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Seinkmane E, Edmondson A, Peak-Chew SY, Zeng A, Rzechorzek NM, James NR, West J, Munns J, Wong DC, Beale AD, O'Neill JS. Circadian regulation of macromolecular complex turnover and proteome renewal. EMBO J 2024; 43:2813-2833. [PMID: 38778155 PMCID: PMC11217436 DOI: 10.1038/s44318-024-00121-5] [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: 11/03/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.
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Affiliation(s)
- Estere Seinkmane
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anna Edmondson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Aiwei Zeng
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nina M Rzechorzek
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan R James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - James West
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jack Munns
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Cs Wong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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2
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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3
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. CELL REPORTS METHODS 2024; 4:100713. [PMID: 38412836 PMCID: PMC10921036 DOI: 10.1016/j.crmeth.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Protein translational control is critical for ensuring that the fetus develops correctly and that necessary organs and tissues are formed and functional. We developed an in utero method to quantify tissue-specific protein dynamics by monitoring amino acid incorporation into the proteome after pulse injection. Fetuses of pregnant mice were injected with isotopically labeled lysine and arginine via the vitelline vein at various embyonic days, and organs and tissues were harvested. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates were calculated between 3.81E-5 and 0.424 h-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver vs. brain); however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates, which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara E Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William H Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA.
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4
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Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
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Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
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5
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Borteçen T, Müller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. Nat Commun 2023; 14:8237. [PMID: 38086798 PMCID: PMC10716174 DOI: 10.1038/s41467-023-43919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight into the proteomic response that is elicited by specific cues. This can be investigated by pulse-labeling of cells with clickable and stable-isotope-coded amino acids for the enrichment and mass spectrometric characterization of newly synthesized proteins (NSPs), however convoluted protocols prohibit their routine application. Here we report the optimization of multiple steps in sample preparation, mass spectrometry and data analysis, and we integrate them into a semi-automated workflow for the quantitative analysis of the newly synthesized proteome (QuaNPA). Reduced input requirements and data-independent acquisition (DIA) enable the analysis of triple-SILAC-labeled NSP samples, with enhanced throughput while featuring high quantitative accuracy. We apply QuaNPA to investigate the time-resolved cellular response to interferon-gamma (IFNg), observing rapid induction of targets 2 h after IFNg treatment. QuaNPA provides a powerful approach for large-scale investigation of NSPs to gain insight into complex cellular processes.
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Affiliation(s)
- Toman Borteçen
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Torsten Müller
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany.
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6
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Han X, Beck K, Bürgmann H, Frey B, Stierli B, Frossard A. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front Microbiol 2023; 14:1279041. [PMID: 37942081 PMCID: PMC10627841 DOI: 10.3389/fmicb.2023.1279041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.
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Affiliation(s)
- Xingguo Han
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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7
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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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8
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Frates ES, Spietz RL, Silverstein MR, Girguis P, Hatzenpichler R, Marlow JJ. Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment. Front Microbiol 2023; 14:1235906. [PMID: 37744927 PMCID: PMC10512730 DOI: 10.3389/fmicb.2023.1235906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.
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Affiliation(s)
- Erin S. Frates
- Department of Biology, Boston University, Boston, MA, United States
| | - Rachel L. Spietz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | | | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
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9
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Jecmen T, Tuzhilkin R, Sulc M. Photo-Methionine, Azidohomoalanine and Homopropargylglycine Are Incorporated into Newly Synthesized Proteins at Different Rates and Differentially Affect the Growth and Protein Expression Levels of Auxotrophic and Prototrophic E. coli in Minimal Medium. Int J Mol Sci 2023; 24:11779. [PMID: 37511538 PMCID: PMC10380393 DOI: 10.3390/ijms241411779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Residue-specific incorporation of non-canonical amino acids (ncAAs) introduces bio-orthogonal functionalities into proteins. As such, this technique is applied in protein characterization and quantification. Here, we studied protein expression with three methionine analogs, namely photo-methionine (pMet), azidohomoalanine (Aha) and homopropargylglycine (Hpg), in prototrophic E. coli BL-21 and auxotrophic E. coli B834 to maximize ncAA content, thereby assessing the effect of ncAAs on bacterial growth and the expression of cytochrome b5 (b5M46), green fluorescence protein (MBP-GFP) and phage shock protein A. In auxotrophic E. coli, ncAA incorporation ranged from 50 to 70% for pMet and reached approximately 50% for Aha, after 26 h expression, with medium and low expression levels of MBP-GFP and b5M46, respectively. In the prototrophic strain, by contrast, the protein expression levels were higher, albeit with a sharp decrease in the ncAA content after the first hours of expression. Similar expression levels and 70-80% incorporation rates were achieved in both bacterial strains with Hpg. Our findings provide guidance for expressing proteins with a high content of ncAAs, highlight pitfalls in determining the levels of methionine replacement by ncAAs by MALDI-TOF mass spectrometry and indicate a possible systematic bias in metabolic labeling techniques using Aha or Hpg.
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Affiliation(s)
- Tomas Jecmen
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
| | - Roman Tuzhilkin
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
| | - Miroslav Sulc
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
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10
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Ignacio BJ, Dijkstra J, Mora N, Slot EFJ, van Weijsten MJ, Storkebaum E, Vermeulen M, Bonger KM. THRONCAT: metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog. Nat Commun 2023; 14:3367. [PMID: 37291115 PMCID: PMC10250548 DOI: 10.1038/s41467-023-39063-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Profiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insights into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine- or puromycin analogs allow for the selective visualization and enrichment of newly synthesized proteins. However, their applications are limited as they often require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a threonine-derived non-canonical amino acid tagging method based on the bioorthogonal threonine analog β-ethynylserine (βES) that enables efficient labeling of the nascent proteome in complete growth media within minutes. We use THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profile immediate proteome dynamics of B-cells in response to B-cell receptor activation simply by adding βES to the culture medium, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in specific cell types in vivo.
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Affiliation(s)
- Bob J Ignacio
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Jelmer Dijkstra
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalia Mora
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Erik F J Slot
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Margot J van Weijsten
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kimberly M Bonger
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands.
