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Gao X, Pang C, Fan Z, Wang Y, Duan Y, Zhan H. Regulation of newly identified lysine lactylation in cancer. Cancer Lett 2024; 587:216680. [PMID: 38346584 DOI: 10.1016/j.canlet.2024.216680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024]
Abstract
Metabolic reprogramming is a typical hallmark of cancer. Enhanced glycolysis in tumor cells leads to the accumulation of lactate, which is traditionally considered metabolic waste. With the development of high-resolution liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), the lactate-derived, lysine lactylation(Kla), has been identified. Kla can alter the spatial configuration of chromatin and regulate the expression of corresponding genes. Metabolic reprogramming and epigenetic remodeling have been extensively linked. Accumulating studies have subsequently expanded the framework on the key roles of this protein translational modification (PTM) in tumors and have provided a new concept of cancer-specific regulation by Kla.
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Affiliation(s)
- Xin Gao
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Chaoyu Pang
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Zhiyao Fan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China.
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Berthias F, Bilgin N, Mecinović J, Jensen ON. Top-down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms. Proteomics 2024; 24:e2200471. [PMID: 38282202 DOI: 10.1002/pmic.202200471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
Enzymatic catalysis is one of the fundamental processes that drives the dynamic landscape of post-translational modifications (PTMs), expanding the structural and functional diversity of proteins. Here, we assessed enzyme specificity using a top-down ion mobility spectrometry (IMS) and tandem mass spectrometry (MS/MS) workflow. We successfully applied trapped IMS (TIMS) to investigate site-specific N-ε-acetylation of lysine residues of full-length histone H4 catalyzed by histone lysine acetyltransferase KAT8. We demonstrate that KAT8 exhibits a preference for N-ε-acetylation of residue K16, while also adding acetyl groups on residues K5 and K8 as the first degree of acetylation. Achieving TIMS resolving power values of up to 300, we fully separated mono-acetylated regioisomers (H4K5ac, H4K8ac, and H4K16ac). Each of these separated regioisomers produce unique MS/MS fragment ions, enabling estimation of their individual mobility distributions and the exact localization of the N-ε-acetylation sites. This study highlights the potential of top-down TIMS-MS/MS for conducting enzymatic assays at the intact protein level and, more generally, for separation and identification of intact isomeric proteoforms and precise PTM localization.
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Affiliation(s)
- Francis Berthias
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Pienkowski T, Kowalczyk T, Cysewski D, Kretowski A, Ciborowski M. Glioma and post-translational modifications: A complex relationship. Biochim Biophys Acta Rev Cancer 2023; 1878:189009. [PMID: 37913943 DOI: 10.1016/j.bbcan.2023.189009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
Post-translational modifications (PTMs) are common covalent processes in biochemical pathways that alter protein function and activity. These modifications occur through proteolytic cleavage or attachment of modifying groups, such as phosphoryl, methyl, glycosyl, or acetyl groups, with one or more amino acid residues of a single protein. Some PTMs also present crosstalk abilities that affect both protein functionality and structure, creating new proteoforms. Any alteration in organism homeostasis may be a cancer hallmark. Cataloging PTMs and consequently, emerging proteoforms, present new therapeutic targets, approaches, and opportunities to discover additional discriminatory biomarkers in disease diagnostics. In this review, we focus on experimentally confirmed PTMs and their potential crosstalk in glioma research to introduce new opportunities for this tumor type, which emerge within the PTMomics area.
