1
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Zhang Y, Xu W, Peng C, Ren S, Zhang C. Intricate effects of post-translational modifications in liver cancer: mechanisms to clinical applications. J Transl Med 2024; 22:651. [PMID: 38997696 PMCID: PMC11245821 DOI: 10.1186/s12967-024-05455-6] [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: 04/14/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024] Open
Abstract
Liver cancer is a significant global health challenge, with hepatocellular carcinoma (HCC) being the most prevalent form, characterized by high incidence and mortality rates. Despite advances in targeted therapies and immunotherapies, the prognosis for advanced liver cancer remains poor. This underscores the urgent need for a deeper understanding of the molecular mechanisms underlying HCC to enable early detection and the development of novel therapeutic strategies. Post-translational modifications (PTMs) are crucial regulatory mechanisms in cellular biology, affecting protein functionality, interactions, and localization. These modifications, including phosphorylation, acetylation, methylation, ubiquitination, and glycosylation, occur after protein synthesis and play vital roles in various cellular processes. Recent advances in proteomics and molecular biology have highlighted the complex networks of PTMs, emphasizing their critical role in maintaining cellular homeostasis and disease pathogenesis. Dysregulation of PTMs has been associated with several malignant cellular processes in HCC, such as altered cell proliferation, migration, immune evasion, and metabolic reprogramming, contributing to tumor growth and metastasis. This review aims to provide a comprehensive understanding of the pathological mechanisms and clinical implications of various PTMs in liver cancer. By exploring the multifaceted interactions of PTMs and their impact on liver cancer progression, we highlight the potential of PTMs as biomarkers and therapeutic targets. The significance of this review lies in its potential to inform the development of novel therapeutic approaches and improve prognostic tools for early intervention in the fight against liver cancer.
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Affiliation(s)
- Yu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weihao Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenli Ren
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Cheng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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2
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Wang X, Wang H, Li J, Li L, Wang Y, Li A. Salt-induced phosphoproteomic changes in the subfornical organ in rats with chronic kidney disease. Ren Fail 2023; 45:2171886. [PMID: 36715439 PMCID: PMC9888458 DOI: 10.1080/0886022x.2023.2171886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVES Subfornical organ (SFO) is vital in chronic kidney disease (CKD) progression caused by high salt levels. The current study investigated the effects of high salt on phosphoproteomic changes in SFO in CKD rats. METHODS 5/6 nephrectomized rats were fed a normal-salt diet (0.4%) (NC group) or a high-salt diet (4%) (HC group) for three weeks, while sham-operated rats were fed a normal-salt diet (0.4%) (NS group). For phosphoproteomic analysis of SFO in different groups, TiO2 enrichment, isobaric tags for relative and absolute quantification (iTRAQ) labeling, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used. RESULTS There were 6808 distinct phosphopeptides found, which corresponded to 2661 phosphoproteins. NC group had 168 upregulated and 250 downregulated phosphopeptides compared to NS group. Comparison to NC group, HC group had 154 upregulated and 124 downregulated phosphopeptides. Growth associated protein 43 (GAP43) and heat shock protein 27 (Hsp27) were significantly upregulated phosphoproteins and may protect against high-salt damage. Differential phosphoproteins with tight functional connection were synapse proteins and microtubule-associated proteins, implying that high-salt diet disrupted brain's structure and function. Furthermore, differential phosphoproteins in HC/NC comparison group were annotated to participate in GABAergic synapse signaling pathway and aldosterone synthesis and secretion, which attenuated inhibitory neurotransmitter effects and increased sympathetic nerve activity (SNA). DISCUSSION This large scale phosphoproteomic profiling of SFO sheds light on how salt aggravates CKD via the central nervous system.
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Affiliation(s)
- Xin Wang
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Clinical Research Center for Kidney Disease, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huizhen Wang
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Clinical Research Center for Kidney Disease, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiawen Li
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lanying Li
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yifan Wang
- Anshun People’s Hospital of Guizhou Province, Anshun, China
| | - Aiqing Li
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Clinical Research Center for Kidney Disease, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China,CONTACT Aiqing Li National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Clinical Research Center for Kidney Disease, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
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3
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Amirian R, Azadi Badrbani M, Izadi Z, Samadian H, Bahrami G, Sarvari S, Abdolmaleki S, Nabavi SM, Derakhshankhah H, Jaymand M. Targeted protein modification as a paradigm shift in drug discovery. Eur J Med Chem 2023; 260:115765. [PMID: 37659194 DOI: 10.1016/j.ejmech.2023.115765] [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: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Targeted Protein Modification (TPM) is an umbrella term encompassing numerous tools and approaches that use bifunctional agents to induce a desired modification over the POI. The most well-known TPM mechanism is PROTAC-directed protein ubiquitination. PROTAC-based targeted degradation offers several advantages over conventional small-molecule inhibitors, has shifted the drug discovery paradigm, and is acquiring increasing interest as over ten PROTACs have entered clinical trials in the past few years. Targeting the protein of interest for proteasomal degradation by PROTACS was the pioneer of various toolboxes for selective protein degradation. Nowadays, the ever-increasing number of tools and strategies for modulating and modifying the POI has expanded far beyond protein degradation, which phosphorylation and de-phosphorylation of the protein of interest, targeted acetylation, and selective modification of protein O-GlcNAcylation are among them. These novel strategies have opened new avenues for achieving more precise outcomes while remaining feasible and minimizing side effects. This field, however, is still in its infancy and has a long way to precede widespread use and translation into clinical practice. Herein, we investigate the pros and cons of these novel strategies by exploring the latest advancements in this field. Ultimately, we briefly discuss the emerging potential applications of these innovations in cancer therapy, neurodegeneration, viral infections, and autoimmune and inflammatory diseases.
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Affiliation(s)
- Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Azadi Badrbani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hadi Samadian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Sarvari
- Department of Pharmaceutical Science, School of Pharmacy, West Virginia University, Morgantown, WV, USA.
| | - Sara Abdolmaleki
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Seyed Mohammad Nabavi
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy.
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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4
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Hu GS, Zheng ZZ, He YH, Wang DC, Liu W. CPPA: A Web Tool for Exploring Proteomic and Phosphoproteomic Data in Cancer. J Proteome Res 2022; 22:368-373. [PMID: 36507870 PMCID: PMC9904288 DOI: 10.1021/acs.jproteome.2c00512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A tremendous amount of proteomic and phosphoproteomic data has been produced over the years with the development of mass spectrometry techniques, providing us with new opportunities to explore and understand the proteome and phosphoproteome as well as the function of proteins and protein phosphorylation sites. However, a lack of powerful tools that we can utilize to explore these valuable data limits our understanding of the proteome and phosphoproteome, particularly in diseases such as cancer. To address these unmet needs, we established CPPA (Cancer Proteome and Phosphoproteome Atlas), a web tool to mine abnormalities of the proteome and phosphoproteome in cancer based on published data sets. All analysis results are presented in CPPA with a flexible web interface to provide key customization utilities, including general analysis, differential expression profiling, statistical analysis of protein phosphorylation sites, correlation analysis, similarity analysis, survival analysis, pathological stage analysis, etc. CPPA greatly facilitates the process of data mining and therapeutic target discovery by providing a comprehensive analysis of proteomic and phosphoproteomic data in normal and tumor tissues with a simple click, which helps to unlock the precious value of mass spectrometry data by bridging the gap between raw data and experimental biologists. CPPA is currently available at https://cppa.site/cppa.