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11
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Yin K, Tong M, Suttapitugsakul S, Xu S, Wu R. Global quantification of newly synthesized proteins reveals cell type- and inhibitor-specific effects on protein synthesis inhibition. PNAS NEXUS 2023; 2:pgad168. [PMID: 37275259 PMCID: PMC10235912 DOI: 10.1093/pnasnexus/pgad168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
Manipulation of protein synthesis is commonly applied to uncover protein functions and cellular activities. Multiple inhibitors with distinct mechanisms have been widely investigated and employed in bio-related research, but it is extraordinarily challenging to measure and evaluate the synthesis inhibition efficiencies of individual proteins by different inhibitors at the proteome level. Newly synthesized proteins are the immediate and direct products of protein synthesis, and thus their comprehensive quantification provides a unique opportunity to study protein inhibition. Here, we systematically investigate protein inhibition and evaluate different popular inhibitors, i.e. cycloheximide, puromycin, and anisomycin, through global quantification of newly synthesized proteins in several types of human cells (A549, MCF-7, Jurkat, and THP-1 cells). The inhibition efficiencies of protein synthesis are comprehensively measured by integrating azidohomoalanine-based protein labeling, selective enrichment, a boosting approach, and multiplexed proteomics. The same inhibitor results in dramatic variation of the synthesis inhibition efficiencies for different proteins in the same cells, and each inhibitor exhibits unique preferences. Besides cell type- and inhibitor-specific effects, some universal rules are unraveled. For instance, nucleolar and ribosomal proteins have relatively higher inhibition efficiencies in every type of cells treated with each inhibitor. Moreover, proteins intrinsically resistant or sensitive to the inhibition are identified and found to have distinct functions. Systematic investigation of protein synthesis inhibition in several types of human cells by different inhibitors provides valuable information about the inhibition of protein synthesis, advancing our understanding of inhibiting protein synthesis.
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Affiliation(s)
| | | | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- To whom correspondence should be addressed:
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12
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541242. [PMID: 37293076 PMCID: PMC10245746 DOI: 10.1101/2023.05.18.541242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein translational control is highly regulated step in the gene expression program during mammalian development that is critical for ensuring that the fetus develops correctly and that all of the necessary organs and tissues are formed and functional. Defects in protein expression during fetal development can lead to severe developmental abnormalities or premature death. Currently, quantitative techniques to monitor protein synthesis rates in a developing fetus (in utero) are limited. Here, we developed a novel in utero stable isotope labeling approach to quantify tissue-specific protein dynamics of the nascent proteome during mouse fetal development. Fetuses of pregnant C57BL/6J mice were injected with isotopically labeled lysine (Lys8) and arginine (Arg10) via the vitelline vein at various gestational days. After treatment, fetal organs/tissues including brain, liver, lung, and heart were harvested for sample preparation and proteomic analysis. We show that the mean incorporation rate for injected amino acids into all organs was 17.50 ± 0.6%. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates (kobs) were calculated between 3.81E-5 and 0.424 hour-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver versus brain), however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Contributed equally to this work
| | - Barbara E. Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Contributed equally to this work
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - William H. Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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13
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Villalobos-Cantor S, Barrett RM, Condon AF, Arreola-Bustos A, Rodriguez KM, Cohen MS, Martin I. Rapid cell type-specific nascent proteome labeling in Drosophila. eLife 2023; 12:83545. [PMID: 37092974 PMCID: PMC10125018 DOI: 10.7554/elife.83545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
Controlled protein synthesis is required to regulate gene expression and is often carried out in a cell type-specific manner. Protein synthesis is commonly measured by labeling the nascent proteome with amino acid analogs or isotope-containing amino acids. These methods have been difficult to implement in vivo as they require lengthy amino acid replacement procedures. O-propargyl-puromycin (OPP) is a puromycin analog that incorporates into nascent polypeptide chains. Through its terminal alkyne, OPP can be conjugated to a fluorophore-azide for directly visualizing nascent protein synthesis, or to a biotin-azide for capture and identification of newly-synthesized proteins. To achieve cell type-specific OPP incorporation, we developed phenylacetyl-OPP (PhAc-OPP), a puromycin analog harboring an enzyme-labile blocking group that can be removed by penicillin G acylase (PGA). Here, we show that cell type-specific PGA expression in Drosophila can be used to achieve OPP labeling of newly-synthesized proteins in targeted cell populations within the brain. Following a brief 2 hr incubation of intact brains with PhAc-OPP, we observe robust imaging and affinity purification of OPP-labeled nascent proteins in PGA-targeted cell populations. We apply this method to show a pronounced age-related decline in neuronal protein synthesis in the fly brain, demonstrating the capability of PhAc-OPP to quantitatively capture in vivo protein synthesis states. This method, which we call POPPi (PGA-dependent OPP incorporation), should be applicable for rapidly visualizing protein synthesis and identifying nascent proteins synthesized under diverse physiological and pathological conditions with cellular specificity in vivo.
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Affiliation(s)
- Stefanny Villalobos-Cantor
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Ruth M Barrett
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alec F Condon
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alicia Arreola-Bustos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Kelsie M Rodriguez
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
- Parkinson Center of Oregon, Oregon Health and Science University, Portland, United States
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14
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Steinert ND, Jorgenson KW, Lin KH, Hermanson JB, Lemens JL, Hornberger TA. A novel method for visualizing in-vivo rates of protein degradation provides insight into how TRIM28 regulates muscle size. iScience 2023; 26:106526. [PMID: 37070069 PMCID: PMC10105291 DOI: 10.1016/j.isci.2023.106526] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle size is controlled by the balance between protein synthesis and protein degradation. Given the essential role of skeletal muscle in maintaining a high quality of life, understanding the mechanisms that modulate this balance are of critical importance. Previously, we demonstrated that muscle-specific knockout of TRIM28 reduces muscle size and function and in the current study, we discovered that this effect is associated with an increase in protein degradation and a dramatic reduction in the expression of Mettl21c. Importantly, we also determined that overexpression of Mettl21c is sufficient to induce hypertrophy in both control and TRIM28 knockout muscles. Moreover, we developed a simple pulse-chase biorthogonal non-canonical amino acid tagging technique that enabled us to visualize the in vivo rate of protein degradation, and with this technique were able to conclude that the hypertrophic effect of Mettl21c is due, at least in part, to an inhibition of protein degradation.
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Affiliation(s)
- Nathaniel D. Steinert
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Kent W. Jorgenson
- Department of Molecular and Cellular Pharmacology, University of Wisconsin - Madison, Madison, WI, USA
- School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, USA
| | - Kuan-Hung Lin
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake B. Hermanson
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake L. Lemens
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
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15
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Zimbelman AR, Wong B, Murray CH, Wolf ME, Stefanik MT. Dopamine D1 and NMDA receptor co-regulation of protein translation in cultured nucleus accumbens neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535293. [PMID: 37034633 PMCID: PMC10081306 DOI: 10.1101/2023.04.02.535293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Protein translation is essential for some forms of synaptic plasticity. We used nucleus accumbens (NAc) medium spiny neurons (MSN), co-cultured with cortical neurons to restore excitatory synapses, to examine whether dopamine modulates protein translation in NAc MSN. FUNCAT was used to measure translation in MSNs under basal conditions and after disinhibiting excitatory transmission using the GABAA receptor antagonist bicuculline (2 hr). Under basal conditions, translation was not altered by the D1-class receptor (D1R) agonist SKF81297 or the D2-class receptor (D2R) agonist quinpirole. Bicuculline alone robustly increased translation. This was reversed by quinpirole but not SKF81297. It was also reversed by co-incubation with the D1R antagonist SCH23390, but not the D2R antagonist eticlopride, suggesting dopaminergic tone at D1Rs. This was surprising because no dopamine neurons are present. An alternative explanation is that bicuculline activates translation by increasing glutamate tone at NMDA receptors (NMDAR) within D1R/NMDAR heteromers, which have been described in other cell types. Supporting this, immunocytochemistry and proximity ligation assays revealed D1/NMDAR heteromers on NAc cells both in vitro and in vivo. Further, bicuculline's effect was reversed to the same extent by SCH23390 alone, the NMDAR antagonist APV alone, or SCH23390+APV. These results suggest that: 1) excitatory synaptic transmission stimulates translation in NAc MSNs, 2) this is opposed when glutamate activates D1R/NMDAR heteromers, even in the absence of dopamine, and 3) antagonist occupation of D1Rs within the heteromers prevents their activation. Our study is the first to suggest a role for D2 receptors and D1R/NMDAR heteromers in regulating protein translation.
