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Li JD, Taipale M, Blencowe BJ. Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25. Mol Cell 2024; 84:2573-2589.e5. [PMID: 38917795 DOI: 10.1016/j.molcel.2024.05.028] [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: 09/15/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Efficient targeted control of splicing is a major goal of functional genomics and therapeutic applications. Guide (g)RNA-directed, deactivated (d)Cas CRISPR enzymes fused to splicing effectors represent a promising strategy due to the flexibility of these systems. However, efficient, specific, and generalizable activation of endogenous exons using this approach has not been previously reported. By screening over 300 dCasRx-splicing factor fusion proteins tethered to splicing reporters, we identify dCasRx-RBM25 as a potent activator of exons. Moreover, dCasRx-RBM25 efficiently activates the splicing of ∼90% of targeted endogenous alternative exons and displays high on-target specificity. Using gRNA arrays for combinatorial targeting, we demonstrate that dCasRx-RBM25 enables multiplexed activation and repression of exons. Using this feature, the targeting of neural-regulated exons in Ptpb1 and Puf60 in embryonic stem cells reveals combinatorial effects on downstream alternative splicing events controlled by these factors. Collectively, our results enable versatile, combinatorial exon-resolution functional assays and splicing-directed therapeutic applications.
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Affiliation(s)
- Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mikko Taipale
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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2
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Zhang J, Chen WQ, Yang K, Wang ZX, Sun DL, Peng YY, Yu M, Wang SX, Guo Q. RBM25 induces trophoblast epithelial-mesenchymal transition and preeclampsia disorder by enhancing the positive feedback loop between Grhl2 and RBM25. Exp Biol Med (Maywood) 2023; 248:1267-1277. [PMID: 37728157 PMCID: PMC10621477 DOI: 10.1177/15353702231191199] [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: 01/15/2023] [Accepted: 05/08/2023] [Indexed: 09/21/2023] Open
Abstract
Defects in migration and invasion caused by dysregulation of trophoblast epithelial-mesenchymal transformation (EMT) are one of the key factors in the pathogenesis of preeclampsia (PE). RNA-binding motif protein 25 (RBM25) is an RNA-binding protein involved in a variety of cellular processes, including cell proliferation, apoptosis, cell migration and invasion, and EMT. However, the expression and function of RBM25 in placental of PE remain unclear. In this study, we reveal that the expression of RBM25 is significantly elevated in PE placental tissue. RBM25 depletion and over-expression in trophoblast cells increase and decrease, respectively, cell migration and invasion by regulating EMT marker E-cadherin and Vimentin expression. Mechanistically, Grhl2 is involved in RBM25-regulated trophoblast cell migration, invasion, and EMT through RBM25-facilitated mRNA stabilization. Furthermore, the upregulation of Grhl2 enhances the expression of RBM25 through transcription and forms a positive feedback regulation in the progression of PE. These findings suggest that upregulation of RBM25 induces dysregulation of trophoblast EMT by enhancing positive feedback regulation of Grhl2 and RBM25, leading to defects in cell migration and invasion. Targeting this newly identified regulatory axis may provide benefits in the prevention and treatment of PE.
