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Cable JM, Reinoso-Vizcaino NM, White RE, Luftig MA. Epstein-Barr virus protein EBNA-LP engages YY1 through leucine-rich motifs to promote naïve B cell transformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574580. [PMID: 38260266 PMCID: PMC10802455 DOI: 10.1101/2024.01.07.574580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Epstein-Barr Virus (EBV) is associated with numerous cancers including B cell lymphomas. In vitro, EBV transforms primary B cells into immortalized Lymphoblastoid Cell Lines (LCLs) which serves as a model to study the role of viral proteins in EBV malignancies. EBV induced cellular transformation is driven by viral proteins including EBV-Nuclear Antigens (EBNAs). EBNA-LP is important for the transformation of naïve but not memory B cells. While EBNA-LP was thought to promote gene activation by EBNA2, EBNA-LP Knock Out (LPKO) virus-infected cells express EBNA2-activated genes efficiently. Therefore, a gap in knowledge exists as to what roles EBNA-LP plays in naïve B cell transformation. We developed a trans-complementation assay wherein transfection with wild-type EBNA-LP rescues the transformation of peripheral blood- and cord blood-derived naïve B cells by LPKO virus. Despite EBNA-LP phosphorylation sites being important in EBNA2 co-activation; neither phospho-mutant nor phospho-mimetic EBNA-LP was defective in rescuing naïve B cell outgrowth. However, we identified conserved leucine-rich motifs in EBNA-LP that were required for transformation of adult naïve and cord blood B cells. Because cellular PPAR-γ coactivator (PGC) proteins use leucine-rich motifs to engage transcription factors including YY1, a key regulator of DNA looping and metabolism, we examined the role of EBNA-LP in engaging cellular transcription factors. We found a significant overlap between EBNA-LP and YY1 in ChIP-Seq data and confirmed their biochemical association in LCLs by endogenous co-immunoprecipitation. Moreover, we found that the EBNA-LP leucine-rich motifs were required for YY1 interaction in LCLs. Finally, we used Cas9 to knockout YY1 in primary total B cells and naïve B cells prior to EBV infection and found YY1 to be essential for EBV-mediated transformation. We propose that EBNA-LP engages YY1 through conserved leucine-rich motifs to promote EBV transformation of naïve B cells.
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Affiliation(s)
- Jana M Cable
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Nicolás M Reinoso-Vizcaino
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Robert E. White
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
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2
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Hardt R, Dehghani A, Schoor C, Gödderz M, Cengiz Winter N, Ahmadi S, Sharma R, Schork K, Eisenacher M, Gieselmann V, Winter D. Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing. Cell Mol Life Sci 2023; 80:260. [PMID: 37594553 PMCID: PMC10439241 DOI: 10.1007/s00018-023-04892-8] [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: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Oligodendrocytes are generated via a two-step mechanism from pluripotent neural stem cells (NSCs): after differentiation of NSCs to oligodendrocyte precursor/NG2 cells (OPCs), they further develop into mature oligodendrocytes. The first step of this differentiation process is only incompletely understood. In this study, we utilized the neurosphere assay to investigate NSC to OPC differentiation in a time course-dependent manner by mass spectrometry-based (phospho-) proteomics. We identify doublecortin-like kinase 1 (Dclk1) as one of the most prominently regulated proteins in both datasets, and show that it undergoes a gradual transition between its short/long isoform during NSC to OPC differentiation. This is regulated by phosphorylation of its SP-rich region, resulting in inhibition of proteolytic Dclk1 long cleavage, and therefore Dclk1 short generation. Through interactome analyses of different Dclk1 isoforms by proximity biotinylation, we characterize their individual putative interaction partners and substrates. All data are available via ProteomeXchange with identifier PXD040652.
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Affiliation(s)
- Robert Hardt
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Alireza Dehghani
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Carmen Schoor
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Markus Gödderz
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Nur Cengiz Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931, Cologne, Germany
| | - Shiva Ahmadi
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Bayer Pharmaceuticals, 42113, Wuppertal, Germany
| | - Ramesh Sharma
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany.
