1
|
Zhu Y, Yang Y, Bu H, Huang H, Chen H, Ran J, Qin L, Ni Y, Yao M, Song T, Li M, Yang Y, Guo T, Chao N, Liu Z, Li W, Zhang L. Apelin‐mediated deamidation of
HMGA1
promotes tumorigenesis by enhancing
SREBP1
activity and lipid synthesis. Cancer Sci 2022; 113:3722-3734. [PMID: 36087034 PMCID: PMC9633285 DOI: 10.1111/cas.15515] [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: 01/07/2022] [Revised: 06/27/2022] [Accepted: 07/15/2022] [Indexed: 02/05/2023] Open
Abstract
Enhanced fatty acid synthesis provides proliferation and survival advantages for tumor cells. Apelin is an adipokine, which serves as a ligand of G protein–coupled receptors that promote tumor growth in malignant cancers. Here, we confirmed that apelin increased sterol regulatory element–binding protein 1 (SREBP1) activity and induced the expression of glutamine amidotransferase for deamidating high‐mobility group A 1 (HMGA1) to promote fatty acid synthesis and proliferation of lung cancer cells. This post‐translational modification stabilized the HMGA1 expression and enhanced the formation of the apelin‐HMGA1‐SREBP1 complex to facilitate SREBP1 activity for lipid metabolism and lung cancer cell growth. We uncovered the pivotal role of apelin‐mediated deamidation of HMGA1 in lipid metabolism and tumorigenesis of lung cancer cells.
Collapse
Affiliation(s)
- Yihan Zhu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital Sichuan University Chengdu China
| | - Ying Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Hong Bu
- Department of Pathology, West China Hospital Sichuan University Chengdu China
| | - Hong Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital Sichuan University Chengdu China
| | - Hongyu Chen
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital Sichuan University Chengdu China
| | - Jingjing Ran
- Laboratory of Human Diseases and Immunotherapies, West China Hospital Sichuan University Chengdu China
| | - Liwen Qin
- Administration of Research Park, West China Hospital Sichuan University Chengdu China
| | - Yinyun Ni
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Menglin Yao
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Tingting Song
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Mufeng Li
- Department of Nuclear Medicine, West China Hospital Sichuan University Chengdu China
| | - Yongfeng Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Tingting Guo
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Ningning Chao
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Zhiqing Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| | - Li Zhang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease‐related Molecular Network, West China Hospital Sichuan University Chengdu China
| |
Collapse
|
2
|
Wang L, Zhang J, Xia M, Liu C, Zu X, Zhong J. High Mobility Group A1 (HMGA1): Structure, Biological Function, and Therapeutic Potential. Int J Biol Sci 2022; 18:4414-4431. [PMID: 35864955 PMCID: PMC9295051 DOI: 10.7150/ijbs.72952] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
High mobility group A1 (HMGA1) is a nonhistone chromatin structural protein characterized by no transcriptional activity. It mainly plays a regulatory role by modifying the structure of DNA. A large number of studies have confirmed that HMGA1 regulates genes related to tumours in the reproductive system, digestive system, urinary system and haematopoietic system. HMGA1 is rare in adult cells and increases in highly proliferative cells such as embryos. After being stimulated by external factors, it will produce effects through the Wnt/β-catenin, PI3K/Akt, Hippo and MEK/ERK pathways. In addition, HMGA1 also affects the ageing, apoptosis, autophagy and chemotherapy resistance of cancer cells, which are linked to tumorigenesis. In this review, we summarize the mechanisms of HMGA1 in cancer progression and discuss the potential clinical application of targeted HMGA1 therapy, indicating that targeted HMGA1 is of great significance in the diagnosis and treatment of malignancy.
Collapse
Affiliation(s)
- Lu Wang
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Ji Zhang
- Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518033, Guangdong, China
| | - Min Xia
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Chang Liu
- Department of Endocrinology and Metabolism, The First People's Hospital of Chenzhou, First School of Clinical Medicine, University of Southern Medical, Guangzhou 510515, Guangdong, China
| | - Xuyu Zu
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Jing Zhong
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| |
Collapse
|
3
|
H2B Type 1-K Accumulates in Senescent Fibroblasts with Persistent DNA Damage along with Methylated and Phosphorylated Forms of HMGA1. Proteomes 2021; 9:proteomes9020030. [PMID: 34205514 PMCID: PMC8293446 DOI: 10.3390/proteomes9020030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 11/27/2022] Open
Abstract
Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The in vivo identification of senescent cells is difficult due to the absence of universal biomarkers. Chromatin modifications are key aspects of the senescence transition and may provide novel biomarkers. We used a combined protein profiling and bottom-up mass spectrometry approach to characterize the isoforms and post-translational modifications of chromatin proteins over time in post-mitotic human fibroblasts in vitro. We show that the H2B type 1-K variant is specifically enriched in deep senescent cells with persistent DNA damage. This accumulation was not observed in quiescent cells or in cells induced into senescence without DNA damage by expression of the RAF kinase. Similarly, HMGA1a di-methylated and HMGA1b tri-phosphorylated forms accumulated exclusively in the chromatin of cells in deep senescent conditions with persistent DNA damage. H2B type 1-K and modified HMGA1 may thus represent novel biomarkers of senescent cells containing persistent DNA damage.
