1
|
Wang P, Li Z, Kim SH, Xu H, Huang H, Yang C, Snape A, Choi JH, Bermudez S, Boivin MN, Ferry N, Karamchandani J, Nagar B, Sonenberg N. PPM1G dephosphorylates eIF4E in control of mRNA translation and cell proliferation. Life Sci Alliance 2024; 7:e202402755. [PMID: 39111820 PMCID: PMC11306785 DOI: 10.26508/lsa.202402755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
The mRNA 5'cap-binding eukaryotic translation initiation factor 4E (eIF4E) plays a critical role in the control of mRNA translation in health and disease. One mechanism of regulation of eIF4E activity is via phosphorylation of eIF4E by MNK kinases, which promotes the translation of a subset of mRNAs encoding pro-tumorigenic proteins. Work on eIF4E phosphatases has been paltry. Here, we show that PPM1G is the phosphatase that dephosphorylates eIF4E. We describe the eIF4E-binding motif in PPM1G that is similar to 4E-binding proteins (4E-BPs). We demonstrate that PPM1G inhibits cell proliferation by targeting phospho-eIF4E-dependent mRNA translation.
Collapse
Affiliation(s)
- Peng Wang
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
- Clinical Biological Imaging and Genetic (C-BIG) Repository, Montreal Neurological Institute-Hospital, Montreal, Canada
| | - Zixian Li
- https://ror.org/01pxwe438 Department of Biochemistry, Francesco Bellini Life Sciences Building, McGill University, Montreal, Canada
| | - Sung-Hoon Kim
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Haijin Xu
- https://ror.org/01pxwe438 Department of Physiology, McIntyre Medical Sciences Building, McGill University, Montreal, Canada
| | - Hao Huang
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Chutong Yang
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Abby Snape
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Jung-Hyun Choi
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Sara Bermudez
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Marie-Noelle Boivin
- Clinical Biological Imaging and Genetic (C-BIG) Repository, Montreal Neurological Institute-Hospital, Montreal, Canada
| | - Nicolas Ferry
- Clinical Biological Imaging and Genetic (C-BIG) Repository, Montreal Neurological Institute-Hospital, Montreal, Canada
| | - Jason Karamchandani
- Clinical Biological Imaging and Genetic (C-BIG) Repository, Montreal Neurological Institute-Hospital, Montreal, Canada
| | - Bhushan Nagar
- https://ror.org/01pxwe438 Department of Biochemistry, Francesco Bellini Life Sciences Building, McGill University, Montreal, Canada
| | - Nahum Sonenberg
- https://ror.org/01pxwe438 Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Canada
| |
Collapse
|
2
|
Hu W, Ma SL, Qiong L, Du Y, Gong LP, Pan YH, Sun LP, Wen JY, Chen JN, Guan XY, Shao CK. PPM1G promotes cell proliferation via modulating mutant GOF p53 protein expression in hepatocellular carcinoma. iScience 2024; 27:109116. [PMID: 38384839 PMCID: PMC10879691 DOI: 10.1016/j.isci.2024.109116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/25/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The serine/threonine protein phosphatase family involves series of cellular processes, such as pre-mRNA splicing. The function of one of its members, protein phosphatase, Mg2+/Mn2+ dependent 1G (PPM1G), remains unclear in hepatocellular carcinoma (HCC). Our results demonstrated that PPM1G was significantly overexpressed in HCC cells and tumor tissues compared with the normal liver tissues at both protein and RNA levels. High PPM1G expression is associated with shorter overall survival (p < 0.0001) and disease-free survival (p = 0.004) in HCC patients. Enhanced expression of PPM1G increases the cell proliferation rate, and knockdown of PPM1G led to a significant reduction in tumor volume in vivo. Further experiments illustrated that upregulated-PPM1G expression increased the protein expression of gain-of-function (GOF) mutant p53. Besides, the immunoprecipitation analysis revealed a direct interaction between PPM1G and GOF mutant p53. Collectively, PPM1G can be a powerful prognostic predictor and potential drug-target molecule.
Collapse
Affiliation(s)
- Wen Hu
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shao-Lin Ma
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, China
| | - Liang Qiong
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yu Du
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Li-Ping Gong
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yu-Hang Pan
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Li-Ping Sun
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Jing-Yun Wen
- Department of Oncology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Jian-Ning Chen
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Department of Clinical Oncology, the University of Hong Kong, Hong Kong, China
| | - Chun-Kui Shao
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| |
Collapse
|
3
|
Jia R, Zheng ZM. Oncogenic SRSF3 in health and diseases. Int J Biol Sci 2023; 19:3057-3076. [PMID: 37416784 PMCID: PMC10321290 DOI: 10.7150/ijbs.83368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Serine/arginine rich splicing factor 3 (SRSF3) is an important multi-functional splicing factor, and has attracted increasing attentions in the past thirty years. The importance of SRSF3 is evidenced by its impressively conserved protein sequences in all animals and alternative exon 4 which represents an autoregulatory mechanism to maintain its proper cellular expression level. New functions of SRSF3 have been continuously discovered recently, especially its oncogenic function. SRSF3 plays essential roles in many cellular processes by regulating almost all aspects of RNA biogenesis and processing of many target genes, and thus, contributes to tumorigenesis when overexpressed or disregulated. This review updates and highlights the gene, mRNA, and protein structure of SRSF3, the regulatory mechanisms of SRSF3 expression, and the characteristics of SRSF3 targets and binding sequences that contribute to SRSF3's diverse molecular and cellular functions in tumorigenesis and human diseases.
Collapse
Affiliation(s)
- Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
4
|
Jiang Y, Zhang C, Chen Y, Zhao S, He Y, He J. Prognostic risk assessment model for alternative splicing events and splicing factors in malignant pleural mesothelioma. Cancer Med 2023; 12:4895-4906. [PMID: 36031798 PMCID: PMC9972025 DOI: 10.1002/cam4.5174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is a rare and highly malignant thoracic tumor. Although alternative splicing (AS) is associated with tumor prognosis, the prognostic significance of AS in MPM is unknown. METHODS Transcriptomic data, clinical information, and splicing percentage values for MPM were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analyses were performed to establish a model affecting the prognosis of MPM. Survival and ROC analyses were used to test the effects of the prognostic model. LASSO/multivariate Cox analysis was used to construct the MPM prognostic splicing factor (SF) model. The SF-AS interaction network was analyzed using Spearman correlation and visualized using Cytoscape. The association between the MPM prognostic SF model and drug sensitivity to chemotherapeutic agents such as cisplatin was analyzed using pRRophetic.R. RESULTS The LASSO/multivariate Cox analysis identified 41 AS events and 2 SFs that were mostly associated with survival. Nine prognostic prediction models (i.e., seven types of AS model, total AS model, and SF model) were developed. An MPM prognostic SF-AS regulatory network was subsequently constructed with decreased drug sensitivity in the SF model high-risk group (p = 0.025). CONCLUSION This study provides the first comprehensive analysis of the prognostic value of AS events and SFs in MPM. The SF-AS regulatory network established in this study and our drug sensitivity analysis using the SF model may provide novel targets for pharmacological studies of MPM.
Collapse
Affiliation(s)
- Yue Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Chengda Zhang
- Department of Gastroenterology, The Third Hospital of Mian Yang (Sichuan Mental Health Center), Mianyang, China
| | - Yang Chen
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Shiyu Zhao
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Yipeng He
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jun He
- Department of Oncology, The Third Hospital of Mian Yang (Sichuan Mental Health Center), Mianyang, China
| |
Collapse
|
5
|
Detering NT, Schüning T, Hensel N, Claus P. The phospho-landscape of the survival of motoneuron protein (SMN) protein: relevance for spinal muscular atrophy (SMA). Cell Mol Life Sci 2022; 79:497. [PMID: 36006469 PMCID: PMC11071818 DOI: 10.1007/s00018-022-04522-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/27/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
Spinal muscular atrophy (SMA) is caused by low levels of the survival of motoneuron (SMN) Protein leading to preferential degeneration of lower motoneurons in the ventral horn of the spinal cord and brain stem. However, the SMN protein is ubiquitously expressed and there is growing evidence of a multisystem phenotype in SMA. Since a loss of SMN function is critical, it is important to decipher the regulatory mechanisms of SMN function starting on the level of the SMN protein itself. Posttranslational modifications (PTMs) of proteins regulate multiple functions and processes, including activity, cellular trafficking, and stability. Several PTM sites have been identified within the SMN sequence. Here, we map the identified SMN PTMs highlighting phosphorylation as a key regulator affecting localization, stability and functions of SMN. Furthermore, we propose SMN phosphorylation as a crucial factor for intracellular interaction and cellular distribution of SMN. We outline the relevance of phosphorylation of the spinal muscular atrophy (SMA) gene product SMN with regard to basic housekeeping functions of SMN impaired in this neurodegenerative disease. Finally, we compare SMA patient mutations with putative and verified phosphorylation sites. Thus, we emphasize the importance of phosphorylation as a cellular modulator in a clinical perspective as a potential additional target for combinatorial SMA treatment strategies.
Collapse
Affiliation(s)
- Nora Tula Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Niko Hensel
- Ottawa Hospital Research Institute (OHRI), Ottawa, Canada
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany.
- Center for Systems Neuroscience (ZSN), Hannover, Germany.
| |
Collapse
|
6
|
Chen D, Zhao Z, Chen L, Li Q, Zou J, Liu S. PPM1G promotes the progression of hepatocellular carcinoma via phosphorylation regulation of alternative splicing protein SRSF3. Cell Death Dis 2021; 12:722. [PMID: 34290239 PMCID: PMC8295330 DOI: 10.1038/s41419-021-04013-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022]
Abstract
Emerging evidence has demonstrated that alternative splicing has a vital role in regulating protein function, but how alternative splicing factors can be regulated remains unclear. We showed that the PPM1G, a protein phosphatase, regulated the phosphorylation of SRSF3 in hepatocellular carcinoma (HCC) and contributed to the proliferation, invasion, and metastasis of HCC. PPM1G was highly expressed in HCC tissues compared to adjacent normal tissues, and higher levels of PPM1G were observed in adverse staged HCCs. The higher levels of PPM1G were highly correlated with poor prognosis, which was further validated in the TCGA cohort. The knockdown of PPM1G inhibited the cell growth and invasion of HCC cell lines. Further studies showed that the knockdown of PPM1G inhibited tumor growth in vivo. The mechanistic analysis showed that the PPM1G interacted with proteins related to alternative splicing, including SRSF3. Overexpression of PPM1G promoted the dephosphorylation of SRSF3 and changed the alternative splicing patterns of genes related to the cell cycle, the transcriptional regulation in HCC cells. In addition, we also demonstrated that the promoter of PPM1G was activated by multiple transcription factors and co-activators, including MYC/MAX and EP300, MED1, and ELF1. Our study highlighted the essential role of PPM1G in HCC and shed new light on unveiling the regulation of alternative splicing in malignant transformation.
