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
|
Xiao Y, Cai G, Feng X, Li Y, Guo W, Guo Q, Huang Y, Su T, Li C, Luo X, Zheng Y, Yang M. Splicing factor YBX1 regulates bone marrow stromal cell fate during aging. EMBO J 2023; 42:e111762. [PMID: 36943004 PMCID: PMC10152142 DOI: 10.15252/embj.2022111762] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
Senescence and altered differentiation potential of bone marrow stromal cells (BMSCs) lead to age-related bone loss. As an important posttranscriptional regulatory pathway, alternative splicing (AS) regulates the diversity of gene expression and has been linked to induction of cellular senescence. However, the role of splicing factors in BMSCs during aging remains poorly defined. Herein, we found that the expression of the splicing factor Y-box binding protein 1 (YBX1) in BMSCs decreased with aging in mice and humans. YBX1 deficiency resulted in mis-splicing in genes linked to BMSC osteogenic differentiation and senescence, such as Fn1, Nrp2, Sirt2, Sp7, and Spp1, thus contributing to BMSC senescence and differentiation shift during aging. Deletion of Ybx1 in BMSCs accelerated bone loss in mice, while its overexpression stimulated bone formation. Finally, we identified a small compound, sciadopitysin, which attenuated the degradation of YBX1 and bone loss in old mice. Our study demonstrated that YBX1 governs cell fate of BMSCs via fine control of RNA splicing and provides a potential therapeutic target for age-related osteoporosis.
Collapse
Affiliation(s)
- Ye Xiao
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Guang‐Ping Cai
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Xu Feng
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Yu‐Jue Li
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Wan‐Hui Guo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Yan Huang
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Tian Su
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Chang‐Jun Li
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Xiang‐Hang Luo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| | - Yong‐Jun Zheng
- Department of Burn SurgeryThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Mi Yang
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| |
Collapse
|
4
|
Sitosari H, Morimoto I, Weng Y, Zheng Y, Fukuhara Y, Ikegame M, Okamura H. Inhibition of protein phosphatase 2A by okadaic acid induces translocation of nucleocytoplasmic O-GlcNAc transferase. Biochem Biophys Res Commun 2023; 646:50-55. [PMID: 36706705 DOI: 10.1016/j.bbrc.2023.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Post-translational modification (PTM) is crucial for many biological events, such as the modulation of bone metabolism. Phosphorylation and O-GlcNAcylation are two examples of PTMs that can occur at the same site in the protein: serine and threonine residues. This phenomenon may cause crosstalk and possible interactions between the molecules involved. Protein phosphatase 2 A (PP2A) is widely expressed throughout the body and plays a major role in dephosphorylation. At the same location where PP2A acts, O-GlcNAc transferase (OGT) can introduce uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) molecules and mediates O-GlcNAc modifications. To examine the effects of PP2A inhibition on OGT localization and expression, osteoblastic MC3T3-E1 cells were treated with Okadaic Acid (OA), a potent PP2A inhibitor. In the control cells, OGT was strictly localized in the nucleus. However, OGT was observed diffusely in the cytoplasm of the OA-treated cells. This change in localization from the nucleus to the cytoplasm resulted from an increase in mitochondrial OGT expression and translocation of the nucleocytoplasmic isoform. Furthermore, knockdown of PP2A catalytic subunit α isoform (PP2A Cα) significantly affected OGT expression (p < 0.05), and there was a correlation between PP2A Cα and OGT expression (r = 0.93). These results suggested a possible interaction between PP2A and OGT, which strengthens the notion of an interaction between phosphorylation and O-GlcNAcylation.
Collapse
Affiliation(s)
- Heriati Sitosari
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan; Department of Oral Biology, Faculty of Dentistry, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Ikkei Morimoto
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan
| | - Yao Weng
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan; Department of Oral Rehabilitation and Implantology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan
| | - Yilin Zheng
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan
| | - Yoko Fukuhara
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan
| | - Mika Ikegame
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan
| | - Hirohiko Okamura
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 770-8525, Japan.
| |
Collapse
|
5
|
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
|
6
|
Jo SH, Park HJ, Lee A, Jung H, Park JM, Kwon SY, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress. THE PLANT CELL 2022; 34:2383-2403. [PMID: 35262729 PMCID: PMC9134067 DOI: 10.1093/plcell/koac084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/05/2022] [Indexed: 05/13/2023]
Abstract
In plants, heat stress induces changes in alternative splicing, including intron retention; these events can rapidly alter proteins or downregulate protein activity, producing nonfunctional isoforms or inducing nonsense-mediated decay of messenger RNA (mRNA). Nuclear cyclophilins (CYPs) are accessory proteins in the spliceosome complexes of multicellular eukaryotes. However, whether plant CYPs are involved in pre-mRNA splicing remain unknown. Here, we found that Arabidopsis thaliana CYP18-1 is necessary for the efficient removal of introns that are retained in response to heat stress during germination. CYP18-1 interacts with Step II splicing factors (PRP18a, PRP22, and SWELLMAP1) and associates with the U2 and U5 small nuclear RNAs in response to heat stress. CYP18-1 binds to phospho-PRP18a, and increasing concentrations of CYP18-1 are associated with increasing dephosphorylation of PRP18a. Furthermore, interaction and protoplast transfection assays revealed that CYP18-1 and the PP2A-type phosphatase PP2A B'η co-regulate PRP18a dephosphorylation. RNA-seq and RT-qPCR analysis confirmed that CYP18-1 is essential for splicing introns that are retained under heat stress. Overall, we reveal the mechanism of action by which CYP18-1 activates the dephosphorylation of PRP18 and show that CYP18-1 is crucial for the efficient splicing of retained introns and rapid responses to heat stress in plants.
