201
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Qin GM, Li RY, Zhao XM. PhosD: inferring kinase-substrate interactions based on protein domains. Bioinformatics 2017; 33:1197-1204. [PMID: 28031187 DOI: 10.1093/bioinformatics/btw792] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022] Open
Abstract
Motivation Identifying the kinase-substrate relationships is vital to understanding the phosphorylation events and various biological processes, especially signal transductions. Although large amount of phosphorylation sites have been detected, unfortunately, it is rarely known which kinases activate those sites. Despite distinct computational approaches have been proposed to predict the kinase-substrate interactions, the prediction accuracy still needs to be improved. Results In this paper, we propose a novel probabilistic model named as PhosD to predict kinase-substrate relationships based on protein domains with the assumption that kinase-substrate interactions are accomplished with kinase-domain interactions. By further taking into account protein-protein interactions, our PhosD outperforms other popular approaches on several benchmark datasets with higher precision. In addition, some of our predicted kinase-substrate relationships are validated by signaling pathways, indicating the predictive power of our approach. Furthermore, we notice that given a kinase, the more substrates are known for the kinase the more accurate its predicted substrates will be, and the domains involved in kinase-substrate interactions are found to be more conserved across proteins phosphorylated by multiple kinases. These findings can help develop more efficient computational approaches in the future. Availability and Implementation The data and results are available at http://comp-sysbio.org/phosd. Contact xm_zhao@tongji.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gui-Min Qin
- School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China.,School of Software
| | - Rui-Yi Li
- School of Computer Science and Technology, Xidian University, Xi'an 710071, China
| | - Xing-Ming Zhao
- School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China
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202
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Abstract
Alzheimer's disease (AD) is characterized by accumulation of the β-amyloid peptide (Aβ), which is generated through sequential proteolysis of the amyloid precursor protein (APP), first by the action of β-secretase, generating the β-C-terminal fragment (βCTF), and then by the Presenilin 1 (PS1) enzyme in the γ-secretase complex, generating Aβ. γ-Secretase is an intramembranous protein complex composed of Aph1, Pen2, Nicastrin, and Presenilin 1. Although it has a central role in the pathogenesis of AD, knowledge of the mechanisms that regulate PS1 function is limited. Here, we show that phosphorylation of PS1 at Ser367 does not affect γ-secretase activity, but has a dramatic effect on Aβ levels in vivo. We identified CK1γ2 as the endogenous kinase responsible for the phosphorylation of PS1 at Ser367. Inhibition of CK1γ leads to a decrease in PS1 Ser367 phosphorylation and an increase in Aβ levels in cultured cells. Transgenic mice in which Ser367 of PS1 was mutated to Ala, show dramatic increases in Aβ peptide and in βCTF levels in vivo. Finally, we show that this mutation impairs the autophagic degradation of βCTF, resulting in its accumulation and increased levels of Aβ peptide and plaque load in the brain. Our results demonstrate that PS1 regulates Aβ levels by a unique bifunctional mechanism. In addition to its known role as the catalytic subunit of the γ-secretase complex, selective phosphorylation of PS1 on Ser367 also decreases Aβ levels by increasing βCTF degradation through autophagy. Elucidation of the mechanism by which PS1 regulates βCTF degradation may aid in the development of potential therapies for Alzheimer's disease.
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203
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Bezabih G, Cheng H, Han B, Feng M, Xue Y, Hu H, Li J. Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera). Sci Rep 2017; 7:1973. [PMID: 28512345 PMCID: PMC5434016 DOI: 10.1038/s41598-017-02192-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/24/2017] [Indexed: 11/09/2022] Open
Abstract
The honeybee brain is a central organ in regulating wide ranges of honeybee biology, including life transition from nurse to forager bees. Knowledge is still lacking on how protein phosphorylation governs the neural activity to drive the age-specific labor division. The cerebral phosphoproteome of nurse and forager honeybees was characterized using Ti4+-IMAC phosphopeptide enrichment mass-spectrometry-based proteomics and protein kinases (PKs) were predicted. There were 3,077 phosphosites residing on 3,234 phosphopeptides from 1004 phosphoproteins in the nurse bees. For foragers the numbers were 3,056, 3,110, and 958, respectively. Notably, among the total 231 PKs in honeybee proteome, 179 novel PKs were predicted in the honeybee brain, of which 88 were experimentally identified. Proteins involved in wide scenarios of pathways were phosphorylated depending on age: glycolysis/gluconeogenesis, AGE/RAGE and phosphorylation in nurse bees and metal ion transport, ATP metabolic process and phototransduction in forager bees. These observations suggest that phosphorylation is vital to the tuning of protein activity to regulate cerebral function according to the biological duties as nursing and foraging bees. The data provides valuable information on phosphorylation signaling in the honeybee brain and potentially useful resource to understand the signaling mechanism in honeybee neurobiology and in other social insects as well.
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Affiliation(s)
- Gebreamlak Bezabih
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, 100093, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Bin Han
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, 100093, China
| | - Mao Feng
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, 100093, China
| | - Yu Xue
- Department of Bioinformatics & Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Han Hu
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, 100093, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, 100093, China.
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204
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Quan Q, Feng J, Lui LT, Shi T, Chu IK. Phosphoproteome of crab-eating macaque cerebral cortex characterized through multidimensional reversed-phase liquid chromatography/mass spectrometry with tandem anion/cation exchange columns. J Chromatogr A 2017; 1498:196-206. [DOI: 10.1016/j.chroma.2017.01.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/06/2023]
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205
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Wang B, Wang M, Li A. Prediction of post-translational modification sites using multiple kernel support vector machine. PeerJ 2017; 5:e3261. [PMID: 28462053 PMCID: PMC5410141 DOI: 10.7717/peerj.3261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/01/2017] [Indexed: 01/12/2023] Open
Abstract
Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.
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Affiliation(s)
- BingHua Wang
- University of Science and Technology of China, School of Information Science and Technology, Hefei, China
| | - Minghui Wang
- University of Science and Technology of China, School of Information Science and Technology, Hefei, China
- University of Science and Technology of China, Centers for Biomedical Engineering, Hefei, China
| | - Ao Li
- University of Science and Technology of China, School of Information Science and Technology, Hefei, China
- University of Science and Technology of China, Centers for Biomedical Engineering, Hefei, China
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206
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Xu X, Huang S, Zhang B, Huang F, Chi W, Fu J, Wang G, Li S, Jiang Q, Zhang C. DNA replication licensing factor Cdc6 and Plk4 kinase antagonistically regulate centrosome duplication via Sas-6. Nat Commun 2017; 8:15164. [PMID: 28447620 PMCID: PMC5414174 DOI: 10.1038/ncomms15164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 03/03/2017] [Indexed: 12/12/2022] Open
Abstract
Centrosome number is tightly controlled during the cell cycle to ensure proper spindle assembly and cell division. However, the underlying mechanism that controls centrosome number remains largely unclear. We show herein that the DNA replication licensing factor Cdc6 is recruited to the proximal side of the centrioles via cyclin A to negatively regulate centrosome duplication by binding and inhibiting the cartwheel protein Sas-6 from forming a stable complex with another centriole duplication core protein, STIL. We further demonstrate that Cdc6 colocalizes with Plk4 at the centrosome, and interacts with Plk4 during S phase. Plk4 disrupts the interaction between Sas-6 and Cdc6, and suppresses the inhibitory role of Cdc6 on Sas-6 by phosphorylating Cdc6. Overexpressing wild-type Cdc6 or Plk4-unphosphorylatable Cdc6 mutant 2A reduces centrosome over-duplication caused by Plk4 overexpression or hydroxyurea treatment. Taken together, our data demonstrate that Cdc6 and Plk4 antagonistically control proper centrosome duplication during the cell cycle. Centrosome duplication is synchronized with cell cycle events but how this is regulated at a molecular level is unclear. Here, the authors show that the DNA replication licensing factor Cdc6 restrains centrosome duplication via binding and inhibiting Sas-6, and the inhibition of Cdc6 on Sas-6 is negatively regulated by Plk4 phosphorylation.
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Affiliation(s)
- Xiaowei Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shijiao Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Boyan Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Fan Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wangfei Chi
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jingyan Fu
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Gang Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Si Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Qing Jiang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Chuanmao Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
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207
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Geng Q, Liu J, Gong Z, Chen S, Chen S, Li X, Lu Y, Zhu X, Lin HK, Xu D. Phosphorylation by mTORC1 stablizes Skp2 and regulates its oncogenic function in gastric cancer. Mol Cancer 2017; 16:83. [PMID: 28446188 PMCID: PMC5407005 DOI: 10.1186/s12943-017-0649-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 04/05/2017] [Indexed: 12/17/2022] Open
Abstract
Background Both mTOR and Skp2 play critical roles in gastric cancer (GC) tumorigenesis. However, potential mechanisms for the association between these two proteins remains unidentified. Methods The regulatory role for mTORC1 in Skp2 stability was tested using ubiquitination assay. The functions of p-Skp2 (phosphorylation of Skp2) were studied in vitro and in vivo. Expression of p-Skp2 and p-mTOR (phosphorylation of mTOR) were shown in GC lines and in 169 human primary GC tissues. Results mTORC1 can directly interact with Skp2 and phosphorylated Skp2 at Ser64, which sequentially protect Skp2 from ubiquitination and degradation. Furthermore, the phospho-deficient p-Skp2 (S64) mutant significantly suppresses GC cell proliferation and tumorigenesis. The expression of p-Skp2 was associated with p-mTOR in GC cell lines and tissues. Interestingly, the combination of p-Skp2 and p-mTOR was a better predictor of survival than either factor alone. Conclusion The mTORC1 function to regulate Skp2 by Ser64 phosphorylation may represent an oncogenic event in GC tumorigenesis. Moreover, our study also indicates that Skp2 Ser64 expression is a potential indicator in the treatment of GC patients using mTORC1 inhibitor. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0649-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qirong Geng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Hematology Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jianjun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Gastric Surgery, Sun Yat-sen University Cancer Center, 651# East Dongfeng road, Guangzhou, 510060, Guangdong Province, China
| | - Zhaohui Gong
- Institute of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Shangxiang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Gastric Surgery, Sun Yat-sen University Cancer Center, 651# East Dongfeng road, Guangzhou, 510060, Guangdong Province, China
| | - Shuai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiaoxing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yue Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Hematology Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaofeng Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hui-Kuan Lin
- Department of Molecular and Cellular Oncology, M.D. Anderson Cancer Center, The University of Texas, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Dazhi Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China. .,Department of Gastric Surgery, Sun Yat-sen University Cancer Center, 651# East Dongfeng road, Guangzhou, 510060, Guangdong Province, China.
