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Wang R, Yang D, Tian T, An Y, Wan C, Chang Q, Liang M, Hou Z, Wang Y, Zhang L, Li Z. Low-Toxicity Sulfonium-Based Probes for Cysteine-Specific Profiling in Live Cells. Anal Chem 2022; 94:4366-4372. [PMID: 35244395 DOI: 10.1021/acs.analchem.1c05129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite being a low-abundance amino acid, cysteine plays an essential role in regulating protein function and serves as a satisfactory target of post-translational modifications and drug developments. To comprehensively assess reactive-cysteine-containing proteins, the development of chemical proteomic probes to label cysteine residues in human cells is an important objective. Cysteine modification using sulfonium-based probes is a novel method to identify reactive cysteine residues in proteins. Herein, we reported a set of "cysteine-reactive sulfonium-based (C-Sul)" probes to label the reactive cysteine sites in cellular proteins. Notably, water-soluble C-Sul probes have a significantly enhanced stability and cellular uptakes, displaying a high specificity toward reactive cysteines and compatibility with quantitative proteomic profiling. In comparison to the conventional iodoacetamide-based probe, C-Sul particularly has no inhibitory effects on cell viability, enabling its application in proteomic profiling of reactive cysteine residues under biorelevant conditions. We propose C-Sul probes as optimal tools of cysteine profiling for further broadly basic research.
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Affiliation(s)
- Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Dongyan Yang
- Innovative Institute for Plant Health, College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Tian Tian
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Qi Chang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Ying Wang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
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2
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Hou Z, Jin Y, Li Y, Fan H, Xiao C, Li Q, Zhang Y. Immobilization of peroxisome proliferator-activated receptor gamma and the application in screening modulators of the receptor from herbal medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1190:123098. [PMID: 35026651 DOI: 10.1016/j.jchromb.2022.123098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
Screening and identification of potential compounds from herbal medicine is a prevailing way to find a lead for the development of innovative drugs. This promotes the development of new methods that are feasible in complex matrices. Here, we described a one-step reversible methodology to immobilize nuclear peroxisome proliferator-activated receptor gamma (PPARγ) onto amino microsphere coated with a DNA strand specifically binding to the receptor. The specific interaction allowed us to achieve the immobilization of PPARγ by mixing the DNA modified microspheres with E. coli lysates expressing the receptor. Characterization of the immobilized receptor was carried out by morphology and binding specificity analysis. Feasibility of immobilized PPARγ in the drug-receptor interaction analysis was performed by an injection amount-dependent method. Besides, immobilized PPARγ was also applied in screening modulators of the receptor from Coptidis Rhizoma extract. The binding of the screened compounds to PPARγ was examined by time-resolved fluorescence resonance energy transfer assay. The results showed that immobilized PPARγ was stable for thirty days with a high-specificity of ligand recognition at the subtype receptor level. Berberine and palmatine were the bioactive compounds of Coptidis Rhizoma specifically binding to PPARγ. The two compounds exhibited half maximal inhibitory concentrations of 4.11 and 2.98 μM during their binding to the receptor. We concluded that the current method is possible to become a common strategy for the immobilization of nuclear receptors, and the immobilized receptor is a high throughput method for recognizing and separating the receptor modulators from complex matrices including herbal medicine.
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Affiliation(s)
- Zhaoling Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Yan Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Yuxin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Hushuai Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Chaoni Xiao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Yajun Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Ministry of Life Sciences and Medicine, Northwest University, Xi'an 710069, China.