Collapse
Affiliation(s)
- Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University
of Science and Technology, Daejeon 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo
Bio, Anseong 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology
Institute/Green Bio Science and Technology, Seoul National University,
Pyeongchang 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major
in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National
University, Seoul 08826, Korea
| | | |
Collapse
|
7
|
Xiong DL, Li Q, Wang H, Jin WL, Fan XM, Ma YY. High expression of PPM1G is associated with the progression and poor prognosis of hepatocellular carcinoma. Cancer Biomark 2021; 34:13-22. [PMID: 34366322 DOI: 10.3233/cbm-203248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND PPM1G, a member of the serine/threonine protease family, dephosphorylates various proteins and may be involved in cancer development. The role and mechanism of PPM1G in HCC still needs to be verified. OBJECTIVE This study aims to explore the role of PPM1G in the occurrence, development and prognosis of HCC. METHODS Using bioinformatics (UALCAN, cBioPortal, Linkedomics, STRING and GSEA) to analyze the expression of PPM1G mRNA in HCC, its clinical relevance and possible involved signaling pathways. The expression of PPM1G protein was determined by immunohistochemistry in 311 cases of HCC to evaluate the association between PPM1G and clinical features and prognosis. RESULTS The expression of PPM1G was significantly upregulated in HCC (P< 0.001), correlated with the metastasis (P= 0.020), pathological grade of HCC (P= 0.032), microvascular invasion (P= 0.040), and HBV infection (P= 0.041). Cox multivariate regression showed high expression of PPM1G was an independent prognostic factor for HCC. Its role in HCC may relate to methylation and frequency mutation. Furthermore, the database showed PPM1G is involved in the signal pathway such as cell cycle, WNT pathway, and mTOR pathway in HCC. CONCLUSION PPM1G showed an essential function involving in tumor-related pathways in HCC, providing a biological basis for targeted treatment of HCC clinically.
Collapse
Affiliation(s)
- Dan-Lei Xiong
- Department of Ultrasound, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China.,Department of Ultrasound, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Qian Li
- Graduate Department, Bengbu Medical College, Bengbu, Anhui, China.,Department of Ultrasound, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Heng Wang
- Graduate Department, Bengbu Medical College, Bengbu, Anhui, China
| | - Wei-Li Jin
- Department of Gastroenterology, Nanxun People's Hospital (Zhejiang Provincial People's Hospital Nanxun Branch), Huzhou, Zhejiang, China
| | - Xiao-Ming Fan
- Department of Ultrasound, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ying-Yu Ma
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| |
Collapse
|
8
|
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
|
9
|
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
|
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
|
Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y. Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. J Biol Chem 2019; 294:10998-11010. [PMID: 31160337 PMCID: PMC6635445 DOI: 10.1074/jbc.ra119.007545] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/26/2019] [Indexed: 01/07/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π-π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.
Collapse
Affiliation(s)
- Xiao-Juan Yang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Hong Zhu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Shi-Rong Mu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Wen-Juan Wei
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Xun Yuan
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Meng Wang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Yanchao Liu
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Jingyi Hui
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and , To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-54921354; E-mail:
| | - Ying Huang
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China, To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-20778200; E-mail:
| |
Collapse
|
12
|
Whole Genome Analysis and Prognostic Model Construction Based on Alternative Splicing Events in Endometrial Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2686875. [PMID: 31355251 PMCID: PMC6634061 DOI: 10.1155/2019/2686875] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022]
Abstract
Objectives A growing body of evidence has shown that aberrant alternative splicing (AS) is closely related to the occurrence and development of cancer. However, prior studies mainly have concentrated on a few genes that exhibit aberrant AS. This study aimed to determine AS events through whole genome analysis and construct a prognostic model of endometrial cancer (EC). Methods We downloaded gene expression RNAseq data from UCSC Xena, and seven types of AS events from TCGA SpliceSeq. Univariate Cox regression was employed to analyze the prognostic-related alternative splicing events (PASEs) and splicing factors; multivariate Cox regression was conducted to analyze the effect of risk score (All) and clinicopathological parameters on EC prognosis. An underlying interaction network of PASEs of EC was constructed by Cytoscape Reactome FI, GO, and KEGG pathway enrichment was performed by DAVID. ROC curves and Kaplan-Meir analysis were used to assess the diagnostic value of prognostic model. The correlation between PASEs and splicing factors was analyzed by GraphPad Prism; then a network was constructed using Cytoscape. Results In total, 28,281 AS events in EC were identified, which consisted of 1166 PASEs. RNPS1, NEK2, and CTNNB1 were the hub genes in the network of the top 600 PASEs. The area under the curve (AUC) of risk score (All) reached 0.819. Risk score (All) together with FIGO stage, cancer status, and primary therapy outcome success was risk factors of the prognosis of EC patients. Splicing factors YBX1, HNRNPDL, and HNRNPA1 were significantly related to the overall survival (OS). The splicing network indicated that the expression of splicing factors was significantly correlated with percent-splice-in (PSI) value of PASEs. Conclusion We constructed a model for predicting the prognosis of EC patients based on PASEs using whole genome analysis of AS events and thereby provided a reliable theoretical basis for EC clinical prognosis evaluation.
Collapse
|
13
|
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
|
14
|
Rios de la Rosa JM, Tirella A, Tirelli N. Receptor-Targeted Drug Delivery and the (Many) Problems We Know of: The Case of CD44 and Hyaluronic Acid. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Julio M. Rios de la Rosa
- NorthWest Centre for Advanced Drug Delivery (NoWCADD); School of Health Sciences; University of Manchester; Oxford Road Manchester M13 9PT UK
| | - Annalisa Tirella
- NorthWest Centre for Advanced Drug Delivery (NoWCADD); School of Health Sciences; University of Manchester; Oxford Road Manchester M13 9PT UK
| | - Nicola Tirelli
- NorthWest Centre for Advanced Drug Delivery (NoWCADD); School of Health Sciences; University of Manchester; Oxford Road Manchester M13 9PT UK
- Laboratory of Polymers and Biomaterials; Fondazione Istituto Italiano di Tecnologia; Genova 16163 Italy
| |
Collapse
|
15
|
Sciuto MR, Warnken U, Schnölzer M, Valvo C, Brunetto L, Boe A, Biffoni M, Krammer PH, De Maria R, Haas TL. Two-Step Coimmunoprecipitation (TIP) Enables Efficient and Highly Selective Isolation of Native Protein Complexes. Mol Cell Proteomics 2017; 17:993-1009. [PMID: 29217617 DOI: 10.1074/mcp.o116.065920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Coimmunoprecipitation (co-IP) is one of the most frequently used techniques to study protein-protein (PPIs) or protein-nucleic acid interactions (PNIs). However, the presence of coprecipitated contaminants is a well-recognized issue associated with single-step co-IPs. To overcome this limitation, we developed the two-step co-IP (TIP) strategy that enables sequential coimmunoprecipitations of endogenous protein complexes. TIP can be performed with a broad range of mono- and polyclonal antibodies targeting a single protein or different components of a given complex. TIP results in a highly selective enrichment of protein complexes and thus outperforms single-step co-IPs for downstream applications such as mass spectrometry for the identification of PPIs and quantitative PCR for the analysis of PNIs. We benchmarked TIP for the identification of CD95/FAS-interacting proteins in primary human CD4+ T cells, which recapitulated all major known interactors, but also enabled the proteomics discovery of PPM1G and IPO7 as new interaction partners. For its feasibility and high performance, we propose TIP as an advanced tool for the isolation of highly purified protein-protein and protein-nucleic acid complexes under native expression conditions.