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208
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Kishore A, Hall RA. Disease-associated extracellular loop mutations in the adhesion G protein-coupled receptor G1 (ADGRG1; GPR56) differentially regulate downstream signaling. J Biol Chem 2017; 292:9711-9720. [PMID: 28424266 DOI: 10.1074/jbc.m117.780551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/17/2017] [Indexed: 12/31/2022] Open
Abstract
Mutations to the adhesion G protein-coupled receptor ADGRG1 (G1; also known as GPR56) underlie the neurological disorder bilateral frontoparietal polymicrogyria. Disease-associated mutations in G1 studied to date are believed to induce complete loss of receptor function through disruption of either receptor trafficking or signaling activity. Given that N-terminal truncation of G1 and other adhesion G protein-coupled receptors has been shown to significantly increase the receptors' constitutive signaling, we examined two different bilateral frontoparietal polymicrogyria-inducing extracellular loop mutations (R565W and L640R) in the context of both full-length and N-terminally truncated (ΔNT) G1. Interestingly, we found that these mutations reduced surface expression of full-length G1 but not G1-ΔNT in HEK-293 cells. Moreover, the mutations ablated receptor-mediated activation of serum response factor luciferase, a classic measure of Gα12/13-mediated signaling, but had no effect on G1-mediated signaling to nuclear factor of activated T cells (NFAT) luciferase. Given these differential signaling results, we sought to further elucidate the pathway by which G1 can activate NFAT luciferase. We found no evidence that ΔNT activation of NFAT is dependent on Gαq/11-mediated or β-arrestin-mediated signaling but rather involves liberation of Gβγ subunits and activation of calcium channels. These findings reveal that disease-associated mutations to the extracellular loops of G1 differentially alter receptor trafficking, depending on the presence of the N terminus, and differentially alter signaling to distinct downstream pathways.
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Affiliation(s)
- Ayush Kishore
- From the Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Randy A Hall
- From the Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322
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209
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de Polo A, Luo Z, Gerarduzzi C, Chen X, Little JB, Yuan ZM. AXL receptor signalling suppresses p53 in melanoma through stabilization of the MDMX-MDM2 complex. J Mol Cell Biol 2017; 9:154-165. [PMID: 27927748 PMCID: PMC5907837 DOI: 10.1093/jmcb/mjw045] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
Deregulation of the tyrosine kinase signalling is often associated with tumour progression and drug resistance, but its underlying mechanisms are only partly understood. In this study, we investigated the effects of the receptor tyrosine kinase AXL on the stability of the MDMX-MDM2 heterocomplex and the activity of p53 in melanoma cells. Our data demonstrated that AXL overexpression or activation through growth arrest-specific 6 (Gas6) ligand stimulation increases MDMX and MDM2 protein levels and decreases p53 activity. Upon activation, AXL stabilizes MDMX through a post-translational modification that involves phosphorylation of MDMX on the phosphosite Ser314, leading to increased affinity between MDMX and MDM2 and favouring MDMX nuclear translocation. Ser314 phosphorylation can also protect MDMX from MDM2-mediated degradation, leading to stabilization of the MDMX-MDM2 complex. We identified CDK4/6 and p38 MAPK as the two kinases mediating AXL-induced modulation of the MDMX-MDM2 complex, and demonstrated that suppression of AXL, either through siRNA silencing or pharmacological inhibition, increases expression levels of p53 target genes P21, MDM2, and PUMA, improves p53 pathway response to chemotherapy, and sensitizes cells to both Cisplatin and Vemurafenib. Our findings offer an insight into a novel signalling axis linking AXL to p53 and provide a potentially druggable pathway to restore p53 function in melanoma.
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Affiliation(s)
- Anna de Polo
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zhongling Luo
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Casimiro Gerarduzzi
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - John B. Little
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zhi-Min Yuan
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Correspondence to: Zhi-Min Yuan, E-mail:
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210
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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211
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Godínez-Palma SK, Rosas-Bringas FR, Rosas-Bringas OG, García-Ramírez E, Zamora-Zaragoza J, Vázquez-Ramos JM. Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D-cyclin-dependent kinase complexes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1585-1597. [PMID: 28369656 PMCID: PMC5444471 DOI: 10.1093/jxb/erx054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The family of maize Kip-related proteins (KRPs) has been studied and a nomenclature based on the relationship to rice KRP genes is proposed. Expression studies of KRP genes indicate that all are expressed at 24 h of seed germination but expression is differential in the different tissues of maize plantlets. Recombinant KRP1;1 and KRP4;2 proteins, members of different KRP classes, were used to study association to and inhibitory activity on different maize cyclin D (CycD)-cyclin-dependent kinase (CDK) complexes. Kinase activity in CycD2;2-CDK, CycD4;2-CDK, and CycD5;3-CDK complexes was inhibited by both KRPs; however, only KRP1;1 inhibited activity in the CycD6;1-CDK complex, not KRP4;2. Whereas KRP1;1 associated with either CycD2;2 or CycD6;1, and to cyclin-dependent kinase A (CDKA) recombinant proteins, forming ternary complexes, KRP4;2 bound CDKA and CycD2;2 but did not bind CycD6;1, establishing a differential association capacity. All CycD-CDK complexes included here phosphorylated both the retinoblastoma-related (RBR) protein and the two KRPs; interestingly, while KRP4;2 phosphorylated by the CycD2;2-CDK complex increased its inhibitory capacity, when phosphorylated by the CycD6;1-CDK complex the inhibitory capacity was reduced or eliminated. Evidence suggests that the phosphorylated residues in KRP4;2 may be different for every kinase, and this would influence its performance as a cyclin-CDK inhibitor.
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Affiliation(s)
- Silvia K Godínez-Palma
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Fernando R Rosas-Bringas
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
- I. Medizinische Klinik and Poliklinik, Universitätsmedizin der Johannes Gutenberg-Universität Mainz Obere Zahlbacherstr. 63 55131 Mainz, Germany
| | - Omar G Rosas-Bringas
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Jorge Zamora-Zaragoza
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Jorge M Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
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212
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Baravalle R, Di Nardo G, Bandino A, Barone I, Catalano S, Andò S, Gilardi G. Impact of R264C and R264H polymorphisms in human aromatase function. J Steroid Biochem Mol Biol 2017; 167:23-32. [PMID: 27702664 DOI: 10.1016/j.jsbmb.2016.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/20/2016] [Accepted: 09/28/2016] [Indexed: 12/23/2022]
Abstract
The cytochrome P450 aromatase is involved in the last step of sex hormones biosynthesis by converting androgens into estrogens. The human enzyme is highly polymorphic and literature data correlate aromatase single nucleotide polymorphisms to the onset of pathologies such as breast cancer and neurodegenerative diseases. The aims of this study were i) to study the influence of the mutations R264C and R264H on the structure-function of the enzyme also upon phosphorylation by selected kinases and ii) to compare the activity of the variants to that of aromatase wild type in two different cell lines. Far-UV circular dichroism spectroscopy, thermal denaturation experiments and CO-binding assay showed that the two polymorphic variants are correctly folded. Steady-state kinetics experiments showed that rArom R264C and R264H exhibit a 1.5 and 3.4 folds lower catalytic efficiency, respectively, when compared to the wild type protein. Since R264 is part of the consensus motif of PKA and PKG1, phosphorylation experiments were performed to study the effect on aromatase function. Phosphorylation by PKA caused a decrease in activity by 36.2%, 49.3% and 27.9% in the wild type, R264C and R264H proteins respectively. Phosphorylation by PKG1 was also found to decrease the activity by 30.3%, 30.5% and 15.4% in the wild type, R264C and R264H proteins respectively. Experiments performed on the three full-length proteins expressed in human MCF-7 breast cancer cells and rat ST14A neuronal cells showed that, depending on the cell line used, the activity of the proteins is different, implicating different cellular mechanisms modulating aromatase activity. This work demonstrate that R264 polymorphism causes an intrinsic alteration of aromatase activity together with a different consensus for phosphorylation by different kinases, indicating that estrogen production can be different when such mutations are present. These findings are significant in understanding the onset and treatment of pathologies in which aromatase has been shown to be involved.
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Affiliation(s)
- Roberta Baravalle
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; CrisDi, Interdepartmental Center for Crystallography, via Pietro Giuria 7, 10125, Torino, Italy
| | - Andrea Bandino
- Department of Medicine and Experimental Oncology, University of Torino, Via Michelangelo 27, 10126, Torino, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy; CrisDi, Interdepartmental Center for Crystallography, via Pietro Giuria 7, 10125, Torino, Italy.
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213
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Cassier E, Gallay N, Bourquard T, Claeysen S, Bockaert J, Crépieux P, Poupon A, Reiter E, Marin P, Vandermoere F. Phosphorylation of β-arrestin2 at Thr 383 by MEK underlies β-arrestin-dependent activation of Erk1/2 by GPCRs. eLife 2017; 6. [PMID: 28169830 PMCID: PMC5325621 DOI: 10.7554/elife.23777] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/06/2017] [Indexed: 01/14/2023] Open
Abstract
In addition to their role in desensitization and internalization of G protein-coupled receptors (GPCRs), β-arrestins are essential scaffolds linking GPCRs to Erk1/2 signaling. However, their role in GPCR-operated Erk1/2 activation differs between GPCRs and the underlying mechanism remains poorly characterized. Here, we show that activation of serotonin 5-HT2C receptors, which engage Erk1/2 pathway via a β-arrestin-dependent mechanism, promotes MEK-dependent β-arrestin2 phosphorylation at Thr383, a necessary step for Erk recruitment to the receptor/β-arrestin complex and Erk activation. Likewise, Thr383 phosphorylation is involved in β-arrestin-dependent Erk1/2 stimulation elicited by other GPCRs such as β2-adrenergic, FSH and CXCR4 receptors, but does not affect the β-arrestin-independent Erk1/2 activation by 5-HT4 receptor. Collectively, these data show that β-arrestin2 phosphorylation at Thr383 underlies β-arrestin-dependent Erk1/2 activation by GPCRs. DOI:http://dx.doi.org/10.7554/eLife.23777.001
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Affiliation(s)
- Elisabeth Cassier
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France.,INSERM, U1191, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Nathalie Gallay
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRS, UMR7247, Nouzilly, France.,Université François Rabelais, Tours, France
| | - Thomas Bourquard
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRS, UMR7247, Nouzilly, France.,Université François Rabelais, Tours, France
| | - Sylvie Claeysen
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France.,INSERM, U1191, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Joël Bockaert
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France.,INSERM, U1191, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Pascale Crépieux
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRS, UMR7247, Nouzilly, France.,Université François Rabelais, Tours, France
| | - Anne Poupon
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRS, UMR7247, Nouzilly, France.,Université François Rabelais, Tours, France
| | - Eric Reiter
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRS, UMR7247, Nouzilly, France.,Université François Rabelais, Tours, France
| | - Philippe Marin
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France.,INSERM, U1191, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Franck Vandermoere
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France.,INSERM, U1191, Montpellier, France.,Université de Montpellier, Montpellier, France
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214
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Abstract
Progression through the meiotic cell cycle must be strictly regulated in oocytes to generate viable embryos and offspring. During mitosis, the kinesin motor protein Kif4 is indispensable for chromosome condensation and separation, midzone formation and cytokinesis. Additionally, the bioactivity of Kif4 is dependent on phosphorylation via Aurora Kinase B and Cdk1, which regulate Kif4 function throughout mitosis. Here, we examine the role of Kif4 in mammalian oocyte meiosis. Kif4 localized in the cytoplasm throughout meiosis I and II, but was also observed to have a dynamic subcellular distribution, associating with both microtubules and kinetochores at different stages of development. Co-localization and proximity ligation assays revealed that the kinetochore proteins, CENP-C and Ndc80, are potential Kif4 interacting proteins. Functional analysis of Kif4 in oocytes via antisense knock-down demonstrated that this protein was not essential for meiosis I completion. However, Kif4 depleted oocytes displayed enlarged polar bodies and abnormal metaphase II spindles, indicating an essential role for this protein for correct asymmetric cell division in meiosis I. Further investigation of the phosphoregulation of meiotic Kif4 revealed that Aurora Kinase and Cdk activity is critical for Kif4 kinetochore localization and interaction with Ndc80 and CENP-C. Finally, Kif4 protein but not gene expression was found to be upregulated with age, suggesting a role for this protein in the decline of oocyte quality with age.
