1
|
Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
Collapse
Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
2
|
Hogg EKJ, Findlay GM. Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders. FEBS Lett 2023; 597:2375-2415. [PMID: 37607329 PMCID: PMC10952393 DOI: 10.1002/1873-3468.14723] [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: 06/05/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023]
Abstract
Human developmental disorders encompass a wide range of debilitating physical conditions and intellectual disabilities. Perturbation of protein kinase signalling underlies the development of some of these disorders. For example, disrupted SRPK signalling is associated with intellectual disabilities, and the gene dosage of DYRKs can dictate the pathology of disorders including Down's syndrome. Here, we review the emerging roles of the CMGC kinase families SRPK, CLK, DYRK, and sub-family HIPK during embryonic development and in developmental disorders. In particular, SRPK, CLK, and DYRK kinase families have key roles in developmental signalling and stem cell regulation, and can co-ordinate neuronal development and function. Genetic studies in model organisms reveal critical phenotypes including embryonic lethality, sterility, musculoskeletal errors, and most notably, altered neurological behaviours arising from defects of the neuroectoderm and altered neuronal signalling. Further unpicking the mechanisms of specific kinases using human stem cell models of neuronal differentiation and function will improve our understanding of human developmental disorders and may provide avenues for therapeutic strategies.
Collapse
Affiliation(s)
- Elizabeth K. J. Hogg
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
| | - Greg M. Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
| |
Collapse
|
3
|
Araki S, Ohori M, Yugami M. Targeting pre-mRNA splicing in cancers: roles, inhibitors, and therapeutic opportunities. Front Oncol 2023; 13:1152087. [PMID: 37342192 PMCID: PMC10277747 DOI: 10.3389/fonc.2023.1152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/22/2023] Open
Abstract
Accumulating evidence has indicated that pre-mRNA splicing plays critical roles in a variety of physiological processes, including development of multiple diseases. In particular, alternative splicing is profoundly involved in cancer progression through abnormal expression or mutation of splicing factors. Small-molecule splicing modulators have recently attracted considerable attention as a novel class of cancer therapeutics, and several splicing modulators are currently being developed for the treatment of patients with various cancers and are in the clinical trial stage. Novel molecular mechanisms modulating alternative splicing have proven to be effective for treating cancer cells resistant to conventional anticancer drugs. Furthermore, molecular mechanism-based combination strategies and patient stratification strategies for cancer treatment targeting pre-mRNA splicing must be considered for cancer therapy in the future. This review summarizes recent progress in the relationship between druggable splicing-related molecules and cancer, highlights small-molecule splicing modulators, and discusses future perspectives of splicing modulation for personalized and combination therapies in cancer treatment.
Collapse
|
4
|
Zheng K, Ren Z, Wang Y. Serine-arginine protein kinases and their targets in viral infection and their inhibition. Cell Mol Life Sci 2023; 80:153. [PMID: 37198350 PMCID: PMC10191411 DOI: 10.1007/s00018-023-04808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Accumulating evidence has consolidated the interaction between viral infection and host alternative splicing. Serine-arginine (SR) proteins are a class of highly conserved splicing factors critical for the spliceosome maturation, alternative splicing and RNA metabolism. Serine-arginine protein kinases (SRPKs) are important kinases that specifically phosphorylate SR proteins to regulate their distribution and activities in the central pre-mRNA splicing and other cellular processes. In addition to the predominant SR proteins, other cytoplasmic proteins containing a serine-arginine repeat domain, including viral proteins, have been identified as substrates of SRPKs. Viral infection triggers a myriad of cellular events in the host and it is therefore not surprising that viruses explore SRPKs-mediated phosphorylation as an important regulatory node in virus-host interactions. In this review, we briefly summarize the regulation and biological function of SRPKs, highlighting their involvement in the infection process of several viruses, such as viral replication, transcription and capsid assembly. In addition, we review the structure-function relationships of currently available inhibitors of SRPKs and discuss their putative use as antivirals against well-characterized viruses or newly emerging viruses. We also highlight the viral proteins and cellular substrates targeted by SRPKs as potential antiviral therapeutic candidates.
Collapse
Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518055, China.
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| |
Collapse
|
5
|
Schröder M, Leiendecker M, Grädler U, Braun J, Blum A, Wanior M, Berger BT, Krämer A, Müller S, Esdar C, Knapp S, Heinrich T. MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core. J Med Chem 2023; 66:837-854. [PMID: 36516476 DOI: 10.1021/acs.jmedchem.2c01705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The highly conserved catalytic sites in protein kinases make it difficult to identify ATP competitive inhibitors with kinome-wide selectivity. Serendipitously, during a dedicated fragment campaign for the focal adhesion kinase (FAK), a scaffold that had lost its initial FAK affinity showed remarkable potency and selectivity for serine-arginine-protein kinases 1-3 (SRPK1-3). Non-conserved interactions with the uniquely structured hinge region of the SRPK family were the key drivers of the exclusive selectivity of the discovered fragment hit. Structure-guided medicinal chemistry efforts led to the SRPK inhibitor MSC-1186, which fulfills all hallmarks of a reversible chemical probe, including nanomolar cellular potency and excellent kinome-wide selectivity. The combination of MSC-1186 with CDC2-like kinase (CLK) inhibitors showed additive attenuation of SR-protein phosphorylation compared to the single agents. MSC-1186 and negative control (MSC-5360) are chemical probes available via the Structural Genomics Consortium chemical probe program (https://www.sgc-ffm.uni-frankfurt.de/).
Collapse
Affiliation(s)
- Martin Schröder
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | | | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Juliane Braun
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Andreas Blum
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Marek Wanior
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Christina Esdar
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Stefan Knapp
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| |
Collapse
|
6
|
Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Van Nest SJ, Koundouros N, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews DA, tenOever BR, Cantley LC, Blenis J, Heaton NS. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Sci Signal 2022; 15:eabm0808. [PMID: 36282911 PMCID: PMC9830954 DOI: 10.1126/scisignal.abm0808] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.