Collapse
Affiliation(s)
- Maria Rita Sciuto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy;
| | - Uwe Warnken
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Martina Schnölzer
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cecilia Valvo
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Lidia Brunetto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Boe
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mauro Biffoni
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Peter H Krammer
- ‖Department of Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ruggero De Maria
- ¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Tobias L Haas
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; .,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| |
Collapse
|
16
|
Abstract
Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing. Splicing is an RNA editing step allowing to produce multiple transcripts from a single gene. The gene itself is organized in chromatin, associating DNA and multiple proteins. Some proteins regulating the compaction of the chromatin also affect RNA splicing. Yet, it was unclear whether these chromatin proteins were exceptions or whether chromatin very generally affected the outcome of splicing. Here, we show that a subset of chromatin proteins is physically in interaction with the enzyme responsible for RNA splicing. In addition, several chromatin proteins not found directly associated with the splicing machinery were also able to influence RNA splicing, suggesting that chromatin compaction very globally plays a role in splicing. This finding was confirmed using the first in vitro assay combining transcription and splicing in the context of chromatin; this assay showed that assembling DNA with chromatin proteins influences the efficiency of splicing.
Collapse
|
17
|
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
|
18
|
Gudipaty SA, McNamara RP, Morton EL, D'Orso I. PPM1G Binds 7SK RNA and Hexim1 To Block P-TEFb Assembly into the 7SK snRNP and Sustain Transcription Elongation. Mol Cell Biol 2015; 35:3810-28. [PMID: 26324325 PMCID: PMC4609742 DOI: 10.1128/mcb.00226-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/11/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022] Open
Abstract
Transcription elongation programs are vital for the precise regulation of several biological processes. One key regulator of such programs is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) once released from the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. Although mechanisms of P-TEFb release from the snRNP are becoming clearer, how P-TEFb remains in the 7SK-unbound state to sustain transcription elongation programs remains unknown. Here we report that the PPM1G phosphatase (inducibly recruited by nuclear factor κB [NF-κB] to target promoters) directly binds 7SK RNA and the kinase inhibitor Hexim1 once P-TEFb has been released from the 7SK snRNP. This dual binding activity of PPM1G blocks P-TEFb reassembly onto the snRNP to sustain NF-κB-mediated Pol II transcription in response to DNA damage. Notably, the PPM1G-7SK RNA interaction is direct, kinetically follows the recruitment of PPM1G to promoters to activate NF-κB transcription, and is reversible, since the complex disassembles before resolution of the program. Strikingly, we found that the ataxia telangiectasia mutated (ATM) kinase regulates the interaction between PPM1G and the 7SK snRNP through site-specific PPM1G phosphorylation. The precise and temporally regulated interaction of a cellular enzyme and a noncoding RNA provides a new paradigm for simultaneously controlling the activation and maintenance of inducible transcription elongation programs.
Collapse
Affiliation(s)
- Swapna Aravind Gudipaty
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ryan P McNamara
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Emily L Morton
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
19
|
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
|
20
|
Abstract
Ribonucleoprotein complexes involved in pre-mRNA splicing and mRNA decay are often regulated by phosphorylation of RNA-binding proteins. Cells use phosphorylation-dependent signaling pathways to turn on and off gene expression. Not much is known about how phosphorylation-dependent signals transmitted by exogenous factors or cell cycle checkpoints regulate RNA-mediated gene expression at the atomic level. Several human diseases are linked to an altered phosphorylation state of an RNA binding protein. Understanding the structural response to the phosphorylation "signal" and its effect on ribonucleoprotein assembly provides mechanistic understanding, as well as new information for the design of novel drugs. In this review, I highlight recent structural studies that reveal the mechanisms by which phosphorylation can regulate protein-protein and protein-RNA interactions in ribonucleoprotein complexes.
Collapse
Affiliation(s)
- Roopa Thapar
- BioSciences
at Rice, Biochemistry
and Cell Biology, Rice University, Houston, Texas 77251-1892, United States
| |
Collapse
|
21
|
Pan C, Tang JY, Xu YF, Xiao P, Liu HD, Wang HA, Wang WB, Meng FG, Yu X, Sun JP. The catalytic role of the M2 metal ion in PP2Cα. Sci Rep 2015; 5:8560. [PMID: 25708299 PMCID: PMC5390078 DOI: 10.1038/srep08560] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/26/2015] [Indexed: 01/16/2023] Open
Abstract
PP2C family phosphatases (the type 2C family of protein phosphatases; or metal-dependent phosphatase, PPM) constitute an important class of signaling enzymes that regulate many fundamental life activities. All PP2C family members have a conserved binuclear metal ion active center that is essential for their catalysis. However, the catalytic role of each metal ion during catalysis remains elusive. In this study, we discovered that mutations in the structurally buried D38 residue of PP2Cα (PPM1A) redefined the water-mediated hydrogen network in the active site and selectively disrupted M2 metal ion binding. Using the D38A and D38K mutations of PP2Cα as specific tools in combination with enzymology analysis, our results demonstrated that the M2 metal ion determines the rate-limiting step of substrate hydrolysis, participates in dianion substrate binding and stabilizes the leaving group after P-O bond cleavage. The newly characterized catalytic role of the M2 metal ion in this family not only provides insight into how the binuclear metal centers of the PP2C phosphatases are organized for efficient catalysis but also helps increase our understanding of the function and substrate specificity of PP2C family members.