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Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example. PLoS Comput Biol 2021; 17:e1009682. [PMID: 34879076 PMCID: PMC8687584 DOI: 10.1371/journal.pcbi.1009682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/20/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
Many computational classifiers have been developed to predict different types of post-translational modification sites. Their performances are measured using cross-validation or independent test, in which experimental data from different sources are mixed and randomly split into training and test sets. However, the self-reported performances of most classifiers based on this measure are generally higher than their performances in the application of new experimental data. It suggests that the cross-validation method overestimates the generalization ability of a classifier. Here, we proposed a generalization estimate method, dubbed experiment-split test, where the experimental sources for the training set are different from those for the test set that simulate the data derived from a new experiment. We took the prediction of lysine methylome (Kme) as an example and developed a deep learning-based Kme site predictor (called DeepKme) with outstanding performance. We assessed the experiment-split test by comparing it with the cross-validation method. We found that the performance measured using the experiment-split test is lower than that measured in terms of cross-validation. As the test data of the experiment-split method were derived from an independent experimental source, this method could reflect the generalization of the predictor. Therefore, we believe that the experiment-split method can be applied to benchmark the practical performance of a given PTM model. DeepKme is free accessible via https://github.com/guoyangzou/DeepKme. The performance of a model for predicting post-translational modification sites is commonly evaluated using the cross-validation method, where the data derived from different experimental sources are mixed and randomly separated into the training dataset and validation dataset. However, the performance measured through cross-validation is generally higher than the performance in the application of new experimental data, indicating that the cross-validation method overestimates the generalization of a model. In this study, we proposed a generalization estimate method, dubbed experiment-split test, where the experimental sources for the training set are different from those for the test set that simulate the data derived from a new experiment. We took the prediction of lysine methylome as an example and developed a deep learning-based Kme site predictor DeepKme with outstanding performance. We found that the performance measured by the experiment-split method is lower than that measured in terms of cross-validation. As the test data of the experiment-split method were derived from an independent experimental source, this method could reflect the generalization of the prediction model. Therefore, the experiment-split method can be applied to benchmark the practical prediction performance.
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Gladyshev VN, Kritchevsky SB, Clarke SG, Cuervo AM, Fiehn O, de Magalhães JP, Mau T, Maes M, Moritz R, Niedernhofer LJ, Van Schaftingen E, Tranah GJ, Walsh K, Yura Y, Zhang B, Cummings SR. Molecular Damage in Aging. NATURE AGING 2021; 1:1096-1106. [PMID: 36846190 PMCID: PMC9957516 DOI: 10.1038/s43587-021-00150-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/04/2021] [Indexed: 11/09/2022]
Abstract
Cellular metabolism generates molecular damage affecting all levels of biological organization. Accumulation of this damage over time is thought to play a central role in the aging process, but damage manifests in diverse molecular forms complicating its assessment. Insufficient attention has been paid to date to the role of molecular damage in aging-related phenotypes, particularly in humans, in part because of the difficulty in measuring its various forms. Recently, omics approaches have been developed that begin to address this challenge, because they are able to assess a sizeable proportion of age-related damage at the level of small molecules, proteins, RNA, DNA, organelles and cells. This review describes the concept of molecular damage in aging and discusses its diverse aspects from theoretical models to experimental approaches. Measurement of multiple types of damage enables studies of the role of damage in human aging outcomes and lays a foundation for testing interventions to reduce the burden of molecular damage, opening new approaches to slowing aging and reducing its consequences.
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Affiliation(s)
- Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen B. Kritchevsky
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ana Maria Cuervo
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
- Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Theresa Mau
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
| | - Michal Maes
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Robert Moritz
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Emile Van Schaftingen
- De Duve Institute, Université catholique de Louvain, Bruxelles, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Bruxelles, Belgium
| | - Gregory J. Tranah
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia-School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshimitsu Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia-School of Medicine, Charlottesville, VA 22908, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Steven R. Cummings
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
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Proteome-wide Prediction of Lysine Methylation Leads to Identification of H2BK43 Methylation and Outlines the Potential Methyllysine Proteome. Cell Rep 2021; 32:107896. [PMID: 32668242 DOI: 10.1016/j.celrep.2020.107896] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/29/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022] Open
Abstract
Protein Lys methylation plays a critical role in numerous cellular processes, but it is challenging to identify Lys methylation in a systematic manner. Here we present an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We develop MethylSight, a program that predicts Kme events solely on the physicochemical properties of residues surrounding the putative methylation sites, which then requires validation by targeted MS. Using this approach, we identify 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts that Lys methylation is a prevalent post-translational modification in the human proteome. Our work provides a useful resource for guiding systematic exploration of the role of Lys methylation in human health and disease.
