151
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Epand RM, So V, Jennings W, Khadka B, Gupta RS, Lemaire M. Diacylglycerol Kinase-ε: Properties and Biological Roles. Front Cell Dev Biol 2016. [PMID: 27803897 DOI: 10.3389/fcell.2016.00112)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In mammals there are at least 10 isoforms of diacylglycerol kinases (DGK). All catalyze the phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PA). Among DGK isoforms, DGKε has several unique features. It is the only DGK isoform with specificity for a particular species of DAG, i.e., 1-stearoyl-2-arachidonoyl glycerol. The smallest of all known DGK isoforms, DGKε, is also the only DGK devoid of a regulatory domain. DGKε is the only DGK isoform that has a hydrophobic segment that is predicted to form a transmembrane helix. As the only membrane-bound, constitutively active DGK isoform with exquisite specificity for particular molecular species of DAG, the functional overlap between DGKε and other DGKs is predicted to be minimal. DGKε exhibits specificity for DAG containing the same acyl chains as those found in the lipid intermediates of the phosphatidylinositol-cycle. It has also been shown that DGKε affects the acyl chain composition of phosphatidylinositol in whole cells. It is thus likely that DGKε is responsible for catalyzing one step in the phosphatidylinositol-cycle. Steps of this cycle take place in both the plasma membrane and the endoplasmic reticulum membrane. DGKε is likely present in both of these membranes. DGKε is the only DGK isoform that is associated with a human disease. Indeed, recessive loss-of-function mutations in DGKε cause atypical hemolytic-uremic syndrome (aHUS). This condition is characterized by thrombosis in the small vessels of the kidney. It causes acute renal insufficiency in infancy and most patients develop end-stage renal failure before adulthood. Disease pathophysiology is poorly understood and there is no therapy. There are also data suggesting that DGKε may play a role in epilepsy and Huntington disease. Thus, DGKε has many unique molecular and biochemical properties when compared to all other DGK isoforms. DGKε homologs also contain a number of conserved sequence features that are distinctive characteristics of either the rodents or specific groups of primate homologs. How cells, tissues and organisms harness DGKε's catalytic prowess remains unclear. The discovery of DGKε's role in causing aHUS will hopefully boost efforts to unravel the mechanisms by which DGKε dysfunction causes disease.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Vincent So
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences CentreHamilton, ON, Canada; Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Mathieu Lemaire
- Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada; Department of Biochemistry, University of TorontoToronto, ON, Canada; Institute of Medicine, University of TorontoToronto, ON, Canada
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152
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Zou X, Blank M. Targeting p38 MAP kinase signaling in cancer through post-translational modifications. Cancer Lett 2016; 384:19-26. [PMID: 27725227 DOI: 10.1016/j.canlet.2016.10.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/26/2016] [Accepted: 10/02/2016] [Indexed: 12/31/2022]
Abstract
The p38 MAPK signaling pathway is a key signal transduction cascade that cancer cells employ to sense and adapt to a plethora of environmental stimuli, and has attracted much attention as a promising target for cancer therapy. Accumulating evidence suggests a dual role of p38 signaling in various types of cancers, wherein the p38 pathway can both suppress and promote tumor growth, metastasis and chemoresistance. This dual role of p38 signaling, along with its context dependence and versatility, poses a great challenge for developing efficient anticancer treatment. An increasing number of studies showed that p38 signaling is subject to regulation by a variety of post-translational modifications (PTMs). Recently, large-scale proteomics profilings have identified a large number of PTMs on key components of the p38 pathway. However, the majority of these modifications and their biological significance in cancer remain uncharacterized. In this review, we highlight a series of studies that focus on the PTMs in the p38 cascade landscape, and discuss the complexity and implications of these PTMs in p38 MAPK signaling regulation.
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Affiliation(s)
- Xiao Zou
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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153
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Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal 2016; 14:17. [PMID: 27549312 PMCID: PMC4994250 DOI: 10.1186/s12964-016-0140-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Smirnova
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jamie J Kwan
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Siu
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Xin Gao
- Division of Computer, Computational Bioscience Research Center, Electrical and Mathematical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Georg Zoidl
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.,Department of Psychology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7760 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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154
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Wieczorek E, Kędracka–Krok S, Sołtys K, Jankowska U, Hołubowicz R, Seliga J, Ożyhar A. Is Transthyretin a Regulator of Ubc9 SUMOylation? PLoS One 2016; 11:e0160536. [PMID: 27501389 PMCID: PMC4976990 DOI: 10.1371/journal.pone.0160536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/20/2016] [Indexed: 12/21/2022] Open
Abstract
Ageing and mutations of transthyretin (TTR), the thyroid hormones and retinol transporting protein lead to amyloidosis by destabilizing the structure of TTR. Because protein structure is regulated through posttranslational modifications, we investigated the Small Ubiquitin-like Modifier (SUMO)ylation of TTR. We chose the widely used Ubc9 fusion-directed SUMOylation system, which is based on a fusion of the SUMOylation substrate of interest with Ubc9, a sole SUMO conjugating enzyme. Surprisingly, despite our presumptions, we found that Ubc9 fused to TTR was SUMOylated at a unique set of lysine residues. Three unknown SUMOylation sites of Ubc9-K154, K18 and K65-were revealed by mass spectrometry (MS). The previously reported SUMOylation at K49 of Ubc9 was also observed. SUMOylation of the lysine residues of TTR fused to Ubc9 was hardly detectable. However, non-fused TTR was SUMOylated via trans-SUMOylation by Ubc9 fused to TTR. Interestingly, mutating the catalytic residue of Ubc9 fused to TTR did not result in complete loss of the SUMOylation signal, suggesting that Ubc9 linked to TTR is directly cross-SUMOylated by the SUMO-activating enzyme E1. Ubc9, TTR or fusion proteins composed of TTR and Ubc9 specifically affected the global SUMOylation of cellular proteins. TTR or Ubc9 alone increased global SUMOylation, whereas concomitant presence of TTR and Ubc9 did not further increase the amount of high-molecular weight (HMW) SUMO conjugates. Our data suggest that TTR may influence the SUMOylation of Ubc9, thereby altering signalling pathways in the cell.
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Affiliation(s)
- Elżbieta Wieczorek
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, Poland
- * E-mail:
| | - Sylwia Kędracka–Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Katarzyna Sołtys
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, Poland
| | - Urszula Jankowska
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, Poland
| | - Justyna Seliga
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, Poland
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155
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Cahill MA, Jazayeri JA, Catalano SM, Toyokuni S, Kovacevic Z, Richardson DR. The emerging role of progesterone receptor membrane component 1 (PGRMC1) in cancer biology. Biochim Biophys Acta Rev Cancer 2016; 1866:339-349. [PMID: 27452206 DOI: 10.1016/j.bbcan.2016.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 01/09/2023]
Abstract
Progesterone receptor membrane component 1 (PGRMC1) is a multi-functional protein with a heme-binding moiety related to that of cytochrome b5, which is a putative progesterone receptor. The recently solved PGRMC1 structure revealed that heme-binding involves coordination by a tyrosinate ion at Y113, and induces dimerization which is stabilized by hydrophobic stacking of heme on adjacent monomers. Dimerization is required for association with cytochrome P450 (cyP450) enzymes, which mediates chemoresistance to doxorubicin and may be responsible for PGRMC1's anti-apoptotic activity. Here we review the multiple attested involvement of PGRMC1 in diverse functions, including regulation of cytochrome P450, steroidogenesis, vesicle trafficking, progesterone signaling and mitotic spindle and cell cycle regulation. Its wide range of biological functions is attested to particularly by its emerging association with cancer and progesterone-responsive female reproductive tissues. PGRMC1 exhibits all the hallmarks of a higher order nexus signal integration hub protein. It appears capable of acting as a detector that integrates information from kinase/phosphatase pathways with heme and CO levels and probably redox status.
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Affiliation(s)
- Michael A Cahill
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
| | - Jalal A Jazayeri
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Susan M Catalano
- Cognition Therapeutics Inc., Pittsburgh, PA 15203, United States
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Zaklina Kovacevic
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Des R Richardson
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia.
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156
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Abstract
Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response.
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157
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Gupta A, Leslie NR. Controlling PTEN (Phosphatase and Tensin Homolog) Stability: A DOMINANT ROLE FOR LYSINE 66. J Biol Chem 2016; 291:18465-73. [PMID: 27405757 DOI: 10.1074/jbc.m116.727750] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/06/2022] Open
Abstract
Phosphatase and tensin homolog (PTEN) is a phosphoinositide lipid phosphatase and one of the most frequently disrupted tumor suppressors in many forms of cancer, with even small reductions in the expression levels of PTEN promoting cancer development. Although the post-translational ubiquitination of PTEN can control its stability, activity, and localization, a detailed understanding of how PTEN ubiquitination integrates with other cellular regulatory processes and may be dysregulated in cancer has been hampered by a poor understanding of the significance of ubiquitination at individual sites. Here we show that Lys(66) is not required for cellular activity, yet dominates over other PTEN ubiquitination sites in the regulation of protein stability. Notably, combined mutation of other sites (Lys(13), Lys(80), and Lys(289)) has relatively little effect on protein expression, protein stability, or PTEN polyubiquitination. The present work identifies a key role for Lys(66) in the regulation of PTEN expression and provides both an opportunity to improve the stability of PTEN as a protein therapy and a mechanistic basis for efforts to stabilize endogenous PTEN.
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Affiliation(s)
- Amit Gupta
- From the Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, James Nasmyth Building, Riccarton Campus, Edinburgh EH14 4AS, United Kingdom
| | - Nicholas R Leslie
- From the Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, James Nasmyth Building, Riccarton Campus, Edinburgh EH14 4AS, United Kingdom
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158
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Kim SM, Wang Y, Nabavi N, Liu Y, Correia MA. Hepatic cytochromes P450: structural degrons and barcodes, posttranslational modifications and cellular adapters in the ERAD-endgame. Drug Metab Rev 2016; 48:405-33. [PMID: 27320797 DOI: 10.1080/03602532.2016.1195403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants.
