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Grimes KM, Maillet M, Swoboda CO, Bowers SLK, Millay DP, Molkentin JD. MEK1-ERK1/2 signaling regulates the cardiomyocyte non-sarcomeric actin cytoskeletal network. Am J Physiol Heart Circ Physiol 2024; 326:H180-H189. [PMID: 37999644 DOI: 10.1152/ajpheart.00612.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
During select pathological conditions, the heart can hypertrophy and remodel in either a dilated or concentric ventricular geometry, which is associated with lengthening or widening of cardiomyocytes, respectively. The mitogen-activated protein kinase kinase 1 (MEK1) and extracellular signal-related kinase 1 and 2 (ERK1/2) pathway has been implicated in these differential types of growth such that cardiac overexpression of activated MEK1 causes profound concentric hypertrophy and cardiomyocyte thickening, while genetic ablation of the genes encoding ERK1/2 in the mouse heart causes dilation and cardiomyocyte lengthening. However, the mechanisms by which this kinase signaling pathway controls cardiomyocyte directional growth as well as its downstream effectors are poorly understood. To investigate this, we conducted an unbiased phosphoproteomic screen in cultured neonatal rat ventricular myocytes treated with an activated MEK1 adenovirus, the MEK1 inhibitor U0126, or an eGFP adenovirus control. Bioinformatic analysis identified cytoskeletal-related proteins as the largest subset of differentially phosphorylated proteins. Phos-tag and traditional Western blotting were performed to confirm that many cytoskeletal proteins displayed changes in phosphorylation with manipulations in MEK1-ERK1/2 signaling. From this, we hypothesized that the actin cytoskeleton would be changed in vivo in the mouse heart. Indeed, we found that activated MEK1 transgenic mice and gene-deleted mice lacking ERK1/2 protein had enhanced non-sarcomeric actin expression in cardiomyocytes compared with wild-type control hearts. Consistent with these results, cytoplasmic β- and γ-actin were increased at the subcortical intracellular regions of adult cardiomyocytes. Together, these data suggest that MEK1-ERK1/2 signaling influences the non-sarcomeric cytoskeletal actin network, which may be important for facilitating the growth of cardiomyocytes in length and/or width.NEW & NOTEWORTHY Here, we performed an unbiased analysis of the total phosphoproteome downstream of MEK1-ERK1/2 kinase signaling in cardiomyocytes. Pathway analysis suggested that proteins of the non-sarcomeric cytoskeleton were the most differentially affected. We showed that cytoplasmic β-actin and γ-actin isoforms, regulated by MEK1-ERK1/2, are localized to the subcortical space at both lateral membranes and intercalated discs of adult cardiomyocytes suggesting how MEK1-ERK1/2 signaling might underlie directional growth of adult cardiomyocytes.
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Affiliation(s)
- Kelly M Grimes
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Marjorie Maillet
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Casey O Swoboda
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Stephanie L K Bowers
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Doug P Millay
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
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2
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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3
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Abstract
Mass spectrometry (MS)-based proteomics is currently the most successful approach to measure and compare peptides and proteins in a large variety of biological samples. Modern mass spectrometers, equipped with high-resolution analyzers, provide large amounts of data output. This is the case of shotgun/bottom-up proteomics, which consists in the enzymatic digestion of protein into peptides that are then measured by MS-instruments through a data dependent acquisition (DDA) mode. Dedicated bioinformatic tools and platforms have been developed to face the increasing size and complexity of raw MS data that need to be processed and interpreted for large-scale protein identification and quantification. This chapter illustrates the most popular bioinformatics solution for the analysis of shotgun MS-proteomics data. A general description will be provided on the data preprocessing options and the different search engines available, including practical suggestions on how to optimize the parameters for peptide search, based on hands-on experience.
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Affiliation(s)
- Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Federica Marini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy.
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Quintieri L, Fanelli F, Zühlke D, Caputo L, Logrieco AF, Albrecht D, Riedel K. Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage. Front Microbiol 2020; 11:991. [PMID: 32670211 PMCID: PMC7326052 DOI: 10.3389/fmicb.2020.00991] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/23/2020] [Indexed: 12/22/2022] Open
Abstract
In food chain, Pseudomonas spp. cause spoilage by reducing shelf life of fresh products, especially during cold storage, with a high economic burden for industries. However, recent studies have shed new light on health risks occurring when they colonize immunocompromised patient tissues. Likewise to P. aeruginosa, they exhibit antibiotic resistance and biofilm formation, responsible for their spread and persistence in the environment. Biofilm formation might be induced by environmental stresses, such as temperature fluctuations causing physiological and metabolic changes exacerbating food spoilage (by protease and pigment synthesis), and the production of adhesion molecules, chemotactic or underestimated virulence factors. In order to provide a new insight into phenotypic biodiversity of Pseudomonas spoilers isolated from cold stored cheese, in this work 19 Pseudomonas spp. were investigated for biofilm, pigments, exopolysaccharide production and motility at low temperature. Only nine strains showed these phenotypic traits and the blue pigmenting cheese strain P. fluorescens ITEM 17298 was the most distinctive. In addition, this strain decreased the survival probability of infected Galleria mellonella larvae, showing, for the first time, a pathogenic potential. Genomic and proteomic analyses performed on the ITEM 17298 planktonic cells treated or not with lactoferrin derived antibiofilm peptides allowed to reveal specific biofilm related-pathways as well as proteins involved in pathogenesis. Indeed, several genes were found related to signaling system by cGMP-dependent protein kinases, cellulose, rhamnolipid and alginate synthesis, antibiotic resistance, adhesion and virulence factors. The proteome of the untreated ITEM 17298, growing at low temperature, showed that most of the proteins associated with biofilm regulation, pigmentation motility, antibiotic resistance and pathogenecity were repressed, or decreased their levels in comparison to that of the untreated cultures. Thus, the results of this work shed light on the complex pathways network allowing psychrotrophic pseudomonads to adapt themselves to food-refrigerated conditions and enhance their spoilage. In addition, the discovery of virulence factors and antibiotic resistance determinants raises some questions about the need to deeper investigate these underestimated bacteria in order to increase awareness and provide input to update legislation on their detection limits in foods.
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Affiliation(s)
- Laura Quintieri
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Francesca Fanelli
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Leonardo Caputo
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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McCann JJ, Vasilevskaya IA, Poudel Neupane N, Shafi AA, McNair C, Dylgjeri E, Mandigo AC, Schiewer MJ, Schrecengost RS, Gallagher P, Stanek TJ, McMahon SB, Berman-Booty LD, Ostrander WF, Knudsen KE. USP22 Functions as an Oncogenic Driver in Prostate Cancer by Regulating Cell Proliferation and DNA Repair. Cancer Res 2020; 80:430-443. [PMID: 31740444 PMCID: PMC7814394 DOI: 10.1158/0008-5472.can-19-1033] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/02/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]
Abstract
Emerging evidence indicates the deubiquitinase USP22 regulates transcriptional activation and modification of target substrates to promote pro-oncogenic phenotypes. Here, in vivo characterization of tumor-associated USP22 upregulation and unbiased interrogation of USP22-regulated functions in vitro demonstrated critical roles for USP22 in prostate cancer. Specifically, clinical datasets validated that USP22 expression is elevated in prostate cancer, and a novel murine model demonstrated a hyperproliferative phenotype with prostate-specific USP22 overexpression. Accordingly, upon overexpression or depletion of USP22, enrichment of cell-cycle and DNA repair pathways was observed in the USP22-sensitive transcriptome and ubiquitylome using prostate cancer models of clinical relevance. Depletion of USP22 sensitized cells to genotoxic insult, and the role of USP22 in response to genotoxic insult was further confirmed using mouse adult fibroblasts from the novel murine model of USP22 expression. As it was hypothesized that USP22 deubiquitylates target substrates to promote protumorigenic phenotypes, analysis of the USP22-sensitive ubiquitylome identified the nucleotide excision repair protein, XPC, as a critical mediator of the USP22-mediated response to genotoxic insult. Thus, XPC undergoes deubiquitylation as a result of USP22 function and promotes USP22-mediated survival to DNA damage. Combined, these findings reveal unexpected functions of USP22 as a driver of protumorigenic phenotypes and have significant implications for the role of USP22 in therapeutic outcomes. SIGNIFICANCE: The studies herein present a novel mouse model of tumor-associated USP22 overexpression and implicate USP22 in modulation of cellular survival and DNA repair, in part through regulation of XPC.
