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PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses. PLoS One 2017; 12:e0180478. [PMID: 28678890 PMCID: PMC5498030 DOI: 10.1371/journal.pone.0180478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic protein phosphatase 4 (PP4) is a PP2A-type protein phosphatase that is part of a conserved complex with regulatory factors PSY2 and PP4R2. Various lines of Arabidopsis thaliana with mutated PP4 subunit genes were constructed to study the so far completely unknown functions of PP4 in plants. Mutants with knocked out putative functional homolog of the PSY2 LIKE (PSY2L) gene were dwarf and bushy, while plants with knocked out PP4R2 LIKE (PP4R2L) looked very similar to WT. The psy2l seedlings had short roots with disorganized morphology and impaired meristem. Seedling growth was sensitive to the genotoxin cisplatin. Global transcript analysis (RNA-seq) of seedlings and rosette leaves revealed several groups of genes, shared between both types of tissues, strongly influenced by knocked out PSY2L. Receptor kinases, CRINKLY3 and WAG1, important for growth and development, were down-regulated 3–7 times. EUKARYOTIC ELONGATION FACTOR5A1 was down-regulated 4–6 fold. Analysis of hormone sensitive genes indicated that abscisic acid levels were high, while auxin, cytokinin and gibberellic acid levels were low in psy2l. Expression of specific transcription factors involved in regulation of anthocyanin synthesis were strongly elevated, e.g. the master regulator PAP1, and intriguingly TT8, which is otherwise mainly expressed in seeds. The psy2l mutants accumulated anthocyanins under conditions where WT did not, pointing to PSY2L as a possible upstream negative regulator of PAP1 and TT8. Expression of the sugar-phosphate transporter GPT2, important for cellular sugar and phosphate homeostasis, was enhanced 7–8 times. Several DNA damage response genes, including the cell cycle inhibitor gene WEE1, were up-regulated in psy2l. The activation of DNA repair signaling genes, in combination with phenotypic traits showing aberrant root meristem and sensitivity to the genotoxic cisplatin, substantiate the involvement of Arabidopsis PSY2L in maintenance of genome integrity.
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Eleftheriadou O, Boguslavskyi A, Longman MR, Cowan J, Francois A, Heads RJ, Wadzinski BE, Ryan A, Shattock MJ, Snabaitis AK. Expression and regulation of type 2A protein phosphatases and alpha4 signalling in cardiac health and hypertrophy. Basic Res Cardiol 2017; 112:37. [PMID: 28526910 PMCID: PMC5438423 DOI: 10.1007/s00395-017-0625-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/02/2017] [Indexed: 01/25/2023]
Abstract
Cardiac physiology and hypertrophy are regulated by the phosphorylation status of many proteins, which is partly controlled by a poorly defined type 2A protein phosphatase-alpha4 intracellular signalling axis. Quantitative PCR analysis revealed that mRNA levels of the type 2A catalytic subunits were differentially expressed in H9c2 cardiomyocytes (PP2ACβ > PP2ACα > PP4C > PP6C), NRVM (PP2ACβ > PP2ACα = PP4C = PP6C), and adult rat ventricular myocytes (PP2ACα > PP2ACβ > PP6C > PP4C). Western analysis confirmed that all type 2A catalytic subunits were expressed in H9c2 cardiomyocytes; however, PP4C protein was absent in adult myocytes and only detectable following 26S proteasome inhibition. Short-term knockdown of alpha4 protein expression attenuated expression of all type 2A catalytic subunits. Pressure overload-induced left ventricular (LV) hypertrophy was associated with an increase in both PP2AC and alpha4 protein expression. Although PP6C expression was unchanged, expression of PP6C regulatory subunits (1) Sit4-associated protein 1 (SAP1) and (2) ankyrin repeat domain (ANKRD) 28 and 44 proteins was elevated, whereas SAP2 expression was reduced in hypertrophied LV tissue. Co-immunoprecipitation studies demonstrated that the interaction between alpha4 and PP2AC or PP6C subunits was either unchanged or reduced in hypertrophied LV tissue, respectively. Phosphorylation status of phospholemman (Ser63 and Ser68) was significantly increased by knockdown of PP2ACα, PP2ACβ, or PP4C protein expression. DNA damage assessed by histone H2A.X phosphorylation (γH2A.X) in hypertrophied tissue remained unchanged. However, exposure of cardiomyocytes to H2O2 increased levels of γH2A.X which was unaffected by knockdown of PP6C expression, but was abolished by the short-term knockdown of alpha4 expression. This study illustrates the significance and altered activity of the type 2A protein phosphatase-alpha4 complex in healthy and hypertrophied myocardium.
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Affiliation(s)
- Olga Eleftheriadou
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science Engineering and Computing, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE, UK
| | - Andrii Boguslavskyi
- Cardiovascular Division, King's College London British Heart Foundation Centre, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Michael R Longman
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science Engineering and Computing, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE, UK
| | - Jonathan Cowan
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science Engineering and Computing, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE, UK
| | - Asvi Francois
- Cardiovascular Division, King's College London British Heart Foundation Centre, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Richard J Heads
- Cardiovascular Division, King's College London British Heart Foundation Centre, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Brian E Wadzinski
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Ali Ryan
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science Engineering and Computing, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE, UK
| | - Michael J Shattock
- Cardiovascular Division, King's College London British Heart Foundation Centre, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Andrew K Snabaitis
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science Engineering and Computing, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE, UK.
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53
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Cellular Dynamics Controlled by Phosphatases. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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54
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Winfree LM, Speese SD, Logan MA. Protein phosphatase 4 coordinates glial membrane recruitment and phagocytic clearance of degenerating axons in Drosophila. Cell Death Dis 2017; 8:e2623. [PMID: 28230857 PMCID: PMC5386485 DOI: 10.1038/cddis.2017.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/15/2022]
Abstract
Neuronal damage induced by injury, stroke, or neurodegenerative disease elicits swift immune responses from glial cells, including altered gene expression, directed migration to injury sites, and glial clearance of damaged neurons through phagocytic engulfment. Collectively, these responses hinder further cellular damage, but the mechanisms that underlie these important protective glial reactions are still unclear. Here, we show that the evolutionarily conserved trimeric protein phosphatase 4 (PP4) serine/threonine phosphatase complex is a novel set of factors required for proper glial responses to nerve injury in the adult Drosophila brain. Glial-specific knockdown of PP4 results in reduced recruitment of glia to severed axons and delayed glial clearance of degenerating axonal debris. We show that PP4 functions downstream of the the glial engulfment receptor Draper to drive glial morphogenesis through the guanine nucleotide exchange factor SOS and the Rho GTPase Rac1, revealing that PP4 molecularly couples Draper to Rac1-mediated cytoskeletal remodeling to ensure glial infiltration of injury sites and timely removal of damaged neurons from the CNS.
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Affiliation(s)
- Lilly M Winfree
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Sean D Speese
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mary A Logan
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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Kim BR, Kwon Y, Rho SB. BMI-1 interacts with sMEK1 and inactivates sMEK1-induced apoptotic cell death. Oncol Rep 2016; 37:579-586. [PMID: 27878292 DOI: 10.3892/or.2016.5262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/05/2022] Open
Abstract
The B lymphoma Mo-MLV insertion region 1 homolog (BMI-1) protein is activated in various types of tumors and associated with cancer development and tumor progression. However, the working role of BMI-1 in cellular signaling is not understood completely. In this study, we revealed one possible biologic mechanism of BMI-1 in cancer progression in vitro using a human ovarian tumor cell system. Suppressor of MEK1 (sMEK1), a pivotal regulator involved in the cellular biological response mechanism, was identified as a BMI-1-binding protein. Ectopic expression of BMI-1 activated cell growth by reducing sMEK1-stimulated apoptotic cell death and suppressing p21, p27 and p53 expression, while enhancing cyclin D1, CDK4 and Bcl-2 expression. The effect of BMI-1 on cell cycle and apoptotic regulatory proteins was also confirmed via silencing of BMI-1 expression. Subsequently, the promoter activities of p21 and p53 were inactivated significantly. However, BMI-1 overexpression noticeably increased Bcl-2 and NF-κB activities. In addition, BMI-1 activated the PI3K/mTOR/4E-BP1 signaling pathways, and sMEK1 significantly inhibited BMI-1-stimulated oncogenesis. These insights provide evidence that BMI-1 activates cell growth and suppresses apoptosis. Collectively, our data indicate that BMI-1 plays a pivotal role in the progression of ovarian cancer, thus representing a novel target for antitumor therapy of ovarian cancer.