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Affiliation(s)
- Sung-Mi Kim
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - YongQiang Wang
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Noushin Nabavi
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Yi Liu
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Maria Almira Correia
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA ;,b Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , CA , USA ;,c Department of Bioengineering and Therapeutic Sciences , University of California San Francisco , San Francisco , CA , USA ;,d The Liver Center, University of California San Francisco , San Francisco , CA , USA
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159
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Heidelberger JB, Wagner SA, Beli P. Mass Spectrometry-Based Proteomics for Investigating DNA Damage-Associated Protein Ubiquitylation. Front Genet 2016; 7:109. [PMID: 27379159 PMCID: PMC4905943 DOI: 10.3389/fgene.2016.00109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Modification of proteins with the 76 amino acid protein ubiquitin plays essential roles in cellular signaling. Development of methods for specific enrichment of ubiquitin remnant peptides and advances in high-resolution mass spectrometry have enabled proteome-wide identification of endogenous ubiquitylation sites. Moreover, ubiquitin remnant profiling has emerged as a powerful approach for investigating changes in protein ubiquitylation in response to cellular perturbations, such as DNA damage, as well as for identification of substrates of ubiquitin-modifying enzymes. Despite these advances, interrogation of ubiquitin chain topologies on substrate proteins remains a challenging task. Here, we describe mass spectrometry-based approaches for quantitative analyses of site-specific protein ubiquitylation and highlight recent studies that employed these methods for investigation of ubiquitylation in the context of the cellular DNA damage response. Furthermore, we provide an overview of experimental strategies for probing ubiquitin chain topologies on proteins and discuss how these methods can be applied to analyze functions of ubiquitylation in the DNA damage response.
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Affiliation(s)
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology Mainz, Germany
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160
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Nguyen VN, Huang KY, Weng JTY, Lai KR, Lee TY. UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw054. [PMID: 27114492 PMCID: PMC4843525 DOI: 10.1093/database/baw054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/20/2016] [Indexed: 12/19/2022]
Abstract
Protein ubiquitylation catalyzed by E3 ubiquitin ligases are crucial in the regulation of many cellular processes. Owing to the high throughput of mass spectrometry-based proteomics, a number of methods have been developed for the experimental determination of ubiquitylation sites, leading to a large collection of ubiquitylation data. However, there exist no resources for the exploration of E3-ligase-associated regulatory networks of for ubiquitylated proteins in humans. Therefore, the UbiNet database was developed to provide a full investigation of protein ubiquitylation networks by incorporating experimentally verified E3 ligases, ubiquitylated substrates and protein-protein interactions (PPIs). To date, UbiNet has accumulated 43 948 experimentally verified ubiquitylation sites from 14 692 ubiquitylated proteins of humans. Additionally, we have manually curated 499 E3 ligases as well as two E1 activating and 46 E2 conjugating enzymes. To delineate the regulatory networks among E3 ligases and ubiquitylated proteins, a total of 430 530 PPIs were integrated into UbiNet for the exploration of ubiquitylation networks with an interactive network viewer. A case study demonstrated that UbiNet was able to decipher a scheme for the ubiquitylation of tumor proteins p63 and p73 that is consistent with their functions. Although the essential role of Mdm2 in p53 regulation is well studied, UbiNet revealed that Mdm2 and additional E3 ligases might be implicated in the regulation of other tumor proteins by protein ubiquitylation. Moreover, UbiNet could identify potential substrates for a specific E3 ligase based on PPIs and substrate motifs. With limited knowledge about the mechanisms through which ubiquitylated proteins are regulated by E3 ligases, UbiNet offers users an effective means for conducting preliminary analyses of protein ubiquitylation. The UbiNet database is now freely accessible via http://csb.cse.yzu.edu.tw/UbiNet/ The content is regularly updated with the literature and newly released data.Database URL: http://csb.cse.yzu.edu.tw/UbiNet/.
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Affiliation(s)
- Van-Nui Nguyen
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan University of Information and Communication Technology, Thai Nguyen University, Vietnam and
| | - Kai-Yao Huang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan
| | - Julia Tzu-Ya Weng
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan Innovation Center for Big Data and Digital Convergence, Yuan Ze University, 320, Taiwan
| | - K Robert Lai
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan Innovation Center for Big Data and Digital Convergence, Yuan Ze University, 320, Taiwan
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan Innovation Center for Big Data and Digital Convergence, Yuan Ze University, 320, Taiwan
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161
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Jouffe C, Gobet C, Martin E, Métairon S, Morin-Rivron D, Masoodi M, Gachon F. Perturbed rhythmic activation of signaling pathways in mice deficient for Sterol Carrier Protein 2-dependent diurnal lipid transport and metabolism. Sci Rep 2016; 6:24631. [PMID: 27097688 PMCID: PMC4838911 DOI: 10.1038/srep24631] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/29/2016] [Indexed: 01/22/2023] Open
Abstract
Through evolution, most of the living species have acquired a time keeping system to anticipate daily changes caused by the rotation of the Earth. In all of the systems this pacemaker is based on a molecular transcriptional/translational negative feedback loop able to generate rhythmic gene expression with a period close to 24 hours. Recent evidences suggest that post-transcriptional regulations activated mostly by systemic cues play a fundamental role in the process, fine tuning the time keeping system and linking it to animal physiology. Among these signals, we consider the role of lipid transport and metabolism regulated by SCP2. Mice harboring a deletion of the Scp2 locus present a modulated diurnal accumulation of lipids in the liver and a perturbed activation of several signaling pathways including PPARα, SREBP, LRH-1, TORC1 and its upstream regulators. This defect in signaling pathways activation feedbacks upon the clock by lengthening the circadian period of animals through post-translational regulation of core clock regulators, showing that rhythmic lipid transport is a major player in the establishment of rhythmic mRNA and protein expression landscape.
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Affiliation(s)
- Céline Jouffe
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, CH-1011, Switzerland.,Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Eva Martin
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Sylviane Métairon
- Functional Genomic, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Delphine Morin-Rivron
- Department of Gastro-Intestinal Health &Microbiome, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Mojgan Masoodi
- Department of Gastro-Intestinal Health &Microbiome, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland.,Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 3E2, Canada
| | - Frédéric Gachon
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, CH-1011, Switzerland.,Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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162
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Thanh Nguyen H, Andrejeva D, Gupta R, Choudhary C, Hong X, Eichhorn PJA, Loya AC, Cohen SM. Deubiquitylating enzyme USP9x regulates hippo pathway activity by controlling angiomotin protein turnover. Cell Discov 2016; 2:16001. [PMID: 27462448 PMCID: PMC4849470 DOI: 10.1038/celldisc.2016.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022] Open
Abstract
The Hippo pathway has been identified as a key barrier for tumorigenesis, acting through downregulation of YAP/TAZ activity. Elevated YAP/TAZ activity has been documented in many human cancers. Ubiquitylation has been shown to play a key role in regulating YAP/TAZ activity through downregulation of a number of Hippo pathway components. Several ubiquitin ligase complexes have been implicated in this process, however, little is known about the deubiquitylating enzymes that counteract these activities to regulate YAP/TAZ. Here we identify the deubiquitylating enzyme USP9x as a regulator of YAP/TAZ activity. We demonstrate that USPx regulates ubiquitin-mediated turnover of the YAP inhibitor, Angiomotin. USP9x acts to deubiquitylate Angiomotin at lysine 496, resulting in stabilization of Angiomotin and lower YAP/TAZ activity. USP9x mRNA levels were reduced in several cancers. Clinically, USP9x mRNA levels were reduced in several cancers with low USPx expression correlating with poor prognosis in renal clear cell carcinoma. Our data indicate that USP9x may be a useful biomarker for renal clear cell carcinoma.
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Affiliation(s)
- Hung Thanh Nguyen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Diana Andrejeva
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rajat Gupta
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Xin Hong
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anand C Loya
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Stephen M Cohen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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163
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Dart AE, Box GM, Court W, Gale ME, Brown JP, Pinder SE, Eccles SA, Wells CM. PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion. J Cell Biol 2016; 211:863-79. [PMID: 26598620 PMCID: PMC4657161 DOI: 10.1083/jcb.201501072] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
PAK4, via a novel kinase-independent mechanism, protects RhoU from a Rab40A/Cullin 5 ubiquitin ligase complex–driven K48 ubiquitination to regulate breast cancer cell adhesion. P21-activated kinase 4 (PAK4) is a Cdc42 effector protein thought to regulate cell adhesion disassembly in a kinase-dependent manner. We found that PAK4 expression is significantly higher in high-grade human breast cancer patient samples, whereas depletion of PAK4 modifies cell adhesion dynamics of breast cancer cells. Surprisingly, systematic analysis of PAK4 functionality revealed that PAK4-driven adhesion turnover is neither dependent on Cdc42 binding nor kinase activity. Rather, reduced expression of PAK4 leads to a concomitant loss of RhoU expression. We report that RhoU is targeted for ubiquitination by the Rab40A–Cullin 5 complex and demonstrate that PAK4 protects RhoU from ubiquitination in a kinase-independent manner. Overexpression of RhoU rescues the PAK4 depletion phenotype, whereas loss of RhoU expression reduces cell adhesion turnover and migration. These data support a new kinase-independent mechanism for PAK4 function, where an important role of PAK4 in cellular adhesions is to stabilize RhoU protein levels. Thus, PAK4 and RhoU cooperate to drive adhesion turnover and promote cell migration.