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Affiliation(s)
- Jennifer J McCann
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Irina A Vasilevskaya
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | | | - Ayesha A Shafi
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Amy C Mandigo
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Randy S Schrecengost
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Peter Gallagher
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Timothy J Stanek
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Steven B McMahon
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Lisa D Berman-Booty
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - William F Ostrander
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania.
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6
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Van den Eynden J, Umapathy G, Ashouri A, Cervantes-Madrid D, Szydzik J, Ruuth K, Koster J, Larsson E, Guan J, Palmer RH, Hallberg B. Phosphoproteome and gene expression profiling of ALK inhibition in neuroblastoma cell lines reveals conserved oncogenic pathways. Sci Signal 2018; 11:11/557/eaar5680. [PMID: 30459281 DOI: 10.1126/scisignal.aar5680] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Anaplastic lymphoma kinase (ALK) is a tyrosine kinase receptor that is a clinical target of major interest in cancer. Mutations and rearrangements in ALK trigger the activation of the encoded receptor and its downstream signaling pathways. ALK mutations have been identified in both familial and sporadic neuroblastoma cases as well as in 30 to 40% of relapses, which makes ALK a bona fide target in neuroblastoma therapy. Tyrosine kinase inhibitors (TKIs) that target ALK are currently in clinical use for the treatment of patients with ALK-positive non-small cell lung cancer. However, monotherapy with the ALK inhibitor crizotinib has been less encouraging in neuroblastoma patients with ALK alterations, raising the question of whether combinatorial therapy would be more effective. In this study, we established both phosphoproteomic and gene expression profiles of ALK activity in neuroblastoma cells exposed to first- and third-generation ALK TKIs, to identify the underlying molecular mechanisms and identify relevant biomarkers, signaling networks, and new therapeutic targets. This analysis has unveiled various important leads for novel combinatorial treatment strategies for patients with neuroblastoma and an increased understanding of ALK signaling involved in this disease.
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Affiliation(s)
- Jimmy Van den Eynden
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden.,Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, 9000 Ghent, Belgium
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Arghavan Ashouri
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | | | - Joanna Szydzik
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Kristina Ruuth
- Institution for Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden.,Children's Hospital affiliated with Zhengzhou University, 450018 Zhengzhou, China
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden.
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden.
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7
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Control of CCND1 ubiquitylation by the catalytic SAGA subunit USP22 is essential for cell cycle progression through G1 in cancer cells. Proc Natl Acad Sci U S A 2018; 115:E9298-E9307. [PMID: 30224477 PMCID: PMC6176615 DOI: 10.1073/pnas.1807704115] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Overexpression of the deubiquitylase ubiquitin-specific peptidase 22 (USP22) is a marker of aggressive cancer phenotypes like metastasis, therapy resistance, and poor survival. Functionally, this overexpression of USP22 actively contributes to tumorigenesis, as USP22 depletion blocks cancer cell cycle progression in vitro, and inhibits tumor progression in animal models of lung, breast, bladder, ovarian, and liver cancer, among others. Current models suggest that USP22 mediates these biological effects via its role in epigenetic regulation as a subunit of the Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional cofactor complex. Challenging the dogma, we report here a nontranscriptional role for USP22 via a direct effect on the core cell cycle machinery: that is, the deubiquitylation of the G1 cyclin D1 (CCND1). Deubiquitylation by USP22 protects CCND1 from proteasome-mediated degradation and occurs separately from the canonical phosphorylation/ubiquitylation mechanism previously shown to regulate CCND1 stability. We demonstrate that control of CCND1 is a key mechanism by which USP22 mediates its known role in cell cycle progression. Finally, USP22 and CCND1 levels correlate in patient lung and colorectal cancer samples and our preclinical studies indicate that targeting USP22 in combination with CDK inhibitors may offer an approach for treating cancer patients whose tumors exhibit elevated CCND1.
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Ramachandran B, Stabley JN, Cheng SL, Behrmann AS, Gay A, Li L, Mead M, Kozlitina J, Lemoff A, Mirzaei H, Chen Z, Towler DA. A GTPase-activating protein-binding protein (G3BP1)/antiviral protein relay conveys arteriosclerotic Wnt signals in aortic smooth muscle cells. J Biol Chem 2018; 293:7942-7968. [PMID: 29626090 DOI: 10.1074/jbc.ra118.002046] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
In aortic vascular smooth muscle (VSM), the canonical Wnt receptor LRP6 inhibits protein arginine (Arg) methylation, a new component of noncanonical Wnt signaling that stimulates nuclear factor of activated T cells (viz NFATc4). To better understand how methylation mediates these actions, MS was performed on VSM cell extracts from control and LRP6-deficient mice. LRP6-dependent Arg methylation was regulated on >500 proteins; only 21 exhibited increased monomethylation (MMA) with concomitant reductions in dimethylation. G3BP1, a known regulator of arteriosclerosis, exhibited a >30-fold increase in MMA in its C-terminal domain. Co-transfection studies confirm that G3BP1 (G3BP is Ras-GAP SH3 domain-binding protein) methylation is inhibited by LRP6 and that G3BP1 stimulates NFATc4 transcription. NFATc4 association with VSM osteopontin (OPN) and alkaline phosphatase (TNAP) chromatin was increased with LRP6 deficiency and reduced with G3BP1 deficiency. G3BP1 activation of NFATc4 mapped to G3BP1 domains supporting interactions with RIG-I (retinoic acid inducible gene I), a stimulus for mitochondrial antiviral signaling (MAVS) that drives cardiovascular calcification in humans when mutated in Singleton-Merten syndrome (SGMRT2). Gain-of-function SGMRT2/RIG-I mutants increased G3BP1 methylation and synergized with osteogenic transcription factors (Runx2 and NFATc4). A chemical antagonist of G3BP, C108 (C108 is 2-hydroxybenzoic acid, 2-[1-(2-hydroxyphenyl)ethylidene]hydrazide CAS 15533-09-2), down-regulated RIG-I-stimulated G3BP1 methylation, Wnt/NFAT signaling, VSM TNAP activity, and calcification. G3BP1 deficiency reduced RIG-I protein levels and VSM osteogenic programs. Like G3BP1 and RIG-I deficiency, MAVS deficiency reduced VSM osteogenic signals, including TNAP activity and Wnt5-dependent nuclear NFATc4 levels. Aortic calcium accumulation is decreased in MAVS-deficient LDLR-/- mice fed arteriosclerotic diets. The G3BP1/RIG-I/MAVS relay is a component of Wnt signaling. Targeting this relay may help mitigate arteriosclerosis.