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Affiliation(s)
- Alexa R. Zimbelman
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
| | - Benjamin Wong
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
| | - Conor H. Murray
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- Present address: Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL
| | - Marina E. Wolf
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- These authors contributed equally
- Present address: Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97212
| | - Michael T. Stefanik
- Department of Psychology and Neuroscience, North Central College, Naperville, IL 60540
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064
- These authors contributed equally
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16
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Saleh AM, VanDyk TG, Jacobson KR, Khan SA, Calve S, Kinzer-Ursem TL. An Integrative Biology Approach to Quantify the Biodistribution of Azidohomoalanine In Vivo. Cell Mol Bioeng 2023; 16:99-115. [PMID: 37096070 PMCID: PMC10121978 DOI: 10.1007/s12195-023-00760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Background Identification and quantitation of newly synthesized proteins (NSPs) are critical to understanding protein dynamics in development and disease. Probing the nascent proteome can be achieved using non-canonical amino acids (ncAAs) to selectively label the NSPs utilizing endogenous translation machinery, which can then be quantitated with mass spectrometry. We have previously demonstrated that labeling the in vivo murine proteome is feasible via injection of azidohomoalanine (Aha), an ncAA and methionine (Met) analog, without the need for Met depletion. Aha labeling can address biological questions wherein temporal protein dynamics are significant. However, accessing this temporal resolution requires a more complete understanding of Aha distribution kinetics in tissues. Results To address these gaps, we created a deterministic, compartmental model of the kinetic transport and incorporation of Aha in mice. Model results demonstrate the ability to predict Aha distribution and protein labeling in a variety of tissues and dosing paradigms. To establish the suitability of the method for in vivo studies, we investigated the impact of Aha administration on normal physiology by analyzing plasma and liver metabolomes following various Aha dosing regimens. We show that Aha administration induces minimal metabolic alterations in mice. Conclusions Our results demonstrate that we can reproducibly predict protein labeling and that the administration of this analog does not significantly alter in vivo physiology over the course of our experimental study. We expect this model to be a useful tool to guide future experiments utilizing this technique to study proteomic responses to stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00760-4.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
| | - Shaheryar A. Khan
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Center, 427 UCB, Boulder, CO 80309 USA
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
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17
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Combining Metabolic Pulse Labeling and Quantitative Proteomics to Monitor Protein Synthesis Upon Viral Infection. Methods Mol Biol 2022; 2610:149-165. [PMID: 36534289 DOI: 10.1007/978-1-0716-2895-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viruses like influenza A virus (IAV) hijack host cells in order to replicate. To actively and abundantly synthesize viral proteins, they reprogram the cellular transcriptional and translational landscape. Here, we present a proteomic approach that allows us to quantify the differences in host and viral protein synthesis comparatively for different strains of IAV. The method is based on combining quantitative proteomics using stable isotope labelling by amino acids in cell culture (SILAC) and bioorthogonal labeling with methionine analogs. This methodology accurately quantifies synthesis of host and viral proteins with high temporal resolution and faithfully detects global changes in cellular translation capacity. It thus provides unique insights into the dynamics of protein synthesis as the infection progresses.
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18
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Hu M, Ling Z, Ren X. Extracellular matrix dynamics: tracking in biological systems and their implications. J Biol Eng 2022; 16:13. [PMID: 35637526 PMCID: PMC9153193 DOI: 10.1186/s13036-022-00292-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/11/2022] [Indexed: 12/23/2022] Open
Abstract
The extracellular matrix (ECM) constitutes the main acellular microenvironment of cells in almost all tissues and organs. The ECM not only provides mechanical support, but also mediates numerous biochemical interactions to guide cell survival, proliferation, differentiation, and migration. Thus, better understanding the everchanging temporal and spatial shifts in ECM composition and structure – the ECM dynamics – will provide fundamental insight regarding extracellular regulation of tissue homeostasis and how tissue states transition from one to another during diverse pathophysiological processes. This review outlines the mechanisms mediating ECM-cell interactions and highlights how changes in the ECM modulate tissue development and disease progression, using the lung as the primary model organ. We then discuss existing methodologies for revealing ECM compositional dynamics, with a particular focus on tracking newly synthesized ECM proteins. Finally, we discuss the ramifications ECM dynamics have on tissue engineering and how to implement spatial and temporal specific extracellular microenvironments into bioengineered tissues. Overall, this review communicates the current capabilities for studying native ECM dynamics and delineates new research directions in discovering and implementing ECM dynamics to push the frontier forward.
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Affiliation(s)
- Michael Hu
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Zihan Ling
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
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19
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Zhang Z, Zeng M, Han X, Hou Z, Wang Z, Su T, Zhao W, Liu J, Liu H. A nascent protein labeling strategy disclosed mitochondrial proteomic responses in punicalagin intervened insulin resistance of HepG2 cells. Food Funct 2022; 13:1180-1191. [PMID: 35018929 DOI: 10.1039/d1fo02749b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Insulin resistance (IR), as a common pathophysiological basis, is closely related to a variety of metabolic diseases, such as obesity and diabetes. IR is often accompanied by mitochondrial dysfunction which could be induced by a high fat diet. Punicalagin (PU), a natural compound extracted from pomegranate, could ameliorate palmitate-induced IR. However, the underlying mechanisms are not well known. We propose that understanding the proteomic response of mitochondria may help define the mechanisms of PU in the prevention of IR. Most of the mitochondrial proteins are encoded by nuclear genes and transported from cytoplasm. To distinguish newly incorporated proteins responding to stimuli from pre-existing mitochondrial proteome, nascent proteins in HepG2 cells were pulse labeled by an amino acid analog L-azidohomoalanine. Nascent nuclear encoded mitochondrial proteins were enriched by click reaction followed by mass detection. Our data showed that PU increased nuclear encoded protein incorporation to mitochondria in general though the total protein levels remained immobile. To decipher this phenomenon, we tested the protein and mRNA levels of genes related to mitophagy and mitochondrial biogenesis and found that the mitochondrial turnover was accelerated by PU treatment. By the nascent protein labeling strategy and pathway analysis, we enriched the newly incorporated proteins of mitochondria for responding to PU treatment and found that PU induced nascent protein incorporation into mitochondria and enhanced mitochondrial turnover. These findings demonstrate that PU prevents IR by targeting mitochondria, and thus, is an effective natural nutrient beneficial for mitochondrial turnover.