Collapse
Affiliation(s)
- Dawei Chen
- Department of Hepatopancreatobiliary Surgery, Jiangyin People's Hospital, School of Medicine, Southeast University, No. 163, Shoushan Road, Jiangyin, 214400, Jiangsu Province, China
| | - Zhenguo Zhao
- Department of Hepatopancreatobiliary Surgery, Jiangyin People's Hospital, School of Medicine, Southeast University, No. 163, Shoushan Road, Jiangyin, 214400, Jiangsu Province, China
| | - Lu Chen
- Department of Hepatopancreatobiliary Surgery, Jiangyin People's Hospital, School of Medicine, Southeast University, No. 163, Shoushan Road, Jiangyin, 214400, Jiangsu Province, China
| | - Qinghua Li
- Department of Hepatopancreatobiliary Surgery, Jiangyin People's Hospital, School of Medicine, Southeast University, No. 163, Shoushan Road, Jiangyin, 214400, Jiangsu Province, China
| | - Jixue Zou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China.
| | - Shuanghai Liu
- Department of Hepatopancreatobiliary Surgery, Jiangyin People's Hospital, School of Medicine, Southeast University, No. 163, Shoushan Road, Jiangyin, 214400, Jiangsu Province, China.
| |
Collapse
|
7
|
Yu K, Tian H, Deng H. PPM1G restricts innate immune signaling mediated by STING and MAVS and is hijacked by KSHV for immune evasion. SCIENCE ADVANCES 2020; 6:6/47/eabd0276. [PMID: 33219031 PMCID: PMC7679160 DOI: 10.1126/sciadv.abd0276] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
The adaptor proteins, STING and MAVS, are components of critical pathogen-sensing pathways that induce innate immunity. Phosphorylation of either adaptor results in activation of the type I interferon pathway. How this phosphorylation is regulated and how it is manipulated by pathogens remain largely unknown. Here, we identified host protein phosphatase, Mg2+/Mn2+ dependent 1G (PPM1G) as a negative regulator of innate immune pathways and showed that this host system is hijacked by Kaposi's sarcoma-associated herpesvirus (KSHV). Mechanistically, KSHV tegument protein ORF33 interacts with STING/MAVS and enhances recruitment of PPM1G to dephosphorylate p-STING/p-MAVS for immunosuppression. Inhibition of PPM1G expression improves the antiviral response against both DNA and RNA viruses. Collectively, our study shows that PPM1G restricts both cytosolic DNA- and RNA-sensing pathways to naturally balance the intensity of the antiviral response. Manipulation of PPM1G by KSHV provides an important strategy for immune evasion.
Collapse
Affiliation(s)
- Kuai Yu
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
8
|
Cellular Identification and In Silico Characterization of Protein Phosphatase 2C (PP2C) of Cryptosporidium parvum. Acta Parasitol 2020; 65:704-715. [PMID: 32347536 DOI: 10.2478/s11686-020-00209-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/25/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Cryptosporidium parvum is an Apicomplexa parasite that causes watery diarrhea (cryptosporidiosis), especially in children and immunocompromised adults (the latter in a very severe form). No effective treatment exists against infection by this parasite. Phosphatases participate in the regulation of various cellular functions and are thus considered potential therapeutic targets in many diseases. The aim of the present study was to indirectly identify and in silico characterize a protein phosphatase 2C of C. parvum. METHODS Western blot and indirect immunofluorescence microscopy were performed with a polyclonal antibody against Leishmania major PP2C. Possible cross-reactivity with LmPP2C was assessed by in silico sequence homology to analyze phylogenetic relationships between distinct C. parvum PP2Cs. In addition, another bioinformatics approach was used to predict the possible relationship and function of C. parvum PP2C in the regulation of several cellular processes. RESULTS Western blotting showed a protein of approximately 72 kDa. With immunofluorescence, PP2C was localized in the nucleus of oocysts (with some additional labeling in the cytoplasm) and at the apical region of sporozoites. By aligning C. parvum PP2C with known ortholog sequences and carrying out PPI analysis, a determination could be made of the degree of conservation of these enzymes, their possible relationship, and their function in the regulation of several cellular processes associated with a likely nuclear location. CONCLUSION Microscopic localization by immunofluorescence identified CpPP2C at the nucleus in oocysts and at the apical end of the sporozoite body. Hence, this enzyme could be associated with proteins that have an important role in the regulation of transcription and other processes orchestrated by MAPK kinases, according to in silico analysis.
Collapse
|
9
|
Su J, Zhu D, Huo Z, Gingold JA, Ang YS, Tu J, Zhou R, Lin Y, Luo H, Yang H, Zhao R, Schaniel C, Moore KA, Lemischka IR, Lee DF. Genomic Integrity Safeguards Self-Renewal in Embryonic Stem Cells. Cell Rep 2020; 28:1400-1409.e4. [PMID: 31390555 PMCID: PMC6708277 DOI: 10.1016/j.celrep.2019.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 01/06/2023] Open
Abstract
A multitude of signals are coordinated to maintain self-renewal in embryonic stem cells (ESCs). To unravel the essential internal and external signals required for sustaining the ESC state, we expand upon a set of ESC pluripotency-associated phosphoregulators (PRs) identified previously by short hairpin RNA (shRNA) screening. In addition to the previously described Aurka, we identify 4 additional PRs (Bub1b, Chek1, Ppm1g, and Ppp2r1b) whose depletion compromises self-renewal and leads to consequent differentiation. Global gene expression profiling and computational analyses reveal that knockdown of the 5 PRs leads to DNA damage/genome instability, activating p53 and culminating in ESC differentiation. Similarly, depletion of genome integrity-associated genes involved in DNA replication and checkpoint, mRNA processing, and Charcot-Marie-Tooth disease lead to compromise of ESC self-renewal via an increase in p53 activity. Our studies demonstrate an essential link between genomic integrity and developmental cell fate regulation in ESCs.
Collapse
Affiliation(s)
- Jie Su
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zijun Huo
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Julian A Gingold
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Women's Health Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Yen-Sin Ang
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Tu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Ruoji Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yu Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Haidan Luo
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Huiling Yang
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kateri A Moore
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dung-Fang Lee
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
10
|
Kumar P, Tathe P, Chaudhary N, Maddika S. PPM1G forms a PPP-type phosphatase holoenzyme with B56δ that maintains adherens junction integrity. EMBO Rep 2019; 20:e46965. [PMID: 31432583 PMCID: PMC6776900 DOI: 10.15252/embr.201846965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 07/26/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Serine/threonine phosphatases achieve substrate diversity by forming distinct holoenzyme complexes in cells. Although the PPP family of serine/threonine phosphatase family members such as PP1 and PP2A are well known to assemble and function as holoenzymes, none of the PPM family members were so far shown to act as holoenzymes. Here, we provide evidence that PPM1G, a member of PPM family of serine/threonine phosphatases, forms a distinct holoenzyme complex with the PP2A regulatory subunit B56δ. B56δ promotes the re-localization of PPM1G to the cytoplasm where the phosphatase can access a discrete set of substrates. Further, we unveil α-catenin, a component of adherens junction, as a new substrate for the PPM1G-B56 phosphatase complex in the cytoplasm. B56δ-PPM1G dephosphorylates α-catenin at serine 641, which is necessary for the appropriate assembly of adherens junctions and the prevention of aberrant cell migration. Collectively, we reveal a new holoenzyme with PPM1G-B56δ as integral components, in which the regulatory subunit provides accessibility to distinct substrates for the phosphatase by defining its cellular localization.
Collapse
Affiliation(s)
- Parveen Kumar
- Laboratory of Cell Death & Cell SurvivalCentre for DNA Fingerprinting and Diagnostics (CDFD)Uppal, HyderabadIndia
- Graduate StudiesManipal Academy of Higher EducationManipalIndia
| | - Prajakta Tathe
- Laboratory of Cell Death & Cell SurvivalCentre for DNA Fingerprinting and Diagnostics (CDFD)Uppal, HyderabadIndia
- Graduate StudiesManipal Academy of Higher EducationManipalIndia
| | - Neelam Chaudhary
- Laboratory of Cell Death & Cell SurvivalCentre for DNA Fingerprinting and Diagnostics (CDFD)Uppal, HyderabadIndia
| | - Subbareddy Maddika
- Laboratory of Cell Death & Cell SurvivalCentre for DNA Fingerprinting and Diagnostics (CDFD)Uppal, HyderabadIndia
| |
Collapse
|
11
|
Pyo J, Ryu J, Kim W, Choi JS, Jeong JW, Kim JE. The Protein Phosphatase PPM1G Destabilizes HIF-1α Expression. Int J Mol Sci 2018; 19:ijms19082297. [PMID: 30081604 PMCID: PMC6121667 DOI: 10.3390/ijms19082297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/23/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
Hypoxia-inducible factors (HIFs) are key regulators of hypoxic responses, and their stability and transcriptional activity are controlled by several kinases. However, the regulation of HIF by protein phosphatases has not been thoroughly investigated. Here, we found that overexpression of Mg2+/Mn2+-dependent protein phosphatase 1 gamma (PPM1G), one of Ser/Thr protein phosphatases, downregulated protein expression of ectopic HIF-1α under normoxic or acute hypoxic conditions. In addition, the deficiency of PPM1G upregulated protein expression of endogenous HIF-1α under normoxic or acute oxidative stress conditions. PPM1G decreased expression of HIF-1α via the proteasomal pathway. PPM1G-mediated HIF-1α degradation was dependent on prolyl hydroxylase (PHD), but independent of von Hippel-Lindau (VHL). These data suggest that PPM1G is critical for the control of HIF-1α-dependent responses.
Collapse
Affiliation(s)
- Jaehyuk Pyo
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
| | - Jaewook Ryu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
| | - Wootae Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
| | - Jae-Sun Choi
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
| | - Joo-Won Jeong
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
- Department of Anatomy and Neurobiology, School of Medicine, Kyung Hee University, Seoul 02447, Korea.
| | - Ja-Eun Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea.
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul 02447, Korea.
| |
Collapse
|
12
|
Xu K, Wang L, Feng W, Feng Y, Shu HK. Phosphatidylinositol-3 kinase-dependent translational regulation of Id1 involves the PPM1G phosphatase. Oncogene 2016; 35:5807-5816. [PMID: 27065332 PMCID: PMC5064830 DOI: 10.1038/onc.2016.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/04/2016] [Accepted: 01/22/2016] [Indexed: 12/30/2022]
Abstract
Id1 is a helix-loop-helix transcriptional modulator that increases the aggressiveness of malignant glial neoplasms. Since most glioblastomas (GBMs) show increased phosphatidylinositol-3 kinase (PI-3K) signaling, we sought to determine whether this pathway regulates Id1 expression. Higher basal Id1 expression correlates with dysregulated PI-3K signaling in multiple established GBM cell lines. Further characterization of PI-3K-dependent Id1 regulation reveals that chemical or genetic inhibition of PI-3K signaling reduces Id1 protein but not mRNA expression. Overall, PI-3K signaling appears to enhance Id1 translation with no significant effect on its stability. PI-3K signaling is known to regulate protein translation through mTORC1-dependent phosphorylation of 4E-BP1, which reduces its association with and inhibition of the translation initiation factor eIF4E. Interestingly, while inhibition of PI-3K and AKT lowers 4E-BP1 phosphorylation and expression of Id1 in all cases, inhibition of TORC1 with rapamycin does not consistently have a similar effect suggesting an alternative mechanism for PI-3K-dependent regulation of Id1 translation. We now identify a potential role for the serine-threonine phosphatase PPM1G in translational regulation of Id1 protein expression. PPM1G knockdown by siRNA increase both 4E-BP1 phosphorylation and Id1 expression and PPM1G and 4E-BP1 co-associates in GBM cells. Furthermore, PPM1G is a phosphoprotein and this phosphorylation appears to be regulated by PI-3K activity. Finally, PI-3K inhibition increases PPM1G activity when assessed by an in vitro phosphatase assay. Our findings provide the first evidence that the PI-3K/AKT signaling pathway modulates PPM1G activity resulting in a shift in the balance between hyper- and hypo-phosphorylated 4E-BP1 and translational regulation of Id1 expression.