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3
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White PJ, McGarrah RW, Grimsrud PA, Tso SC, Yang WH, Haldeman JM, Grenier-Larouche T, An J, Lapworth AL, Astapova I, Hannou SA, George T, Arlotto M, Olson LB, Lai M, Zhang GF, Ilkayeva O, Herman MA, Wynn RM, Chuang DT, Newgard CB. The BCKDH Kinase and Phosphatase Integrate BCAA and Lipid Metabolism via Regulation of ATP-Citrate Lyase. Cell Metab 2018; 27:1281-1293.e7. [PMID: 29779826 PMCID: PMC5990471 DOI: 10.1016/j.cmet.2018.04.015] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/27/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Branched-chain amino acids (BCAA) are strongly associated with dysregulated glucose and lipid metabolism, but the underlying mechanisms are poorly understood. We report that inhibition of the kinase (BDK) or overexpression of the phosphatase (PPM1K) that regulates branched-chain ketoacid dehydrogenase (BCKDH), the committed step of BCAA catabolism, lowers circulating BCAA, reduces hepatic steatosis, and improves glucose tolerance in the absence of weight loss in Zucker fatty rats. Phosphoproteomics analysis identified ATP-citrate lyase (ACL) as an alternate substrate of BDK and PPM1K. Hepatic overexpression of BDK increased ACL phosphorylation and activated de novo lipogenesis. BDK and PPM1K transcript levels were increased and repressed, respectively, in response to fructose feeding or expression of the ChREBP-β transcription factor. These studies identify BDK and PPM1K as a ChREBP-regulated node that integrates BCAA and lipid metabolism. Moreover, manipulation of the BDK:PPM1K ratio relieves key metabolic disease phenotypes in a genetic model of severe obesity.
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Affiliation(s)
- Phillip J White
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Robert W McGarrah
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Paul A Grimsrud
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Shih-Chia Tso
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen-Hsuan Yang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Jonathan M Haldeman
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Thomas Grenier-Larouche
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Jie An
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Amanda L Lapworth
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Inna Astapova
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Sarah A Hannou
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Tabitha George
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Michelle Arlotto
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Lyra B Olson
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Michelle Lai
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Guo-Fang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Mark A Herman
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA.
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Dehghani A, Gödderz M, Winter D. Tip-Based Fractionation of Batch-Enriched Phosphopeptides Facilitates Easy and Robust Phosphoproteome Analysis. J Proteome Res 2017; 17:46-54. [DOI: 10.1021/acs.jproteome.7b00256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alireza Dehghani
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Markus Gödderz
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Dominic Winter
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
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5
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Impact of the in vitro gastrointestinal digestion protocol on casein phosphopeptide profile of Grana Padano cheese digestates. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.11.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Sandhu P, Naeem MM, Lu C, Kumarathasan P, Gomes J, Basak A. Ser 422 phosphorylation blocks human Tau cleavage by caspase-3: Biochemical implications to Alzheimer's Disease. Bioorg Med Chem Lett 2016; 27:642-652. [PMID: 27989667 DOI: 10.1016/j.bmcl.2016.11.087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 12/16/2022]
Abstract
Proteolytic truncation of microtubule associated human (h) Tau protein by caspase-3 at the carboxy (C) terminus has been linked to the pathogenesis of Alzheimer's Disease (AD). This cleavage likely occurs between Asp421↓Ser422 leading to the formation of 421-mer truncated Tau protein which has been found to be present as aggregate in high level after phosphorylation in mortal AD brain tissue compared to normal. At least 50 phosphorylation sites involving Ser, Thr and Tyr residues have been identified or proposed in hTau and a selected number of them have been implicated in hTau aggregation following latter's proteolytic truncation. Interestingly, it is further noted that Ser422 residue present in the P1' position of hTau caspase-3 cleavage region is a potential phosphorylation site. So we became interested to examine in vitro the effect of phospho-Ser422 residue on hTau cleavage by caspase-3 which is a crucial upstream event associated with hTau self-assembly leading to AD pathogenesis. The goal of this project is to study in vitro the caspase-3 cleavage site of hTau protein and to examine the kinetics of this cleavage following Ser422 phosphorylation and treatment with caspase-3 inhibitors. This is achieved by designing peptides from the sequence of hTau protein containing the proposed caspase-3 cleavage region. Peptides were designed from 441-mer major human Tau protein sequence that encompasses the proposed caspase-3 cleavage site [Asp421↓Ser422]. Corresponding phospho-, dextro-Ser422 and dextro-Asp421 analogs were also designed. Peptides were synthesized by solid phase chemistry, purified and fully characterized by mass spectrometry. These were then incubated with recombinant caspase-3 enzyme under identical condition for digestion and analyzed for cleavage by mass spectrometry and RP-HPLC chromatograms. Our results indicated that while the control peptide is efficiently cleaved by caspase-3 at Asp421↓Ser422 site producing the expected N- and C-terminal fragment peptides, the corresponding phospho-Ser422 peptide remained completely resistant to the cleavage. Substitution of Asp421 by its dextro isoform also blocks peptide cleavage by caspase-3. However substitution of Ser422 by its dextro isoform in the peptide did not affect the cleavage significantly. The above results were further confirmed by caspase-3 digestion experiment in the presence of varying amounts of caspase-3 inhibitor (Ac-DQVD-aldehyde) which was found to block this cleavage in a highly effective manner. Our results highlighted the crucial significance of Ser422 phosphorylation and suggest that the kinase associated with this Ser-phosphorylation may protect Tau from aggregation. Thus specific promoters/activators of this kinase may find useful therapeutic benefits in arresting Tau truncation by caspase-3 and the progression of AD. In addition our data demonstrated that Tau-peptides where Ser422 or Asp421 are substituted by their respective dextro isomers, exhibit different cleavage kinetics by caspase-3 and this may have important implications in therapeutic intervention of Tau aggregation and associated AD.