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Affiliation(s)
- Anna E Dart
- Division of Cancer Studies, King's College London, London SE1 1UL, England, UK
| | - Gary M Box
- Tumour Biology and Metastasis, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, England, UK
| | - William Court
- Tumour Biology and Metastasis, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, England, UK
| | - Madeline E Gale
- Division of Cancer Studies, King's College London, London SE1 1UL, England, UK
| | - John P Brown
- Breast Research Pathology, Department of Research Oncology, Division of Cancer Studies, School of Medicine, Guy's Hospital, King's College London, London SE1 9RT, England, UK
| | - Sarah E Pinder
- Breast Research Pathology, Department of Research Oncology, Division of Cancer Studies, School of Medicine, Guy's Hospital, King's College London, London SE1 9RT, England, UK
| | - Suzanne A Eccles
- Tumour Biology and Metastasis, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, England, UK
| | - Claire M Wells
- Division of Cancer Studies, King's College London, London SE1 1UL, England, UK
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164
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Naik E, Dixit VM. Usp9X Is Required for Lymphocyte Activation and Homeostasis through Its Control of ZAP70 Ubiquitination and PKCβ Kinase Activity. THE JOURNAL OF IMMUNOLOGY 2016; 196:3438-51. [PMID: 26936881 DOI: 10.4049/jimmunol.1403165] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/09/2016] [Indexed: 11/19/2022]
Abstract
To achieve a durable adaptive immune response, lymphocytes must undergo clonal expansion and induce a survival program that enables the persistence of Ag-experienced cells and the development of memory. During the priming phase of this response, CD4(+)T lymphocytes either remain tolerized or undergo clonal expansion. In this article, we show that Usp9X functions as a positive regulatory switch during T lymphocyte priming through removal of inhibitory monoubiquitination from ZAP70. In the absence of Usp9X, an increased amount of ZAP70 localized to early endosomes consistent with the role of monoubiquitin in endocytic sorting. Usp9X becomes competent to deubiquitinate ZAP70 through TCR-dependent phosphorylation and enhancement of its catalytic activity and association with the LAT signalosome. In B lymphocytes, Usp9X is required for the induction of PKCβ kinase activity after BCR-dependent activation. Accordingly, inUsp9Xknockout B cells, there was a significant reduction in phospho-CARMA1 levels that resulted in reduced CARMA1/Bcl-10/MALT-1 complex formation and NF-κB-dependent cell survival. The pleiotropic effect of Usp9X during Ag-receptor signaling highlights its importance for the development of an effective and durable adaptive immune response.
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Affiliation(s)
- Edwina Naik
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, CA 94080
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, CA 94080
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165
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Hayes MP, Roman DL. Regulator of G Protein Signaling 17 as a Negative Modulator of GPCR Signaling in Multiple Human Cancers. AAPS JOURNAL 2016; 18:550-9. [PMID: 26928451 DOI: 10.1208/s12248-016-9894-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/15/2016] [Indexed: 02/08/2023]
Abstract
Regulators of G protein signaling (RGS) proteins modulate G protein-coupled receptor (GPCR) signaling networks by terminating signals produced by active Gα subunits. RGS17, a member of the RZ subfamily of RGS proteins, is typically only expressed in appreciable amounts in the human central nervous system, but previous works have shown that RGS17 expression is selectively upregulated in a number of malignancies, including lung, breast, prostate, and hepatocellular carcinoma. In addition, this upregulation of RGS17 is associated with a more aggressive cancer phenotype, as increased proliferation, migration, and invasion are observed. Conversely, decreased RGS17 expression diminishes the response of ovarian cancer cells to agents commonly used during chemotherapy. These somewhat contradictory roles of RGS17 in cancer highlight the need for selective, high-affinity inhibitors of RGS17 to use as chemical probes to further the understanding of RGS17 biology. Based on current evidence, these compounds could potentially have clinical utility as novel chemotherapeutics in the treatment of lung, prostate, breast, and liver cancers. Recent advances in screening technologies to identify potential inhibitors coupled with increasing knowledge of the structural requirements of RGS-Gα protein-protein interaction inhibitors make the future of drug discovery efforts targeting RGS17 promising. This review highlights recent findings related to RGS17 as both a canonical and atypical RGS protein, its role in various human disease states, and offers insights on small molecule inhibition of RGS17.
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Affiliation(s)
- Michael P Hayes
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa, USA
| | - David L Roman
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa, USA. .,Cancer Signaling and Experimental Therapeutics Program, Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA. .,, 115 S. Grand Avenue, S327 PHAR, Iowa City, Iowa, 52242, USA.
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166
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Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T. Deubiquitylation of Protein Cargo Is Not an Essential Step in Exosome Formation. Mol Cell Proteomics 2016; 15:1556-71. [PMID: 26884507 DOI: 10.1074/mcp.m115.054965] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Indexed: 01/02/2023] Open
Abstract
Exosomes, derived from multivesicular bodies (MVBs), contain proteins and genetic materials from their cell of origin and are secreted from various cells types, including kidney epithelial cells. In general, it is thought that protein cargo is ubiquitylated but that ubiquitin is cleaved by specific deubiquitylases during the process of cargo incorporation into MVBs. Here, we provide direct evidence that, in vivo, deubiquitylation is not essential. Ubiquitin was detected within human MVBs and urinary exosomes by electron microscopy. Of the >6000 proteins identified in human urinary exosomes was mass spectrometry, 15% were ubiquitylated with various topologies (Lys63>Lys48> Lys11>Lys6>Lys29>Lys33>Lys27). A significant preference for basic amino acids upstream of ubiquitylation sites suggests specific ubiquitylation motifs. The current studies demonstrate that, in vivo, deubiquitylation of proteins is not necessary for their incorporation into MVBs and highlight that urinary exosomes are an enriched source for studying ubiquitin modifications in physiological or disease states.
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Affiliation(s)
- Alyssa R Huebner
- From the ‡Department of Biomedicine and Center for Interactions of Proteins in Epithelial Transport, Aarhus University, Denmark
| | - Lei Cheng
- From the ‡Department of Biomedicine and Center for Interactions of Proteins in Epithelial Transport, Aarhus University, Denmark
| | | | - Mark A Knepper
- ¶Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603
| | - Robert A Fenton
- From the ‡Department of Biomedicine and Center for Interactions of Proteins in Epithelial Transport, Aarhus University, Denmark;
| | - Trairak Pisitkun
- From the ‡Department of Biomedicine and Center for Interactions of Proteins in Epithelial Transport, Aarhus University, Denmark; §Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand;
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167
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Aretz I, Hardt C, Wittig I, Meierhofer D. An Impaired Respiratory Electron Chain Triggers Down-regulation of the Energy Metabolism and De-ubiquitination of Solute Carrier Amino Acid Transporters. Mol Cell Proteomics 2016; 15:1526-38. [PMID: 26852163 DOI: 10.1074/mcp.m115.053181] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 12/25/2022] Open
Abstract
Hundreds of genes have been associated with respiratory chain disease (RCD), the most common inborn error of metabolism so far. Elimination of the respiratory electron chain by depleting the entire mitochondrial DNA (mtDNA, ρ(0) cells) has therefore one of the most severe impacts on the energy metabolism in eukaryotic cells. In this study, proteomic data sets including the post-translational modifications (PTMs) phosphorylation and ubiquitination were integrated with metabolomic data sets and selected enzyme activities in the osteosarcoma cell line 143B.TK(-) A shotgun based SILAC LC-MS proteomics and a targeted metabolomics approach was applied to elucidate the consequences of the ρ(0) state. Pathway and protein-protein interaction (PPI) network analyses revealed a nonuniform down-regulation of the respiratory electron chain, the tricarboxylic acid (TCA) cycle, and the pyruvate metabolism in ρ(0) cells. Metabolites of the TCA cycle were dysregulated, such as a reduction of citric acid and cis-aconitic acid (six and 2.5-fold), and an increase of lactic acid, oxalacetic acid (both twofold), and succinic acid (fivefold) in ρ(0) cells. Signaling pathways such as GPCR, EGFR, G12/13 alpha, and Rho GTPases were up-regulated in ρ(0) cells, which could be indicative for the mitochondrial retrograde response, a pathway of communication from mitochondria to the nucleus. This was supported by our phosphoproteome data, which revealed two main processes, GTPase-related signal transduction and cytoskeleton organization. Furthermore, a general de-ubiquitination in ρ(0) cells was observed, for example, 80S ribosomal proteins were in average threefold and SLC amino acid transporters fivefold de-ubiquitinated. The latter might cause the observed significant increase of amino acid levels in ρ(0) cells. We conclude that an elimination of the respiratory electron chain, e.g. mtDNA depletion, not only leads to an uneven down-regulation of mitochondrial energy pathways, but also triggers the retrograde response.
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Affiliation(s)
- Ina Aretz
- From the ‡Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany; §Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Takustraße 3, 14195 Berlin, Germany
| | - Christopher Hardt
- From the ‡Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Ilka Wittig
- ¶Functional Proteomics, Faculty of Medicine, Goethe-University, Theodor Stern Kai 7, Haus 26, D-60590 Frankfurt am Main, Germany
| | - David Meierhofer
- From the ‡Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany;
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168
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Aragonès G, Auguet T, Guiu-Jurado E, Berlanga A, Curriu M, Martinez S, Alibalic A, Aguilar C, Hernández E, Camara ML, Canela N, Herrero P, Ruyra X, Martín-Paredero V, Richart C. Proteomic Profile of Unstable Atheroma Plaque: Increased Neutrophil Defensin 1, Clusterin, and Apolipoprotein E Levels in Carotid Secretome. J Proteome Res 2016; 15:933-44. [PMID: 26795031 DOI: 10.1021/acs.jproteome.5b00936] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because of the clinical significance of carotid atherosclerosis, the search for novel biomarkers has become a priority. The aim of the present study was to compare the protein secretion profile of the carotid atherosclerotic plaque (CAP, n = 12) and nonatherosclerotic mammary artery (MA, n = 10) secretomes. We used a nontargeted proteomic approach that incorporated tandem immunoaffinity depletion, iTRAQ labeling, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 162 proteins were quantified, of which 25 showed statistically significant differences in secretome levels between carotid atherosclerotic plaque and nondiseased mammary artery. We found increased levels of neutrophil defensin 1, apolipoprotein E, clusterin, and zinc-alpha-2-glycoprotein in CAP secretomes. Results were validated by ELISA assays. Also, differentially secreted proteins are involved in pathways such as focal adhesion and leukocyte transendothelial migration. In conclusion, this study provides a subset of identified proteins that are differently expressed in secretomes of clinical significance.
