1
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Zn(II)-DPA functionalized graphene oxide two-dimensional nanocomposites for N-phosphoproteins enrichment. Talanta 2022; 243:123384. [DOI: 10.1016/j.talanta.2022.123384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/15/2022]
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2
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Incel A, Arribas Díez I, Wierzbicka C, Gajoch K, Jensen ON, Sellergren B. Selective Enrichment of Histidine Phosphorylated Peptides Using Molecularly Imprinted Polymers. Anal Chem 2021; 93:3857-3866. [PMID: 33591162 PMCID: PMC8023515 DOI: 10.1021/acs.analchem.0c04474] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Protein histidine
phosphorylation
(pHis) is involved in molecular signaling networks in bacteria, fungi,
plants, and higher eukaryotes including mammals and is implicated
in human diseases such as cancer. Detailed investigations of the pHis
modification are hampered due to its acid-labile nature and consequent
lack of tools to study this post-translational modification (PTM).
We here demonstrate three molecularly imprinted polymer (MIP)-based
reagents, MIP1–MIP3, for enrichment of pHis peptides and subsequent
characterization by chromatography and mass spectrometry (LC–MS).
The combination of MIP1 and β-elimination provided some selectivity
for improved detection of pHis peptides. MIP2 was amenable to larger
pHis peptides, although with poor selectivity. Microsphere-based MIP3
exhibited improved selectivity and was amenable to enrichment and
detection by LC–MS of pHis peptides in tryptic digests of protein
mixtures. These MIP protocols do not involve any acidic solvents during
sample preparation and enrichment, thus preserving the pHis modification.
The presented proof-of-concept results will lead to new protocols
for highly selective enrichment of labile protein phosphorylations
using molecularly imprinted materials.
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Affiliation(s)
- Anıl Incel
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ignacio Arribas Díez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Celina Wierzbicka
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Katarzyna Gajoch
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
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3
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Su J, Li Y, Gu W, Liu X. Spiropyran-modified upconversion nanocomposite as a fluorescent sensor for diagnosis of histidinemia. RSC Adv 2020; 10:26664-26670. [PMID: 35515791 PMCID: PMC9055446 DOI: 10.1039/d0ra03711g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Histidinemia is a congenital metabolic disorder where the histidine (His) metabolism is blocked, resulting in increased concentrations of His in blood and urine. The disease causes an abnormal development of the patient's nervous system, which leads to many serious illnesses. Therefore, it is very important to diagnose early. In this study, we developed a novel fluorescent nanosensor NaGdF4:Yb3+, Er3+@SiO2–spiropyran (UCNP@SiO2–SP). The nanosensor displayed a “turn-off” fluorescence response towards His. When His was mixed with UCNP@SiO2–SP, His could specifically bind to SP, which could cause the isomerization of SP. The structure of SP was changed from spiroform into merocyanine form. The luminescence of the sensor was overlapped with the absorption of the merocyanine form. As a result, His will lead to fluorescence quenching of the sensor based on inner filter effects (IFE), which can be used to detect His. Importantly, as the first report of a UCNP@SiO2–SP nanosensor for detecting His, this method exhibits good selectivity and anti-interference capability. The detection limit is 4.4 μM. In addition, the amount of His in urine was also measured, suggesting the applicability of this sensor for histidinemia diagnosis. A novel sensor based on upconversion fluorescent nanoparticles was developed and used to diagnose histidinemia.![]()
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Affiliation(s)
- Jian Su
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Yiwei Li
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Wen Gu
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Xin Liu
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
- Collaborative Innovation Center of Chemical Science and Engineering
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4
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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5
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Jia S, He D, Chang CJ. Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation. J Am Chem Soc 2019; 141:7294-7301. [PMID: 31017395 DOI: 10.1021/jacs.8b11912] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Site-selective bioconjugation to native protein residues is a powerful tool for protein functionalization, with cysteine and lysine side chains being the most common points for attachment owing to their high nucleophilicity. We now report a strategy for histidine modification using thiophosphorodichloridate reagents that mimic post-translational histidine phosphorylation, enabling fast and selective labeling of protein histidines under mild conditions where various payloads can be introduced via copper-assisted alkyne-azide cycloaddition (CuAAC) chemistry. We establish that these reagents are particularly effective at covalent modification of His-tags, which are common motifs to facilitate protein purification, as illustrated by selective attachment of polyarginine cargoes to enhance the uptake of proteins into living cells. This work provides a starting point for probing and enhancing protein function using histidine-directed chemistry.