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Affiliation(s)
- Priya Sandhu
- Interdisciplinary School of Health Sciences, Faculty of Health Science, U Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Mansur Mohammad Naeem
- Interdisciplinary School of Health Sciences, Faculty of Health Science, U Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Chunyu Lu
- Interdisciplinary School of Health Sciences, Faculty of Health Science, U Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Premkumari Kumarathasan
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - James Gomes
- Interdisciplinary School of Health Sciences, Faculty of Health Science, U Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Ajoy Basak
- Interdisciplinary School of Health Sciences, Faculty of Health Science, U Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Chronic Disease Program, Ottawa Hospital Research Institute, 725 Parkdale Ave., Ottawa, ON K1Y 4E9, Canada.
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7
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Wierød L, Cameron J, Strøm TB, Leren TP. Studies of the autoinhibitory segment comprising residues 31-60 of the prodomain of PCSK9: Possible implications for the mechanism underlying gain-of-function mutations. Mol Genet Metab Rep 2016; 9:86-93. [PMID: 27896130 PMCID: PMC5121147 DOI: 10.1016/j.ymgmr.2016.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/14/2016] [Indexed: 01/07/2023] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the low density lipoprotein receptor (LDLR) at the cell surface and is internalized as a complex with the LDLR. In the acidic milieu of the sorting endosome, PCSK9 remains bound to the LDLR and prevents the LDLR from folding over itself to adopt a closed conformation. As a consequence, the LDLR fails to recycle back to the cell membrane. Even though it is the catalytic domain of PCSK9 that interacts with the LDLR at the cell surface, the structurally disordered segment consisting of residues 31–60 and which is rich in acidic residues, has a negative effect both on autocatalytic cleavage and on the activity of PCSK9 towards the LDLR. Thus, this unstructured segment represents an autoinhibitory domain of PCSK9. One may speculate that post-translational modifications within residues 31–60 may affect the inhibitory activity of this segment, and represent a mechanism for fine-tuning the activity of PCSK9 towards the LDLR. Our data indicate that the inhibitory effect of this unstructured segment results from an interaction with basic residues of the catalytic domain of PCSK9. Mutations in the catalytic domain which involve charged residues, could therefore be gain-of-function mutations by affecting the positioning of this segment.
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Affiliation(s)
- Lene Wierød
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jamie Cameron
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Thea Bismo Strøm
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trond P Leren
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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8
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Jacot D, Frénal K, Marq JB, Sharma P, Soldati-Favre D. Assessment of phosphorylation inToxoplasmaglideosome assembly and function. Cell Microbiol 2014; 16:1518-32. [DOI: 10.1111/cmi.12307] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/16/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Damien Jacot
- Department of Microbiology & Molecular Medicine; CMU/University of Geneva; Rue Michel-Servet 1 CH-1211 Geneva 4 Switzerland
| | - Karine Frénal
- Department of Microbiology & Molecular Medicine; CMU/University of Geneva; Rue Michel-Servet 1 CH-1211 Geneva 4 Switzerland
| | - Jean-Baptiste Marq
- Department of Microbiology & Molecular Medicine; CMU/University of Geneva; Rue Michel-Servet 1 CH-1211 Geneva 4 Switzerland
| | - Pushkar Sharma
- Eukaryotic Gene Expression Laboratory; National Institute of Immunology; New Delhi 110067 India
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine; CMU/University of Geneva; Rue Michel-Servet 1 CH-1211 Geneva 4 Switzerland
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Dickhut C, Feldmann I, Lambert J, Zahedi RP. Impact of digestion conditions on phosphoproteomics. J Proteome Res 2014; 13:2761-70. [PMID: 24724590 DOI: 10.1021/pr401181y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the past few years, the focus of phosphoproteomics has shifted from merely qualitative to quantitative and targeted studies. Tryptic digestion is a critical step that directly affects quantification and that can be impaired by phosphorylation. Therefore, we systematically characterized the digestion efficiency of 19 nonmodified and phosphorylated model peptides. Whereas we quantified a strong reduction of tryptic cleavage within phosphorylated PKA motifs (R)-R-X-pS/pT and also R-X-X-pT sequences, (R)-R-X-pY sequences were almost unaffected. Structural prediction implied the formation of salt bridges between R/K cleavage sites and phosphoamino acids pS/pT as the main reason for impaired tryptic digestion. We evaluated different conditions to optimize the digestion of such "resistant" phosphopeptides, yielding a substantial improvement of digestion efficiency. We performed a quantitative large-scale phosphoproteomic analysis of human platelets to validate our findings in a complex biological sample. Here, increasing trypsin concentrations up to a trypsin to peptide ratio of 1:10 led to a significant gain (i) in the overall number of phosphorylation sites (up to 9%) and (ii) in the intensities of individual phosphopeptides, thereby improving the sensitivity of phosphopeptide quantification. Still, for certain sequences, the negative impact of phosphorylation on digestion efficiency will further complicate the analysis of phosphorylation stoichiometry.