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6
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Zhao X, Jin Y, Yuan X, Hou Z, Chen Z, Fu X, Li Q, Wang J, Zhang Y. Covalent Inhibitor-Based One-Step Method for Endothelin Receptor A Immobilization: from Ligand Recognition to Lead Identification. Anal Chem 2020; 92:13750-13758. [DOI: 10.1021/acs.analchem.0c01807] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Yahui Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Xinyi Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Zhaoling Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Ziyue Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Xiaoying Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Yajun Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education; College of Life Sciences, Northwest University, Xi’an 710069, China
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7
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Rashid A, Wang R, Zhang L, Yue J, Yang M, Yen A. Dissecting the novel partners of nuclear c-Raf and its role in all-trans retinoic acid (ATRA)-induced myeloblastic leukemia cells differentiation. Exp Cell Res 2020; 394:111989. [PMID: 32283065 PMCID: PMC10656057 DOI: 10.1016/j.yexcr.2020.111989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 01/09/2023]
Abstract
All-trans retinoic acid (ATRA) is an anti-cancer differentiation therapy agent effective for acute promyelocytic leukemia (APL) but not acute myeloid leukemia (AML) in general. Using the HL-60 human non-APL AML model where ATRA causes nuclear enrichment of c-Raf that drives differentiation and G1/G0 cell cycle arrest, we now observe that c-Raf in the nucleus showed novel interactions with several prominent regulators of the cell cycle and cell differentiation. One is cyclin-dependent kinase 2 (Cdk2). ATRA treatment caused c-Raf to dissociate from Cdk2. This was associated with enhanced binding of Cdk2 with retinoic acid receptor α (RARα). Consistent with this novel Raf/CDK2/RARα axis contributing to differentiation, CD38 expression per cell, which is transcriptionally regulated by a retinoic acid response element (RARE), is enhanced. The RB tumor suppressor, a fundamental regulator of G1 cell cycle progression or arrest, was also targeted by c-Raf in the nucleus. RB and specifically the S608 phosphorylated form (pS608RB) complexed with c-Raf. ATRA treatment induced S608RB-hypophosphorylation associated with G1/G0 cell cycle arrest and release of c-Raf from RB. We also found that nuclear c-Raf interacted with SMARCD1, a pioneering component of the SWI/SNF chromatin remodeling complex. ATRA treatment diminished the amount of this protein bound to c-Raf. The data suggest that ATRA treatment to HL-60 human cells re-directed c-Raf from its historically pro-proliferation functions in the cytoplasm to pro-differentiation functions in the nucleus.
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Affiliation(s)
- Asif Rashid
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Rui Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jianbo Yue
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
| | - Andrew Yen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
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Li L, Liu M, Yue L, Wang R, Zhang N, Liang Y, Zhang L, Cheng L, Xia J, Wang R. Host-Guest Protein Assembly for Affinity Purification of Methyllysine Proteomes. Anal Chem 2020; 92:9322-9329. [PMID: 32510198 DOI: 10.1021/acs.analchem.0c01643] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions drive self-assembly of biomacromolecules and thus enable important physiological functions at a cellular level. Supramolecular chemists have developed artificial host-guest interactions that are similar with, yet distinct from and orthogonal to, the natural protein-protein interactions. For instance, cucurbit[n]urils are synthetic receptors that can specifically recognize proteins with N-terminal aromatic residues with high affinities, yet this interaction can be reversed by the competition of small molecules such as amantadine. Herein, we develop a site-specific, oriented protein-display method by combining the host-guest interaction based on cucurbit[7]uril and a covalent protein-peptide reaction. A methyllysine-binding protein HP1β chromodomain (CD) is immobilized via host-guest interactions and used as the "bait" to capture methyllysine proteomes from cancer cells. The captured "fish"-methyllysine-containing proteins-can be released via competitive displacement by amantadine in a nondenaturing and traceless manner. This affinity purification method found 73 novel methyllysine sites from 101 identified sites among 66 methylated proteins from 255 HP1β CD-binding proteins in cancer cells via subsequent mass spectrometric analysis. This work thereby presents a new strategy of artificial host-guest protein assembly in affinity purification of methyllysine proteins in coupling to mass spectrometry.