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Affiliation(s)
- Guo-sheng Hu
- State
Key Laboratory of Cellular Stress Biology, School of Life Sciences,
Faculty of Medicine and Life Sciences, Xiamen
University, Xiang’an South Road, Xiamen, Fujian 361102, China,Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zao-zao Zheng
- State
Key Laboratory of Cellular Stress Biology, School of Life Sciences,
Faculty of Medicine and Life Sciences, Xiamen
University, Xiang’an South Road, Xiamen, Fujian 361102, China,Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Yao-hui He
- State
Key Laboratory of Cellular Stress Biology, School of Life Sciences,
Faculty of Medicine and Life Sciences, Xiamen
University, Xiang’an South Road, Xiamen, Fujian 361102, China,Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Du-chuang Wang
- State
Key Laboratory of Cellular Stress Biology, School of Life Sciences,
Faculty of Medicine and Life Sciences, Xiamen
University, Xiang’an South Road, Xiamen, Fujian 361102, China,Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- State
Key Laboratory of Cellular Stress Biology, School of Life Sciences,
Faculty of Medicine and Life Sciences, Xiamen
University, Xiang’an South Road, Xiamen, Fujian 361102, China,Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China,
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5
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Wang S, Chen YZ, Fu S, Zhao Y. In silico approaches uncovering the systematic function of N-phosphorylated proteins in human cells. Comput Biol Med 2022; 151:106280. [PMID: 36375414 DOI: 10.1016/j.compbiomed.2022.106280] [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: 07/03/2022] [Revised: 10/12/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Phosphorylation plays a key role in the regulation of protein function. In addition to the extensively studied O-phosphorylation of serine, threonine, and tyrosine, emerging evidence suggests that the non-canonical phosphorylation of histidine, lysine, and arginine termed N-phosphorylation, exists widely in eukaryotes. At present, the study of N-phosphorylation is still in its infancy, and its regulatory role and specific biological functions in mammalian cells are still unknown. Here, we report the in silico analysis of the systematic biological significance of N-phosphorylated proteins in human cells. The protein structural and functional domain enrichment analysis revealed that N-phosphorylated proteins are rich in RNA recognition motif, nucleotide-binding and alpha-beta plait domains. The most commonly enriched biological pathway is the metabolism of RNA. Besides, arginine phosphorylated (pArg) proteins are highly related to DNA repair, while histidine phosphorylated (pHis) proteins may play a role in the regulation of the cell cycle, and lysine phosphorylated (pLys) proteins are linked to cellular stress response, intracellular signal transduction, and intracellular transport, which are of great significance for maintaining cell homeostasis. Protein-protein interaction (PPI) network analysis revealed important hub proteins (i.e., SRSF1, HNRNPA1, HNRNPC, SRSF7, HNRNPH1, SRSF2, SRSF11, HNRNPD, SRRM2 and YBX1) which are closely related to neoplasms, nervous system diseases, and virus infection and have potential as therapeutic targets. Those proteins with clinical significance are worthy of attention, and the rational considerations of N-phosphorylation in occurrence and progression of diseases might be beneficial for further translational applications.
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Affiliation(s)
- Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Yu Zong Chen
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Songsen Fu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
| | - Yufen Zhao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China; Key Lab of Bioorganic Phosphorus Chemistry&Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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6
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Zhang M, Zhang Q, Cao Z, Cai X, Liu J, Jiang Y, Zhu Y, Zhou J, Yu L, Zhen X, Hu Y, Yan G, Sun H. MEKK4-mediated Phosphorylation of HOXA10 at Threonine 362 facilitates embryo adhesion to the endometrial epithelium. Cell Death Dis 2022; 8:415. [PMID: 36216824 PMCID: PMC9550837 DOI: 10.1038/s41420-022-01203-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/10/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022]
Abstract
Embryo adhesion is a very important step in the embryo implantation process. Homeobox A10 (HOXA10), a key transcriptional factor of endometrial receptivity, is indispensable for embryo adhesion. However, how to control the activation status of HOXA10 remains elusive. Here, we found that Mitogen-activated protein kinase kinase kinase 4 (MEKK4) was associated with HOXA10 and directly phosphorylated HOXA10 at threonine 362. This MEKK4-mediated phosphorylation enhanced HOXA10-mediated transcriptional responses and adhesion between the embryo and endometrial epithelium. Specific deletion or kinase inactivation of MEKK4 in endometrial epithelial cells attenuates adhesion between embryo and epithelium. Therefore, the identification of MEKK4 as a novel physiological positive regulator of HOXA10 activation provides mechanistic insights to improve embryo implantation success. Moreover, when Thr362 was mutated to alanine (T362A) to mimic its dephosphorylation, the protein stability and transcriptional regulation of HOXA10 were decreased. In addition, HOXA10 -promoted embryo adhesion was weakened after the mutation of Thr362, suggesting that the phosphorylation of HOXA10 at this site may be a new indicator for evaluating endometrial receptivity and judging the ‘implantation window’.
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Affiliation(s)
- Mei Zhang
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Qun Zhang
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Zhiwen Cao
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Xinyu Cai
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Jingyu Liu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Yue Jiang
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Yingchun Zhu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Jidong Zhou
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Lina Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Xin Zhen
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China
| | - Yali Hu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China.
| | - Guijun Yan
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China. .,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China. .,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210008, China.
| | - Haixiang Sun
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China. .,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, 210008, China. .,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211116, China.
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7
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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8
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Hong Y, Flinkman D, Suomi T, Pietilä S, James P, Coffey E, Elo LL. PhosPiR: an automated phosphoproteomic pipeline in R. Brief Bioinform 2021; 23:6456296. [PMID: 34882763 PMCID: PMC8787428 DOI: 10.1093/bib/bbab510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 01/01/2023] Open
Abstract
Large-scale phosphoproteome profiling using mass spectrometry (MS) provides functional insight that is crucial for disease biology and drug discovery. However, extracting biological understanding from these data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from large-scale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phosphosite annotation and translation across species, multilevel enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge.