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Affiliation(s)
- Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund 44227, Germany
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10
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In vitro gastrointestinal digestion of bovine αS1- and αS2-casein variants gives rise to different IgE-binding epitopes. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Boehm ME, Seidler J, Hahn B, Lehmann WD. Site-specific degree of phosphorylation in proteins measured by liquid chromatography-electrospray mass spectrometry. Proteomics 2012; 12:2167-78. [PMID: 22653803 DOI: 10.1002/pmic.201100561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review focuses on quantitative protein phosphorylation analysis based on coverage of both the phosphorylated and nonphosphorylated forms. In this way, site-specific data on the degree of phosphorylation can be measured, generating the most detailed level of phosphorylation status analysis of proteins. To highlight the experimental challenges in this type of quantitative protein phosphorylation analysis, we discuss the typical workflows for mass spectrometry-based proteomics with a focus on the quantitative analysis of peptide/phosphopeptide ratios. We review workflows for measuring site-specific degrees of phosphorylation including the label-free approach, differential stable isotope labeling of analytes, and methods based on the addition of stable isotope labeled peptide/phosphopeptide pairs as internal standards. The discussion also includes the determination of phosphopeptide isoform abundance data for multiply phosphorylated motifs that contain information about the connectivity of phosphorylation events. The review closes with a prospective on the use of intact stable isotope labeled proteins as internal standards and a summarizing discussion of the typical accuracies of the individual methods.
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Affiliation(s)
- Martin E Boehm
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Winter D, Hung CW, Jaskolla TW, Karas M, Lehmann WD. Enzyme-cleavable tandem peptides for quantitative studies in MS-based proteomics. Proteomics 2012; 12:3470-4. [DOI: 10.1002/pmic.201200290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/13/2012] [Accepted: 10/01/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Dominic Winter
- Molecular Structure Analysis; German Cancer Research Center; Heidelberg; Germany
| | - Chien-Wen Hung
- Molecular Structure Analysis; German Cancer Research Center; Heidelberg; Germany
| | - Thorsten W. Jaskolla
- Cluster of Excellence Macromolecular Complexes; Institute of Pharmaceutical Chemistry; Goethe-University Frankfurt; Frankfurt; Germany
| | - Michael Karas
- Cluster of Excellence Macromolecular Complexes; Institute of Pharmaceutical Chemistry; Goethe-University Frankfurt; Frankfurt; Germany
| | - Wolf D. Lehmann
- Molecular Structure Analysis; German Cancer Research Center; Heidelberg; Germany
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13
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Jacot D, Soldati-Favre D. Does protein phosphorylation govern host cell entry and egress by the Apicomplexa? Int J Med Microbiol 2012; 302:195-202. [DOI: 10.1016/j.ijmm.2012.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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14
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Thomas DC, Ahmed A, Gilberger TW, Sharma P. Regulation of Plasmodium falciparum glideosome associated protein 45 (PfGAP45) phosphorylation. PLoS One 2012; 7:e35855. [PMID: 22558243 PMCID: PMC3338798 DOI: 10.1371/journal.pone.0035855] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/23/2012] [Indexed: 01/08/2023] Open
Abstract
The actomyosin motor complex of the glideosome provides the force needed by apicomplexan parasites such as Toxoplasma gondii (Tg) and Plasmodium falciparum (Pf) to invade their host cells and for gliding motility of their motile forms. Glideosome Associated Protein 45 (PfGAP45) is an essential component of the glideosome complex as it facilitates anchoring and effective functioning of the motor. Dissection of events that regulate PfGAP45 may provide insights into how the motor and the glideosome operate. We found that PfGAP45 is phosphorylated in response to Phospholipase C (PLC) and calcium signaling. It is phosphorylated by P. falciparum kinases Protein Kinase B (PfPKB) and Calcium Dependent Protein Kinase 1 (PfCDPK1), which are calcium dependent enzymes, at S89, S103 and S149. The Phospholipase C pathway influenced the phosphorylation of S103 and S149. The phosphorylation of PfGAP45 at these sites is differentially regulated during parasite development. The localization of PfGAP45 and its association may be independent of the phosphorylation of these sites. PfGAP45 regulation in response to calcium fits in well with the previously described role of calcium in host cell invasion by malaria parasite.
