J, Schosserer M. OPP Labeling Enables Total Protein Synthesis Quantification in CHO Production Cell Lines at the Single-Cell Level. Biotechnol J 2018; 13:e1700492. [PMID: 29369524 DOI: 10.1002/biot.201700492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 01/19/2018] [Indexed: 01/21/2023]
Abstract
Accurate measurement of global and specific protein synthesis rates is becoming increasingly important, especially in the context of biotechnological applications such as process modeling or selection of production cell clones. While quantification of total protein translation across whole cell populations is easily achieved, methods that are capable of tracking population dynamics at the single-cell level are still lacking. To address this need, we apply O-propargyl-puromycin (OPP) labeling to assess total protein synthesis in single recombinant Chinese hamster ovary (CHO) cells by flow cytometry. Thereby we demonstrate that global protein translation rates slightly increase with progression through the cell cycle during exponential growth. Stable CHO cell lines producing recombinant protein display similar levels of total protein synthesis as their parental CHO host cell line. Global protein translation does not correlate with intracellular product content of three model proteins, but the host cell line with high transient productivity has a higher OPP signal. This indicates that production cell lines with increased overall protein synthesis capacity can be identified by our method at the single-cell level. In conclusion, OPP-labeling allows rapid and reproducible assessment of global protein synthesis in single CHO cells, and can be multiplexed with DNA staining or any type of immunolabeling of specific proteins or markers for organelles.
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Affiliation(s)
- Fabian Nagelreiter
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Michael T Coats
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Gerald Klanert
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Elisabeth Gludovacz
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria.,Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria.,ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria.,Christian Doppler Laboratory for Biotechnology of Skin Aging, Vienna, Austria.,Evercyte GmbH, Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
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23
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Guo H, Li Z. Developments of bioorthogonal handle-containing photo-crosslinkers for photoaffinity labeling. MEDCHEMCOMM 2017; 8:1585-1591. [PMID: 30108869 PMCID: PMC6071706 DOI: 10.1039/c7md00217c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/14/2017] [Indexed: 01/14/2023]
Abstract
Photoaffinity labeling (PAL) has been widely applied in various research areas such as medicinal chemistry, chemical biology and structural biology, owing to its capability of investigating non-covalent ligand-protein interactions under native environments and elucidating protein structures, functions etc. One important application of this technique is to use affinity-based proteome profiling (AfBP) coupled with bioimaging for profiling drug-target interactions in situ. In order to accurately report drug-target interactions via these approaches, several considerations as follows need to be made: (1) maximally retaining bioactivities of photoprobes upon functionalization with a photoreactive group and a reporter tag from a parental compound; (2) performing proteome profiling and imaging in situ simultaneously, to monitor drug-target interactions in different manners; and (3) developing excellent photo-crosslinkers capable of photo-crosslinking and fluorescence turn-on at the same time. With these considerations in mind, we have developed three versions of "minimalist" bioorthogonal handle-containing photo-crosslinkers (L3-L6) during the years and successfully applied them in all kinds of small bioactive molecules for protein labeling and cellular imaging studies. In this mini-review, the features and functions of these linkers are specifically highlighted and summarized.
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Affiliation(s)
- Haijun Guo
- College of Pharmacy , Jinan University , Guangzhou , 510632 China .
| | - Zhengqiu Li
- College of Pharmacy , Jinan University , Guangzhou , 510632 China .
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24
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry; Institute of Molecular Functional Materials; Chemical Biology Centre and Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong China
- HKU Shenzhen Institute of Research and Innovation; Shenzhen 518053 China
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25
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Fung SK, Zou T, Cao B, Lee PY, Fung YME, Hu D, Lok CN, Che CM. Cyclometalated Gold(III) Complexes Containing N-Heterocyclic Carbene Ligands Engage Multiple Anti-Cancer Molecular Targets. Angew Chem Int Ed Engl 2017; 56:3892-3896. [PMID: 28247451 DOI: 10.1002/anie.201612583] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 01/03/2023]
Abstract
Metal N-heterocyclic carbene (NHC) complexes are a promising class of anti-cancer agents displaying potent in vitro and in vivo activities. Taking a multi-faceted approach employing two clickable photoaffinity probes, herein we report the identification of multiple molecular targets for anti-cancer active pincer gold(III) NHC complexes. These complexes display potent and selective cytotoxicity against cultured cancer cells and in vivo anti-tumor activities in mice bearing xenografts of human cervical and lung cancers. Our experiments revealed the specific engagement of the gold(III) complexes with multiple cellular targets, including HSP60, vimentin, nucleophosmin, and YB-1, accompanied by expected downstream mechanisms of action. Additionally, PtII and PdII analogues can also bind the cellular proteins targeted by the gold(III) complexes, uncovering a distinct pincer cyclometalated metal-NHC scaffold in the design of anti-cancer metal medicines with multiple molecular targets.
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Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Pui-Yan Lee
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Di Hu
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
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26
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Guo H, Xu J, Hao P, Ding K, Li Z. Competitive affinity-based proteome profiling and imaging to reveal potential cellular targets of betulinic acid. Chem Commun (Camb) 2017; 53:9620-9623. [DOI: 10.1039/c7cc04190j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Affinity-based proteome profiling (AfBP) coupled with bioimaging to uncover cellular targets of betulinic acid.
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Affiliation(s)
- Haijun Guo
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Jiaqian Xu
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Piliang Hao
- School of Life Science and Technology
- ShanghaiTech University
- Shanghai 201210
- China
| | - Ke Ding
- College of Pharmacy
- Jinan University
- Guangzhou
- China
| | - Zhengqiu Li
- College of Pharmacy
- Jinan University
- Guangzhou
- China
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