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Affiliation(s)
- Ye Hong
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Dani Flinkman
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Lund University, Lund, Sweden
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Peter James
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Lund University, Lund, Sweden
| | - Eleanor Coffey
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
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9
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Yang X, Wei R, Shi Y, Liu LL, Wu Y, Zhao Y, Stephan DW. Oxyphosphoranes as precursors to bridging phosphate-catecholate ligands. Chem Commun (Camb) 2021; 57:1194-1197. [PMID: 33439178 DOI: 10.1039/d0cc07736d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examples of chelating ligands that incorporate P-O donors are seldom encountered. Herein, a series of novel bridging diphosphate ligand supported bimetallic Zr(iv), V(iii) and Ni(ii) complexes have been derived from reactions of the oxyphosphorane (C6Cl4O2)P(OEt)3 with the corresponding metal halides. The mechanism is probed and shown to involve elimination of ethyl halide, and ring opening affording the chelating phosphate-catecholate ligands.
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Affiliation(s)
- Xin Yang
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China.
| | - Rui Wei
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yaping Shi
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China.
| | - Liu Leo Liu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yile Wu
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Douglas W Stephan
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Department of Chemistry, University of Toronto, 80 St. George St, Toronto, ON M5S3H6, Canada.
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10
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Hadj-Moussa H, Wade SC, Childers CL, Storey KB. Mind the GAP: Purification and characterization of urea resistant GAPDH during extreme dehydration. Proteins 2020; 89:544-557. [PMID: 33368595 DOI: 10.1002/prot.26038] [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: 07/24/2020] [Revised: 11/24/2020] [Accepted: 12/12/2020] [Indexed: 11/12/2022]
Abstract
The African clawed frog (Xenopus laevis) withstands prolonged periods of extreme whole-body dehydration that lead to impaired blood flow, global hypoxia, and ischemic stress. During dehydration, these frogs shift from oxidative metabolism to a reliance on anaerobic glycolysis. In this study, we purified the central glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to electrophoretic homogeneity and investigated structural, kinetic, subcellular localization, and post-translational modification properties between control and 30% dehydrated X. laevis liver. GAPDH from dehydrated liver displayed a 25.4% reduction in maximal velocity and a 55.7% increase in its affinity for GAP, as compared to enzyme from hydrated frogs. Under dehydration mimicking conditions (150 mM urea and 1% PEG), GAP affinity was reduced with a Km value 53.8% higher than controls. Frog dehydration also induced a significant increase in serine phosphorylation, methylation, acetylation, beta-N-acetylglucosamination, and cysteine nitrosylation, post-translational modifications (PTMs). These modifications were bioinformatically predicted and experimentally validated to govern protein stability, enzymatic activity, and nuclear translocation, which increased during dehydration. These dehydration-responsive protein modifications, however, did not appear to affect enzymatic thermostability as GAPDH melting temperatures remained unchanged when tested with differential scanning fluorimetry. PTMs could promote extreme urea resistance in dehydrated GAPDH since the enzyme from dehydrated animals had a urea I50 of 7.3 M, while the I50 from the hydrated enzyme was 5.3 M. The physiological consequences of these dehydration-induced molecular modifications of GAPDH likely suppress GADPH glycolytic functions during the reduced circulation and global hypoxia experienced in dehydrated X. laevis.
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Affiliation(s)
- Hanane Hadj-Moussa
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Steven C Wade
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Christine L Childers
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada.,National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
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11
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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12
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Wang Y, Wei H, Tong J, Ji M, Yang J. pSynGAP1 disturbance-mediated hippocampal oscillation network impairment might contribute to long-term neurobehavioral abnormities in sepsis survivors. Aging (Albany NY) 2020; 12:23146-23164. [PMID: 33203791 PMCID: PMC7746391 DOI: 10.18632/aging.104080] [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: 01/08/2020] [Accepted: 08/17/2020] [Indexed: 02/01/2023]
Abstract
Although more patients survive sepsis and are increasingly discharged from the hospital, they often experience long-term cognitive and psychological impairment with significant socioeconomic impact. However, the pathophysiological mechanisms have not been fully elucidated. In the present study, we showed that LPS induced long-term neurobehavioral abnormities, as reflected by significantly decreased freezing time to context and sucrose preference. Using a high-throughput quantitative proteomic screen, we showed that phosphorylation of synaptic GTPase-activating protein 1 (pSynGAP1) was identified as the hub of synaptic plasticity and was significantly decreased following LPS exposure. This decreased pSynGAP was associated with significantly lower theta and gamma oscillations in the CA1 of the hippocampus. Notably, restoration of pSynGAP1 by roscovitine was able to reverse most of these abnormities. Taken together, our study suggested that pSynGAP1 disturbance-mediated hippocampal oscillation network impairment might play a critical role in long-term neurobehavioral abnormities of sepsis survivors.
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Affiliation(s)
- Yong Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hua Wei
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianhua Tong
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Muhuo Ji
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianjun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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13
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Suwanmajo T, Ramesh V, Krishnan J. Exploring cyclic networks of multisite modification reveals origins of information processing characteristics. Sci Rep 2020; 10:16542. [PMID: 33024185 PMCID: PMC7539153 DOI: 10.1038/s41598-020-73045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
Multisite phosphorylation (and generally multisite modification) is a basic way of encoding substrate function and circuits/networks of post-translational modifications (PTM) are ubiquitous in cell signalling. The information processing characteristics of PTM systems are a focal point of broad interest. The ordering of modifications is a key aspect of multisite modification, and a broad synthesis of the impact of ordering of modifications is still missing. We focus on a basic class of multisite modification circuits: the cyclic mechanism, which corresponds to the same ordering of phosphorylation and dephosphorylation, and examine multiple variants involving common/separate kinases and common/separate phosphatases. This is of interest both because it is encountered in concrete cellular contexts, and because it serves as a bridge between ordered (sequential) mechanisms (representing one type of ordering) and random mechanisms (which have no ordering). We show that bistability and biphasic dose response curves of the maximally modified phosphoform are ruled out for basic structural reasons independent of parameters, while oscillations can result with even just one shared enzyme. We then examine the effect of relaxing some basic assumptions about the ordering of modification. We show computationally and analytically how bistability, biphasic responses and oscillations can be generated by minimal augmentations to the cyclic mechanism even when these augmentations involved reactions operating in the unsaturated limit. All in all, using this approach we demonstrate (1) how the cyclic mechanism (with single augmentations) represents a modification circuit using minimal ingredients (in terms of shared enzymes and sequestration of enzymes) to generate bistability and oscillations, when compared to other mechanisms, (2) new design principles for rationally designing PTM systems for a variety of behaviour, (3) a basis and a necessary step for understanding the origins and robustness of behaviour observed in basic multisite modification systems.
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Affiliation(s)
- Thapanar Suwanmajo
- Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Vaidhiswaran Ramesh
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK
| | - J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK.
- Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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14
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Galego L, Barahona S, Romão CV, Arraiano CM. Phosphorylation status of BolA affects its role in transcription and biofilm development. FEBS J 2020; 288:961-979. [PMID: 32535996 DOI: 10.1111/febs.15447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022]
Abstract
BolA has been characterized as an important transcriptional regulator, which is induced in stationary phase of growth, and in response to several stresses. In Escherichia coli, its cellular function is associated with cell wall synthesis and division, morphology, permeability, motility and biofilm formation. Phosphorylation has been widely described as one of the most important events involved in the modulation of the activity of many transcription factors. In the present work, we have demonstrated in vivo and by mass spectrometry that BolA is phosphorylated in four highly conserved protein positions: S26, S45, T81 and S95. S95 is located in the C terminus unstructured region of the protein, and the other three sites are in the DNA-binding domain. These positions were mutated to nonphosphorylated residues, and their effects were investigated on different known BolA functions. Using northern blot experiments, we showed that the regulation of the expression of these Ser/Thr BolA mutants is performed at the post-translational level. Western blot results revealed that the stability/turnover of the mutated BolA proteins is differently affected depending on the dephosphorylated residue. Moreover, we provide evidences that phosphorylation events are crucial in the modulation of BolA activity as a transcription factor and as a regulator of cell morphology and biofilm development. Here, we propose that phosphorylation affects BolA downstream functions and discuss the possible significance of these phosphoresidues in the protein structure, stability, dimerization and function as a transcription factor.
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Affiliation(s)
- Lisete Galego
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana Barahona
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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15
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Dong Z, Gao M, Li C, Xu M, Liu S. LncRNA UCA1 Antagonizes Arsenic-Induced Cell Cycle Arrest through Destabilizing EZH2 and Facilitating NFATc2 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903630. [PMID: 32537408 PMCID: PMC7284218 DOI: 10.1002/advs.201903630] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/17/2020] [Accepted: 03/08/2020] [Indexed: 05/17/2023]
Abstract
Arsenic (As) is a widespread metalloid contaminant, and its internal exposure is demonstrated to cause serious detrimental health problems. Albeit considerable studies are performed to interrogate the molecular mechanisms responsible for As-induced toxicities, the exact mechanisms are not fully understood yet, especially at the epigenetic regulation level. In the present study, it is identified that long non-coding RNA (lncRNA) urothelial cancer associated 1 (UCA1) alleviates As-induced G2/M phase arrest in human liver cells. Intensive mechanistic investigations illustrate that UCA1 interacts with enhancer of zeste homolog 2 (EZH2) and accelerates the latter's protein turnover rate under normal and As-exposure conditions. The phosphorylation of EZH2 at the Thr-487 site by cyclin dependent kinase 1 (CDK1) is responsible for As-induced EZH2 protein degradation, and UCA1 enhances this process through increasing the interaction between CDK1 and EZH2. As a consequence, the cell cycle regulator nuclear factor of activated T cells 2 (NFATc2), a downstream target of EZH2, is upregulated to resist As-blocked cell cycle progress and cytotoxicity. In conclusion, the findings decipher a novel prosurvival signaling pathway underlying As toxicity from the perspective of epigenetic regulation: UCA1 facilitates the ubiquitination of EZH2 to upregulate NFATc2 and further antagonizes As-induced cell cycle arrest.
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Affiliation(s)
- Zheng Dong
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Ming Gao
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Changying Li
- Liver Research CenterBeijing Friendship HospitalCapital Medical UniversityBeijing100050China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
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16
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Fallek A, Weiss-Shtofman M, Kramer M, Dobrovetsky R, Portnoy M. Phosphorylation Organocatalysts Highly Active by Design. Org Lett 2020; 22:3722-3727. [PMID: 32319783 DOI: 10.1021/acs.orglett.0c01226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The activity of nucleophilic organocatalysts for alcohol/phenol phosphorylation was enhanced through attaching oligoether appendages to a benzyl substituent on imidazole- or aminopyridine-based active units, presumably because of stabilizing n-cation interactions of the ethereal oxygens with the positively charged aza-heterocycle in the catalytic intermediates, and was substantially higher than that of known benchmark catalysts for a range of substrates. Density functional theory calculations and the study of analogues having a lower potential for such stabilizing interactions support our hypothesis.
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Affiliation(s)
- Amit Fallek
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Mor Weiss-Shtofman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Kramer
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roman Dobrovetsky
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moshe Portnoy
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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17
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Link AJ, Niu X, Weaver CM, Jennings JL, Duncan DT, McAfee KJ, Sammons M, Gerbasi VR, Farley AR, Fleischer TC, Browne CM, Samir P, Galassie A, Boone B. Targeted Identification of Protein Interactions in Eukaryotic mRNA Translation. Proteomics 2020; 20:e1900177. [PMID: 32027465 DOI: 10.1002/pmic.201900177] [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: 05/14/2019] [Revised: 12/13/2019] [Indexed: 11/09/2022]
Abstract
To identify protein-protein interactions and phosphorylated amino acid sites in eukaryotic mRNA translation, replicate TAP-MudPIT and control experiments are performed targeting Saccharomyces cerevisiae genes previously implicated in eukaryotic mRNA translation by their genetic and/or functional roles in translation initiation, elongation, termination, or interactions with ribosomal complexes. Replicate tandem affinity purifications of each targeted yeast TAP-tagged mRNA translation protein coupled with multidimensional liquid chromatography and tandem mass spectrometry analysis are used to identify and quantify copurifying proteins. To improve sensitivity and minimize spurious, nonspecific interactions, a novel cross-validation approach is employed to identify the most statistically significant protein-protein interactions. Using experimental and computational strategies discussed herein, the previously described protein composition of the canonical eukaryotic mRNA translation initiation, elongation, and termination complexes is calculated. In addition, statistically significant unpublished protein interactions and phosphorylation sites for S. cerevisiae's mRNA translation proteins and complexes are identified.
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Affiliation(s)
- Andrew J Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xinnan Niu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Connie M Weaver
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jennifer L Jennings
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Dexter T Duncan
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - K Jill McAfee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Morgan Sammons
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Vince R Gerbasi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Adam R Farley
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Tracey C Fleischer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | | | - Parimal Samir
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Allison Galassie
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Braden Boone
- Department of Bioinformatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
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18
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Suwanmajo T, Krishnan J. Exploring the intrinsic behaviour of multisite phosphorylation systems as part of signalling pathways. J R Soc Interface 2019; 15:rsif.2018.0109. [PMID: 29950514 DOI: 10.1098/rsif.2018.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023] Open
Abstract
Multisite phosphorylation is a basic way of chemically encoding substrate function and a recurring feature of cell signalling pathways. A number of studies have explored information processing characteristics of multisite phosphorylation, through studies of the intrinsic kinetics. Many of these studies focus on the module in isolation. In this paper, we build a bridge to connect the behaviour of multisite modification in isolation to that as part of pathways. We study the effect of activation of the enzymes (which are basic ways in which the module may be regulated), as well the effects of the modified substrates being involved in further modifications or exiting reaction compartments. We find that these effects can induce multiple kinds of transitions, including to behaviour not seen intrinsically in the multisite modification module. We then build on these insights to investigate how these multisite modification systems can be tuned by enzyme activation to realize a range of information processing outcomes for the design of synthetic phosphorylation circuits. Connecting the complexity of multisite modification kinetics, with the pathways in which they are embedded, serves as a basis for teasing out many aspects of their interaction, providing insights of relevance in systems biology, synthetic biology/chemistry and chemical information processing.