Collapse
Affiliation(s)
- Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA.,Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine/Memorial Sloan Kettering Cancer Center/The Rockefeller University, New York, NY 10021, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.,Corresponding author. (N.S.H.); (J.B.); (L.C.C.); (B.R.t.); (B.E.H.)
| | | | - Jared L. Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tristan X. Jordan
- New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Benjamin M. Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY 10065, USA
| | - Katarina M. Liberatore
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Danielle K. Bulaon
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Samantha J. Van Nest
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nikos Koundouros
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Edward R. Kastenhuber
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marisa N. Mercadante
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kripa Shobana-Ganesh
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY 10065, USA
| | - Long He
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Robert E. Schwartz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Harel Weinstein
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Elena Piskounova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Dermatology, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA 92868, USA
| | - Joseph D. Trimarco
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kaitlyn N. Burke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cait E. Hamele
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ryan R. Chaparian
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alfred T. Harding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M. Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | | | | | - François Aguet
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.,Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Kate Heesom
- Proteomics Facility, University of Bristol, Bristol, BS8 1TD, UK
| | | | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Benjamin R. tenOever
- New York University, Grossman School of Medicine, New York, NY 10016, USA.,Corresponding author. (N.S.H.); (J.B.); (L.C.C.); (B.R.t.); (B.E.H.)
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.,Corresponding author. (N.S.H.); (J.B.); (L.C.C.); (B.R.t.); (B.E.H.)
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.,Corresponding author. (N.S.H.); (J.B.); (L.C.C.); (B.R.t.); (B.E.H.)
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Duke University School of Medicine Durham, NC 27710, USA.,Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Corresponding author. (N.S.H.); (J.B.); (L.C.C.); (B.R.t.); (B.E.H.)
| |
Collapse
|
7
|
Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
Collapse
Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
8
|
Naro C, Bielli P, Sette C. Oncogenic dysregulation of pre-mRNA processing by protein kinases: challenges and therapeutic opportunities. FEBS J 2021; 288:6250-6272. [PMID: 34092037 PMCID: PMC8596628 DOI: 10.1111/febs.16057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/13/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing and polyadenylation represent two major steps in pre-mRNA-processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes contributes to oncogenic programmes involved in the onset, progression and evolution of human cancers, which often result in the acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA-processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA-processing mechanisms is played by three main families of protein kinases: serine arginine protein kinase (SRPK), CDC-like kinase (CLK) and cyclin-dependent kinase (CDK). These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells, and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.
Collapse
Affiliation(s)
- Chiara Naro
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Pamela Bielli
- Department of Biomedicine and PreventionUniversity of Rome Tor VergataItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| | - Claudio Sette
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| |
Collapse
|
9
|
Pastor F, Shkreta L, Chabot B, Durantel D, Salvetti A. Interplay Between CMGC Kinases Targeting SR Proteins and Viral Replication: Splicing and Beyond. Front Microbiol 2021; 12:658721. [PMID: 33854493 PMCID: PMC8040976 DOI: 10.3389/fmicb.2021.658721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/27/2022] Open
Abstract
Protein phosphorylation constitutes a major post-translational modification that critically regulates the half-life, intra-cellular distribution, and activity of proteins. Among the large number of kinases that compose the human kinome tree, those targeting RNA-binding proteins, in particular serine/arginine-rich (SR) proteins, play a major role in the regulation of gene expression by controlling constitutive and alternative splicing. In humans, these kinases belong to the CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group and several studies indicate that they also control viral replication via direct or indirect mechanisms. The aim of this review is to describe known and emerging activities of CMGC kinases that share the common property to phosphorylate SR proteins, as well as their interplay with different families of viruses, in order to advance toward a comprehensive knowledge of their pro- or anti-viral phenotype and better assess possible translational opportunities.
Collapse
Affiliation(s)
- Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David Durantel
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| |
Collapse
|
10
|
Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews D, tenOever BR, Cantley LC, Blenis J, Heaton NS. The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32817937 DOI: 10.1101/2020.08.14.251207] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3a/b and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.
Collapse
|
11
|
Wang G, Sheng W, Tang J, Li X, Zhou J, Dong M. Cooperation of SRPK2, Numb and p53 in the malignant biology and chemosensitivity of colorectal cancer. Biosci Rep 2020; 40:BSR20191488. [PMID: 31898732 PMCID: PMC6970084 DOI: 10.1042/bsr20191488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 12/29/2019] [Accepted: 12/31/2019] [Indexed: 01/24/2023] Open
Abstract
Serine-arginine protein kinase 2 (SRPK2) is aberrantly expressed in human malignancies including colorectal cancer (CRC). However, little is known about the molecular mechanisms, and the role of SRPK2 in chemosensitivity remains unexplored in CRC. We recently showed that SRPK2 promotes pancreatic cancer progression by down-regulating Numb and p53. Therefore, we investigated the cooperation between SRPK2, Numb and p53 in the cell migration, invasion and chemosensitivity of CRC in vitro. Here, we showed that SRPK2 expression was higher in CRC tumors than in nontumor tissues. SRPK2 expression was positively associated with clinicopathological characteristics of CRC patients, including tumor differentiation, T stage, N stage and UICC stage. Additionally, SRPK2 had no association with mutant p53 (mtp53) in SW480 and SW620 cells, but negatively regulated Numb and wild-type p53 (wtp53) in response to 5-fluorouracil or cisplatin treatment in HCT116 cells. Moreover, SRPK2, Numb and p53 coimmunoprecipitated into a triple complex with or without the treatment of 5-fluorouracil in HCT116 cells, and p53 knockdown reversed the up-regulation of wtp53 induced by SRPK2 silencing with chemical agent treatment. Furthermore, overexpression of SRPK2 increased cell migration and invasion and decreased chemosensitivity to 5-fluorouracil or cisplatin in HCT116 cells. Conversely, SRPK2 silencing decreased cell migration and invasion and increased chemosensitivity to 5-fluorouracil or cisplatin, yet these effects could be reversed by p53 knockdown under chemical agent treatment. These results thus reveal a novel role of SRPK2-Numb-p53 signaling in the progression of CRC and demonstrate that SRPK2 is a potential therapeutic target for CRC clinical therapy.