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Affiliation(s)
- Tomasz Pienkowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Tomasz Kowalczyk
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
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Hu H, Burrow MF, Leung WK. Proteomic profile of in situ acquired pellicle on tooth and restorative material surfaces. J Dent 2023; 129:104389. [PMID: 36526084 DOI: 10.1016/j.jdent.2022.104389] [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: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To evaluate and compare the proteomic profile of acquired pellicle on smooth bovine tooth and tooth-coloured restorative materials, including resin composite (RC), glass ionomer cement (GIC), and casein phosphopeptide-amorphous calcium phosphate modified GIC (CPP-ACP GIC). METHODS Two-hour in situ pellicles on tooth/materials specimens mounted in oral appliances worn by ten healthy adults were investigated. Pellicle proteins and corresponding unstimulated whole saliva were quantitatively analysed through liquid chromatography-tandem mass spectrometry. RESULTS Significantly higher amounts of protein were adsorbed onto tooth surface than restorative materials tested (4.11 ± 0.69 vs. 2.54 ± 0.38/2.98 ± 0.80/3.01 ± 0.37 µg, RC/GIC/CPP-ACP GIC). From the ten participants, 1,444 (487-1,086/person), 1,454 (645-1,051/person), 1,731 (454-1,475/person), or 1,597 (423-1,261/person) pellicle proteins were detected at least once on bovine tooth, RC, GIC, or CPP-ACP GIC, respectively, and with 1,072 (304-793/person) salivary proteins identified. Comparative quantification revealed minor differences between tooth and restorative materials pellicle profiles. High inter-individual variations in pellicle protein composition were demonstrated. Compared to the salivary protein profile, 214/57 proteins showed significantly increased/decreased abundance in pellicle formed on at least one substrate (fold change > 3.325/fold change < 0.301). Gene Ontology enrichment analysis showed some pellicle proteins detected with increased affinity to tooth/material surface were identified as being related to "calcium-dependent protein binding" or "cell-cell adhesion mediator activity". CONCLUSION Similar protein quantity and composition was observed in 2 h in situ pellicles formed on different smooth restorative material surfaces. The proteomic profile of pellicles appeared distinct from that of the corresponding unstimulated whole saliva. CLINICAL SIGNIFICANCE Host backgrounds appeared more influential on the proteomic profile of the in situ acquired pellicle than the underlying substrate characteristics among systemically and orally healthy adults. Pellicle proteins preferentially adsorbed on tooth/materials were putatively associated with calcium ion homeostasis or host-microbiota interaction.
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Affiliation(s)
- Hongying Hu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China
| | - Michael Francis Burrow
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China
| | - Wai Keung Leung
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China.
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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Brandi J, Noberini R, Bonaldi T, Cecconi D. Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications. J Chromatogr A 2022; 1678:463352. [PMID: 35896048 DOI: 10.1016/j.chroma.2022.463352] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Post-translational modifications (PTMs) occur during or after protein biosynthesis and increase the functional diversity of proteome. They comprise phosphorylation, acetylation, methylation, glycosylation, ubiquitination, sumoylation (among many other modifications), and influence all aspects of cell biology. Mass-spectrometry (MS)-based proteomics is the most powerful approach for PTM analysis. Despite this, it is challenging due to low abundance and labile nature of many PTMs. Hence, enrichment of modified peptides is required for MS analysis. This review provides an overview of most common PTMs and a discussion of current enrichment methods for MS-based proteomics analysis. The traditional affinity strategies, including immunoenrichment, chromatography and protein pull-down, are outlined together with their strengths and shortcomings. Moreover, a special attention is paid to chemical enrichment strategies, such as capture by chemoselective probes, metabolic and chemoenzymatic labelling, which are discussed with an emphasis on their recent progress. Finally, the challenges and future trends in the field are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy.
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy.
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
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Detection of single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of Phi29 DNA packaging motor. Biomaterials 2021; 276:121022. [PMID: 34298441 DOI: 10.1016/j.biomaterials.2021.121022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 12/22/2022]
Abstract
Protein post-translational modification (PTM) is crucial to modulate protein interactions and activity in various biological processes. Emerging evidence has revealed PTM patterns participate in the pathology onset and progression of various diseases. Current PTM identification relies mainly on mass spectrometry-based approaches that limit the assessment to the entire protein population in question. Here we report a label-free method for the detection of the single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of phi29 DNA packaging motor, which bears the deletion of 25-amino acids (AA) at the C-terminus or 17-AA at the internal loop of the channel. The mutant channels were used to detect propionylation modification via single-molecule fingerprinting in either the traditional patch-clamp or the portable MinION™ platform of Oxford Nanopore Technologies. Up to 2000 channels are available in the MinION™ Flow Cells. The current signatures and dwell time of individual channels were identified. Peptides with only one propionylation were differentiated. Excitingly, identification of single or multiple modifications on the MinION™ system was achieved. The successful application of PTM differentiation on the MinION™ system represents a significant advance towards developing a label-free and high-throughput detection platform utilizing nanopores for clinical diagnosis based on PTM.