Collapse
Affiliation(s)
- K Xu
- Department of Radiation Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - L Wang
- Department of Radiation Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - W Feng
- Department of Pharmacology, Emory University, Atlanta, GA, USA
| | - Y Feng
- Department of Pharmacology, Emory University, Atlanta, GA, USA
| | - H-Kg Shu
- Department of Radiation Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| |
Collapse
|
13
|
Yu F, Wu Y, Xie Q. Ubiquitin-Proteasome System in ABA Signaling: From Perception to Action. MOLECULAR PLANT 2016; 9:21-33. [PMID: 26455462 DOI: 10.1016/j.molp.2015.09.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 05/18/2023]
Abstract
Protein post-translational modification (PTM) by ubiquitination has been observed during many aspects of plant growth, development, and stress responses. The ubiquitin-proteasome system precisely regulates phytohormone signaling by affecting protein activity, localization, assembly, and interaction ability. Abscisic acid (ABA) is a major phytohormone, and plays important roles in plants under normal or stressed growth conditions. The ABA signaling pathway is composed of phosphatases, kinases, transcription factors, and membrane ion channels. It has been reported that multiple ABA signaling transducers are subjected to the regulations by ubiquitination. In particular, recent studies have identified different types of E3 ligases that mediate ubiquitination of ABA receptors in different cell compartments. This review focuses on modulation of these components by monoubiquitination or polyubiquitination that occurs in the plasma membrane, endomembranes, and from the cytosol to the nucleus; this implies the existence of retrograde and trafficking processes that are regulated by ubiquitination in ABA signaling. A number of single-unit E3 ligases, components of multi-subunit E3 ligases, E2s, and specific subunits of the 26S proteasome involved in ABA signal regulation are discussed. Dissecting the precise functions of ubiquitination in the ABA pathway may help us understand key factors in the signaling of other phytohormones regulated by ubiquitination and other types of PTMs.
Collapse
Affiliation(s)
- Feifei Yu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
| |
Collapse
|
14
|
Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
Collapse
Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| |
Collapse
|
15
|
Dago DN, Scafoglio C, Rinaldi A, Memoli D, Giurato G, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A. Estrogen receptor beta impacts hormone-induced alternative mRNA splicing in breast cancer cells. BMC Genomics 2015; 16:367. [PMID: 25956916 PMCID: PMC4424892 DOI: 10.1186/s12864-015-1541-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/17/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Estrogens play an important role in breast cancer (BC) development and progression; when the two isoforms of the estrogen receptor (ERα and ERβ) are co-expressed each of them mediate specific effects of these hormones in BC cells. ERβ has been suggested to exert an antagonist role toward the oncogenic activities of ERα, and for this reason it is considered an oncosuppressor. As clinical evidence regarding a prognostic role for this receptor subtype in hormone-responsive BC is still limited and conflicting, more knowledge is required on the biological functions of ERβ in cancer cells. We have previously described the ERβ and ERα interactomes from BC cells, identifying specific and distinct patterns of protein interactions for the two receptors. In particular, we identified factors involved in mRNA splicing and maturation as important components of both ERα and ERβ pathways. Guided by these findings, here we performed RNA sequencing to investigate in depth the differences in the early transcriptional events and RNA splicing patterns induced by estradiol in cells expressing ERα alone or ERα and ERβ. RESULTS Exon skipping was the most abundant splicing event in the post-transcriptional regulation by estradiol. We identified several splicing events induced by ERα alone and by ERα+ERβ, demonstrating for the first time that ERβ significantly affects estrogen-induced splicing in BC cells, as revealed by modification of a subset of ERα-dependent splicing by ERβ, as well as by the presence of splicing isoforms only in ERβ+cells. In particular, we observed that ERβ+BC cell lines exhibited around 2-fold more splicing events than the ERβ- cells. Interestingly, we identified putative direct targets of ERβ-mediated alternative splicing by correlating the genomic locations of ERβ and ERα binding sites with estradiol-induced differential splicing in the corresponding genes. CONCLUSIONS Taken together, these results demonstrate that ERβ significantly affects estrogen-induced early transcription and mRNA splicing in hormone-responsive BC cells, providing novel information on the biological role of ERβ in these tumors.
Collapse
Affiliation(s)
- Dougba Noel Dago
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy. .,UFR Sciences Biologiques, Université Peleforo Gon Coulibaly, Korhogo, Ivory Coast.
| | - Claudio Scafoglio
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA.
| | - Antonio Rinaldi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Via S. Allende, 1, Baronissi, SA, 84081, Italy. .,Molecular Pathology and Medical Genomics, "SS. Giovanni di Dio e Ruggi d'Aragona - Schola Medica Salernitana" Hospital of the University of Salerno, Salerno, Italy.
| |
Collapse
|
16
|
Liu MT, Nagre NN, Ryan K. Structurally diverse low molecular weight activators of the mammalian pre-mRNA 3' cleavage reaction. Bioorg Med Chem 2014; 22:834-41. [PMID: 24373842 PMCID: PMC4018835 DOI: 10.1016/j.bmc.2013.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/23/2013] [Accepted: 12/03/2013] [Indexed: 11/15/2022]
Abstract
The 3' end formation of mammalian pre-mRNA contributes to gene expression regulation by setting the downstream boundary of the 3' untranslated region, which in many genes carries regulatory sequences. A large number of protein cleavage factors participate in this pre-mRNA processing step, but chemical tools to manipulate this process are lacking. Guided by a hypothesis that a PPM1 family phosphatase negatively regulates the 3' cleavage reaction, we have found a variety of new small molecule activators of the in vitro reconstituted pre-mRNA 3' cleavage reaction. New activators include a cyclic peptide PPM1D inhibitor, a dipeptide with modifications common to histone tails, abscisic acid and an improved l-arginine β-naphthylamide analog. The minimal concentration required for in vitro cleavage has been improved from 200μM to the 200nM-100μM range. These compounds provide unexpected leads in the search for small molecule tools able to affect pre-mRNA 3' end formation.
Collapse
Affiliation(s)
- Min Ting Liu
- Department of Chemistry, The City College of New York, The City University of New York, New York, NY 10031, USA
| | - Nagaraja N Nagre
- Department of Chemistry, The City College of New York, The City University of New York, New York, NY 10031, USA
| | - Kevin Ryan
- Department of Chemistry, The City College of New York, The City University of New York, New York, NY 10031, USA.
| |
Collapse
|
17
|
RNA splicing: a new player in the DNA damage response. Int J Cell Biol 2013; 2013:153634. [PMID: 24159334 PMCID: PMC3789447 DOI: 10.1155/2013/153634] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/16/2022] Open
Abstract
It is widely accepted that tumorigenesis is a multistep process characterized by the sequential accumulation of genetic alterations. However, the molecular basis of genomic instability in cancer is still partially understood. The observation that hereditary cancers are often characterized by mutations in DNA repair and checkpoint genes suggests that accumulation of DNA damage is a major contributor to the oncogenic transformation. It is therefore of great interest to identify all the cellular pathways that contribute to the response to DNA damage. Recently, RNA processing has emerged as a novel pathway that may contribute to the maintenance of genome stability. In this review, we illustrate several different mechanisms through which pre-mRNA splicing and genomic stability can influence each other. We specifically focus on the role of splicing factors in the DNA damage response and describe how, in turn, activation of the DDR can influence the activity of splicing factors.
Collapse
|
18
|
Naro C, Sette C. Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
Collapse
Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
| |
Collapse
|
19
|
Foster WH, Langenbacher A, Gao C, Chen J, Wang Y. Nuclear phosphatase PPM1G in cellular survival and neural development. Dev Dyn 2013; 242:1101-9. [PMID: 23723158 DOI: 10.1002/dvdy.23990] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/27/2013] [Accepted: 05/14/2013] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND PPM1G is a nuclear localized serine/threonine phosphatase implicated to be a regulator of chromatin remodeling, mRNA splicing, and DNA damage. However, its in vivo function is unknown. RESULTS Here we show that ppm1g expression is highly enriched in the central nervous system during mouse and zebrafish development. ppm1g(-/-) mice were embryonic lethal with incomplete penetrance after E12.5. Rostral defects, including neural tube and craniofacial defects were observed in ppm1g(-/-) embryos associated with increased cell death in the neural epithelium. In zebrafish, loss of ppm1g also led to neural defects with aberrant neural marker gene expression. Primary fibroblasts from ppm1g(-/-) embryos failed to grow without immortalization while immortalized ppm1g(-/-) fibroblasts had increased cell death upon oxidative and genotoxic stress when compared to wild type fibroblasts. CONCLUSIONS Our in vivo and in vitro studies revealed a critical role for PPM1G in normal development and cell survival.
Collapse
Affiliation(s)
- William H Foster
- Molecular, Cellular and Integrated Physiology Program, University of California at Los Angeles, Los Angeles, California, USA
| | | | | | | | | |
Collapse
|
20
|
Lee KM, Tarn WY. Coupling pre-mRNA processing to transcription on the RNA factory assembly line. RNA Biol 2013; 10:380-90. [PMID: 23392244 DOI: 10.4161/rna.23697] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It has been well-documented that nuclear processing of primary transcripts of RNA polymerase II occurs co-transcriptionally and is functionally coupled to transcription. Moreover, increasing evidence indicates that transcription influences pre-mRNA splicing and even several post-splicing RNA processing events. In this review, we discuss the issues of how RNA polymerase II modulates co-transcriptional RNA processing events via its carboxyl terminal domain, and the protein domains involved in coupling of transcription and RNA processing events. In addition, we describe how transcription influences the expression or stability of mRNAs through the formation of distinct mRNP complexes. Finally, we delineate emerging findings that chromatin modifications function in the regulation of RNA processing steps, especially splicing, in addition to transcription. Overall, we provide a comprehensive view that transcription could integrate different control systems, from epigenetic to post-transcriptional control, for efficient gene expression.
