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Chen S, Li D, Zeng Z, Zhang W, Xie H, Tang J, Liao S, Cai W, Liu F, Tang D, Dai Y. Analysis of proteome and post-translational modifications of 2-hydroxyisobutyrylation reveals the glycolysis pathway in oral adenoid cystic carcinoma. World J Surg Oncol 2023; 21:301. [PMID: 37741973 PMCID: PMC10517466 DOI: 10.1186/s12957-023-03155-x] [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: 05/18/2023] [Accepted: 08/19/2023] [Indexed: 09/25/2023] Open
Abstract
PURPOSE Oral adenoid cystic carcinoma (OACC) has high rates of both local-regional recurrence and distant metastasis. The objective of this study is to investigate the impact of Khib on OACC and its potential as a targeted therapeutic intervention. EXPERIMENTAL DESIGN: We investigated the DEPs (differentially expressed proteins) and DHMPs between OACC-T and OACC-N using LC-MS/MS-based quantitative proteomics and using several bioinformatics methods, including GO enrichment analysis, KEGG pathway analysis, subcellular localization prediction, MEA (motif enrichment analysis), and PPI (protein-protein interaction networks) to illustrate how Khib modification interfere with OACC evolution. RESULTS Compared OACC-tumor samples (OACC-T) with the adjacent normal samples (OACC-N), there were 3243 of the DEPs and 2011 Khib sites were identified on 764 proteins (DHMPs). DEPs and DHMPs were strongly associated to glycolysis pathway. GAPDH of K254, ENO of K228, and PGK1 of K323 were modified by Khib in OACC-T. Khib may increase the catalytic efficiency to promote glycolysis pathway and favor OACC progression. CONCLUSIONS AND CLINICAL RELEVANCE Khib may play a significant role in the mechanism of OACC progression by influencing the enzyme activity of the glycolysis pathway. These findings may provide new therapeutic options of OACC.
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Affiliation(s)
- Sining Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
- Nephrology Department, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China
| | - Dandan Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
- Experimental Center, Shenzhen Pingle Orthopedic Hospital (Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, Guangdong, 518118, China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
| | - Wei Zhang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
| | - Hongliang Xie
- Department of Oral and Maxillofacial Surgery, Stomatological Medical Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Jianming Tang
- Department of Oral and Maxillofacial Surgery, Stomatological Medical Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Shengyou Liao
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
| | - Wanxia Cai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China
| | - Fanna Liu
- Nephrology Department, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China.
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China.
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, Guangdong, China.
- Comprehensive health Industry Research Center, Taizhou Research Institute, Southern University of Science and Technology, Taizhou, 318000, China.
- Department of Organ Transplantation, No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guilin, 541002, China.
- The first affiliated hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, 232001, China.
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2
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Head PE, Myung S, Chen Y, Schneller JL, Wang C, Duncan N, Hoffman P, Chang D, Gebremariam A, Gucek M, Manoli I, Venditti CP. Aberrant methylmalonylation underlies methylmalonic acidemia and is attenuated by an engineered sirtuin. Sci Transl Med 2022; 14:eabn4772. [PMID: 35613279 PMCID: PMC10468269 DOI: 10.1126/scitranslmed.abn4772] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organic acidemias such as methylmalonic acidemia (MMA) are a group of inborn errors of metabolism that typically arise from defects in the catabolism of amino and fatty acids. Accretion of acyl-CoA species is postulated to underlie disease pathophysiology, but the mechanism(s) remain unknown. Here, we surveyed hepatic explants from patients with MMA and unaffected donors, in parallel with samples from various mouse models of methylmalonyl-CoA mutase deficiency. We found a widespread posttranslational modification, methylmalonylation, that inhibited enzymes in the urea cycle and glycine cleavage pathway in MMA. Biochemical studies and mouse genetics established that sirtuin 5 (SIRT5) controlled the metabolism of MMA-related posttranslational modifications. SIRT5 was engineered to resist acylation-driven inhibition via lysine to arginine mutagenesis. The modified SIRT5 was used to create an adeno-associated viral 8 (AAV8) vector and systemically delivered to mutant and control mice. Gene therapy ameliorated hyperammonemia and reduced global methylmalonylation in the MMA mice.
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Affiliation(s)
- PamelaSara E. Head
- National Institute of General Medical Sciences, NIH, 45 Center Drive MSC 6200 Bethesda, MD, 20892-6200 USA
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Sangho Myung
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Yong Chen
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Jessica L. Schneller
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Cindy Wang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Nicholas Duncan
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Pauline Hoffman
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - David Chang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Abigael Gebremariam
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Marjan Gucek
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Irini Manoli
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Charles P. Venditti
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
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3
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Yang M, Zhu Z, Zhuang Z, Bai Y, Wang S, Ge F. Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production. Mol Cell Proteomics 2020; 20:100013. [PMID: 33568340 PMCID: PMC7950108 DOI: 10.1074/mcp.ra120.002144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.