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215
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An Y, Wang J, Li C, Revote J, Zhang Y, Naderer T, Hayashida M, Akutsu T, Webb GI, Lithgow T, Song J. SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. Sci Rep 2017; 7:41031. [PMID: 28112271 PMCID: PMC5253721 DOI: 10.1038/srep41031] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/14/2016] [Indexed: 12/28/2022] Open
Abstract
Bacteria translocate effector molecules to host cells through highly evolved secretion systems. By definition, the function of these effector proteins is to manipulate host cell biology and the sequence, structural and functional annotations of these effector proteins will provide a better understanding of how bacterial secretion systems promote bacterial survival and virulence. Here we developed a knowledgebase, termed SecretEPDB (Bacterial Secreted Effector Protein DataBase), for effector proteins of type III secretion system (T3SS), type IV secretion system (T4SS) and type VI secretion system (T6SS). SecretEPDB provides enriched annotations of the aforementioned three classes of effector proteins by manually extracting and integrating structural and functional information from currently available databases and the literature. The database is conservative and strictly curated to ensure that every effector protein entry is supported by experimental evidence that demonstrates it is secreted by a T3SS, T4SS or T6SS. The annotations of effector proteins documented in SecretEPDB are provided in terms of protein characteristics, protein function, protein secondary structure, Pfam domains, metabolic pathway and evolutionary details. It is our hope that this integrated knowledgebase will serve as a useful resource for biological investigation and the generation of new hypotheses for research efforts aimed at bacterial secretion systems.
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Affiliation(s)
- Yi An
- College of Information Engineering, Northwest A&F University, Yangling 712100, China.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Jiawei Wang
- School of Electronic and Computer Engineering, Peking University, Beijing 100871, China
| | - Chen Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - Yang Zhang
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Thomas Naderer
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Morihiro Hayashida
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Jiangning Song
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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216
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Awan FM, Obaid A, Ikram A, Janjua HA. Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach. Int J Mol Sci 2017; 18:ijms18010139. [PMID: 28085066 PMCID: PMC5297772 DOI: 10.3390/ijms18010139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022] Open
Abstract
Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC). Post-translational modifications (PTMs) and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A), 1 in LC3B (S92C), 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H) and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C) coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.
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Affiliation(s)
- Faryal Mehwish Awan
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad 44000, Pakistan.
| | - Ayesha Obaid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad 44000, Pakistan.
| | - Aqsa Ikram
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad 44000, Pakistan.
| | - Hussnain Ahmed Janjua
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12 Islamabad 44000, Pakistan.
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217
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Alfonzo-Méndez MA, Alcántara-Hernández R, García-Sáinz JA. Novel Structural Approaches to Study GPCR Regulation. Int J Mol Sci 2016; 18:E27. [PMID: 28025563 PMCID: PMC5297662 DOI: 10.3390/ijms18010027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/15/2016] [Accepted: 12/21/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Upon natural agonist or pharmacological stimulation, G protein-coupled receptors (GPCRs) are subjected to posttranslational modifications, such as phosphorylation and ubiquitination. These posttranslational modifications allow protein-protein interactions that turn off and/or switch receptor signaling as well as trigger receptor internalization, recycling or degradation, among other responses. Characterization of these processes is essential to unravel the function and regulation of GPCR. METHODS In silico analysis and methods such as mass spectrometry have emerged as novel powerful tools. Both approaches have allowed proteomic studies to detect not only GPCR posttranslational modifications and receptor association with other signaling macromolecules but also to assess receptor conformational dynamics after ligand (agonist/antagonist) association. RESULTS this review aims to provide insights into some of these methodologies and to highlight how their use is enhancing our comprehension of GPCR function. We present an overview using data from different laboratories (including our own), particularly focusing on free fatty acid receptor 4 (FFA4) (previously known as GPR120) and α1A- and α1D-adrenergic receptors. From our perspective, these studies contribute to the understanding of GPCR regulation and will help to design better therapeutic agents.
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Affiliation(s)
- Marco A Alfonzo-Méndez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Rocío Alcántara-Hernández
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - J Adolfo García-Sáinz
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico.
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218
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The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport. Pharmaceuticals (Basel) 2016; 9:ph9040080. [PMID: 28009816 PMCID: PMC5198054 DOI: 10.3390/ph9040080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022] Open
Abstract
The pleiotropic serine/threonine protein kinase CK2 was the first kinase discovered. It is renowned for its role in cell proliferation and anti-apoptosis. The complexity of this kinase is well reflected by the findings of past decades in terms of its heterotetrameric structure, subcellular location, constitutive activity and the extensive catalogue of substrates. With the advent of non-biased high-throughput functional genomics such as genome-wide deletion mutant screening, novel aspects of CK2 functionality have been revealed. Our recent discoveries using the model organism Saccharomyces cerevisiae and mammalian cells demonstrate that CK2 regulates metal toxicity. Extensive literature search reveals that there are few but elegant works on the role of CK2 in regulating the sodium and zinc channels. As both CK2 and metal ions are key players in cell biology and oncogenesis, understanding the details of CK2’s regulation of metal ion homeostasis has a direct bearing on cancer research. In this review, we aim to garner the recent data and gain insights into the role of CK2 in metal ion transport.
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219
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Cheng Z, Zhu Q, Dee R, Opheim Z, Mack CP, Cyr DM, Taylor JM. Focal Adhesion Kinase-mediated Phosphorylation of Beclin1 Protein Suppresses Cardiomyocyte Autophagy and Initiates Hypertrophic Growth. J Biol Chem 2016; 292:2065-2079. [PMID: 27994061 DOI: 10.1074/jbc.m116.758268] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/15/2016] [Indexed: 01/11/2023] Open
Abstract
Autophagy is an evolutionarily conserved intracellular degradation/recycling system that is essential for cellular homeostasis but is dysregulated in a number of diseases, including myocardial hypertrophy. Although it is clear that limiting or accelerating autophagic flux can result in pathological cardiac remodeling, the physiological signaling pathways that fine-tune cardiac autophagy are poorly understood. Herein, we demonstrated that stimulation of cardiomyocytes with phenylephrine (PE), a well known hypertrophic agonist, suppresses autophagy and that activation of focal adhesion kinase (FAK) is necessary for PE-stimulated autophagy suppression and subsequent initiation of hypertrophic growth. Mechanistically, we showed that FAK phosphorylates Beclin1, a core autophagy protein, on Tyr-233 and that this post-translational modification limits Beclin1 association with Atg14L and reduces Beclin1-dependent autophagosome formation. Remarkably, although ectopic expression of wild-type Beclin1 promoted cardiomyocyte atrophy, expression of a Y233E phosphomimetic variant of Beclin1 failed to affect cardiomyocyte size. Moreover, genetic depletion of Beclin1 attenuated PE-mediated/FAK-dependent initiation of myocyte hypertrophy in vivo Collectively, these findings identify FAK as a novel negative regulator of Beclin1-mediated autophagy and indicate that this pathway can facilitate the promotion of compensatory hypertrophic growth. This novel mechanism to limit Beclin1 activity has important implications for treating a variety of pathologies associated with altered autophagic flux.
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Affiliation(s)
| | | | | | | | | | - Douglas M Cyr
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joan M Taylor
- From the Department of Pathology, .,McAllister Heart Institute, and
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220
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Vaclová T, Woods NT, Megías D, Gomez-Lopez S, Setién F, García Bueno JM, Macías JA, Barroso A, Urioste M, Esteller M, Monteiro ANA, Benítez J, Osorio A. Germline missense pathogenic variants in the BRCA1 BRCT domain, p.Gly1706Glu and p.Ala1708Glu, increase cellular sensitivity to PARP inhibitor olaparib by a dominant negative effect. Hum Mol Genet 2016; 25:5287-5299. [PMID: 27742776 DOI: 10.1093/hmg/ddw343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/03/2016] [Indexed: 12/29/2022] Open
Abstract
BRCA1-deficient cells show defects in DNA repair and rely on other members of the DNA repair machinery, which makes them sensitive to PARP inhibitors (PARPi). Although carrying a germline pathogenic variant in BRCA1/2 is the best determinant of response to PARPi, a significant percentage of the patients do not show sensitivity and/or display increased toxicity to the agent. Considering previously suggested mutation-specific BRCA1 haploinsufficiency, we aimed to investigate whether there are any differences in cellular response to PARPi olaparib depending on the BRCA1 mutation type. Lymphoblastoid cell lines derived from carriers of missense pathogenic variants in the BRCA1 BRCT domain (c.5117G > A, p.Gly1706Glu and c.5123C > A, p.Ala1708Glu) showed higher sensitivity to olaparib than cells with truncating variants or wild types (WT). Response to olaparib depended on a basal PARP enzymatic activity, but did not correlate with PARP1 expression. Interestingly, cellular sensitivity to the agent was associated with the level of BRCA1 recruitment into γH2AX foci, being the lowest in cells with missense variants. Since these variants lead to partially stable protein mutants, we propose a model in which the mutant protein acts in a dominant negative manner on the WT BRCA1, impairing the recruitment of BRCA1 into DNA damage sites and, consequently, increasing cellular sensitivity to PARPi. Taken together, our results indicate that carriers of different BRCA1 mutations could benefit from olaparib in a distinct way and show different toxicities to the agent, which could be especially relevant for a potential future use of PARPi as prophylactic agents in BRCA1 mutation carriers.