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Affiliation(s)
- Boh-Ram Kim
- Research Institute, National Cancer Center, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Global Top 5 Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Seung Bae Rho
- Research Institute, National Cancer Center, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
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56
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Kim BR, Seo SH, Park MS, Lee SH, Kwon Y, Rho SB. sMEK1 inhibits endothelial cell proliferation by attenuating VEGFR-2-dependent-Akt/eNOS/HIF-1α signaling pathways. Oncotarget 2016; 6:31830-43. [PMID: 26378810 PMCID: PMC4741643 DOI: 10.18632/oncotarget.5570] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 08/15/2015] [Indexed: 12/31/2022] Open
Abstract
The suppressor of MEK null (sMEK1) protein possesses pro-apoptotic activities. In the current study, we reveal that sMEK1 functions as a novel anti-angiogenic factor by suppressing vascular endothelial growth factor (VEGF)-induced cell proliferation, migration, and capillary-like tubular structure in vitro. In addition, sMEK1 inhibited the phosphorylation of the signaling components up- and downstream of Akt, including phospholipase Cγ1 (PLC-γ1), 3-phosphoinositide-dependent protein kinase 1 (PDK1), endothelial nitric oxide synthetase (eNOS), and hypoxia-inducible factor 1 (HIF-1α) during ovarian tumor progression via binding with vascular endothelial growth factor receptor 2 (VEGFR-2). Furthermore, sMEK1 decreased tumor vascularity and inhibited tumor growth in a xenograft human ovarian tumor model. These results supply convincing evidence that sMEK1 controls endothelial cell function and subsequent angiogenesis by suppressing VEGFR-2-mediated PI3K/Akt/eNOS signaling pathway. Taken together, our results clearly suggest that sMEK1 might be a novel anti-angiogenic and anti-tumor agent for use in ovarian tumor.
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Affiliation(s)
- Boh-Ram Kim
- Research Institute, National Cancer Center, Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea.,College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Global Top 5 Program, Ewha Womans University, Seoul, Republic of Korea
| | - Seung Hee Seo
- Research Institute, National Cancer Center, Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea
| | - Mi Sun Park
- Research Institute, National Cancer Center, Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea
| | - Seung-Hoon Lee
- Department of Life Science, Yong In University, Samga-dong, Cheoin-gu, Yongin-si Gyeonggi-do, Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Global Top 5 Program, Ewha Womans University, Seoul, Republic of Korea
| | - Seung Bae Rho
- Research Institute, National Cancer Center, Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea
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Hwang J, Lee JA, Pallas DC. Leucine Carboxyl Methyltransferase 1 (LCMT-1) Methylates Protein Phosphatase 4 (PP4) and Protein Phosphatase 6 (PP6) and Differentially Regulates the Stable Formation of Different PP4 Holoenzymes. J Biol Chem 2016; 291:21008-21019. [PMID: 27507813 DOI: 10.1074/jbc.m116.739920] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 11/06/2022] Open
Abstract
The protein phosphatase 2A (PP2A) subfamily of phosphatases, PP2A, PP4, and PP6, are multifunctional serine/threonine protein phosphatases involved in many cellular processes. Carboxyl methylation of the PP2A catalytic subunit (PP2Ac) C-terminal leucine is regulated by the opposing activities of leucine carboxyl methyltransferase 1 (LCMT-1) and protein phosphatase methylesterase 1 (PME-1) and regulates PP2A holoenzyme formation. The site of methylation on PP2Ac is conserved in the catalytic subunits of PP4 and PP6, and PP4 is also methylated on that site, but the identities of the methyltransferase enzyme for PP4 are not known. Whether PP6 is methylated is also not known. Here we use antibodies specific for the unmethylated phosphatases to show that PP6 is carboxyl-methylated and that LCMT-1 is the major methyltransferase for PP2A, PP4, and PP6 in mouse embryonic fibroblasts (MEFs). Analysis of PP2A and PP4 complexes by blue native polyacrylamide gel electrophoresis (BN-PAGE) indicates that PP4 holoenzyme complexes, like those of PP2A, are differentially regulated by LCMT-1, with the PP4 regulatory subunit 1 (PP4R1)-containing PP4 complex being the most dramatically affected by the LCMT-1 loss. MEFs derived from LCMT-1 knock-out mouse embryos have reduced levels of PP2A B regulatory subunit and PP4R1 relative to control MEFs, indicating that LCMT-1 is important for maintaining normal levels of these subunits. Finally, LCMT-1 homozygous knock-out MEFs exhibited hyperphosphorylation of HDAC3, a reported target of the methylation-dependent PP4R1-PP4c complex. Collectively, our data suggest that LCMT-1 coordinately regulates the carboxyl methylation of PP2A-related phosphatases and, consequently, their holoenzyme assembly and function.
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Affiliation(s)
- Juyeon Hwang
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Jocelyn A Lee
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
| | - David C Pallas
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
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58
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The protein phosphatase 4 - PEA15 axis regulates the survival of breast cancer cells. Cell Signal 2016; 28:1389-1400. [PMID: 27317964 DOI: 10.1016/j.cellsig.2016.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND The control of breast cell survival is of critical importance for preventing breast cancer initiation and progression. The activity of many proteins which regulate cell survival is controlled by reversible phosphorylation, so that the relevant kinases and phosphatases play crucial roles in determining cell fate. Several protein kinases act as oncoproteins in breast cancer and changes in their activities contribute to the process of transformation. Through counteracting the activity of oncogenic kinases, the protein phosphatases are also likely to be important players in breast cancer development, but this class of molecules is relatively poorly understood. Here we have investigated the role of the serine/threonine protein phosphatase 4 in the control of cell survival of breast cancer cells. METHODS The breast cancer cell lines, MCF7 and MDA-MB-231, were transfected with expression vectors encoding the catalytic subunit of protein phosphatase 4 (PP4c) or with PP4c siRNAs. Culture viability, apoptosis, cell migration and cell cycle were assessed. The involvement of phosphoprotein enriched in astrocytes 15kDa (PEA15) in PP4c action was investigated by immunoblotting approaches and by siRNA-mediated silencing of PEA15. RESULTS In this study we showed that PP4c over-expression inhibited cell proliferation, enhanced spontaneous apoptosis and decreased the migratory and colony forming abilities of breast cancer cells. Moreover, PP4c down-regulation produced complementary effects. PP4c is demonstrated to regulate the phosphorylation of PEA15, and PEA15 itself regulates the apoptosis of breast cancer cells. The inhibitory effects of PP4c on breast cancer cell survival and growth were lost in PEA15 knockdown cells, confirming that PP4c action is mediated, at least in part, through the de-phosphorylation of apoptosis regulator PEA15. CONCLUSION Our work shows that PP4 regulates breast cancer cell survival and identifies a novel PP4c-PEA15 signalling axis in the control of breast cancer cell survival. The dysfunction of this axis may be important in the development and progression of breast cancer.
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59
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Chattopadhyay D, Swingle MR, Salter EA, Wood E, D'Arcy B, Zivanov C, Abney K, Musiyenko A, Rusin SF, Kettenbach A, Yet L, Schroeder CE, Golden JE, Dunham WH, Gingras AC, Banerjee S, Forbes D, Wierzbicki A, Honkanen RE. Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C. Biochem Pharmacol 2016; 109:14-26. [PMID: 27002182 DOI: 10.1016/j.bcp.2016.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/15/2016] [Indexed: 12/24/2022]
Abstract
Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.
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Affiliation(s)
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Edward A Salter
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Eric Wood
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA; Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Brandon D'Arcy
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Catherine Zivanov
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA; Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Kevin Abney
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Scott F Rusin
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Arminja Kettenbach
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Larry Yet
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Chad E Schroeder
- Department of Medicinal Chemistry, University of Kansas Specialized Chemistry Center, Lawrence, KS 66047, USA
| | - Jennifer E Golden
- Department of Medicinal Chemistry, University of Kansas Specialized Chemistry Center, Lawrence, KS 66047, USA
| | - Wade H Dunham
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Surajit Banerjee
- Northeastern Collaborative Access Team (NE-CAT) Cornell University, Lemont, IL, USA
| | - David Forbes
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA.
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Zhang X, Damacharla D, Ma D, Qi Y, Tagett R, Draghici S, Kowluru A, Yi Z. Quantitative proteomics reveals novel protein interaction partners of PP2A catalytic subunit in pancreatic β-cells. Mol Cell Endocrinol 2016; 424:1-11. [PMID: 26780722 PMCID: PMC4779412 DOI: 10.1016/j.mce.2016.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/15/2015] [Accepted: 01/07/2016] [Indexed: 12/19/2022]
Abstract
Protein phosphatase 2A (PP2A) is one of the major serine/threonine phosphatases. We hypothesize that PP2A regulates signaling cascades in pancreatic β-cells in the context of glucose-stimulated insulin secretion (GSIS). Using co-immunoprecipitation (co-IP) and tandem mass spectrometry, we globally identified the protein interaction partners of the PP2A catalytic subunit (PP2Ac) in insulin-secreting pancreatic β-cells. Among the 514 identified PP2Ac interaction partners, 476 were novel. This represents the first global view of PP2Ac protein-protein interactions caused by hyperglycemic conditions. Additionally, numerous PP2Ac partners were found involved in a variety of signaling pathways in the β-cell function, such as insulin secretion. Our data suggest that PP2A interacts with various signaling proteins necessary for physiological insulin secretion as well as signaling proteins known to regulate cell dysfunction and apoptosis in the pancreatic β-cells.