Collapse
Affiliation(s)
- Chang Pan
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China
| | - Jun-yi Tang
- 1] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [2] Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Yun-fei Xu
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China
| | - Peng Xiao
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hong-da Liu
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China [3] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hao-an Wang
- Department of Human Biology, University of Toronto, Toronto, Ontario, Canada
| | - Wen-bo Wang
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China [3] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Fan-guo Meng
- Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Xiao Yu
- 1] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [2] Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Jin-peng Sun
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [3] Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| |
Collapse
|
22
|
Alidousty C, Rauen T, Hanssen L, Wang Q, Alampour-Rajabi S, Mertens PR, Bernhagen J, Floege J, Ostendorf T, Raffetseder U. Calcineurin-mediated YB-1 dephosphorylation regulates CCL5 expression during monocyte differentiation. J Biol Chem 2014; 289:21401-12. [PMID: 24947514 DOI: 10.1074/jbc.m114.562991] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Y-box (YB) protein-1 serves as a master regulator in gene transcription and mRNA translation. YB-1 itself is regulated at various levels, e.g. through post-translational modifications. In our previous work, we identified RANTES/CCL5 as a transcriptional target of YB-1. We previously demonstrated that YB-1 protein is transiently up-regulated during monocyte/macrophage differentiation evidenced in monocytic cells (THP-1 cells) that were differentiated using phorbol myristate acetate (PMA). Here we provide evidence that YB-1 phosphorylation, specifically at its serine residue 102 (Ser-102), increases early on in THP-1 cells following PMA treatment as well as in differentiated primary human monocytes. This process is mediated through the Akt signaling pathway. Ser-102-phosphorylated YB-1 displays stronger binding affinity and trans-activating capacity at the CCL5 gene promoter. Notably, Ser-102-phosphorylated YB-1 disappears at later stages of the monocyte/macrophage differentiation process. We demonstrate that serine-threonine phosphatase calcineurin (CN) dephosphorylates YB-1 preventing it from binding to and trans-activating the CCL5 promoter. Co-immunoprecipitation assays prove a direct YB-1/CN interaction. Furthermore, analyses in kidney tissues from mice that were treated with the CN inhibitor cyclosporine A revealed an in vivo effect of CN on the YB-1 phosphorylation status. We conclude that YB-1 phosphorylation at Ser-102 is an important prerequisite for CCL5 promoter activation during macrophage differentiation. Our findings point to a critical role of YB-1 in the resolution of inflammatory processes which may largely be due to CN-mediated dephosphorylation.
Collapse
Affiliation(s)
- Christina Alidousty
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Thomas Rauen
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Lydia Hanssen
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Qiang Wang
- the Department of Rheumatology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Setareh Alampour-Rajabi
- the Department of Cell and Molecular Biology, Institute of Biochemistry and Molecular Cell Biology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany, and
| | - Peter R Mertens
- the Department of Nephrology, Hypertension, Diabetes, and Endocrinology, Otto-von-Guericke-University, 39120 Magdeburg, Germany
| | - Jürgen Bernhagen
- the Department of Cell and Molecular Biology, Institute of Biochemistry and Molecular Cell Biology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany, and
| | - Jürgen Floege
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Tammo Ostendorf
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Ute Raffetseder
- From the Department of Nephrology and Clinical Immunology, University Hospital RWTH-Aachen, Pauwelsstrasse 30, 52057 Aachen, Germany,
| |
Collapse
|
23
|
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
|
24
|
Bebee TW, Cieply BW, Carstens RP. Genome-wide activities of RNA binding proteins that regulate cellular changes in the epithelial to mesenchymal transition (EMT). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:267-302. [PMID: 25201109 DOI: 10.1007/978-1-4939-1221-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The epithelial to mesenchymal transition (EMT) and reverse mesenchymal to epithelial transition (MET) are developmentally conserved processes that are essential for patterning of developing embryos and organs. The EMT/MET are further utilized in wound healing, but they can also be hijacked by cancer cells to promote tumor progression and metastasis. The molecular pathways governing these processes have historically focused on the transcriptional regulation and networks that control them. Indeed, global profiling of transcriptional changes has provided a wealth of information into how these networks are regulated, the downstream targets, and functional consequence of alterations to the global transcriptome. However, recent evidence has revealed that the posttranscriptional landscape of the cell is also dramatically altered during the EMT/MET and contributes to changes in cell behavior and phenotypes. While studies of this aspect of EMT biology are still in their infancy, recent progress has been achieved by the identification of several RNA binding proteins (RBPs) that regulate splicing, polyadenylation, mRNA stability, and translational control during EMT. This chapter focuses on the global impact of RBPs that regulate mRNA maturation as well as outlines the functional impact of several key posttranscriptional changes during the EMT. The growing evidence of RBP involvement in the cellular transformation during EMT underscores that a coordinated regulation of both transcriptional and posttranscriptional changes is essential for EMT. Furthermore, new discoveries into these events will paint a more detailed picture of the transcriptome during the EMT/MET and provide novel molecular targets for treatment of human diseases.
Collapse
Affiliation(s)
- Thomas W Bebee
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | | | | |
Collapse
|
25
|
Allemand E, Hastings ML. Expression and purification of splicing proteins from mammalian cells. Methods Mol Biol 2014; 1126:205-16. [PMID: 24549667 DOI: 10.1007/978-1-62703-980-2_16] [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] [Indexed: 01/20/2023]
Abstract
Pre-mRNA splicing is a complex process that is carried out by a large ribonucleoprotein enzyme, termed the spliceosome, which comprises up to 200 proteins. Despite this complexity, the role of individual spliceosomal proteins in the splicing reaction has been successfully investigated using cell-free assays. In many cases, the splicing factor of interest must be expressed and purified in order to study its function in vitro. Posttranslational modifications such as phosphorylation, methylation, acetylation, and ubiquitination of splicing factors are important for activity. Thus, their purification from mammalian cells presents numerous advantages. Here, we describe a method for expression and purification of splicing proteins from mammalian cells.
Collapse
Affiliation(s)
- Eric Allemand
- Unité de Régulation Epigénétique, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | | |
Collapse
|
26
|
Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation. Cell Rep 2013; 5:1256-68. [PMID: 24316072 DOI: 10.1016/j.celrep.2013.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/02/2013] [Accepted: 11/02/2013] [Indexed: 12/19/2022] Open
Abstract
The transition from transcription initiation into elongation is controlled by transcription factors, which recruit positive transcription elongation factor b (P-TEFb) to promoters to phosphorylate RNA polymerase II. A fraction of P-TEFb is recruited as part of the inhibitory 7SK small nuclear ribonucleoprotein particle (snRNP), which inactivates the kinase and prevents elongation. However, it is unclear how P-TEFb is captured from the promoter-bound 7SK snRNP to activate elongation. Here, we describe a mechanism by which transcription factors mediate the enzymatic release of P-TEFb from the 7SK snRNP at promoters to trigger activation in a gene-specific manner. We demonstrate that Tat recruits PPM1G/PP2Cγ to locally disassemble P-TEFb from the 7SK snRNP at the HIV promoter via dephosphorylation of the kinase T loop. Similar to Tat, nuclear factor (NF)-κB recruits PPM1G in a stimulus-dependent manner to activate elongation at inflammatory-responsive genes. Recruitment of PPM1G to promoter-assembled 7SK snRNP provides a paradigm for rapid gene activation through transcriptional pause release.