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Affiliation(s)
- Tereza Vaclová
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nicholas T Woods
- Eppley Institute for Research in Cancer and Allied Diseases, Molecular and Biochemical Etiology Program, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Diego Megías
- Confocal Microscopy Core Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sergio Gomez-Lopez
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fernando Setién
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | | | - José Antonio Macías
- Hereditary Cancer Unit, Medical Oncology Service, Hospital Morales Meseguer, Murcia, Spain
| | - Alicia Barroso
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alvaro N A Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, FL, USA
| | - Javier Benítez
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Spanish Network on Rare Diseases (CIBERER), Madrid, Spain.,Genotyping Unit (CEGEN), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
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221
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WSB1 overcomes oncogene-induced senescence by targeting ATM for degradation. Cell Res 2016; 27:274-293. [PMID: 27958289 DOI: 10.1038/cr.2016.148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/20/2022] Open
Abstract
Oncogene-induced senescence (OIS) or apoptosis through the DNA-damage response is an important barrier of tumorigenesis. Overcoming this barrier leads to abnormal cell proliferation, genomic instability, and cellular transformation, and finally allows cancers to develop. However, it remains unclear how the OIS barrier is overcome. Here, we show that the E3 ubiquitin ligase WD repeat and SOCS box-containing protein 1 (WSB1) plays a role in overcoming OIS. WSB1 expression in primary cells helps the bypass of OIS, leading to abnormal proliferation and cellular transformation. Mechanistically, WSB1 promotes ATM ubiquitination, resulting in ATM degradation and the escape from OIS. Furthermore, we identify CDKs as the upstream kinase of WSB1. CDK-mediated phosphorylation activates WSB1 by promoting its monomerization. In human cancer tissue and in vitro models, WSB1-induced ATM degradation is an early event during tumorigenic progression. We suggest that WSB1 is one of the key players of early oncogenic events through ATM degradation and destruction of the tumorigenesis barrier. Our work establishes an important mechanism of cancer development and progression in premalignant lesions.
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222
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McKenzie C, Bassi ZI, Debski J, Gottardo M, Callaini G, Dadlez M, D'Avino PP. Cross-regulation between Aurora B and Citron kinase controls midbody architecture in cytokinesis. Open Biol 2016; 6:rsob.160019. [PMID: 27009191 PMCID: PMC4821246 DOI: 10.1098/rsob.160019] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytokinesis culminates in the final separation, or abscission, of the two daughter cells at the end of cell division. Abscission relies on an organelle, the midbody, which forms at the intercellular bridge and is composed of various proteins arranged in a precise stereotypic pattern. The molecular mechanisms controlling midbody organization and function, however, are obscure. Here we show that proper midbody architecture requires cross-regulation between two cell division kinases, Citron kinase (CIT-K) and Aurora B, the kinase component of the chromosomal passenger complex (CPC). CIT-K interacts directly with three CPC components and is required for proper midbody architecture and the orderly arrangement of midbody proteins, including the CPC. In addition, we show that CIT-K promotes Aurora B activity through phosphorylation of the INCENP CPC subunit at the TSS motif. In turn, Aurora B controls CIT-K localization and association with its central spindle partners through phosphorylation of CIT-K's coiled coil domain. Our results identify, for the first time, a cross-regulatory mechanism between two kinases during cytokinesis, which is crucial for establishing the stereotyped organization of midbody proteins.
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Affiliation(s)
- Callum McKenzie
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Zuni I Bassi
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Janusz Debski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Warszawa 02-106, Poland
| | - Marco Gottardo
- Department of Life Sciences, University of Siena, Via A. Moro 4, Siena 53100, Italy
| | - Giuliano Callaini
- Department of Life Sciences, University of Siena, Via A. Moro 4, Siena 53100, Italy
| | - Michal Dadlez
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Warszawa 02-106, Poland
| | - Pier Paolo D'Avino
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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223
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Blondeau-Bidet E, Bossus M, Maugars G, Farcy E, Lignot JH, Lorin-Nebel C. Molecular characterization and expression of Na +/K +-ATPase α1 isoforms in the European sea bass Dicentrarchus labrax osmoregulatory tissues following salinity transfer. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:1647-1664. [PMID: 27289588 DOI: 10.1007/s10695-016-0247-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/01/2016] [Indexed: 05/14/2023]
Abstract
The Na+/K+-ATPase (NKA) is considered as the main pump involved in active ion transport. In the European sea bass, Dicentrarchus labrax, we found two genes encoding for the alpha 1 subunit isoforms (NKA α1a and NKA α1b). NKA α1a and NKA α1b isoform amino acid (aa) sequences were compared through phylogeny and regarding key functional motifs between salmonids and other acanthomorph species. Analysis of aa sequences of both isoforms revealed a high degree of conservation across teleosts. The expression pattern of both nka α1a and nka α1b was measured in the gill, kidney and posterior intestine of fish in seawater (SW) and transferred to fresh water (FW) at different exposure times. Nka α1a was more expressed than nka α1b whatever the condition and the tissue analyzed. After long-term salinity acclimation (2.5 years) either in FW or SW, transcript levels of nka α1a were higher in the kidney followed by the posterior intestine and the gill. Compared to SW conditions, expression of nka α1a in FW was significantly increased or decreased, respectively, in gill and posterior intestine. In contrast, branchial nka α1b was significantly decreased in FW-acclimated fish. Short-term FW acclimation seems to rapidly increase nka α1a transcript levels in the kidney unlike in gill tissues where different gene expression levels are detected only after long-term acclimation.
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Affiliation(s)
- Eva Blondeau-Bidet
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Maryline Bossus
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Gersende Maugars
- Unité Biologie des Organismes et écosystèmes aquatiques (BOREA, UMR 7208), CNRS, IRD 207, Sorbonne Universités, Muséum national d'Histoire naturelle, Université Pierre et Marie Curie, Université de Caen Basse Normandie, CP32, 7 rue Cuvier, 75005, Paris, France
| | - Emilie Farcy
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Jehan-Hervé Lignot
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Catherine Lorin-Nebel
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France.
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224
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Phosphorylation Requirement of Murine Leukemia Virus p12. J Virol 2016; 90:11208-11219. [PMID: 27707931 DOI: 10.1128/jvi.01178-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/28/2016] [Indexed: 11/20/2022] Open
Abstract
The p12 protein of murine leukemia virus (MLV) Gag is associated with the preintegration complex (PIC), and mutants of p12 (PM14) exhibit defects in nuclear entry/retention. Mutants of the phosphorylated serine 61 also have been reported to have defects in the early life cycle. Here we show that a phosphorylated peptide motif derived from human papillomavirus 8 (HPV-8), the E2 hinge region including residues 240 to 255, can functionally replace the main phosphorylated motif of MLV p12 and can rescue the viral titer of a strain with the lethal p12-PM14 mutation. Complementation with the HPV-8 E2 hinge motif generated multiple second-site mutations in live viral passage assays. Additional p12 phosphorylation sites were detected, including the late domain of p12 (PPPY) as well as the late domain/protease cleavage site of matrix (LYPAL), by mass spectrometry and Western blotting. Chromatin binding of p12-green fluorescent protein (GFP) fusion protein and functional complementation of p12-PM14 occurred in a manner independent of the E2 hinge region phosphorylation. Replacement of serine 61 by alanine within the minimal tethering domain (61SPMASRLRGRR71) maintained tethering, but in the context of the full-length p12, mutants with substitutions in S61 remained untethered and lost infectivity, indicating phosphorylation of p12 serine 61 functions to temporally regulate early and late p12 functions. IMPORTANCE The p12 protein, required for both early and late viral functions, is the predominant phosphorylated viral protein of Moloney MLV and is required for virus viability. Our studies indicate that the N terminus of p12 represses the early function of the chromatin binding domain and that deletion of the N terminus activates chromatin binding in the wild-type Moloney MLV p12 protein. Mass spectrometry and mutagenesis studies suggest that phosphorylation of both the repression domain and the chromatin binding domain acts to temporally regulate this process at the appropriate stages during infection.
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225
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Sakai M, Tujimura-Hayakawa T, Yagi T, Yano H, Mitsushima M, Unoki-Kubota H, Kaburagi Y, Inoue H, Kido Y, Kasuga M, Matsumoto M. The GCN5-CITED2-PKA signalling module controls hepatic glucose metabolism through a cAMP-induced substrate switch. Nat Commun 2016; 7:13147. [PMID: 27874008 PMCID: PMC5121418 DOI: 10.1038/ncomms13147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/08/2016] [Indexed: 01/31/2023] Open
Abstract
Hepatic gluconeogenesis during fasting results from gluconeogenic gene activation via the glucagon-cAMP-protein kinase A (PKA) pathway, a process whose dysregulation underlies fasting hyperglycemia in diabetes. Such transcriptional activation requires epigenetic changes at promoters by mechanisms that have remained unclear. Here we show that GCN5 functions both as a histone acetyltransferase (HAT) to activate fasting gluconeogenesis and as an acetyltransferase for the transcriptional co-activator PGC-1α to inhibit gluconeogenesis in the fed state. During fasting, PKA phosphorylates GCN5 in a manner dependent on the transcriptional coregulator CITED2, thereby increasing its acetyltransferase activity for histone and attenuating that for PGC-1α. This substrate switch concomitantly promotes both epigenetic changes associated with transcriptional activation and PGC-1α-mediated coactivation, thereby triggering gluconeogenesis. The GCN5-CITED2-PKA signalling module and associated GCN5 substrate switch thus serve as a key driver of gluconeogenesis. Disruption of this module ameliorates hyperglycemia in obese diabetic animals, offering a potential therapeutic strategy for such conditions.