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Affiliation(s)
- Shang Jia
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Dan He
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Christopher J Chang
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States.,Howard Hughes Medical Institute , University of California , Berkeley , California 94720 , United States
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6
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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7
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Kaur S, Baldi B, Vuong J, O'Donoghue SI. Visualization and Analysis of Epiproteome Dynamics. J Mol Biol 2019; 431:1519-1539. [PMID: 30769119 DOI: 10.1016/j.jmb.2019.01.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 12/28/2022]
Abstract
The epiproteome describes the set of all post-translational modifications (PTMs) made to the proteins comprising a cell or organism. The extent of the epiproteome is still largely unknown; however, advances in experimental techniques are beginning to produce a deluge of data, tracking dynamic changes to the epiproteome in response to cellular stimuli. These data have potential to revolutionize our understanding of biology and disease. This review covers a range of recent visualization methods and tools developed specifically for dynamic epiproteome data sets. These methods have been designed primarily for data sets on phosphorylation, as this the most studied PTM; however, most of these methods are also applicable to other types of PTMs. Unfortunately, the currently available methods are often inadequate for existing data sets; thus, realizing the potential buried in epiproteome data sets will require new, tailored bioinformatics methods that will help researchers analyze, visualize, and interactively explore these complex data sets.
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Affiliation(s)
- Sandeep Kaur
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
| | - Benedetta Baldi
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Jenny Vuong
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Seán I O'Donoghue
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
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8
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Shi HJ, Liu WB, Xu C, Zhang DD, Wang BK, Zhang L, Li XF. Molecular Characterization of the RNA-Binding Protein Quaking-a in Megalobrama amblycephala: Response to High-Carbohydrate Feeding and Glucose/Insulin/Glucagon Treatment. Front Physiol 2018; 9:434. [PMID: 29740344 PMCID: PMC5928497 DOI: 10.3389/fphys.2018.00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
The RNA-binding protein quaking-a (Qkia) was cloned from the liver of blunt snout bream Megalobrama amblycephala through the rapid amplification of cDNA ends method, with its potential role in glucose metabolism investigated. The full-length cDNA of qkia covered 1,718 bp, with an open reading frame of 1,572 bp, which encodes 383 AA. Sequence alignment and phylogenetic analysis revealed a high degree of conservation (97–99%) among most fish and other higher vertebrates. The mRNA of qkia was detected in all examined organs/tissues. Then, the plasma glucose levels and tissue qkia expressions were determined in fish intraperitoneally injected with glucose [1.67 g per kg body weight (BW)], insulin (0.052 mg/kg BW), and glucagon (0.075 mg/kg BW) respectively, as well as in fish fed two dietary carbohydrate levels (31 and 41%) for 12 weeks. Glucose administration induced a remarkable increase of plasma glucose with the highest value being recorded at 1 h. Thereafter, it reduced to the basal value. After glucose administration, qkia expressions significantly decreased with the lowest value being recorded at 1 h in liver and muscle and 8 h in brain, respectively. Then they gradually returned to the basal value. The insulin injection induced a significant decrease of plasma glucose with the lowest value being recorded at 1 h, whereas the opposite was true after glucagon load (the highest value was gained at 4 h). Subsequently, glucose levels gradually returned to the basal value. After insulin administration, the qkia expressions significantly decreased with the lowest value being attained at 2 h in brain and muscle and 1 h in liver, respectively. However, glucagon significantly stimulated the expressions of qkia in tissues with the highest value being gained at 6 h. Moreover, high dietary carbohydrate levels remarkably increased plasma glucose levels, but down-regulated the transcriptions of qkia in tissues. These results indicated that the gene of blunt snout bream shared a high similarity with that of the other vertebrates. Glucose and insulin administration, as well as high-carbohydrate feeding, remarkably down-regulated its transcriptions in brain, muscle and liver, whereas the opposite was true after the glucagon load.
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Affiliation(s)
- Hua-Juan Shi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wen-Bin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chao Xu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ding-Dong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Bing-Ke Wang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Li Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiang-Fei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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9
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Hindupur SK, Colombi M, Fuhs SR, Matter MS, Guri Y, Adam K, Cornu M, Piscuoglio S, Ng CKY, Betz C, Liko D, Quagliata L, Moes S, Jenoe P, Terracciano LM, Heim MH, Hunter T, Hall MN. The protein histidine phosphatase LHPP is a tumour suppressor. Nature 2018; 555:678-682. [PMID: 29562234 DOI: 10.1038/nature26140] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 02/14/2018] [Indexed: 12/13/2022]
Abstract
Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver tumours. Sustained, hepatic expression of LHPP in the hepatocellular carcinoma mouse model reduced tumour burden and prevented the loss of liver function. Finally, in patients with hepatocellular carcinoma, low expression of LHPP correlated with increased tumour severity and reduced overall survival. Thus, LHPP is a protein histidine phosphatase and tumour suppressor, suggesting that deregulated histidine phosphorylation is oncogenic.