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Affiliation(s)
- Divya Catherine Thomas
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Anwar Ahmed
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Tim Wolf Gilberger
- Department of Molecular Parasitology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- M. G. DeGroote Institute for Infectious Disease Research and Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Pushkar Sharma
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail:
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15
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Holder AA, Mohd Ridzuan MA, Green JL. Calcium dependent protein kinase 1 and calcium fluxes in the malaria parasite. Microbes Infect 2012; 14:825-30. [PMID: 22584104 DOI: 10.1016/j.micinf.2012.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/11/2012] [Accepted: 04/11/2012] [Indexed: 01/20/2023]
Abstract
Calcium dependent protein kinases (CDPKs) are found only in plants and alveolates and are distinguished from other kinases by an activation domain that binds calcium directly. Plants contain families of these kinases and their functions are modulated by post translational modifications as well as calcium activation. Apicomplexan parasites also contain CDPK families and this review is focused on CDPK1 in Plasmodium spp. This enzyme has been implicated in parasite motility and host cell invasion and at least two substrates associated with the actomyosin motor complex have been identified. By analogy with the plant CDPKs we propose that its activity is modulated both by post translational modifications and by its subcellular location in a compartment within the parasite's pellicle, which may regulate the calcium concentration required for activation.
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Affiliation(s)
- Anthony A Holder
- Division of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Nebl T, Prieto JH, Kapp E, Smith BJ, Williams MJ, Yates JR, Cowman AF, Tonkin CJ. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex. PLoS Pathog 2011; 7:e1002222. [PMID: 21980283 PMCID: PMC3182922 DOI: 10.1371/journal.ppat.1002222] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 07/05/2011] [Indexed: 01/29/2023] Open
Abstract
Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. Apicomplexan parasites are a group of obligate intracellular pathogens of wide medical and agricultural significance. Included within this phylum is Plasmodium spp, the causative agents to malaria and the ubiquitous parasite Toxoplasma, which inflicts disease burden on AIDS patients, transplant recipients and the unborn fetus. No matter the host cell that they target, all apicomplexan parasites must activate invasion upon host cell contact. Calcium-mediated signal transduction pathways modulate this process, yet the molecular processes are largely unknown. Using a range of proteomics approaches we reveal proteins in Toxoplasma that are phosphorylated upon calcium signaling, and furthermore, identify phosphorylation sites on a range of proteins that may play crucial roles in regulating parasite motility and microneme secretion. By quantitatively monitoring phosphorylation deposition upon calcium signaling we define putative regulatory domains of GAP45 and MLC1 and further show evidence that the invasion motor potentially more strongly associates upon calcium signaling. We also identified that a new Calmodulin-like protein is part of the invasion motor and this suggests that direct Ca2+ binding may also modulate motor activity.
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Affiliation(s)
- Thomas Nebl
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Judith Helena Prieto
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eugene Kapp
- Joint Proteomics Facility, The Ludwig Institute for Cancer Research and the Walter and Eliza Hall Institute, Victoria, Australia
| | - Brian J. Smith
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Melanie J. Williams
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Christopher J. Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, Australia
- * E-mail:
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Gao J, Gao G, Zhang Y, Wang F. Proteomic analysis of human epithelial ovarian cancer xenografts in immunodeficient mice exposed to chronic psychological stress. SCIENCE CHINA-LIFE SCIENCES 2011; 54:112-20. [DOI: 10.1007/s11427-010-4126-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 10/13/2010] [Indexed: 01/23/2023]
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Hahn B, Böhm M, Raia V, Zinn N, Möller P, Klingmüller U, Lehmann WD. One-source peptide/phosphopeptide standards for accurate phosphorylation degree determination. Proteomics 2011; 11:490-4. [DOI: 10.1002/pmic.201000569] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/04/2010] [Accepted: 11/08/2010] [Indexed: 11/08/2022]
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Abstract
The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
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Affiliation(s)
- Joerg Seidler
- Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
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