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Affiliation(s)
- Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Wen-qi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Kai Yang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing 100026, China
| | - Zhao-xi Wang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Dong-lan Sun
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Yuan-yuan Peng
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Mei Yu
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Shao-xiong Wang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
| | - Qing Guo
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Key Laboratory of Maternal and Fetal Medicine, Shijiazhuang 050011, China
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3
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Zhang YF, Wang YX, Zhang N, Lin ZH, Wang LR, Feng Y, Pan Q, Wang L. Prognostic alternative splicing regulatory network of RBM25 in hepatocellular carcinoma. Bioengineered 2021; 12:1202-1211. [PMID: 33830865 PMCID: PMC8806338 DOI: 10.1080/21655979.2021.1908812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
RNA-binding motif protein 25 (RBM25) is a poorly characterized RNA-binding protein that is involved in several biological processes and regulates the proliferation and metastasis of tumor cells. The regulatory role of RBM25 in hepatocellular carcinoma (HCC) is unknown. Here, RBM25 expression and outcomes in HCC patients were evaluated using The Cancer Genome Atlas database. RBM25 was overexpressed in HCC patients compared with the healthy group. The high expression of RBM25 in tumor tissues was significantly related to poor overall survival (P<0.001). Overexpression of RBM25 significantly contributed to poorer survival in male patients and N0 stage patients (P<0.001). Spearman analysis and weighted gene co-expression network analysis identified 694 RBM25-related genes. Protein-protein interaction network analysis revealed the Cluster with the highest score, which positively correlated with RBM25. CDCA5 and INCENP were identified as the core functional genes related to RBM25. The overexpression of CDCA5 and INCENP in HCC patients was examined using the Human Protein Atlas database. The findings collectively indicated that RBM25 may interact with CDCA5 and INCENP to regulate HCC. Our detailed characterization of RBM25 protein interactions and related core functional genes provides a basis for further studies aimed at identifying molecular regulatory pathways or splicing events.
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Affiliation(s)
- Yong-Fa Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Xiu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning- Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen-Hai Lin
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Long-Rong Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun Feng
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Pan
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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4
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Jenkins T, Northall SJ, Ptchelkine D, Lever R, Cubbon A, Betts H, Taresco V, Cooper CDO, McHugh PJ, Soultanas P, Bolt EL. The HelQ human DNA repair helicase utilizes a PWI-like domain for DNA loading through interaction with RPA, triggering DNA unwinding by the HelQ helicase core. NAR Cancer 2021; 3:zcaa043. [PMID: 34316696 PMCID: PMC8210318 DOI: 10.1093/narcan/zcaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Genome instability is a characteristic enabling factor for carcinogenesis. HelQ helicase is a component of human DNA maintenance systems that prevent or reverse genome instability arising during DNA replication. Here, we provide details of the molecular mechanisms that underpin HelQ function-its recruitment onto ssDNA through interaction with replication protein A (RPA), and subsequent translocation of HelQ along ssDNA. We describe for the first time a functional role for the non-catalytic N-terminal region of HelQ, by identifying and characterizing its PWI-like domain. We present evidence that this domain of HelQ mediates interaction with RPA that orchestrates loading of the helicase domains onto ssDNA. Once HelQ is loaded onto the ssDNA, ATP-Mg2+ binding in the catalytic site activates the helicase core and triggers translocation along ssDNA as a dimer. Furthermore, we identify HelQ-ssDNA interactions that are critical for the translocation mechanism. Our data are novel and detailed insights into the mechanisms of HelQ function relevant for understanding how human cells avoid genome instability provoking cancers, and also how cells can gain resistance to treatments that rely on DNA crosslinking agents.
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Affiliation(s)
- Tabitha Jenkins
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Sarah J Northall
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | | | - Rebecca Lever
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Andrew Cubbon
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Hannah Betts
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Vincenzo Taresco
- School of Pharmacy, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Christopher D O Cooper
- Department of Biological and Geographical Sciences, School of Applied Sciences, The University of Huddersfield, HD1 3DH, Huddersfield, UK
| | - Peter J McHugh
- MRC Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, OX3 9DS, Oxford, UK
| | - Panos Soultanas
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Edward L Bolt
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
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5
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Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PLoS Genet 2020; 16:e1009176. [PMID: 33137164 PMCID: PMC7660927 DOI: 10.1371/journal.pgen.1009176] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/12/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
The ataxia telangiectasia and Rad3-related (ATR) protein kinase is a key regulator of the cellular response to DNA damage. Due to increased amount of replication stress, cancer cells heavily rely on ATR to complete DNA replication and cell cycle progression. Thus, ATR inhibition is an emerging target in cancer therapy, with multiple ATR inhibitors currently undergoing clinical trials. Here, we describe dual genome-wide CRISPR knockout and CRISPR activation screens employed to comprehensively identify genes that regulate the cellular resistance to ATR inhibitors. Specifically, we investigated two different ATR inhibitors, namely VE822 and AZD6738, in both HeLa and MCF10A cells. We identified and validated multiple genes that alter the resistance to ATR inhibitors. Importantly, we show that the mechanisms of resistance employed by these genes are varied, and include restoring DNA replication fork progression, and prevention of ATR inhibitor-induced apoptosis. In particular, we describe a role for MED12-mediated inhibition of the TGFβ signaling pathway in regulating replication fork stability and cellular survival upon ATR inhibition. Our dual genome-wide screen findings pave the way for personalized medicine by identifying potential biomarkers for ATR inhibitor resistance.