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Affiliation(s)
- Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Divyasri Damacharla
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Danjun Ma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Yue Qi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Rebecca Tagett
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, MI, USA
| | - Anjaneyulu Kowluru
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA; β-Cell Biochemistry Laboratory, John D. Dingell VA Medical Center, Detroit, MI, 48201, USA
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
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Feng J, Duan Y, Sun W, Qin Y, Zhuang Z, Zhu D, Sun X, Jiang L. CaTip41 regulates protein phosphatase 2A activity, CaRad53 deactivation and the recovery of DNA damage-induced filamentation to yeast form in Candida albicans. FEMS Yeast Res 2016; 16:fow009. [PMID: 26851402 DOI: 10.1093/femsyr/fow009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation and dephosphorylation of the checkpoint kinase CaRad53 is crucial for fungal cells in response to genotoxic stresses. The protein phosphatase 2A (PP2A) CaPph3/CaPsy2 phosphatase complex is involved in CaRad53 dephosphorylation in Candida albicans. In view of the role of ScTip41/ScTap42 in regulating PP2A phosphatases in Saccharomyces cerevisiae, we have explored the function of CaTip41 in C. albicans. Here, we show that CaTIP41 is a functional ortholog of ScTIP41 in the sensitivity of S. cerevisiae cells to rapamycin. Deletion of CaTIP41 causes C. albicans cells to be sensitive to DNA damaging agents, methylmethane sulfonate (MMS) and cisplatin, and resistant to both rapamycin and caffeine. Accordingly, expression of CaTip41 increases in response to MMS and cisplatin. In addition, C. albicans cells lacking CaTIP41 show a delay in the recovery from MMS-induced filamentation to yeast form, decreased PP2A activity and a defect in deactivation of CaRad53 during recovery from DNA damage. Through yeast two-hybrid assay we show that CaTip41 interacts with either CaPph3, CaPsy2 or CaTap42. Therefore, CaTip41 plays regulatory roles in both the CaRad53 deactivation during recovery from DNA damage and the target of rapamycin signaling pathway.
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Affiliation(s)
- Jinrong Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yinong Duan
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Wei Sun
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yongwei Qin
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Zhong Zhuang
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Dandan Zhu
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Xiaolei Sun
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Linghuo Jiang
- The National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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TIPRL Inhibits Protein Phosphatase 4 Activity and Promotes H2AX Phosphorylation in the DNA Damage Response. PLoS One 2015; 10:e0145938. [PMID: 26717153 PMCID: PMC4696667 DOI: 10.1371/journal.pone.0145938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/10/2015] [Indexed: 11/19/2022] Open
Abstract
Despite advances in our understanding of protein kinase regulation in the DNA damage response, the mechanism that controls protein phosphatase activity in this pathway is unclear. Unlike kinases, the activity and specificity of serine/threonine phosphatases is governed largely by their associated proteins. Here we show that Tip41-like protein (TIPRL), an evolutionarily conserved binding protein for PP2A-family phosphatases, is a negative regulator of protein phosphatase 4 (PP4). Knockdown of TIPRL resulted in increased PP4 phosphatase activity and formation of the active PP4-C/PP4R2 complex known to dephosphorylate γ-H2AX. Thus, overexpression of TIPRL promotes phosphorylation of H2AX, and increases γ-H2AX positive foci in response to DNA damage, whereas knockdown of TIPRL inhibits γ-H2AX phosphorylation. In correlation with γ-H2AX levels, we found that TIPRL overexpression promotes cell death in response to genotoxic stress, and knockdown of TIPRL protects cells from genotoxic agents. Taken together, these data demonstrate that TIPRL inhibits PP4 activity to allow for H2AX phosphorylation and the subsequent DNA damage response.
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Loss of flfl Triggers JNK-Dependent Cell Death in Drosophila. BIOMED RESEARCH INTERNATIONAL 2015; 2015:623573. [PMID: 26583122 PMCID: PMC4637051 DOI: 10.1155/2015/623573] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/05/2015] [Indexed: 01/21/2023]
Abstract
falafel (flfl) encodes a Drosophila homolog of human SMEK whose in vivo functions remain elusive. In this study, we performed gain-of-function and loss-of-function analysis in Drosophila and identified flfl as a negative regulator of JNK pathway-mediated cell death. While ectopic expression of flfl suppresses TNF-triggered JNK-dependent cell death, loss of flfl promotes JNK activation and cell death in the developing eye and wing. These data report for the first time an essential physiological function of flfl in maintaining tissue homeostasis and organ development. As the JNK signaling pathway has been evolutionary conserved from fly to human, a similar role of PP4R3 in JNK-mediated physiological process is speculated.
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Haider S, Lipinszki Z, Przewloka MR, Ladak Y, D’Avino PP, Kimata Y, Lio’ P, Glover DM. DAPPER: a data-mining resource for protein-protein interactions. BioData Min 2015; 8:30. [PMID: 26405458 PMCID: PMC4581157 DOI: 10.1186/s13040-015-0063-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes. With increasing volumes of such datasets, especially in model organisms such as Drosophila melanogaster, there exists a pressing need for specialised tools, which can seamlessly collect, integrate and analyse these data. Here we describe a database coupled with a mining tool for protein-protein interactions (DAPPER), developed as a rich resource for studying multi-protein complexes in Drosophila melanogaster. RESULTS This proteomics database is compiled through mass spectrometric analyses of many protein complexes affinity purified from Drosophila tissues and cultured cells. The web access to DAPPER is provided via an accelerated version of BioMart software enabling data-mining through customised querying and output formats. The protein-protein interaction dataset is annotated with FlyBase identifiers, and further linked to the Ensembl database using BioMart's data-federation model, thereby enabling complex multi-dataset queries. DAPPER is open source, with all its contents and source code are freely available. CONCLUSIONS DAPPER offers an easy-to-navigate and extensible platform for real-time integration of diverse resources containing new and existing protein-protein interaction datasets of Drosophila melanogaster.
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Affiliation(s)
- Syed Haider
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD UK
| | - Zoltan Lipinszki
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Marcin R. Przewloka
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Yaseen Ladak
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
- Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Pier Paolo D’Avino
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Yuu Kimata
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Pietro Lio’
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD UK
| | - David M. Glover
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
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Wu G, Ma Z, Qian J, Liu B. PP4R1 accelerates cell growth and proliferation in HepG2 hepatocellular carcinoma. Onco Targets Ther 2015; 8:2067-74. [PMID: 26300649 PMCID: PMC4535559 DOI: 10.2147/ott.s77709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC), as the fifth most common cancer worldwide, has become the third leading cause of cancer-related deaths. It is reported that protein phosphatase 4 (PP4) is an essential protein for nucleation, growth, and stabilization of microtubules in centrosomes/spindle bodies during cell division. Besides, previous studies have identified protein phosphatase 4 regulatory subunit 1 (PP4R1) as a constitutive interaction partner of PP4 catalytic subunit PP4C. The PP4C-PP4R1 PP4 complex plays a role in dephosphorylation, regulation of histone acetylation, and NF-κB activation. However, little is known about the pathological functions of PP4R1 in human cancers. Thus, in order to investigate how PP4R1 functions in human HCC, two common hepatocarcinogenesis HCC cell lines HepG2 and SMMC-7721 were employed, transduced with recombinant lentivirus expressing PP4R1 short hairpin RNA. Compared with the controls, the cells treated with Lv-shPP4R1 showed a significant decrease in cell proliferation and colony formation. The results of flow cytometry showed that the knockdown of PP4R1 caused HepG2 cells arrest at G2/M phase in the cell cycle. Furthermore, the transduction of Lv-shPP4R1 into HepG2 cells led to the inactivation of two major mitogen-activated protein kinase signaling cascades: p38 and c-Jun N-terminal kinase (JNK), indicating that PP4R1 could promote cell proliferation, which might be regulated by p38 and c-Jun N-terminal kinase pathways. In a word, this study highlights the crucial role of PP4R1 in promoting HCC cell growth, which might elucidate the pathological mechanism of HCC.
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Affiliation(s)
- Gang Wu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Zhenyu Ma
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jianmin Qian
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Bin Liu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
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Lant B, Yu B, Goudreault M, Holmyard D, Knight JDR, Xu P, Zhao L, Chin K, Wallace E, Zhen M, Gingras AC, Derry WB. CCM-3/STRIPAK promotes seamless tube extension through endocytic recycling. Nat Commun 2015; 6:6449. [PMID: 25743393 DOI: 10.1038/ncomms7449] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/29/2015] [Indexed: 01/25/2023] Open
Abstract
The mechanisms governing apical membrane assembly during biological tube development are poorly understood. Here, we show that extension of the C. elegans excretory canal requires cerebral cavernous malformation 3 (CCM-3), independent of the CCM1 orthologue KRI-1. Loss of ccm-3 causes canal truncations and aggregations of canaliculular vesicles, which form ectopic lumen (cysts). We show that CCM-3 localizes to the apical membrane, and in cooperation with GCK-1 and STRIPAK, promotes CDC-42 signalling, Golgi stability and endocytic recycling. We propose that endocytic recycling is mediated through the CDC-42-binding kinase MRCK-1, which interacts physically with CCM-3-STRIPAK. We further show canal membrane integrity to be dependent on the exocyst complex and the actin cytoskeleton. This work reveals novel in vivo roles of CCM-3·STRIPAK in regulating tube extension and membrane integrity through small GTPase signalling and vesicle dynamics, which may help explain the severity of CCM3 mutations in patients.