Collapse
Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences; Academia Sinica; Taipei, Taiwan
| | | |
Collapse
|
21
|
Manning AK, Hivert MF, Scott RA, Grimsby JL, Bouatia-Naji N, Chen H, Rybin D, Liu CT, Bielak LF, Prokopenko I, Amin N, Barnes D, Cadby G, Hottenga JJ, Ingelsson E, Jackson AU, Johnson T, Kanoni S, Ladenvall C, Lagou V, Lahti J, Lecoeur C, Liu Y, Martinez-Larrad MT, Montasser ME, Navarro P, Perry JRB, Rasmussen-Torvik LJ, Salo P, Sattar N, Shungin D, Strawbridge RJ, Tanaka T, van Duijn CM, An P, de Andrade M, Andrews JS, Aspelund T, Atalay M, Aulchenko Y, Balkau B, Bandinelli S, Beckmann JS, Beilby JP, Bellis C, Bergman RN, Blangero J, Boban M, Boehnke M, Boerwinkle E, Bonnycastle LL, Boomsma DI, Borecki IB, Böttcher Y, Bouchard C, Brunner E, Budimir D, Campbell H, Carlson O, Chines PS, Clarke R, Collins FS, Corbatón-Anchuelo A, Couper D, de Faire U, Dedoussis GV, Deloukas P, Dimitriou M, Egan JM, Eiriksdottir G, Erdos MR, Eriksson JG, Eury E, Ferrucci L, Ford I, Forouhi NG, Fox CS, Franzosi MG, Franks PW, Frayling TM, Froguel P, Galan P, de Geus E, Gigante B, Glazer NL, Goel A, Groop L, Gudnason V, Hallmans G, Hamsten A, Hansson O, Harris TB, Hayward C, Heath S, Hercberg S, Hicks AA, Hingorani A, Hofman A, Hui J, Hung J, Jarvelin MR, Jhun MA, Johnson PC, Jukema JW, Jula A, Kao W, Kaprio J, Kardia SLR, Keinanen-Kiukaanniemi S, Kivimaki M, Kolcic I, Kovacs P, Kumari M, Kuusisto J, Kyvik KO, Laakso M, Lakka T, Lannfelt L, Lathrop GM, Launer LJ, Leander K, Li G, Lind L, Lindstrom J, Lobbens S, Loos RJF, Luan J, Lyssenko V, Mägi R, Magnusson PKE, Marmot M, Meneton P, Mohlke KL, Mooser V, Morken MA, Miljkovic I, Narisu N, O’Connell J, Ong KK, Oostra BA, Palmer LJ, Palotie A, Pankow JS, Peden JF, Pedersen NL, Pehlic M, Peltonen L, Penninx B, Pericic M, Perola M, Perusse L, Peyser PA, Polasek O, Pramstaller PP, Province MA, Räikkönen K, Rauramaa R, Rehnberg E, Rice K, Rotter JI, Rudan I, Ruokonen A, Saaristo T, Sabater-Lleal M, Salomaa V, Savage DB, Saxena R, Schwarz P, Seedorf U, Sennblad B, Serrano-Rios M, Shuldiner AR, Sijbrands EJ, Siscovick DS, Smit JH, Small KS, Smith NL, Smith AV, Stančáková A, Stirrups K, Stumvoll M, Sun YV, Swift AJ, Tönjes A, Tuomilehto J, Trompet S, Uitterlinden AG, Uusitupa M, Vikström M, Vitart V, Vohl MC, Voight BF, Vollenweider P, Waeber G, Waterworth DM, Watkins H, Wheeler E, Widen E, Wild SH, Willems SM, Willemsen G, Wilson JF, Witteman JC, Wright AF, Yaghootkar H, Zelenika D, Zemunik T, Zgaga L, Wareham NJ, McCarthy MI, Barroso I, Watanabe RM, Florez JC, Dupuis J, Meigs JB, Langenberg C. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Nat Genet 2012; 44:659-69. [PMID: 22581228 PMCID: PMC3613127 DOI: 10.1038/ng.2274] [Citation(s) in RCA: 599] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 04/13/2012] [Indexed: 12/15/2022]
Abstract
Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and β-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 × 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.
Collapse
Affiliation(s)
- Alisa K. Manning
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts
| | - Marie-France Hivert
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Jonna L. Grimsby
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Nabila Bouatia-Naji
- Institut Pasteur de Lille, Lille, France
- Lille Nord de France University, Lille, France
| | - Han Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, Massachusetts, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lawrence F. Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Inga Prokopenko
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel Barnes
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research. Toronto, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Jouke-Jan Hottenga
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Toby Johnson
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, Cambridge, UK
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
| | - Vasiliki Lagou
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Cecile Lecoeur
- Institut Pasteur de Lille, Lille, France
- Lille Nord de France University, Lille, France
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Maria Teresa Martinez-Larrad
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain
| | - May E. Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, Maryland, USA
| | - Pau Navarro
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - John R. B. Perry
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Perttu Salo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - Dmitry Shungin
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Genetic Epidemiology & Clinical Research Group, Umeå University Hospital, Umeå, Sweden
- Department of Odontology, Umeå University, Sweden
| | - Rona J. Strawbridge
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland, USA
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Centre for medical systems biology, Netherlands Genomics Initiative, The Hague
- Netherlands Genomics Initiative and the Netherlands Consortium for Healthy Aging, Rotterdam, The Netherlands
| | - Ping An
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Thor Aspelund
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Mustafa Atalay
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Yurii Aulchenko
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Beverley Balkau
- Inserm, CESP Centre for research in Epidemiology and Population Health, Villejuif, France
- University Paris Sud 11, Villejuif, France
| | | | - Jacques S. Beckmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - John P. Beilby
- PathWest Laboratory Medicine of WA, J Block, QEII Medical Centre, Nedlands, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Australia
- Busselton Population Medical Research Foundation, B Block, QEII Medical Centre, Nedlands, Australia
| | - Claire Bellis
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Richard N. Bergman
- Department of Physiology & Biophysics, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - John Blangero
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mladen Boban
- Department of Pharmacology, Faculty of Medicine, University of Split, Croatia
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Dorret I. Boomsma
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Ingrid B. Borecki
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Claude Bouchard
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
| | - Eric Brunner
- University College London, Department of Epidemiology & Public Health, London, UK
| | - Danijela Budimir
- Department of Pharmacology, Faculty of Medicine, University of Split, Croatia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Olga Carlson
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, Maryland, USA
| | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Robert Clarke
- Clinical Trial Service Unit, University of Oxford, Oxford, UK
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Arturo Corbatón-Anchuelo
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain
| | - David Couper
- Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - George V Dedoussis
- Department of Nutrition - Dietetics, Harokopio University, Athens, Greece
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, Cambridge, UK
| | - Maria Dimitriou
- Department of Nutrition - Dietetics, Harokopio University, Athens, Greece
| | - Josephine M Egan
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, Maryland, USA
| | | | - Michael R. Erdos
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Johan G. Eriksson
- Department of General Practice and Primary health Care, University of Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
- Folkhalsan Research Centre, Helsinki, Finland
- Vaasa Central Hospital, Vaasa, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Elodie Eury
- Institut Pasteur de Lille, Lille, France
- Lille Nord de France University, Lille, France
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, Baltimore, Maryland, USA
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, UK
| | - Nita G. Forouhi
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Caroline S Fox
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, USA
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Grazia Franzosi
- Department of Cardiovascular Research, Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - Paul W Franks
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Genetic Epidemiology & Clinical Research Group, Umeå University Hospital, Umeå, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
- Institut National de la Recherche Agronomique, Université Paris, Bobigny Cedex, France
| | - Timothy M Frayling
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
| | - Philippe Froguel
- Institut Pasteur de Lille, Lille, France
- Lille Nord de France University, Lille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Pilar Galan
- Institut National de la Santé et de la Recherche Médicale, Université Paris, Bobigny Cedex, France
| | - Eco de Geus
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Bruna Gigante
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicole L. Glazer
- Department of Medicine, Section of Preventive Medicine and Epidemiology, BU School of Medicine, Boston, Massachusetts, USA
- Department of Epidemiology, BU School of Public Health, Boston, Massachusetts, USA
| | - Anuj Goel
- Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Göran Hallmans
- Department of Public Health & Clinical Medicine, Nutrition Research, Umeå University, Sweden
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ola Hansson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
| | - Tamara B. Harris
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Simon Heath
- Centre National de Génotypage, Commissariat à L’Energie Atomique, Institut de Génomique, Evry, France
| | - Serge Hercberg
- Institut National de la Santé et de la Recherche Médicale, Université Paris, Bobigny Cedex, France
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano, Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Aroon Hingorani
- Genetic epidemiology group, University College London, Department of Epidemiology & Public Health, London, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative and the Netherlands Consortium for Healthy Aging, Rotterdam, The Netherlands
| | - Jennie Hui
- PathWest Laboratory Medicine of WA, J Block, QEII Medical Centre, Nedlands, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Australia
- Busselton Population Medical Research Foundation, B Block, QEII Medical Centre, Nedlands, Australia
- School of Population Health, The University of Western Australia, Nedlands, Australia
| | - Joseph Hung
- Busselton Population Medical Research Foundation, B Block, QEII Medical Centre, Nedlands, Australia
- Sir Charles Gairdner Hospital Unit, School of Medicine & Pharmacology, University of Western Australia, Australia
| | - Marjo Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-HPA Centre for Environment and Health, Faculty of Medicine, Imperial College London, UK
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- National Institute of Health and Welfare, Oulu, Finland
| | - Min A. Jhun
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - J Wouter Jukema
- Department of Cardiology C5-P, Leiden University Medical Center, Leiden, the Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
| | - Antti Jula
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - W.H. Kao
- Division of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Jaakko Kaprio
- National Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Hjelt Institute, Dept of Public Health, University of Helsinki, Finland
| | - Sharon L. R. Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sirkka Keinanen-Kiukaanniemi
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Mika Kivimaki
- University College London, Department of Epidemiology & Public Health, London, UK
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine, University of Split, Croatia
| | - Peter Kovacs
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Meena Kumari
- Genetic epidemiology group, University College London, Department of Epidemiology & Public Health, London, UK
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kirsten Ohm Kyvik
- Institute of Regional Health Services Research and Professor Odense Patient data Explorative Network (OPEN)
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences, Uppsala University, Rudbecklaboratoriet, Uppsala, Sweden
| | - G Mark Lathrop
- Centre National de Génotypage, Commissariat à L’Energie Atomique, Institut de Génomique, Evry, France
| | - Lenore J. Launer
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Karin Leander
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA
| | - Lars Lind
- Department of Medical Sciences, University Hospital, Uppsala University, Uppsala, Sweden
| | - Jaana Lindstrom
- Diabetes Prevention Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stéphane Lobbens
- Institut Pasteur de Lille, Lille, France
- Lille Nord de France University, Lille, France
| | - Ruth J. F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Jian’an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Lund University Diabetes Centre, Malmö, Sweden
| | - Reedik Mägi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Michael Marmot
- University College London, Department of Epidemiology & Public Health, London, UK
| | - Pierre Meneton
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Paris, France
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Vincent Mooser
- Division of Genetics, GlaxoSmithKline, Philadelphia, Pennsylvania, USA
| | - Mario A. Morken
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Iva Miljkovic
- Department of Epidemiology, Center for Aging and Population Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Jeff O’Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, Maryland, USA
| | - Ken K. Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research. Toronto, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Aarno Palotie
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, Cambridge, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki and Helsinki University Central Hospital, Finland
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
| | - John F. Peden
- Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marina Pehlic
- Department of Biology, Faculty of Medicine, University of Split, Croatia
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, Cambridge, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Brenda Penninx
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department Psychiatry, EMGO Institute for Health and Care Research and Institute for Neurosciences, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Markus Perola
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Louis Perusse
- Department of Preventive Medicine, Laval University, Quebec, Canada
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ozren Polasek
- Department of Public Health, Faculty of Medicine, University of Split, Croatia
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano, Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Michael A. Province
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Katri Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Emil Rehnberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | | | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
- Centre for Global Health, University of Split, Croatia
| | - Aimo Ruokonen
- Institute of Clinical Medicine, University of Oulu, Finland
| | - Timo Saaristo
- Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Maria Sabater-Lleal
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - David B. Savage
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peter Schwarz
- Department of Medicine, Division Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Udo Seedorf
- Leibniz Institute for Arteriosclerosis Research, University of Munster, Germany
| | - Bengt Sennblad
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Manuel Serrano-Rios
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, Spain
| | - Alan R. Shuldiner
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, Maryland, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland, USA
| | | | - David S. Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Johannes H. Smit
- Department of Psychiatry, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Nicholas L. Smith
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, USA
- Seattle Epidemiologic Research and Information Center, Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kathleen Stirrups
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, Cambridge, UK
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Division of Endocrinology and Diabetes, Leipzig, Germany
| | - Yan V. Sun
- Department of Epidemiology, Emory University, Atlanta, Georgia, US
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Anke Tönjes
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Division of Endocrinology and Diabetes, Leipzig, Germany
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
- Hospital Universitario La Paz, Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
| | - Stella Trompet
- Department of Cardiology C5-P, Leiden University Medical Center, Leiden, the Netherlands
| | - Andre G. Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative and the Netherlands Consortium for Healthy Aging, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Easten Finland, Kuopio, Finland
- Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Max Vikström
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Marie-Claude Vohl
- Department of Food Science and Nutrition, Laval University, Quebec, Canada
| | - Benjamin F. Voight
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Dawn M Waterworth
- Division of Genetics, GlaxoSmithKline, Philadelphia, Pennsylvania, USA
| | - Hugh Watkins
- Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eleanor Wheeler
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Sarah H. Wild
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Sara M. Willems
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Gonneke Willemsen
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Jacqueline C.M. Witteman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative and the Netherlands Consortium for Healthy Aging, Rotterdam, The Netherlands
| | - Alan F. Wright
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
| | - Diana Zelenika
- Centre National de Génotypage, Commissariat à L’Energie Atomique, Institut de Génomique, Evry, France
| | - Tatijana Zemunik
- Department of Biology, Faculty of Medicine, University of Split, Croatia
| | - Lina Zgaga
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
- Department of medical statistics, epidemiology and medical informatics, University of Zagreb, Zagreb, Croatia
| | | | | | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Ines Barroso
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, UK
- University of Cambridge, Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Richard M. Watanabe
- Department of Physiology & Biophysics, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Jose C. Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Diabetes Research Center, Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, USA
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| |
Collapse
|
22
|
Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C. Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. Mol Cell 2012; 46:212-25. [PMID: 22424773 PMCID: PMC3565437 DOI: 10.1016/j.molcel.2012.01.026] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 12/06/2011] [Accepted: 01/30/2012] [Indexed: 12/12/2022]
Abstract
The regulatory networks of the DNA damage response (DDR) encompass many proteins and posttranslational modifications. Here, we use mass spectrometry-based proteomics to analyze the systems-wide response to DNA damage by parallel quantification of the DDR-regulated phosphoproteome, acetylome, and proteome. We show that phosphorylation-dependent signaling networks are regulated more strongly compared to acetylation. Among the phosphorylated proteins identified are many putative substrates of DNA-PK, ATM, and ATR kinases, but a majority of phosphorylated proteins do not share the ATM/ATR/DNA-PK target consensus motif, suggesting an important role of downstream kinases in amplifying DDR signals. We show that the splicing-regulator phosphatase PPM1G is recruited to sites of DNA damage, while the splicing-associated protein THRAP3 is excluded from these regions. Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair.