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Affiliation(s)
- Bindu Ramachandran
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - John N Stabley
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Su-Li Cheng
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Abraham S Behrmann
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Austin Gay
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Li Li
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Megan Mead
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Julia Kozlitina
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Dwight A Towler
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
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Nguyen DTT, Richter D, Michel G, Mitschka S, Kolanus W, Cuevas E, Wulczyn FG. The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation. Cell Death Differ 2017; 24:1063-1078. [PMID: 28430184 PMCID: PMC5442473 DOI: 10.1038/cdd.2017.54] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/04/2017] [Accepted: 03/17/2017] [Indexed: 12/13/2022] Open
Abstract
Rapidity and specificity are characteristic features of proteolysis mediated by the ubiquitin-proteasome system. Therefore, the UPS is ideally suited for the remodeling of the embryonic stem cell proteome during the transition from pluripotent to differentiated states and its inverse, the generation of inducible pluripotent stem cells. The Trim-NHL family member LIN41 is among the first E3 ubiquitin ligases to be linked to stem cell pluripotency and reprogramming. Initially discovered in C. elegans as a downstream target of the let-7 miRNA, LIN41 is now recognized as a critical regulator of stem cell fates as well as the timing of neurogenesis. Despite being indispensable for embryonic development and neural tube closure in mice, the underlying mechanisms for LIN41 function in these processes are poorly understood. To better understand the specific contributions of the E3 ligase activity for the stem cell functions of LIN41, we characterized global changes in ubiquitin or ubiquitin-like modifications using Lin41-inducible mouse embryonic stem cells. The tumor suppressor protein p53 was among the five most strongly affected proteins in cells undergoing neural differentiation in response to LIN41 induction. We show that LIN41 interacts with p53, controls its abundance by ubiquitination and antagonizes p53-dependent pro-apoptotic and pro-differentiation responses. In vivo, the lack of LIN41 is associated with upregulation of Grhl3 and widespread caspase-3 activation, two downstream effectors of p53 with essential roles in neural tube closure. As Lin41-deficient mice display neural tube closure defects, we conclude that LIN41 is critical for the regulation of p53 functions in cell fate specification and survival during early brain development.
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Affiliation(s)
- Duong Thi Thuy Nguyen
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
| | - Daniel Richter
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
| | - Geert Michel
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Forschungseinrichtung für Experimentelle Medizin, Krahmerstraße 6-10, Berlin 12207, Germany
| | - Sibylle Mitschka
- University of Bonn, Life &Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, Carl-Troll-Straße 31, Bonn 53115, Germany
| | - Waldemar Kolanus
- University of Bonn, Life &Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, Carl-Troll-Straße 31, Bonn 53115, Germany
| | - Elisa Cuevas
- UCL Institute of Child Health, Stem Cells &Regenerative Medicine Section, 30 Guilford Street, London WC1N 1EH, Great Britain, UK
| | - F Gregory Wulczyn
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
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10
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Negative regulation of TCR signaling by ubiquitination of Zap-70 Lys-217. Mol Immunol 2016; 73:19-28. [PMID: 27032069 DOI: 10.1016/j.molimm.2016.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/26/2016] [Accepted: 03/15/2016] [Indexed: 02/08/2023]
Abstract
The tyrosine kinase Zap-70 is a key regulator of T cell receptor (TCR) signaling downstream of antigen presentation, with coordinated regulation of Zap-70 kinase activity critical for proper T cell proliferation, differentiation, and effector function during an immune response. Zap-70 is cytosolic in unstimulated T cells, but is rapidly recruited to the TCR complex following receptor stimulation. Its activity is regulated both by binding to subunits of the TCR and by phosphorylation on multiple tyrosine residues. Zap-70 also has been reported to be ubiquitinated following TCR stimulation. Herein, we confirm the ubiquitination of Zap-70 in T cell lines and in primary human and mouse T cells, and report the identification of nine novel Zap-70 ubiquitination sites. Three sites, including Lys-193, Lys-217, and Lys-376, displayed greater than 20-fold increase in modification levels following TCR stimulation. Abrogation of Lys-217 ubiquitination results in increased kinase activation, enhanced activation of downstream signaling pathways, and elevated IL-2 production following TCR stimulation. These data suggest that Zap-70 ubiquitination contributes to the regulation of Zap-70 signaling following TCR stimulation.
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11
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Affiliation(s)
- David S. Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta Edmonton Alberta Canada
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12
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Methyl-Arginine Profile of Brain from Aged PINK1-KO+A53T-SNCA Mice Suggests Altered Mitochondrial Biogenesis. PARKINSONS DISEASE 2016; 2016:4686185. [PMID: 27034888 PMCID: PMC4791501 DOI: 10.1155/2016/4686185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/29/2022]
Abstract
Hereditary Parkinson's disease can be triggered by an autosomal dominant overdose of alpha-Synuclein (SNCA) or the autosomal recessive deficiency of PINK1. We recently showed that the combination of PINK1-knockout with overexpression of A53T-SNCA in double mutant (DM) mice potentiates phenotypes and reduces survival. Now we studied brain hemispheres of DM mice at age of 18 months in a hypothesis-free approach, employing a quantitative label-free global proteomic mass spectrometry scan of posttranslational modifications focusing on methyl-arginine. The strongest effects were documented for the adhesion modulator CMAS, the mRNA decapping/deadenylation factor PATL1, and the synaptic plasticity mediator CRTC1/TORC1. In addition, an intriguing effect was observed for the splicing factor PSF/SFPQ, known to interact with the dopaminergic differentiation factor NURR1 as well as with DJ-1, the protein responsible for the autosomal recessive PARK7 variant of PD. CRTC1, PSF, and DJ-1 are modulators of PGC1alpha and of mitochondrial biogenesis. This pathway was further stressed by dysregulations of oxygen sensor EGLN3 and of nuclear TMPO. PSF and TMPO cooperate with dopaminergic differentiation factors LMX1B and NURR1. Further dysregulations concerned PRR18, TRIO, HNRNPA1, DMWD, WAVE1, ILDR2, DBNDD1, and NFM. Thus, we report selective novel endogenous stress responses in brain, which highlight early dysregulations of mitochondrial homeostasis and midbrain vulnerability.
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Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A deeper look into Comet--implementation and features. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1865-74. [PMID: 26115965 PMCID: PMC4607604 DOI: 10.1007/s13361-015-1179-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 05/04/2023]
Abstract
The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington's academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these details in depth and highlight new features available in the latest release. Comet is freely available for download at http://comet-ms.sourceforge.net or it can be accessed as a component of a number of larger software projects into which it has been incorporated. Graphical Abstract ᅟ.