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Affiliation(s)
| | - Marco Colombi
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Stephen R Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Matthias S Matter
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Yakir Guri
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Marion Cornu
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Charles Betz
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Dritan Liko
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Suzette Moes
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Paul Jenoe
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Markus H Heim
- Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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10
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Makwana MV, Muimo R, Jackson RF. Advances in development of new tools for the study of phosphohistidine. J Transl Med 2018; 98:291-303. [PMID: 29200202 DOI: 10.1038/labinvest.2017.126] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 01/04/2023] Open
Abstract
Protein phosphorylation is an important post-translational modification that is an integral part of cellular function. The O-phosphorylated amino-acid residues, such as phosphoserine (pSer), phosphothreonine (pThr) and phosphotyrosine (pTyr), have dominated the literature while the acid labile N-linked phosphorylated amino acids, such as phosphohistidine (pHis), have largely been historically overlooked because of the acidic conditions routinely used in amino-acid detection and analysis. This review highlights some misinterpretations that have arisen in the existing literature, pinpoints outstanding questions and potential future directions to clarify the role of pHis in mammalian signalling systems. Particular emphasis is placed on pHis isomerization and the hybrid functionality for both pHis and pTyr of the proposed τ-pHis analogue bearing the triazole residue.
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Affiliation(s)
- Mehul V Makwana
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
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11
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Renvoisé M, Bonhomme L, Davanture M, Zivy M, Lemaire C. Phosphoproteomic Analysis of Isolated Mitochondria in Yeast. Methods Mol Biol 2017; 1636:283-299. [PMID: 28730486 DOI: 10.1007/978-1-4939-7154-1_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mitochondria play a central role in cellular energy metabolism and cell death. Deregulation of mitochondrial functions is associated with several human pathologies (neurodegenerative diseases, neuromuscular diseases, type II diabetes, obesity, cancer). The steadily increasing number of identified mitochondrial phosphoproteins, kinases, and phosphatases in recent years suggests that reversible protein phosphorylation plays an important part in the control of mitochondrial processes. In addition, many mitochondrial phosphoproteins probably still remain to be identified, considering that 30% of proteins are expected to be phosphorylated in eukaryotes. In this chapter, we describe two procedures for the analysis of the mitochondrial phosphoproteome. The first one is a qualitative method that combines blue native and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D-BN/SDS-PAGE) and specific phosphoprotein staining. The second one is a quantitative approach that associates mitochondrial peptide labeling, phosphopeptide enrichment, and mass spectrometry.
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Affiliation(s)
- Margaux Renvoisé
- UMR 9198 CNRS, Institute for Integrative Biology of the Cell (I2BC), B3S, LPSM-CEA Saclay, 91191, Gif-sur-Yvette cedex, France
| | - Ludovic Bonhomme
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 63039, Clermont-Ferrand, France
| | - Marlène Davanture
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, UniversitÕ Paris-Saclay, Ferme du Moulon, 91191, Gif-sur-Yvette, France
| | - Michel Zivy
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, UniversitÕ Paris-Saclay, Ferme du Moulon, 91191, Gif-sur-Yvette, France
| | - Claire Lemaire
- UMR 9198 CNRS, Institute for Integrative Biology of the Cell (I2BC), B3S, LPSM-CEA Saclay, 91191, Gif-sur-Yvette cedex, France.
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12
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Abstract
Reversible protein phosphorylation is critically important in biology and medicine. Hundreds of thousands of sites of protein phosphorylation have been discovered but our understanding of the functions of the vast majority of these post-translational modifications is lacking. This review describes several chemical and biochemical methods that are under development and in current use to install phospho-amino acids and their mimics site-specifically into proteins. The relative merits of total chemical synthesis, semisynthesis, and nonsense suppression strategies for studying protein phosphorylation are discussed in terms of technical simplicity, scope, and versatility.
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Affiliation(s)
- Zan Chen
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States.
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13
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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14
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Nguyen HTH, Shaffer CJ, Tureček F. Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction. J Phys Chem B 2015; 119:3948-61. [PMID: 25688483 DOI: 10.1021/jp511717c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase.
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Affiliation(s)
- Huong T H Nguyen
- Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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15
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Kee JM, Oslund RC, Couvillon AD, Muir TW. A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org Lett 2014; 17:187-9. [PMID: 25531910 DOI: 10.1021/ol503320p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein histidine phosphorylation plays a crucial role in cell signaling and central metabolism. However, its detailed functions remain elusive due to technical challenges in detecting and isolating proteins bearing phosphohistidine (pHis), a labile posttranslational modification (PTM). To address this issue, we previously developed the first pHis-specific antibodies using stable, synthetic triazole-based pHis analogs. A second-generation, pyrazole-based pHis analog that enabled the development of a pan-pHis antibody with much improved pHis specificity is now reported.
