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Wilkin S, Lanigan LT, Montes N, Sharma M, Avanzi C, Sejdiu D, Majander K, Pfrengle S, Chiang Y, Kunz L, Dittmann A, Rühli F, Singh P, Coll MF, Collins MJ, Taurozzi AJ, Schuenemann VJ. Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen. iScience 2024; 27:109663. [PMID: 38655200 PMCID: PMC11035369 DOI: 10.1016/j.isci.2024.109663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/30/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
This study investigates the efficacy of proteomic analysis of human remains to identify active infections in the past through the detection of pathogens and the host response to infection. We advance leprosy as a case study due to the sequestering of sufferers in leprosaria and the suggestive skeletal lesions that can result from the disease. Here we present a sequential enzyme extraction protocol, using trypsin followed by ProAlanase, to reduce the abundance of collagen peptides and in so doing increase the detection of non-collagenous proteins. Through our study of five individuals from an 11th to 18th century leprosarium, as well as four from a contemporaneous non-leprosy associated cemetery in Barcelona, we show that samples from 2 out of 5 leprosarium individuals extracted with the sequential digestion methodology contain numerous host immune proteins associated with modern leprosy. In contrast, individuals from the non-leprosy associated cemetery and all samples extracted with a trypsin-only protocol did not. Through this study, we advance a palaeoproteomic methodology to gain insights into the health of archaeological individuals and take a step toward a proteomics-based method to study immune responses in past populations.
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Affiliation(s)
- Shevan Wilkin
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Max Planck Institute of Geoanthropology, Jena, Germany
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
| | - Liam T. Lanigan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nuria Montes
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mukul Sharma
- Microbial Pathogenesis and Genomics, National Institute of Research in Tribal Health, Jabalpur, MP, India
| | - Charlotte Avanzi
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Donikë Sejdiu
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Yun Chiang
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Kunz
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pushpendra Singh
- Microbial Pathogenesis and Genomics, National Institute of Research in Tribal Health, Jabalpur, MP, India
- Model Rural Health Research Unit, Badoni, Datia (MP), India
| | | | - Matthew J. Collins
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, West Tower, Downing St, Cambridge CB2 3ER, UK
| | - Alberto J. Taurozzi
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Young JW, Pfitzner E, van Wee R, Kirschbaum C, Kukura P, Robinson CV. Characterization of membrane protein interactions by peptidisc-mediated mass photometry. iScience 2024; 27:108785. [PMID: 38303728 PMCID: PMC10831248 DOI: 10.1016/j.isci.2024.108785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Membrane proteins perform numerous critical functions in the cell, making many of them primary drug targets. However, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using the ABC transporter BtuCD, we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.
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Affiliation(s)
- John William Young
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emanuel Pfitzner
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raman van Wee
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Carla Kirschbaum
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philipp Kukura
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Sealover NE, Theard PT, Hughes JM, Linke AJ, Daley BR, Kortum RL. In situ modeling of acquired resistance to RTK/RAS-pathway-targeted therapies. iScience 2024; 27:108711. [PMID: 38226159 PMCID: PMC10788224 DOI: 10.1016/j.isci.2023.108711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024] Open
Abstract
Intrinsic and acquired resistance limit the window of effectiveness for oncogene-targeted cancer therapies. Here, we describe an in situ resistance assay (ISRA) that reliably models acquired resistance to RTK/RAS-pathway-targeted therapies across cell lines. Using osimertinib resistance in EGFR-mutated lung adenocarcinoma (LUAD) as a model system, we show that acquired osimertinib resistance can be significantly delayed by inhibition of proximal RTK signaling using SHP2 inhibitors. Isolated osimertinib-resistant populations required SHP2 inhibition to resensitize cells to osimertinib and reduce MAPK signaling to block the effects of enhanced activation of multiple parallel RTKs. We additionally modeled resistance to targeted therapies including the KRASG12C inhibitors adagrasib and sotorasib, the MEK inhibitor trametinib, and the farnesyl transferase inhibitor tipifarnib. These studies highlight the tractability of in situ resistance assays to model acquired resistance to targeted therapies and provide a framework for assessing the extent to which synergistic drug combinations can target acquired drug resistance.
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Affiliation(s)
- Nancy E. Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Patricia T. Theard
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacob M. Hughes
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Amanda J. Linke
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Brianna R. Daley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Robert L. Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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Choi J. Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner. iScience 2023; 26:106911. [PMID: 37305691 PMCID: PMC10250834 DOI: 10.1016/j.isci.2023.106911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high computational power. In this study, a novel method has been suggested to predict protein interaction partners by investigating narrow funnel-like interaction energy distribution. In this study, it was demonstrated that various protein interactions including kinases and E3 ubiquitin ligases have narrow funnel-like interaction energy distribution. To analyze protein interaction distribution, modified scores of iRMS and TM-score are introduced. Then, using these scores, algorithm and deep learning model for prediction of protein interaction partner and substrate of kinase and E3 ubiquitin ligase were developed. The prediction accuracy was similar to or even better than that of yeast two-hybrid screening. Ultimately, this knowledge-free protein interaction prediction method will broaden our understanding of protein interaction networks.