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Affiliation(s)
- Jimmy K Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | | | - Tahmina A Jahan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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14
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Brechenmacher L, Nguyen THN, Zhang N, Jun TH, Xu D, Mian MAR, Stacey G. Identification of Soybean Proteins and Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation. J Proteome Res 2015; 14:4137-46. [PMID: 26350764 DOI: 10.1021/acs.jproteome.5b00146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Soybean aphid is an important pest causing significant yield losses. The Rag2 locus confers resistance to soybean aphid biotypes 1 and 2. Transcriptomic and proteomic analyses were done over a 48 h period after aphid infestation using near isogenic lines (NILs) differing at the Rag2 locus. Comparing the Rag2 and/or rag2 lines identified 3445 proteins, of which 396 were differentially regulated between the two lines, including proteins involved in cell wall metabolism, carbohydrate metabolism, and stress response. RNA-seq transcriptomic analysis identified 2361 genes significantly regulated between the resistant and susceptible lines. Genes upregulated in the Rag2 line were annotated as being involved in cell wall, secondary, and hormone metabolism as well as in stress, signaling, and transcriptional responses. Genes downregulated in the Rag2 line were annotated as being involved in photosynthesis and carbon metabolism. Interestingly, two genes (unknown and mitochondrial protease) located within the defined Rag2 locus were expressed significantly higher in the resistant genotype. The expression of a putative NBS-LRR resistant gene within the Rag2 locus was not different between the two soybean lines, but a second NBL-LRR gene located just at the border of the defined Rag2 locus was. Therefore, this gene may be a candidate R gene controlling aphid resistance.
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Affiliation(s)
| | | | | | - Tae-Hwan Jun
- USDA-ARS, Department of Horticulture and Crop Science, The Ohio State University , 1680 Madison Avenue, Wooster, Ohio 44691, United States
| | | | - M A Rouf Mian
- USDA-ARS, Department of Horticulture and Crop Science, The Ohio State University , 1680 Madison Avenue, Wooster, Ohio 44691, United States
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15
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Ryder DJ, Judge SM, Beharry AW, Farnsworth CL, Silva JC, Judge AR. Identification of the Acetylation and Ubiquitin-Modified Proteome during the Progression of Skeletal Muscle Atrophy. PLoS One 2015; 10:e0136247. [PMID: 26302492 PMCID: PMC4547751 DOI: 10.1371/journal.pone.0136247] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/31/2015] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle atrophy is a consequence of several physiological and pathophysiological conditions including muscle disuse, aging and diseases such as cancer and heart failure. In each of these conditions, the predominant mechanism contributing to the loss of skeletal muscle mass is increased protein turnover. Two important mechanisms which regulate protein stability and degradation are lysine acetylation and ubiquitination, respectively. However our understanding of the skeletal muscle proteins regulated through acetylation and ubiquitination during muscle atrophy is limited. Therefore, the purpose of the current study was to conduct an unbiased assessment of the acetylation and ubiquitin-modified proteome in skeletal muscle during a physiological condition of muscle atrophy. To induce progressive, physiologically relevant, muscle atrophy, rats were cast immobilized for 0, 2, 4 or 6 days and muscles harvested. Acetylated and ubiquitinated peptides were identified via a peptide IP proteomic approach using an anti-acetyl lysine antibody or a ubiquitin remnant motif antibody followed by mass spectrometry. In control skeletal muscle we identified and mapped the acetylation of 1,326 lysine residues to 425 different proteins and the ubiquitination of 4,948 lysine residues to 1,131 different proteins. Of these proteins 43, 47 and 50 proteins were differentially acetylated and 183, 227 and 172 were differentially ubiquitinated following 2, 4 and 6 days of disuse, respectively. Bioinformatics analysis identified contractile proteins as being enriched among proteins decreased in acetylation and increased in ubiquitination, whereas histone proteins were enriched among proteins increased in acetylation and decreased in ubiquitination. These findings provide the first proteome-wide identification of skeletal muscle proteins exhibiting changes in lysine acetylation and ubiquitination during any atrophy condition, and provide a basis for future mechanistic studies into how the acetylation and ubiquitination status of these identified proteins regulates the muscle atrophy phenotype.
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Affiliation(s)
- Daniel J. Ryder
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | - Sarah M. Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | - Adam W. Beharry
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
| | | | - Jeffrey C. Silva
- Cell Signaling Technology, Danvers, MA, United States of America
| | - Andrew R. Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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16
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Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways. J Biol Chem 2015; 290:14963-78. [PMID: 25882841 DOI: 10.1074/jbc.m114.627794] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 11/06/2022] Open
Abstract
Target of rapamycin is a Ser/Thr kinase that operates in two conserved multiprotein complexes, TORC1 and TORC2. Unlike TORC1, TORC2 is insensitive to rapamycin, and its functional characterization is less advanced. Previous genetic studies demonstrated that TORC2 depletion leads to loss of actin polarization and loss of endocytosis. To determine how TORC2 regulates these readouts, we engineered a yeast strain in which TORC2 can be specifically and acutely inhibited by the imidazoquinoline NVP-BHS345. Kinetic analyses following inhibition of TORC2, supported with quantitative phosphoproteomics, revealed that TORC2 regulates these readouts via distinct pathways as follows: rapidly through direct protein phosphorylation cascades and slowly through indirect changes in the tensile properties of the plasma membrane. The rapid signaling events are mediated in large part through the phospholipid flippase kinases Fpk1 and Fpk2, whereas the slow signaling pathway involves increased plasma membrane tension resulting from a gradual depletion of sphingolipids. Additional hits in our phosphoproteomic screens highlight the intricate control TORC2 exerts over diverse aspects of eukaryote cell physiology.
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Affiliation(s)
- Delphine Rispal
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Sandra Eltschinger
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Michael Stahl
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Stefania Vaga
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich
| | - Bernd Bodenmiller
- the Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich
| | - Yann Abraham
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ireos Filipuzzi
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - N Rao Movva
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ruedi Aebersold
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, the Faculty of Science, University of Zürich, 8057 Zürich, and
| | - Stephen B Helliwell
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel,
| | - Robbie Loewith
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva, the National Centre for Competence in Research Chemical Biology, 1211 Geneva, Switzerland
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17
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Abstract
Experiments are described that allowed cross-linking of analogs of a 13-amino acid peptide into the binding site of a model G protein-coupled receptor. Syntheses of peptide analogs that were used for photochemical or chemical cross-linking were carried out using solid-phase peptide synthesis. Chemical cross-linking utilized 3,4-dihydroxy-l-phenylalanine-incorporated peptides and subsequent periodate-mediated activation, whereas photochemical cross-linking was mediated by p-benzoyl-l-phenylalanine (Bpa)-labeled peptides and UV-initiated activation. Mass spectrometry was employed to locate the site(s) in the receptor that formed the cross-links to the ligand. We also describe a method called unnatural amino acid replacement that allowed capture of a peptide ligand into the receptor. In this method, the receptor was genetically modified by replacement of a natural amino acid with Bpa. The modified receptor was UV-irradiated to capture the ligand. The approaches described are applicable to other peptide-binding proteins and can reveal the ligand-binding site in atomic detail.