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Affiliation(s)
- Benjamin Lant
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Bin Yu
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Marilyn Goudreault
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - Doug Holmyard
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - James D R Knight
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - Peter Xu
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Linda Zhao
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Kelly Chin
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Evan Wallace
- 1] Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4 [2] Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Mei Zhen
- 1] Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5 [2] Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Anne-Claude Gingras
- 1] Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5 [2] Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - W Brent Derry
- 1] Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4 [2] Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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67
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Restricted protein phosphatase 2A targeting by Merkel cell polyomavirus small T antigen. J Virol 2015; 89:4191-200. [PMID: 25631078 DOI: 10.1128/jvi.00157-15] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Merkel cell polyomavirus (MCV) is a newly discovered human cancer virus encoding a small T (sT) oncoprotein. We performed MCV sT FLAG-affinity purification followed by mass spectroscopy (MS) analysis, which identified several protein phosphatases (PP), including PP2A A and C subunits and PP4C, as potential cellular interacting proteins. PP2A targeting is critical for the transforming properties of nonhuman polyomaviruses, such as simian virus 40 (SV40), but is not required for MCV sT-induced rodent cell transformation. We compared similarities and differences in PP2A binding between MCV and SV40 sT. While SV40 sT coimmunopurified with subunits PP2A Aα and PP2A C, MCV sT coimmunopurified with PP2A Aα, PP2A Aβ, and PP2A C. Scanning alanine mutagenesis at 29 sites across the MCV sT protein revealed that PP2A-binding domains lie on the opposite molecular surface from a previously described large T stabilization domain (LSD) loop that binds E3 ligases, such as Fbw7. MCV sT-PP2A interactions can be functionally distinguished by mutagenesis from MCV sT LSD-dependent 4E-BP1 hyperphosphorylation and viral DNA replication enhancement. MCV sT has a restricted range for PP2A B subunit substitution, inhibiting only the assembly of B56α into the phosphatase holoenzyme. In contrast, SV40 sT inhibits the assembly of B55α, B56α and B56ε into PP2A. We conclude that MCV sT is required for Merkel cell carcinoma growth, but its in vitro transforming activity depends on LSD interactions rather than PP2A targeting. IMPORTANCE Merkel cell polyomavirus is a newly discovered human cancer virus that promotes cancer, in part, through expression of its small T (sT) oncoprotein. Animal polyomavirus sT oncoproteins have been found to cause experimental tumors by blocking the activities of a group of phosphatases called protein phosphatase 2A (PP2A). Our structural analysis reveals that MCV sT also displaces the B subunit of PP2A to inhibit PP2A activity. MCV sT, however, only displaces a restricted subset of PP2A B subunits, which is insufficient to cause tumor cell formation in vitro. MCV sT instead transforms tumor cells through another region called the large T stabilization domain. The PP2A targeting and transforming activities lie on opposite faces of the MCV sT molecule and can be genetically separated from each other.
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68
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Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell 2015; 57:273-89. [PMID: 25533186 PMCID: PMC5706562 DOI: 10.1016/j.molcel.2014.11.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/16/2014] [Accepted: 11/14/2014] [Indexed: 12/25/2022]
Abstract
Mec1-Ddc2 (ATR-ATRIP) controls the DNA damage checkpoint and shows differential cell-cycle regulation in yeast. To find regulators of Mec1-Ddc2, we exploited a mec1 mutant that retains catalytic activity in G2 and recruitment to stalled replication forks, but which is compromised for the intra-S phase checkpoint. Two screens, one for spontaneous survivors and an E-MAP screen for synthetic growth effects, identified loss of PP4 phosphatase, pph3Δ and psy2Δ, as the strongest suppressors of mec1-100 lethality on HU. Restored Rad53 phosphorylation accounts for part, but not all, of the pph3Δ-mediated survival. Phosphoproteomic analysis confirmed that 94% of the mec1-100-compromised targets on HU are PP4 regulated, including a phosphoacceptor site within Mec1 itself, mutation of which confers damage sensitivity. Physical interaction between Pph3 and Mec1, mediated by cofactors Psy2 and Ddc2, is shown biochemically and through FRET in subnuclear repair foci. This establishes a physical and functional Mec1-PP4 unit for regulating the checkpoint response.
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Affiliation(s)
- Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Monika Tsai-Pflugfelder
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Bhupinder Bhullar
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Fabrikstrasse 22, 4056 Basel, Switzerland
| | - Hanneke Vlaming
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Aude Guénolé
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Haico van Attikum
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Rohith Srivas
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland.
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69
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Lipinszki Z, Lefevre S, Savoian MS, Singleton MR, Glover DM, Przewloka MR. Centromeric binding and activity of Protein Phosphatase 4. Nat Commun 2015; 6:5894. [PMID: 25562660 PMCID: PMC4354016 DOI: 10.1038/ncomms6894] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/18/2014] [Indexed: 02/02/2023] Open
Abstract
The cell division cycle requires tight coupling between protein phosphorylation and dephosphorylation. However, understanding the cell cycle roles of multimeric protein phosphatases has been limited by the lack of knowledge of how their diverse regulatory subunits target highly conserved catalytic subunits to their sites of action. Phosphoprotein phosphatase 4 (PP4) has been recently shown to participate in the regulation of cell cycle progression. We now find that the EVH1 domain of the regulatory subunit 3 of Drosophila PP4, Falafel (Flfl), directly interacts with the centromeric protein C (CENP-C). Unlike other EVH1 domains that interact with proline-rich ligands, the crystal structure of the Flfl amino-terminal EVH1 domain bound to a CENP-C peptide reveals a new target-recognition mode for the phosphatase subunit. We also show that binding of Flfl to CENP-C is required to bring PP4 activity to centromeres to maintain CENP-C and attached core kinetochore proteins at chromosomes during mitosis.
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Affiliation(s)
- Zoltan Lipinszki
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Stephane Lefevre
- Macromolecular Structure and Function Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, UK
| | - Matthew S. Savoian
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Martin R. Singleton
- Macromolecular Structure and Function Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, UK
| | - David M. Glover
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Marcin R. Przewloka
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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70
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Haesen D, Sents W, Lemaire K, Hoorne Y, Janssens V. The Basic Biology of PP2A in Hematologic Cells and Malignancies. Front Oncol 2014; 4:347. [PMID: 25566494 PMCID: PMC4263090 DOI: 10.3389/fonc.2014.00347] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/20/2014] [Indexed: 12/30/2022] Open
Abstract
Reversible protein phosphorylation plays a crucial role in regulating cell signaling. In normal cells, phosphoregulation is tightly controlled by a network of protein kinases counterbalanced by several protein phosphatases. Deregulation of this delicate balance is widely recognized as a central mechanism by which cells escape external and internal self-limiting signals, eventually resulting in malignant transformation. A large fraction of hematologic malignancies is characterized by constitutive or unrestrained activation of oncogenic kinases. This is in part achieved by activating mutations, chromosomal rearrangements, or constitutive activation of upstream kinase regulators, in part by inactivation of their anti-oncogenic phosphatase counterparts. Protein phosphatase 2A (PP2A) represents a large family of cellular serine/threonine phosphatases with suspected tumor suppressive functions. In this review, we highlight our current knowledge about the complex structure and biology of these phosphatases in hematologic cells, thereby providing the rationale behind their diverse signaling functions. Eventually, this basic knowledge is a key to truly understand the tumor suppressive role of PP2A in leukemogenesis and to allow further rational development of therapeutic strategies targeting PP2A.
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Affiliation(s)
- Dorien Haesen
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Ward Sents
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Katleen Lemaire
- Gene Expression Unit, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Yana Hoorne
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven , Leuven , Belgium
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71
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Lillo C, Kataya ARA, Heidari B, Creighton MT, Nemie-Feyissa D, Ginbot Z, Jonassen EM. Protein phosphatases PP2A, PP4 and PP6: mediators and regulators in development and responses to environmental cues. PLANT, CELL & ENVIRONMENT 2014; 37:2631-48. [PMID: 24810976 DOI: 10.1111/pce.12364] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 05/23/2023]
Abstract
The three closely related groups of serine/threonine protein phosphatases PP2A, PP4 and PP6 are conserved throughout eukaryotes. The catalytic subunits are present in trimeric and dimeric complexes with scaffolding and regulatory subunits that control activity and confer substrate specificity to the protein phosphatases. In Arabidopsis, three scaffolding (A subunits) and 17 regulatory (B subunits) proteins form complexes with five PP2A catalytic subunits giving up to 255 possible combinations. Three SAP-domain proteins act as regulatory subunits of PP6. Based on sequence similarities with proteins in yeast and mammals, two putative PP4 regulatory subunits are recognized in Arabidopsis. Recent breakthroughs have been made concerning the functions of some of the PP2A and PP6 regulatory subunits, for example the FASS/TON2 in regulation of the cellular skeleton, B' subunits in brassinosteroid signalling and SAL proteins in regulation of auxin transport. Reverse genetics is starting to reveal also many more physiological functions of other subunits. A system with key regulatory proteins (TAP46, TIP41, PTPA, LCMT1, PME-1) is present in all eukaryotes to stabilize, activate and inactivate the catalytic subunits. In this review, we present the status of knowledge concerning physiological functions of PP2A, PP4 and PP6 in Arabidopsis, and relate these to yeast and mammals.
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Affiliation(s)
- Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
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Gao J, Wang H, Wong AHH, Zeng G, Huang Z, Wang Y, Sang J, Wang Y. Regulation of Rfa2 phosphorylation in response to genotoxic stress in Candida albicans. Mol Microbiol 2014; 94:141-55. [PMID: 25109320 DOI: 10.1111/mmi.12749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 01/10/2023]
Abstract
Successful pathogens must be able to swiftly respond to and repair DNA damages inflicted by the host defence. The replication protein A (RPA) complex plays multiple roles in DNA damage response and is regulated by phosphorylation. However, the regulators of RPA phosphorylation remain unclear. Here, we investigated Rfa2 phosphorylation in the pathogenic fungus Candida albicans. Rfa2, a RFA subunit, is phosphorylated when DNA replication is inhibited by hydroxyurea and dephosphorylated during the recovery. By screening a phosphatase mutant library, we found that Pph3 associates with different regulatory subunits to differentially control Rfa2 dephosphorylation in stressed and unstressed cells. Site-directed mutagenesis revealed T11, S18, S29, and S30 being critical for Rfa2 phosphorylation in response to genotoxic insult. We obtained evidence that the genome integrity checkpoint kinase Mec1 and the cyclin-dependent kinase Clb2-Cdc28 mediate Rfa2 phosphorylation. Although cells expressing either a phosphomimetic or a non-phosphorylatable version of Rfa2 had defects, the latter exhibited greater sensitivity to genotoxic challenge, failure to repair DNA damages and to deactivate Rad53-mediated checkpoint pathways in a dosage-dependent manner. These mutants were also less virulent in mice. Our results provide important new insights into the regulatory mechanism and biological significance of Rfa2 phosphorylation in C. albicans.