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Affiliation(s)
- Jung-Min Kee
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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16
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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17
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Sensitive detection of biothiols and histidine based on the recovered fluorescence of the carbon quantum dots-Hg(II) system. Anal Chim Acta 2014; 859:72-8. [DOI: 10.1016/j.aca.2014.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/01/2014] [Accepted: 12/10/2014] [Indexed: 12/11/2022]
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18
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Evidence of histidine and aspartic acid phosphorylation in human prostate cancer cells. Naunyn Schmiedebergs Arch Pharmacol 2014; 388:161-73. [DOI: 10.1007/s00210-014-1063-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
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19
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McAllister TE, Horner KA, Webb ME. Evaluation of the interaction between phosphohistidine analogues and phosphotyrosine binding domains. Chembiochem 2014; 15:1088-91. [PMID: 24771713 PMCID: PMC4159583 DOI: 10.1002/cbic.201402090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/16/2022]
Abstract
We have investigated the interaction of peptides containing phosphohistidine analogues and their homologues with the prototypical phosphotyrosine binding SH2 domain from the eukaryotic cell signalling protein Grb2 by using a combination of isothermal titration calorimetry and a fluorescence anisotropy competition assay. These investigations demonstrated that the triazole class of phosphohistidine analogues are capable of binding too, suggesting that phosphohistidine could potentially be detected by this class of proteins in vivo.
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Affiliation(s)
- Tom E McAllister
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Katherine A Horner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
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20
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Fíla J, Čapková V, Honys D. Phosphoproteomic studies in Arabidopsis and tobacco male gametophytes. Biochem Soc Trans 2014; 42:383-7. [PMID: 24646248 DOI: 10.1042/bst20130249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Mature pollen represents an extremely resistant quiescent structure surrounded by a tough cell wall. After its hydration on stigma papillary cells, pollen tube growth starts rapidly. Massive metabolic changes are likely to be accompanied by changes in protein phosphorylation. Protein phosphorylation belongs among the most rapid post-translational modifications. To date, only Arabidopsis thaliana and tobacco (Nicotiana tabacum) mature pollen have been subjected to phosphoproteomic studies in order to identify the phosphoproteins present. In the present mini-review, Arabidopsis and tobacco datasets were compared with each other. The representation of the O-phosphorylated amino acids was compared between these two datasets, and the putative pollen-specific or pollen-abundant phosphopeptides were highlighted. Finally, the phosphorylation sites common for both Arabidopsis and tobacco phosphoproteins are listed as well as the phosphorylation motifs identified.
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Affiliation(s)
| | - Věra Čapková
- *Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Praha 6, Czech Republic
| | - David Honys
- *Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Praha 6, Czech Republic
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21
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Abstract
It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.
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22
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Loroch S, Dickhut C, Zahedi RP, Sickmann A. Phosphoproteomics--more than meets the eye. Electrophoresis 2013; 34:1483-92. [PMID: 23576030 DOI: 10.1002/elps.201200710] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/22/2013] [Accepted: 03/10/2013] [Indexed: 12/16/2022]
Abstract
PTMs enable cells to adapt to internal and external stimuli in the milliseconds to seconds time regime. Protein phosphorylation is probably the most important of these modifications as it affects protein structure and interactions, critically influencing the life cycle of a cell. In the last 15 years, new insights into phosphorylation have been provided by highly sensitive MS-based approaches combined with specific phosphopeptide enrichment strategies. Although so far research has mainly focused on the discovery and characterization of O-phosphorylation, this review also briefly outlines the current knowledge about N-phosphorylation depicting its ubiquitous relevance. Further, common pitfalls in sample preparation, LC-MS analysis, and subsequent data analysis are discussed as well as issues regarding quality and comparability of studies on protein phosphorylation.