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Affiliation(s)
- Gemma Aragonès
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain
| | - Teresa Auguet
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain.,Servei Medicina Interna, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
| | - Esther Guiu-Jurado
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain
| | - Alba Berlanga
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain
| | - Marta Curriu
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain
| | - Salomé Martinez
- Servei Anatomia Patològica, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
| | - Ajla Alibalic
- Servei Medicina Interna, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
| | - Carmen Aguilar
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain
| | - Esteban Hernández
- Servei Angiologia i Cirurgia Vascular, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
| | - María-Luisa Camara
- Servei de Cirurgia Cardíaca, Hospital Germans Trias i Pujol , Badalona 08916, Spain
| | - Núria Canela
- Group of Research on Omic Methodologies (GROM), Centre for Omic Sciences (COS) , Reus 43204, Spain
| | - Pol Herrero
- Group of Research on Omic Methodologies (GROM), Centre for Omic Sciences (COS) , Reus 43204, Spain
| | - Xavier Ruyra
- Servei de Cirurgia Cardíaca, Hospital Germans Trias i Pujol , Badalona 08916, Spain
| | - Vicente Martín-Paredero
- Servei Angiologia i Cirurgia Vascular, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
| | - Cristóbal Richart
- Grup de Recerca GEMMAIR - Medicina Aplicada, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili (URV), Institut Investigació Sanitària Pere Virgili (IISPV). Tarragona 43007, Spain.,Servei Medicina Interna, Hospital Universitari Joan XXIII , Tarragona 43007, Spain
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169
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Rinschen MM, Bharill P, Wu X, Kohli P, Reinert MJ, Kretz O, Saez I, Schermer B, Höhne M, Bartram MP, Aravamudhan S, Brooks BR, Vilchez D, Huber TB, Müller RU, Krüger M, Benzing T. The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes. Hum Mol Genet 2016; 25:1328-44. [PMID: 26792178 DOI: 10.1093/hmg/ddw016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/16/2016] [Indexed: 11/13/2022] Open
Abstract
The PHB-domain protein podocin maintains the renal filtration barrier and its mutation is an important cause of hereditary nephrotic syndrome. Podocin and its Caenorhabditis elegans orthologue MEC-2 have emerged as key components of mechanosensitive membrane protein signalling complexes. Whereas podocin resides at a specialized cell junction at the podocyte slit diaphragm, MEC-2 is found in neurons required for touch sensitivity. Here, we show that the ubiquitin ligase Ubr4 is a key component of the podocin interactome purified both from cultured podocytes and native glomeruli. It colocalizes with podocin and regulates its stability. In C. elegans, this process is conserved. Here, Ubr4 is responsible for the degradation of mislocalized MEC-2 multimers. Ubiquitylomic analysis of mouse glomeruli revealed that podocin is ubiquitylated at two lysine residues. These sites were Ubr4-dependent and were conserved across species. Molecular dynamics simulations revealed that ubiquitylation of one site, K301, do not only target podocin/MEC-2 for proteasomal degradation, but may also affect stability and disassembly of the multimeric complex. We suggest that Ubr4 is a key regulator of podocyte foot process proteostasis.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,
| | - Puneet Bharill
- Department II of Internal Medicine, Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priyanka Kohli
- Department II of Internal Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | | | - Oliver Kretz
- Renal Division, University Hospital Freiburg, Freiburg, Germany, Neuroanatomy, University of Freiburg, Freiburg, Germany
| | - Isabel Saez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Bernhard Schermer
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | | | - Sriram Aravamudhan
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany and
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Vilchez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Tobias B Huber
- Renal Division, University Hospital Freiburg, Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Marcus Krüger
- Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Thomas Benzing
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,
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170
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USP2-45 Is a Circadian Clock Output Effector Regulating Calcium Absorption at the Post-Translational Level. PLoS One 2016; 11:e0145155. [PMID: 26756164 PMCID: PMC4710524 DOI: 10.1371/journal.pone.0145155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/01/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian circadian clock influences most aspects of physiology and behavior through the transcriptional control of a wide variety of genes, mostly in a tissue-specific manner. About 20 clock-controlled genes (CCGs) oscillate in virtually all mammalian tissues and are generally considered as core clock components. One of them is Ubiquitin-Specific Protease 2 (Usp2), whose status remains controversial, as it may be a cogwheel regulating the stability or activity of core cogwheels or an output effector. We report here that Usp2 is a clock output effector related to bodily Ca2+ homeostasis, a feature that is conserved across evolution. Drosophila with a whole-body knockdown of the orthologue of Usp2, CG14619 (dUsp2-kd), predominantly die during pupation but are rescued by dietary Ca2+ supplementation. Usp2-KO mice show hyperabsorption of dietary Ca2+ in small intestine, likely due to strong overexpression of the membrane scaffold protein NHERF4, a regulator of the Ca2+ channel TRPV6 mediating dietary Ca2+ uptake. In this tissue, USP2-45 is found in membrane fractions and negatively regulates NHERF4 protein abundance in a rhythmic manner at the protein level. In clock mutant animals (Cry1/Cry2-dKO), rhythmic USP2-45 expression is lost, as well as the one of NHERF4, confirming the inverse relationship between USP2-45 and NHERF4 protein levels. Finally, USP2-45 interacts in vitro with NHERF4 and endogenous Clathrin Heavy Chain. Taken together these data prompt us to define USP2-45 as the first clock output effector acting at the post-translational level at cell membranes and possibly regulating membrane permeability of Ca2+.
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171
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Ramirez J, Min M, Barrio R, Lindon C, Mayor U. Isolation of Ubiquitinated Proteins to High Purity from In Vivo Samples. Methods Mol Biol 2016; 1449:193-202. [PMID: 27613036 DOI: 10.1007/978-1-4939-3756-1_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ubiquitination pathways are widely used within eukaryotic cells. The complexity of ubiquitin signaling gives rise to a number of problems in the study of specific pathways. One problem is that not all processes regulated by ubiquitin are shared among the different cells of an organism (e.g., neurotransmitter release is only carried out in neuronal cells). Moreover, these processes are often highly temporally dynamic. It is essential therefore to use the right system for each biological question, so that we can characterize pathways specifically in the tissue or cells of interest. However, low stoichiometry, and the unstable nature of many ubiquitin conjugates, presents a technical barrier to studying this modification in vivo. Here, we describe two approaches to isolate ubiquitinated proteins to high purity. The first one favors isolation of the whole mixture of ubiquitinated material from a given tissue or cell type, generating a survey of the ubiquitome landscape for a specific condition. The second one favors the isolation of just one specific protein, in order to facilitate the characterization of its ubiquitinated fraction. In both cases, highly stringent denaturing buffers are used to minimize the presence of contaminating material in the sample.
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Affiliation(s)
- Juanma Ramirez
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Mingwei Min
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Catherine Lindon
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
| | - Ugo Mayor
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain.
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172
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Giovannoni I, Callea F, Bellacchio E, Torre G, De Ville De Goyet J, Francalanci P. Genetics and Molecular Modeling of New Mutations of Familial Intrahepatic Cholestasis in a Single Italian Center. PLoS One 2015; 10:e0145021. [PMID: 26678486 PMCID: PMC4683058 DOI: 10.1371/journal.pone.0145021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 11/28/2015] [Indexed: 12/15/2022] Open
Abstract
Familial intrahepatic cholestases (FICs) are a heterogeneous group of autosomal recessive disorders of childhood that disrupt bile formation and present with cholestasis of hepatocellular origin. Three distinct forms are described: FIC1 and FIC2, associated with low/normal GGT level in serum, which are caused by impaired bile salt secretion due to defects in ATP8B1 encoding the FIC1 protein and defects in ABCB11 encoding bile salt export pump protein, respectively; FIC3, linked to high GGT level, involves impaired biliary phospholipid secretion due to defects in ABCB4, encoding multidrug resistance 3 protein. Different mutations in these genes may cause either a progressive familial intrahepatic cholestasis (PFIC) or a benign recurrent intrahepatic cholestasis (BRIC). For the purposes of the present study we genotyped 27 children with intrahepatic cholestasis, diagnosed on either a clinical or histological basis. Two BRIC, 23 PFIC and 2 BRIC/PFIC were identified. Thirty-four different mutations were found of which 11 were novel. One was a 2Mb deletion (5’UTR- exon 18) in ATP8B1. In another case microsatellite analysis of chromosome 2, including ABCB11, showed uniparental disomy. Two cases were compound heterozygous for BRIC/PFIC2 mutations. Our results highlight the importance of the pathogenic role of novel mutations in the three genes and unusual modes of their transmission.
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Affiliation(s)
- Isabella Giovannoni
- Dept. Pathology and Molecular Histopathology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Francesco Callea
- Dept. Pathology and Molecular Histopathology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Giuliano Torre
- Dept. Hepatology, Gastroenterology and Nutrition Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Jean De Ville De Goyet
- Dept. Pediatric Surgery and Transplantation, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paola Francalanci
- Dept. Pathology and Molecular Histopathology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- * E-mail:
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173
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Regulation of Shootin1 Gene Expression Involves NGF-induced Alternative Splicing during Neuronal Differentiation of PC12 Cells. Sci Rep 2015; 5:17931. [PMID: 26648138 PMCID: PMC4673418 DOI: 10.1038/srep17931] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Shootin1 is a protein involved in neuronal polarization, and has been shown to be a key molecule for the positive/negative feedback loop for axon induction required during neuronal symmetry breaking. To better understand the molecular basis of shootin1 dynamics, we analysed the regulatory pathways and the expressional status of shootin1 gene during NGF-induced neuronal differentiation. We demonstrated that the isoform-1 and isoform-2 of shootin1 is differentially expressed during neuronal differentiation. By blocking individual downstream pathways of NGF signalling, we found that PI3K/Akt pathway plays a major role in the expression of shootin1 isoform-2. Western blot and RT-PCR results showed that the isoform-1 of shootin1 is constitutively expressed, while the isoform-2 is expressed in a manner that is strictly dependent on NGF-stimulation. Isoform-specific RT-PCR results demonstrated that the differential expression of the isoform-1 and isoform-2 of shootin1 is a consequence of alternative splicing of shootin1 pre-mRNA, in response to NGF-signalling. Collectively these findings provide the first information on the molecular mechanisms regulating the expression of shootin1 gene and represent the first example of NGF-induced alternative splicing process that has a regulatory role in neuritogenesis.