Collapse
Affiliation(s)
- Guosen Wang
- Department of General Surgery, The First Affliated Hospital, Nanchang University, Nanchang 330006, Jiangxi, China
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| | - Weiwei Sheng
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| | - Jingtong Tang
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| | - Xin Li
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| | - Jianping Zhou
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| | - Ming Dong
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang 110001, Liaoning, China
| |
Collapse
|
12
|
Li X, Yang S, Zhang M, Xie S, Xie Z. Downregulation of SRPK2 promotes cell cycle arrest though E2F1 in non-small cell lung cancer. Eur J Histochem 2019; 63. [PMID: 31833327 PMCID: PMC6945924 DOI: 10.4081/ejh.2019.3067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
Serine-arginine protein kinase (SRPK) belongs to a class of cell cycle regulating kinases that can phosphorylate proteins containing serine/arginine-Rich (SR) regions. SR proteins are a family of RNA binding phosphoproteins that control both constitutive and alternative pre-mRNA splicing events. However, little is known about their role in non-small cell lung cancer (NSCLC). In the present study, we found that serine-arginine protein kinase 2 (SRPK2) expression was upregulated in NSCLC tissues compared with adjacent normal tissues. Kaplan-Meier curve analyses showed that the overall survival time of NSCLC patients with high SRPK2 expression was shorter than those with low SRPK2 expression. Overexpression of SRPK2 promoted NSCLC cell proliferation and cell cycle arrest, while knockdown of SRPK2 inhibited proliferation and promoted cell cycle arrest in NSCLC cell lines. SRPK2 promoted the transcriptional regulation of E2F1 on downstream cell cycle related genes through phosphorylation of SC35. Xenograft model showed that SRPK2 promoted tumor growth in vivo. SRPK2 phosphorylated SC35 and phosphorylated SC35 activated E2F1 transcription of cyclin-related proteins, thereby promoting the cycle progression of NSCLC. Our findings demonstrated that SRPK2 may be a potential therapeutic target for NSCLC clinical therapy, which plays an important role in the progression of NSCLC.
Collapse
Affiliation(s)
- Xin Li
- Department of Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou.
| | | | | | | | | |
Collapse
|
13
|
Serine-Arginine Protein Kinase SRPK2 Modulates the Assembly of the Active Zone Scaffolding Protein CAST1/ERC2. Cells 2019; 8:cells8111333. [PMID: 31671734 PMCID: PMC6912806 DOI: 10.3390/cells8111333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 01/10/2023] Open
Abstract
Neurons release neurotransmitters at a specialized region of the presynaptic membrane, the active zone (AZ), where a complex meshwork of proteins organizes the release apparatus. The formation of this proteinaceous cytomatrix at the AZ (CAZ) depends on precise homo- and hetero-oligomerizations of distinct CAZ proteins. The CAZ protein CAST1/ERC2 contains four coiled-coil (CC) domains that interact with other CAZ proteins, but also promote self-assembly, which is an essential step for its integration during AZ formation. The self-assembly and synaptic recruitment of the Drosophila protein Bruchpilot (BRP), a partial homolog of CAST1/ERC2, is modulated by the serine-arginine protein kinase (SRPK79D). Here, we demonstrate that overexpression of the vertebrate SRPK2 regulates the self-assembly of CAST1/ERC2 in HEK293T, SH-SY5Y and HT-22 cells and the CC1 and CC4 domains are involved in this process. Moreover, the isoform SRPK2 forms a complex with CAST1/ERC2 when co-expressed in HEK293T and SH-SY5Y cells. More importantly, SRPK2 is present in brain synaptic fractions and synapses, suggesting that this protein kinase might control the level of self-aggregation of CAST1/ERC2 in synapses, and thereby modulate presynaptic assembly.
Collapse
|
14
|
Wang G, Sheng W, Shi X, Li X, Zhou J, Dong M. Serine/arginine protein-specific kinase 2 promotes the development and progression of pancreatic cancer by downregulating Numb and p53. FEBS J 2019; 286:1668-1682. [PMID: 30724469 DOI: 10.1111/febs.14778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/16/2018] [Accepted: 02/04/2019] [Indexed: 01/18/2023]
Abstract
Serine/arginine protein-specific kinase 2 (SRPK2) plays a vital role in the progression of a range of different malignancies, including pancreatic cancer. However, the mechanisms are poorly understood. Previous studies have shown that in hepatocellular carcinoma, SRPK2 knockdown leads to the upregulation of the cell fate determining protein Numb, and in pancreatic cancer cells, Numb knockdown prevents ubiquitin-mediated degradation of p53. In this study, we investigated the relationship between SRPK2, Numb and p53 in the development of pancreatic cancer with or without chemical agent treatment in vitro. SRPK2 expression was upregulated in pancreatic cancer tissues and associated with decreased overall survival in pancreatic cancer patients, indicating that expression of this protein can be used as a marker of unfavourable prognosis. Expression of SRPK2 was positively associated with tumour T stage and Union for International Cancer Control (UICC) stage, and negatively associated with Numb expression in serial tissue sections. In pancreatic cancer cells, SRPK2 downregulation or overexpression led to modulation of Numb and wild-type p53 protein expression in response to oxaliplatin treatment. Furthermore, these three endogenous proteins could be coimmunoprecipitated as a triple complex. Numb or p53 knockdown reversed the upregulation of p53 that was induced by silencing SRPK2. SRPK2 overexpression promoted cell invasion and migration, and decreased chemosensitivity of cancer cells to gemcitabine or oxaliplatin treatment. Conversely, SRPK2 silencing decreased cell invasion and migration and increased chemosensitivity; these effects were reversed by silencing p53 in oxaliplatin-treated pancreatic cancer cells. Our data suggest that SRPK2 negatively regulates p53 by downregulating Numb under chemical agent treatment. Thus, SRPK2 promotes the development and progression of pancreatic cancer in a p53-dependent manner.
Collapse
Affiliation(s)
- Guosen Wang
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Weiwei Sheng
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Xiaoyang Shi
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Xin Li
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Jianping Zhou
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Ming Dong
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
| |
Collapse
|
15
|
Wang ZH, Liu P, Liu X, Yu SP, Wang JZ, Ye K. Delta-secretase (AEP) mediates tau-splicing imbalance and accelerates cognitive decline in tauopathies. J Exp Med 2018; 215:3038-3056. [PMID: 30373880 PMCID: PMC6279401 DOI: 10.1084/jem.20180539] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 08/16/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023] Open
Abstract
Wang et al. demonstrate that AEP cleaves SRPK2 in tauopathies and plays a functional role in mediating tau-splicing imbalance and accelerating cognitive decline in mouse models of tauopathy. SRPK2 is abnormally activated in tauopathies including Alzheimer’s disease (AD). SRPK2 is known to play an important role in pre–mRNA splicing by phosphorylating SR-splicing factors. Dysregulation of tau exon 10 pre–mRNA splicing causes pathological imbalances in 3R- and 4R-tau, leading to neurodegeneration; however, the role of SRPK2 in these processes remains unclear. Here we show that delta-secretase (also known as asparagine endopeptidase; AEP), which is activated in AD, cleaves SRPK2 and increases its nuclear translocation as well as kinase activity, augmenting exon 10 inclusion. Conversely, AEP-uncleavable SRPK2 N342A mutant increases exon 10 exclusion. Lentiviral expression of truncated SRPK2 increases 4R-tau isoforms and accelerates cognitive decline in htau mice. Uncleavable SRPK2 N342A expression improves synaptic functions and prevents spatial memory deficits in tau intronic mutant FTDP-17 transgenic mice. Hence, AEP mediates tau-splicing imbalance in tauopathies via cleaving SRPK2.