Collapse
|
4
|
Sumter TF, Xian L, Huso T, Koo M, Chang YT, Almasri TN, Chia L, Inglis C, Reid D, Resar LMS. The High Mobility Group A1 (HMGA1) Transcriptome in Cancer and Development. Curr Mol Med 2016; 16:353-93. [PMID: 26980699 DOI: 10.2174/1566524016666160316152147] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 02/15/2016] [Accepted: 03/10/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND & OBJECTIVES Chromatin structure is the single most important feature that distinguishes a cancer cell from a normal cell histologically. Chromatin remodeling proteins regulate chromatin structure and high mobility group A (HMGA1) proteins are among the most abundant, nonhistone chromatin remodeling proteins found in cancer cells. These proteins include HMGA1a/HMGA1b isoforms, which result from alternatively spliced mRNA. The HMGA1 gene is overexpressed in cancer and high levels portend a poor prognosis in diverse tumors. HMGA1 is also highly expressed during embryogenesis and postnatally in adult stem cells. Overexpression of HMGA1 drives neoplastic transformation in cultured cells, while inhibiting HMGA1 blocks oncogenic and cancer stem cell properties. Hmga1 transgenic mice succumb to aggressive tumors, demonstrating that dysregulated expression of HMGA1 causes cancer in vivo. HMGA1 is also required for reprogramming somatic cells into induced pluripotent stem cells. HMGA1 proteins function as ancillary transcription factors that bend chromatin and recruit other transcription factors to DNA. They induce oncogenic transformation by activating or repressing specific genes involved in this process and an HMGA1 "transcriptome" is emerging. Although prior studies reveal potent oncogenic properties of HMGA1, we are only beginning to understand the molecular mechanisms through which HMGA1 functions. In this review, we summarize the list of putative downstream transcriptional targets regulated by HMGA1. We also briefly discuss studies linking HMGA1 to Alzheimer's disease and type-2 diabetes. CONCLUSION Further elucidation of HMGA1 function should lead to novel therapeutic strategies for cancer and possibly for other diseases associated with aberrant HMGA1 expression.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - L M S Resar
- Department of Medicine, Faculty of the Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross Research Building, Room 1025, Baltimore, MD 21205-2109, USA.
| |
Collapse
|
5
|
Molden RC, Garcia BA. Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications. ACTA ACUST UNITED AC 2014; 77:23.7.1-23.7.28. [PMID: 25081742 DOI: 10.1002/0471140864.ps2307s77] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Histones are chromatin proteins that are highly modified with many different types of post-translational modifications. These modifications act in concert to regulate a number of chromatin-related processes. However, identification and quantification of co-occurring histone post-translational modifications is challenging because there are many potential combinations of modifications and because the commonly used strategy of fragmenting proteins using trypsin or an alternative protease prior to LC-MS/MS analysis results in the loss of connectivity between modifications on different peptides. In this unit, mass spectrometric methods to analyze combinatorial histone modifications on histone tails (middle-down mass spectrometry) and on intact histones (top-down mass spectrometry) are described.
Collapse
Affiliation(s)
- Rosalynn C Molden
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
6
|
Cannon JR, Kluwe C, Ellington A, Brodbelt JS. Characterization of green fluorescent proteins by 193 nm ultraviolet photodissociation mass spectrometry. Proteomics 2014; 14:1165-73. [PMID: 24596159 PMCID: PMC4071602 DOI: 10.1002/pmic.201300364] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/07/2013] [Accepted: 01/13/2014] [Indexed: 11/05/2022]
Abstract
We investigate the utility of 193 nm ultraviolet photodissociation (UVPD) in comparison to CID, higher energy CID (HCD), and electron transfer dissociation (ETD) for top down fragmentation of highly homologous green fluorescent proteins (GFP) in the gas phase. Several GFP variants were constructed via mutation of surface residues to charged moieties, demonstrating different pIs and presenting a challenge for identification by mass spectrometry. Presented is a comparison of fragmentation techniques utilized for top down characterization of four variants with varying levels of surface charge. UVPD consistently resulted in identification of more fragment ions relative to other MS/MS methods, allowing higher confidence identification. In addition to the high number of fragment ions, the sites of fragmentation were more evenly spread throughout the protein backbone, which proved key for localizing the point mutations.