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Affiliation(s)
- Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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23
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Schmidt A, Ammerer G, Mechtler K. Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization. Proteomics 2013; 13:945-54. [DOI: 10.1002/pmic.201200240] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/10/2012] [Accepted: 10/01/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas Schmidt
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
- Institute for Molecular Pathology (IMP); Vienna Austria
| | - Gustav Ammerer
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
| | - Karl Mechtler
- Institute for Molecular Pathology (IMP); Vienna Austria
- Institute for Molecular Biotechnology of the Austrian Academy of Sciences (IMBA); Vienna Austria
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24
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Guo M, Huang BX. Integration of phosphoproteomic, chemical, and biological strategies for the functional analysis of targeted protein phosphorylation. Proteomics 2013; 13:424-37. [PMID: 23125184 DOI: 10.1002/pmic.201200274] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/04/2012] [Accepted: 09/20/2012] [Indexed: 12/20/2022]
Abstract
Reversible phosphorylation, tightly controlled by protein kinases and phosphatases, plays a central role in mediating biological processes, such as protein-protein interactions, subcellular translocation, and activation of cellular enzymes. MS-based phosphoproteomics has now allowed the detection and quantification of tens of thousands of phosphorylation sites from a typical biological sample in a single experiment, which has posed new challenges in functional analysis of each and every phosphorylation site on specific signaling phosphoproteins of interest. In this article, we review recent advances in the functional analysis of targeted phosphorylation carried out by various chemical and biological approaches in combination with the MS-based phosphoproteomics. This review focuses on three types of strategies, including forward functional analysis, defined for the result-driven phosphoproteomics efforts in determining the substrates of a specific protein kinase; reverse functional analysis, defined for tracking the kinase(s) for specific phosphosite(s) derived from the discovery-driven phosphoproteomics efforts; and MS-based analysis on the structure-function relationship of phosphoproteins. It is expected that this review will provide a state-of-the-art overview of functional analysis of site-specific phosphorylation and explore new perspectives and outline future challenges.
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Affiliation(s)
- Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
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25
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Covian R, Balaban RS. Cardiac mitochondrial matrix and respiratory complex protein phosphorylation. Am J Physiol Heart Circ Physiol 2012; 303:H940-66. [PMID: 22886415 DOI: 10.1152/ajpheart.00077.2012] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It has become appreciated over the last several years that protein phosphorylation within the cardiac mitochondrial matrix and respiratory complexes is extensive. Given the importance of oxidative phosphorylation and the balance of energy metabolism in the heart, the potential regulatory effect of these classical signaling events on mitochondrial function is of interest. However, the functional impact of protein phosphorylation and the kinase/phosphatase system responsible for it are relatively unknown. Exceptions include the well-characterized pyruvate dehydrogenase and branched chain α-ketoacid dehydrogenase regulatory system. The first task of this review is to update the current status of protein phosphorylation detection primarily in the matrix and evaluate evidence linking these events with enzymatic function or protein processing. To manage the scope of this effort, we have focused on the pathways involved in energy metabolism. The high sensitivity of modern methods of detecting protein phosphorylation and the low specificity of many kinases suggests that detection of protein phosphorylation sites without information on the mole fraction of phosphorylation is difficult to interpret, especially in metabolic enzymes, and is likely irrelevant to function. However, several systems including protein translocation, adenine nucleotide translocase, cytochrome c, and complex IV protein phosphorylation have been well correlated with enzymatic function along with the classical dehydrogenase systems. The second task is to review the current understanding of the kinase/phosphatase system within the matrix. Though it is clear that protein phosphorylation occurs within the matrix, based on (32)P incorporation and quantitative mass spectrometry measures, the kinase/phosphatase system responsible for this process is ill-defined. An argument is presented that remnants of the much more labile bacterial protein phosphoryl transfer system may be present in the matrix and that the evaluation of this possibility will require the application of approaches developed for bacterial cell signaling to the mitochondria.
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Affiliation(s)
- Raul Covian
- Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, Bethesda, Maryland 20817, USA
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26
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Fan F, Williams HJ, Boyer JG, Graham TL, Zhao H, Lehr R, Qi H, Schwartz B, Raushel FM, Meek TD. On the catalytic mechanism of human ATP citrate lyase. Biochemistry 2012; 51:5198-211. [PMID: 22657152 DOI: 10.1021/bi300611s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ATP citrate lyase (ACL) catalyzes an ATP-dependent biosynthetic reaction which produces acetyl-coenzyme A and oxaloacetate from citrate and coenzyme A (CoA). Studies were performed with recombinant human ACL to ascertain the nature of the catalytic phosphorylation that initiates the ACL reaction and the identity of the active site residues involved. Inactivation of ACL by treatment with diethylpyrocarbonate suggested the catalytic role of an active site histidine (i.e., His760), which was proposed to form a phosphohistidine species during catalysis. The pH-dependence of the pre-steady-state phosphorylation of ACL with [γ-(33)P]-ATP revealed an ionizable group with a pK(a) value of ~7.5, which must be unprotonated for the catalytic phosphorylation of ACL to occur. Mutagenesis of His760 to an alanine results in inactivation of the biosynthetic reaction of ACL, in good agreement with the involvement of a catalytic histidine. The nature of the formation of the phospho-ACL was further investigated by positional isotope exchange using [γ-(18)O(4)]-ATP. The β,γ-bridge to nonbridge positional isotope exchange rate of [γ-(18)O(4)]-ATP achieved its maximal rate of 14 s(-1) in the absence of citrate and CoA. This rate decreased to 5 s(-1) when citrate was added, and was found to be 10 s(-1) when both citrate and CoA were present. The rapid positional isotope exchange rates indicated the presence of one or more catalytically relevant, highly reversible phosphorylated intermediates. Steady-state measurements in the absence of citrate and CoA showed that MgADP was produced by both wild type and H760A forms of ACL, with rates at three magnitudes lower than that of k(cat) for the full biosynthetic reaction. The ATPase activity of ACL, along with the small yet significant positional isotope exchange rate observed in H760A mutant ACL (~150 fold less than wild type), collectively suggested the presence of a second, albeit unproductive, phosphoryl transfer in ACL. Mathematical analysis and computational simulation suggested that the desorption of MgADP at a rate of ~7 s(-1) was the rate-limiting step in the biosynthesis of AcCoA and oxaloacetate.