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Affiliation(s)
- Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04017, South Korea
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Lee S, Cui M, Lee D, Han K, Sun W, Lee D. A rationally designed optochemogenetic switch for activating canonical Wnt signaling. iScience 2023; 26:106233. [PMID: 36915690 PMCID: PMC10006827 DOI: 10.1016/j.isci.2023.106233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Accurate spatiotemporal control of multicellular self-organization by various signaling pathways is essential for developmental stages. In particular, evolutionarily conserved Wnt signaling serves as a major morphogenetic switch to determine the anteroposterior axis of the embryo. Here, we developed a genetically encoded optochemogenetic Wnt switch, named optochemoWnt, by coupling a blue light-inducible CRY2olig and rapamycin-inducible LRP6c clustering. The rationally designed optochemoWnt successfully modulated Wnt signaling with AND-gated patterns and demonstrated an improved signal-to-noise ratio (SNR). The dual-triggered switch provides a safeguard to prevent signal leakage resulting from ambient light sources under general laboratory conditions. OptochemoWnt expands the molecular toolbox available for the fields of developmental biology and tissue engineering. In addition, the AND-gated strategy of optochemoWnt may be used for other biomedical applications that integrate user defined switch elements with Boolean logic gates.
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Affiliation(s)
- Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.,Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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Wang Y, Zhong B, Xu C, Zhan D, Zhao S, Wu H, Liu M, Lan X, Cai D, Ding Q, Zheng B, Lan J, Lv Q, Wang Y, Qin J. Global profiling of AMG510 modified proteins identified tumor suppressor KEAP1 as an off-target. iScience 2023; 26:106080. [PMID: 36824285 DOI: 10.1016/j.isci.2023.106080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2022] [Accepted: 01/23/2023] [Indexed: 01/30/2023] Open
Abstract
KRAS inhibitor AMG510 covalently modifies the G12C residue and inactivates the KRAS/G12C function. Because there are many reactive cysteines in the proteome, it is important to characterize AMG510 on-target modification and off-targets. Here, we presented a streamlined workflow to measure abundant AMG510 modified peptides including that of KRAS/G12C by direct profiling, and a pan-AMG510 antibody peptide IP workflow to profile less abundant AMG510 off-targets. We identified over 300 off-target sites with three distinct kinetic patterns, expanding the AMG510 modified proteome involved in the nucleocytoplasmic transport, response to oxidative stress, adaptive immune system, and glycolysis. We found that AMG510 covalently modified cys339 of ALDOA and inhibited its enzyme activity. Moreover, AMG510 modified KEAP1 cys288 and induced NRF2 accumulation in the nuclear of NSCLC cells independent of KRAS/G12C mutation. Our study provides a comprehensive resource of protein off-targets of AMG510 and elucidates potential toxicological sideeffects for this covalent KRASG12C inhibitor.
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Harne S, Gayathri P. Characterization of heterologously expressed Fibril, a shape and motility determining cytoskeletal protein of the helical bacterium Spiroplasma. iScience 2022; 25:105055. [PMID: 36157586 PMCID: PMC9489929 DOI: 10.1016/j.isci.2022.105055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
Fibril is a constitutive filament-forming cytoskeletal protein of unidentified fold, exclusive to members of genus Spiroplasma. It is hypothesized to undergo conformational changes necessary to bring about Spiroplasma motility through changes in cell helicity. However, the mechanism driving conformational changes in Fibril remains unknown. We expressed Fibril from S. citri in E. coli for its purification and characterization. Sodium dodecyl sulfate solubilized Fibril filaments and facilitated purification by affinity chromatography. An alternative protocol for obtaining enriched insoluble Fibril filaments was standardized using density gradient centrifugation. Electron microscopy of Fibril purified by these protocols revealed filament bundles. Probable domain boundaries of Fibril protein were identified based on mass spectrometric analysis of proteolytic fragments. Presence of α-helical and β-sheet signatures in FT-IR measurements suggests that Fibril filaments consist of an assembly of folded globular domains, and not a β-strand-based aggregation like amyloid fibrils. Codon-optimized Spiroplasma citri Fibril was expressed in E. coli SDS treatment does not denature Fibril filaments Fibril possesses α helices and β sheet and is not an amyloid-like protein Domain boundaries were predicted using mass spectrometry of proteolytic fragments
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Affiliation(s)
- Shrikant Harne
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Pananghat Gayathri
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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Ogawa Y, Imamoto N. Methods to separate nuclear soluble fractions reflecting localizations in living cells. iScience 2021; 24:103503. [PMID: 34934922 DOI: 10.1016/j.isci.2021.103503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/15/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022] Open
Abstract
To understand various intranuclear functions, it is important to know when, what, and how proteins enter the nucleus. Although many methods and commercial kits for nuclear fractionation have been developed, there are still no methods for obtaining a complete nuclear proteome. Soluble nuclear proteins are often lost during fractionation. We developed remarkably improved methods to obtain nuclear soluble fractions by optimizing the conditions of selective permeabilization of the plasma membrane. As a result, 10 million cells could be separated into the cytoplasmic and nuclear soluble fractions more precisely in a 1.5-mL test tube. Moreover, the addition of an inhibitor to prevent leakage from the nucleus retained small proteins in the nucleus. Because of the simple protocols and easy application for multiple samples, our methods are expected to be applied to various studies on spatiotemporal changes of dynamic nuclear proteins, such as signal transduction.