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Affiliation(s)
- Mashito Sakai
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Tomoko Tujimura-Hayakawa
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Takashi Yagi
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.,Department of Bioregulation, Nippon Medical School, 1-396 Kosugi-machi, Nakahara-ku, Kawasaki 211-8533, Japan
| | - Hiroyuki Yano
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.,Department of Bioregulation, Nippon Medical School, 1-396 Kosugi-machi, Nakahara-ku, Kawasaki 211-8533, Japan
| | - Masaru Mitsushima
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Hiroyuki Unoki-Kubota
- Department of Diabetic Complications, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Yasushi Kaburagi
- Department of Diabetic Complications, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Hiroshi Inoue
- Metabolism and Nutrition Research Unit, Innovative Integrated Bio-research Core, Institute for Frontier Science Initiative, Kanazawa University, 13-1 Takara-machi, Kanazawa 920-8641, Japan
| | - Yoshiaki Kido
- Division of Medical Chemistry, Department of Metabolism and Disease, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe 654-0142, Japan.,Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Masato Kasuga
- National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Michihiro Matsumoto
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
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226
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Lee KY, Chen YH, Hsu SC, Yu MJ. Phosphorylation of Serine 235 of the Hepatitis C Virus Non-Structural Protein NS5A by Multiple Kinases. PLoS One 2016; 11:e0166763. [PMID: 27875595 PMCID: PMC5119781 DOI: 10.1371/journal.pone.0166763] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
Phosphorylation at serine 235 (S235) of the hepatitis C virus (HCV) non-structural protein 5A (NS5A) plays a critical role in the viral life cycle. For medical and virological interests, we exploited the HEK293T kidney cells to test 3 candidate protein kinases on NS5A S235 phosphorylation. Inhibitors that inhibit casein kinase I α (CKIα), polo-like kinase I (PlKI) or calmodulin-dependent kinase II (CaMKII) all reduced NS5A S235 phosphorylation. CKIα was studied previously and PlKI had severe cytotoxicity, thus CaMKII was selected for validation in the Huh7.5.1 liver cells. In the HCV (J6/JFH1)-infected Huh7.5.1 cells, CaMKII inhibitor reduced NS5A S235 phosphorylation and HCV RNA levels without apparent cytotoxicity. RT-PCR analysis showed expression of CaMKII γ and δ isoforms in the Huh7.5.1 cells. Both CaMKII γ and δ directly phosphorylated NS5A S235 in vitro. CaMKII γ or δ single knockdown did not affect NS5A S235 phosphorylation but elevated the HCV RNA levels in the infected cells. CKIα plus CaMKII (γ or δ) double knockdown reduced NS5A S235 phosphorylation and reduced HCV RNA levels; however, the HCV RNA levels were higher than those in the infected cells with CKIα single knockdown. We conclude that CKIα-mediated NS5A S235 phosphorylation is critical for HCV replication. CaMKII γ and δ may have negative roles in the HCV life cycle.
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Affiliation(s)
- Kuan-Ying Lee
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Yi-Hung Chen
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Shih-Chin Hsu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Ming-Jiun Yu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
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227
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Mammalian FMRP S499 Is Phosphorylated by CK2 and Promotes Secondary Phosphorylation of FMRP. eNeuro 2016; 3:eN-NWR-0092-16. [PMID: 27957526 PMCID: PMC5116651 DOI: 10.1523/eneuro.0092-16.2016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/29/2022] Open
Abstract
The fragile X mental retardation protein (FMRP) is an mRNA-binding regulator of protein translation that associates with 4-6% of brain transcripts and is central to neurodevelopment. Autism risk genes’ transcripts are overrepresented among FMRP-binding mRNAs, and FMRP loss-of-function mutations are responsible for fragile X syndrome, the most common cause of monogenetic autism. It is thought that FMRP-dependent translational repression is governed by the phosphorylation of serine residue 499 (S499). However, recent evidence suggests that S499 phosphorylation is not modulated by metabotropic glutamate receptor class I (mGluR-I) or protein phosphatase 2A (PP2A), two molecules shown to regulate FMRP translational repression. Moreover, the mammalian FMRP S499 kinase remains unknown. We found that casein kinase II (CK2) phosphorylates murine FMRP S499. Further, we show that phosphorylation of FMRP S499 permits phosphorylation of additional, nearby residues. Evidence suggests that these nearby residues are modulated by mGluR-I and PP2A pathways. These data support an alternative phosphodynamic model of FMRP that is harmonious with prior studies and serves as a framework for further investigation.
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228
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Abstract
Phosphatases play key roles in normal physiology and diseases. Studying phosphatases has been both essential and challenging, and the application of conventional genetic and biochemical methods has led to crucial but still limited understanding of their mechanisms, substrates, and exclusive functions within highly intricate networks. With the advances in technologies such as cellular imaging and molecular and chemical biology in terms of sensitive tools and methods, the phosphatase field has thrived in the past years and has set new insights for cell signaling studies and for therapeutic development. In this review, we give an overview of the existing interdisciplinary tools for phosphatases, give examples on how they have been applied to increase our understanding of these enzymes, and suggest how they-and other tools yet barely used in the phosphatase field-might be adapted to address future questions and challenges.
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Affiliation(s)
- Sara Fahs
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Pablo Lujan
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
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229
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Temporal quantitative phosphoproteomics of ADP stimulation reveals novel central nodes in platelet activation and inhibition. Blood 2016; 129:e1-e12. [PMID: 28060719 DOI: 10.1182/blood-2016-05-714048] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 11/03/2016] [Indexed: 01/01/2023] Open
Abstract
Adenosine diphosphate (ADP) enhances platelet activation by virtually any other stimulant to complete aggregation. It binds specifically to the G-protein-coupled membrane receptors P2Y1 and P2Y12, stimulating intracellular signaling cascades, leading to integrin αIIbβ3 activation, a process antagonized by endothelial prostacyclin. P2Y12 inhibitors are among the most successful antiplatelet drugs, however, show remarkable variability in efficacy. We reasoned whether a more detailed molecular understanding of ADP-induced protein phosphorylation could identify (1) critical hubs in platelet signaling toward aggregation and (2) novel molecular targets for antiplatelet treatment strategies. We applied quantitative temporal phosphoproteomics to study ADP-mediated signaling at unprecedented molecular resolution. Furthermore, to mimic the antagonistic efficacy of endothelial-derived prostacyclin, we determined how Iloprost reverses ADP-mediated signaling events. We provide temporal profiles of 4797 phosphopeptides, 608 of which showed significant regulation. Regulated proteins are implicated in well-known activating functions such as degranulation and cytoskeletal reorganization, but also in less well-understood pathways, involving ubiquitin ligases and GTPase exchange factors/GTPase-activating proteins (GEF/GAP). Our data demonstrate that ADP-triggered phosphorylation occurs predominantly within the first 10 seconds, with many short rather than sustained changes. For a set of phosphorylation sites (eg, PDE3ASer312, CALDAG-GEFISer587, ENSASer109), we demonstrate an inverse regulation by ADP and Iloprost, suggesting that these are central modulators of platelet homeostasis. This study demonstrates an extensive spectrum of human platelet protein phosphorylation in response to ADP and Iloprost, which inversely overlap and represent major activating and inhibitory pathways.
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230
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Rucki AA, Foley K, Zhang P, Xiao Q, Kleponis J, Wu AA, Sharma R, Mo G, Liu A, Van Eyk J, Jaffee EM, Zheng L. Heterogeneous Stromal Signaling within the Tumor Microenvironment Controls the Metastasis of Pancreatic Cancer. Cancer Res 2016; 77:41-52. [PMID: 27821486 DOI: 10.1158/0008-5472.can-16-1383] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/13/2016] [Accepted: 10/11/2016] [Indexed: 12/16/2022]
Abstract
Understanding how stromal signals regulate the development of pancreatic ductal adenocarcinoma (PDAC) may suggest novel therapeutic interventions in this disease. In this study, we assessed the metastatic role of stromal signals suggested to be important in the PDAC microenvironment. Src and IGF-1R phosphorylated the prometastatic molecule Annexin A2 (AnxA2) at Y23 and Y333 in response to stromal signals HGF and IGF-1, respectively, and IGF-1 expression was regulated by the Sonic Hedgehog (Shh) pathway. Both Shh and HGF were heterogeneously expressed in PDAC stroma, and only dual inhibition of these pathways could significantly suppress AnxA2 phosphorylation, PDAC growth, and metastasis. Taken together, our results illuminate tumor-stromal interactions, which drive metastasis, and provide a mechanism-based rationale for a stroma-directed therapy for PDAC. Cancer Res; 77(1); 41-52. ©2016 AACR.
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Affiliation(s)
- Agnieszka A Rucki
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Graduate Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kelly Foley
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Graduate Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pingbo Zhang
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qian Xiao
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jennifer Kleponis
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Annie A Wu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rajni Sharma
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guanglan Mo
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Skip Viragh Center for Pancreatic Cancer, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angen Liu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jennifer Van Eyk
- Department of Medicine, Biological Chemistry and Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth M Jaffee
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Graduate Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Skip Viragh Center for Pancreatic Cancer, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lei Zheng
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Graduate Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Skip Viragh Center for Pancreatic Cancer, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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231
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Payá-Milans M, Aznar-Moreno JA, Balbuena TS, Haslam RP, Gidda SK, Pérez-Hormaeche J, Mullen RT, Thelen JJ, Napier JA, Salas JJ, Garcés R, Martínez-Force E, Venegas-Calerón M. Sunflower HaGPAT9-1 is the predominant GPAT during seed development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:42-52. [PMID: 27717477 DOI: 10.1016/j.plantsci.2016.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 05/25/2023]
Abstract
In oil crops, triacylglycerol biosynthesis is an important metabolic pathway in which glycerol-3-phosphate acyltransferase (GPAT) performs the first acylation step. Mass spectrometry analysis of developing sunflower (Helianthus annuus) seed membrane fractions identified an abundant GPAT, HaGPAT9 isoform 1, with a N-terminal peptide that possessed two phosphorylated residues with possible regulatory function. HaGPAT9-1 belongs to a broad eukaryotic GPAT family, similar to mammalian GPAT3, and it represents one of the two sunflower GPAT9 isoforms, sharing 90% identity with HaGPAT9-2. Both sunflower genes are expressed during seed development and in vegetative tissues, with HaGPAT9-1 transcripts accumulating at relatively higher levels than those for HaGPAT9-2. Green fluorescent protein tagging of HaGPAT9-1 confirmed its subcellular accumulation in the endoplasmic reticulum. Despite their overall sequence similarities, the two sunflower isoforms displayed significant differences in their enzymatic activities. For instance, HaGPAT9-1 possesses in vivo GPAT activity that rescues the lethal phenotype of the cmy228 yeast strain, while in vitro assays revealed a preference of HaGPAT9-1 for palmitoyl-, oleoyl- and linoleoyl-CoAs of one order of magnitude, with the highest increase in yield for oleoyl- and linoleoyl-CoAs. By contrast, no enzymatic activity could be detected for HaGPAT9-2, even though its over-expression modified the TAG profile of yeast.
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Affiliation(s)
- Miriam Payá-Milans
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jose Antonio Aznar-Moreno
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS 66506, United States
| | - Tiago S Balbuena
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States; Department of Technology, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Javier Pérez-Hormaeche
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jay J Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Joaquín J Salas
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Rafael Garcés
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Enrique Martínez-Force
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Mónica Venegas-Calerón
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain.