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Affiliation(s)
- Zhengyi Zhang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Mengqi Zeng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Xiao Han
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Zhen Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Tian Su
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Wei Zhao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
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20
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Kern M, Ferreira-Cerca S. Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea. Methods Mol Biol 2022; 2533:229-246. [PMID: 35796992 PMCID: PMC9761519 DOI: 10.1007/978-1-0716-2501-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .
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Affiliation(s)
- Michael Kern
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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21
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Ke X, Li C, Luo D, Wang T, Liu Y, Tan Z, Du M, He Z, Wang H, Zheng Z, Zhang Y. Metabolic labeling of enterovirus 71 with quantum dots for the study of virus receptor usage. J Nanobiotechnology 2021; 19:295. [PMID: 34583708 PMCID: PMC8477995 DOI: 10.1186/s12951-021-01046-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
Fluorescent labeling and dynamic tracking is a powerful tool for exploring virus infection mechanisms. However, for small-sized viruses, virus tracking studies are usually hindered by a lack of appropriate labeling methods that do not dampen virus yield or infectivity. Here, we report a universal strategy for labeling viruses with chemical dyes and Quantum dots (QDs). Enterovirus 71 (EV71) was produced in a cell line that stably expresses a mutant methionyl-tRNA synthetase (MetRS), which can charge azidonorleucine (ANL) to the methionine sites of viral proteins during translation. Then, the ANL-containing virus was easily labeled with DBCO-AF647 and DBCO-QDs. The labeled virus shows sufficient yield and no obvious decrease in infectivity and can be used for imaging the virus entry process. Using the labeled EV71, different functions of scavenger receptor class B, member 2 (SCARB2), and heparan sulfate (HS) in EV71 infection were comparatively studied. The cell entry process of a strong HS-binding EV71 strain was investigated by real-time dynamic visualization of EV71-QDs in living cells. Taken together, our study described a universal biocompatible virus labeling method, visualized the dynamic viral entry process, and reported details of the receptor usage of EV71.
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Affiliation(s)
- Xianliang Ke
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Chunjie Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Dan Luo
- Department of Gastroenterology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430015, Wuhan, China
| | - Ting Wang
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430100, China
| | - Yan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhongyuan Tan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Mingyuan Du
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, China
| | - Hanzhong Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhenhua Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yuan Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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22
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Tivendale ND, Fenske R, Duncan O, Millar AH. In vivo homopropargylglycine incorporation enables sampling, isolation and characterization of nascent proteins from Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1260-1276. [PMID: 34152049 DOI: 10.1111/tpj.15376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Determining which proteins are actively synthesized at a given point in time and extracting a representative sample for analysis is important to understand plant responses. Here we show that the methionine (Met) analogue homopropargylglycine (HPG) enables Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT) of a small sample of the proteins being synthesized in Arabidopsis plants or cell cultures, facilitating their click-chemistry enrichment for analysis. The sites of HPG incorporation could be confirmed by peptide mass spectrometry at Met sites throughout protein amino acid sequences and correlation with independent studies of protein labelling with 15 N verified the data. We provide evidence that HPG-based BONCAT tags a better sample of nascent plant proteins than azidohomoalanine (AHA)-based BONCAT in Arabidopsis and show that the AHA induction of Met metabolism and greater inhibition of cell growth rate than HPG probably limits AHA incorporation at Met sites in Arabidopsis. We show HPG-based BONCAT provides a verifiable method for sampling, which plant proteins are being synthesized at a given time point and enriches a small portion of new protein molecules from the bulk protein pool for identification, quantitation and subsequent biochemical analysis. Enriched nascent polypeptides samples were found to contain significantly fewer common post-translationally modified residues than the same proteins from whole plant extracts, providing evidence for age-related accumulation of post-translational modifications in plants.
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Affiliation(s)
- Nathan D Tivendale
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Owen Duncan
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
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23
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Marlow J, Spietz R, Kim K, Ellisman M, Girguis P, Hatzenpichler R. Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environ Microbiol 2021; 23:4756-4777. [PMID: 34346142 PMCID: PMC8456820 DOI: 10.1111/1462-2920.15667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/08/2021] [Indexed: 01/04/2023]
Abstract
Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%-22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.
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Affiliation(s)
- Jeffrey Marlow
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Rachel Spietz
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
| | - Keun‐Young Kim
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
| | - Mark Ellisman
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
- Department of PharmacologyUniversity of CaliforniaSan DiegoLa JollaCalifornia92161USA
| | - Peter Girguis
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
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24
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Amino Acid Analog Induces Stress Response in Marine Synechococcus. Appl Environ Microbiol 2021; 87:e0020021. [PMID: 33990310 DOI: 10.1128/aem.00200-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Characterizing the cell-level metabolic trade-offs that phytoplankton exhibit in response to changing environmental conditions is important for predicting the impact of these changes on marine food web dynamics and biogeochemical cycling. The time-selective proteome-labeling approach, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to provide insight into differential allocation of resources at the cellular level, especially when coupled with proteomics. However, the application of this technique in marine phytoplankton remains limited. We demonstrate that the marine cyanobacteria Synechococcus sp. and two groups of eukaryotic algae take up the modified amino acid l-homopropargylglycine (HPG), suggesting that BONCAT can be used to detect translationally active phytoplankton. However, the impact of HPG addition on growth dynamics varied between groups of phytoplankton. In addition, proteomic analysis of Synechococcus cells grown with HPG revealed a physiological shift in nitrogen metabolism, general protein stress, and energy production, indicating a potential limitation for the use of BONCAT in understanding the cell-level response of Synechococcus sp. to environmental change. Variability in HPG sensitivity between algal groups and the impact of HPG on Synechococcus physiology indicates that particular considerations should be taken when applying this technique to other marine taxa or mixed marine microbial communities. IMPORTANCE Phytoplankton form the base of the marine food web and substantially impact global energy and nutrient flow. Marine picocyanobacteria of the genus Synechococcus comprise a large portion of phytoplankton biomass in the ocean and therefore are important model organisms. The technical challenges of environmental proteomics in mixed microbial communities have limited our ability to detect the cell-level adaptations of phytoplankton communities to a changing environment. The proteome labeling technique, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to address some of these challenges by simplifying proteomic analyses. This study explores the ability of marine phytoplankton to take up the modified amino acid, l-homopropargylglycine (HPG), required for BONCAT, and investigates the proteomic response of Synechococcus to HPG. We not only demonstrate that cyanobacteria can take up HPG but also highlight the physiological impact of HPG on Synechococcus, which has implications for future applications of this technique in the marine environment.