Collapse
Affiliation(s)
- Zhi-Hao Wang
- Department of Pathophysiology, Key Laboratory of Ministry of Education of Neurological Diseases, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Pai Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Xia Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Shan Ping Yu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA
| | - Jian-Zhi Wang
- Department of Pathophysiology, Key Laboratory of Ministry of Education of Neurological Diseases, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China .,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA .,Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
16
|
Czubaty A, Piekiełko-Witkowska A. Protein kinases that phosphorylate splicing factors: Roles in cancer development, progression and possible therapeutic options. Int J Biochem Cell Biol 2017; 91:102-115. [PMID: 28552434 DOI: 10.1016/j.biocel.2017.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/30/2022]
Abstract
Disturbed alternative splicing is a common feature of human tumors. Splicing factors that control alternative splicing are phosphorylated by multiple kinases, including these that specifically add phosphoryl groups to serine-arginine rich proteins (e.g. SR-protein kinases, cdc2-like kinases, topoisomerase 1), and protein kinases that govern key cellular signaling pathways (i.e. AKT). Phosphorylation of splicing factors regulates their subcellular localization and interactions with target transcripts and protein partners, and thus significantly contributes the final result of splicing reactions. In this review we aim to summarize the current knowledge on the role of splicing kinases in cancer. Published studies and recently released data of The Cancer Genome Atlas demonstrate that expressions and activities of splicing kinases are commonly disturbed in cancers. Aberrant functioning of splicing kinases results in changed alternative splicing of tumor suppressors (e.g. p53) and regulators of cell signaling (e.g. MAPKs), apoptosis (e.g. MCL), and angiogenesis (VEGF). Splicing kinases act in complicated regulatory networks in which they mutually affect each other's activity to provide tight control of cellular signaling. Dysregulation of these regulatory networks contributes to oncogenic transformation, uncontrolled proliferation, enhanced migration and invasion. Furthermore, the activities of splicing kinases significantly contribute to cellular responses to genotoxic stress. In conclusion, published data provide strong evidence that splicing kinases emerge as important regulators of key processes governing malignant transformation, progression, and response to therapeutic treatments, suggesting their potential as clinically relevant targets.
Collapse
Affiliation(s)
- Alicja Czubaty
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
| |
Collapse
|
17
|
Wang J, Wu HF, Shen W, Xu DY, Ruan TY, Tao GQ, Lu PH. SRPK2 promotes the growth and migration of the colon cancer cells. Gene 2016; 586:41-7. [PMID: 27041240 DOI: 10.1016/j.gene.2016.03.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/09/2016] [Accepted: 03/18/2016] [Indexed: 10/21/2022]
Abstract
Colon cancer is one of the major causes of cancer-related death in the world. Understanding the molecular mechanism underlying this malignancy will facilitate the diagnosis and treatment. Serine-arginine protein kinase 2 (SRPK2) has been reported to be upregulated in several cancer types. However, its expression and functions in colon cancer remains unknown. In this study, it was found that the expression of SRPK2 was up-regulated in the clinical colon cancer samples. Overexpression of SRPK2 promoted the growth and migration of colon cancer cells, while knocking down the expression of SRPK2 inhibited the growth, migration and tumorigenecity of colon cancer cells. Molecular mechanism studies revealed that SRPK2 activated ERK signaling in colon cancer cells. Taken together, our study demonstrated the tumor promoting roles of SRPK2 in colon cancer cells and SRPK2 might be a promising therapeutic target for colon cancer.
Collapse
Affiliation(s)
- Jian Wang
- Department of Gastrointestinal Surgery, Huai'an Hospital Affiliated of Xuzhou Medical College and Huai'an Second People's Hospital, No. 62, Huai-hai South Road, Hua'an, 223200, Jiangsu, China
| | - Hai-Feng Wu
- Department of Critical Care Medicine, Affiliated Yixing People's Hospital, Jiangsu University, No. 75, Tongzhenguan Road, Yixing, 214200, Jiangsu, China
| | - Wei Shen
- Department of General Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, Jiangsu Province, China
| | - Dong-Yan Xu
- Department of Gastroenterology, Huai'an Hospital Affiliated of Xuzhou Medical College and Huai'an Second People's Hospital, No. 62, Huai-hai South Road, Huai'an, 223200, Jiangsu, China
| | - Ting-Yan Ruan
- Department of Medical Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu Province, China
| | - Guo-Qing Tao
- Department of General Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, Jiangsu Province, China
| | - Pei-Hua Lu
- Department of Medical Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu Province, China.
| |
Collapse
|
18
|
Nancy MM, Nora RM, Rebeca MC. Peptidic tools applied to redirect alternative splicing events. Peptides 2015; 67:1-11. [PMID: 25748022 DOI: 10.1016/j.peptides.2015.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 01/25/2023]
Abstract
Peptides are versatile and attractive biomolecules that can be applied to modulate genetic mechanisms like alternative splicing. In this process, a single transcript yields different mature RNAs leading to the production of protein isoforms with diverse or even antagonistic functions. During splicing events, errors can be caused either by mutations present in the genome or by defects or imbalances in regulatory protein factors. In any case, defects in alternative splicing have been related to several genetic diseases including muscular dystrophy, Alzheimer's disease and cancer from almost every origin. One of the most effective approaches to redirect alternative splicing events has been to attach cell-penetrating peptides to oligonucleotides that can modulate a single splicing event and restore correct gene expression. Here, we summarize how natural existing and bioengineered peptides have been applied over the last few years to regulate alternative splicing and genetic expression. Under different genetic and cellular backgrounds, peptides have been shown to function as potent vehicles for splice correction, and their therapeutic benefits have reached clinical trials and patenting stages, emphasizing the use of regulatory peptides as an exciting therapeutic tool for the treatment of different genetic diseases.