Collapse
|
27
|
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
|
28
|
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
|
29
|
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
|
30
|
Kim MH, Sonoda Y, Sasaki K, Kaminaka H, Imai R. Interactome analysis reveals versatile functions of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 in RNA processing within the nucleus and cytoplasm. Cell Stress Chaperones 2013; 18:517-25. [PMID: 23334891 PMCID: PMC3682024 DOI: 10.1007/s12192-012-0398-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 12/13/2012] [Accepted: 12/18/2012] [Indexed: 02/06/2023] Open
Abstract
Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 (AtCSP3) shares an RNA chaperone function with E. coli cold shock proteins and regulates freezing tolerance during cold acclimation. Here, we screened for AtCSP3-interacting proteins using a yeast two-hybrid system and 38 candidate interactors were identified. Sixteen of these were further confirmed in planta interaction between AtCSP3 by a bi-molecular fluorescence complementation assay. We found that AtCSP3 interacts with CONSTANS-LIKE protein 15 and nuclear poly(A)-binding proteins in nuclear speckles. Three 60S ribosomal proteins (RPL26A, RPL40A/UBQ2, and RPL36aB) and the Gar1 RNA-binding protein interacted with AtCSP3 in the nucleolus and nucleoplasm, suggesting that AtCSP3 functions in ribosome biogenesis. Interactions with LOS2/enolase and glycine-rich RNA-binding protein 7 that are cold inducible, and an mRNA decapping protein 5 (DCP5) were observed in the cytoplasm. These data suggest that AtCSP3 participates in multiple complexes that reside in nuclear and cytoplasmic compartments and possibly regulates RNA processing and functioning.
Collapse
Affiliation(s)
- Myung-Hee Kim
- />Crop Breeding Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555 Japan
| | - Yutaka Sonoda
- />Crop Breeding Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555 Japan
| | - Kentaro Sasaki
- />Crop Breeding Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555 Japan
| | - Hironori Kaminaka
- />Laboratory of Plant Molecular Biology, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Ryozo Imai
- />Crop Breeding Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555 Japan
| |
Collapse
|
31
|
Conklin PL, DePaolo D, Wintle B, Schatz C, Buckenmeyer G. Identification of Arabidopsis VTC3 as a putative and unique dual function protein kinase::protein phosphatase involved in the regulation of the ascorbic acid pool in plants. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2793-804. [PMID: 23749562 DOI: 10.1093/jxb/ert140] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ascorbic acid (AsA) is present at high levels in plants and is a potent antioxidant and cellular reductant. The major plant AsA biosynthetic pathway is through the intermediates D-mannose and L-galactose. Although there is ample evidence that plants respond to fluctuating environmental conditions with changes in the pool size of AsA, it is unclear how this regulation occurs. The AsA-deficient Arabidopsis thaliana mutants vtc3-1 and vtc3-2 define a locus that has been identified by positional cloning as At2g40860. Confirmation of this identification was through the study of AsA-deficient At2g40860 insertion mutants and by transgenic complementation of the AsA deficiency in vtc3-1 and vtc3-2 with wild-type At2g40860 cDNA. The very unusual VTC3 gene is predicted to encode a novel polypeptide with an N-terminal protein kinase domain tethered covalently to a C-terminal protein phosphatase type 2C domain. Homologues of this gene exist only within the Viridiplantae/Chloroplastida and the gene may therefore have arisen along with the D-mannose/L-galactose AsA biosynthetic pathway. The vtc3 mutant plants are defective in the ability to elevate the AsA pool in response to light and heat, suggestive of an important role for VTC3 in the regulation of the AsA pool size.
Collapse
Affiliation(s)
- Patricia L Conklin
- Biological Sciences Department, State University of New York at Cortland, Bowers Hall, Cortland, NY 13045, USA.
| | | | | | | | | |
Collapse
|
32
|
Identification of a new Schistosoma mansoni SMYB1 partner: putative roles in RNA metabolism. Parasitology 2013; 140:1085-95. [PMID: 23673212 DOI: 10.1017/s0031182013000413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SMYB1 is a Schistosoma mansoni protein highly similar to members of the Y-box binding protein family. Similar to other homologues, SMYB1 is able to bind double- and single-stranded DNA, as well as RNA molecules. The characterization of proteins involved in the regulation of gene expression in S. mansoni is of great importance for the understanding of molecular events that control morphological and physiological changes in this parasite. Here we demonstrate that SMYB1 is located in the cytoplasm of cells from different life-cycle stages of S. mansoni, suggesting that this protein is probably acting in mRNA metabolism in the cytoplasm and corroborating previous findings from our group that showed its ability to bind RNA. Protein-protein interactions are important events in all biological processes, since most proteins execute their functions through large supramolecular structures. Yeast two-hybrid screenings using SMYB1 as bait identified a partner in S. mansoni similar to the SmD3 protein of Drosophila melanogaster (SmRNP), which is important in the assembly of small nuclear ribonucleoprotein complexes. Also, pull-down assays were conducted using immobilized GST-SMYB1 proteins and confirmed the SMYB1-SmRNP interaction. The interaction of SMYB1 with a protein involved in mRNA processing suggests that it may act in processes such as turnover, transport and stabilization of RNA molecules.
Collapse
|
33
|
Shimada M, Nakanishi M. Response to DNA damage: why do we need to focus on protein phosphatases? Front Oncol 2013; 3:8. [PMID: 23386996 PMCID: PMC3560363 DOI: 10.3389/fonc.2013.00008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 01/09/2013] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are continuously threatened by unavoidable errors during normal DNA replication or various sources of genotoxic stresses that cause DNA damage or stalled replication. To maintain genomic integrity, cells have developed a coordinated signaling network, known as the DNA damage response (DDR). Following DNA damage, sensor molecules detect the presence of DNA damage and transmit signals to downstream transducer molecules. This in turn conveys the signals to numerous effectors, which initiate a large number of specific biological responses, including transient cell cycle arrest mediated by checkpoints, DNA repair, and apoptosis. It is recently becoming clear that dephosphorylation events are involved in keeping DDR factors inactive during normal cell growth. Moreover, dephosphorylation is required to shut off checkpoint arrest following DNA damage and has been implicated in the activation of the DDR. Spatial and temporal regulation of phosphorylation events is essential for the DDR, and fine-tuning of phosphorylation is partly mediated by protein phosphatases. While the role of kinases in the DDR has been well documented, the complex roles of protein dephosphorylation have only recently begun to be investigated. Therefore, it is important to focus on the role of phosphatases and to determine how their activity is regulated upon DNA damage. In this work, we summarize current knowledge on the involvement of serine/threonine phosphatases, especially the protein phosphatase 1, protein phosphatase 2A, and protein phosphatase Mg2+/Mn2+-dependent families, in the DDR.