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174
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Stoichiometry of the eIF2B complex is maintained by mutual stabilization of subunits. Biochem J 2015; 473:571-80. [PMID: 26614765 DOI: 10.1042/bj20150828] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/26/2015] [Indexed: 12/30/2022]
Abstract
The eukaryotic translation initiation factor eIF2B is a multi-subunit complex with a crucial role in the regulation of global protein synthesis in the cell. The complex comprises five subunits, termed α through ε in order of increasing size, arranged as a heterodecamer with two copies of each subunit. Regulation of the co-stoichiometric expression of the eIF2B subunits is crucial for the proper function and regulation of the eIF2B complex in cells. We have investigated the control of stoichiometric eIF2B complexes through mutual stabilization of eIF2B subunits. Our data show that the stable expression of the catalytic eIF2Bε subunit in human cells requires co-expression of eIF2Bγ. Similarly, stable expression of eIF2Bδ requires both eIF2Bβ and eIF2Bγ+ε. The expression of these subunits decreases despite there being no change in either the levels or the translation of their mRNAs. Instead, these subunits are targeted for degradation by the ubiquitin-proteasome system. The data allow us to propose a model for the formation of stoichiometric eIF2B complexes which can ensure their stoichiometric incorporation into the holocomplex.
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175
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Borggrefe T, Lauth M, Zwijsen A, Huylebroeck D, Oswald F, Giaimo BD. The Notch intracellular domain integrates signals from Wnt, Hedgehog, TGFβ/BMP and hypoxia pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:303-13. [PMID: 26592459 DOI: 10.1016/j.bbamcr.2015.11.020] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 01/12/2023]
Abstract
Notch signaling is a highly conserved signal transduction pathway that regulates stem cell maintenance and differentiation in several organ systems. Upon activation, the Notch receptor is proteolytically processed, its intracellular domain (NICD) translocates into the nucleus and activates expression of target genes. Output, strength and duration of the signal are tightly regulated by post-translational modifications. Here we review the intracellular post-translational regulation of Notch that fine-tunes the outcome of the Notch response. We also describe how crosstalk with other conserved signaling pathways like the Wnt, Hedgehog, hypoxia and TGFβ/BMP pathways can affect Notch signaling output. This regulation can happen by regulation of ligand, receptor or transcription factor expression, regulation of protein stability of intracellular key components, usage of the same cofactors or coregulation of the same key target genes. Since carcinogenesis is often dependent on at least two of these pathways, a better understanding of their molecular crosstalk is pivotal.
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Affiliation(s)
| | - Matthias Lauth
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Germany
| | - An Zwijsen
- VIB Center for the Biology of Disease and Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Franz Oswald
- University Medical Center Ulm, Department of Internal Medicine I, Ulm, Germany
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176
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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177
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Lussier MP, Sanz-Clemente A, Roche KW. Dynamic Regulation of N-Methyl-d-aspartate (NMDA) and α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors by Posttranslational Modifications. J Biol Chem 2015; 290:28596-603. [PMID: 26453298 DOI: 10.1074/jbc.r115.652750] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many molecular mechanisms underlie the changes in synaptic glutamate receptor content that are required by neuronal networks to generate cellular correlates of learning and memory. During the last decade, posttranslational modifications have emerged as critical regulators of synaptic transmission and plasticity. Notably, phosphorylation, ubiquitination, and palmitoylation control the stability, trafficking, and synaptic expression of glutamate receptors in the central nervous system. In the current review, we will summarize some of the progress made by the neuroscience community regarding our understanding of phosphorylation, ubiquitination, and palmitoylation of the NMDA and AMPA subtypes of glutamate receptors.
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Affiliation(s)
- Marc P Lussier
- From the Département de Chimie, Université du Québec à Montréal, Montréal, Québec H3C 3P8, Canada
| | - Antonio Sanz-Clemente
- the Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, and
| | - Katherine W Roche
- the Receptor Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20892
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178
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Boylston JA, Sun J, Chen Y, Gucek M, Sack MN, Murphy E. Characterization of the cardiac succinylome and its role in ischemia-reperfusion injury. J Mol Cell Cardiol 2015; 88:73-81. [PMID: 26388266 DOI: 10.1016/j.yjmcc.2015.09.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022]
Abstract
Succinylation refers to modification of lysine residues with succinyl groups donated by succinyl-CoA. Sirtuin5 (Sirt5) is a mitochondrial NAD(+)-dependent deacylase that catalyzes the removal of succinyl groups from proteins. Sirt5 and protein succinylation are conserved across species, suggesting functional importance of the modification. Sirt5 loss impacts liver metabolism but the role of succinylation in the heart has not been explored. We combined affinity enrichment with proteomics and mass spectrometry to analyze total succinylated lysine content of mitochondria isolated from WT and Sirt5(-/-) mouse hearts. We identified 887 succinylated lysine residues in 184 proteins. 44 peptides (5 proteins) occurred uniquely in WT samples, 289 (46 proteins) in Sirt5(-/-) samples, and 554 (133 proteins) were common to both groups. The 46 unique proteins in Sirt5(-/-) heart participate in metabolic processes such as fatty acid β-oxidation (Eci2) and branched chain amino acid catabolism, and include respiratory chain proteins (Ndufa7, 12, 13, Dhsa). We performed label-free analysis of the peptides common to WT and Sirt5(-/-) hearts. 16 peptides from 9 proteins were significantly increased in Sirt5(-/-) by at least 30%. The adenine nucleotide transporter 1 showed the highest increase in succinylation in Sirt5(-/-) (108.4 fold). The data indicate that succinylation is widespread in the heart and enriched in metabolic pathways. We examined whether the loss of Sirt5 would impact ischemia-reperfusion (I/R) injury and we found an increase in infarct size in Sirt5(-/-) hearts compared to WT littermates (68.5(+)/-1.1% Sirt5(-/-) vs 39.6(+)/(-) 6.8% WT) following 20min of ischemia and 90-min reperfusion. We further demonstrate that I/R injury in Sirt5(-/-) heart is restored to WT levels by pretreatment with dimethyl malonate, a competitive inhibitor of succinate dehydrogenase (SDH), implicating alteration in SDH activity as causative of the injury.
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Affiliation(s)
| | - Junhui Sun
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Yong Chen
- Proteomics Core Facility, NHLBI, NIH, Bethesda, MD, United States
| | - Marjan Gucek
- Proteomics Core Facility, NHLBI, NIH, Bethesda, MD, United States
| | - Michael N Sack
- Center for Molecular Medicine, NHLBI, NIH, Bethesda, MD, United States
| | - Elizabeth Murphy
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States.
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179
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Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P, Förster F, Auble DT, Hopfner KP. Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1. eLife 2015; 4. [PMID: 26258880 PMCID: PMC4565979 DOI: 10.7554/elife.07432] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/08/2015] [Indexed: 12/28/2022] Open
Abstract
Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex. DOI:http://dx.doi.org/10.7554/eLife.07432.001 An organism’s DNA contains thousands of genes, not all of which are active at the same time. Cells use a number of methods to carefully control when particular genes are switched on or off. For example, proteins called transcription factors can activate a gene by binding to particular regions of DNA called promoters. One such transcription factor is called the TATA-binding protein (TBP for short). Mot1 is a remodeling enzyme that can form a “complex” with TBP by binding to it, and in doing so remove TBP from DNA. This silences the genes at those sites. The freed TBP can then bind to other promoters that lack Mot1 and activate the genes found there. In 2011, researchers revealed the structure of the complex formed between TBP and Mot1 after TBP has been detached from DNA. However, the structure of the complex that forms while TBP is still bound to the DNA molecule was not known. Butryn et al. – including several of the researchers involved in the 2011 work – have now described the structure of this complex using X-ray crystallography and electron microscopy. Another protein called negative cofactor 2 is also part of the complex, and helps to stabilize it. Butryn et al. found that Mot1 reduces the strength of the interactions between DNA and both TBP and negative cofactor 2. Binding to TBP and negative cofactor 2 causes the DNA molecule to bend; however, if Mot1 is also in the complex, the DNA becomes less bent. By making these changes, Mot1 is likely to prime TBP to detach from the DNA. Since the current structures do not yet reveal the atomic structure of Mot1’s ATP dependent DNA motor domain, the next challenge is to visualize the entire complex at atomic resolution. DOI:http://dx.doi.org/10.7554/eLife.07432.002
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Affiliation(s)
- Agata Butryn
- Gene Center, Department of Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Jan M Schuller
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, , Germany
| | - Gabriele Stoehr
- Gene Center, Department of Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Petra Runge-Wollmann
- Gene Center, Department of Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, , Germany
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, United States
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig Maximilian University, Munich, Germany
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180
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Chen IT, Hsu PH, Hsu WC, Chen NJ, Tseng PH. Polyubiquitination of Transforming Growth Factor β-activated Kinase 1 (TAK1) at Lysine 562 Residue Regulates TLR4-mediated JNK and p38 MAPK Activation. Sci Rep 2015; 5:12300. [PMID: 26189595 PMCID: PMC4507259 DOI: 10.1038/srep12300] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022] Open
Abstract
Toll-like receptor 4 (TLR4) plays an important role in innate immunity by eliciting inflammation. Upon receptor engagement, transforming growth factor β-activated kinase 1 (TAK1) is an essential mediator that transmits a signal from the receptor to downstream effectors, IκB kinase (IKK) and the mitogen-activated protein kinases (MAPKs), which control the production of inflammatory cytokines. However, the association between phosphorylation and ubiquitination of TAK1 is not yet clear. Here, we examined the crosstalk between phosphorylation and polyubiquitination of TAK1 and further investigated the mechanism of distinct activation of MAPKs and IKK. Inhibition of TAK1 phosphorylation enhanced Lys63-linked polyubiquitination of TAK1. Conversely, ubiquitin modification was counteracted by phospho-mimic TAK1 mutant, T(184,187)D. Moreover, using LC-MS analysis, Lys562 of TAK1 was identified as a novel Lys63-linked ubiquitination site and as the key residue in the feedback regulation. Mutation of Lys562 of TAK1 leads to a decrease in TAK1 phosphorylation and specific inhibition of the MAPK pathway, but has no effect on formation of the TAK1-containing complex. Our findings demonstrate a feedback loop for phosphorylation and ubiquitination of TAK1, indicating a dynamic regulation between TAK1 polyubiquitiantion and phosphorylated activation, and the molecular mechanism by which IKK and MAPKs are differentially activated in the TLR4 pathway.