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Affiliation(s)
| | - Fred Naider
- Chemistry Department, College of Staten Island, City University of New York
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18
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Bouchut A, Chawla AR, Jeffers V, Hudmon A, Sullivan WJ. Proteome-wide lysine acetylation in cortical astrocytes and alterations that occur during infection with brain parasite Toxoplasma gondii. PLoS One 2015; 10:e0117966. [PMID: 25786129 PMCID: PMC4364782 DOI: 10.1371/journal.pone.0117966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
Lysine acetylation is a reversible post-translational modification (PTM) that has been detected on thousands of proteins in nearly all cellular compartments. The role of this widespread PTM has yet to be fully elucidated, but can impact protein localization, interactions, activity, and stability. Here we present the first proteome-wide survey of lysine acetylation in cortical astrocytes, a subtype of glia that is a component of the blood-brain barrier and a key regulator of neuronal function and plasticity. We identified 529 lysine acetylation sites across 304 proteins found in multiple cellular compartments that largely function in RNA processing/transcription, metabolism, chromatin biology, and translation. Two hundred and seventy-seven of the acetylated lysines we identified on 186 proteins have not been reported previously in any other cell type. We also mapped an acetylome of astrocytes infected with the brain parasite, Toxoplasma gondii. It has been shown that infection with T. gondii modulates host cell gene expression, including several lysine acetyltransferase (KAT) and deacetylase (KDAC) genes, suggesting that the host acetylome may also be altered during infection. In the T. gondii-infected astrocytes, we identified 34 proteins exhibiting a level of acetylation >2-fold and 24 with a level of acetylation <2-fold relative to uninfected astrocytes. Our study documents the first acetylome map for cortical astrocytes, uncovers novel lysine acetylation sites, and demonstrates that T. gondii infection produces an altered acetylome.
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Affiliation(s)
- Anne Bouchut
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Aarti R. Chawla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Victoria Jeffers
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Andy Hudmon
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- * E-mail:
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19
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Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Mol Syst Biol 2014; 10:767. [PMID: 25492886 PMCID: PMC4300490 DOI: 10.15252/msb.20145112] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cells respond to environmental stimuli via specialized signaling pathways. Concurrent stimuli trigger multiple pathways that integrate information, predominantly via protein phosphorylation. Budding yeast responds to NaCl and pheromone via two mitogen-activated protein kinase cascades, the high osmolarity, and the mating pathways, respectively. To investigate signal integration between these pathways, we quantified the time-resolved phosphorylation site dynamics after pathway co-stimulation. Using shotgun mass spectrometry, we quantified 2,536 phosphopeptides across 36 conditions. Our data indicate that NaCl and pheromone affect phosphorylation events within both pathways, which thus affect each other at more levels than anticipated, allowing for information exchange and signal integration. We observed a pheromone-induced down-regulation of Hog1 phosphorylation due to Gpd1, Ste20, Ptp2, Pbs2, and Ptc1. Distinct Ste20 and Pbs2 phosphosites responded differently to the two stimuli, suggesting these proteins as key mediators of the information exchange. A set of logic models was then used to assess the role of measured phosphopeptides in the crosstalk. Our results show that the integration of the response to different stimuli requires complex interconnections between signaling pathways.
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Affiliation(s)
- Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland
| | - Marti Bernardo-Faura
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK
| | - Thomas Cokelaer
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK
| | - Alessio Maiolica
- Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland
| | - Christopher A Barnes
- Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Ludovic C Gillet
- Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland
| | - Björn Hegemann
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Frank van Drogen
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Hoda Sharifian
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Edda Klipp
- Department of Biology, Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland Faculty of Science, University of Zurich, Zurich, Switzerland
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20
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Proteomic analysis of ubiquitin-like posttranslational modifications induced by the adenovirus E4-ORF3 protein. J Virol 2014; 89:1744-55. [PMID: 25410875 DOI: 10.1128/jvi.02892-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Viruses interact with and regulate many host metabolic pathways in order to advance the viral life cycle and counteract intrinsic and extrinsic antiviral responses. The human adenovirus (Ad) early protein E4-ORF3 forms a unique scaffold throughout the nuclei of infected cells and inhibits multiple antiviral defenses, including a DNA damage response (DDR) and an interferon response. We previously reported that the Ad5 E4-ORF3 protein induces sumoylation of Mre11 and Nbs1, which are essential for the DDR, and their relocalization into E4-ORF3-induced nuclear inclusions is required for this modification to occur. In this study, we sought to analyze a global change in ubiquitin-like (Ubl) modifications, with particular focus on SUMO3, by the Ad5 E4-ORF3 protein and to identify new substrates with these modifications. By a comparative proteome-wide approach utilizing immunoprecipitation/mass spectrometry, we found that Ubl modifications of 166 statistically significant lysine sites in 51 proteins are affected by E4-ORF3, and the proteome of modifications spans a diverse range of cellular functions. Ubl modifications of 92% of these identified sites were increased by E4-ORF3. We further analyzed SUMO3 conjugation of several identified proteins. Our findings demonstrated a role for the Ad5 E4-ORF3 protein as a regulator of Ubl modifications and revealed new SUMO3 substrates induced by E4-ORF3. IMPORTANCE The adenovirus E4-ORF3 protein induces dynamic structural changes in the nuclei of infected cells and counteracts host antiviral responses. One of the mechanisms that accounts for this process is the relocalization and sequestration of cellular proteins into an E4-ORF3 nuclear scaffold, but little is known about how this small viral protein affects diverse cellular responses. In this study, we analyzed for the first time the global pattern of ubiquitin-like (Ubl) modifications, with particular focus on SUMO3, altered by E4-ORF3 expression. The results suggest a role for the Ad5 E4-ORF3 protein as a regulator of Ubl modifications and reveal new SUMO3 substrates targeted by E4-ORF3. Our findings propose Ubl modifications as a new mechanism by which E4-ORF3 may modulate cellular protein functions in addition to subnuclear relocalization.
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21
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Rahman M, Nirala NK, Singh A, Zhu LJ, Taguchi K, Bamba T, Fukusaki E, Shaw LM, Lambright DG, Acharya JK, Acharya UR. Drosophila Sirt2/mammalian SIRT3 deacetylates ATP synthase β and regulates complex V activity. ACTA ACUST UNITED AC 2014; 206:289-305. [PMID: 25023514 PMCID: PMC4107778 DOI: 10.1083/jcb.201404118] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sirtuin-mediated deacetylation of the catalytic subunit of mitochondrial complex V increases complex activity. Adenosine triphosphate (ATP) synthase β, the catalytic subunit of mitochondrial complex V, synthesizes ATP. We show that ATP synthase β is deacetylated by a human nicotinamide adenine dinucleotide (NAD+)–dependent protein deacetylase, sirtuin 3, and its Drosophila melanogaster homologue, dSirt2. dsirt2 mutant flies displayed increased acetylation of specific Lys residues in ATP synthase β and decreased complex V activity. Overexpression of dSirt2 increased complex V activity. Substitution of Lys 259 and Lys 480 with Arg in human ATP synthase β, mimicking deacetylation, increased complex V activity, whereas substitution with Gln, mimicking acetylation, decreased activity. Mass spectrometry and proteomic experiments from wild-type and dsirt2 mitochondria identified the Drosophila mitochondrial acetylome and revealed dSirt2 as an important regulator of mitochondrial energy metabolism. Additionally, we unravel a ceramide–NAD+–sirtuin axis wherein increased ceramide, a sphingolipid known to induce stress responses, resulted in depletion of NAD+ and consequent decrease in sirtuin activity. These results provide insight into sirtuin-mediated regulation of complex V and reveal a novel link between ceramide and Drosophila acetylome.