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25
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Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M. One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife 2021; 10:59303. [PMID: 33594971 PMCID: PMC7932693 DOI: 10.7554/elife.59303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
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Affiliation(s)
| | | | | | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Daniele Peroni
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Romina Belli
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jacopo Zasso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
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26
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Narayanan N, Calve S. Extracellular matrix at the muscle - tendon interface: functional roles, techniques to explore and implications for regenerative medicine. Connect Tissue Res 2021; 62:53-71. [PMID: 32856502 PMCID: PMC7718290 DOI: 10.1080/03008207.2020.1814263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The muscle-tendon interface is an anatomically specialized region that is involved in the efficient transmission of force from muscle to tendon. Due to constant exposure to loading, the interface is susceptible to injury. Current treatment methods do not meet the socioeconomic demands of reduced recovery time without compromising the risk of reinjury, requiring the need for developing alternative strategies. The extracellular matrix (ECM) present in muscle, tendon, and at the interface of these tissues consists of unique molecules that play significant roles in homeostasis and repair. Better, understanding the function of the ECM during development, injury, and aging has the potential to unearth critical missing information that is essential for accelerating the repair at the muscle-tendon interface. Recently, advanced techniques have emerged to explore the ECM for identifying specific roles in musculoskeletal biology. Simultaneously, there is a tremendous increase in the scope for regenerative medicine strategies to address the current clinical deficiencies. Advancements in ECM research can be coupled with the latest regenerative medicine techniques to develop next generation therapies that harness ECM for treating defects at the muscle-tendon interface. The current work provides a comprehensive review on the role of muscle and tendon ECM to provide insights about the role of ECM in the muscle-tendon interface and discusses the latest research techniques to explore the ECM to gathered information for developing regenerative medicine strategies.
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Affiliation(s)
- Naagarajan Narayanan
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Drive, Boulder, Colorado 80309 – 0427
| | - Sarah Calve
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Drive, Boulder, Colorado 80309 – 0427
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27
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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28
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McClatchy DB, Martínez-Bartolomé S, Gao Y, Lavallée-Adam M, Yates JR. Quantitative analysis of global protein stability rates in tissues. Sci Rep 2020; 10:15983. [PMID: 32994440 PMCID: PMC7524747 DOI: 10.1038/s41598-020-72410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Protein degradation is an essential mechanism for maintaining proteostasis in response to internal and external perturbations. Disruption of this process is implicated in many human diseases. We present a new technique, QUAD (Quantification of Azidohomoalanine Degradation), to analyze the global degradation rates in tissues using a non-canonical amino acid and mass spectrometry. QUAD analysis reveals that protein stability varied within tissues, but discernible trends in the data suggest that cellular environment is a major factor dictating stability. Within a tissue, different organelles and protein functions were enriched with different stability patterns. QUAD analysis demonstrated that protein stability is enhanced with age in the brain but not in the liver. Overall, QUAD allows the first global quantitation of protein stability rates in tissues, which will allow new insights and hypotheses in basic and translational research.
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Affiliation(s)
- Daniel B McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Yu Gao
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Mathieu Lavallée-Adam
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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29
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Abstract
The mammalian target of rapamycin and the integrated stress response are central cellular hubs regulating translation upon stress. The precise proteins and pathway specificity of translation targets of these pathways remained largely unclear. We recently described a new method for quantitative translation proteomics and found that both pathways control translation of the same sets of proteins.
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Affiliation(s)
- Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt Am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt Am Main, Germany.,Frankfurt Cancer Institute, Frankfurt Am Main, Germany.,Cardio-Pulmonary Institute, Frankfurt Am Main, Germany
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30
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Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun 2020; 11:3244. [PMID: 32591520 PMCID: PMC7320153 DOI: 10.1038/s41467-020-17010-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets. Here the authors describe PhosID, an enrichment strategy using phosphonate-handles, that combines click chemistry and IMAC-based phospho-enrichment for quantitative proteomics analysis of newly synthesized proteins.
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Affiliation(s)
- Fleur Kleinpenning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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31
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Valentini TD, Lucas SK, Binder KA, Cameron LC, Motl JA, Dunitz JM, Hunter RC. Bioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota. Nat Commun 2020; 11:2287. [PMID: 32385294 PMCID: PMC7210995 DOI: 10.1038/s41467-020-16163-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Culture-independent studies of cystic fibrosis lung microbiota have provided few mechanistic insights into the polymicrobial basis of disease. Deciphering the specific contributions of individual taxa to CF pathogenesis requires comprehensive understanding of their ecophysiology at the site of infection. We hypothesize that only a subset of CF microbiota are translationally active and that these activities vary between subjects. Here, we apply bioorthogonal non-canonical amino acid tagging (BONCAT) to visualize and quantify bacterial translational activity in expectorated sputum. We report that the percentage of BONCAT-labeled (i.e. active) bacterial cells varies substantially between subjects (6-56%). We use fluorescence-activated cell sorting (FACS) and genomic sequencing to assign taxonomy to BONCAT-labeled cells. While many abundant taxa are indeed active, most bacterial species detected by conventional molecular profiling show a mixed population of both BONCAT-labeled and unlabeled cells, suggesting heterogeneous growth rates in sputum. Differentiating translationally active subpopulations adds to our evolving understanding of CF lung disease and may help guide antibiotic therapies targeting bacteria most likely to be susceptible.
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Affiliation(s)
- Talia D Valentini
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN, 55455, United States
| | - Sarah K Lucas
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN, 55455, United States
| | - Kelsey A Binder
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN, 55455, United States
| | - Lydia C Cameron
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN, 55455, United States
| | - Jason A Motl
- Academic Health Center, University Flow Cytometry Resource, University of Minnesota, 6th St SE, Minneapolis, MN, 55455, United States
| | - Jordan M Dunitz
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, University of Minnesota, 420 Delaware St. SE, Minneapolis, MN, 55455, United States
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN, 55455, United States.