Collapse
Affiliation(s)
- Martínez-Montiel Nancy
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Rosas-Murrieta Nora
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Martínez-Contreras Rebeca
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico.
| |
Collapse
|
19
|
Shilo A, Siegfried Z, Karni R. The role of splicing factors in deregulation of alternative splicing during oncogenesis and tumor progression. Mol Cell Oncol 2015; 2:e970955. [PMID: 27308389 PMCID: PMC4905244 DOI: 10.4161/23723548.2014.970955] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 04/18/2023]
Abstract
In past decades, cancer research has focused on genetic alterations that are detected in malignant tissues and contribute to the initiation and progression of cancer. These changes include mutations, copy number variations, and translocations. However, it is becoming increasingly clear that epigenetic changes, including alternative splicing, play a major role in cancer development and progression. There are relatively few studies on the contribution of alternative splicing and the splicing factors that regulate this process to cancer development and progression. Recently, multiple studies have revealed altered splicing patterns in cancers and several splicing factors were found to contribute to tumor development. Studies using high-throughput genomic analysis have identified mutations in components of the core splicing machinery and in splicing factors in several cancers. In this review, we will highlight new findings on the role of alternative splicing and its regulators in cancer initiation and progression, in addition to novel approaches to correct oncogenic splicing.
Collapse
Affiliation(s)
- Asaf Shilo
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
- Correspondence to: Rotem Karni;
| |
Collapse
|
20
|
Primary structural features of SR-like protein acinusS govern the phosphorylation mechanism by SRPK2. Biochem J 2014; 459:181-91. [PMID: 24444330 DOI: 10.1042/bj20131091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SRPKs (serine/arginine protein kinases) are highly specific kinases that recognize and phosphorylate RS (Arg-Ser) dipeptide repeats. It has been shown previously that SRPK1 phosphorylates the RS domain of SRSF1 (serine/arginine splicing factor 1) at multiple sites using a directional and processive mechanism. Such ability to processively phosphorylate substrates is proposed to be an inherent characteristic of SRPKs. SRPK2 is highly related to SRPK1 in sequence and in vitro properties, yet it has been shown to have distinct substrate specificity and physiological function in vivo. To study the molecular basis for substrate specificity of SRPK2, we investigated the roles of the non-kinase regions and a conserved docking groove of SRPK2 in the recognition and phosphorylation of different substrates: SRSF1 and acinusS. Our results reveal that a conserved electronegative docking groove in SRPK2, but not its non-kinase regions, is responsible for substrate binding regardless of their identities. Although SRPK2 phosphorylates SRSF1 in a processive manner as predicted, an electronegative region on acinusS restricts SRPK2 phosphorylation to a single specific site despite the presence of multiple RS dipeptides. These results suggest that primary structural elements on the substrates serve as key regulatory roles in determining the phosphorylation mechanism of SRPK2.
Collapse
|
21
|
Identification of a novel function of CX-4945 as a splicing regulator. PLoS One 2014; 9:e94978. [PMID: 24743259 PMCID: PMC3990583 DOI: 10.1371/journal.pone.0094978] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/21/2014] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks) in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR) proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3-90 nM) was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.
Collapse
|
22
|
Xiang S, Gapsys V, Kim HY, Bessonov S, Hsiao HH, Möhlmann S, Klaukien V, Ficner R, Becker S, Urlaub H, Lührmann R, de Groot B, Zweckstetter M. Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 2013; 21:2162-74. [PMID: 24183573 DOI: 10.1016/j.str.2013.09.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 11/25/2022]
Abstract
Serine/arginine-rich (SR) proteins are important players in RNA metabolism and are extensively phosphorylated at serine residues in RS repeats. Here, we show that phosphorylation switches the RS domain of the serine/arginine-rich splicing factor 1 from a fully disordered state to a partially rigidified arch-like structure. Nuclear magnetic resonance spectroscopy in combination with molecular dynamics simulations revealed that the conformational switch is restricted to RS repeats, critically depends on the phosphate charge state and strongly decreases the conformational entropy of RS domains. The dynamic switch also occurs in the 100 kDa SR-related protein hPrp28, for which phosphorylation at the RS repeat is required for spliceosome assembly. Thus, a phosphorylation-induced dynamic switch is common to the class of serine/arginine-rich proteins and provides a molecular basis for the functional redundancy of serine/arginine-rich proteins and the profound influence of RS domain phosphorylation on protein-protein and protein-RNA interactions.
Collapse
Affiliation(s)
- Shengqi Xiang
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Paraquat modulates alternative pre-mRNA splicing by modifying the intracellular distribution of SRPK2. PLoS One 2013; 8:e61980. [PMID: 23613995 PMCID: PMC3628584 DOI: 10.1371/journal.pone.0061980] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/16/2013] [Indexed: 11/24/2022] Open
Abstract
Paraquat (PQ) is a neurotoxic herbicide that induces superoxide formation. Although it is known that its toxic properties are linked to ROS production, the cellular response to PQ is still poorly understood. We reported previously that treatment with PQ induced genome-wide changes in pre-mRNA splicing. Here, we investigated the molecular mechanism underlying PQ-induced pre-mRNA splicing alterations. We show that PQ treatment leads to the phosphorylation and nuclear accumulation of SRPK2, a member of the family of serine/arginine (SR) protein-specific kinases. Concomitantly, we observed increased phosphorylation of SR proteins. Site-specific mutagenesis identified a single serine residue that is necessary and sufficient for nuclear localization of SRPK2. Transfection of a phosphomimetic mutant modified splice site selection of the E1A minigene splicing reporter similar to PQ-treatment. Finally, we found that PQ induces DNA damage and vice versa that genotoxic treatments are also able to promote SRPK2 phosphorylation and nuclear localization. Consistent with these observations, treatment with PQ, cisplatin or γ-radiation promote changes in the splicing pattern of genes involved in DNA repair, cell cycle control, and apoptosis. Altogether, our findings reveal a novel regulatory mechanism that connects PQ to the DNA damage response and to the modulation of alternative splicing via SRPK2 phosphorylation.