Collapse
Affiliation(s)
- Petra Beli
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Natalia Lukashchuk
- The Gurdon Institute, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Sebastian A. Wagner
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Brian T. Weinert
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Linda Baskcomb
- The Gurdon Institute, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Matthias Mann
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried (near Munich), Germany
| | - Stephen P. Jackson
- The Gurdon Institute, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Chunaram Choudhary
- The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| |
Collapse
|
23
|
Hutten S, Prescott A, James J, Riesenberg S, Boulon S, Lam YW, Lamond AI. An intranucleolar body associated with rDNA. Chromosoma 2011; 120:481-99. [PMID: 21698343 PMCID: PMC3232531 DOI: 10.1007/s00412-011-0327-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 05/16/2011] [Accepted: 05/31/2011] [Indexed: 02/07/2023]
Abstract
The nucleolus is the subnuclear organelle responsible for ribosome subunit biogenesis and can also act as a stress sensor. It forms around clusters of ribosomal DNA (rDNA) and is mainly organised in three subcompartments, i.e. fibrillar centre, dense fibrillar component and granular component. Here, we describe the localisation of 21 protein factors to an intranucleolar region different to these main subcompartments, called the intranucleolar body (INB). These factors include proteins involved in DNA maintenance, protein turnover, RNA metabolism, chromatin organisation and the post-translational modifiers SUMO1 and SUMO2/3. Increase in the size and number of INBs is promoted by specific types of DNA damage and depends on the functional integrity of the nucleolus. INBs are abundant in nucleoli of unstressed cells during S phase and localise in close proximity to rDNA with heterochromatic features. The data suggest the INB is linked with regulation of rDNA transcription and/or maintenance of rDNA.
Collapse
Affiliation(s)
- Saskia Hutten
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | | | | | | | | | | | | |
Collapse
|
24
|
Suh EJ, Kim YJ, Kim SH. Protein phosphatase 2Cgamma regulates the level of p21Cip1/WAF1 by Akt signaling. Biochem Biophys Res Commun 2009; 386:467-70. [PMID: 19538940 DOI: 10.1016/j.bbrc.2009.06.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 06/12/2009] [Indexed: 12/25/2022]
Abstract
PP2Cgamma is a splicing factor that dephosphorylates specific substrates required for the formation of the spliceosome. In a previous study, we reported that the degradation of p21(Cip1/WAF1)was affected by PP2Cgamma, causing an accumulation of cells in S phase. Here, we demonstrate that the PP2Cgamma-induced degradation of p21(Cip1/WAF1) is mediated by Akt signaling. In cells expressing PP2Cgamma, Akt1 protein was phosphorylated. When PP2Cgamma expression was knocked down, the phosphorylation of Akt1 was reduced and the level of p21(Cip1/WAF1) protein was increased. Interestingly, the stability of p21(Cip1/WAF1) was highly maintained in Akt1-depleted cells despite the ectopic expression of PP2Cgamma. Taken together, these results suggest that PP2Cgamma is a novel regulator of p21(Cip1/WAF1) protein stability via the Akt signaling pathway.
Collapse
Affiliation(s)
- Eun-Jung Suh
- Department of Biology, Kyung Hee University, 1 Hoegi-dong Dongdaemoon-ku, Seoul 130-701, Republic of Korea
| | | | | |
Collapse
|
25
|
Hearst SM, Gilder AS, Negi SS, Davis MD, George EM, Whittom AA, Toyota CG, Husedzinovic A, Gruss OJ, Hebert MD. Cajal-body formation correlates with differential coilin phosphorylation in primary and transformed cell lines. J Cell Sci 2009; 122:1872-81. [PMID: 19435804 DOI: 10.1242/jcs.044040] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cajal bodies (CBs) are nuclear structures that are thought to have diverse functions, including small nuclear ribonucleoprotein (snRNP) biogenesis. The phosphorylation status of coilin, the CB marker protein, might impact CB formation. We hypothesize that primary cells, which lack CBs, contain different phosphoisoforms of coilin compared with that found in transformed cells, which have CBs. Localization, self-association and fluorescence recovery after photobleaching (FRAP) studies on coilin phosphomutants all suggest this modification impacts the function of coilin and may thus contribute towards CB formation. Two-dimensional gel electrophoresis demonstrates that coilin is hyperphosphorylated in primary cells compared with transformed cells. mRNA levels of the nuclear phosphatase PPM1G are significantly reduced in primary cells and expression of PPM1G in primary cells induces CBs. Additionally, PPM1G can dephosphorylate coilin in vitro. Surprisingly, however, expression of green fluorescent protein alone is sufficient to form CBs in primary cells. Taken together, our data support a model whereby coilin is the target of an uncharacterized signal transduction cascade that responds to the increased transcription and snRNP demands found in transformed cells.
Collapse
Affiliation(s)
- Scoty M Hearst
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Ryan K, Khleborodova A, Pan J, Ryan XP. Small molecule activators of pre-mRNA 3' cleavage. RNA (NEW YORK, N.Y.) 2009; 15:483-92. [PMID: 19155323 PMCID: PMC2657006 DOI: 10.1261/rna.1262509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 12/08/2008] [Indexed: 05/27/2023]
Abstract
3' Cleavage and polyadenylation are obligatory steps in the biogenesis of most mammalian pre-mRNAs. In vitro reconstitution of the 3' cleavage reaction from human cleavage factors requires high concentrations of creatine phosphate (CP), though how CP activates cleavage is not known. Previously, we proposed that CP might work by competitively inhibiting a cleavage-suppressing serine/threonine (S/T) phosphatase. Here we show that fluoride/EDTA, a general S/T phosphatase inhibitor, activates in vitro cleavage in place of CP. Subsequent testing of inhibitors specific for different S/T phosphatases showed that inhibitors of the PPM family of S/T phosphatases, which includes PP2C, but not the PPP family, which includes PP1, PP2A, and PP2B, activated 3' cleavage in vitro. In particular, NCI 83633, an inhibitor of PP2C, activated extensive 3' cleavage at a concentration 50-fold below that required by fluoride or CP. The testing of structural analogs led to the identification of a more potent compound that activated 3' cleavage at 200 microM. While testing CP analogs to understand the origin of its cleavage activation effect, we found phosphocholine to be a more effective activator than CP. The minimal structural determinants of 3' cleavage activation by phosphocholine were identified. Our results describe a much improved small molecule activator of in vitro pre-mRNA cleavage, identify the molecular determinants of cleavage activation by phosphoamines such as phosphocholine, and suggest that a PPM family phosphatase is involved in the negative regulation of mammalian pre-mRNA 3' cleavage.
Collapse
Affiliation(s)
- Kevin Ryan
- Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, USA.
| | | | | | | |
Collapse
|
27
|
Xie J. Control of alternative pre-mRNA splicing by Ca(++) signals. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1779:438-52. [PMID: 18258215 PMCID: PMC3500379 DOI: 10.1016/j.bbagrm.2008.01.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 12/18/2007] [Accepted: 01/08/2008] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a common way of gene expression regulation in metazoans. The selective use of specific exons can be modulated in response to various manipulations that alter Ca(++) signals, particularly in neurons. A number of splicing factors have also been found to be controlled by Ca(++) signals. Moreover, pre-mRNA elements have been identified that are essential and sufficient to mediate Ca(++)-regulated splicing, providing model systems for dissecting the involved molecular components. In neurons, this regulation likely contributes to the fine-tuning of neuronal properties.
Collapse
Affiliation(s)
- Jiuyong Xie
- Department of Physiology, Faculty of Medicine, University of Manitoba, 730 William Avenue, Winnipeg, Canada MB R3E 3J7.
| |
Collapse
|
28
|
Hai Y, Cao W, Liu G, Hong SP, Elela SA, Klinck R, Chu J, Xie J. A G-tract element in apoptotic agents-induced alternative splicing. Nucleic Acids Res 2008; 36:3320-31. [PMID: 18440980 PMCID: PMC2425498 DOI: 10.1093/nar/gkn207] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice variant. Targeted mutagenesis analyses narrowed down a critical sequence to a 16-nt G-tract element (Gt16). Transferring this element to a heterologous gene conferred Ro response on an otherwise constitutive exon. The Ro effect was reduced by okadaic acid, an inhibitor of protein phosphatases PP1 and PP2A, in a concentration-dependent manner. Search in the human genome followed by RT–PCR identified a group of genes that contain similar exonic G-tract elements and are responsive to Ro. Moreover, the Gt16 element also mediates the regulation of alternative splicing by other cell apoptosis-inducers particularly retinoic acid. Therefore, the G-tract element likely plays a role in the apoptotic agents-induced alternative splicing of a group of genes. The functions of these genes imply that this regulation will have impact on cell growth/death.