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32
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Steward KF, Eilers B, Tripet B, Fuchs A, Dorle M, Rawle R, Soriano B, Balasubramanian N, Copié V, Bothner B, Hatzenpichler R. Metabolic Implications of Using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for Tracking Protein Synthesis. Front Microbiol 2020; 11:197. [PMID: 32117186 PMCID: PMC7031258 DOI: 10.3389/fmicb.2020.00197] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) is a powerful tool for tracking protein synthesis on the level of single cells within communities and whole organisms. A basic premise of BONCAT is that the non-canonical amino acids (NCAA) used to track translational activity do not significantly alter cellular physiology. If the NCAA would induce changes in the metabolic state of cells, interpretation of BONCAT studies could be challenging. To address this knowledge-gap, we have used a global metabolomics analyses to assess the intracellular effects of NCAA incorporation. Two NCAA were tested: L-azidohomoalanine (AHA) and L-homopropargylglycine (HPG); L-methionine (MET) was used as a minimal stress baseline control. Liquid Chromatography Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance (NMR) were used to characterize intracellular metabolite profiles of Escherichia coli cultures, with multivariate statistical analysis using XCMS and MetaboAnalyst. Results show that doping with NCAA induces metabolic changes, however, the metabolic impact was not dramatic. A second set of experiments in which cultures were placed under mild stress to simulate real-world environmental conditions showed a more consistent and more robust perturbation. Pathways that changed include amino acid and protein synthesis, choline and betaine, and the TCA cycle. Globally, these changes were statistically minor, indicating that NCAA are unlikely to exert a significant impact on cells during incorporation. Our results are consistent with previous reports of NCAA doping under replete conditions and extend these results to bacterial growth under environmentally relevant conditions. Our work highlights the power of metabolomics studies in detecting cellular response to growth conditions and the complementarity of NMR and LCMS as omics tools.
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Affiliation(s)
- Katherine F Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Brian Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Amanda Fuchs
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Michael Dorle
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Rachel Rawle
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Berliza Soriano
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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33
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Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbiome function at single cell level. Nat Rev Microbiol 2020; 18:241-256. [PMID: 32055027 DOI: 10.1038/s41579-020-0323-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/14/2022]
Abstract
The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.
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Affiliation(s)
- Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
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34
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Analysis of a fully infectious bio-orthogonally modified human virus reveals novel features of virus cell entry. PLoS Pathog 2019; 15:e1007956. [PMID: 31589653 PMCID: PMC6797222 DOI: 10.1371/journal.ppat.1007956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/17/2019] [Accepted: 09/12/2019] [Indexed: 12/28/2022] Open
Abstract
We report the analysis of a complex enveloped human virus, herpes simplex virus (HSV), assembled after in vivo incorporation of bio-orthogonal methionine analogues homopropargylglycine (HPG) or azidohomoalanine (AHA). We optimised protocols for the production of virions incorporating AHA (termed HSVAHA), identifying conditions which resulted in normal yields of HSV and normal particle/pfu ratios. Moreover we show that essentially every single HSVAHA capsid-containing particle was detectable at the individual particle level by chemical ligation of azide-linked fluorochromes to AHA-containing structural proteins. This was a completely specific chemical ligation, with no capsids assembled under normal methionine-containing conditions detected in parallel. We demonstrate by quantitative mass spectrometric analysis that HSVAHA virions exhibit no qualitative or quantitative differences in the repertoires of structural proteins compared to virions assembled under normal conditions. Individual proteins and AHA incorporation sites were identified in capsid, tegument and envelope compartments, including major essential structural proteins. Finally we reveal novel aspects of entry pathways using HSVAHA and chemical fluorochrome ligation that were not apparent from conventional immunofluorescence. Since ligation targets total AHA-containing protein and peptides, our results demonstrate the presence of abundant AHA-labelled products in cytoplasmic macrodomains and tubules which no longer contain intact particles detectable by immunofluorescence. Although these do not co-localise with lysosomal markers, we propose they may represent sites of proteolytic virion processing. Analysis of HSVAHA also enabled the discrimination from primary entering from secondary assembling virions, demonstrating assembly and second round infection within 6 hrs of initial infection and dual infections of primary and secondary virus in spatially restricted cytoplasmic areas of the same cell. Together with other demonstrated applications e.g., in genome biology, lipid and protein trafficking, this work further exemplifies the utility and potential of bio-orthogonal chemistry for studies in many aspects of virus-host interactions.
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35
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Dynamics of Non-Canonical Amino Acid-Labeled Intra- and Extracellular Proteins in the Developing Mouse. Cell Mol Bioeng 2019; 12:495-509. [PMID: 31719929 DOI: 10.1007/s12195-019-00592-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/17/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction Mapping protein synthesis and turnover during development will provide insight into functional tissue assembly; however, quantitative in vivo characterization has been hindered by a lack of tools. To address this gap, we previously demonstrated murine embryos can be labeled with the non-canonical amino acid azidohomoalanine (Aha), which enables the enrichment and identification of newly synthesized proteins. Using this technique, we now show how protein turnover varies as a function of both time and cellular compartment during murine development. Methods Pregnant C57BL/6 mice were injected with Aha or PBS (control) at different embryonic time points. Aha-labeled proteins from homogenized E12.5 and E15.5 embryos were conjugated with diazo biotin-alkyne, bound to NeutrAvidin beads, selectively released, then processed for either SDS-PAGE or LC-MS/MS. For turnover studies, embryos were harvested 0-48 h after Aha injection at E12.5, separated into different cellular fractions based on solubility, and analyzed via western blotting. Results We developed an enhanced method for isolating Aha-labeled proteins from embryos that minimizes background signal from unlabeled proteins and avidin contamination. Approximately 50% of all identified proteins were found only in Aha samples. Comparing proteins present in both Aha and PBS samples, 90% were > 2-fold enriched in Aha-treated embryos. Furthermore, this method could resolve differences in the Aha-labeled proteome between developmental time points. Newly synthesized Aha-labeled proteins were observed by 3 h and peak labeling was around 6 h. Notably, extracellular matrix and cytoskeletal turnover appeared lower than the cytosolic fraction. Conclusions The methods developed in this work enable the identification and quantification of protein synthesis and turnover in different tissue fractions during development. This will provide insight into functional tissue assembly and ultimately inform the design of regenerative therapies that seek to promote growth and repair.
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36
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Grandi P, Bantscheff M. Advanced proteomics approaches to unravel protein homeostasis. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:99-108. [PMID: 31200865 DOI: 10.1016/j.ddtec.2019.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Quantitative proteomics methods are instrumental in measuring the interplay between protein synthesis and protein degradation in cells and tissues in different conditions and substantially contribute to the understanding of control mechanisms for protein homeostasis. Proteomics and chemoproteomics approaches enable the characterization of small molecule modifiers of protein degradation for therapeutic applications. Here, we review recent developments and applications of mass spectrometry-based (chemo-)proteomics methods for the study of cellular homeostasis.
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Affiliation(s)
- Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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37
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Discovery of NV-5138, the first selective Brain mTORC1 activator. Sci Rep 2019; 9:4107. [PMID: 30858438 PMCID: PMC6412019 DOI: 10.1038/s41598-019-40693-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/20/2019] [Indexed: 12/21/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) has been linked to several important chronic medical conditions many of which are associated with advancing age. A variety of inputs including the amino acid leucine are required for full mTORC1 activation. The cytoplasmic proteins Sestrin1 and Sestrin2 specifically bind to the multiprotein complex GATOR2 and communicate leucine sufficiency to the mTORC1 pathway activation complex. Herein, we report NV-5138, a novel orally bioavailable compound that binds to Sestrin2 and activates mTORC1 both in vitro and in vivo. NV-5138 like leucine transiently activates mTORC1 in several peripheral tissues, but in contrast to leucine uniquely activates this complex in the brain due lack of metabolism and utilization in protein synthesis. As such, NV-5138 will permit the exploration in areas of unmet medical need including neuropsychiatric conditions and cognition which have been linked to the activation status of mTORC1.