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Affiliation(s)
- Motiur Rahman
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Niraj K Nirala
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Alka Singh
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Lihua Julie Zhu
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kaori Taguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Leslie M Shaw
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - David G Lambright
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jairaj K Acharya
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, Frederick, MD 21702
| | - Usha R Acharya
- Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605Program in Gene Function and Expression, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, and Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
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22
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Escobar-Hoyos LF, Yang J, Zhu J, Cavallo JA, Zhai H, Burke S, Koller A, Chen EI, Shroyer KR. Keratin 17 in premalignant and malignant squamous lesions of the cervix: proteomic discovery and immunohistochemical validation as a diagnostic and prognostic biomarker. Mod Pathol 2014; 27:621-30. [PMID: 24051697 PMCID: PMC4026928 DOI: 10.1038/modpathol.2013.166] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 12/20/2022]
Abstract
Most previously described immunohistochemical markers of cervical high-grade squamous intraepithelial lesion (HSIL) and squamous cell carcinoma may help to improve diagnostic accuracy but have a minimal prognostic value. The goals of the current study were to identify and validate novel candidate biomarkers that could potentially improve diagnostic and prognostic accuracy for cervical HSIL and squamous cell carcinoma. Microdissected tissue sections from formalin-fixed paraffin-embedded normal ectocervical squamous mucosa, low-grade squamous intraepithelial lesion (LSIL), HSIL and squamous cell carcinoma sections were analyzed by mass spectrometry-based shotgun proteomics for biomarker discovery. The diagnostic specificity of candidate biomarkers was subsequently evaluated by immunohistochemical analysis of tissue microarrays. Among 1750 proteins identified by proteomic analyses, keratin 4 (KRT4) and keratin 17 (KRT17) showed reciprocal patterns of expression in the spectrum of cases ranging from normal ectocervical squamous mucosa to squamous cell carcinoma. Immunohistochemical studies confirmed that KRT4 expression was significantly decreased in squamous cell carcinoma compared with the other diagnostic categories. By contrast, KRT17 expression was significantly increased in HSIL and squamous cell carcinoma compared with normal ectocervical squamous mucosa and LSIL. KRT17 was also highly expressed in immature squamous metaplasia and in endocervical reserve cells but was generally not detected in mature squamous metaplasia. Furthermore, high levels of KRT17 expression were significantly associated with poor survival of squamous cell carcinoma patients (Hazard ratio=14.76, P=0.01). In summary, both KRT4 and KRT17 expressions are related to the histopathology of the cervical squamous mucosa; KRT17 is highly overexpressed in immature squamous metaplasia, in HSIL, and in squamous cell carcinoma and the level of KRT17 in squamous cell carcinoma may help to identify patients who are at greatest risk for cervical cancer mortality.
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Affiliation(s)
- Luisa F Escobar-Hoyos
- Department of Pharmacological Sciences, Stony Brook School of Medicine, Stony Brook, NY, USA,Department of Pathology, Stony Brook School of Medicine, Stony Brook, NY, USA,Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education, Universidad del Cauca, Popayán, Colombia
| | - Jie Yang
- Department of Applied Mathematics and Statistics, Stony Brook School of Medicine, Stony Brook, NY, USA,Department of Preventive Medicine, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Jiawen Zhu
- Department of Applied Mathematics and Statistics, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Julie-Ann Cavallo
- Department of Pharmacological Sciences, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Haiyan Zhai
- Department of Pathology, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Stephanie Burke
- Department of Pathology, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Antonius Koller
- Proteomics Center, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Emily I Chen
- Department of Pharmacological Sciences, Stony Brook School of Medicine, Stony Brook, NY, USA,Department of Pathology, Stony Brook School of Medicine, Stony Brook, NY, USA,Proteomics Center, Stony Brook School of Medicine, Stony Brook, NY, USA
| | - Kenneth R Shroyer
- Department of Pathology, Stony Brook School of Medicine, Stony Brook, NY, USA
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Interactome analysis of AMP-activated protein kinase (AMPK)-α1 and -β1 in INS-1 pancreatic beta-cells by affinity purification-mass spectrometry. Sci Rep 2014; 4:4376. [PMID: 24625528 PMCID: PMC3953747 DOI: 10.1038/srep04376] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/26/2014] [Indexed: 12/23/2022] Open
Abstract
The heterotrimeric enzyme AMP-activated protein kinase (AMPK) is a major metabolic factor that regulates the homeostasis of cellular energy. In particular, AMPK mediates the insulin resistance that is associated with type 2 diabetes. Generally, cellular processes require tight regulation of protein kinases, which is effected through their formation of complex with other proteins and substrates. Despite their critical function in regulation and pathogenesis, there are limited data on the interaction of protein kinases. To identify proteins that interact with AMPK, we performed large-scale affinity purification (AP)-mass spectrometry (MS) of the AMPK-α1 and -β1 subunits. Through a comprehensive analysis, using a combination of immunoprecipitaion and ion trap mass spectrometry, we identified 381 unique proteins in the AMPKα/β interactomes: 325 partners of AMPK-α1 and 243 for AMPK-β1. Further, we identified 196 novel protein-protein interactions with AMPK-α1 and AMPK-β1. Notably, in our bioinformatics analysis, the novel interaction partners mediated functions that are related to the regulation of actin organization. Specifically, several such proteins were linked to pancreatic beta-cell functions, including glucose-stimulated insulin secretion, beta-cell development, beta-cell differentiation, and cell-cell communication.
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Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, Luthi-Carter R, Beaumont V, Bates GP. HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo. PLoS One 2013; 8:e80849. [PMID: 24278330 PMCID: PMC3838388 DOI: 10.1371/journal.pone.0080849] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/09/2013] [Indexed: 11/24/2022] Open
Abstract
Reversible protein acetylation provides a central mechanism for controlling gene expression and cellular signaling events. It is governed by the antagonistic commitment of two enzymes families: the histone acetyltransferases (HATs) and the histone deacetylases (HDACs). HDAC4, like its class IIa counterparts, is a potent transcriptional repressor through interactions with tissue specific transcription factors via its N-terminal domain. Whilst the lysine deacetylase activity of the class IIa HDACs is much less potent than that of the class I enzymes, HDAC4 has been reported to influence protein deacetylation through its interaction with HDAC3. To investigate the influence of HDAC4 on protein acetylation we employed the immunoaffinity-based AcetylScan proteomic method. We identified many proteins known to be modified by acetylation, but found that the absence of HDAC4 had no effect on the acetylation profile of the murine neonate brain. This is consistent with the biochemical data suggesting that HDAC4 may not function as a lysine deacetylase, but these in vivo data do not support the previous report showing that the enzymatic activity of HDAC3 might be modified by its interaction with HDAC4. To complement this work, we used Affymetrix arrays to investigate the effect of HDAC4 knock-out on the transcriptional profile of the postnatal murine brain. There was no effect on global transcription, consistent with the absence of a differential histone acetylation profile. Validation of the array data by Taq-man qPCR indicated that only protamine 1 and Igfbp6 mRNA levels were increased by more than one-fold and only Calml4 was decreased. The lack of a major effect on the transcriptional profile is consistent with the cytoplasmic location of HDAC4 in the P3 murine brain.