Collapse
Affiliation(s)
- Yan Hai
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College. Kunming, China
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Lammers T, Lavi S. Role of type 2C protein phosphatases in growth regulation and in cellular stress signaling. Crit Rev Biochem Mol Biol 2008; 42:437-61. [PMID: 18066953 DOI: 10.1080/10409230701693342] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A number of interesting features, phenotypes, and potential clinical applications have recently been ascribed to the type 2C family of protein phosphatases. Thus far, 16 different PP2C genes have been identified in the human genome, encoding (by means of alternative splicing) for at least 22 different isozymes. Virtually ever since their discovery, type 2C phosphatases have been predominantly linked to cell growth and to cellular stress signaling. Here, we provide an overview of the involvement of type 2C phosphatases in these two processes, and we show that four of them (PP2Calpha, PP2Cbeta, ILKAP, and PHLPP) can be expected to function as tumor suppressor proteins, and one as an oncoprotein (PP2Cdelta /Wip1). In addition, we demonstrate that in virtually all cases in which they have been linked to the stress response, PP2Cs act as inhibitors of cellular stress signaling. Based on the vast amount of experimental evidence obtained thus far, it therefore seems justified to conclude that type 2C protein phosphatases are important physiological regulators of cell growth and of cellular stress signaling.
Collapse
Affiliation(s)
- Twan Lammers
- Department of Innovative Cancer Diagnosis and Therapy, German Cancer Research Center, Heidelberg, Germany.
| | | |
Collapse
|
30
|
A complex signaling pathway regulates SRp38 phosphorylation and pre-mRNA splicing in response to heat shock. Mol Cell 2008; 28:79-90. [PMID: 17936706 DOI: 10.1016/j.molcel.2007.08.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2007] [Revised: 07/20/2007] [Accepted: 08/02/2007] [Indexed: 11/22/2022]
Abstract
Although pre-mRNA splicing is known to be regulated by cell signaling, the underlying mechanisms are poorly understood. SRp38 is a member of the SR protein family and, when dephosphorylated, functions as a general and potent splicing repressor in response to heat shock. Here we show that SRp38 is dephosphorylated by the phosphatase PP1, which is activated by dissociation of its inhibitors, including NIPP1. PP1 is targeted to SRp38 through direct interaction via its arginine/serine-rich (RS) domain. The specific dephosphorylation of SRp38 and not other SR proteins is determined largely by the low activities of SR protein kinases for it compared to other SR proteins. Finally, we show that 14-3-3 proteins associate with SRp38 and protect it from dephosphorylation under nonstress conditions, but dissociate upon heat shock. Together, our study delineates a complex mechanism involving multiple factors by which a stress signaling pathway regulates protein phosphorylation and, in turn, pre-mRNA splicing.
Collapse
|
31
|
Dieker J, Cisterna B, Monneaux F, Decossas M, van der Vlag J, Biggiogera M, Muller S. Apoptosis-linked changes in the phosphorylation status and subcellular localization of the spliceosomal autoantigen U1-70K. Cell Death Differ 2008; 15:793-804. [PMID: 18202700 DOI: 10.1038/sj.cdd.4402312] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Apoptosis consists of highly regulated pathways involving post-translational modifications and cleavage of proteins leading to sequential inactivation of the main cellular processes. Here, we focused on the apoptotic processing of one of the essential components of the mRNA splicing machinery, the U1-70K snRNP protein. We found that at an early stage of apoptosis, before the cleavage of the C-terminal part of the protein by caspase-3, the basal phosphorylation of the Ser140 residue located within the RNA recognition motif, increases very significantly. A caspase-dependent, PP1-mediated dephosphorylation of other serine residues takes place in a subset of U1-70K proteins. The U1-70K protein phosphorylated at Ser140 is clustered in heterogeneous ectopic RNP-derived structures, which are finally extruded in apoptotic bodies. The elaborate processing of the spliceosomal U1-70K protein we identified might play an important role in the regulated breakdown of the mRNA splicing machinery during early apoptosis. In addition, these specific changes in the phosphorylation/dephosphorylation balance and the subcellular localization of the U1-70K protein might explain why the region encompassing the Ser140 residue becomes a central autoantigen during the autoimmune disease systemic lupus erythematosus.
Collapse
Affiliation(s)
- J Dieker
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | | | | | | | | | | | | |
Collapse
|
32
|
Lu G, Wang Y. FUNCTIONAL DIVERSITY OF MAMMALIAN TYPE 2C PROTEIN PHOSPHATASE ISOFORMS: NEW TALES FROM AN OLD FAMILY. Clin Exp Pharmacol Physiol 2008; 35:107-12. [DOI: 10.1111/j.1440-1681.2007.04843.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
33
|
Petri S, Grimmler M, Over S, Fischer U, Gruss OJ. Dephosphorylation of survival motor neurons (SMN) by PPM1G/PP2Cgamma governs Cajal body localization and stability of the SMN complex. ACTA ACUST UNITED AC 2007; 179:451-65. [PMID: 17984321 PMCID: PMC2064792 DOI: 10.1083/jcb.200704163] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The survival motor neuron (SMN) complex functions in maturation of uridine-rich small nuclear ribonucleoprotein (RNP) particles. SMN mediates the cytoplasmic assembly of Sm proteins onto uridine-rich small RNAs, and then participates in targeting RNPs to nuclear Cajal bodies (CBs). Recent studies have suggested that phosphorylation might control localization and function of the SMN complex. Here, we show that the nuclear phosphatase PPM1G/PP2Cgamma interacts with and dephosphorylates the SMN complex. Small interfering RNA knockdown of PPM1G leads to an altered phosphorylation pattern of SMN and Gemin3, loss of SMN from CBs, and reduced stability of SMN. Accumulation in CBs is restored upon overexpression of catalytically active, but not that of inactive, PPM1G. This demonstrates that PPM1G's phosphatase activity is necessary to maintain SMN subcellular distribution. Concomitant knockdown of unr interacting protein (unrip), a component implicated in cytoplasmic retention of the SMN complex, also rescues the localization defects. Our data suggest that an interplay between PPM1G and unrip determine compartment-specific phosphorylation patterns, localization, and function of the SMN complex.
Collapse
Affiliation(s)
- Sebastian Petri
- Zentrum für Molekulare Biologie der Universität Heidelberg, 69120 Heidelberg, Germany
| | | | | | | | | |
Collapse
|
34
|
Stamm S. Regulation of alternative splicing by reversible protein phosphorylation. J Biol Chem 2007; 283:1223-7. [PMID: 18024427 DOI: 10.1074/jbc.r700034200] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The vast majority of human protein-coding genes are subject to alternative splicing, which allows the generation of more than one protein isoform from a single gene. Cells can change alternative splicing patterns in response to a signal, which creates protein variants with different biological properties. The selection of alternative splice sites is governed by the dynamic formation of protein complexes on the processed pre-mRNA. A unique set of these splicing regulatory proteins assembles on different pre-mRNAs, generating a "splicing" or "messenger ribonucleoprotein code" that determines exon recognition. By influencing protein/protein and protein/RNA interactions, reversible protein phosphorylation modulates the assembly of regulatory proteins on pre-mRNA and therefore contributes to the splicing code. Studies of the serine/arginine-rich protein class of regulators identified different kinases and protein phosphatase 1 as the molecules that control reversible phosphorylation, which controls not only splice site selection, but also the localization of serine/arginine-rich proteins and mRNA export. The involvement of protein phosphatase 1 explains why second messengers like cAMP and ceramide that control the activity of this phosphatase influence alternative splicing. The emerging mechanistic links between splicing regulatory proteins and known signal transduction pathways now allow in detail the understanding how cellular signals modulate gene expression by influencing alternative splicing. This knowledge can be applied to human diseases that are caused by the selection of wrong splice sites.
Collapse
Affiliation(s)
- Stefan Stamm
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536-0509, USA.
| |
Collapse
|
35
|
Novoyatleva T, Heinrich B, Tang Y, Benderska N, Butchbach MER, Lorson CL, Lorson MA, Ben-Dov C, Fehlbaum P, Bracco L, Burghes AHM, Bollen M, Stamm S. Protein phosphatase 1 binds to the RNA recognition motif of several splicing factors and regulates alternative pre-mRNA processing. Hum Mol Genet 2007; 17:52-70. [PMID: 17913700 DOI: 10.1093/hmg/ddm284] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative splicing emerges as one of the most important mechanisms to generate transcript diversity. It is regulated by the formation of protein complexes on pre-mRNA. We demonstrate that protein phosphatase 1 (PP1) binds to the splicing factor transformer2-beta1 (tra2-beta1) via a phylogenetically conserved RVDF sequence located on the RNA recognition motif (RRM) of tra2-beta1. PP1 binds directly to tra2-beta1 and dephosphorylates it, which regulates the interaction between tra2-beta1 and other proteins. Eight other proteins, including SF2/ASF and SRp30c, contain an evolutionary conserved PP1 docking motif in the beta-4 strand of their RRMs indicating that binding to PP1 is a new function of some RRMs. Reducing PP1 activity promotes usage of numerous alternative exons, demonstrating a role of PP1 activity in splice site selection. PP1 inhibition promotes inclusion of the survival of motoneuron 2 exon 7 in a mouse model expressing the human gene. This suggests that reducing PP1 activity could be a new therapeutic principle to treat spinal muscular atrophy and other diseases caused by missplicing events. Our data indicate that the binding of PP1 to evolutionary conserved motifs in several RRMs is the link between known signal transduction pathways regulating PP1 activity and pre-mRNA processing.
Collapse
|
36
|
Sasaki M, Ohnishi M, Tashiro F, Niwa H, Suzuki A, Miyazaki JI, Kobayashi T, Tamura S. Disruption of the mouse protein Ser/Thr phosphatase 2Cβ gene leads to early pre-implantation lethality. Mech Dev 2007; 124:489-99. [PMID: 17499977 DOI: 10.1016/j.mod.2007.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 03/17/2007] [Accepted: 04/02/2007] [Indexed: 11/29/2022]
Abstract
Protein phosphatase 2Cbeta (PP2Cbeta) is a member of a family of protein Ser/Thr phosphatases (PP2C) that is composed of at least twelve different gene products. Recent studies have revealed that PP2Cbeta mRNA accumulates in mature sperm, unfertilized metaphase II-arrested oocytes and zygotes, but that the mRNA level then decreases sharply between the early two-cell and eight-cell stages, remaining at low levels during the 16-cell to blastocyst stages of mice. These observations raised the possibility that PP2Cbeta plays a crucial role during gametogenesis, fertilization, and/or early stages of embryonic development. In this study, we employed a gene knockout technique in mice to test this possibility. We found that PP2Cbeta(Delta/wt) mice generate normal mature gametes. However, PP2Cbeta(Delta/Delta) embryos die between the two-cell and eight-cell stages. To our interest, PP2Cbeta(Delta/Delta) ES cells which had been generated by transfecting PP2Cbeta(3lox/3lox) ES cells with Cre-expressing plasmid were viable. In addition, knockdown of PP2Cbeta using siRNA did not affect the proliferation of wild-type ES cells. These observations suggest that relatively high PP2Cbeta expression is specifically required during the early stages of pre-implantation development. The possible mechanisms for the early pre-implantation lethality of PP2Cbeta(Delta/Delta) mice are discussed.