Collapse
|
24
|
Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma 2013; 122:191-207. [PMID: 23525660 DOI: 10.1007/s00412-013-0407-z] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022]
Abstract
Genomic sequencing reveals similar but limited numbers of protein-coding genes in different genomes, which begs the question of how organismal diversities are generated. Alternative pre-mRNA splicing, a widespread phenomenon in higher eukaryotic genomes, is thought to provide a mechanism to increase the complexity of the proteome and introduce additional layers for regulating gene expression in different cell types and during development. Among a large number of factors implicated in the splicing regulation are the SR protein family of splicing factors and SR protein-specific kinases. Here, we summarize the rules for SR proteins to function as splicing regulators, which depend on where they bind in exons versus intronic regions, on alternative exons versus flanking competing exons, and on cooperative as well as competitive binding between different SR protein family members on many of those locations. We review the importance of cycles of SR protein phosphorylation/dephosphorylation in the splicing reaction with emphasis on the recent molecular insight into the role of SR protein phosphorylation in early steps of spliceosome assembly. Finally, we highlight recent discoveries of SR protein-specific kinases in transducing growth signals to regulate alternative splicing in the nucleus and the connection of both SR proteins and SR protein kinases to human diseases, particularly cancer.
Collapse
|
25
|
SRPK1 inhibition in vivo: modulation of VEGF splicing and potential treatment for multiple diseases. Biochem Soc Trans 2012; 40:831-5. [PMID: 22817743 DOI: 10.1042/bst20120051] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SRPK1 (serine-arginine protein kinase 1) is a protein kinase that specifically phosphorylates proteins containing serine-arginine-rich domains. Its substrates include a family of SR proteins that are key regulators of mRNA AS (alternative splicing). VEGF (vascular endothelial growth factor), a principal angiogenesis factor contains an alternative 3' splice site in the terminal exon that defines a family of isoforms with a different amino acid sequence at the C-terminal end, resulting in anti-angiogenic activity in the context of VEGF165-driven neovascularization. It has been shown recently in our laboratories that SRPK1 regulates the choice of this splice site through phosphorylation of the splicing factor SRSF1 (serine/arginine-rich splicing factor 1). The present review summarizes progress that has been made to understand how SRPK1 inhibition may be used to manipulate the balance of pro- and anti-angiogenic VEGF isoforms in animal models in vivo and therefore control abnormal angiogenesis and other pathophysiological processes in multiple disease states.
Collapse
|
26
|
Ogawa Y, Hagiwara M. Challenges to congenital genetic disorders with “RNA-targeting” chemical compounds. Pharmacol Ther 2012; 134:298-305. [DOI: 10.1016/j.pharmthera.2012.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 11/16/2022]
|
27
|
Saitoh N, Sakamoto C, Hagiwara M, Agredano-Moreno LT, Jiménez-García LF, Nakao M. The distribution of phosphorylated SR proteins and alternative splicing are regulated by RANBP2. Mol Biol Cell 2012; 23:1115-28. [PMID: 22262462 PMCID: PMC3302738 DOI: 10.1091/mbc.e11-09-0783] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
SR splicing factors are distributed in the speckled pattern in the nucleus. Alternative pre-mRNA splicing is regulated through nuclear distribution of phosphorylated SR splicing factors, which is specifically regulated by the RANBP2 system in mammalian cell lines, as well as in mouse tissues. The mammalian cell nucleus is functionally compartmentalized into various substructures. Nuclear speckles, also known as interchromatin granule clusters, are enriched with SR splicing factors and are implicated in gene expression. Here we report that nuclear speckle formation is developmentally regulated; in certain cases phosphorylated SR proteins are absent from the nucleus and are instead localized at granular structures in the cytoplasm. To investigate how the nuclear architecture is formed, we performed a phenotypic screen of HeLa cells treated with a series of small interfering RNAs. Depletion of Ran-binding protein 2 induced cytoplasmic intermediates of nuclear speckles in G1 phase. Detailed analyses of these structures suggested that a late step in the sequential nuclear entry of mitotic interchromatin granule components was disrupted and that phosphorylated SR proteins were sequestered in an SR protein kinase–dependent manner. As a result, the cells had an imbalanced subcellular distribution of phosphorylated and hypophosphorylated SR proteins, which affected alternative splicing patterns. This study demonstrates that the speckled distribution of phosphorylated pre-mRNA processing factors is regulated by the nucleocytoplasmic transport system in mammalian cells and that it is important for alternative splicing.
Collapse
Affiliation(s)
- Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan.
| | | | | | | | | | | |
Collapse
|
28
|
Biselli-Chicote PM, Oliveira ARCP, Pavarino EC, Goloni-Bertollo EM. VEGF gene alternative splicing: pro- and anti-angiogenic isoforms in cancer. J Cancer Res Clin Oncol 2011; 138:363-70. [PMID: 22045472 DOI: 10.1007/s00432-011-1073-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 09/21/2011] [Indexed: 12/28/2022]
Abstract
Tumor growth and progression depend on angiogenesis, a process of new blood vessels formation from a preexisting vascular endothelium. Tumors promote angiogenesis by secreting or activating angiogenic factors that stimulate endothelial proliferation and migration and capillary morphogenesis. The newly formed blood vessels provide nutrients and oxygen to the tumor, increasing its growth. Thus, angiogenesis plays a key role in cancer progression and development of metastases. An important growth factor that promotes angiogenesis and participates in a variety of physiological and pathological processes is the vascular endothelial growth factor (VEGF-A or VEGF). Overexpression of VEGF results in increased angiogenesis in normal and pathological conditions. The existence of an alternative site of splicing at the 3' untranslated region of the mRNA results in the expression of isoforms with a C-terminal region which are downregulated in tumors and may have differential inhibitory effects. This suggests that control of splicing can be an important regulatory mechanism of angiogenesis in cancer.