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Kassab S, Albalawi Z, Daghistani H, Kitmitto A. Mitochondrial Arrest on the Microtubule Highway-A Feature of Heart Failure and Diabetic Cardiomyopathy? Front Cardiovasc Med 2021; 8:689101. [PMID: 34277734 PMCID: PMC8282893 DOI: 10.3389/fcvm.2021.689101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/08/2021] [Indexed: 01/16/2023] Open
Abstract
A pathophysiological consequence of both type 1 and 2 diabetes is remodelling of the myocardium leading to the loss of left ventricular pump function and ultimately heart failure (HF). Abnormal cardiac bioenergetics associated with mitochondrial dysfunction occurs in the early stages of HF. Key factors influencing mitochondrial function are the shape, size and organisation of mitochondria within cardiomyocytes, with reports identifying small, fragmented mitochondria in the myocardium of diabetic patients. Cardiac mitochondria are now known to be dynamic organelles (with various functions beyond energy production); however, the mechanisms that underpin their dynamism are complex and links to motility are yet to be fully understood, particularly within the context of HF. This review will consider how the outer mitochondrial membrane protein Miro1 (Rhot1) mediates mitochondrial movement along microtubules via crosstalk with kinesin motors and explore the evidence for molecular level changes in the setting of diabetic cardiomyopathy. As HF and diabetes are recognised inflammatory conditions, with reports of enhanced activation of the NLRP3 inflammasome, we will also consider evidence linking microtubule organisation, inflammation and the association to mitochondrial motility. Diabetes is a global pandemic but with limited treatment options for diabetic cardiomyopathy, therefore we also discuss potential therapeutic approaches to target the mitochondrial-microtubule-inflammatory axis.
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Affiliation(s)
- Sarah Kassab
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Zainab Albalawi
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Hussam Daghistani
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Ashraf Kitmitto
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
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Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
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10
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Roychowdhury T, Chattopadhyay S. Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation. Front Cell Dev Biol 2020; 8:602994. [PMID: 33409278 PMCID: PMC7779526 DOI: 10.3389/fcell.2020.602994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023] Open
Abstract
Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.
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Affiliation(s)
- Tanaya Roychowdhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
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Gamon LF, Guo C, He J, Hägglund P, Hawkins CL, Davies MJ. Absolute quantitative analysis of intact and oxidized amino acids by LC-MS without prior derivatization. Redox Biol 2020; 36:101586. [PMID: 32505089 PMCID: PMC7276450 DOI: 10.1016/j.redox.2020.101586] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/15/2023] Open
Abstract
The precise characterization and quantification of oxidative protein damage is a significant challenge due to the low abundance, large variety, and heterogeneity of modifications. Mass spectrometry (MS)-based techniques at the peptide level (proteomics) provide a detailed but limited picture due to incomplete sequence coverage and imperfect enzymatic digestion. This is particularly problematic with oxidatively modified and cross-linked/aggregated proteins. There is a pressing need for methods that can quantify large numbers of modified amino acids, which are often present in low abundance compared to the high background of non-damaged amino acids, in a rapid and reliable fashion. We have developed a protocol using zwitterionic ion-exchange chromatography coupled with LC-MS to simultaneously quantify both parent amino acids and their respective oxidation products. Proteins are hydrolyzed with methanesulfonic acid in the presence of tryptamine and purified by strong cation exchange solid phase extraction. The method was validated for the common amino acids (excluding Gln, Asn, Cys) and the oxidation products 3-chlorotyrosine (3-ClTyr), 3-nitrotyrosine (3-NO2Tyr), di-tyrosine, Nε-(1-carboxymethyl)-l-lysine, o,o’-di-tyrosine, 3,4,-dihydroxyphenylalanine, hydroxy-tryptophan and kynurenine. Linear standard curves were observed over ~3 orders of magnitude dynamic range (2–1000 pmol for parent amino acids, 80 fmol–20 pmol for oxidation products) with limit-of-quantification values as low as 200 fmol (o,o’-di-tyrosine). The validated method was used to quantify Tyr and Trp loss, and formation of 3-NO2Tyr on the isolated protein anastellin treated with peroxynitrous acid, and for 3-ClTyr formation (over a 2 orders of magnitude range) in cell lysates and complex protein mixtures treated with hypochlorous acid. Identification and quantification of oxidative protein damage is a major challenge. A versatile LC-MS assay is reported that involves hydrolysis to free amino acids. Quantification is possible for both parent amino acids and products in single runs. A dynamic range of 2-3 orders of magnitude is available for most analytes. Example of use with pure proteins, extracellular matrix and cell lysates are given.
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Affiliation(s)
- Luke F Gamon
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chaorui Guo
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jianfei He
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Hägglund
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Clare L Hawkins
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
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