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232
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Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Vieitez C, Sole C, Swaney DL, Stanford LB, Liachko I, Bottcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villen J. Evolution of protein phosphorylation across 18 fungal species. Science 2016; 354:229-232. [DOI: 10.1126/science.aaf2144] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 08/16/2016] [Indexed: 12/28/2022]
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233
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Zhao YW, Lai HY, Tang H, Chen W, Lin H. Prediction of phosphothreonine sites in human proteins by fusing different features. Sci Rep 2016; 6:34817. [PMID: 27698459 PMCID: PMC5048138 DOI: 10.1038/srep34817] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/20/2016] [Indexed: 01/24/2023] Open
Abstract
Phosphorylation is one of the most important protein post-translation modifications. With the rapid development of high-throughput mass spectrometry, phosphorylation site data is rapidly accumulating, which provides us an opportunity to systematically investigate and predict phosphorylation in proteins. The phosphorylation of threonine is the addition of a phosphoryl group to its polar side chains group. In this work, we statistically analyzed the distribution of the different properties including position conservation, secondary structure, accessibility and some other physicochemical properties of the residues surrounding the phosphothreonine site and non-phosphothreonine site. We found that the distributions of those features are non-symmetrical. Based on the distribution of properties, we developed a new model by using optimal window size strategy and feature selection technique. The cross-validated results show that the area under receiver operating characteristic curve reaches to 0.847, suggesting that our model may play a complementary role to other existing methods for predicting phosphothreonine site in proteins.
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Affiliation(s)
- Ya-Wei Zhao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hong-Yan Lai
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou 646000, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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234
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Duan H, Wang C, Wang M, Gao X, Yan M, Akram S, Peng W, Zou H, Wang D, Zhou J, Chu Y, Dou Z, Barrett G, Green HN, Wang F, Tian R, He P, Wang W, Liu X, Yao X. Phosphorylation of PP1 Regulator Sds22 by PLK1 Ensures Accurate Chromosome Segregation. J Biol Chem 2016; 291:21123-21136. [PMID: 27557660 PMCID: PMC5076521 DOI: 10.1074/jbc.m116.745372] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/22/2016] [Indexed: 11/06/2022] Open
Abstract
During cell division, accurate chromosome segregation is tightly regulated by Polo-like kinase 1 (PLK1) and opposing activities of Aurora B kinase and protein phosphatase 1 (PP1). However, the regulatory mechanisms underlying the aforementioned hierarchical signaling cascade during mitotic chromosome segregation have remained elusive. Sds22 is a conserved regulator of PP1 activity, but how it regulates PP1 activity in space and time during mitosis remains elusive. Here we show that Sds22 is a novel and cognate substrate of PLK1 in mitosis, and the phosphorylation of Sds22 by PLK1 elicited an inhibition of PP1-mediated dephosphorylation of Aurora B at threonine 232 (Thr232) in a dose-dependent manner. Overexpression of a phosphomimetic mutant of Sds22 causes a dramatic increase in mitotic delay, whereas overexpression of a non-phosphorylatable mutant of Sds22 results in mitotic arrest. Mechanistically, the phosphorylation of Sds22 by PLK1 strengthens the binding of Sds22 to PP1 and inhibits the dephosphorylation of Thr232 of Aurora B to ensure a robust, error-free metaphase-anaphase transition. These findings delineate a conserved signaling hierarchy that orchestrates dynamic protein phosphorylation and dephosphorylation of critical mitotic regulators during chromosome segregation to guard chromosome stability.
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Affiliation(s)
- Hequan Duan
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China, the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310
| | - Chunli Wang
- the National Chromatographic Research and Analysis Center, Chinesse Academy of Sciences, Dalian 116023, China
| | - Ming Wang
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Xinjiao Gao
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Maomao Yan
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Saima Akram
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Wei Peng
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Hanfa Zou
- the National Chromatographic Research and Analysis Center, Chinesse Academy of Sciences, Dalian 116023, China
| | - Dong Wang
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Jiajia Zhou
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Youjun Chu
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China, the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310
| | - Zhen Dou
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China
| | - Gregory Barrett
- the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310
| | - Hadiyah-Nicole Green
- the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310
| | - Fangjun Wang
- the National Chromatographic Research and Analysis Center, Chinesse Academy of Sciences, Dalian 116023, China
| | - Ruijun Tian
- the Guangzhou Women and Children's Medical Center, Guangzhou 510623, China, and the Center of Molecular Proteomics, South University of Science & Technology of China, Shenzhen 518055, China
| | - Ping He
- the Guangzhou Women and Children's Medical Center, Guangzhou 510623, China, and the Center of Molecular Proteomics, South University of Science & Technology of China, Shenzhen 518055, China
| | - Wenwen Wang
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China, the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310,
| | - Xing Liu
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China, the Morehouse School of Medicine and Atlanta Clinical & Translational Science Institute, Atlanta, Georgia 30310,
| | - Xuebiao Yao
- From the Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, MOE Collaborative Innovation Center of Chemistry for Life Sciences, University of Science & Technology of China, Hefei 230027, China,
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235
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Tyshchuk O, Völger HR, Ferrara C, Bulau P, Koll H, Mølhøj M. Detection of a phosphorylated glycine-serine linker in an IgG-based fusion protein. MAbs 2016; 9:94-103. [PMID: 27661266 PMCID: PMC5240648 DOI: 10.1080/19420862.2016.1236165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Molecular mass determination by electrospray ionization mass spectrometry of a recombinant IgG-based fusion protein (mAb1-F) produced in human embryonic kidney (HEK) cells demonstrated the presence of a dominant +79 Da product variant. Using LC-MS tryptic peptide mapping analysis and collision-induced dissociation (CID) and electron-transfer/higher-energy collision dissociation fragmentations, the modification was localized to the C-terminal serine residue of a glycine-serine linker [(G4S)2] of a fused heavy chain containing in total 2 (G4S)2-linkers. The modification was identified as a phosphorylation (+79.97 Da) by the presence of a 98 Da neutral loss reaction with CID, by spiking a synthetic phosphoserine peptide, and by dephosphorylation with alkaline phosphatase. A thermolysin digest combined with higher-energy collision dissociation (HCD) positioned the phosphoserine to one specific glycine-serine linker of the fused heavy chain, and the relative level of phosphorylated linker was determined to be 11.3% and 0.4% by LC-MS when the fusion protein was transiently expressed in HEK or in stably transformed Chinese hamster ovary cells, respectively. This observation demonstrates that fusions with glycine-serine linker sequences should be carefully evaluated during drug development to prevent the introduction of a phosphorylation site in therapeutic fusion proteins.
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Affiliation(s)
- Oksana Tyshchuk
- a Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH , Penzberg , Germany
| | - Hans Rainer Völger
- a Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH , Penzberg , Germany
| | - Claudia Ferrara
- b Oncology Discovery & Translational Area, Roche Innovation Center Zurich , Schlieren , Switzerland
| | - Patrick Bulau
- c Roche Pharma Technical Development Penzberg, Roche Diagnostics GmbH , Penzberg , Germany
| | - Hans Koll
- a Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH , Penzberg , Germany
| | - Michael Mølhøj
- a Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH , Penzberg , Germany
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236
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Kim HY, Kim YS, Yun HH, Im CN, Ko JH, Lee JH. ERK-mediated phosphorylation of BIS regulates nuclear translocation of HSF1 under oxidative stress. Exp Mol Med 2016; 48:e260. [PMID: 27659916 PMCID: PMC5050300 DOI: 10.1038/emm.2016.84] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 12/28/2022] Open
Abstract
B-cell lymphoma (BCL)-2-interacting cell death suppressor (BIS) has diverse cellular functions depending on its binding partners. However, little is known about the effects of biochemical modification of BIS on its various activities under oxidative stress conditions. In this study, we showed that H2O2 reduced BIS mobility on SDS–polyacrylamide gels in a time-dependent manner via the activation of extracellular signaling-regulated kinase (ERK). The combined results of mass spectroscopy and computational prediction identified Thr285 and Ser289 in BIS as candidate residues for phosphorylation by ERK under oxidative stress conditions. Deletion of these sites resulted in a partial reduction in the H2O2-induced mobility shift relative to that of the wild-type BIS protein; overexpression of the deletion mutant sensitized A172 cells to H2O2-induced cell death without increasing the level of intracellular reactive oxygen species. Expression of the BIS deletion mutant decreased the level of heat shock protein (HSP) 70 mRNA following H2O2 treatment, which was accompanied by impaired nuclear translocation of heat shock transcription factor (HSF) 1. Co-immunoprecipitation assays revealed that the binding of wild-type BIS to HSF1 was decreased by oxidative stress, while the binding of the BIS deletion mutant to HSF1 was not affected. These results indicate that ERK-dependent phosphorylation of BIS has a role in the regulation of nuclear translocation of HSF1 likely through modulation of its interaction affinity with HSF1, which affects HSP70 expression and sensitivity to oxidative stress.
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Affiliation(s)
- Hye Yun Kim
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yong-Sam Kim
- Aging Intervention Research Center, Aging Research Institute, KRIBB, Daejeon, Republic of Korea.,Korea University of Science and Technology. Daejeon, Republic of Korea
| | - Hye Hyeon Yun
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chang-Nim Im
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-Heon Ko
- Aging Intervention Research Center, Aging Research Institute, KRIBB, Daejeon, Republic of Korea.,Korea University of Science and Technology. Daejeon, Republic of Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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237
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Chang CW, Abhinav K, Di Cara F, Panagakou I, Vass S, Heck MMS. A role for the metalloprotease invadolysin in insulin signaling and adipogenesis. Biol Chem 2016; 398:373-393. [PMID: 27622830 DOI: 10.1515/hsz-2016-0226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/04/2016] [Indexed: 01/24/2023]
Abstract
Invadolysin is a novel metalloprotease conserved amongst metazoans that is essential for life in Drosophila. We previously showed that invadolysin was essential for the cell cycle and cell migration, linking to metabolism through a role in lipid storage and interaction with mitochondrial proteins. In this study we demonstrate that invadolysin mutants exhibit increased autophagy and decreased glycogen storage - suggestive of a role for invadolysin in insulin signaling in Drosophila. Consistent with this, effectors of insulin signaling were decreased in invadolysin mutants. In addition, we discovered that invadolysin was deposited on newly synthesized lipid droplets in a PKC-dependent manner. We examined two in vitro models of adipogenesis for the expression and localization of invadolysin. The level of invadolysin increased during both murine 3T3-L1 and human Simpson-Golabi-Behmel syndrome (SGBS), adipogenesis. Invadolysin displayed a dynamic localization to lipid droplets over the course of adipogenesis, which may be due to the differential expression of distinct invadolysin variants. Pharmacological inhibition of adipogenesis abrogated the increase in invadolysin. In summary, our results on in vivo and in vitro systems highlight an important role for invadolysin in insulin signaling and adipogenesis.