Collapse
Affiliation(s)
- Masato Sasaki
- Department of Biochemistry, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Hastings ML, Allemand E, Duelli DM, Myers MP, Krainer AR. Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF(65). PLoS One 2007; 2:e538. [PMID: 17579712 PMCID: PMC1888729 DOI: 10.1371/journal.pone.0000538] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/22/2007] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA splicing is a crucial step in gene expression, and accurate recognition of splice sites is an essential part of this process. Splice sites with weak matches to the consensus sequences are common, though it is not clear how such sites are efficiently utilized. Using an in vitro splicing-complementation approach, we identified PUF60 as a factor that promotes splicing of an intron with a weak 3′ splice-site. PUF60 has homology to U2AF65, a general splicing factor that facilitates 3′ splice-site recognition at the early stages of spliceosome assembly. We demonstrate that PUF60 can functionally substitute for U2AF65in vitro, but splicing is strongly stimulated by the presence of both proteins. Reduction of either PUF60 or U2AF65 in cells alters the splicing pattern of endogenous transcripts, consistent with the idea that regulation of PUF60 and U2AF65 levels can dictate alternative splicing patterns. Our results indicate that recognition of 3′ splice sites involves different U2AF-like molecules, and that modulation of these general splicing factors can have profound effects on splicing.
Collapse
Affiliation(s)
- Michelle L. Hastings
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eric Allemand
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dominik M. Duelli
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Michael P. Myers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
38
|
Allemand E, Hastings ML, Murray MV, Myers MP, Krainer AR. Alternative splicing regulation by interaction of phosphatase PP2Cgamma with nucleic acid-binding protein YB-1. Nat Struct Mol Biol 2007; 14:630-8. [PMID: 17572683 DOI: 10.1038/nsmb1257] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 05/02/2007] [Indexed: 01/29/2023]
Abstract
Kinases and phosphatases participate in precursor messenger RNA (pre-mRNA) splicing regulation, but their precise roles and the identities of their cofactors and substrates remain poorly understood. The human Ser/Thr phosphatase PP2Cgamma promotes spliceosome assembly. We show that PP2Cgamma's distinctive acidic domain is essential for its activity in splicing and interacts with YB-1, a spliceosome-associated factor. Moreover, PP2Cgamma is a phosphoprotein in vivo, and its acidic domain is phosphorylated under splicing conditions in vitro. PP2Cgamma phosphorylation enhances its interaction with YB-1 and is reversed by the phosphatase in cis. PP2Cgamma knockdown leaves constitutive splicing unaffected but inhibits cell proliferation and affects alternative splicing of CD44, a YB-1 target. This effect on splicing regulation is mediated by PP2Cgamma's acidic domain, which is essential to promote inclusion of CD44 exons v4 and v5 in vivo. We propose that PP2Cgamma modulates alternative splicing of specific pre-mRNAs coregulated by YB-1.
Collapse
Affiliation(s)
- Eric Allemand
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | | | | | | | | |
Collapse
|
39
|
Moorhead GBG, Trinkle-Mulcahy L, Ulke-Lemée A. Emerging roles of nuclear protein phosphatases. Nat Rev Mol Cell Biol 2007; 8:234-44. [PMID: 17318227 DOI: 10.1038/nrm2126] [Citation(s) in RCA: 263] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phosphorylation state of any protein represents a balance of the actions of specific protein kinases and protein phosphatases. Many protein phosphatases are highly enriched in, or exclusive to, the nuclear compartment, where they dephosphorylate key substrates to regulate various nuclear processes. In this review we will discuss recent findings that define the role of nuclear protein phosphatases in controlling transforming growth factor-beta (TGFbeta) and bone-morphogenetic protein (BMP) signalling, the DNA-damage response, RNA processing, cell-cycle progression and gene transcription.
Collapse
Affiliation(s)
- Greg B G Moorhead
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary Alberta, Canada T2N 1N4.
| | | | | |
Collapse
|
40
|
Shu Y, Rintala-Maki ND, Wall VE, Wang K, Goard CA, Langdon CE, Sutherland LC. The apoptosis modulator and tumour suppressor protein RBM5 is a phosphoprotein. Cell Biochem Funct 2007; 25:643-53. [PMID: 16927403 DOI: 10.1002/cbf.1366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
RBM5/LUCA-15/H37 is a nuclear SR-related RNA binding protein with the ability to modulate both apoptosis and the cell cycle, and retard tumour formation. How RBM5 functions to carry out these, potentially interrelated, biological activities is unknown. Since reversible phosphorylation has been shown to play an important role in the regulation of SR protein function, apoptosis and cell cycle control, in an attempt to elucidate the underlying mechanisms regulating RBM5 function, the phosphorylation status of RBM5 was investigated. Whole cell lysate from growing cell cultures was treated with the broad phosphatase spectrum of CIP, resulting in a decrease in the molecular mass of RBM5. A similar decrease in molecular mass, of a subset of RBM5 proteins, was observed during growth factor deprivation, in a manner consistent with partial dephosphorylation of RBM5. Molecular mass increased upon growth factor addition, demonstrating that this apoptosis-associated alteration in molecular mass was a reversible process. Immunoprecipitation and mutagenesis experiments strongly suggested that phosphotyrosines are not present in RBM5 under normal growth conditions, and that serine 69 is phosphorylated, but not by Akt kinase. Taken together, these results suggest that reversible phosphorylation of RBM5 is a mechanism capable of regulating RBM5 participation in modulating apoptosis, and perhaps tumour suppression.
Collapse
Affiliation(s)
- Yanjun Shu
- Tumour Biology Group, Regional Cancer Program of the Hôpital régional de Sudbury Regional Hospital, Sudbury, Ontario, Canada
| | | | | | | | | | | | | |
Collapse
|
41
|
Stern A, Privman E, Rasis M, Lavi S, Pupko T. Evolution of the Metazoan Protein Phosphatase 2C Superfamily. J Mol Evol 2006; 64:61-70. [PMID: 17160364 DOI: 10.1007/s00239-006-0033-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 10/04/2006] [Indexed: 01/22/2023]
Abstract
Members of the protein phosphatase 2C (PP2C) superfamily are Mg(2+)/Mn(2+)-dependent serine/threonine phosphatases, which are essential for regulation of cell cycle and stress signaling pathways in cells. In this study, a comprehensive genomic analysis of all available metazoan PP2C sequences was conducted. The phylogeny of PP2C was reconstructed, revealing the existence of 15 vertebrate families which arose following a series of gene duplication events. Relative dating of these duplications showed that they occurred in two active periods: before the divergence of bilaterians and before vertebrate diversification. PP2C families which duplicated during the first period take part in different signaling pathways, whereas PP2C families which diverged in the second period display tissue expression differences yet participate in similar signaling pathways. These differences were found to involve variation of expression in tissues which show higher complexity in vertebrates, such as skeletal muscle and the nervous system. Further analysis was performed with the aim of identifying the functional domains of PP2C. The conservation pattern across the entire PP2C superfamily revealed an extensive domain of more than 50 amino acids which is highly conserved throughout all PP2C members. Several insertion or deletion events were found which may have led to the specialization of each PP2C family.
Collapse
Affiliation(s)
- Adi Stern
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | | | | |
Collapse
|
42
|
Shi Y, Reddy B, Manley JL. PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. Mol Cell 2006; 23:819-29. [PMID: 16973434 DOI: 10.1016/j.molcel.2006.07.022] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 06/05/2006] [Accepted: 07/26/2006] [Indexed: 11/22/2022]
Abstract
Pre-mRNA splicing is a complex and dynamic process in which protein phosphorylation and dephosphorylation both play important roles. Although specific phosphatases, such as PP1 and PP2A, have been implicated in splicing, direct evidence for their involvement has been lacking, and their exact function(s) in this process remain unknown. In this study, we show that PP1 and certain PP2A family phosphatases play essential but redundant roles in splicing. Unexpectedly, we found that these phosphatases are required principally for the second step of the splicing reaction. Furthermore, we provide evidence that components of U2 and U5 snRNPs, specifically SAP155 and U5-116 kDa, are the key spliceosomal substrates for these phosphatases. Based on these data, we propose that dephosphorylation of U2 and U5 snRNP components by PP1/PP2A family phosphatases facilitates essential structural rearrangements in the spliceosome during the transition from the first to the second step.
Collapse
Affiliation(s)
- Yongsheng Shi
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | |
Collapse
|
43
|
Lopato S, Borisjuk L, Milligan AS, Shirley N, Bazanova N, Parsley K, Langridge P. Systematic identification of factors involved in post-transcriptional processes in wheat grain. PLANT MOLECULAR BIOLOGY 2006; 62:637-53. [PMID: 16941218 DOI: 10.1007/s11103-006-9046-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 07/06/2006] [Indexed: 05/11/2023]
Abstract
Post-transcriptional processing of primary transcripts can significantly affect both the quantity and the structure of mature mRNAs and the corresponding protein products. It is an important mechanism of gene regulation in animals, yeast and plants. Here we have investigated the interactive networks of pre-mRNA processing factors in the developing grain of wheat (Triticum aestivum), one of the world's major food staples. As a first step we isolated a homologue of the plant specific AtRSZ33 splicing factor, which has been shown to be involved in the early stages of embryo development in Arabidopsis. Real-time PCR showed that the wheat gene, designated TaRSZ38, is expressed mainly in young, developing organs (flowers, root, stem), and expression peaks in immature grain. In situ hybridization and immunodetection revealed preferential abundance of TaRSZ38 in mitotically active tissues of the major storage organ of the grain, the endosperm. The protein encoded by TaRSZ38 was subsequently used as a starting bait in a two-hybrid screen to identify additional factors in grain that are involved in pre-mRNA processing. Most of the identified proteins showed high homology to known splicing factors and splicing related proteins, supporting a role for TaRSZ38 in spliceosome formation and 5' site selection. Several clones were selected as baits in further yeast two-hybrid screens. In total, cDNAs for 16 proteins were isolated. Among these proteins, TaRSZ22, TaSRp30, TaU1-70K, and the large and small subunits of TaU2AF, are wheat homologues of known plant splicing factors. Several, additional proteins are novel for plants and show homology to known pre-mRNA splicing, splicing related and mRNA export factors from yeast and mammals.