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Affiliation(s)
- Thapanar Suwanmajo
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, UK.,Centre of Excellence in Materials Science and Technology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, UK .,Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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19
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Quantitative and functional posttranslational modification proteomics reveals that TREPH1 plays a role in plant touch-delayed bolting. Proc Natl Acad Sci U S A 2018; 115:E10265-E10274. [PMID: 30291188 DOI: 10.1073/pnas.1814006115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Environmental mechanical forces, such as wind and touch, trigger gene-expression regulation and developmental changes, called "thigmomorphogenesis," in plants, demonstrating the ability of plants to perceive such stimuli. In Arabidopsis, a major thigmomorphogenetic response is delayed bolting, i.e., emergence of the flowering stem. The signaling components responsible for mechanotransduction of the touch response are largely unknown. Here, we performed a high-throughput SILIA (stable isotope labeling in Arabidopsis)-based quantitative phosphoproteomics analysis to profile changes in protein phosphorylation resulting from 40 seconds of force stimulation in Arabidopsis thaliana Of the 24 touch-responsive phosphopeptides identified, many were derived from kinases, phosphatases, cytoskeleton proteins, membrane proteins, and ion transporters. In addition, the previously uncharacterized protein TOUCH-REGULATED PHOSPHOPROTEIN1 (TREPH1) became rapidly phosphorylated in touch-stimulated plants, as confirmed by immunoblots. TREPH1 fractionates as a soluble protein and is shown to be required for the touch-induced delay of bolting and gene-expression changes. Furthermore, a nonphosphorylatable site-specific isoform of TREPH1 (S625A) failed to restore touch-induced flowering delay of treph1-1, indicating the necessity of S625 for TREPH1 function and providing evidence consistent with the possible functional relevance of the touch-regulated TREPH1 phosphorylation. Taken together, these findings identify a phosphoprotein player in Arabidopsis thigmomorphogenesis regulation and provide evidence that TREPH1 and its touch-induced phosphorylation may play a role in touch-induced bolting delay, a major component of thigmomorphogenesis.
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20
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Chakraborty A. The inositol pyrophosphate pathway in health and diseases. Biol Rev Camb Philos Soc 2018; 93:1203-1227. [PMID: 29282838 PMCID: PMC6383672 DOI: 10.1111/brv.12392] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Inositol pyrophosphates (IPPs) are present in organisms ranging from plants, slime moulds and fungi to mammals. Distinct classes of kinases generate different forms of energetic diphosphate-containing IPPs from inositol phosphates (IPs). Conversely, polyphosphate phosphohydrolase enzymes dephosphorylate IPPs to regenerate the respective IPs. IPPs and/or their metabolizing enzymes regulate various cell biological processes by modulating many proteins via diverse mechanisms. In the last decade, extensive research has been conducted in mammalian systems, particularly in knockout mouse models of relevant enzymes. Results obtained from these studies suggest impacts of the IPP pathway on organ development, especially of brain and testis. Conversely, deletion of specific enzymes in the pathway protects mice from various diseases such as diet-induced obesity (DIO), type-2 diabetes (T2D), fatty liver, bacterial infection, thromboembolism, cancer metastasis and aging. Furthermore, pharmacological inhibition of the same class of enzymes in mice validates the therapeutic importance of this pathway in cardio-metabolic diseases. This review critically analyses these findings and summarizes the significance of the IPP pathway in mammalian health and diseases. It also evaluates benefits and risks of targeting this pathway in disease therapies. Finally, future directions of mammalian IPP research are discussed.
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Affiliation(s)
- Anutosh Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO 63104, U.S.A
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21
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. Mol Cell Proteomics 2018; 17:335-348. [PMID: 29183913 PMCID: PMC5795395 DOI: 10.1074/mcp.ra117.000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/19/2022] Open
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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22
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. MOLECULAR & CELLULAR PROTEOMICS : MCP 2017. [PMID: 29183913 DOI: 10.1074/mcp.ra117.000378.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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23
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Karki M, Gibard C, Bhowmik S, Krishnamurthy R. Nitrogenous Derivatives of Phosphorus and the Origins of Life: Plausible Prebiotic Phosphorylating Agents in Water. Life (Basel) 2017; 7:E32. [PMID: 28758921 PMCID: PMC5617957 DOI: 10.3390/life7030032] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 12/02/2022] Open
Abstract
Phosphorylation under plausible prebiotic conditions continues to be one of the defining issues for the role of phosphorus in the origins of life processes. In this review, we cover the reactions of alternative forms of phosphate, specifically the nitrogenous versions of phosphate (and other forms of reduced phosphorus species) from a prebiotic, synthetic organic and biochemistry perspective. The ease with which such amidophosphates or phosphoramidate derivatives phosphorylate a wide variety of substrates suggests that alternative forms of phosphate could have played a role in overcoming the "phosphorylation in water problem". We submit that serious consideration should be given to the search for primordial sources of nitrogenous versions of phosphate and other versions of phosphorus.
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Affiliation(s)
- Megha Karki
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Clémentine Gibard
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Subhendu Bhowmik
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
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24
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Abstract
Multi-site phosphorylation is ubiquitous in cell biology and has been widely studied experimentally and theoretically. The underlying chemical modification mechanisms are typically assumed to be distributive or processive. In this paper, we study the behaviour of mixed mechanisms that can arise either because phosphorylation and dephosphorylation involve different mechanisms or because phosphorylation and/or dephosphorylation can occur through a combination of mechanisms. We examine a hierarchy of models to assess chemical information processing through different mixed mechanisms, using simulations, bifurcation analysis and analytical work. We demonstrate how mixed mechanisms can show important and unintuitive differences from pure distributive and processive mechanisms, in some cases resulting in monostable behaviour with simple dose-response behaviour, while in other cases generating new behaviour-like oscillations. Our results also suggest patterns of information processing that are relevant as the number of modification sites increases. Overall, our work creates a framework to examine information processing arising from complexities of multi-site modification mechanisms and their impact on signal transduction.