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Affiliation(s)
- Linting Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Min Liu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ludan Yue
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518000, P. R. China
| | - Ning Zhang
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Yujie Liang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
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Lee KY, Chopra A, Burke GL, Chen Z, Greenblatt JF, Biggar KK, Meneghini MD. A crucial RNA-binding lysine residue in the Nab3 RRM domain undergoes SET1 and SET3-responsive methylation. Nucleic Acids Res 2020; 48:2897-2911. [PMID: 31960028 PMCID: PMC7102954 DOI: 10.1093/nar/gkaa029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/07/2020] [Accepted: 01/18/2020] [Indexed: 11/13/2022] Open
Abstract
The Nrd1-Nab3-Sen1 (NNS) complex integrates molecular cues to direct termination of noncoding transcription in budding yeast. NNS is positively regulated by histone methylation as well as through Nrd1 binding to the initiating form of RNA PolII. These cues collaborate with Nrd1 and Nab3 binding to target RNA sequences in nascent transcripts through their RRM RNA recognition motifs. In this study, we identify nine lysine residues distributed amongst Nrd1, Nab3 and Sen1 that are methylated, suggesting novel molecular inputs for NNS regulation. We identify mono-methylation of one these residues (Nab3-K363me1) as being partly dependent on the H3K4 methyltransferase, Set1, a known regulator of NNS function. Moreover, the accumulation of Nab3-K363me1 is essentially abolished in strains lacking SET3, a SET domain containing protein that is positively regulated by H3K4 methylation. Nab3-K363 resides within its RRM and physically contacts target RNA. Mutation of Nab3-K363 to arginine (Nab3-K363R) decreases RNA binding of the Nab3 RRM in vitro and causes transcription termination defects and slow growth. These findings identify SET3 as a potential contextual regulator of Nab3 function through its role in methylation of Nab3-K363. Consistent with this hypothesis, we report that SET3 exhibits genetic activation of NAB3 that is observed in a sensitized context.
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Affiliation(s)
- Kwan Yin Lee
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Giovanni L Burke
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ziyan Chen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jack F Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Marc D Meneghini
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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10
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Protein lysine methylation in the regulation of anoxia tolerance in the red eared slider turtle, Trachemys scripta elegans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100660. [PMID: 32066095 DOI: 10.1016/j.cbd.2020.100660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/23/2022]
Abstract
The red eared slider turtle (Trachemys scripta elegans) is a champion vertebrate facultative anaerobe, capable of surviving for several months under conditions of exceptionally low oxygen availability. The ability of the turtle to facilitate this impressive tolerance to oxygen restriction is accomplished through a dramatic reduction in non-essential cellular processes. This is done in an attempt to conserve limited ATP stores and match demand in the anoxic state, with ATP supplied primarily through anaerobic glycolysis. Determining both the non-essential and the essential cellular processes that are deemed to be anoxia-responsive in the turtle has been an intense area of study over the past few decades. As a result, recent advancements have established the influence of global metabolic controls, such as post-transcriptional and post-translational regulation of gene expression in anoxia adaptation. A remaining question is whether or not epigenetic-level regulatory mechanisms are also utilized to allow for local control over gene expression. Recently, research has begun to document lysine methylation as an anoxia-responsive post-translational histone modification, as the activities of a number of methyl-lysine regulatory enzymes are extraordinarily sensitive to oxygen availability. As a result, oxygen-dependent methyl-lysine regulatory enzymes have been of particular interest to several recent studies of animal oxygen sensitivity, including the freshwater turtle. This review will introduce the concept of lysine methylation as an oxygen-sensitive protein modification as well as a prospectus on how this modification may contribute to anoxia tolerance in the turtle.
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11
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Cornett EM, Ferry L, Defossez PA, Rothbart SB. Lysine Methylation Regulators Moonlighting outside the Epigenome. Mol Cell 2020; 75:1092-1101. [PMID: 31539507 DOI: 10.1016/j.molcel.2019.08.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
Abstract
Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
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Affiliation(s)
- Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Laure Ferry
- Université de Paris, Epigenetics and Cell Fate, CNRS, 75013 Paris, France
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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Mezey N, Cho WCS, Biggar KK. Intriguing Origins of Protein Lysine Methylation: Influencing Cell Function Through Dynamic Methylation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:551-557. [PMID: 32194241 PMCID: PMC7212469 DOI: 10.1016/j.gpb.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 03/05/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
Affiliation(s)
- Natalie Mezey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China.
| | - Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada.
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