Collapse
Affiliation(s)
- P M Biselli-Chicote
- Genetics and Molecular Biology Research Unit - UPGEM, Medical School of Sao Jose do Rio Preto - FAMERP, Av. Brigadeiro Faria Lima, 5416, Bloco U6, Sao Jose do Rio Preto, SP 15090-000, Brazil
| | | | | | | |
Collapse
|
29
|
Ninomiya K, Kataoka N, Hagiwara M. Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor. ACTA ACUST UNITED AC 2011; 195:27-40. [PMID: 21949414 PMCID: PMC3187705 DOI: 10.1083/jcb.201107093] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A nuclear pool of partially spliced Clk1/4 pre-mRNAs matures in response to stress and induces SR protein phosphorylation and activation. It has been assumed that premessenger ribonucleic acids (RNAs; pre-mRNAs) are spliced cotranscriptionally in the process of gene expression. However, in this paper, we report that splicing of Clk1/4 mRNAs is suspended in tissues and cultured cells and that intermediate forms retaining specific introns are abundantly pooled in the nucleus. Administration of the Cdc2-like kinase–specific inhibitor TG003 increased the level of Clk1/4 mature mRNAs by promoting splicing of the intron-retaining RNAs. Under stress conditions, splicing of general pre-mRNAs was inhibited by dephosphorylation of SR splicing factors, but exposure to stresses, such as heat shock and osmotic stress, promoted the maturation of Clk1/4 mRNAs. Clk1/4 proteins translated after heat shock catalyzed rephosphorylation of SR proteins, especially SRSF4 and SRSF10. These findings suggest that Clk1/4 expression induced by stress-responsive splicing serves to maintain the phosphorylation state of SR proteins.
Collapse
Affiliation(s)
- Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | |
Collapse
|
30
|
Giannakouros T, Nikolakaki E, Mylonis I, Georgatsou E. Serine-arginine protein kinases: a small protein kinase family with a large cellular presence. FEBS J 2011; 278:570-86. [DOI: 10.1111/j.1742-4658.2010.07987.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
31
|
Inhibition of hepatitis C virus replication by a specific inhibitor of serine-arginine-rich protein kinase. Antimicrob Agents Chemother 2010; 54:3179-86. [PMID: 20498328 DOI: 10.1128/aac.00113-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Splicing of messenger RNAs is regulated by site-specific binding of members of the serine-arginine-rich (SR) protein family, and SR protein kinases (SRPK) 1 and 2 regulate overall activity of the SR proteins by phosphorylation of their RS domains. We have reported that specifically designed SRPK inhibitors suppressed effectively several DNA and RNA viruses in vitro and in vivo. Here, we show that an SRPK inhibitor, SRPIN340, suppressed in a dose-dependent fashion expression of a hepatitis C virus (HCV) subgenomic replicon and replication of the HCV-JFH1 clone in vitro. The inhibitory effects were not associated with antiproliferative or nonspecific cytotoxic effects on the host cells. Overexpression of SRPK1 or SRPK2 resulted in augmentation of HCV replication, while small interfering RNA (siRNA) knockdown of the SRPKs suppressed HCV replication significantly. Immunocytochemistry showed that SRPKs and the HCV core and NS5A proteins colocalized to some extent in the perinuclear area. Our results demonstrate that SRPKs are host factors essential for HCV replication and that functional inhibitors of these kinases may constitute a new class of antiviral agents against HCV infection.
Collapse
|
32
|
Xu Y, Yu W, Xiong Y, Xie H, Ren Z, Xu D, Lei M, Zuo B, Feng X. Molecular characterization and expression patterns of serine/arginine-rich specific kinase 3 (SPRK3) in porcine skeletal muscle. Mol Biol Rep 2010; 38:2903-9. [PMID: 20127522 DOI: 10.1007/s11033-010-9952-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/15/2010] [Indexed: 11/26/2022]
Abstract
SRPK3 is a protein kinase belonging to serine/arginine protein kinases (SRPK) family, which phosphorylates serine/arginine repeat-containing proteins, and is controlled by a muscle-specific enhancer directly regulated by MEF2. In this study, a full-length cDNA of the porcine SRPK3 gene encoding a 566 amino acid protein was isolated. It contains 14 exons over approximately 4.3 kb. The deduced amino acid sequence of porcine SRPK3 contains a bipartite kinase domain, and shows high similarities to their corresponding human and cattle homologues. Tissue distribution analysis indicated that porcine SRPK3 mRNAs are highly expressed in heart and skeletal muscle especially in uterus and parorchis, but at low level in brain, stomach, small intestine, and ovary. Expression pattern of SRPK3 was similar in Large White and Chinese Meishan breeds. Both the two breeds had the highest expression levels at fetal 65 days (P < 0.01), and decreased while the age increased until 60 days old, then increased at 120 days (P < 0.01) and decreased at 180 days (P < 0.05). However, at fetal 65 days, the mRNA abundance of SRPK3 in Large White was 12.5-fold higher than in Meishan pigs (P < 0.01), whereas at 180 days, the abundance in Meishan was 3.4-fold higher than in Large White pigs (P < 0.01). These results suggest that the SRPK3 gene might be an important gene of skeletal muscle development and also provides basic molecular information useful for further studies on its roles in porcine skeletal muscle.
Collapse
Affiliation(s)
- Yongjie Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 1 Shizishan Street, 430070 Wuhan, Hubei, People's Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Rapid-response splicing reporter screens identify differential regulators of constitutive and alternative splicing. Mol Cell Biol 2010; 30:1718-28. [PMID: 20123975 DOI: 10.1128/mcb.01301-09] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bioactive compounds have been invaluable for dissecting the mechanisms, regulation, and functions of cellular processes. However, very few such reagents have been described for pre-mRNA splicing. To facilitate their systematic discovery, we developed a high-throughput cell-based assay that measures pre-mRNA splicing by utilizing a quantitative reporter system with advantageous features. The reporter, consisting of a destabilized, intron-containing luciferase expressed from a short-lived mRNA, allows rapid screens (<4 h), thereby obviating the potential toxicity of splicing inhibitors. We describe three inhibitors (out of >23,000 screened), all pharmacologically active: clotrimazole, flunarizine, and chlorhexidine. Interestingly, none was a general splicing inhibitor. Rather, each caused distinct splicing changes of numerous genes. We further discovered the target of action of chlorhexidine and show that it is a selective inhibitor of specific Cdc2-like kinases (Clks) that phosphorylate serine-arginine-rich (SR) protein splicing factors. Our findings reveal unexpected activities of clinically used drugs in splicing and uncover differential regulation of constitutively spliced introns.