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Affiliation(s)
- Jiaxin Gao
- Key Laboratory of Cell Proliferation and Regulation Biology, College of Life Sciences, Beijing Normal University, Beijing, China; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
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73
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Distinct phosphatases antagonize the p53 response in different phases of the cell cycle. Proc Natl Acad Sci U S A 2014; 111:7313-8. [PMID: 24711418 DOI: 10.1073/pnas.1322021111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The basic machinery that detects DNA damage is the same throughout the cell cycle. Here, we show, in contrast, that reversal of DNA damage responses (DDRs) and recovery are fundamentally different in G1 and G2 phases of the cell cycle. We find that distinct phosphatases are required to counteract the checkpoint response in G1 vs. G2. Whereas WT p53-induced phosphatase 1 (Wip1) promotes recovery in G2-arrested cells by antagonizing p53, it is dispensable for recovery from a G1 arrest. Instead, we identify phosphoprotein phosphatase 4 catalytic subunit (PP4) to be specifically required for cell cycle restart after DNA damage in G1. PP4 dephosphorylates Krüppel-associated box domain-associated protein 1-S473 to repress p53-dependent transcriptional activation of p21 when the DDR is silenced. Taken together, our results show that PP4 and Wip1 are differentially required to counteract the p53-dependent cell cycle arrest in G1 and G2, by antagonizing early or late p53-mediated responses, respectively.
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74
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Lee DH, Acharya SS, Kwon M, Drane P, Guan Y, Adelmant G, Kalev P, Shah J, Pellman D, Marto JA, Chowdhury D. Dephosphorylation enables the recruitment of 53BP1 to double-strand DNA breaks. Mol Cell 2014; 54:512-25. [PMID: 24703952 DOI: 10.1016/j.molcel.2014.03.020] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/27/2014] [Accepted: 03/12/2014] [Indexed: 01/01/2023]
Abstract
Excluding 53BP1 from chromatin is required to attenuate the DNA damage response during mitosis, yet the functional relevance and regulation of this exclusion are unclear. Here we show that 53BP1 is phosphorylated during mitosis on two residues, T1609 and S1618, located in its well-conserved ubiquitination-dependent recruitment (UDR) motif. Phosphorylating these sites blocks the interaction of the UDR motif with mononuclesomes containing ubiquitinated histone H2A and impedes binding of 53BP1 to mitotic chromatin. Ectopic recruitment of 53BP1-T1609A/S1618A to mitotic DNA lesions was associated with significant mitotic defects that could be reversed by inhibiting nonhomologous end-joining. We also reveal that protein phosphatase complex PP4C/R3β dephosphorylates T1609 and S1618 to allow the recruitment of 53BP1 to chromatin in G1 phase. Our results identify key sites of 53BP1 phosphorylation during mitosis, identify the counteracting phosphatase complex that restores the potential for DDR during interphase, and establish the physiological importance of this regulation.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Sciences, College of Science, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Sanket S Acharya
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mijung Kwon
- Department of Cell Biology, Harvard Medical School, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pascal Drane
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yinghua Guan
- Department of Systems Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Guillaume Adelmant
- Department of Biological Chemistry Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter Kalev
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jagesh Shah
- Department of Systems Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David Pellman
- Department of Cell Biology, Harvard Medical School, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Biological Chemistry Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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75
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Psy2 targets the PP4 family phosphatase Pph3 to dephosphorylate Mth1 and repress glucose transporter gene expression. Mol Cell Biol 2013; 34:452-63. [PMID: 24277933 DOI: 10.1128/mcb.00279-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The reversible nature of protein phosphorylation dictates that any protein kinase activity must be counteracted by protein phosphatase activity. How phosphatases target specific phosphoprotein substrates and reverse the action of kinases, however, is poorly understood in a biological context. We address this question by elucidating a novel function of the conserved PP4 family phosphatase Pph3-Psy2, the yeast counterpart of the mammalian PP4c-R3 complex, in the glucose-signaling pathway. Our studies show that Pph3-Psy2 specifically targets the glucose signal transducer protein Mth1 via direct binding of the EVH1 domain of the Psy2 regulatory subunit to the polyproline motif of Mth1. This activity is required for the timely dephosphorylation of the downstream transcriptional repressor Rgt1 upon glucose withdrawal, a critical event in the repression of HXT genes, which encode glucose transporters. Pph3-Psy2 dephosphorylates Mth1, an Rgt1 associated corepressor, but does not dephosphorylate Rgt1 at sites associated with inactivation, in vitro. We show that Pph3-Psy2 phosphatase antagonizes Mth1 phosphorylation by protein kinase A (PKA), the major protein kinase activated in response to glucose, in vitro and regulates Mth1 function via putative PKA phosphorylation sites in vivo. We conclude that the Pph3-Psy2 phosphatase modulates Mth1 activity to facilitate precise regulation of HXT gene expression by glucose.
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76
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Lyu J, Kim HR, Yamamoto V, Choi SH, Wei Z, Joo CK, Lu W. Protein phosphatase 4 and Smek complex negatively regulate Par3 and promote neuronal differentiation of neural stem/progenitor cells. Cell Rep 2013; 5:593-600. [PMID: 24209749 PMCID: PMC3855259 DOI: 10.1016/j.celrep.2013.09.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 08/22/2013] [Accepted: 09/23/2013] [Indexed: 01/24/2023] Open
Abstract
Neural progenitor cells (NPCs) are multipotent cells that can self-renew and differentiate into neurons and glial cells. However, mechanisms that control their fate decisions are poorly understood. Here, we show that Smek1, a regulatory subunit of the serine/threonine protein phosphatase PP4, promotes neuronal differentiation and suppresses the proliferative capacity of NPCs. We identify the cell polarity protein Par3, a negative regulator of neuronal differentiation, as a Smek1 substrate and demonstrate that Smek1 suppresses its activity. We also show that Smek1, which is predominantly nuclear in NPCs, is excluded from the nucleus during mitosis, allowing it to interact with cortical/cytoplasmic Par3 and mediate its dephosphorylation by the catalytic subunit PP4c. These results identify the PP4/Smek1 complex as a key regulator of neurogenesis.
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Affiliation(s)
- Jungmook Lyu
- Catholic Institute for Visual Science, Department of Ophthalmology and Visual Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Los Angeles, California 90042, USA
| | - Hee-Ryang Kim
- Catholic Institute for Visual Science, Department of Ophthalmology and Visual Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Vicky Yamamoto
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Los Angeles, California 90042, USA
| | - Si Ho Choi
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Los Angeles, California 90042, USA
| | - Zong Wei
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Los Angeles, California 90042, USA
| | - Choun-Ki Joo
- Catholic Institute for Visual Science, Department of Ophthalmology and Visual Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Wange Lu
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Los Angeles, California 90042, USA
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77
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Vandamme D, Minke BA, Fitzmaurice W, Kholodenko BN, Kolch W. Systems biology-embedded target validation: improving efficacy in drug discovery. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:1-11. [PMID: 24214316 DOI: 10.1002/wsbm.1253] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/24/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022]
Abstract
The pharmaceutical industry is faced with a range of challenges with the ever-escalating costs of drug development and a drying out of drug pipelines. By harnessing advances in -omics technologies and moving away from the standard, reductionist model of drug discovery, there is significant potential to reduce costs and improve efficacy. Embedding systems biology approaches in drug discovery, which seek to investigate underlying molecular mechanisms of potential drug targets in a network context, will reduce attrition rates by earlier target validation and the introduction of novel targets into the currently stagnant market. Systems biology approaches also have the potential to assist in the design of multidrug treatments and repositioning of existing drugs, while stratifying patients to give a greater personalization of medical treatment.
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Affiliation(s)
- Drieke Vandamme
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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78
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Uhrig RG, Labandera AM, Moorhead GB. Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines. TRENDS IN PLANT SCIENCE 2013; 18:505-13. [PMID: 23790269 DOI: 10.1016/j.tplants.2013.05.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/14/2013] [Accepted: 05/17/2013] [Indexed: 05/20/2023]
Abstract
The major plant serine/threonine protein phosphatases belong to the phosphoprotein phosphatase (PPP) family. Over the past few years the complement of Arabidopsis thaliana PPP family of catalytic subunits has been cataloged and many regulatory subunits identified. Specific roles for PPPs have been characterized, including roles in auxin and brassinosteroid signaling, in phototropism, in regulating the target of rapamycin pathway, and in cell stress responses. In this review, we provide a framework for understanding the PPP family by exploring the fundamental role of the phosphatase regulatory subunits that drive catalytic engine specificity. Although there are fewer plant protein phosphatases compared with their protein kinase partners, their function is now recognized to be as dynamic and as regulated as that of protein kinases.