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238
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Xue X, Ramakrishnan SK, Weisz K, Triner D, Xie L, Attili D, Pant A, Győrffy B, Zhan M, Carter-Su C, Hardiman KM, Wang TD, Dame MK, Varani J, Brenner D, Fearon ER, Shah YM. Iron Uptake via DMT1 Integrates Cell Cycle with JAK-STAT3 Signaling to Promote Colorectal Tumorigenesis. Cell Metab 2016; 24:447-461. [PMID: 27546461 PMCID: PMC5023486 DOI: 10.1016/j.cmet.2016.07.015] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/07/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022]
Abstract
Dietary iron intake and systemic iron balance are implicated in colorectal cancer (CRC) development, but the means by which iron contributes to CRC are unclear. Gene expression and functional studies demonstrated that the cellular iron importer, divalent metal transporter 1 (DMT1), is highly expressed in CRC through hypoxia-inducible factor 2α-dependent transcription. Colon-specific Dmt1 disruption resulted in a tumor-selective inhibitory effect of proliferation in mouse colon tumor models. Proteomic and genomic analyses identified an iron-regulated signaling axis mediated by cyclin-dependent kinase 1 (CDK1), JAK1, and STAT3 in CRC progression. A pharmacological inhibitor of DMT1 antagonized the ability of iron to promote tumor growth in a CRC mouse model and a patient-derived CRC enteroid orthotopic model. Our studies implicate a growth-promoting signaling network instigated by elevated intracellular iron levels in tumorigenesis, offering molecular insights into how a key dietary component may contribute to CRC.
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Affiliation(s)
- Xiang Xue
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sadeesh K Ramakrishnan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kevin Weisz
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Triner
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liwei Xie
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Durga Attili
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asha Pant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest 1117, Hungary; 2nd Department of Pediatrics, Semmelweis University, Budapest 1085, Hungary
| | - Mingkun Zhan
- Department of Plastic Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, China
| | - Christin Carter-Su
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karin M Hardiman
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas D Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James Varani
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dean Brenner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric R Fearon
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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239
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Richter E, Mostertz J, Hochgräfe F. Proteomic discovery of host kinase signaling in bacterial infections. Proteomics Clin Appl 2016; 10:994-1010. [PMID: 27440122 PMCID: PMC5096009 DOI: 10.1002/prca.201600035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/08/2016] [Accepted: 07/18/2016] [Indexed: 12/15/2022]
Abstract
Protein phosphorylation catalyzed by protein kinases acts as a reversible molecular switch in signal transduction, providing a mechanism for the control of protein function in cellular processes. During microbial infection, cellular signaling essentially contributes to immune control to restrict the dissemination of invading pathogens within the host organism. However, pathogenic microbes compete for the control of host signaling to create a beneficial environment for successful invasion and infection. Although efforts to achieve a better understanding of the host–pathogen interaction and its molecular consequences have been made, there is urgent need for a comprehensive characterization of infection‐related host signaling processes. System‐wide and hypothesis‐free analysis of phosphorylation‐mediated host signaling during host–microbe interactions by mass spectrometry (MS)‐based methods is not only promising in view of a greater understanding of the pathogenesis of the infection but also may result in the identification of novel host targets for preventive or therapeutic intervention. Here, we review state‐of‐the‐art MS‐based techniques for the system‐wide identification and quantitation of protein phosphorylation and compare them to array‐based phosphoprotein analyses. We also provide an overview of how phosphoproteomics and kinomics have contributed to our understanding of protein kinase‐driven phosphorylation networks that operate during host–microbe interactions.
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Affiliation(s)
- Erik Richter
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany
| | - Jörg Mostertz
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany
| | - Falko Hochgräfe
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany.
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240
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Singec I, Crain AM, Hou J, Tobe BTD, Talantova M, Winquist AA, Doctor KS, Choy J, Huang X, La Monaca E, Horn DM, Wolf DA, Lipton SA, Gutierrez GJ, Brill LM, Snyder EY. Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling. Stem Cell Reports 2016; 7:527-542. [PMID: 27569059 PMCID: PMC5032292 DOI: 10.1016/j.stemcr.2016.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 10/27/2022] Open
Abstract
Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.
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Affiliation(s)
- Ilyas Singec
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Andrew M Crain
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Junjie Hou
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Brian T D Tobe
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Maria Talantova
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alicia A Winquist
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kutbuddin S Doctor
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jennifer Choy
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiayu Huang
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Esther La Monaca
- Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - David M Horn
- Thermo Fisher Scientific Inc., San Jose, CA 95134, USA
| | - Dieter A Wolf
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Stuart A Lipton
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Gustavo J Gutierrez
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Laurence M Brill
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Evan Y Snyder
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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241
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Ohta S, Kimura M, Takagi S, Toramoto I, Ishihama Y. Identification of Mitosis-Specific Phosphorylation in Mitotic Chromosome-Associated Proteins. J Proteome Res 2016; 15:3331-41. [PMID: 27504668 DOI: 10.1021/acs.jproteome.6b00512] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
During mitosis, phosphorylation of chromosome-associated proteins is a key regulatory mechanism. Mass spectrometry has been successfully applied to determine the complete protein composition of mitotic chromosomes, but not to identify post-translational modifications. Here, we quantitatively compared the phosphoproteome of isolated mitotic chromosomes with that of chromosomes in nonsynchronized cells. We identified 4274 total phosphorylation sites and 350 mitosis-specific phosphorylation sites in mitotic chromosome-associated proteins. Significant mitosis-specific phosphorylation in centromere/kinetochore proteins was detected, although the chromosomal association of these proteins did not change throughout the cell cycle. This mitosis-specific phosphorylation might play a key role in regulation of mitosis. Further analysis revealed strong dependency of phosphorylation dynamics on kinase consensus patterns, thus linking the identified phosphorylation sites to known key mitotic kinases. Remarkably, chromosomal axial proteins such as non-SMC subunits of condensin, TopoIIα, and Kif4A, together with the chromosomal periphery protein Ki67 involved in the establishment of the mitotic chromosomal structure, demonstrated high phosphorylation during mitosis. These findings suggest a novel mechanism for regulation of chromosome restructuring in mitosis via protein phosphorylation. Our study generated a large quantitative database on protein phosphorylation in mitotic and nonmitotic chromosomes, thus providing insights into the dynamics of chromatin protein phosphorylation at mitosis onset.
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Affiliation(s)
- Shinya Ohta
- Center for Innovative and Translational Medicine Medical School, Kochi University Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Michiko Kimura
- Graduate School of Pharmaceutical Sciences, Kyoto University 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shunsuke Takagi
- Graduate School of Pharmaceutical Sciences, Kyoto University 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Iyo Toramoto
- Center for Innovative and Translational Medicine Medical School, Kochi University Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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242
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Bolinger MT, Ramshekar A, Waldschmidt HV, Larsen SD, Bewley MC, Flanagan JM, Antonetti DA. Occludin S471 Phosphorylation Contributes to Epithelial Monolayer Maturation. Mol Cell Biol 2016; 36:2051-66. [PMID: 27185880 PMCID: PMC4946429 DOI: 10.1128/mcb.00053-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/19/2016] [Accepted: 05/10/2016] [Indexed: 12/25/2022] Open
Abstract
Multiple organ systems require epithelial barriers for normal function, and barrier loss is a hallmark of diseases ranging from inflammation to epithelial cancers. However, the molecular processes regulating epithelial barrier maturation are not fully elucidated. After contact, epithelial cells undergo size-reductive proliferation and differentiate, creating a dense, highly ordered monolayer with high resistance barriers. We provide evidence that the tight junction protein occludin contributes to the regulation of epithelial cell maturation upon phosphorylation of S471 in its coiled-coil domain. Overexpression of a phosphoinhibitory occludin S471A mutant prevents size-reductive proliferation and subsequent tight junction maturation in a dominant manner. Inhibition of cell proliferation in cell-contacted but immature monolayers recapitulated this phenotype. A kinase screen identified G-protein-coupled receptor kinases (GRKs) targeting S471, and GRK inhibitors delayed epithelial packing and junction maturation. We conclude that occludin contributes to the regulation of size-reductive proliferation and epithelial cell maturation in a phosphorylation-dependent manner.
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Affiliation(s)
- Mark T Bolinger
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Aniket Ramshekar
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Helen V Waldschmidt
- Vahlteich Medicinal Chemistry Core, Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria C Bewley
- Departments of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - John M Flanagan
- Departments of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - David A Antonetti
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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243
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Udgata A, Qureshi R, Mukhopadhyay S. Transduction of Functionally Contrasting Signals by Two Mycobacterial PPE Proteins Downstream of TLR2 Receptors. THE JOURNAL OF IMMUNOLOGY 2016; 197:1776-87. [DOI: 10.4049/jimmunol.1501816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 06/01/2016] [Indexed: 02/02/2023]
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244
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Wang M, Jiang Y, Xu X. A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles. MOLECULAR BIOSYSTEMS 2016; 11:3092-100. [PMID: 26344496 DOI: 10.1039/c5mb00384a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Post-translational modifications (PTMs) regulate many aspects of biological behaviours including protein-protein interactions and cellular processes. Identification of PTM sites is helpful for understanding the PTM regulatory mechanisms. The PTMs on serine and threonine sites include phosphorylation, O-linked glycosylation and acetylation. Although a lot of computational approaches have been developed for PTM site prediction, currently most of them generate the predictive models by employing only local sequence information and few of them consider the relationship between different PTMs. In this paper, by adopting the site-modification network (SMNet) profiles that efficiently incorporate in situ PTM information, we develop a novel method to predict PTM sites on serine and threonine. PTM data are collected from various PTM databases and the SMNet is built to reflect the relationship between multiple PTMs, from which SMNet profiles are extracted to train predictive models based on SVM. Performance analysis of the SVM models shows that the SMNet profiles play an important role in accurately predicting PTM sites on serine and threonine. Furthermore, the proposed method is compared with existing PTM prediction approaches. The results from 10-fold cross-validation demonstrate that the proposed method with SMNet profiles performs remarkably better than existing methods, suggesting the power of SMNet profiles in identifying PTM sites.