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6
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Ge Y, Schuster MB, Pundhir S, Rapin N, Bagger FO, Sidiropoulos N, Hashem N, Porse BT. The splicing factor RBM25 controls MYC activity in acute myeloid leukemia. Nat Commun 2019; 10:172. [PMID: 30635567 PMCID: PMC6329799 DOI: 10.1038/s41467-018-08076-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022] Open
Abstract
Cancer sequencing studies have implicated regulators of pre-mRNA splicing as important disease determinants in acute myeloid leukemia (AML), but the underlying mechanisms have remained elusive. We hypothesized that "non-mutated" splicing regulators may also play a role in AML biology and therefore conducted an in vivo shRNA screen in a mouse model of CEBPA mutant AML. This has led to the identification of the splicing regulator RBM25 as a novel tumor suppressor. In multiple human leukemic cell lines, knockdown of RBM25 promotes proliferation and decreases apoptosis. Mechanistically, we show that RBM25 controls the splicing of key genes, including those encoding the apoptotic regulator BCL-X and the MYC inhibitor BIN1. This mechanism is also operative in human AML patients where low RBM25 levels are associated with high MYC activity and poor outcome. Thus, we demonstrate that RBM25 acts as a regulator of MYC activity and sensitizes cells to increased MYC levels.
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Affiliation(s)
- Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Frederik Otzen Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nikos Sidiropoulos
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nadia Hashem
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark. .,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark. .,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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7
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Kistowski M, Dębski J, Karczmarski J, Paziewska A, Olędzki J, Mikula M, Ostrowski J, Dadlez M. A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome. Mol Cell Proteomics 2016; 16:213-227. [PMID: 27927741 DOI: 10.1074/mcp.m116.058818] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 11/12/2016] [Indexed: 12/18/2022] Open
Abstract
Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic data sets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected. This sequence consensus indicated neutrophil elastase as a source of the fingerprint. We also found that a large fraction of affected proteins are RNA processing proteins associated with the nuclear fraction and mostly cleaved within their functionally important RNA-binding domains. Thus, we detected a new class of cancer-specific peptides that are possible markers of tumor-infiltrating neutrophil activity, which often correlates with the clinical outcome. Data are available via ProteomeXchange with identifiers: PXD005274 (Data set 1) and PXD004249 (Data set 2). Our results indicate the value of peptide-wise analysis of large global proteomic analysis data sets as opposed to protein-wise analysis, in which outlier differential peptides are usually neglected.