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Affiliation(s)
- Michal Mielcarek
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Tamara Seredenina
- Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Matthew P. Stokes
- Cell Signaling Technology, Danvers, Massachusetts, United States of America
| | - Georgina F. Osborne
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Christian Landles
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Linda Inuabasi
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Sophie A. Franklin
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Jeffrey C. Silva
- Cell Signaling Technology, Danvers, Massachusetts, United States of America
| | - Ruth Luthi-Carter
- Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Vahri Beaumont
- CHDI Management Inc./CHDI Foundation Inc., Los Angeles, California, United States of America
| | - Gillian P. Bates
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- * E-mail:
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25
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Nalepa G, Barnholtz-Sloan J, Enzor R, Dey D, He Y, Gehlhausen JR, Lehmann AS, Park SJ, Yang Y, Yang X, Chen S, Guan X, Chen Y, Renbarger J, Yang FC, Parada LF, Clapp W. The tumor suppressor CDKN3 controls mitosis. ACTA ACUST UNITED AC 2013; 201:997-1012. [PMID: 23775190 PMCID: PMC3691455 DOI: 10.1083/jcb.201205125] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitosis is controlled by a network of kinases and phosphatases. We screened a library of small interfering RNAs against a genome-wide set of phosphatases to comprehensively evaluate the role of human phosphatases in mitosis. We found four candidate spindle checkpoint phosphatases, including the tumor suppressor CDKN3. We show that CDKN3 is essential for normal mitosis and G1/S transition. We demonstrate that subcellular localization of CDKN3 changes throughout the cell cycle. We show that CDKN3 dephosphorylates threonine-161 of CDC2 during mitotic exit and we visualize CDC2(pThr-161) at kinetochores and centrosomes in early mitosis. We performed a phosphokinome-wide mass spectrometry screen to find effectors of the CDKN3-CDC2 signaling axis. We found that one of the identified downstream phosphotargets, CKβ phosphorylated at serine 209, localizes to mitotic centrosomes and controls the spindle checkpoint. Finally, we show that CDKN3 protein is down-regulated in brain tumors. Our findings indicate that CDKN3 controls mitosis through the CDC2 signaling axis. These results have implications for targeted anticancer therapeutics.
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Affiliation(s)
- Grzegorz Nalepa
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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26
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Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich KP. Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics. Mol Cell Proteomics 2013; 12:2070-80. [PMID: 23608596 DOI: 10.1074/mcp.m112.027052] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although K-Ras, Cdc42, and PAK4 signaling are commonly deregulated in cancer, only a few studies have sought to comprehensively examine the spectrum of phosphorylation-mediated signaling downstream of each of these key signaling nodes. In this study, we completed a label-free quantitative analysis of oncogenic K-Ras, activated Cdc42, and PAK4-mediated phosphorylation signaling, and report relative quantitation of 2152 phosphorylated peptides on 1062 proteins. We define the overlap in phosphopeptides regulated by K-Ras, Cdc42, and PAK4, and find that perturbation of these signaling components affects phosphoproteins associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. These findings provide a resource for future studies to characterize novel targets of oncogenic K-Ras signaling and validate biomarkers of PAK4 inhibition.
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Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080, USA.
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27
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A two-component system (XydS/R) controls the expression of genes encoding CBM6-containing proteins in response to straw in Clostridium cellulolyticum. PLoS One 2013; 8:e56063. [PMID: 23418511 PMCID: PMC3572039 DOI: 10.1371/journal.pone.0056063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 12/17/2022] Open
Abstract
The composition of the cellulosomes (multi enzymatic complexes involved in the degradation of plant cell wall polysaccharides) produced by Clostridium cellulolyticum differs according to the growth substrate. In particular, the expression of a cluster of 14 hemicellulase-encoding genes (called xyl-doc) seems to be induced by the presence of straw and not of cellulose. Genes encoding a putative two-component regulation system (XydS/R) were found upstream of xyl-doc. First evidence for the involvement of the response regulator, XydR, part of this two-component system, in the expression of xyl-doc genes was given by the analysis of the cellulosomes produced by a regulator overproducing strain when grown on cellulose. Nano-LC MS/MS analysis allowed the detection of the products of all xyl-doc genes and of the product of the gene at locus Ccel_1656 predicted to bear a carbohydrate binding domain targeting hemicellulose. RT-PCR experiments further demonstrated that the regulation occurs at the transcriptional level and that all xyl-doc genes are transcriptionally linked. mRNA quantification in a regulator knock-out strain and in its complemented derivative confirmed the involvement of the regulator in the expression of xyl-doc genes and of the gene at locus Ccel_1656 in response to straw. Electrophoretic mobility shift assays using the purified regulator further demonstrated that the regulator binds to DNA regions located upstream of the first gene of the xyl-doc gene cluster and upstream of the gene at locus Ccel_1656.
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28
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Bontron S, Jaquenoud M, Vaga S, Talarek N, Bodenmiller B, Aebersold R, De Virgilio C. Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. Cell Rep 2012; 3:16-22. [PMID: 23273919 DOI: 10.1016/j.celrep.2012.11.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/12/2012] [Accepted: 11/28/2012] [Indexed: 01/31/2023] Open
Abstract
The TORC1 and PKA protein kinases are central elements of signaling networks that regulate eukaryotic cell proliferation in response to growth factors and/or nutrients. In yeast, attenuation of signaling by these kinases following nitrogen and/or carbon limitation activates the protein kinase Rim15, which orchestrates the initiation of a reversible cellular quiescence program to ensure normal chronological life span. The molecular elements linking Rim15 to distal readouts including the expression of Msn2/4- and Gis1-dependent genes involve the endosulfines Igo1/2. Here, we show that Rim15, analogous to the greatwall kinase in Xenopus, phosphorylates endosulfines to directly inhibit the Cdc55-protein phosphatase 2A (PP2A(Cdc55)). Inhibition of PP2A(Cdc55) preserves Gis1 in a phosphorylated state and consequently promotes its recruitment to and activation of transcription from promoters of specific nutrient-regulated genes. These results close a gap in our perception of and delineate a role for PP2A(Cdc55) in TORC1-/PKA-mediated regulation of quiescence and chronological life span.
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Affiliation(s)
- Séverine Bontron
- Department of Biology, Division of Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland
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29
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Quantitative profiling of DNA damage and apoptotic pathways in UV damaged cells using PTMScan Direct. Int J Mol Sci 2012; 14:286-307. [PMID: 23344034 PMCID: PMC3565264 DOI: 10.3390/ijms14010286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/04/2012] [Accepted: 12/10/2012] [Indexed: 02/07/2023] Open
Abstract
Traditional methods for analysis of peptides using liquid chromatography and tandem mass spectrometry (LC-MS/MS) lack the specificity to comprehensively monitor specific biological processes due to the inherent duty cycle limitations of the MS instrument and the stochastic nature of the analytical platform. PTMScan Direct is a novel, antibody-based method that allows quantitative LC-MS/MS profiling of specific peptides from proteins that reside in the same signaling pathway. New PTMScan Direct reagents have been produced that target peptides from proteins involved in DNA Damage/Cell Cycle and Apoptosis/Autophagy pathways. Together, the reagents provide access to 438 sites on 237 proteins in these signaling cascades. These reagents have been used to profile the response to UV damage of DNA in human cell lines. UV damage was shown to activate canonical DNA damage response pathways through ATM/ATR-dependent signaling, stress response pathways and induce the initiation of apoptosis, as assessed by an increase in the abundance of peptides corresponding to cleaved, activated caspases. These data demonstrate the utility of PTMScan Direct as a multiplexed assay for profiling specific cellular responses to various stimuli, such as UV damage of DNA.
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30
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Hines HB. Microbial proteomics using mass spectrometry. Methods Mol Biol 2012; 881:159-86. [PMID: 22639214 DOI: 10.1007/978-1-61779-827-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.