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Affiliation(s)
- Thapanar Suwanmajo
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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25
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Childers CL, Storey KB. Post-translational Regulation of Hexokinase Function and Protein Stability in the Aestivating Frog Xenopus laevis. Protein J 2016; 35:61-71. [DOI: 10.1007/s10930-016-9647-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Diculescu VC, Oliveira-Brett AM. In situ electrochemical evaluation of dsDNA interaction with the anticancer drug danusertib nitrenium radical product using the DNA-electrochemical biosensor. Bioelectrochemistry 2015; 107:50-7. [PMID: 26523506 DOI: 10.1016/j.bioelechem.2015.10.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/22/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022]
Abstract
Danusertib is a kinase inhibitor and anti-cancer drug. The evaluation of the interaction between danusertib and dsDNA was investigated in bulk solution and using the dsDNA-electrochemical biosensor. The dsDNA-danusertib interaction occurs in two sequential steps. First, danusertib binds electrostatically todsDNA phosphate backbone through the positively charged piperazine moiety. The second step involved the pyrrolo-pyrazolemoiety and led to small morphological modifications in the dsDNA double helix which were electrochemically characterised through the changes of guanine and adenine residue oxidation peaks and confirmed by electrophoretic and spectrophotometric measurements. The nitrenium cation radical product of danusertib amino group oxidation was electrochemically generated in situ on the dsDNA-electrochemical biosensor surface. The danusertib nitrenium cation radical redox metabolite was covalently attached to the C8 of guanine residues preventing their oxidation. An interaction mechanism of dsDNA-danusertib is proposed and the formation of the danusertib redox nitrenium radical metabolite-guanine adduct explained.
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Affiliation(s)
- Victor Constantin Diculescu
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Ana Maria Oliveira-Brett
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535, Coimbra, Portugal.
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27
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Valimberti I, Tiberti M, Lambrughi M, Sarcevic B, Papaleo E. E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft. Sci Rep 2015; 5:14849. [PMID: 26463729 PMCID: PMC4604453 DOI: 10.1038/srep14849] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/19/2015] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation is a modification that offers a dynamic and reversible mechanism to regulate the majority of cellular processes. Numerous diseases are associated with aberrant regulation of phosphorylation-induced switches. Phosphorylation is emerging as a mechanism to modulate ubiquitination by regulating key enzymes in this pathway. The molecular mechanisms underpinning how phosphorylation regulates ubiquitinating enzymes, however, are elusive. Here, we show the high conservation of a functional site in E2 ubiquitin-conjugating enzymes. In catalytically active E2s, this site contains aspartate or a phosphorylatable serine and we refer to it as the conserved E2 serine/aspartate (CES/D) site. Molecular simulations of substrate-bound and -unbound forms of wild type, mutant and phosphorylated E2s, provide atomistic insight into the role of the CES/D residue for optimal E2 activity. Both the size and charge of the side group at the site play a central role in aligning the substrate lysine toward E2 catalytic cysteine to control ubiquitination efficiency. The CES/D site contributes to the fingerprint of the E2 superfamily. We propose that E2 enzymes can be divided into constitutively active or regulated families. E2s characterized by an aspartate at the CES/D site signify constitutively active E2s, whereas those containing a serine can be regulated by phosphorylation.
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Affiliation(s)
- Ilaria Valimberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Tiberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Lambrughi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Boris Sarcevic
- Cell Cycle and Cancer Unit, St. Vincent's Institute of Medical Research and The Department of Medicine, St. Vincent's Hospital, The University of Melbourne, Fitzroy, Melbourne, Victoria 3065, Australia
| | - Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
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28
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Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 2015; 126:24-33. [DOI: 10.1016/j.jprot.2015.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 12/25/2022]
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29
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Khemiri A, Jouenne T, Cosette P. Proteomics dedicated to biofilmology: What have we learned from a decade of research? Med Microbiol Immunol 2015; 205:1-19. [PMID: 26068406 DOI: 10.1007/s00430-015-0423-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 06/03/2015] [Indexed: 12/31/2022]
Abstract
Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.
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Affiliation(s)
- Arbia Khemiri
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France.
- University of Normandy, UR, Mont-Saint-Aignan, France.
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France.
| | - Thierry Jouenne
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
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30
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Popa OM, Diculescu VC. Direct electrochemical oxidation of Abelson tyrosine-protein kinase 1 and evaluation of its interaction with synthetic substrate, ATP and inhibitors. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.01.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Ni F, Fu C, Gao X, Liu Y, Xu P, Liu L, Lv Y, Fu S, Sun Y, Han D, Li Y, Zhao Y. N-phosphoryl amino acid models for P-N bonds in prebiotic chemical evolution. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5321-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Jouy F, Müller SA, Wagner J, Otto W, von Bergen M, Tomm JM. Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance. Proteomics 2014; 15:25-33. [DOI: 10.1002/pmic.201400119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 09/23/2014] [Accepted: 10/21/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Florent Jouy
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Stephan A. Müller
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Juliane Wagner
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Wolfgang Otto
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
- Department of Biotechnology and Environmental Engineering; University of Aalborg; Aalborg Denmark
| | - Janina M. Tomm
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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33
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Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014; 5:263. [PMID: 25177341 PMCID: PMC4133750 DOI: 10.3389/fgene.2014.00263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks.
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Affiliation(s)
- Robert H Newman
- Department of Biology, North Carolina Agricultural and Technical State University Greensboro, NC, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; High-Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University Baltimore, MD, USA
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34
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Characterization of the polyproline region of the hepatitis E virus in immunocompromised patients. J Virol 2014; 88:12017-25. [PMID: 25100839 DOI: 10.1128/jvi.01625-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Little is known about virus adaptation in immunocompromised patients with chronic genotype 3 hepatitis E virus (HEV3) infections. Virus-host recombinant strains have been isolated recently from chronically infected patients. The nature and incidence of such recombinant events occurring during infections of solid-organ transplant (SOT) recipients are essentially unknown. The polyproline region (PPR) of strains isolated from SOT patients was sequenced during the acute-infection phase (n = 59) and during follow-up of patients whose infections became chronic (n = 27). These 27 HEV strains included 3 (11%) that showed recombinant events 12, 34, 48, or 88 months after infection. In one strain, parts of the PPR and the RNA-dependent RNA polymerase were concomitantly inserted. In the second, a fragment of a human tyrosine aminotransferase (TAT) gene was inserted first, followed by a fragment of PPR. A fragment of the human inter-α-trypsin inhibitor (ITI) gene was inserted in the third. All the inserted sequences were rich in aliphatic and basic amino acids. In vitro growth experiments suggest that the ITI insertion promoted more vigorous virus growth. In silico studies showed that the inserted sequences could provide potential acetylation, ubiquitination, and phosphorylation sites. We found that recombinant events had occurred in the HEV PPR in approximately 11% of the strains isolated from chronically infected transplant patients followed up in Toulouse University Hospital. These inserted fragments came from the HEV genome or a human gene and could enhance virus replication. Importance: Hepatitis E virus (HEV) can cause chronic infections in immunocompromised patients, including solid-organ transplant (SOT) recipients. Two strains that had undergone recombination with human ribosomal genes were described recently. The strains with inserted sequences replicated better in vitro. Little is known about the frequency of such recombinant events or how such an insertion enhances replication. We therefore investigated 59 SOT patients infected with HEV and found 3 strains with 4 recombinant events in 27 of these patients whose infection became chronic. The 4 inserted sequences were of different origins (human gene or HEV genome), but all were enriched in aliphatic and basic amino acids and provided potential regulation sites. Our data indicate that recombinant events occur in approximately 11% of strains isolated from chronically infected patients. The structures of the inserted sequences provide new clues as to how the inserted sequences could foster virus replication.