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Affiliation(s)
- R Glen Uhrig
- Department of Biological Sciences, University of Calgary, Canada
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79
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Voss M, Campbell K, Saranzewa N, Campbell DG, Hastie CJ, Peggie MW, Martin-Granados C, Prescott AR, Cohen PTW. Protein phosphatase 4 is phosphorylated and inactivated by Cdk in response to spindle toxins and interacts with γ-tubulin. Cell Cycle 2013; 12:2876-87. [PMID: 23966160 PMCID: PMC3899200 DOI: 10.4161/cc.25919] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many pharmaceuticals used to treat cancer target the cell cycle or mitotic spindle dynamics, such as the anti-tumor drug, paclitaxel, which stabilizes microtubules. Here we show that, in cells arrested in mitosis with the spindle toxins, nocodazole, or paclitaxel, the endogenous protein phosphatase 4 (Ppp4) complex Ppp4c-R2-R3A is phosphorylated on its regulatory (R) subunits, and its activity is inhibited. The phosphorylations are blocked by roscovitine, indicating that they may be mediated by Cdk1-cyclin B. Endogenous Ppp4c is enriched at the centrosomes in the absence and presence of paclitaxel, nocodazole, or roscovitine, and the activity of endogenous Ppp4c-R2-R3A is inhibited from G1/S to the G2/M phase of the cell cycle. Endogenous γ-tubulin and its associated protein, γ-tubulin complex protein 2, both of which are essential for nucleation of microtubules at centrosomes, interact with the Ppp4 complex. Recombinant γ-tubulin can be phosphorylated by Cdk1-cyclin B or Brsk1 and dephosphorylated by Ppp4c-R2-R3A in vitro. The data indicate that Ppp4c-R2-R3A regulates microtubule organization at centrosomes during cell division in response to stress signals such as spindle toxins, paclitaxel, and nocodazole, and that inhibition of the Ppp4 complex may be advantageous for treatment of some cancers.
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Affiliation(s)
- Martin Voss
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit; College of Life Sciences; University of Dundee; Dundee, Scotland, UK
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80
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Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis N, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJR, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 2013; 10:730-6. [PMID: 23921808 PMCID: PMC3773500 DOI: 10.1038/nmeth.2557] [Citation(s) in RCA: 1095] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 05/18/2013] [Indexed: 02/07/2023]
Abstract
Affinity purification coupled with mass spectrometry (AP-MS) is a widely used approach for the identification of protein-protein interactions. However, for any given protein of interest, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants (for example, proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. The standard approach is to identify nonspecific interactions using one or more negative-control purifications, but many small-scale AP-MS studies do not capture a complete, accurate background protein set when available controls are limited. Fortunately, negative controls are largely bait independent. Hence, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. Here we present the contaminant repository for affinity purification (the CRAPome) and describe its use for scoring protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely accessible at http://www.crapome.org/.
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Affiliation(s)
- Dattatreya Mellacheruvu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Zachary Wright
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Amber L. Couzens
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Nicole St-Denis
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Tuo Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yana V. Miteva
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Simon Hauri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Teck Yew Low
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Vincentius A. Halim
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Richard D. Bagshaw
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Nina C. Hubner
- Department of Molecular Biology; Faculty of Science; Nijmegen Centre for Molecular Life Sciences; Radboud University; Nijmegen, The Netherlands
| | - Abdallah al-Hakim
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Annie Bouchard
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Denis Faubert
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Wade H. Dunham
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marilyn Goudreault
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Zhen-Yuan Lin
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Beatriz Gonzalez Badillo
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Tony Pawson
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Daniel Durocher
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Benoit Coulombe
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Mike P. Washburn
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Brian Raught
- Ontario Cancer Institute, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Rob M. Ewing
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Science, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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81
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Nakashima A, Tanimura-Ito K, Oshiro N, Eguchi S, Miyamoto T, Momonami A, Kamada S, Yonezawa K, Kikkawa U. A positive role of mammalian Tip41-like protein, TIPRL, in the amino-acid dependent mTORC1-signaling pathway through interaction with PP2A. FEBS Lett 2013; 587:2924-9. [DOI: 10.1016/j.febslet.2013.07.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 12/25/2022]
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82
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Su YW, Chen YP, Chen MY, Reth M, Tan TH. The serine/threonine phosphatase PP4 is required for pro-B cell development through its promotion of immunoglobulin VDJ recombination. PLoS One 2013; 8:e68804. [PMID: 23874770 PMCID: PMC3712940 DOI: 10.1371/journal.pone.0068804] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/31/2013] [Indexed: 12/15/2022] Open
Abstract
PP4 phosphatase regulates a number of crucial processes but the role of PP4 in B cells has never been reported. We generated B cell-specific pp4 knockout mice and have identified an essential role for PP4 in B cell development. Deficiency of PP4 in B lineage cells leads to a strong reduction in pre-B cell numbers, an absence in immature B cells, and a complete loss of mature B cells. In PP4-deficient pro-B cells, immunoglobulin (Ig) DJ(H) recombination is impaired and Ig µ heavy chain expression is greatly decreased. In addition, PP4-deficient pro-B cells show an increase of DNA double-strand breaks at Ig loci. Consistent with their reduced numbers, residual PP4-deficient pre-B cells accumulate in the G1 phase, exhibit excessive DNA damage, and undergo increased apoptosis. Overexpression of transgenic Ig in PP4-deficient mice rescues the defect in B cell development such that the animals have normal numbers of IgM(+) B cells. Our study therefore reveals a novel function for PP4 in pro-B cell development through its promotion of V(H)DJ(H) recombination.
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Affiliation(s)
- Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
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83
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Fedorov DV, Kovaltsova SV, Evstuhina TA, Peshekhonov VT, Chernenkov AY, Korolev VG. HSM6 gene is identical to PSY4 gene in Saccharomyces cerevisiae yeasts. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413020063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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84
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Peters MJ, Broer L, Willemen HLDM, Eiriksdottir G, Hocking LJ, Holliday KL, Horan MA, Meulenbelt I, Neogi T, Popham M, Schmidt CO, Soni A, Valdes AM, Amin N, Dennison EM, Eijkelkamp N, Harris TB, Hart DJ, Hofman A, Huygen FJPM, Jameson KA, Jones GT, Launer LJ, Kerkhof HJM, de Kruijf M, McBeth J, Kloppenburg M, Ollier WE, Oostra B, Payton A, Rivadeneira F, Smith BH, Smith AV, Stolk L, Teumer A, Thomson W, Uitterlinden AG, Wang K, van Wingerden SH, Arden NK, Cooper C, Felson D, Gudnason V, Macfarlane GJ, Pendleton N, Slagboom PE, Spector TD, Völzke H, Kavelaars A, van Duijn CM, Williams FMK, van Meurs JBJ. Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region. Ann Rheum Dis 2013; 72:427-36. [PMID: 22956598 PMCID: PMC3691951 DOI: 10.1136/annrheumdis-2012-201742] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 07/19/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND OBJECTIVES Chronic widespread pain (CWP) is a common disorder affecting ∼10% of the general population and has an estimated heritability of 48-52%. In the first large-scale genome-wide association study (GWAS) meta-analysis, we aimed to identify common genetic variants associated with CWP. METHODS We conducted a GWAS meta-analysis in 1308 female CWP cases and 5791 controls of European descent, and replicated the effects of the genetic variants with suggestive evidence for association in 1480 CWP cases and 7989 controls. Subsequently, we studied gene expression levels of the nearest genes in two chronic inflammatory pain mouse models, and examined 92 genetic variants previously described associated with pain. RESULTS The minor C-allele of rs13361160 on chromosome 5p15.2, located upstream of chaperonin-containing-TCP1-complex-5 gene (CCT5) and downstream of FAM173B, was found to be associated with a 30% higher risk of CWP (minor allele frequency=43%; OR=1.30, 95% CI 1.19 to 1.42, p=1.2×10(-8)). Combined with the replication, we observed a slightly attenuated OR of 1.17 (95% CI 1.10 to 1.24, p=4.7×10(-7)) with moderate heterogeneity (I2=28.4%). However, in a sensitivity analysis that only allowed studies with joint-specific pain, the combined association was genome-wide significant (OR=1.23, 95% CI 1.14 to 1.32, p=3.4×10(-8), I2=0%). Expression levels of Cct5 and Fam173b in mice with inflammatory pain were higher in the lumbar spinal cord, not in the lumbar dorsal root ganglions, compared to mice without pain. None of the 92 genetic variants previously described were significantly associated with pain (p>7.7×10(-4)). CONCLUSIONS We identified a common genetic variant on chromosome 5p15.2 associated with joint-specific CWP in humans. This work suggests that CCT5 and FAM173B are promising targets in the regulation of pain.