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Affiliation(s)
- Mingkun Yang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhuo Zhu
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youhuang Bai
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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4
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Yakubu RR, Nieves E, Weiss LM. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:169-198. [PMID: 31347048 DOI: 10.1007/978-3-030-15950-4_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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5
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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6
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Yang M, Lin X, Liu X, Zhang J, Ge F. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline. MOLECULAR PLANT 2018; 11:1292-1307. [PMID: 30176371 DOI: 10.1016/j.molp.2018.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.
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Affiliation(s)
- Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jia Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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7
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Darling AL, Uversky VN. Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter. Front Genet 2018; 9:158. [PMID: 29780404 PMCID: PMC5945825 DOI: 10.3389/fgene.2018.00158] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins and domains that devoid stable secondary and/or tertiary structure. IDPs/IDPRs are abundantly present in various proteomes, where they are involved in regulation, signaling, and control, thereby serving as crucial regulators of various cellular processes. Various mechanisms are utilized to tightly regulate and modulate biological functions, structural properties, cellular levels, and localization of these important controllers. Among these regulatory mechanisms are precisely controlled degradation and different posttranslational modifications (PTMs). Many normal cellular processes are associated with the presence of the right amounts of precisely activated IDPs at right places and in right time. However, wrecked regulation of IDPs/IDPRs might be associated with various human maladies, ranging from cancer and neurodegeneration to cardiovascular disease and diabetes. Pathogenic transformations of IDPs/IDPRs are often triggered by altered PTMs. This review considers some of the aspects of IDPs/IDPRs and their normal and aberrant regulation by PTMs.
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Affiliation(s)
- April L Darling
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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8
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Liu Q, Remmelzwaal S, Heck AJR, Akhmanova A, Liu F. Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry. Sci Rep 2017; 7:13453. [PMID: 29044157 PMCID: PMC5647383 DOI: 10.1038/s41598-017-13663-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/25/2017] [Indexed: 10/27/2022] Open
Abstract
Characterization of protein interaction domains is crucial for understanding protein functions. Here we combine cross-linking mass spectrometry (XL-MS) with deletion analysis to accurately locate minimal protein interaction domains. As a proof of concept, we investigated in detail the binding interfaces of two protein assemblies: the complex formed by MICAL3, ELKS and Rab8A, which is involved in exocytosis, and the complex of SLAIN2, CLASP2 and ch-TOG, which controls microtubule dynamics. We found that XL-MS provides valuable information to efficiently guide the design of protein fragments that are essential for protein interaction. However, we also observed a number of cross-links between polypeptide regions that were dispensable for complex formation, especially among intrinsically disordered sequences. Collectively, our results indicate that XL-MS, which renders distance restrains of linked residue pairs, accelerates the characterization of protein binding regions in combination with other biochemical approaches.
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Affiliation(s)
- Qingyang Liu
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sanne Remmelzwaal
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Fan Liu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands.
- Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany.
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9
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Nguyen VA, Carey LM, Giummarra L, Faou P, Cooke I, Howells DW, Tse T, Macaulay SL, Ma H, Davis SM, Donnan GA, Crewther SG. A Pathway Proteomic Profile of Ischemic Stroke Survivors Reveals Innate Immune Dysfunction in Association with Mild Symptoms of Depression - A Pilot Study. Front Neurol 2016; 7:85. [PMID: 27379006 PMCID: PMC4907034 DOI: 10.3389/fneur.2016.00085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022] Open
Abstract
Depression after stroke is a common occurrence, raising questions as to whether depression could be a long-term biological and immunological sequela of stroke. Early explanations for post-stroke depression (PSD) focused on the neuropsychological/psychosocial effects of stroke on mobility and quality of life. However, recent investigations have revealed imbalances of inflammatory cytokine levels in association with PSD, though to date, there is only one published proteomic pathway analysis testing this hypothesis. Thus, we examined the serum proteome of stroke patients (n = 44, mean age = 63.62 years) and correlated these with the Montgomery–Åsberg Depression Rating Scale (MADRS) scores at 3 months post-stroke. Overall, the patients presented with mild depression symptoms on the MADRS, M = 6.40 (SD = 7.42). A discovery approach utilizing label-free relative quantification was employed utilizing an LC-ESI–MS/MS coupled to a LTQ-Orbitrap Elite (Thermo-Scientific). Identified peptides were analyzed using the gene set enrichment approach on several different genomic databases that all indicated significant downregulation of the complement and coagulation systems with increasing MADRS scores. Complement and coagulation systems are traditionally thought to play a key role in the innate immune system and are established precursors to the adaptive immune system through pro-inflammatory cytokine signaling. Both systems are known to be globally affected after ischemic or hemorrhagic stroke. Thus, our results suggest that lowered complement expression in the periphery in conjunction with depressive symptoms post-stroke may be a biomarker for incomplete recovery of brain metabolic needs, homeostasis, and inflammation following ischemic stroke damage. Further proteomic investigations are now required to construct the temporal profile, leading from acute lesion damage to manifestation of depressive symptoms. Overall, the findings provide support for the involvement of inflammatory and immune mechanisms in PSD symptoms and further demonstrate the value and feasibility of the proteomic approach in stroke research.