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35
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Ye X, Li L. Macroporous reversed-phase separation of proteins combined with reversed-phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA-MB-231 cells. Electrophoresis 2014; 35:3479-86. [PMID: 24888630 DOI: 10.1002/elps.201300586] [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: 11/24/2013] [Revised: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 12/13/2022]
Abstract
A new method of combining macroporous RP (mRP) protein fractionation with RPLC peptide separation MS/MS is reported for profiling the phosphoproteome of a complex sample. In this method, an mRP-C18 column was used to fractionate the proteins from a whole cell lysate of a breast cancer cell line, MDA-MB-231, into 38 fractions. Each fraction was subjected to tryptic digestion, sequential phosphopeptide enrichment by immobilized metal ion affinity chromatography and titanium dioxide (TiO2 ), followed by capillary RPLC-MS/MS analysis. For comparison, the conventional method of using strong cation exchange RPLC separation of peptides combined with MS/MS was also used for analyzing the phosphoproteome. Replicate experiments by the mRP-RPLC method identified 1585 distinct phosphoproteins with 4519 phosphopeptides, compared to 1585 phosphoproteins with 4297 phosphopeptides by strong cation exchange RPLC, with a total of 1947 phosphoproteins and 6278 phosphopeptides identified from the combined results. While the two methods have similar ability in the identification of the phosphoproteome, they produce complementary information. The phosphoproteins identified in this study, including 67 novel phosphorylation sites from 56 breast cancer related proteins, can serve as the entry point for future validation with biological implications in breast cancer. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000948 and DOI 10.6019/PXD000948.
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Affiliation(s)
- Xiaoxia Ye
- Department of Chemistry, University of Alberta, Edmonton, Canada
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36
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Ma CWM, Lam H. Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring. J Proteome Res 2014; 13:2262-71. [PMID: 24661115 DOI: 10.1021/pr401006g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Discovering novel post-translational modifications (PTMs) to proteins and detecting specific modification sites on proteins is one of the last frontiers of proteomics. At present, hunting for post-translational modifications remains challenging in widely practiced shotgun proteomics workflows due to the typically low abundance of modified peptides and the greatly inflated search space as more potential mass shifts are considered by the search engines. Moreover, most popular search methods require that the user specifies the modification(s) for which to search; therefore, unexpected and novel PTMs will not be detected. Here a new algorithm is proposed to apply spectral library searching to the problem of open modification searches, namely, hunting for PTMs without prior knowledge of what PTMs are in the sample. The proposed tier-wise scoring method intelligently looks for unexpected PTMs by allowing mass-shifted peak matches but only when the number of matches found is deemed statistically significant. This allows the search engine to search for unexpected modifications while maintaining its ability to identify unmodified peptides effectively at the same time. The utility of the method is demonstrated using three different data sets, in which the numbers of spectrum identifications to both unmodified and modified peptides were substantially increased relative to a regular spectral library search as well as to another open modification spectral search method, pMatch.
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Affiliation(s)
- Chun Wai Manson Ma
- Division of Biomedical Engineering and ‡Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Hong Kong, China
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37
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Gajadhar AS, White FM. System level dynamics of post-translational modifications. Curr Opin Biotechnol 2014; 28:83-7. [PMID: 24441143 DOI: 10.1016/j.copbio.2013.12.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/24/2013] [Indexed: 11/20/2022]
Abstract
Attempts to characterize cellular behaviors with static, univariate measurements cannot fully capture biological complexity and lead to an inadequate interpretation of cellular processes. Significant biological insight can be gleaned by considering the contribution of dynamic protein post-translational modifications (PTMs) utilizing systems-level quantitative analysis. High-resolution mass spectrometry coupled with computational modeling of dynamic signal-response relationships is a powerful tool to reveal PTM-mediated regulatory networks. Recent advances using this approach have defined network kinetics of growth factor signaling pathways, identified systems level responses to cytotoxic perturbations, elucidated kinase-substrate relationships, and unraveled the dynamics of PTM cross-talk. Innovations in multiplex measurement capacity, PTM annotation accuracy, and computational integration of datasets promise enhanced resolution of dynamic PTM networks and further insight into biological intricacies.
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Affiliation(s)
- Aaron S Gajadhar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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38
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Palomo JM. Solid-phase peptide synthesis: an overview focused on the preparation of biologically relevant peptides. RSC Adv 2014. [DOI: 10.1039/c4ra02458c] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Tailor-made design preparation of complex peptide sequence including posttranslational modifications, fluorescent labels, unnatural amino acids are of exceptional value for biological studies of several important diseases. The possibility to obtain these molecules in sufficient amounts in relative short time is thanks to the solid-phase approach.
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Affiliation(s)
- Jose M. Palomo
- Departamento of Biocatalisis
- Instituto de Catalisis (CSIC)
- Madrid, Spain
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39
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Marmelstein AM, Yates LM, Conway JH, Fiedler D. Chemical pyrophosphorylation of functionally diverse peptides. J Am Chem Soc 2013; 136:108-11. [PMID: 24350643 DOI: 10.1021/ja411737c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A highly selective and convenient method for the synthesis of pyrophosphopeptides in solution is reported. The remarkable compatibility with functional groups (alcohol, thiol, amine, carboxylic acid) in the peptide substrates suggests that the intrinsic nucleophilicity of the phosphoserine residue is much higher than previously appreciated. Because the methodology operates in polar solvents, including water, a broad range of pyrophosphopeptides can be accessed. We envision these peptides will find widespread applications in the development of mass spectrometry and antibody-based detection methods for pyrophosphoproteins.
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Affiliation(s)
- Alan M Marmelstein
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
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Hu Y, Lam H. Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications. J Proteome Res 2013; 12:5971-7. [DOI: 10.1021/pr4007443] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yingwei Hu
- Department of Chemical and Biomolecular Engineering and ‡Division of Biomedical
Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Henry Lam
- Department of Chemical and Biomolecular Engineering and ‡Division of Biomedical
Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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41
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Suwanmajo T, Krishnan J. Biphasic responses in multi-site phosphorylation systems. J R Soc Interface 2013; 10:20130742. [PMID: 24108693 DOI: 10.1098/rsif.2013.0742] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-site phosphorylation systems are repeatedly encountered in cellular biology and multi-site modification is a basic building block of post-translational modification. In this paper, we demonstrate how distributive multi-site modification mechanisms by a single kinase/phosphatase pair can lead to biphasic/partial biphasic dose-response characteristics for the maximally phosphorylated substrate at steady state. We use simulations and analysis to uncover a hidden competing effect which is responsible for this and analyse how it may be accentuated. We build on this to analyse different variants of multi-site phosphorylation mechanisms showing that some mechanisms are intrinsically not capable of displaying this behaviour. This provides both a consolidated understanding of how and under what conditions biphasic responses are obtained in multi-site phosphorylation and a basis for discriminating between different mechanisms based on this. We also demonstrate how this behaviour may be combined with other behaviour such as threshold and bistable responses, demonstrating the capacity of multi-site phosphorylation systems to act as complex molecular signal processors.