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Affiliation(s)
- Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Linda Broer
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanneke L D M Willemen
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, The Netherlands
| | | | - Lynne J Hocking
- Aberdeen Pain Research Collaboration (Musculoskeletal Research), University of Aberdeen, Aberdeen, UK
| | - Kate L Holliday
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Michael A Horan
- Mental Health and Neurodegeneration Group, School Community Based Medicine, University of Manchester, Manchester, UK
| | - Ingrid Meulenbelt
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tuhina Neogi
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Maria Popham
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Carsten O Schmidt
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Anushka Soni
- NIHR Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Ana M Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Elaine M Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Niels Eijkelkamp
- Molecular Nociception Group, University College London, London, UK
| | - Tamara B Harris
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Deborah J Hart
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank J P M Huygen
- Department of Anaesthesiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karen A Jameson
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gareth T Jones
- Aberdeen Pain Research Collaboration (Epidemiology Group), University of Aberdeen, Aberdeen, UK
| | - Lenore J Launer
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Hanneke J M Kerkhof
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Marjolein de Kruijf
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
- Department of Anaesthesiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John McBeth
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - William E Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Antony Payton
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Blair H Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Albert V Smith
- Icelandic Heart Association Research Institute, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Alexander Teumer
- Institute of Functional Genomics, Ernst Moritz Arndt University Greifswald, University of Greifswald, Greifswald, Germany
| | - Wendy Thomson
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ke Wang
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sophie H van Wingerden
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nigel K Arden
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - David Felson
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association Research Institute, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Gary J Macfarlane
- Aberdeen Pain Research Collaboration (Epidemiology Group), University of Aberdeen, Aberdeen, UK
| | - Neil Pendleton
- Mental Health and Neurodegeneration Group, School Community Based Medicine, University of Manchester, Manchester, UK
| | - P Eline Slagboom
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Annemieke Kavelaars
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
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85
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Gissot M, Walker R, Delhaye S, Alayi TD, Huot L, Hot D, Callebaut I, Schaeffer-Reiss C, Dorsselaer AV, Tomavo S. Toxoplasma gondii Alba proteins are involved in translational control of gene expression. J Mol Biol 2013; 425:1287-301. [PMID: 23454356 DOI: 10.1016/j.jmb.2013.01.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/29/2012] [Accepted: 01/26/2013] [Indexed: 10/27/2022]
Abstract
Molecular mechanisms controlling gene expression in apicomplexan parasites remain poorly understood. Here, we report the characterization of two Toxoplasma gondii homologs of the ancient archeal Alba proteins named TgAlba1 and TgAlba2. The targeted disruption of TgAlba1 and TgAlba2 genes in both virulent type I and avirulent type II strains of T. gondii reveals that TgAlba proteins may have an important role in regulating stress response. We found that although the steady-state level of the Tgalba2 transcript is increased in the ΔTgalba1 null mutant parasites, the cognate TgAlba2 protein is undetectable, suggesting that TgAlba1 is required for translation of TgAlba2. Using a tandem affinity purification tag strategy combined with proteomic analyses, we provide evidence that many factors known to be involved in the translation machinery are co-purified with TgAlba1 and TgAlba2. We further performed RNA pull-down and microarray analyses to show that TgAlba1 and TgAlba2 bind to more than 30 RNAs including their own transcripts. Moreover, we demonstrate that the tight translational regulation of the TgAlba2 endogenous transcript relies on the presence of both its 3' untranslated region and that of the TgAlba1 protein. Thus, our findings on TgAlba1 and TgAlba2 are consistent with a role in gene-specific translation.
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Affiliation(s)
- Mathieu Gissot
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM 1019, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
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86
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Brechmann M, Mock T, Nickles D, Kiessling M, Weit N, Breuer R, Müller W, Wabnitz G, Frey F, Nicolay JP, Booken N, Samstag Y, Klemke CD, Herling M, Boutros M, Krammer PH, Arnold R. A PP4 holoenzyme balances physiological and oncogenic nuclear factor-kappa B signaling in T lymphocytes. Immunity 2012; 37:697-708. [PMID: 23084358 DOI: 10.1016/j.immuni.2012.07.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 07/09/2012] [Indexed: 11/24/2022]
Abstract
Signal transduction to nuclear factor-kappa B (NF-κB) involves multiple kinases and phosphorylated target proteins, but little is known about signal termination by dephosphorylation. By RNAi screening, we have identified protein phosphatase 4 regulatory subunit 1 (PP4R1) as a negative regulator of NF-κB activity in T lymphocytes. PP4R1 formed part of a distinct PP4 holoenzyme and bridged the inhibitor of NF-κB kinase (IKK) complex and the phosphatase PP4c, thereby directing PP4c activity to dephosphorylate and inactivate the IKK complex. PP4R1 expression was triggered upon activation and proliferation of primary human T lymphocytes and deficiency for PP4R1 caused sustained and increased IKK activity, T cell hyperactivation, and aberrant NF-κB signaling in NF-κB-addicted T cell lymphomas. Collectively, our results unravel PP4R1 as a previously unknown activation-associated negative regulator of IKK activity in lymphocytes whose downregulation promotes oncogenic NF-κB signaling in a subgroup of T cell lymphomas.
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Affiliation(s)
- Markus Brechmann
- Division of Immunogenetics, Tumor Immunology Program, German Cancer Research Center, Heidelberg, Germany
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87
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Moir RD, Willis IM. Regulation of pol III transcription by nutrient and stress signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:361-75. [PMID: 23165150 DOI: 10.1016/j.bbagrm.2012.11.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/06/2012] [Accepted: 11/08/2012] [Indexed: 12/29/2022]
Abstract
Transcription by RNA polymerase III (pol III) is responsible for ~15% of total cellular transcription through the generation of small structured RNAs such as tRNA and 5S RNA. The coordinate synthesis of these molecules with ribosomal protein mRNAs and rRNA couples the production of ribosomes and their tRNA substrates and balances protein synthetic capacity with the growth requirements of the cell. Ribosome biogenesis in general and pol III transcription in particular is known to be regulated by nutrient availability, cell stress and cell cycle stage and is perturbed in pathological states. High throughput proteomic studies have catalogued modifications to pol III subunits, assembly, initiation and accessory factors but most of these modifications have yet to be linked to functional consequences. Here we review our current understanding of the major points of regulation in the pol III transcription apparatus, the targets of regulation and the signaling pathways known to regulate their function. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Robyn D Moir
- Departments of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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88
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Nesvizhskii AI. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 2012; 12:1639-55. [PMID: 22611043 DOI: 10.1002/pmic.201100537] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Analysis of protein interaction networks and protein complexes using affinity purification and mass spectrometry (AP/MS) is among most commonly used and successful applications of proteomics technologies. One of the foremost challenges of AP/MS data is a large number of false-positive protein interactions present in unfiltered data sets. Here we review computational and informatics strategies for detecting specific protein interaction partners in AP/MS experiments, with a focus on incomplete (as opposite to genome wide) interactome mapping studies. These strategies range from standard statistical approaches, to empirical scoring schemes optimized for a particular type of data, to advanced computational frameworks. The common denominator among these methods is the use of label-free quantitative information such as spectral counts or integrated peptide intensities that can be extracted from AP/MS data. We also discuss related issues such as combining multiple biological or technical replicates, and dealing with data generated using different tagging strategies. Computational approaches for benchmarking of scoring methods are discussed, and the need for generation of reference AP/MS data sets is highlighted. Finally, we discuss the possibility of more extended modeling of experimental AP/MS data, including integration with external information such as protein interaction predictions based on functional genomics data.
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89
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Dunham WH, Mullin M, Gingras AC. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 2012; 12:1576-90. [PMID: 22611051 DOI: 10.1002/pmic.201100523] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.
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Affiliation(s)
- Wade H Dunham
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
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90
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Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmuller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global Gene Deletion Analysis Exploring Yeast Filamentous Growth. Science 2012; 337:1353-6. [DOI: 10.1126/science.1224339] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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91
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Byun HJ, Kim BR, Yoo R, Park SY, Rho SB. sMEK1 enhances gemcitabine anti-cancer activity through inhibition of phosphorylation of Akt/mTOR. Apoptosis 2012; 17:1095-103. [DOI: 10.1007/s10495-012-0751-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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92
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Abstract
Cell cycle transitions depend on protein phosphorylation and dephosphorylation. The discovery of cyclin-dependent kinases (CDKs) and their mode of activation by their cyclin partners explained many important aspects of cell cycle control. As the cell cycle is basically a series of recurrences of a defined set of events, protein phosphatases must obviously be as important as kinases. However, our knowledge about phosphatases lags well behind that of kinases. We still do not know which phosphatase(s) is/are truly responsible for dephosphorylating CDK substrates, and we know very little about whether and how protein phosphatases are regulated. Here, we summarize our present understanding of the phosphatases that are important in the control of the cell cycle and pose the questions that need to be answered as regards the regulation of protein phosphatases.
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93
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A novel 4EHP-GIGYF2 translational repressor complex is essential for mammalian development. Mol Cell Biol 2012; 32:3585-93. [PMID: 22751931 DOI: 10.1128/mcb.00455-12] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The binding of the eukaryotic initiation factor 4E (eIF4E) to the mRNA 5' cap structure is a rate-limiting step in mRNA translation initiation. eIF4E promotes ribosome recruitment to the mRNA. In Drosophila, the eIF4E homologous protein (d4EHP) forms a complex with binding partners to suppress the translation of distinct mRNAs by competing with eIF4E for binding the 5' cap structure. This repression mechanism is essential for the asymmetric distribution of proteins and normal embryonic development in Drosophila. In contrast, the physiological role of the mammalian 4EHP (m4EHP) was not known. In this study, we have identified the Grb10-interacting GYF protein 2 (GIGYF2) and the zinc finger protein 598 (ZNF598) as components of the m4EHP complex. GIGYF2 directly interacts with m4EHP, and this interaction is required for stabilization of both proteins. Disruption of the m4EHP-GIGYF2 complex leads to increased translation and perinatal lethality in mice. We propose a model by which the m4EHP-GIGYF2 complex represses translation of a subset of mRNAs during embryonic development, as was previously reported for d4EHP.