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Affiliation(s)
- I-Ting Chen
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan (ROC)
| | - Pang-Hung Hsu
- 1] Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan (ROC) [2] Institute of Bioscience and Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung20224, Taiwan (ROC)
| | - Wan-Ching Hsu
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan (ROC)
| | - Nien-Jung Chen
- 1] Institute of Microbiology and Immunology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan (ROC) [2] Infection and Immunity Research Center, National Yang-Ming University, Taipei 11221, Taiwan (ROC)
| | - Ping-Hui Tseng
- 1] Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan (ROC) [2] Infection and Immunity Research Center, National Yang-Ming University, Taipei 11221, Taiwan (ROC)
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181
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Chesarino NM, McMichael TM, Yount JS. Regulation of the trafficking and antiviral activity of IFITM3 by post-translational modifications. Future Microbiol 2015; 9:1151-63. [PMID: 25405885 DOI: 10.2217/fmb.14.65] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IFITM3 restricts cellular infection by multiple important viral pathogens, and is particularly critical for the innate immune response against influenza virus. Expression of IFITM3 expands acidic endolysosomal compartments and prevents fusion of endocytosed viruses, leading to their degradation. This small, 133 amino acid, antiviral protein is controlled by at least four distinct post-translational modifications. Positive regulation of IFITM3 antiviral activity is provided by S-palmitoylation, while negative regulatory mechanisms include lysine ubiquitination, lysine methylation and tyrosine phosphorylation. Herein, we describe specific insights into IFITM3 trafficking and activity that were provided by studies of IFITM3 post-translational modifications, and discuss evidence suggesting that IFITM3 adopts multiple membrane topologies involving at least one intramembrane domain in its antivirally active conformation.
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Affiliation(s)
- Nicholas M Chesarino
- Department of Microbial Infection & Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210, USA
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182
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Small GTP-binding protein Ran is regulated by posttranslational lysine acetylation. Proc Natl Acad Sci U S A 2015; 112:E3679-88. [PMID: 26124124 DOI: 10.1073/pnas.1505995112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ran is a small GTP-binding protein of the Ras superfamily regulating fundamental cellular processes: nucleo-cytoplasmic transport, nuclear envelope formation and mitotic spindle assembly. An intracellular Ran•GTP/Ran•GDP gradient created by the distinct subcellular localization of its regulators RCC1 and RanGAP mediates many of its cellular effects. Recent proteomic screens identified five Ran lysine acetylation sites in human and eleven sites in mouse/rat tissues. Some of these sites are located in functionally highly important regions such as switch I and switch II. Here, we show that lysine acetylation interferes with essential aspects of Ran function: nucleotide exchange and hydrolysis, subcellular Ran localization, GTP hydrolysis, and the interaction with import and export receptors. Deacetylation activity of certain sirtuins was detected for two Ran acetylation sites in vitro. Moreover, Ran was acetylated by CBP/p300 and Tip60 in vitro and on transferase overexpression in vivo. Overall, this study addresses many important challenges of the acetylome field, which will be discussed.
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183
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Cesaro L, Pinna LA, Salvi M. A Comparative Analysis and Review of lysyl Residues Affected by Posttranslational Modifications. Curr Genomics 2015; 16:128-38. [PMID: 26085811 PMCID: PMC4467303 DOI: 10.2174/1389202916666150216221038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 11/22/2022] Open
Abstract
Post-translational modification is the most common mechanism of regulating protein function. If
phosphorylation is considered a key event in many signal transduction pathways, other modifications must be
considered as well. In particular the side chain of lysine residues is a target of different modifications; notably
acetylation, methylation, ubiquitylation, sumoylation, neddylation, etc. Mass spectrometry approaches combining
highly sensitive instruments and specific enrichment strategies have enabled the identification of modified
sites on a large scale. Here we make a comparative analysis of the most representative lysine modifications
(ubiquitylation, acetylation, sumoylation and methylation) identified in the human proteome. This review focuses on
conserved amino acids, secondary structures preference, subcellular localization of modified proteins, and signaling pathways
where these modifications are implicated. We discuss specific differences and similarities between these modifications,
characteristics of the crosstalk among lysine post translational modifications, and single nucleotide polymorphisms
that could influence lysine post-translational modifications in humans.
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Affiliation(s)
- Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy ; Institute of Neurosciences, V.le G. Colombo 3, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
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184
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Prabhu L, Hartley AV, Martin M, Warsame F, Sun E, Lu T. Role of post-translational modification of the Y box binding protein 1 in human cancers. Genes Dis 2015; 2:240-246. [PMID: 30258867 PMCID: PMC6150071 DOI: 10.1016/j.gendis.2015.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/12/2015] [Indexed: 12/21/2022] Open
Abstract
Y box binding protein-1 (YBX1) belongs to a DNA- and RNA-binding family of transcription factors, containing the highly conserved cold shock domain (CSD). YBX1 is involved in a number of cellular functions including transcription, translation, DNA damage repair etc., and it is upregulated during times of environmental stress. YBX1 is localized in both the cytoplasm and the nucleus. There, its nuclear translocation is observed in a number of cancers and is associated with poor prognosis and disease progression. Additionally, YBX1 expression is upregulated in a variety of cancers, pointing towards its role as a potential oncogene. Under certain circumstances, YBX1 also promotes the expression of multidrug resistance 1 (MDR1) gene, which is involved in the development of drug resistance. Thus, it is critical to understand the mechanism of YBX1 regulation and its downstream effects on promoting cancer development. A number of recent studies have highlighted the mechanisms of YBX1 regulation. Mass spectrometric analyses have reported several post-translational modifications that possibly play an important role in modulating YBX1 function. Phosphorylation is the most widely occurring post-translational modification in YBX1. In vivo analyses of sites like S102 and more recently, S165 illustrate the relationship of post-translational regulation of YBX1 in promoting cell proliferation and tumor growth. This review provides a comprehensive and up-to-date account of post-translational modifications identified in YBX1. This knowledge is a key in allowing us to better understand the mechanism of YBX1 regulation, which will aid in development of novel therapeutic strategies to target YBX1 in many types of cancer in the future.
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Affiliation(s)
- Lakshmi Prabhu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Antja-Voy Hartley
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Matthew Martin
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Fadumo Warsame
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Emily Sun
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Tao Lu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.,Department of Medical and Molecular Genetics, 975 West Walnut Street, Medical Research and Library Building, Indianapolis, IN 46202, USA
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185
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Metformin increases degradation of phospholamban via autophagy in cardiomyocytes. Proc Natl Acad Sci U S A 2015; 112:7165-70. [PMID: 26040000 DOI: 10.1073/pnas.1508815112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phospholamban (PLN) is an effective inhibitor of the sarco(endo)plasmic reticulum Ca(2+) ATPase (SERCA). Here, we examined PLN stability and degradation in primary cultured mouse neonatal cardiomyocytes (CMNCs) and mouse hearts using immunoblotting, molecular imaging, and [(35)S]methionine pulse-chase experiments, together with lysosome (chloroquine and bafilomycin A1) and autophagic (3-methyladenine and Atg5 siRNA) antagonists. Inhibiting lysosomal and autophagic activities promoted endogenous PLN accumulation, whereas accelerating autophagy with metformin enhanced PLN degradation in CMNCs. This reduction in PLN levels was functionally correlated with an increased rate of SERCA2a activity, accounting for an inotropic effect of metformin. Metabolic labeling reaffirmed that metformin promoted wild-type and R9C PLN degradation. Immunofluorescence showed that PLN and the autophagy marker, microtubule light chain 3, became increasingly colocalized in response to chloroquine and bafilomycin treatments. Mechanistically, pentameric PLN was polyubiquitinylated at the K3 residue and this modification was required for p62-mediated selective autophagy trafficking. Consistently, attenuated autophagic flux in HECT domain and ankyrin repeat-containing E3 ubiquitin protein ligase 1-null mouse hearts was associated with increased PLN levels determined by immunoblots and immunofluorescence. Our study identifies a biological mechanism that traffics PLN to the lysosomes for degradation in mouse hearts.