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Affiliation(s)
- Vinh A Nguyen
- Occupational Therapy, College of Science Health and Engineering, School of Allied Health, La Trobe University, Melbourne, VIC, Australia; Neurorehabilitation and Recovery, Stroke, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia; School of Psychology and Public Health, La Trobe University, Melbourne, VIC, Australia
| | - Leeanne M Carey
- Occupational Therapy, College of Science Health and Engineering, School of Allied Health, La Trobe University, Melbourne, VIC, Australia; Neurorehabilitation and Recovery, Stroke, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Loretta Giummarra
- School of Psychology and Public Health, La Trobe University , Melbourne, VIC , Australia
| | - Pierre Faou
- School of Molecular Sciences, La Trobe University , Melbourne, VIC , Australia
| | - Ira Cooke
- School of Molecular Sciences, La Trobe University , Melbourne, VIC , Australia
| | - David W Howells
- School of Medicine, University of Tasmania , Hobart, TAS , Australia
| | - Tamara Tse
- Occupational Therapy, College of Science Health and Engineering, School of Allied Health, La Trobe University, Melbourne, VIC, Australia; Neurorehabilitation and Recovery, Stroke, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - S Lance Macaulay
- Commonwealth Science and Industrial Research Organisation (CSIRO) , Melbourne, VIC , Australia
| | - Henry Ma
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia; Monash University, Clayton, VIC, Australia
| | - Stephen M Davis
- The University of Melbourne, Parkville, VIC, Australia; Department of Medicine, Melbourne Brain Centre, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Geoffrey A Donnan
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia; The University of Melbourne, Parkville, VIC, Australia
| | - Sheila G Crewther
- Neurorehabilitation and Recovery, Stroke, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia; School of Psychology and Public Health, La Trobe University, Melbourne, VIC, Australia
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10
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Proietto M, Bianchi MM, Ballario P, Brenna A. Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa. Int J Mol Sci 2015; 16:15347-83. [PMID: 26198228 PMCID: PMC4519903 DOI: 10.3390/ijms160715347] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/24/2015] [Accepted: 06/30/2015] [Indexed: 12/15/2022] Open
Abstract
Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC), a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ), the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM). The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.
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Affiliation(s)
- Marco Proietto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Michele Maria Bianchi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Paola Ballario
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Andrea Brenna
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Department of Biology, Division of Biochemistry, University of Fribourg, Chemin du Musée 5, Fribourg 1700, Switzerland.
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Szabo Z, Janaky T. Challenges and developments in protein identification using mass spectrometry. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Butt AQ, McArdle A, Gibson DS, FitzGerald O, Pennington SR. Psoriatic Arthritis Under a Proteomic Spotlight: Application of Novel Technologies to Advance Diagnosis and Management. Curr Rheumatol Rep 2015; 17:35. [DOI: 10.1007/s11926-015-0509-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Woods AG, Wormwood KL, Wetie AGN, Aslebagh R, Crimmins BS, Holsen TM, Darie CC. Autism spectrum disorder: an omics perspective. Proteomics Clin Appl 2014; 9:159-68. [PMID: 25311756 DOI: 10.1002/prca.201400116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/11/2014] [Accepted: 10/07/2014] [Indexed: 01/02/2023]
Abstract
Current directions in autism spectrum disorder (ASD) research may require moving beyond genetic analysis alone, based on the complexity of the disorder, heterogeneity and convergence of genetic alterations at the cellular/functional level. Mass spectrometry (MS) has been increasingly used to study CNS disorders, including ASDs. Proteomic research using MS is directed at understanding endogenous protein changes that occur in ASD. This review focuses on how MS has been used to study ASDs, with particular focus on proteomic analysis. Other neurodevelopmental disorders have been investigated using MS, including fragile X syndrome (FXS) and Smith-Lemli-Opitz Syndrome (SLOS), genetic syndromes highly associated with ASD comorbidity.
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Affiliation(s)
- Alisa G Woods
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA; SUNY Plattsburgh Neuropsychology Clinic and Psychoeducation Services, Plattsburgh, NY, USA
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