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Affiliation(s)
- Yutaka Ogawa
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Furusawa C, Tanabe K, Ishii C, Kagata N, Tomita M, Fukuda S. Decoding gut microbiota by imaging analysis of fecal samples. iScience 2021; 24:103481. [PMID: 34927025 DOI: 10.1016/j.isci.2021.103481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 09/21/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
The gut microbiota plays a crucial role in maintaining health. Monitoring the complex dynamics of its microbial population is, therefore, important. Here, we present a deep convolution network that can characterize the dynamic changes in the gut microbiota using low-resolution images of fecal samples. Further, we demonstrate that the microbial relative abundances, quantified via 16S rRNA amplicon sequencing, can be quantitatively predicted by the neural network. Our approach provides a simple and inexpensive method of gut microbiota analysis. A deep convolution network classifies gut microbiota based on fecal sample images Image-based quantitative prediction of gut microbiota composition is demonstrated This result provides a simple and inexpensive method of gut microbiota analysis
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Shao CS, Zhou XH, Miao YH, Wang P, Zhang QQ, Huang Q. In situ observation of mitochondrial biogenesis as the early event of apoptosis. iScience 2021; 24:103038. [PMID: 34553131 DOI: 10.1016/j.isci.2021.103038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/28/2021] [Accepted: 08/22/2021] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial biogenesis is a cell response to external stimuli which is generally believed to suppress apoptosis. However, during the process of apoptosis, whether mitochondrial biogenesis occurs in the early stage of the apoptotic cells remains unclear. To address this question, we constructed the COX8-EGFP-ACTIN-mCherry HeLa cells with recombinant fluorescent proteins respectively tagged on the nucleus and mitochondria and monitored the mitochondrial changes in the living cells exposed to gamma-ray radiation. Besides in situ detection of mitochondrial fluorescence changes, we also examined the cell viability, nuclear DNA damage, reactive oxygen species (ROS), mitochondrial superoxide, citrate synthase activity, ATP, cytoplasmic and mitochondrial calcium, mitochondrial mass, mitochondrial morphology, and protein expression related to mitochondrial biogenesis, as well as the apoptosis biomarkers. As a result, we confirmed that significant mitochondrial biogenesis took place preceding the radiation-induced apoptosis, and it was closely correlated with the apoptotic cells at late stage. The involved mechanism was also discussed. Dual fluorescence approach was used for in situ observation of living cell processes Radiation-induced effects of mitochondrial biogenesis and apoptosis were observed Relationship between mitochondrial biogenesis and apoptosis was revisited Assessing early mitochondrial biogenesis is critical for predicting later fate of cells
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Huang Y, Bai X, Guo Z, Dong H, Fu Y, Zhang H, Zhai G, Tian S, Wang Y, Zhang K. DNA-guided photoactivatable probe-based chemical proteomics reveals the reader protein of mRNA methylation. iScience 2021; 24:103046. [PMID: 34553132 PMCID: PMC8441146 DOI: 10.1016/j.isci.2021.103046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 07/27/2021] [Accepted: 08/24/2021] [Indexed: 01/27/2023] Open
Abstract
Chemical modification on mRNA can recruit specific binding proteins (readers/partners) to determine post-transcriptional gene regulation. However, the identification of the reader is extremely limited owing to the rather weak and highly dynamic non-covalent interactions between mRNA modification and reader, and therefore the sensitive and robust approaches are desirable. Here, we report a DNA-guided photoactivatable-based chemical proteomic approach for profiling the readers of mRNA methylation. By use of N6-methyladenosine (m6A), we illustrated that this method can be successfully utilized for labelling and enriching the readers of mRNA modification, as well as for the discovery of new partners. Thus we applied this strategy to a new modification 2'-O-methyladenosine. As a result, DDX1 was identified and verified as a potential binding protein. Our study therefore provides a powerful chemical proteomics tool for identifying the binding factors of mRNA modification and reveals the underlying function of mRNA modification.
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Affiliation(s)
- Yepei Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhenchang Guo
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yun Fu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hui Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ye Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
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