Collapse
Affiliation(s)
- Midori Shimada
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University Nagoya, Japan
| | | |
Collapse
|
34
|
Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. A complex network of factors with overlapping affinities represses splicing through intronic elements. Nat Struct Mol Biol 2012; 20:36-45. [PMID: 23241926 PMCID: PMC3537874 DOI: 10.1038/nsmb.2459] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 11/05/2012] [Indexed: 12/11/2022]
Abstract
To better understand splicing regulation, we used a cell-based screen to identify ten diverse motifs that inhibit splicing from intron. Each motif was validated in another human cell type and gene context, and their presence correlated with in vivo splicing changes. All motifs exhibited exonic splicing enhancer or silencer activity, and grouping these motifs based on their distributions yielded clusters with distinct patterns of context-dependent activity. Candidate regulatory factors associated with each motif were identified, recovering 24 known and novel splicing regulators. Specific domains in selected factors were sufficient to confer ISS activity. Many factors bound multiple distinct motifs with similar affinity, and all motifs were recognized by multiple factors, revealing a complex, overlapping network of protein:RNA interactions. This arrangement enables individual cis-element to function differently in distinct cellular contexts depending on the spectrum of regulatory factors present.
Collapse
Affiliation(s)
- Yang Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Anderson SL, Liu B, Qiu J, Sturm AJ, Schwartz JA, Peters AJ, Sullivan KA, Rubin BY. Nutraceutical-mediated restoration of wild-type levels of IKBKAP-encoded IKAP protein in familial dysautonomia-derived cells. Mol Nutr Food Res 2012; 56:570-9. [PMID: 22495984 DOI: 10.1002/mnfr.201100670] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SCOPE The reported ability to modulate the production of the wild-type transcript in cells bearing the splice-altering familial dysautonomia (FD)-causing mutation in the IKBKAP gene prompted an evaluation of the impact of commonly consumed nutraceuticals on the splicing of this transcript. METHODS AND RESULTS Screening efforts revealed the ability of the isoflavones, genistein, and daidzein, to impact splicing and increase the production of the wild-type, exon-20-containing, transcript, and the full-length IKBKAP-encoded IΚB kinase complex associated protein(IKAP) in FD-derived cells. Genistein was also found to impact splicing in neuronal cells, a cell type profoundly impacted by FD. The simultaneous exposure of FD-derived cells to genistein and epigallocatechin gallate (EGCG) resulted in the almost exclusive production of the exon-20-containing transcript and the production of wild-type amounts of IKAP protein. CONCLUSION This study represents the first demonstration that the isoflavones, genistein and daidzein, possess splice-altering capabilities and that simultaneous treatment with genistein and EGCG reverses the splice-altering impact of the FD-causing mutation. These findings support the clinical evaluation of the therapeutic impact of the combined administration of these two commonly consumed nutraceuticals on this patient population and suggest a broader evaluation of the impact of these nutraceuticals on the in vivo RNA splicing process.
Collapse
Affiliation(s)
- Sylvia L Anderson
- Laboratory for Familial Dysautonomia Research, Department of Biological Sciences, Fordham University, Bronx, NY10458, USA
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Wei WJ, Mu SR, Heiner M, Fu X, Cao LJ, Gong XF, Bindereif A, Hui J. YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts. Nucleic Acids Res 2012; 40:8622-36. [PMID: 22730292 PMCID: PMC3458536 DOI: 10.1093/nar/gks579] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein–protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3′ splice sites in mammalian cells.
Collapse
Affiliation(s)
- Wen-Juan Wei
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
This review traces the historical origins and conceptual developments leading to the current state of knowledge of the three superfamilies of protein Ser/Thr phosphatases. 'PR enzyme' was identified as an enzyme that inactivates glycogen phosphorylase, although it took 10 years before this ugly duckling was recognized for its true identity as a protein Ser/Thr phosphatase. Ethanol denaturation for purification in the 1970s yielded a phosphatase that exhibited broad specificity, which was resolved into type-1 and type-2 phosphatases in the 1980s. More recent developments show that regulation and specificity are achieved through assembly of multisubunit holoenzymes, transient phosphorylation and the action of inhibitor proteins. Still not widely appreciated, there are hundreds of discrete protein Ser/Thr phosphatases available to counteract protein kinases, offering potential therapeutic targets. Signalling networks and modelling schemes need to incorporate the full gamut of protein Ser/Thr phosphatases and their interconnections.
Collapse
Affiliation(s)
- David L Brautigan
- Department of Microbiology, Immunology and Cancer Biology, Center for Cell Signaling, University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.
| |
Collapse
|
38
|
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
|
39
|
Li P, Ham BK, Lucas WJ. CmRBP50 protein phosphorylation is essential for assembly of a stable phloem-mobile high-affinity ribonucleoprotein complex. J Biol Chem 2011; 286:23142-9. [PMID: 21572046 PMCID: PMC3123081 DOI: 10.1074/jbc.m111.244129] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 04/29/2011] [Indexed: 01/30/2023] Open
Abstract
RNA-binding proteins (RBPs) form ribonucleoprotein (RNP) complexes that play crucial roles in RNA processing for gene regulation. The angiosperm sieve tube system contains a unique population of transcripts, some of which function as long-distance signaling agents involved in regulating organ development. These phloem-mobile mRNAs are translocated as RNP complexes. One such complex is based on a phloem RBP named Cucurbita maxima RNA-binding protein 50 (CmRBP50), a member of the polypyrimidine track binding protein family. The core of this RNP complex contains six additional phloem proteins. Here, requirements for assembly of this CmRBP50 RNP complex are reported. Phosphorylation sites on CmRBP50 were mapped, and then coimmunoprecipitation and protein overlay studies established that the phosphoserine residues, located at the C terminus of CmRBP50, are critical for RNP complex assembly. In vitro pull-down experiments revealed that three phloem proteins, C. maxima phloem protein 16, C. maxima GTP-binding protein, and C. maxima phosphoinositide-specific phospholipase-like protein, bind directly with CmRBP50. This interaction required CmRBP50 phosphorylation. Gel mobility-shift assays demonstrated that assembly of the CmRBP50-based protein complex results in a system having enhanced binding affinity for phloem-mobile mRNAs carrying polypyrimidine track binding motifs. This property would be essential for effective long-distance translocation of bound mRNA to the target tissues.