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Affiliation(s)
- Harry B Hines
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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31
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Lysine acetylation is widespread on proteins of diverse function and localization in the protozoan parasite Toxoplasma gondii. EUKARYOTIC CELL 2012; 11:735-42. [PMID: 22544907 DOI: 10.1128/ec.00088-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
While histone proteins are the founding members of lysine acetylation substrates, it is now clear that hundreds of other proteins can be acetylated in multiple compartments of the cell. Our knowledge of the scope of this modification throughout the kingdom of life is beginning to emerge, as proteome-wide lysine acetylation has been documented in prokaryotes, Arabidopsis thaliana, Drosophila melanogaster, and human cells. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify parasite peptides enriched by immunopurification with acetyl-lysine antibody, we produced the first proteome-wide analysis of acetylation for a protozoan organism, the opportunistic apicomplexan parasite Toxoplasma gondii. The results show that lysine acetylation is abundant in the actively proliferating tachyzoite form of the parasite, which causes acute toxoplasmosis. Our approach successfully identified known acetylation marks on Toxoplasma histones and α-tubulin and detected over 400 novel acetylation sites on a wide variety of additional proteins, including those with roles in transcription, translation, metabolism, and stress responses. Importantly, an extensive set of parasite-specific proteins, including those found in organelles unique to Apicomplexa, is acetylated in the parasite. Our data provide a wealth of new information that improves our understanding of the evolution of this vital regulatory modification while potentially revealing novel therapeutic avenues. We conclude from this study that lysine acetylation was prevalent in the early stages of eukaryotic cell evolution and occurs on proteins involved in a remarkably diverse array of cellular functions, including those that are specific to parasites.
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32
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Chang IF, Hsu JL, Hsu PH, Sheng WA, Lai SJ, Lee C, Chen CW, Hsu JC, Wang SY, Wang LY, Chen CC. Comparative phosphoproteomic analysis of microsomal fractions of Arabidopsis thaliana and Oryza sativa subjected to high salinity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:131-42. [PMID: 22325874 DOI: 10.1016/j.plantsci.2011.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 05/20/2023]
Abstract
Plants respond to salt stress by initiating phosphorylation cascades in their cells. Many key phosphorylation events take place at membranes. Microsomal fractions from 400 mM salt-treated Arabidopsis suspension plants were isolated, followed by trypsin shaving, enrichment using Zirconium ion-charged or TiO(2) magnetic beads, and tandem mass spectrometry analyses for site mapping. A total of 27 phosphorylation sites from 20 Arabidopsis proteins including photosystem II reaction center protein H PsbH were identified. In addition to Arabidopsis, microsomal fractions from shoots of 200 mM salt-treated rice was carried out, followed by trypsin digestion using shaving or tube-gel, and enrichment using Zirconium ion-charged or TiO(2) magnetic beads. This yielded identification of 13 phosphorylation sites from 8 proteins including photosystem II reaction center protein H PsbH. Label-free quantitative analysis suggests that the phosphorylation sites of PsbH were regulated by salt stress in Arabidopsis and rice. Sequence alignment of PsbH phosphorylation sites indicates that Thr-2 and Thr-4 are evolutionarily conserved in plants. Four conserved phosphorylation motifs were predicted, and these suggest that a specific unknown kinase or phosphatase is involved in high-salt stress responses in plants.
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Affiliation(s)
- Ing-Feng Chang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
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33
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Stokes MP, Farnsworth CL, Moritz A, Silva JC, Jia X, Lee KA, Guo A, Polakiewicz RD, Comb MJ. PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS. Mol Cell Proteomics 2012; 11:187-201. [PMID: 22322096 DOI: 10.1074/mcp.m111.015883] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Proteomic studies of post-translational modifications by metal affinity or antibody-based methods often employ data-dependent analysis, providing rich data sets that consist of randomly sampled identified peptides because of the dynamic response of the mass spectrometer. This can complicate the primary goal of programs for drug development, mutational analysis, and kinase profiling studies, which is to monitor how multiple nodes of known, critical signaling pathways are affected by a variety of treatment conditions. Cell Signaling Technology has developed an immunoaffinity-based LC-MS/MS method called PTMScan Direct for multiplexed analysis of these important signaling proteins. PTMScan Direct enables the identification and quantification of hundreds of peptides derived from specific proteins in signaling pathways or specific protein types. Cell lines, tissues, or xenografts can be used as starting material. PTMScan Direct is compatible with both SILAC and label-free quantification. Current PTMScan Direct reagents target key nodes of many signaling pathways (PTMScan Direct: Multipathway), serine/threonine kinases, tyrosine kinases, and the Akt/PI3K pathway. Validation of each reagent includes score filtering of MS/MS assignments, filtering by identification of peptides derived from expected targets, identification of peptides homologous to expected targets, minimum signal intensity of peptide ions, and dependence upon the presence of the reagent itself compared with a negative control. The Multipathway reagent was used to study sensitivity of human cancer cell lines to receptor tyrosine kinase inhibitors and showed consistent results with previously published studies. The Ser/Thr kinase reagent was used to compare relative levels of kinase-derived phosphopeptides in mouse liver, brain, and embryo, showing tissue-specific activity of many kinases including Akt and PKC family members. PTMScan Direct will be a powerful quantitative method for elucidation of changes in signaling in a wide array of experimental systems, combining the specificity of traditional biochemical methods with the high number of data points and dynamic range of proteomic methods.
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34
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Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae. Mol Syst Biol 2011; 7:545. [PMID: 22068328 PMCID: PMC3261716 DOI: 10.1038/msb.2011.80] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 09/29/2011] [Indexed: 01/09/2023] Open
Abstract
Nutrient sensing and coordination of metabolic pathways are crucial functions for living cells. A combined analysis of the yeast transcriptome, phosphoproteome and metabolome is used to investigate the interactions between the Snf1 and TORC1 pathways under nutrient-limited conditions. Snf1 regulates a broad range of biological processes, while target of rapamycin complex 1 (TORC1) seems to be repressed under both glucose- and ammonium-limited conditions. Snf1 has a role in regulating amino acids by upregulating the NADP+-dependent glutamate dehydrogenase (encoded by GDH3) under glucose-limited condition. In addition to the accepted role of Snf1 in regulating fatty acid (FA) metabolism, TORC1 may also regulate FA metabolism. Direct interactions between Snf1 and TORC1 pathways are unlikely under nutrient-limited conditions and TORC1 might be repressed in a manner that is independent of Snf1.
Nutrient sensing and coordination of metabolic pathways are crucial functions for all living cells, but details of the coordination under different environmental conditions remain elusive. We therefore undertook a systems biology approach to investigate the interactions between the Snf1 and the target of rapamycin complex 1 (TORC1) in Saccharomyces cerevisiae. We show that Snf1 regulates a much broader range of biological processes compared with TORC1 under both glucose- and ammonium-limited conditions. We also find that Snf1 has a role in upregulating the NADP+-dependent glutamate dehydrogenase (encoded by GDH3) under derepressing condition, and therefore may also have a role in ammonium assimilation and amino-acid biosynthesis, which can be considered as a convergence of Snf1 and TORC1 pathways. In addition to the accepted role of Snf1 in regulating fatty acid (FA) metabolism, we show that TORC1 also regulates FA metabolism, likely through modulating the peroxisome and β-oxidation. Finally, we conclude that direct interactions between Snf1 and TORC1 pathways are unlikely under nutrient-limited conditions and propose that TORC1 is repressed in a manner that is independent of Snf1.
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