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Affiliation(s)
- Michał Kistowski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Janusz Dębski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Jakub Karczmarski
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Agnieszka Paziewska
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jacek Olędzki
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Michał Mikula
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- ¶Department of Gastroenterology Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Dadlez
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw;
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8
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Mohammad DK, Ali RH, Turunen JJ, Nore BF, Smith CIE. B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing. PLoS One 2016; 11:e0160255. [PMID: 27487157 PMCID: PMC4972398 DOI: 10.1371/journal.pone.0160255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/16/2016] [Indexed: 12/19/2022] Open
Abstract
Protein kinase B (AKT) phosphorylates numerous substrates on the consensus motif RXRXXpS/T, a docking site for 14-3-3 interactions. To identify novel AKT-induced phosphorylation events following B cell receptor (BCR) activation, we performed proteomics, biochemical and bioinformatics analyses. Phosphorylated consensus motif-specific antibody enrichment, followed by tandem mass spectrometry, identified 446 proteins, containing 186 novel phosphorylation events. Moreover, we found 85 proteins with up regulated phosphorylation, while in 277 it was down regulated following stimulation. Up regulation was mainly in proteins involved in ribosomal and translational regulation, DNA binding and transcription regulation. Conversely, down regulation was preferentially in RNA binding, mRNA splicing and mRNP export proteins. Immunoblotting of two identified RNA regulatory proteins, RBM25 and MEF-2D, confirmed the proteomics data. Consistent with these findings, the AKT-inhibitor (MK-2206) dramatically reduced, while the mTORC-inhibitor PP242 totally blocked phosphorylation on the RXRXXpS/T motif. This demonstrates that this motif, previously suggested as an AKT target sequence, also is a substrate for mTORC1/2. Proteins with PDZ, PH and/or SH3 domains contained the consensus motif, whereas in those with an HMG-box, H15 domains and/or NF-X1-zinc-fingers, the motif was absent. Proteins carrying the consensus motif were found in all eukaryotic clades indicating that they regulate a phylogenetically conserved set of proteins.
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Affiliation(s)
- Dara K. Mohammad
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska Hospital Huddinge, SE-141 86 Huddinge-Stockholm, Sweden
- Department of Biology, College of Science, University of Salahaddin, 44002 Erbil, Kurdistan Region-Iraq
- * E-mail: ; (DKM); (CIES)
| | - Raja H. Ali
- KTH Royal Institute of Technology, Swedish e-Science Research Center, Science for Life Laboratory, School of Computer Science and Communication, SE-171 77 Solna, Sweden
| | - Janne J. Turunen
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska Hospital Huddinge, SE-141 86 Huddinge-Stockholm, Sweden
| | - Beston F. Nore
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska Hospital Huddinge, SE-141 86 Huddinge-Stockholm, Sweden
- Department of Biochemistry, School of Medicine, University of Sulaimani, Sulaimaniyah, Kurdistan Region-Iraq
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska Hospital Huddinge, SE-141 86 Huddinge-Stockholm, Sweden
- * E-mail: ; (DKM); (CIES)
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9
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Absmeier E, Rosenberger L, Apelt L, Becke C, Santos KF, Stelzl U, Wahl MC. A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein. ACTA ACUST UNITED AC 2015; 71:762-71. [DOI: 10.1107/s1399004715001005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/16/2015] [Indexed: 11/10/2022]
Abstract
The spliceosomal RNA helicase Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. Brr2 exhibits an unusual organization with tandem helicase units, each comprising dual RecA-like domains and a Sec63 homology unit, preceded by a more than 400-residue N-terminal helicase-associated region. Whereas recent crystal structures have provided insights into the molecular architecture and regulation of the Brr2 helicase region, little is known about the structural organization and function of its N-terminal part. Here, a near-atomic resolution crystal structure of a PWI-like domain that resides in the N-terminal region ofChaetomium thermophilumBrr2 is presented. CD spectroscopic studies suggested that this domain is conserved in the yeast and human Brr2 orthologues. Although canonical PWI domains act as low-specificity nucleic acid-binding domains, no significant affinity of the unusual PWI domain of Brr2 for a broad spectrum of DNAs and RNAs was detected in band-shift assays. Consistently, theC. thermophilumBrr2 PWI-like domain, in the conformation seen in the present crystal structure, lacks an expanded positively charged surface patch as observed in at least one canonical, nucleic acid-binding PWI domain. Instead, in a comprehensive yeast two-hybrid screen against human spliceosomal proteins, fragments of the N-terminal region of human Brr2 were found to interact with several other spliceosomal proteins. At least one of these interactions, with the Prp19 complex protein SPF27, depended on the presence of the PWI-like domain. The results suggest that the N-terminal region of Brr2 serves as a versatile protein–protein interaction platform in the spliceosome and that some interactions require or are reinforced by the PWI-like domain.
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