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186
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Thomas SN, Zhang H, Cotter RJ. Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues. Clin Proteomics 2015; 12:14. [PMID: 26019700 PMCID: PMC4445283 DOI: 10.1186/s12014-015-9086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/11/2015] [Indexed: 01/12/2023] Open
Abstract
Background Post-translational modification by ubiquitin is a fundamental regulatory mechanism that is implicated in many cellular processes including the cell cycle, apoptosis, cell adhesion, angiogenesis, and tumor growth. The low stoichiometry of ubiquitylation presents an analytical challenge for the detection of endogenously modified proteins in the absence of enrichment strategies. The recent availability of antibodies recognizing peptides with Lys residues containing a di-Gly ubiquitin remnant (K-ε-GG) has greatly improved the ability to enrich and identify ubiquitylation sites from complex protein lysates via mass spectrometry. To date, there have not been any published studies that quantitatively assess the changes in endogenous ubiquitin-modification protein stoichiometry status at the proteome level from different tissues. Results In this study, we applied an integrated quantitative mass spectrometry based approach using isobaric tags for relative and absolute quantitation (iTRAQ) to interrogate the ubiquitin-modified proteome and the cognate global proteome levels from luminal and basal breast cancer patient-derived xenograft tissues. Among the proteins with quantitative global and ubiquitylation data, 91 % had unchanged levels of total protein relative abundance, and less than 5 % of these proteins had up- or down-regulated ubiquitylation levels. Of particular note, greater than half of the proteins with observed changes in their total protein level also had up- or down-regulated changes in their ubiquitylation level. Conclusions This is the first report of the application of iTRAQ-based quantification to the integrated analysis of the ubiquitylated and global proteomes at the tissue level. Our results underscore the importance of conducting integrated analyses of the global and ubiquitylated proteomes toward elucidating the specific functional significance of ubiquitylation. Electronic supplementary material The online version of this article (doi:10.1186/s12014-015-9086-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefani N Thomas
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, 1550 Orleans Street CRBII Room 3M06, Baltimore, MD 21231 USA
| | - Hui Zhang
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, 1550 Orleans Street CRBII Room 3M06, Baltimore, MD 21231 USA
| | - Robert J Cotter
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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187
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Abstract
Nuclear, casein kinase and cyclin-dependent kinase substrate (NUCKS), a protein similar to the HMG (high-mobility group) protein family, is one of the most modified proteins in the mammalian proteome. Although very little is known about the biological roles of NUCKS, emerging clinical evidence suggests that this protein can be a biomarker and therapeutic target in various human ailments, including several types of cancer. An inverse correlation between NUCKS protein levels and body mass index in humans has also been observed. Depletion of NUCKS in mice has been reported to lead to obesity and impaired glucose homoeostasis. Genome-wide genomic and proteomic approaches have revealed that NUCKS is a chromatin regulator that affects transcription. The time is now ripe for further understanding of the role of this novel biomarker of cancer and the metabolic syndrome, and how its sundry modifications can affect its function. Such studies could reveal how NUCKS could be a link between physiological cues and human ailments.
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188
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Bavelloni A, Piazzi M, Raffini M, Faenza I, Blalock WL. Prohibitin 2: At a communications crossroads. IUBMB Life 2015; 67:239-54. [PMID: 25904163 DOI: 10.1002/iub.1366] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023]
Abstract
Prohibitins (PHBs) are a highly conserved class of proteins first discovered as inhibitors of cellular proliferation. Since then PHBs have been found to have a significant role in transcription, nuclear signaling, mitochondrial structural integrity, cell division, and cellular membrane metabolism, placing these proteins among the key regulators of pathologies such as cancer, neuromuscular degeneration, and other metabolic diseases. The human genome encodes two PHB proteins, prohibitin 1 (PHB1) and prohibitin 2 (PHB2), which function not only as a heterodimeric complex, but also independently. While many previous reviews have focused on the better characterized prohibitin, PHB1, this review focuses on PHB2 and new data concerning its cellular functions both in complex with PHB1 and independent of PHB1.
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Affiliation(s)
- Alberto Bavelloni
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Manuela Piazzi
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - Mirco Raffini
- Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Irene Faenza
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - William L Blalock
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
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189
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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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190
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Hölper S, Nolte H, Bober E, Braun T, Krüger M. Dissection of metabolic pathways in the Db/Db mouse model by integrative proteome and acetylome analysis. MOLECULAR BIOSYSTEMS 2015; 11:908-22. [DOI: 10.1039/c4mb00490f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An in vivo SILAC-based quantitative proteomics approach to analyse protein abundances and acetylation levels under diabetic conditions.
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Affiliation(s)
- Soraya Hölper
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Hendrik Nolte
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Eva Bober
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
| | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research
- 61231 Bad Nauheim
- Germany
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191
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Hoffmeister M, Prelle C, Küchler P, Kovacevic I, Moser M, Müller-Esterl W, Oess S. The ubiquitin E3 ligase NOSIP modulates protein phosphatase 2A activity in craniofacial development. PLoS One 2014; 9:e116150. [PMID: 25546391 PMCID: PMC4278855 DOI: 10.1371/journal.pone.0116150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/05/2014] [Indexed: 02/05/2023] Open
Abstract
Holoprosencephaly is a common developmental disorder in humans characterised by incomplete brain hemisphere separation and midface anomalies. The etiology of holoprosencephaly is heterogeneous with environmental and genetic causes, but for a majority of holoprosencephaly cases the genes associated with the pathogenesis could not be identified so far. Here we report the generation of knockout mice for the ubiquitin E3 ligase NOSIP. The loss of NOSIP in mice causes holoprosencephaly and facial anomalies including cleft lip/palate, cyclopia and facial midline clefting. By a mass spectrometry based protein interaction screen we identified NOSIP as a novel interaction partner of protein phosphatase PP2A. NOSIP mediates the monoubiquitination of the PP2A catalytic subunit and the loss of NOSIP results in an increase in PP2A activity in craniofacial tissue in NOSIP knockout mice. We conclude, that NOSIP is a critical modulator of brain and craniofacial development in mice and a candidate gene for holoprosencephaly in humans.
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Affiliation(s)
- Meike Hoffmeister
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
| | - Carola Prelle
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
| | - Philipp Küchler
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
| | - Igor Kovacevic
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
| | - Markus Moser
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Werner Müller-Esterl
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
| | - Stefanie Oess
- Institute for Biochemistry II, Goethe University Frankfurt Medical School, Frankfurt/Main, Germany
- * E-mail:
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192
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Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem 2014; 290:3308-32. [PMID: 25451919 DOI: 10.1074/jbc.m114.611525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CYP3A4 is an abundant and catalytically dominant human liver endoplasmic reticulum-anchored cytochrome P450 enzyme engaged in the biotransformation of endo- and xenobiotics, including >50% of clinically relevant drugs. Alterations of CYP3A4 protein turnover can influence clinically relevant drug metabolism and bioavailability and drug-drug interactions. This CYP3A4 turnover involves endoplasmic reticulum-associated degradation via the ubiquitin (Ub)-dependent 26 S proteasomal system that relies on two highly complementary E2 Ub-conjugating-E3 Ub-ligase (UBC7-gp78 and UbcH5a-C terminus of Hsc70-interacting protein (CHIP)-Hsc70-Hsp40) complexes, as well as protein kinases (PK) A and C. We have documented that CYP3A4 Ser/Thr phosphorylation (Ser(P)/Thr(P)) by PKA and/or PKC accelerates/enhances its Lys ubiquitination by either of these E2-E3 systems. Intriguingly, CYP3A4 Ser(P)/Thr(P) and ubiquitinated Lys residues reside within the cytosol-accessible surface loop and/or conformationally assembled acidic Asp/Glu clusters, leading us to propose that such post-translational Ser/Thr protein phosphorylation primes CYP3A4 for ubiquitination. Herein, this possibility was examined through various complementary approaches, including site-directed mutagenesis, chemical cross-linking, peptide mapping, and LC-MS/MS analyses. Our findings reveal that such CYP3A4 Asp/Glu/Ser(P)/Thr(P) surface clusters are indeed important for its intermolecular electrostatic interactions with each of these E2-E3 subcomponents. By imparting additional negative charge to these Asp/Glu clusters, such Ser/Thr phosphorylation would generate P450 phosphodegrons for molecular recognition by the E2-E3 complexes, thereby controlling the timing of CYP3A4 ubiquitination and endoplasmic reticulum-associated degradation. Although the importance of phosphodegrons in the CHIP targeting of its substrates is known, to our knowledge this is the first example of phosphodegron involvement in gp78-substrate recruitment, an important step in CYP3A4 proteasomal degradation.
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Affiliation(s)
- YongQiang Wang
- From the Departments of Cellular and Molecular Pharmacology
| | - Sung-Mi Kim
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Yi Liu
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Maria Almira Correia
- From the Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco, San Francisco, California 94158-2517
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193
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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194
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Watts FZ, Baldock R, Jongjitwimol J, Morley SJ. Weighing up the possibilities: Controlling translation by ubiquitylation and sumoylation. ACTA ACUST UNITED AC 2014; 2:e959366. [PMID: 26779408 DOI: 10.4161/2169074x.2014.959366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/01/2014] [Accepted: 05/12/2014] [Indexed: 12/15/2022]
Abstract
Regulation of protein synthesis is of fundamental importance to cells. It has a critical role in the control of gene expression, and consequently cell growth and proliferation. The importance of this control is supported by the fact that protein synthesis is frequently upregulated in tumor cells. The major point at which regulation occurs is the initiation stage. Initiation of translation involves the interaction of several proteins to form the eIF4F complex, the recognition of the mRNA by this complex, and the subsequent recruitment of the 40S ribosomal subunit to the mRNA. This results in the formation of the 48S complex that then scans the mRNA for the start codon, engages the methionyl-tRNA and eventually forms the mature 80S ribosome which is elongation-competent. Formation of the 48S complex is regulated by the availability of individual initiation factors and through specific protein-protein interactions. Both of these events can be regulated by post-translational modification by ubiquitin or Ubls (ubiquitin-like modifiers) such as SUMO or ISG15. We provide here a summary of translation initiation factors that are modified by ubiquitin or Ubls and, where they have been studied in detail, describe the role of these modifications and their effects on regulating protein synthesis.