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Affiliation(s)
- Thapanar Suwanmajo
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, , South Kensington Campus, London SW7 2AZ, UK
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42
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Winquist RJ, Mullane K, Williams M. The fall and rise of pharmacology--(re-)defining the discipline? Biochem Pharmacol 2013; 87:4-24. [PMID: 24070656 DOI: 10.1016/j.bcp.2013.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 09/09/2013] [Indexed: 12/19/2022]
Abstract
Pharmacology is an integrative discipline that originated from activities, now nearly 7000 years old, to identify therapeutics from natural product sources. Research in the 19th Century that focused on the Law of Mass Action (LMA) demonstrated that compound effects were dose-/concentration-dependent eventually leading to the receptor concept, now a century old, that remains the key to understanding disease causality and drug action. As pharmacology evolved in the 20th Century through successive biochemical, molecular and genomic eras, the precision in understanding receptor function at the molecular level increased and while providing important insights, led to an overtly reductionistic emphasis. This resulted in the generation of data lacking physiological context that ignored the LMA and was not integrated at the tissue/whole organism level. As reductionism became a primary focus in biomedical research, it led to the fall of pharmacology. However, concerns regarding the disconnect between basic research efforts and the approval of new drugs to treat 21st Century disease tsunamis, e.g., neurodegeneration, metabolic syndrome, etc. has led to the reemergence of pharmacology, its rise, often in the semantic guise of systems biology. Against a background of limited training in pharmacology, this has resulted in issues in experimental replication with a bioinformatics emphasis that often has a limited relationship to reality. The integration of newer technologies within a pharmacological context where research is driven by testable hypotheses rather than technology, together with renewed efforts in teaching pharmacology, is anticipated to improve the focus and relevance of biomedical research and lead to novel therapeutics that will contain health care costs.
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Affiliation(s)
- Raymond J Winquist
- Department of Pharmacology, Vertex Pharmaceuticals Inc., Cambridge, MA, United States
| | - Kevin Mullane
- Profectus Pharma Consulting Inc., San Jose, CA, United States
| | - Michael Williams
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
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43
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Cohen IR. Autoantibody repertoires, natural biomarkers, and system controllers. Trends Immunol 2013; 34:620-5. [PMID: 23768955 DOI: 10.1016/j.it.2013.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/04/2013] [Accepted: 05/14/2013] [Indexed: 12/20/2022]
Abstract
The immune system is composed of networks of interacting cells and molecules; therefore, to understand and control immune behavior we need to adopt the thinking and tools of systems immunology. This review describes the use of an antigen microarray device and informatics to profile the repertoires of autoantibodies in health and disease. Autoantibody profiling provides an insight into the biomarkers used by the immune system in its dialog with the body. Heat shock protein 60 (HSP60) and HSP70 are cited as examples of key hubs in physiological regulatory networks; HSP molecules and peptides can be viewed as natural regulators because the immune system itself deploys them to modulate inflammatory reactions. The discovery of such natural biomarkers paves the way towards natural control.
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Affiliation(s)
- Irun R Cohen
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Han B, Zhang L, Feng M, Fang Y, Li J. An Integrated Proteomics Reveals Pathological Mechanism of Honeybee (Apis cerena) Sacbrood Disease. J Proteome Res 2013; 12:1881-97. [DOI: 10.1021/pr301226d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bin Han
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Lan Zhang
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Mao Feng
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Yu Fang
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
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Wang M, Wang GX, Xiao FN, Zhao Y, Wang K, Xia XH. Sensitive label-free monitoring of protein kinase activity and inhibition using ferric ions coordinated to phosphorylated sites as electrocatalysts. Chem Commun (Camb) 2013; 49:8788-90. [DOI: 10.1039/c3cc43290d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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46
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Grangeasse C, Nessler S, Mijakovic I. Bacterial tyrosine kinases: evolution, biological function and structural insights. Philos Trans R Soc Lond B Biol Sci 2012; 367:2640-55. [PMID: 22889913 DOI: 10.1098/rstb.2011.0424] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reversible protein phosphorylation is a major mechanism in the regulation of fundamental signalling events in all living organisms. Bacteria have been shown to possess a versatile repertoire of protein kinases, including histidine and aspartic acid kinases, serine/threonine kinases, and more recently tyrosine and arginine kinases. Tyrosine phosphorylation is today recognized as a key regulatory device of bacterial physiology, linked to exopolysaccharide production, virulence, stress response and DNA metabolism. However, bacteria have evolved tyrosine kinases that share no resemblance with their eukaryotic counterparts and are unique in exploiting the ATP/GTP-binding Walker motif to catalyse autophosphorylation and substrate phosphorylation on tyrosine. These enzymes, named BY-kinases (for Bacterial tYrosine kinases), have been identified in a majority of sequenced bacterial genomes, and to date no orthologues have been found in Eukarya. The aim of this review was to present the most recent knowledge about BY-kinases by focusing primarily on their evolutionary origin, structural and functional aspects, and emerging regulatory potential based on recent bacterial phosphoproteomic studies.
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Affiliation(s)
- Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, CNRS, Université de Lyon, UMR 5086, 7 passage du Vercors, 69367 Lyon, France.
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Liu C, Fan D, Shi Y, Zhou Q. A glimpse of enzymology within the idea of systems. SCIENCE CHINA. LIFE SCIENCES 2012; 55:826-33. [PMID: 23015132 PMCID: PMC7088909 DOI: 10.1007/s11427-012-4371-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/21/2012] [Indexed: 12/21/2022]
Affiliation(s)
- ChuanPeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.
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Regulation of adherens junction dynamics by phosphorylation switches. JOURNAL OF SIGNAL TRANSDUCTION 2012; 2012:125295. [PMID: 22848810 PMCID: PMC3403498 DOI: 10.1155/2012/125295] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 12/15/2022]
Abstract
Adherens junctions connect the actin cytoskeleton of neighboring cells through transmembrane cadherin receptors and a network of adaptor proteins. The interactions between these adaptors and cadherin as well as the activity of actin regulators localized to adherens junctions are tightly controlled to facilitate cell junction assembly or disassembly in response to changes in external or internal forces and/or signaling. Phosphorylation of tyrosine, serine, or threonine residues acts as a switch on the majority of adherens junction proteins, turning "on" or "off" their interactions with other proteins and/or their enzymatic activity. Here, we provide an overview of the kinases and phosphatases regulating phosphorylation of adherens junction proteins and bring examples of phosphorylation events leading to the assembly or disassembly of adherens junctions, highlighting the important role of phosphorylation switches in regulating their dynamics.
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