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Dermit M, Dodel M, Mardakheh FK. Methods for monitoring and measurement of protein translation in time and space. MOLECULAR BIOSYSTEMS 2018; 13:2477-2488. [PMID: 29051942 PMCID: PMC5795484 DOI: 10.1039/c7mb00476a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Regulation of protein translation constitutes a crucial step in control of gene expression. Here we review recent methods for system-wide monitoring and measurement of protein translation.
Regulation of protein translation constitutes a crucial step in control of gene expression. In comparison to transcriptional regulation, however, translational control has remained a significantly under-studied layer of gene expression. This trend is now beginning to shift thanks to recent advances in next-generation sequencing, proteomics, and microscopy based methodologies which allow accurate monitoring of protein translation rates, from single target messenger RNA molecules to genome-wide scale studies. In this review, we summarize these recent advances, and discuss how they are enabling researchers to study translational regulation in a wide variety of in vitro and in vivo biological systems, with unprecedented depth and spatiotemporal resolution.
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Affiliation(s)
- Maria Dermit
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - Martin Dodel
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - Faraz K Mardakheh
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
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Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
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Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
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Stefanik MT, Sakas C, Lee D, Wolf ME. Ionotropic and metabotropic glutamate receptors regulate protein translation in co-cultured nucleus accumbens and prefrontal cortex neurons. Neuropharmacology 2018; 140:62-75. [PMID: 30077883 DOI: 10.1016/j.neuropharm.2018.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 01/14/2023]
Abstract
The regulation of protein translation by glutamate receptors and its role in plasticity have been extensively studied in the hippocampus. In contrast, very little is known about glutamatergic regulation of translation in nucleus accumbens (NAc) medium spiny neurons (MSN), despite their critical role in addiction-related plasticity and recent evidence that protein translation contributes to this plasticity. We used a co-culture system, containing NAc MSNs and prefrontal cortex (PFC) neurons, and fluorescent non-canonical amino acid tagging (FUNCAT) to visualize newly synthesized proteins in neuronal processes of NAc MSNs and PFC pyramidal neurons. First, we verified that the FUNCAT signal reflects new protein translation. Next, we examined the regulation of translation by group I metabotropic glutamate receptors (mGluRs) and ionotropic glutamate receptors by incubating co-cultures with agonists or antagonists during the 2-h period of non-canonical amino acid labeling. In NAc MSNs, basal translation was modestly reduced by blocking Ca2+-permeable AMPARs whereas blocking all AMPARs or suppressing constitutive mGluR5 signaling enhanced translation. Activating group I mGluRs with dihydroxyphenylglycine increased translation in an mGluR1-dependent manner in NAc MSNs and PFC pyramidal neurons. Disinhibiting excitatory transmission with bicuculline also increased translation. In MSNs, this was reversed by antagonists of mGluR1, mGluR5, AMPARs or NMDARs. In PFC neurons, AMPAR or NMDAR antagonists blocked bicuculline-stimulated translation. Our study, the first to examine glutamatergic regulation of translation in MSNs, demonstrates regulatory mechanisms specific to MSNs that depend on the level of neuronal activation. This sets the stage for understanding how translation may be altered in addiction.
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Affiliation(s)
- Michael T Stefanik
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Courtney Sakas
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Dennis Lee
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Marina E Wolf
- Department of Neuroscience, The Chicago Medical School at Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response. J Mol Biol 2018; 430:1965-1992. [PMID: 29746850 DOI: 10.1016/j.jmb.2018.04.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/05/2023]
Abstract
In the early stages of infection, gaining control of the cellular protein synthesis machinery including its ribosomes is the ultimate combat objective for a virus. To successfully replicate, viruses unequivocally need to usurp and redeploy this machinery for translation of their own mRNA. In response, the host triggers global shutdown of translation while paradoxically allowing swift synthesis of antiviral proteins as a strategy to limit collateral damage. This fundamental conflict at the level of translational control defines the outcome of infection. As part of this special issue on molecular mechanisms of early virus-host cell interactions, we review the current state of knowledge regarding translational control during viral infection with specific emphasis on protein kinase RNA-activated and mammalian target of rapamycin-mediated mechanisms. We also describe recent technological advances that will allow unprecedented insight into how viruses and host cells battle for ribosomes.
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Adelmund SM, Ruskowitz ER, Farahani PE, Wolfe JV, DeForest CA. Light-Activated Proteomic Labeling via Photocaged Bioorthogonal Non-Canonical Amino Acids. ACS Chem Biol 2018; 13:573-577. [PMID: 29419281 DOI: 10.1021/acschembio.7b01023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work introduces light-activated bioorthogonal noncanonical amino acid tagging (laBONCAT) as a method to selectively label, isolate, and identify proteins newly synthesized at user-defined regions in tissue culture. By photocaging l-azidohomoalanine (Aha), metabolic incorporation into proteins is prevented. The caged compound remains stable for many hours in culture, but can be photochemically liberated rapidly and on demand with spatial control. Upon directed light exposure, the uncaged amino acid is available for local translation, enabling downstream proteomic interrogation via bioorthogonal conjugation. Exploiting the reactive azide moiety present on Aha's amino acid side chain, we demonstrate that newly synthesized proteins can be purified for quantitative proteomics or visualized in synthetic tissues with a new level of spatiotemporal control. Shedding light on when and where proteins are translated within living samples, we anticipate that laBONCAT will aid in understanding the progression of complex protein-related disorders.
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Affiliation(s)
- Steven M. Adelmund
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Emily R. Ruskowitz
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Payam E. Farahani
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Julie V. Wolfe
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Cole A. DeForest
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, Washington 98105, United States
- Institute for Stem Cell & Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular Engineering & Sciences Institute, University of Washington, 3946 W Stevens Way NE, Seattle, Washington 98105, United States
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Lee TA, Bailey-Serres J. Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control. Curr Opin Biotechnol 2018; 49:29-34. [DOI: 10.1016/j.copbio.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
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Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio 2017; 8:mBio.01593-17. [PMID: 29066549 PMCID: PMC5654934 DOI: 10.1128/mbio.01593-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics. We enriched and identified proteins synthesized by cells in these regions. Compared to the entire biofilm proteome, the labeled subpopulation was characterized by a lower abundance of ribosomal proteins and was enriched in proteins of unknown function. We performed a pulse-labeling experiment to determine the dynamic proteomic response of the tolerant subpopulation to supra-MIC treatment with the fluoroquinolone antibiotic ciprofloxacin. The adaptive response included the upregulation of proteins required for sensing and repairing DNA damage and substantial changes in the expression of enzymes involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance. Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms, in which distinct cellular subpopulations can respond differently to stresses, including subpopulations of pathogenic biofilms that are more tolerant to antibiotics. Global proteomic analysis affords insights into cellular physiology but cannot identify proteins expressed in a particular subpopulation of interest. Here, we report a chemical biology method to selectively label, enrich, and identify proteins expressed by cells within distinct regions of biofilm microcolonies. We used this approach to study changes in protein synthesis by the subpopulation of antibiotic-tolerant cells throughout a course of treatment. We found substantial differences between the initial response and the long-term adaptive strategy that biofilm cells use to cope with antibiotic stress. The method we describe is readily applicable to investigations of bacterial heterogeneity in diverse contexts.