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94
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Kean MJ, Couzens AL, Gingras AC. Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins. Methods 2012; 57:400-8. [PMID: 22710030 DOI: 10.1016/j.ymeth.2012.06.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 06/04/2012] [Accepted: 06/08/2012] [Indexed: 12/24/2022] Open
Abstract
Reversible phosphorylation events regulate critical aspects of cellular biology by affecting protein conformation, cellular localization, enzymatic activity and associations with interaction partners. Kinases and phosphatases interact not only with their substrates but also with regulatory subunits and other proteins, including scaffolds. In recent years, affinity purification coupled to mass spectrometry (AP-MS) has proven to be a powerful tool to identify protein-protein interactions (PPIs) involving kinases and phosphatases. In this review we outline general considerations for successful AP-MS, and describe strategies that we have used to characterize the interactions of kinases and phosphatases in human cells.
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Affiliation(s)
- Michelle J Kean
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, 600 University Ave., Rm 992, Toronto, ON, Canada M5G 1X5
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95
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Huang Y, Jeong JS, Okamura J, Sook-Kim M, Zhu H, Guerrero-Preston R, Ratovitski EA. Global tumor protein p53/p63 interactome: making a case for cisplatin chemoresistance. Cell Cycle 2012; 11:2367-79. [PMID: 22672905 DOI: 10.4161/cc.20863] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cisplatin chemoresistance is a clinical problem that leads to treatment failure in various human epithelial cancers. Members of tumor protein (TP) p53 family play various critical roles in the multiple molecular mechanisms underlying the chemoresistance of tumor cells. However, the in-depth mechanisms of the cellular response to cisplatin-induced cell death are still under thorough investigation. We previously showed that squamous cell carcinoma (SCC) cells exposed to cisplatin display an ATM-dependent phosphorylation of ΔNp63α, leading to a specific function of the phosphorylated (p)-ΔNp63α transcription factor in cisplatin-sensitive tumor cells. We further found that SCC cells expressing non-p-ΔNp63α-S385G became cisplatin-resistant. Using quantitative mass-spectrometry of protein complexes labeled with isobaric tags, we showed that TP53 and ΔNp63α are involved in numerous protein-protein interactions, which are likely to be implicated in the response of tumor cells to cisplatin exposure. We found that p-ΔNp63α binds to the splicing complex, leading to repression of mRNA splicing and activation of ACIN1-mediated cell death pathway. In contrast to p-ΔNp63α, non-p-ΔNp63α fails to bind the critical members of the splicing complex, thereby leading to activation of RNA splicing and reduction of cell death pathway. Overall, our studies provide an integrated proteomic platform in making a case for the role of the p53/p63 interactome in cisplatin chemoresistance.
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Affiliation(s)
- Yiping Huang
- Department of Dermatology, Institute of Basic Biomedical Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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96
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Abstract
This review traces the historical origins and conceptual developments leading to the current state of knowledge of the three superfamilies of protein Ser/Thr phosphatases. 'PR enzyme' was identified as an enzyme that inactivates glycogen phosphorylase, although it took 10 years before this ugly duckling was recognized for its true identity as a protein Ser/Thr phosphatase. Ethanol denaturation for purification in the 1970s yielded a phosphatase that exhibited broad specificity, which was resolved into type-1 and type-2 phosphatases in the 1980s. More recent developments show that regulation and specificity are achieved through assembly of multisubunit holoenzymes, transient phosphorylation and the action of inhibitor proteins. Still not widely appreciated, there are hundreds of discrete protein Ser/Thr phosphatases available to counteract protein kinases, offering potential therapeutic targets. Signalling networks and modelling schemes need to incorporate the full gamut of protein Ser/Thr phosphatases and their interconnections.
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Affiliation(s)
- David L Brautigan
- Department of Microbiology, Immunology and Cancer Biology, Center for Cell Signaling, University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.
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97
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Bosio Y, Berto G, Camera P, Bianchi F, Ambrogio C, Claus P, Di Cunto F. PPP4R2 regulates neuronal cell differentiation and survival, functionally cooperating with SMN. Eur J Cell Biol 2012; 91:662-74. [PMID: 22559936 DOI: 10.1016/j.ejcb.2012.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 02/08/2012] [Accepted: 03/12/2012] [Indexed: 01/28/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a human disease caused by reduced levels of the Survival of Motor Neuron (SMN) protein, leading to progressive loss of motor neurons and muscular paralysis. However, it is still not very clear why these cells are specifically sensitive to SMN levels. Therefore, understanding which proteins may functionally interact with SMN in a neuronal context is a very important issue. PPP4R2, a regulatory subunit of the protein phosphatase 4 (PPP4C), was previously identified as a functional interactor of the SMN complex, but has never been studied in neuronal cells. In this report, we show that PPP4R2 displays a very dynamic intracellular localization in mouse and rat neuronal cell lines and in rat primary hippocampal neurons, strongly correlating with differentiation. More importantly, we found that PPP4R2 loss of function impairs the differentiation of the mouse motor-neuronal cell line NSC-34, an effect that can be counteracted by SMN overexpression. In addition, we show that PPP4R2 may specifically protect NSC-34 cells from DNA damage-induced apoptosis and that it is capable to functionally cooperate with SMN in this activity. Our data indicate that PPP4R2 is a SMN partner that may modulate the differentiation and survival of neuronal cells.
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Affiliation(s)
- Ylenia Bosio
- Molecular Biotechnology Center, Department of Genetics, Biology and Biochemistry, University of Turin, Italy
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98
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Sents W, Ivanova E, Lambrecht C, Haesen D, Janssens V. The biogenesis of active protein phosphatase 2A holoenzymes: a tightly regulated process creating phosphatase specificity. FEBS J 2012; 280:644-61. [PMID: 22443683 DOI: 10.1111/j.1742-4658.2012.08579.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protein phosphatase type 2A (PP2A) enzymes constitute a large family of Ser/Thr phosphatases with multiple functions in cellular signaling and physiology. The composition of heterotrimeric PP2A holoenzymes, resulting from the combinatorial assembly of a catalytic C subunit, a structural A subunit, and regulatory B-type subunit, provides the essential determinants for substrate specificity, subcellular targeting, and fine-tuning of phosphatase activity, largely explaining why PP2A is functionally involved in so many diverse physiological processes, sometimes in seemingly opposing ways. In this review, we highlight how PP2A holoenzyme biogenesis and enzymatic activity are controlled by a sophisticatedly coordinated network of five PP2A modulators, consisting of α4, phosphatase 2A phosphatase activator (PTPA), leucine carboxyl methyl transferase 1 (LCMT1), PP2A methyl esterase 1 (PME-1) and, potentially, target of rapamycin signaling pathway regulator-like 1 (TIPRL1), which serve to prevent promiscuous phosphatase activity until the holoenzyme is completely assembled. Likewise, these modulators may come into play when PP2A holoenzymes are disassembled following particular cellular stresses. Malfunctioning of these cellular control mechanisms contributes to human disease. The potential therapeutic benefits or pitfalls of interfering with these regulatory mechanisms will be briefly discussed.
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Affiliation(s)
- Ward Sents
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium
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99
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Gesing S, Schindler D, Fränzel B, Wolters D, Nowrousian M. The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. Mol Microbiol 2012; 84:748-65. [PMID: 22463819 DOI: 10.1111/j.1365-2958.2012.08058.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ascomycetes develop four major types of fruiting bodies that share a common ancestor, and a set of common core genes most likely controls this process. One way to identify such genes is to search for conserved expression patterns. We analysed microarray data of Fusarium graminearum and Sordaria macrospora, identifying 78 genes with similar expression patterns during fruiting body development. One of these genes was asf1 (anti-silencing function 1), encoding a predicted histone chaperone. asf1 expression is also upregulated during development in the distantly related ascomycete Pyronema confluens. To test whether asf1 plays a role in fungal development, we generated an S. macrospora asf1 deletion mutant. The mutant is sterile and can be complemented to fertility by transformation with the wild-type asf1 and its P. confluens homologue. An ASF1-EGFP fusion protein localizes to the nucleus. By tandem-affinity purification/mass spectrometry as well as yeast two-hybrid analysis, we identified histones H3 and H4 as ASF1 interaction partners. Several developmental genes are dependent on asf1 for correct transcriptional expression. Deletion of the histone chaperone genes rtt106 and cac2 did not cause any developmental phenotypes. These data indicate that asf1 of S. macrospora encodes a conserved histone chaperone that is required for fruiting body development.
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Affiliation(s)
- Stefan Gesing
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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100
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Gingras AC, Raught B. Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett 2012; 586:2723-31. [PMID: 22710165 DOI: 10.1016/j.febslet.2012.03.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 03/30/2012] [Accepted: 03/30/2012] [Indexed: 10/28/2022]
Abstract
The past 10 years have witnessed a dramatic proliferation in the availability of protein interaction data. However, for interaction mapping based on affinity purification coupled with mass spectrometry (AP-MS), there is a wealth of information present in the datasets that often goes unrecorded in public repositories, and as such remains largely unexplored. Further, how this type of data is represented and used by bioinformaticians has not been well established. Here, we point out some common mistakes in how AP-MS data are handled, and describe how protein complex organization and interaction dynamics can be inferred using quantitative AP-MS approaches.
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Affiliation(s)
- Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Canada.
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