Collapse
Affiliation(s)
- Joe R. Cannon
- Department of Chemistry, University of Texas at Austin, Austin, Texas
| | - Christien Kluwe
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas
| | - Andrew Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas
| | | |
Collapse
|
7
|
Guzman YA, Sakellari D, Arsenakis M, Floudas CA. Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review. Expert Rev Proteomics 2013; 11:31-41. [PMID: 24308552 DOI: 10.1586/14789450.2014.864953] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Periodontitis is a common chronic and destructive disease whose pathogenetic mechanisms remain unclear. Due to their sensitivity and global scale, proteomics studies offer the opportunity to uncover critical host and pathogen activity indicators and can elucidate clinically applicable biomarkers for improved diagnosis and treatment of the disease. This review summarizes the literature of proteomics studies on periodontitis and comprehensively discusses commonly found candidate biomarkers. Key considerations in the design of an experimental proteomics platform are also outlined. The applicability of protein biomarkers across the progression of periodontitis and unexplored areas of research are highlighted.
Collapse
Affiliation(s)
- Yannis A Guzman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | | | | |
Collapse
|
8
|
Bartke T, Borgel J, DiMaggio PA. Proteomics in epigenetics: new perspectives for cancer research. Brief Funct Genomics 2013; 12:205-18. [PMID: 23401080 PMCID: PMC3662889 DOI: 10.1093/bfgp/elt002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The involvement of epigenetic processes in the origin and progression of cancer is now widely appreciated. Consequently, targeting the enzymatic machinery that controls the epigenetic regulation of the genome has emerged as an attractive new strategy for therapeutic intervention. The development of epigenetic drugs requires a detailed knowledge of the processes that govern chromatin regulation. Over the recent years, mass spectrometry (MS) has become an indispensable tool in epigenetics research. In this review, we will give an overview of the applications of MS-based proteomics in studying various aspects of chromatin biology. We will focus on the use of MS in the discovery and mapping of histone modifications and how novel proteomic approaches are being utilized to identify and study chromatin-associated proteins and multi-subunit complexes. Finally, we will discuss the application of proteomic methods in the diagnosis and prognosis of cancer based on epigenetic biomarkers and comment on their future impact on cancer epigenetics.
Collapse
Affiliation(s)
- Till Bartke
- MRC Clinical Sciences Centre, Imperial College London Faculty of Medicine, Hammersmith Hospital Campus, London W12 0NN, UK.
| | | | | |
Collapse
|
9
|
Lanucara F, Eyers CE. Top-down mass spectrometry for the analysis of combinatorial post-translational modifications. MASS SPECTROMETRY REVIEWS 2013; 32:27-42. [PMID: 22718314 DOI: 10.1002/mas.21348] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/21/2012] [Accepted: 02/21/2012] [Indexed: 06/01/2023]
Abstract
Protein post-translational modifications (PTMs) are critically important in regulating both protein structure and function, often in a rapid and reversible manner. Due to its sensitivity and vast applicability, mass spectrometry (MS) has become the technique of choice for analyzing PTMs. Whilst the "bottom-up' analytical approach, in which proteins are proteolyzed generating peptides for analysis by MS, is routinely applied and offers some advantages in terms of ease of analysis and lower limit of detection, "top-down" MS, describing the analysis of intact proteins, yields unique and highly valuable information on the connectivity and therefore combinatorial effect of multiple PTMs in the same polypeptide chain. In this review, the state of the art in top-down MS will be discussed, covering the main instrumental platforms and ion activation techniques. Moreover, the way that this approach can be used to gain insights on the combinatorial effect of multiple post-translational modifications and how this information can assist in studying physiologically relevant systems at the molecular level will also be addressed.