Collapse
Affiliation(s)
- Pingfang Li
- From the Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616 and
- the Department of Horticulture, Huajiachi Campus, Zhejiang University, Kaixuan Road 268, Hangzhou, 310029, China
| | - Byung-Kook Ham
- From the Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616 and
| | - William J. Lucas
- From the Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616 and
| |
Collapse
|
40
|
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
|
41
|
Zhang B, zur Hausen A, Orlowska-Volk M, Jäger M, Bettendorf H, Stamm S, Hirschfeld M, Yiqin O, Tong X, Gitsch G, Stickeler E. Alternative splicing-related factor YT521: an independent prognostic factor in endometrial cancer. Int J Gynecol Cancer 2010; 20:492-9. [PMID: 20686370 DOI: 10.1111/igc.0b013e3181d66ffe] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND YT521 is a splicing factor involved in alternative splicing regulation of several tumor biological important genes. Two messenger RNA (mRNA) isoforms due to YT521 exon6 alternative splicing exist, with so far unknown functional consequences. Further evidence exists for a direct influence of YT521 expression in tumorigenesis because its mRNA level is changed in tumors compared with physiological tissue. We investigated the potential impact of YT521 expression on tumor biological parameters in endometrial cancer (EC). METHODS Real-time reverse transcription-polymerase chain reaction specifically detecting YT521 exon6-retention and exon6-skipping mRNA isoforms and immunohistochemistry were performed in a cohort of 130 EC tissue samples. RESULTS Whereas YT521 exon6-retention mRNA was detectable in 86 (66.2%), the exon6-skipping isoform mRNA was expressed in only 8 (6.2%) of all EC samples. On the protein level, 104 (80%) of EC samples showed nuclear expression. The mRNA levels of exon6-skipping isoform were not correlated to any of the clinicopathological parameters of EC. In contrast, YT521 exon6-retention mRNA expression was positively correlated to metastasis (R = 0.196, P = 0.026) and inversely correlated to the protein expression levels (R = -0.205, P = 0.019). In univariate analyses, higher levels of YT521 exon6-retention mRNA were correlated to a poorer progression-free survival (P = 0.003), and this is confirmed by multivariate analyses (P = 0.019). The negative YT521 protein expression was correlated to poorer overall and disease-specific survival (P = 0.036 and P = 0.034), respectively, in univariate analyses. They are also confirmed by multivariate analyses (P = 0.021 and P = 0.010, respectively). CONCLUSIONS We characterized for the first time in a clinical setting a new but rare exon6-skipping mRNA splicing isoform of YT521. Furthermore, we identified YT521 as a potential new independent prognostic factor for patients with EC: the lack of YT521 protein in tumor cells was highly predictive for a poor overall and disease-specific survival and independent from the histological subtypes.
Collapse
Affiliation(s)
- Bo Zhang
- Department of Obstetrics and Gynecology, Freiburg University Medical Center, Freiburg, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Cotranscriptional exon skipping in the genotoxic stress response. Nat Struct Mol Biol 2010; 17:1358-66. [PMID: 20972445 DOI: 10.1038/nsmb.1912] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 08/19/2010] [Indexed: 12/14/2022]
Abstract
Pre-mRNA splicing is functionally coupled to transcription, and genotoxic stresses can enhance alternative exon inclusion by affecting elongating RNA polymerase II. We report here that various genotoxic stress inducers, including camptothecin (CPT), inhibit the interaction between Ewing's sarcoma proto-oncoprotein (EWS), an RNA polymerase II-associated factor, and YB-1, a spliceosome-associated factor. This results in the cotranscriptional skipping of several exons of the MDM2 gene, which encodes the main p53 ubiquitin ligase. This reversible exon skipping participates in the regulation of MDM2 expression that may contribute to the accumulation of p53 during stress exposure and its rapid shut-off when stress is removed. Finally, a splicing-sensitive microarray identified numerous exons that are skipped in response to CPT and EWS-YB-1 depletion. These data demonstrate genotoxic stress-induced alteration of the communication between the transcriptional and splicing machineries, which results in widespread exon skipping and plays a central role in the genotoxic stress response.
Collapse
|
43
|
Jodelka FM, Ebert AD, Duelli DM, Hastings ML. A feedback loop regulates splicing of the spinal muscular atrophy-modifying gene, SMN2. Hum Mol Genet 2010; 19:4906-17. [PMID: 20884664 PMCID: PMC2989896 DOI: 10.1093/hmg/ddq425] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neurological disorder characterized by motor neuron degeneration and progressive muscle paralysis. The disease is caused by a reduction in survival of motor neuron (SMN) protein resulting from homozygous deletion of the SMN1 gene. SMN protein is also encoded by SMN2. However, splicing of SMN2 exon 7 is defective, and consequently, the majority of the transcripts produce a truncated, unstable protein. SMN protein itself has a role in splicing. The protein is required for the biogenesis of spliceosomal snRNPs, which are essential components of the splicing reaction. We now show that SMN protein abundance affects the splicing of SMN2 exon 7, revealing a feedback loop inSMN expression. The reduced SMN protein concentration observed in SMA samples and in cells depleted of SMN correlates with a decrease in cellular snRNA levels and a decrease in SMN2 exon 7 splicing. Furthermore, altering the relative abundance or activity of individual snRNPs has distinct effects on exon 7 splicing, demonstrating that core spliceosomal snRNPs influence SMN2 alternative splicing. Our results identify a feedback loop in SMN expression by which low SMN protein levels exacerbate SMN exon 7 skipping, leading to a further reduction in SMN protein. These results imply that a modest increase in SMN protein abundance may cause a disproportionately large increase in SMN expression, a finding that is important for assessing the therapeutic potential of SMA treatments and understanding disease pathogenesis.