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Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio 2017. [PMID: 29066549 DOI: 10.1128/mbio.01593‐17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics. We enriched and identified proteins synthesized by cells in these regions. Compared to the entire biofilm proteome, the labeled subpopulation was characterized by a lower abundance of ribosomal proteins and was enriched in proteins of unknown function. We performed a pulse-labeling experiment to determine the dynamic proteomic response of the tolerant subpopulation to supra-MIC treatment with the fluoroquinolone antibiotic ciprofloxacin. The adaptive response included the upregulation of proteins required for sensing and repairing DNA damage and substantial changes in the expression of enzymes involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance.IMPORTANCE Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms, in which distinct cellular subpopulations can respond differently to stresses, including subpopulations of pathogenic biofilms that are more tolerant to antibiotics. Global proteomic analysis affords insights into cellular physiology but cannot identify proteins expressed in a particular subpopulation of interest. Here, we report a chemical biology method to selectively label, enrich, and identify proteins expressed by cells within distinct regions of biofilm microcolonies. We used this approach to study changes in protein synthesis by the subpopulation of antibiotic-tolerant cells throughout a course of treatment. We found substantial differences between the initial response and the long-term adaptive strategy that biofilm cells use to cope with antibiotic stress. The method we describe is readily applicable to investigations of bacterial heterogeneity in diverse contexts.
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Ramberger E, Dittmar G. Tissue Specific Labeling in Proteomics. Proteomes 2017; 5:proteomes5030017. [PMID: 28718811 PMCID: PMC5620534 DOI: 10.3390/proteomes5030017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
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Affiliation(s)
- Evelyn Ramberger
- Mass-Spectrometry Core Unit, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
- Berlin School of Integrative Oncology (BSIO), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1272 Strassen, Luxembourg.
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Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses. Neuron 2017; 92:358-371. [PMID: 27764671 PMCID: PMC5078608 DOI: 10.1016/j.neuron.2016.09.058] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/16/2016] [Accepted: 09/27/2016] [Indexed: 12/16/2022]
Abstract
Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation. Neither up- nor down-scaling produced changes in the number of different proteins translated. Rather, up- and down-scaling elicited opposing translational regulation of several molecular pathways, producing targeted adjustments in the proteome. We discovered ∼300 differentially regulated proteins involved in neurite outgrowth, axon guidance, filopodia assembly, excitatory synapses, and glutamate receptor complexes. We also identified differentially regulated proteins that are associated with multiple diseases, including schizophrenia, epilepsy, and Parkinson's disease.
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Brandi J, Manfredi M, Speziali G, Gosetti F, Marengo E, Cecconi D. Proteomic approaches to decipher cancer cell secretome. Semin Cell Dev Biol 2017; 78:93-101. [PMID: 28684183 DOI: 10.1016/j.semcdb.2017.06.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 01/17/2023]
Abstract
In this review, we give an overview of the actual proteomic approaches used in the study of cancer cells secretome. In particular, we describe the proteomic strategies to decipher cancer cell secretome initially focusing on the different aspects of sample preparation. We examine the issues related to the presence of low abundant proteins, the analysis of secreted proteins in the conditioned media with or without the removal of fetal bovine serum and strategies developed to reduce intracellular protein contamination. As regards the identification and quantification of secreted proteins, we described the different proteomic approaches used, i.e. gel-based, MS-based (label-based and label-free), and the antibody and array-based methods, together with some of the most recent applications in the field of cancer research. Moreover, we describe the bioinformatics tools developed for the in silico validation and characterization of cancer cells secretome. We also discuss the most important available tools for protein annotation and for prediction of classical and non-classical secreted proteins. In summary in this review advances, concerns and challenges in the field of cancer secretome analysis are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy; ISALIT S.r.l., Novara, Italy.
| | - Giulia Speziali
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Fabio Gosetti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Daniela Cecconi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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Glenn WS, Stone SE, Ho SH, Sweredoski MJ, Moradian A, Hess S, Bailey-Serres J, Tirrell DA. Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue. PLANT PHYSIOLOGY 2017; 173:1543-1553. [PMID: 28104718 PMCID: PMC5338676 DOI: 10.1104/pp.16.01762] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/14/2017] [Indexed: 05/11/2023]
Abstract
Proteomic plasticity undergirds stress responses in plants, and understanding such responses requires accurate measurement of the extent to which proteins levels are adjusted to counter external stimuli. Here, we adapt bioorthogonal noncanonical amino acid tagging (BONCAT) to interrogate protein synthesis in vegetative Arabidopsis (Arabidopsis thaliana) seedlings. BONCAT relies on the translational incorporation of a noncanonical amino acid probe into cellular proteins. In this study, the probe is the Met surrogate azidohomoalanine (Aha), which carries a reactive azide moiety in its amino acid side chain. The azide handle in Aha can be selectively conjugated to dyes and functionalized beads to enable visualization and enrichment of newly synthesized proteins. We show that BONCAT is sensitive enough to detect Arabidopsis proteins synthesized within a 30-min interval defined by an Aha pulse and that the method can be used to detect proteins made under conditions of light stress, osmotic shock, salt stress, heat stress, and recovery from heat stress. We further establish that BONCAT can be coupled to tandem liquid chromatography-mass spectrometry to identify and quantify proteins synthesized during heat stress and recovery from heat stress. Our results are consistent with a model in which, upon the onset of heat stress, translation is rapidly reprogrammed to enhance the synthesis of stress mitigators and is again altered during recovery. All experiments were carried out with commercially available reagents, highlighting the accessibility of the BONCAT method to researchers interested in stress responses as well as translational and posttranslational regulation in plants.
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Affiliation(s)
- Weslee S Glenn
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Shannon E Stone
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Samuel H Ho
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Michael J Sweredoski
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Annie Moradian
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Sonja Hess
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - Julia Bailey-Serres
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering (W.S.G., S.E.S., S.H.H., D.A.T.), and Proteome Exploration Laboratory (M.J.S., A.M., S.H.), California Institute of Technology, Pasadena, California 91125; and
- Center for Plant Cell Biology, University of California, Riverside, California 92521 (J.B.-S.)
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