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Affiliation(s)
- Fan Fan
- Biological Reagents and Assay Development, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA.
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27
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Wilke KE, Francis S, Carlson EE. Activity-based probe for histidine kinase signaling. J Am Chem Soc 2012; 134:9150-3. [PMID: 22606938 DOI: 10.1021/ja3041702] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial two-component systems (TCSs) are signaling pathways composed of two proteins: a histidine kinase (HK) and a response regulator (RR). Upon stimulation, the HK autophosphorylates at a conserved histidine. The phosphoryl group is subsequently transferred to an aspartate on an RR, eliciting an adaptive response, often up- or downregulation of gene expression. TCS signaling controls many functions in bacteria, including development, virulence, and antibiotic resistance, making the proteins involved in these systems potential therapeutic targets. Efficient methods for the profiling of HKs are currently lacking. For direct readout of HK activity, we sought to design a probe that enables detection of the phosphotransfer event; however, analysis of the phosphohistidine species is made difficult by the instability of the P-N bond. We anticipated that use of a γ-thiophosphorylated ATP analogue, which would yield a thiophosphorylated histidine intermediate, could overcome this challenge. We determined that the fluorophore-conjugated probe, BODIPY-FL-ATPγS, labels active HK proteins and is competitive for the ATP binding site. This activity-based probe provides a new strategy for analysis of TCSs and other HK-mediated processes and will facilitate both functional studies and inhibitor identification.
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Affiliation(s)
- Kaelyn E Wilke
- Department of Chemistry, Indiana University, Bloomington, 47405, United States
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28
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Kee JM, Muir TW. Chasing phosphohistidine, an elusive sibling in the phosphoamino acid family. ACS Chem Biol 2012; 7:44-51. [PMID: 22148577 DOI: 10.1021/cb200445w] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This year (2012) marks the 50th anniversary of the discovery of protein histidine phosphorylation. Phosphorylation of histidine (pHis) is now widely recognized as being critical to signaling processes in prokaryotes and lower eukaryotes. However, the modification is also becoming more widely reported in mammalian cellular processes and implicated in certain human disease states such as cancer and inflammation. Nonetheless, much remains to be understood about the role and extent of the modification in mammalian cell biology. Studying the functional role of pHis in signaling, either in vitro or in vivo, has proven devilishly hard, largely due to the chemical instability of the modification. As a consequence, we are currently handicapped by a chronic lack of chemical and biochemical tools with which to study histidine phosphorylation. Here, we discuss the challenges associated with studying the chemical biology of pHis and review recent progress that offers some hope that long-awaited biochemical reagents for studying this elusive posttranslational modification (PTM) might soon be available.
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Affiliation(s)
- Jung-Min Kee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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29
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Stable triazolylphosphonate analogues of phosphohistidine. Amino Acids 2011; 43:857-74. [DOI: 10.1007/s00726-011-1145-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
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30
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Perry J, Koteva K, Wright G. Receptor domains of two-component signal transduction systems. MOLECULAR BIOSYSTEMS 2011; 7:1388-98. [PMID: 21347487 DOI: 10.1039/c0mb00329h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two-component signal transduction systems are found ubiquitously in prokaryotes, and in archaea, fungi, yeast and some plants, where they regulate physiologic and molecular processes at both transcriptional and post-transcriptional levels. Two-component systems sense changes in environmental conditions when a specific ligand binds to the receptor domain of the histidine kinase sensory component. The structures of many histidine kinase receptors are known, including those which sense extracellular and cytoplasmic signals. In this review, we discuss the basic architecture of two-component signalling circuits, including known system ligands, structure and function of both receptor and signalling domains, the chemistry of phosphotransfer, and cross-talk between different two-component pathways. Given the importance of these systems in regulating cellular responses, many biochemical techniques have been developed for their study and analysis. We therefore also review current methods used to study two-component signalling, including a new affinity-based proteomics approach used to study inducible resistance to the antibiotic vancomycin through the VanSR two-component signal transduction system.