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Affiliation(s)
- Felicity Z Watts
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Robert Baldock
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Jirapas Jongjitwimol
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Simon J Morley
- Department of Biochemistry and Biomedical Science; School of Life Sciences; University of Sussex ; Brighton, UK
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195
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Chen Z, Zhou Y, Zhang Z, Song J. Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. Brief Bioinform 2014; 16:640-57. [DOI: 10.1093/bib/bbu031] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/18/2014] [Indexed: 01/25/2023] Open
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196
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Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. Proc Natl Acad Sci U S A 2014; 111:E3880-9. [PMID: 25187565 DOI: 10.1073/pnas.1414748111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Many metabolic pathways are critically regulated during development and aging but little is known about the molecular mechanisms underlying this regulation. One key metabolic cascade in eukaryotes is the mevalonate pathway. It catalyzes the synthesis of sterol and nonsterol isoprenoids, such as cholesterol and ubiquinone, as well as other metabolites. In humans, an age-dependent decrease in ubiquinone levels and changes in cholesterol homeostasis suggest that mevalonate pathway activity changes with age. However, our knowledge of the mechanistic basis of these changes remains rudimentary. We have identified a regulatory circuit controlling the sumoylation state of Caenorhabditis elegans HMG-CoA synthase (HMGS-1). This protein is the ortholog of human HMGCS1 enzyme, which mediates the first committed step of the mevalonate pathway. In vivo, HMGS-1 undergoes an age-dependent sumoylation that is balanced by the activity of ULP-4 small ubiquitin-like modifier protease. ULP-4 exhibits an age-regulated expression pattern and a dynamic cytoplasm-to-mitochondria translocation. Thus, spatiotemporal ULP-4 activity controls the HMGS-1 sumoylation state in a mechanism that orchestrates mevalonate pathway activity with the age of the organism. To expand the HMGS-1 regulatory network, we combined proteomic analyses with knockout studies and found that the HMGS-1 level is also governed by the ubiquitin-proteasome pathway. We propose that these conserved molecular circuits have evolved to govern the level of mevalonate pathway flux during aging, a flux whose dysregulation is associated with numerous age-dependent cardiovascular and cancer pathologies.
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197
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Jang HM, Erf GF, Rowland KC, Kong BW. Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model. BMC Genomics 2014; 15:707. [PMID: 25151476 PMCID: PMC4152579 DOI: 10.1186/1471-2164-15-707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Smyth line (SL) chicken is the only animal model for autoimmune vitiligo that spontaneously displays all clinical and biological manifestations of the human disorder. To understand the genetic components underlying the susceptibility to develop SL vitiligo (SLV), whole genome resequencing analysis was performed in SLV chickens compared with non-vitiliginous parental Brown line (BL) chickens, which maintain a very low incidence rate of vitiligo. RESULTS Illumina sequencing technology and reference based assembly on Red Jungle Fowl genome sequences were used. Results of genome resequencing of pooled DNA of each 10 BL and SL chickens reached 5.1x and 7.0x coverage, respectively. The total number of SNPs was 4.8 and 5.5 million in BL and SL genome, respectively. Through a series of filtering processes, a total of ~1 million unique SNPs were found in the SL alone. Eventually of the 156 reliable marker SNPs, which can induce non-synonymous-, frameshift-, nonsense-, and no-start mutations in amino acid sequences in proteins, 139 genes were chosen for further analysis. Of these, 14 randomly chosen SNPs were examined for SNP verification by PCR and Sanger sequencing to detect SNP positions in 20 BL and 70 SL chickens. The results of the analysis of the 14 SNPs clearly showed differential frequencies of nucleotide bases in the SNP positions between BL and SL chickens. Bioinformatic analysis showed that the 156 most reliable marker SNPs included genes involved in dermatological diseases/conditions such as ADAMTS13, ASPM, ATP6V0A2, BRCA2, COL12A1, GRM5, LRP2, OBSCN, PLAU, RNF168, STAB2, and XIRP1. Intermolecular gene network analysis revealed that candidate genes identified in SLV play a role in networks centered on protein kinases (MAPK, ERK1/2, PKC, PRKDC), phosphatase (PPP1CA), ubiquitinylation (UBC) and amyloid production (APP). CONCLUSIONS Various potential genetic markers showing amino acid changes and potential roles in vitiligo development were identified in the SLV chicken through genome resequencing. The genetic markers and bioinformatic interpretations of amino acid mutations found in SLV chickens may provide insight into the genetic component responsible for the onset and the progression of autoimmune vitiligo and serve as valuable markers to develop diagnostic tools to detect vitiligo susceptibility.
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Affiliation(s)
- Hyeon-Min Jang
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Gisela F Erf
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Kaylee C Rowland
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Byung-Whi Kong
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
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198
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Zong N, Ping P, Lau E, Choi HJH, Ng DCM, Meyer D, Fang C, Li H, Wang D, Zelaya IM, Yates JR, Lam MPY. Lysine ubiquitination and acetylation of human cardiac 20S proteasomes. Proteomics Clin Appl 2014; 8:590-594. [PMID: 24957502 PMCID: PMC5094860 DOI: 10.1002/prca.201400029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/12/2014] [Accepted: 06/10/2014] [Indexed: 11/06/2022]
Abstract
PURPOSE Altered proteasome functions are associated with multiple cardiomyopathies. While the proteasome targets polyubiquitinated proteins for destruction, it itself is modifiable by ubiquitination. We aim to identify the exact ubiquitination sites on cardiac proteasomes and examine whether they are also subject to acetylations. EXPERIMENTAL DESIGN Assembled cardiac 20S proteasome complexes were purified from five human hearts with ischemic cardiomyopathy, then analyzed by high-resolution MS to identify ubiquitination and acetylation sites. We developed a library search strategy that may be used to complement database search in identifying PTM in different samples. RESULTS We identified 63 ubiquitinated lysines from intact human cardiac 20S proteasomes. In parallel, 65 acetylated residues were also discovered, 39 of which shared with ubiquitination sites. CONCLUSION AND CLINICAL RELEVANCE This is the most comprehensive characterization of cardiac proteasome ubiquitination to date. There are significant overlaps between the discovered ubiquitination and acetylation sites, permitting potential crosstalk in regulating proteasome functions. The information presented here will aid future therapeutic strategies aimed at regulating the functions of cardiac proteasomes.
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Affiliation(s)
- Nobel Zong
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Peipei Ping
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Edward Lau
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Howard JH Choi
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Dominic CM Ng
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Meyer
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Caiyun Fang
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Haomin Li
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ding Wang
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ivette M Zelaya
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Maggie PY Lam
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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199
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Xia P, Wang S, Huang G, Du Y, Zhu P, Li M, Fan Z. RNF2 is recruited by WASH to ubiquitinate AMBRA1 leading to downregulation of autophagy. Cell Res 2014; 24:943-58. [PMID: 24980959 PMCID: PMC4123297 DOI: 10.1038/cr.2014.85] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/01/2014] [Accepted: 05/26/2014] [Indexed: 12/17/2022] Open
Abstract
WASH (Wiskott-Aldrich syndrome protein (WASP) and SCAR homolog) was identified to function in endosomal sorting via Arp2/3 activation. We previously demonstrated that WASH is a new interactor of BECN1 and present in the BECN1-PIK3C3 complex with AMBRA1. The AMBRA1-DDB1-CUL4A complex is an E3 ligase for K63-linked ubiquitination of BECN1, which is required for starvation-induced autophagy. WASH suppresses autophagy by inhibition of BECN1 ubiquitination. However, how AMBRA1 is regulated during autophagy remains elusive. Here, we found that RNF2 associates with AMBRA1 to act as an E3 ligase to ubiquitinate AMBRA1 via K48 linkage. RNF2 mediates ubiquitination of AMBRA1 at lysine 45. Notably, RNF2 deficiency enhances autophagy induction. Upon autophagy induction, RNF2 potentiates AMBRA1 degradation with the help of WASH. WASH deficiency impairs the association of RNF2 with AMBRA1 to impede AMBRA1 degradation. Our findings reveal another novel layer of regulation of autophagy through WASH recruitment of RNF2 for AMBRA1 degradation leading to downregulation of autophagy.
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Affiliation(s)
- Pengyan Xia
- 1] Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanling Huang
- 1] Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Li
- 1] Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Iesmantavicius V, Weinert BT, Choudhary C. Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol Cell Proteomics 2014; 13:1979-92. [PMID: 24961812 PMCID: PMC4125731 DOI: 10.1074/mcp.o113.035683] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The target of rapamycin (TOR) kinase senses the availability of nutrients and coordinates cellular growth and proliferation with nutrient abundance. Inhibition of TOR mimics nutrient starvation and leads to the reorganization of many cellular processes, including autophagy, protein translation, and vesicle trafficking. TOR regulates cellular physiology by modulating phosphorylation and ubiquitylation signaling networks; however, the global scope of such regulation is not fully known. Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified. The phosphoproteome was extensively modulated by rapamycin treatment, with more than 900 up-regulated sites one hour after rapamycin treatment. Dynamically regulated phosphoproteins were involved in diverse cellular processes, prominently including transcription, membrane organization, vesicle-mediated transport, and autophagy. Several hundred ubiquitylation sites were increased after rapamycin treatment, and about half as many decreased in abundance. We found that proteome, phosphorylation, and ubiquitylation changes converged on the Rsp5-ubiquitin ligase, Rsp5 adaptor proteins, and Rsp5 targets. Putative Rsp5 targets were biased for increased ubiquitylation, suggesting activation of Rsp5 by rapamycin. Rsp5 adaptor proteins, which recruit target proteins for Rsp5-dependent ubiquitylation, were biased for increased phosphorylation. Furthermore, we found that permeases and transporters, which are often ubiquitylated by Rsp5, were biased for reduced ubiquitylation and reduced protein abundance. The convergence of multiple proteome-level changes on the Rsp5 system indicates a key role of this pathway in the response to rapamycin treatment. Collectively, these data reveal new insights into the global proteome dynamics in response to rapamycin treatment and provide a first detailed view of the co-regulation of phosphorylation- and ubiquitylation-dependent signaling networks by this compound.
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Affiliation(s)
- Vytautas Iesmantavicius
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Brian T Weinert
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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