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Affiliation(s)
- Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, People's Republic of China
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245
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Li YW, Guo J, Shen H, Li J, Yang N, Frangou C, Wilson KE, Zhang Y, Mussell AL, Sudol M, Farooq A, Qu J, Zhang J. Phosphorylation of Tyr188 in the WW domain of YAP1 plays an essential role in YAP1-induced cellular transformation. Cell Cycle 2016; 15:2497-505. [PMID: 27428284 DOI: 10.1080/15384101.2016.1207836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP1, a transcriptional co-activator amplified in mouse and human cancers where it promotes epithelial-to-mesenchymal transition (EMT) and malignant transformation. The Hippo tumor suppressor pathway has been suggested to inhibit the YAP1 function through serine phosphorylation-induced cytoplasmic retention and degradation. Here we report that the tyrosine188 (Y188) site of YAP1 isoform with 2 WW domains (known as YAP1-2) plays an important role in YAP1-induced cellular transformation. IP-Mass Spectrometry analysis of YAP1 identified the phosphorylation of Y188 but not other tyrosine residues. In contrast to the aberrant 3D acinus formation observed in YAP1-WT transduced cells, overexpression of YAP1-Y188F (non-phosphorylated mimic) displayed normal 3D structures. In addition, knockdown of the endogenous YAP1 in MDA-MB231 breast cancer cells inhibited cell proliferation and migration, which were then successfully rescued by the exogenous YAP1-WT and YAP1-Y188E but not Y188F. Mechanistically, we also demonstrated that YAP1-Y188F had a higher affinity to the upstream negative regulator PTPN14 and was extensively localized in the cytoplasm. Since the Y188 is located in the conserved aromatic core of the WW domain of YAP1, our finding has a wide implication for WW domain signaling in general, where Y phosphorylation may act as a common positive regulator of the complex formation via WW domains. In summary, our results indicate that tyrosine 188 plays an important role in the YAP1-induced cellular transformation and its phosphorylation may intriguingly serve as a positive indicator of YAP1 activation.
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Affiliation(s)
- Ying-Wei Li
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Jin Guo
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - He Shen
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Jun Li
- b Department of Pharmaceutical Sciences , New York Center of Excellence in Bioinformatics and Life Sciences, State University of New York , Buffalo , NY , USA
| | - Nuo Yang
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Costa Frangou
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Kayla E Wilson
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Yinglong Zhang
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA.,c Orthopaedic Oncology Institute, Tangdu Hospital, Fourth Military Medical University , Xi'an , Shaanxi , P. R. China
| | - Ashley L Mussell
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Marius Sudol
- d Department of Physiology , National University of Singapore, The Yong Loo Li School of Medicine, Mechanobiology Institute, Institute of Molecular and Cell Biology (IMCB) A*STAR , Singapore , Republic of Singapore
| | - Amjad Farooq
- e Department of Biochemistry & Molecular Biology , Leonard Miller School of Medicine, University of Miami , Miami , FL , USA
| | - Jun Qu
- b Department of Pharmaceutical Sciences , New York Center of Excellence in Bioinformatics and Life Sciences, State University of New York , Buffalo , NY , USA
| | - Jianmin Zhang
- a Department of Cancer Genetics , Roswell Park Cancer Institute , Buffalo , NY , USA
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246
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Trost B, Maleki F, Kusalik A, Napper S. DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites. J Proteome Res 2016; 15:2760-7. [PMID: 27367363 DOI: 10.1021/acs.jproteome.6b00304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The post-translational modification of proteins is critical for regulating their function. Although many post-translational modification sites have been experimentally determined, particularly in certain model organisms, experimental knowledge of these sites is severely lacking for many species. Thus, it is important to be able to predict sites of post-translational modification in such species. Previously, we described DAPPLE, a tool that facilitates the homology-based prediction of one particular post-translational modification, phosphorylation, in an organism of interest using known phosphorylation sites from other organisms. Here, we describe DAPPLE 2, which expands and improves upon DAPPLE in three major ways. First, it predicts sites for many post-translational modifications (20 different types) using data from several sources (15 online databases). Second, it has the ability to make predictions approximately 2-7 times faster than DAPPLE depending on the database size and the organism of interest. Third, it simplifies and accelerates the process of selecting predicted sites of interest by categorizing them based on gene ontology terms, keywords, and signaling pathways. We show that DAPPLE 2 can successfully predict known human post-translational modification sites using, as input, known sites from species that are either closely (e.g., mouse) or distantly (e.g., yeast) related to humans. DAPPLE 2 can be accessed at http://saphire.usask.ca/saphire/dapple2 .
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Affiliation(s)
- Brett Trost
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Farhad Maleki
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Anthony Kusalik
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
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247
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Gao Y, Hao W, Gu J, Liu D, Fan C, Chen Z, Deng L. PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. ACTA ACUST UNITED AC 2016; 23:12. [PMID: 27437197 PMCID: PMC4943517 DOI: 10.1186/s40709-016-0042-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Post-translational modifications (PTMs) occur on almost all proteins and often strongly affect the functions of modified proteins. Phosphorylation is a crucial PTM mechanism with important regulatory functions in biological systems. Identifying the potential phosphorylation sites of a target protein may increase our understanding of the molecular processes in which it takes part. Results In this paper, we propose PredPhos, a computational method that can accurately predict both kinase-specific and non-kinase-specific phosphorylation sites by using optimally selected properties. The optimal combination of features was selected from a set of 153 novel structural neighborhood properties by a two-step feature selection method consisting of a random forest algorithm and a sequential backward elimination method. To overcome the imbalanced problem, we adopt an ensemble method, which combines bootstrap resampling technique, support vector machine-based fusion classifiers and majority voting strategy. We evaluate the proposed method using both tenfold cross validation and independent test. Results show that our method achieves a significant improvement on the prediction performance for both kinase-specific and non-kinase-specific phosphorylation sites. Conclusions The experimental results demonstrate that the proposed method is quite effective in predicting phosphorylation sites. Promising results are derived from the new structural neighborhood properties, the novel way of feature selection, as well as the ensemble method.
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Affiliation(s)
- Yong Gao
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Weilin Hao
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China.,School of Electronics Engineering and Computer Science, Peking University, No. 5 Yiheyuan Road, Beijing, 100871 China
| | - Jing Gu
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Diwei Liu
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Chao Fan
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Zhigang Chen
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China
| | - Lei Deng
- School of Software, Central South University, No. 22 Shaoshan South RD., Changsha, 410075 China.,Shanghai Key Laboratory of Intelligent Information Processing, No. 220 Handan Road, Shanghai, 200433 China
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248
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Heterologous, PKC-Mediated Desensitization of Human Histamine H3 Receptors Expressed in CHO-K1 Cells. Neurochem Res 2016; 41:2415-24. [PMID: 27350581 DOI: 10.1007/s11064-016-1954-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 12/11/2022]
Abstract
Desensitization is a major mechanism to regulate the functional response of G protein-coupled receptors. In this work we studied whether the human histamine H3 receptor of 445 amino acids (hH3R445) experiences heterologous desensitization mediated by PKC activation. Bioinformatic analysis indicated the presence of Serine and Threonine residues susceptible of PKC-mediated phosphorylation on the third intracellular loop and the carboxyl terminus of the hH3R445. In CHO-K1 cells stably transfected with the hH3R445 direct PKC activation by phorbol 12-myristate 13-acetate (TPA, 200 nM) abolished H3R-mediated inhibition of forskolin-stimulated cAMP accumulation. Activation of endogenous purinergic receptors by ATP (adenosine 5'-triphosphate, 10 μM) increased the free calcium intracellular concentration ([Ca(2+)]i) confirming their coupling to phospholipase C stimulation. Incubation with ATP also abolished H3R-mediated inhibition of forskolin-induced cAMP accumulation, and this effect was prevented by the PKC inhibitors Ro-31-8220 and Gö-6976. Pre-incubation with TPA or ATP reduced H3R-mediated stimulation of [(35)S]-GTPγS binding to membranes from CHO-K1-hH3R445 cells by 39.7 and 54.2 %, respectively, with no change in the agonist potency, and the effect was prevented by either Ro-31-8220 or Gö-6976. Exposure to ATP or TPA also resulted in the loss of cell surface H3Rs (-30.4 and -45.1 %) as evaluated by [(3)H]-NMHA binding to intact cells. These results indicate that the hH3R445 undergoes heterologous desensitization upon activation of receptors coupled to PKC stimulation.
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249
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Promotion of Cell Viability and Histone Gene Expression by the Acetyltransferase Gcn5 and the Protein Phosphatase PP2A in Saccharomyces cerevisiae. Genetics 2016; 203:1693-707. [PMID: 27317677 DOI: 10.1534/genetics.116.189506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/27/2016] [Indexed: 01/23/2023] Open
Abstract
Histone modifications direct chromatin-templated events in the genome and regulate access to DNA sequence information. There are multiple types of modifications, and a common feature is their dynamic nature. An essential step for understanding their regulation, therefore, lies in characterizing the enzymes responsible for adding and removing histone modifications. Starting with a dosage-suppressor screen in Saccharomyces cerevisiae, we have discovered a functional interaction between the acetyltransferase Gcn5 and the protein phosphatase 2A (PP2A) complex, two factors that regulate post-translational modifications. We find that RTS1, one of two genes encoding PP2A regulatory subunits, is a robust and specific high-copy suppressor of temperature sensitivity of gcn5∆ and a subset of other gcn5∆ phenotypes. Conversely, loss of both PP2A(Rts1) and Gcn5 function in the SAGA and SLIK/SALSA complexes is lethal. RTS1 does not restore global transcriptional defects in gcn5∆; however, histone gene expression is restored, suggesting that the mechanism of RTS1 rescue includes restoration of specific cell cycle transcripts. Pointing to new mechanisms of acetylation-phosphorylation cross-talk, RTS1 high-copy rescue of gcn5∆ growth requires two residues of H2B that are phosphorylated in human cells. These data highlight the potential significance of dynamic phosphorylation and dephosphorylation of these deeply conserved histone residues for cell viability.
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250
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GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites. Sci Rep 2016; 6:28249. [PMID: 27306108 PMCID: PMC4910163 DOI: 10.1038/srep28249] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/01/2016] [Indexed: 01/19/2023] Open
Abstract
As one of the most common post-translational modifications in eukaryotic cells, lipid modification is an important mechanism for the regulation of variety aspects of protein function. Over the last decades, three classes of lipid modifications have been increasingly studied. The co-regulation of these different lipid modifications is beginning to be noticed. However, due to the lack of integrated bioinformatics resources, the studies of co-regulatory mechanisms are still very limited. In this work, we developed a tool called GPS-Lipid for the prediction of four classes of lipid modifications by integrating the Particle Swarm Optimization with an aging leader and challengers (ALC-PSO) algorithm. GPS-Lipid was proven to be evidently superior to other similar tools. To facilitate the research of lipid modification, we hosted a publicly available web server at http://lipid.biocuckoo.org with not only the implementation of GPS-Lipid, but also an integrative database and visualization tool. We performed a systematic analysis of the co-regulatory mechanism between different lipid modifications with GPS-Lipid. The results demonstrated that the proximal dual-lipid modifications among palmitoylation, myristoylation and prenylation are key mechanism for regulating various protein functions. In conclusion, GPS-lipid is expected to serve as useful resource for the research on lipid modifications, especially on their co-regulation.
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