Collapse
Affiliation(s)
- Francesco Lanucara
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester M1 7DN, UK
| | | |
Collapse
|
10
|
Discovery of lysine post-translational modifications through mass spectrometric detection. Essays Biochem 2012; 52:147-63. [PMID: 22708569 DOI: 10.1042/bse0520147] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complexity of an organism's proteome is in part due to the diversity of post-translational modifications present that can direct the location and function of a protein. To address the growing interest in characterizing these modifications, mass spectrometric-based proteomics has emerged as one of the most essential experimental platforms for their discovery. In searching for post-translational modifications within a target set of proteins to global surveys of particularly modified proteins within a given proteome, various experimental MS (mass spectrometry) and allied techniques have been developed. Out of 20 naturally encoded amino acids, lysine is essentially the most highly post-translationally modified residue. This chapter provides a succinct overview of such methods for the characterization of protein lysine modifications as broadly classified, such as methylation and ubiquitination.
Collapse
|
11
|
Allosteric post-translational modification codes. Trends Biochem Sci 2012; 37:447-55. [DOI: 10.1016/j.tibs.2012.07.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/25/2012] [Accepted: 07/11/2012] [Indexed: 12/24/2022]
|
12
|
Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| |
Collapse
|
13
|
Cui W, Rohrs HW, Gross ML. Top-down mass spectrometry: recent developments, applications and perspectives. Analyst 2011; 136:3854-64. [PMID: 21826297 PMCID: PMC3505190 DOI: 10.1039/c1an15286f] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Top-down mass spectrometry is an emerging approach for the analysis of intact proteins. The term was coined as a contrast with the better-established, bottom-up strategy for analysis of peptide fragments derived from digestion, either enzymatically or chemically, of intact proteins. Although the term top-down originates from proteomics, it can also be applied to mass spectrometric analysis of intact large biomolecules that are constituents of protein assemblies or complexes. Traditionally, mass spectrometry has usually started with intact molecules, and in this regard, top-down approaches reflect the spirit of mass spectrometry. This article provides an overview of the methodologies in top-down mass spectrometry and then reviews applications covering protein posttranslational modifications, protein biophysics, DNAs/RNAs, and protein assemblies. Finally, challenges and future directions are discussed.
Collapse
Affiliation(s)
- Weidong Cui
- NIH NCRR Center for Biomedical and Bio-Organic Mass Spectrometry, Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
| | | | | |
Collapse
|
14
|
Tipton JD, Tran JC, Catherman AD, Ahlf DR, Durbin KR, Kelleher NL. Analysis of intact protein isoforms by mass spectrometry. J Biol Chem 2011; 286:25451-8. [PMID: 21632550 DOI: 10.1074/jbc.r111.239442] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The diverse proteome of an organism arises from such events as single nucleotide substitutions at the DNA level, different RNA processing, and dynamic enzymatic post-translational modifications. This minireview focuses on the measurement of intact proteins to describe the diversity found in proteomes. The field of biological mass spectrometry has steadily advanced, enabling improvements in the characterization of single proteins to proteins derived from cells or tissues. In this minireview, we discuss the basic technology for "top-down" intact protein analysis. Furthermore, examples of studies involved with the qualitative and quantitative analysis of full-length polypeptides are provided.
Collapse
Affiliation(s)
- Jeremiah D Tipton
- Departmen of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | | | | | | | | | | |
Collapse
|
15
|
Tweedie-Cullen RY, Mansuy IM. Towards a better understanding of nuclear processes based on proteomics. Amino Acids 2010; 39:1117-30. [PMID: 20730591 DOI: 10.1007/s00726-010-0723-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 08/09/2010] [Indexed: 12/25/2022]
Abstract
The complex structural and functional organisation of the brain warrants the application of high-throughput approaches to study its functional alterations in physiological and pathological conditions. Such approaches have greatly benefited from advances in proteomics and genomics, and from their combination with computational modelling. They have been particularly instrumental for the analysis of processes such as the post-translational modification (PTM) of proteins, a critical biological process in the nervous system that remains not well studied. Protein PTMs are dynamic covalent marks that can be induced by activity and allow the maintenance of a trace of this activity. In the nucleus, they can modulate histone proteins and the components of the transcriptional machinery, and thereby contribute to regulating gene expression. PTMs do however need to be tightly controlled for proper chromatin functions. This review provides a synopsis of methods available to study PTMs and protein expression based on high-throughput mass spectrometry (MS), and covers basic concepts of traditional 'shot-gun'-based MS. It describes classical and emerging proteomic approaches such as multiple reaction monitoring and electron transfer dissociation, and their application to the analyses of nuclear processes in the brain.
Collapse
Affiliation(s)
- Ry Y Tweedie-Cullen
- Department of Biology of the ETH Zurich and Medical Faculty of the University Zurich, 8057, Zurich, Switzerland.
| | | |
Collapse
|