Collapse
Affiliation(s)
- Sergiy Lopato
- Australian Centre for Plant Functional Genomics, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia.
| | | | | | | | | | | | | |
Collapse
|
44
|
Kimura H, Takizawa N, Allemand E, Hori T, Iborra FJ, Nozaki N, Muraki M, Hagiwara M, Krainer AR, Fukagawa T, Okawa K. A novel histone exchange factor, protein phosphatase 2Cgamma, mediates the exchange and dephosphorylation of H2A-H2B. ACTA ACUST UNITED AC 2006; 175:389-400. [PMID: 17074886 PMCID: PMC2064517 DOI: 10.1083/jcb.200608001] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In eukaryotic nuclei, DNA is wrapped around a protein octamer composed of the core histones H2A, H2B, H3, and H4, forming nucleosomes as the fundamental units of chromatin. The modification and deposition of specific histone variants play key roles in chromatin function. In this study, we established an in vitro system based on permeabilized cells that allows the assembly and exchange of histones in situ. H2A and H2B, each tagged with green fluorescent protein (GFP), are incorporated into euchromatin by exchange independently of DNA replication, and H3.1-GFP is assembled into replicated chromatin, as found in living cells. By purifying the cellular factors that assist in the incorporation of H2A-H2B, we identified protein phosphatase (PP) 2C gamma subtype (PP2Cgamma/PPM1G) as a histone chaperone that binds to and dephosphorylates H2A-H2B. The disruption of PP2Cgamma in chicken DT40 cells increased the sensitivity to caffeine, a reagent that disturbs DNA replication and damage checkpoints, suggesting the involvement of PP2Cgamma-mediated histone dephosphorylation and exchange in damage response or checkpoint recovery in higher eukaryotes.
Collapse
Affiliation(s)
- Hiroshi Kimura
- Nuclear Function and Dynamics Unit, Horizontal Medical Research Organization, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Suh EJ, Kim TY, Kim SH. PP2Cgamma-mediated S-phase accumulation induced by the proteasome-dependent degradation of p21(WAF1/CIP1). FEBS Lett 2006; 580:6100-4. [PMID: 17054950 DOI: 10.1016/j.febslet.2006.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 09/25/2006] [Accepted: 10/04/2006] [Indexed: 11/26/2022]
Abstract
Serine/threonine phosphatases such as PP1, PP2A, and PP2B are well known to regulate the transition phase of the cell cycle. However, the function of PP2Cgamma in cell cycle progression is still unclear. In the present study, we report the characterization of PP2Cgamma in mammalian cells during the cell cycle. After release of synchronized cells from thymidine block, over-expression of PP2Cgamma led to accumulation in the S phase. The amount of endogenous p21(WAF1/CIP1) protein was markedly reduced by the expression of PP2Cgamma. The degradation of p21(WAF1/CIP1) induced by PP2Cgamma was mediated in a proteasome-dependent manner. In addition, the phosphatase activity of PP2Cgamma was capable of repressing the level of p21(WAF1/CIP1) protein. Phosphorylation of Rb was also reduced in cells expressing PP2Cgamma. Taken together, these results indicate that PP2Cgamma-induced S phase accumulation may be associated with proteasome-directed p21(WAF1/CIP1) degradation.
Collapse
Affiliation(s)
- Eun-Jung Suh
- Department of Biology, Kyung Hee University, Republic of Korea
| | | | | |
Collapse
|
46
|
Byrum CA, Walton KD, Robertson AJ, Carbonneau S, Thomason RT, Coffman JA, McClay DR. Protein tyrosine and serine-threonine phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions. Dev Biol 2006; 300:194-218. [PMID: 17087928 PMCID: PMC3045532 DOI: 10.1016/j.ydbio.2006.08.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 08/18/2006] [Accepted: 08/19/2006] [Indexed: 10/24/2022]
Abstract
Protein phosphatases, in coordination with protein kinases, play crucial roles in regulation of signaling pathways. To identify protein tyrosine phosphatases (PTPs) and serine-threonine (ser-thr) phosphatases in the Strongylocentrotus purpuratus genome, 179 annotated sequences were studied (122 PTPs, 57 ser-thr phosphatases). Sequence analysis identified 91 phosphatases (33 conventional PTPs, 31 dual specificity phosphatases, 1 Class III Cysteine-based PTP, 1 Asp-based PTP, and 25 ser-thr phosphatases). Using catalytic sites, levels of conservation and constraint in amino acid sequence were examined. Nine of 25 receptor PTPs (RPTPs) corresponded to human, nematode, or fly homologues. Domain structure revealed that sea urchin-specific RPTPs including two, PTPRLec and PTPRscav, may act in immune defense. Embryonic transcription of each phosphatase was recorded from a high-density oligonucleotide tiling microarray experiment. Most RPTPs are expressed at very low levels, whereas nonreceptor PTPs (NRPTPs) are generally expressed at moderate levels. High expression was detected in MAP kinase phosphatases (MKPs) and numerous ser-thr phosphatases. For several expressed NRPTPs, MKPs, and ser-thr phosphatases, morpholino antisense-mediated knockdowns were performed and phenotypes obtained. Finally, to assess roles of annotated phosphatases in endomesoderm formation, a literature review of phosphatase functions in model organisms was superimposed on sea urchin developmental pathways to predict areas of functional activity.
Collapse
Affiliation(s)
- C A Byrum
- Developmental, Cell, and Molecular Biology Group, Box 91000, Duke University, Durham, NC 27708, USA.
| | | | | | | | | | | | | |
Collapse
|
47
|
Deckert J, Hartmuth K, Boehringer D, Behzadnia N, Will CL, Kastner B, Stark H, Urlaub H, Lührmann R. Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol Cell Biol 2006; 26:5528-43. [PMID: 16809785 PMCID: PMC1592722 DOI: 10.1128/mcb.00582-06] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The spliceosomal B complex is the substrate that undergoes catalytic activation leading to catalysis of pre-mRNA splicing. Previous characterization of this complex was performed in the presence of heparin, which dissociates less stably associated components. To obtain a more comprehensive inventory of the B complex proteome, we isolated this complex under low-stringency conditions using two independent methods. MS2 affinity-selected B complexes supported splicing when incubated in nuclear extract depleted of snRNPs. Mass spectrometry identified over 110 proteins in both independently purified B complex preparations, including approximately 50 non-snRNP proteins not previously found in the spliceosomal A complex. Unexpectedly, the heteromeric hPrp19/CDC5 complex and 10 additional hPrp19/CDC5-related proteins were detected, indicating that they are recruited prior to spliceosome activation. Electron microscopy studies revealed that MS2 affinity-selected B complexes exhibit a rhombic shape with a maximum dimension of 420 A and are structurally more homogeneous than B complexes treated with heparin. These data provide novel insights into the composition and structure of the spliceosome just prior to its catalytic activation and suggest a potential role in activation for proteins recruited at this stage. Furthermore, the spliceosomal complexes isolated here are well suited for complementation studies with purified proteins to dissect factor requirements for spliceosome activation and splicing catalysis.
Collapse
Affiliation(s)
- Jochen Deckert
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Kwekel JC, Burgoon LD, Burt JW, Harkema JR, Zacharewski TR. A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiol Genomics 2005; 23:327-42. [PMID: 16174780 DOI: 10.1152/physiolgenomics.00175.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Physiological, morphological, and transcriptional alterations elicited by ethynyl estradiol in the uteri of Sprague-Dawley rats and C57BL/6 mice were assessed using comparable study designs, microarray platforms, and analysis methods to identify conserved estrogen signaling networks. Comparative analysis identified 153 orthologous gene pairs that were positively correlated, suggesting conserved transcriptional targets important in uterine proliferation. Functional annotation for these responses were associated with angiogenesis, water and solute transport, cell cycle control, redox control, DNA replication, protein synthesis and transport, xenobiotic metabolism, cell-cell communication, energetics, and cholesterol and fatty acid regulation. The identification of conserved temporal expression patterns of these orthologs provides experimental support for the transfer of functional annotation from mouse orthologs to 44 previously unannotated rat expressed sequence tags based on their homology and co-expression patterns. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates the ability of systematic comparative genomic assessments to elucidate important conserved mechanisms in rodent estrogen signaling during uterine proliferation.
Collapse
Affiliation(s)
- Joshua C Kwekel
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | | | | | |
Collapse
|
49
|
Allemand E, Guil S, Myers M, Moscat J, Cáceres JF, Krainer AR. Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock. Proc Natl Acad Sci U S A 2005; 102:3605-10. [PMID: 15738418 PMCID: PMC553333 DOI: 10.1073/pnas.0409889102] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an alternative splicing factor that is mainly nuclear, although it shuttles rapidly between nuclear and cytoplasmic compartments. Cells stressed by osmotic shock (OSM) activate the mitogen-activated protein kinase kinase(3/6)-p38 signaling pathway, which in turn results in accumulation of hnRNP A1 in the cytoplasm. This effect modulates alternative splicing regulation in vivo and correlates with increased hnRNP A1 phosphorylation. We have characterized the molecular mechanism involved in the cytoplasmic accumulation of hnRNP A1 in NIH 3T3 cells subjected to OSM. This treatment results in serine-specific phosphorylation within a C-terminal peptide, dubbed the "F-peptide," which is adjacent to the M9 motif that mediates bidirectional transport of hnRNP A1. Analysis of mutants in which the F-peptide serines were replaced by aspartic acids or alanines showed that F-peptide phosphorylation is required for the subcellular redistribution of hnRNP A1 in cells subjected to OSM. Furthermore, F-peptide phosphorylation modulates the interaction of hnRNP A1 with transportin Trn1. Our findings suggest that the phosphorylation of F-peptide by cell-signaling pathways regulates the rate of hnRNP A1 nuclear import.
Collapse
Affiliation(s)
- Eric Allemand
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | | | | | | | | |
Collapse
|
50
|
Lorkovic ZJ, Lopato S, Pexa M, Lehner R, Barta A. Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins suggest their involvement in pre-mRNA Splicing. J Biol Chem 2004; 279:33890-8. [PMID: 15166240 DOI: 10.1074/jbc.m400270200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ser/Arg (SR)-rich proteins are important splicing factors in both general and alternative splicing. By binding to specific sequences on pre-mRNA and interacting with other splicing factors via their RS domain they mediate different intraspliceosomal contacts, thereby helping in splice site selection and spliceosome assembly. While characterizing new members of this protein family in Arabidopsis, we have identified two proteins, termed CypRS64 and CypRS92, consisting of an N-terminal peptidyl-prolyl cis/trans isomerase domain and a C-terminal domain with many SR/SP dipeptides. Cyclophilins possess a peptidyl-prolyl cis/trans isomerase activity and are implicated in protein folding, assembly, and transport. CypRS64 interacts in vivo and in vitro with a subset of Arabidopsis SR proteins, including SRp30 and SRp34/SR1, two homologs of mammalian SF2/ASF, known to be important for 5' splice site recognition. In addition, both cyclophilins interact with U1-70K and U11-35K, which in turn are binding partners of SRp34/SR1. CypRS64 is a nucleoplasmic protein, but in most cells expressing CypRS64-GFP fusion it was also found in one to six round nuclear bodies. However, co-expression of CypRS64 with its binding partners resulted in re-localization of CypRS64 from the nuclear bodies to nuclear speckles, indicating functional interactions. These findings together with the observation that binding of SRp34/SR1 to CypRS64 is phosphorylation-dependent indicate an involvement of CypRS64 in nuclear pre-mRNA splicing, possibly by regulating phosphorylation/dephosphorylation of SR proteins and other spliceosomal components. Alternatively, binding of CypRS64 to proteins important for 5' splice site recognition suggests its involvement in the dynamics of spliceosome assembly.
Collapse
Affiliation(s)
- Zdravko J Lorkovic
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Department of Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9/3, A-1030 Vienna, Austria.
| | | | | | | | | |
Collapse
|