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Affiliation(s)
- Julie Perry
- MG DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main St W, Hamilton, Ontario, Canada
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31
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Abstract
We report the synthesis of the phosphohistidine analogue, Fmoc-4-diethylphosphonotriazolylalanine 5 and its incorporation into peptides. Our synthesis of 5 has enabled us to demonstrate that the analogue is compatible with Fmoc-solid phase peptide synthesis (SPPS) conditions. Standard cleavage conditions yield the diethyl phosphonate-protected peptide, however this can be subsequently deprotected using trimethylsilyl bromide to yield the free phosphonic acid-containing peptides.
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32
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Abstract
Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by 1H NMR and 31P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested.
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33
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Kee JM, Villani B, Carpenter LR, Muir TW. Development of stable phosphohistidine analogues. J Am Chem Soc 2011; 132:14327-9. [PMID: 20879710 DOI: 10.1021/ja104393t] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is one of the most common and extensively studied posttranslational modifications (PTMs). Compared to the O-phosphorylation of Ser, Thr, and Tyr residues, our understanding of histidine phosphorylation is relatively limited, particularly in higher eukaryotes, due to technical difficulties stemming from the intrinsic instability and isomerism of phosphohistidine (pHis). We report the design and synthesis of stable and nonisomerizable pHis analogues. These pHis analogues were successfully utilized in solid-phase peptide synthesis and semi-synthesis of histone H4. Significantly, the first antibody that specifically recognizes pHis was obtained using the synthetic peptide as the immunogen.
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Affiliation(s)
- Jung-Min Kee
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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34
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Hofmann FT, Lindemann C, Salia H, Adamitzki P, Karanicolas J, Seebeck FP. A phosphoarginine containing peptide as an artificial SH2 ligand. Chem Commun (Camb) 2011; 47:10335-7. [DOI: 10.1039/c1cc13341a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Lapek JD, Tombline G, Friedman AE. Mass spectrometry detection of histidine phosphorylation on NM23-H1. J Proteome Res 2010; 10:751-5. [PMID: 21121676 DOI: 10.1021/pr100905m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphorylation is a ubiquitous protein post-translational modification that is intimately involved in most aspects of cellular regulation. Currently, most proteomic analyses are performed with phosphorylation searches for serine, threonine, and tyrosine modifications, as the phosphorylated residues of histidine and aspartic acid are acid labile and thus undetectable with most proteomic methodologies. Here, we present a novel buffer system to show histidine phosphorylation of NM23-H1, the product of the first identified putative human metastasis suppressor gene (NME1), which catalyzes the transfer of the γ-phosphate from nucleoside triphosphates to nucleoside diphosphates. On the basis of a pH titration of LC elution buffers and MS/MS identification, recombinant NM23-H1 subjected to autophosphorylation was shown to contain phosphorylated histidine at residue 118 at pH 5 and 6, with each level giving over 75% peptide coverage for identification. The solvent system presented permits the detection of all five possible phosphorylation moieties. Application of histidine and aspartic acid phosphorylation modifications to proteomic analyses will significantly advance the understanding of phosphorylation relay signaling in cellular regulation, including elucidation of the role of NM23-H1 in metastasis.
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Affiliation(s)
- John D Lapek
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York 14642, USA
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36
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Himmel S, Wolff S, Becker S, Lee D, Griesinger C. Nachweis und Identifizierung von Protein-Phosphorylierungen in Histidinen mithilfe von HNP-Korrelationen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Himmel S, Wolff S, Becker S, Lee D, Griesinger C. Detection and Identification of Protein-Phosphorylation Sites in Histidines through HNP Correlation Patterns. Angew Chem Int Ed Engl 2010; 49:8971-4. [DOI: 10.1002/anie.201003965] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Prohaska SJ, Stadler PF, Krakauer DC. Innovation in gene regulation: The case of chromatin computation. J Theor Biol 2010; 265:27-44. [DOI: 10.1016/j.jtbi.2010.03.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/06/2010] [Indexed: 11/17/2022]
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39
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Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the masses. ACS Chem Biol 2010; 5:105-19. [PMID: 20047291 DOI: 10.1021/cb900277e] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation serves as a primary mechanism of signal transduction in the cells of biological organisms. Technical advancements over the last several years in mass spectrometry now allow for the large-scale identification and quantitation of in vivo phosphorylation at unprecedented levels. These developments have occurred in the areas of sample preparation, instrumentation, quantitative methodology, and informatics so that today, 10 000-20 000 phosphorylation sites can be identified and quantified within a few weeks. With the rapid development and widespread availability of such data, its translation into biological insight and knowledge is a current obstacle. Here we present an overview of how this technology came to be and is currently applied, as well as future challenges for the field.