Collapse
Affiliation(s)
- Francine M Jodelka
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | | | | | | |
Collapse
|
44
|
Arginine methylation controls the subcellular localization and functions of the oncoprotein splicing factor SF2/ASF. Mol Cell Biol 2010; 30:2762-74. [PMID: 20308322 DOI: 10.1128/mcb.01270-09] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing and posttranslational modifications (PTMs) are major sources of protein diversity in eukaryotic proteomes. The SR protein SF2/ASF is an oncoprotein that functions in pre-mRNA splicing, with additional roles in other posttranscriptional and translational events. Functional studies of SR protein PTMs have focused exclusively on the reversible phosphorylation of Ser residues in the C-terminal RS domain. We confirmed that human SF2/ASF is methylated at residues R93, R97, and R109, which were identified in a global proteomic analysis of Arg methylation, and further investigated whether these methylated residues regulate the properties of SF2/ASF. We show that the three arginines additively control the subcellular localization of SF2/ASF and that both the positive charge and the methylation state are important. Mutations that block methylation and remove the positive charge result in the cytoplasmic accumulation of SF2/ASF. The consequent decrease in nuclear SF2/ASF levels prevents it from modulating the alternative splicing of target genes, results in higher translation stimulation, and abrogates the enhancement of nonsense-mediated mRNA decay. This study addresses the mechanisms by which Arg methylation and the associated positive charge regulate the activities of SF2/ASF and emphasizes the significance of localization control for an oncoprotein with multiple functions in different cellular compartments.
Collapse
|
45
|
Huynh N, Ma CT, Giang N, Hagopian J, Ngo J, Adams J, Ghosh G. Allosteric interactions direct binding and phosphorylation of ASF/SF2 by SRPK1. Biochemistry 2009; 48:11432-40. [PMID: 19886675 DOI: 10.1021/bi901107q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ASF/SF2, a member of the serine-arginine (SR) protein family, has two RRM domains (RRM1 and RRM2) and a C-terminal domain rich in RS dipeptides. SR protein kinase 1 (SRPK1) phosphorylates approximately 12 of these serines using a semiprocessive mechanism. The X-ray structure of the ASF/SF2-SRPK1 complex revealed several features of the complex that raised intriguing questions about how the substrate is phosphorylated by the kinase. The part of the RS domain destined to be phosphorylated at later stages of the reaction docks to a kinase groove distal to the active site while the neighboring RRM2 binds near the active site [Ngo, J. C., et al. (2008) Mol. Cell 29, 563-576]. In this study, we investigate the interplay between the RS domain and RRM2 for stable association and phosphorylation of ASF/SF2. Despite several contacts in the enzyme-substrate complex, free RRM2 does not bind efficiently to SRPK1 unless the docking groove is occupied by the RS domain. This domain cross-talk enhances the processive phosphorylation of the RS domain. The RRM-SRPK1 contact residues control the folding of a critical beta-strand in RRM2. Unfolding of this structural element may force the N-terminal serines of the RS domain into the active site for sequential phosphorylation. Thus, ASF/SF2 represents a new class of substrates that use unique primary sequence to induce allosteric binding, processive phosphorylation, and product release.
Collapse
Affiliation(s)
- Nhat Huynh
- Department of Chemistry and Biochemistry, University of California at San Diego,9500 Gilman Drive, La Jolla, California 92093, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
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
|
47
|
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
|
48
|
Mtango NR, Potireddy S, Latham KE. Expression of microRNA processing machinery genes in rhesus monkey oocytes and embryos of different developmental potentials. Mol Reprod Dev 2009; 76:255-69. [PMID: 18646051 PMCID: PMC2631102 DOI: 10.1002/mrd.20950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs that silence gene expression. In animal cells, miRNAs bind to the 3' untranslated regions of specific mRNAs and inhibit their translation. The correct regulation of mRNA expression by miRNAs is believed to be important for oocyte maturation, early development and implantation. We examined the expression of 25 mRNAs involved in the microRNA processing pathway in a nonhuman primate oocyte and embryo model. We observed that mRNAs related to miRNA splicing are downregulated during oocyte maturation while those related to miRNA processing are upregulated, indicating that there may exist a temporal difference in their activities related to transcriptional activity in germinal vesicle stage oocytes. We also observed that the vast majority of mRNAs examined were insensitive to alpha-amanitin at the 8-16 cell stage. The expression data did not reveal a major impact of embryo culture, and hormonal stimulation protocol affected only a small number of mRNAs, suggesting that the components of the pathway may be accumulated in the oocyte during oogenesis and resistant to exogenous insults. In comparison to published mouse array data, we observed species differences and similarities in the temporal expression patterns of some genes, suggesting that miRNA processing may be regulated differently. These data extend our understanding of the potential roles of miRNA during primate embryogenesis.
Collapse
Affiliation(s)
- Namdori R Mtango
- The Fels Institute for Cancer Research and Molecular Biology, Temple University Medical School, Philadelphia, Pennsylvania 19140, USA
| | | | | |
Collapse
|
49
|
Tazi J, Bakkour N, Stamm S. Alternative splicing and disease. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1792:14-26. [PMID: 18992329 PMCID: PMC5632948 DOI: 10.1016/j.bbadis.2008.09.017] [Citation(s) in RCA: 382] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 09/19/2008] [Accepted: 09/30/2008] [Indexed: 12/11/2022]
Abstract
Almost all protein-coding genes are spliced and their majority is alternatively spliced. Alternative splicing is a key element in eukaryotic gene expression that increases the coding capacity of the human genome and an increasing number of examples illustrates that the selection of wrong splice sites causes human disease. A fine-tuned balance of factors regulates splice site selection. Here, we discuss well-studied examples that show how a disturbance of this balance can cause human disease. The rapidly emerging knowledge of splicing regulation now allows the development of treatment options.
Collapse
Affiliation(s)
- Jamal Tazi
- University of Montpellier II, Institute of Molecular Genetics, Centre Nationale de Recherche Scientifique, 1919 Route de Mende, France
| | | | | |
Collapse
|
50
|
van Alphen RJ, Wiemer EAC, Burger H, Eskens FALM. The spliceosome as target for anticancer treatment. Br J Cancer 2008; 100:228-32. [PMID: 19034274 PMCID: PMC2634708 DOI: 10.1038/sj.bjc.6604801] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The spliceosome is a ribonucleoprotein complex involved in RNA splicing, that is, the removal of non-coding introns from precursor messenger RNA. (Alternative) Splicing events may play an essential role in tumourigenesis. The recent discovery that the spliceosome is a target for novel compounds with anticancer activity opens up new therapeutic avenues.
Collapse
Affiliation(s)
- R J van Alphen
- Department of Medical Oncology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | | | | |
Collapse
|