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Affiliation(s)
| | | | | | - Nicole A. Beauchene
- Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J. Coon
- Departments of Chemistry
- Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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40
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Stepchild phosphohistidine: acid-labile phosphorylation becomes accessible by functional proteomics. Anal Bioanal Chem 2010; 397:3209-12. [PMID: 20063153 DOI: 10.1007/s00216-009-3372-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 11/30/2009] [Accepted: 11/30/2009] [Indexed: 12/22/2022]
Abstract
Bioanalytical techniques were preferentially developed for the investigation of phosphohydroxyamino acids in the past and there is a wealth of information on the detection of serine, threonine and tyrosine phosphorylation in functional proteomics. However, similarly important for protein regulation and signalling is the phosphorylation of other amino acids such as histidine, but its detection is hampered by the sensitivity to acid. Mass spectrometry in conjunction with chromatographic methods is allowing us to start to get a handle on phosphohistidine. (32)P-labelling and amino acid analysis for phosphorylation site determination is increasingly complemented by typical proteomic approaches based on reversed-phase peptide separation and gas-phase fragmentation. Chemical phosphorylation of peptides is a valuable tool, therefore, for the generation of analytical standards for use in method development.
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41
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Carlson HK, Plate L, Price MS, Allen JJ, Shokat KM, Marletta MA. Use of a semisynthetic epitope to probe histidine kinase activity and regulation. Anal Biochem 2009; 397:139-43. [PMID: 19819215 DOI: 10.1016/j.ab.2009.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 11/26/2022]
Abstract
Histidine-aspartic acid phosphotransfer pathways are central components of prokaryotic signal transduction pathways and are also found in many eukaryotes. Tools to study histidine kinases, however, are currently quite limited. In this article, we present a new tool to study histidine-aspartic acid phosphotransfer pathways. We show that many histidine kinases will accept ATPgammaS as a substrate to form a stable thiophosphohistidine even when they do not form stable phosphohistidines using the natural substrate ATP. An antibody that has previously been used to detect thiophosphorylated serine, threonine, and tyrosine residues is shown to recognize thiophosphohistidine and thiophosphoaspartic acid residues. Histidine kinase autothiophosphorylation is regulated by other protein sensor domains in the same way as autophosphorylation, and thiophosphate is transferred to downstream aspartic acid containing response regulators.
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Affiliation(s)
- Hans K Carlson
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
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Mehta A, Orchard S. Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified. Mol Cell Biochem 2009; 329:3-15. [PMID: 19415463 PMCID: PMC2721137 DOI: 10.1007/s11010-009-0114-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 04/02/2009] [Indexed: 12/17/2022]
Abstract
The guest editor (AM) provides his perspective on the most recent advances on nucleoside diphosphate kinase (NDPK, otherwise known as AWD or NM23) showcasing phospho-histidine biochemistry and its impact on diverse pathology when disordered. His co-author (SO) provides state-of-the-art analyses from the European institute of Bioinformatics in an appendix to support the most recent advances made by the NDPK community. Unfortunately, to those outside the field, NDPK is often dismissed as a tiny ‘ancient housekeeper’ protein found in marine sponges, social amoebae, worms, fruit flies, rodents and humans but the state-of-the-art papers overviewed here show that NDPK does not act simply in mindless rote, inter-converting cellular ‘energy currencies’. That two NDPK isoforms regulate fetal erythroid lineage is a developmental case in point. Seminal Cancer Research UK support is gratefully acknowledged that generated additional resources to enable the NDPK community to meet in Dundee in 2007 (www.dundee.ac.uk/mchs/ndpk; next meeting is planned: 2010/Mannheim-Heidelberg). The presented papers illustrate the point that when scientists are left alone ‘shut up in the narrow cell of their laboratory’ (as the philosopher Ortega once said, a sentiment echoed by Erwin Schrödinger), then progress will ultimately occur bridging the gap between specialization and translation for human benefit. To aid translation, this overview initially introduces the NDPK family to the non-specialist, who serendipitously finds these proteins in their biology. This is immediately followed by examples of the diverse biology generated by this self-aggregating group of multi-functional proteins and finally capped by an emerging idea explaining how this diversity might arise.
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Affiliation(s)
- Anil Mehta
- Division of Medical Sciences, Tayside Institute of Child Health, Ninewells Hospital Medical School, Dundee DD19SY, Scotland, UK.
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