Collapse
|
34
|
Schneider M, Hsiao HH, Will CL, Giet R, Urlaub H, Lührmann R. Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation. Nat Struct Mol Biol 2010; 17:216-21. [PMID: 20118938 DOI: 10.1038/nsmb.1718] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 10/09/2009] [Indexed: 11/09/2022]
Abstract
Reversible protein phosphorylation has an essential role during pre-mRNA splicing. Here we identify two previously unidentified phosphoproteins in the human spliceosomal B complex, namely the pre-mRNA processing factors PRP6 and PRP31, both components of the U4/U6-U5 tri-small nuclear ribonucleoprotein (snRNP). We provide evidence that PRP6 and PRP31 are directly phosphorylated by human PRP4 kinase (PRP4K) concomitant with their incorporation into B complexes. Immunodepletion and complementation studies with HeLa splicing extracts revealed that active human PRP4K is required for the phosphorylation of PRP6 and PRP31 and for the assembly of stable, functional B complexes. Thus, the phosphorylation of PRP6 and PRP31 is likely to have a key role during spliceosome assembly. Our data provide new insights into the molecular mechanism by which PRP4K contributes to splicing. They further indicate that numerous phosphorylation events contribute to spliceosome assembly and, thus, that splicing can potentially be modulated at multiple regulatory checkpoints.
Collapse
Affiliation(s)
- Marc Schneider
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, Göttingen, Germany
| | | | | | | | | | | |
Collapse
|
35
|
Nieratschker V, Schubert A, Jauch M, Bock N, Bucher D, Dippacher S, Krohne G, Asan E, Buchner S, Buchner E. Bruchpilot in ribbon-like axonal agglomerates, behavioral defects, and early death in SRPK79D kinase mutants of Drosophila. PLoS Genet 2009; 5:e1000700. [PMID: 19851455 PMCID: PMC2759580 DOI: 10.1371/journal.pgen.1000700] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 09/23/2009] [Indexed: 12/18/2022] Open
Abstract
Defining the molecular structure and function of synapses is a central theme in brain research. In Drosophila the Bruchpilot (BRP) protein is associated with T-shaped ribbons ("T-bars") at presynaptic active zones (AZs). BRP is required for intact AZ structure and normal evoked neurotransmitter release. By screening for mutations that affect the tissue distribution of Bruchpilot, we have identified a P-transposon insertion in gene CG11489 (location 79D) which shows high homology to mammalian genes for SR protein kinases (SRPKs). SRPKs phosphorylate serine-arginine rich splicing factors (SR proteins). Since proteins expressed from CG11489 cDNAs phosphorylate a peptide from a human SR protein in vitro, we name CG11489 the Drosophila Srpk79D gene. We have characterized Srpk79D transcripts and generated a null mutant. Mutation of the Srpk79D gene causes conspicuous accumulations of BRP in larval and adult nerves. At the ultrastructural level, these correspond to extensive axonal agglomerates of electron-dense ribbons surrounded by clear vesicles. Basic synaptic structure and function at larval neuromuscular junctions appears normal, whereas life expectancy and locomotor behavior of adult mutants are significantly impaired. All phenotypes of the mutant can be largely or completely rescued by panneural expression of SRPK79D isoforms. Isoform-specific antibodies recognize panneurally overexpressed GFP-tagged SRPK79D-PC isoform co-localized with BRP at presynaptic active zones while the tagged -PB isoform is found in spots within neuronal perikarya. SRPK79D concentrations in wild type apparently are too low to be revealed by these antisera. We propose that the Drosophila Srpk79D gene characterized here may be expressed at low levels throughout the nervous system to prevent the assembly of BRP containing agglomerates in axons and maintain intact brain function. The discovery of an SR protein kinase required for normal BRP distribution calls for the identification of its substrate and the detailed analysis of SRPK function for the maintenance of nervous system integrity.
Collapse
Affiliation(s)
- Vanessa Nieratschker
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Alice Schubert
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Mandy Jauch
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Nicole Bock
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Daniel Bucher
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Sonja Dippacher
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Georg Krohne
- Department of Electron Microscopy, Julius-Maximilians-University, Würzburg, Germany
| | - Esther Asan
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Sigrid Buchner
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Erich Buchner
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| |
Collapse
|
36
|
Liu S, Zhou Z, Lin Z, Ouyang Q, Zhang J, Tian S, Xing M. Identification of a nuclear localization motif in the serine/arginine protein kinase PSRPK of physarum polycephalum. BMC BIOCHEMISTRY 2009; 10:22. [PMID: 19703313 PMCID: PMC2754491 DOI: 10.1186/1471-2091-10-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 08/25/2009] [Indexed: 11/13/2022]
Abstract
Background Serine/arginine (SR) protein-specific kinases (SRPKs) are conserved in a wide range of organisms, from humans to yeast. Studies showed that SRPKs can regulate the nuclear import of SR proteins in cytoplasm, and regulate the sub-localization of SR proteins in the nucleus. But no nuclear localization signal (NLS) of SRPKs was found. We isolated an SRPK-like protein PSRPK (GenBank accession No. DQ140379) from Physarum polycephalum previously, and identified a NLS of PSRPK in this study. Results We carried out a thorough molecular dissection of the different domains of the PSRPK protein involved in its nuclear localization. By truncation of PSRPK protein, deletion of and single amino acid substitution in a putative NLS and transfection of mammalian cells, we observed the distribution of PSRPK fluorescent fusion protein in mammalian cells using confocal microscopy and found that the protein was mainly accumulated in the nucleus; this indicated that the motif contained a nuclear localization signal (NLS). Further investigation with truncated PSPRK peptides showed that the NLS (318PKKGDKYDKTD328) was localized in the alkaline Ω-loop of a helix-loop-helix motif (HLHM) of the C-terminal conserved domain. If the 318PKKGDK322 sequence was deleted from the loop or K320 was mutated to T320, the PSRPK fluorescent fusion protein could not enter and accumulate in the nucleus. Conclusion This study demonstrated that the 318PKKGDKYDKTD328 peptides localized in the C-terminal conserved domain of PSRPK with the Ω-loop structure could play a crucial role in the NLS function of PSRPK.
Collapse
Affiliation(s)
- Shide Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering and College of Life Science, Shenzhen University, Shenzhen, PR China.
| | | | | | | | | | | | | |
Collapse
|
37
|
Tsianou D, Nikolakaki E, Tzitzira A, Bonanou S, Giannakouros T, Georgatsou E. The enzymatic activity of SR protein kinases 1 and 1a is negatively affected by interaction with scaffold attachment factors B1 and 2. FEBS J 2009; 276:5212-27. [PMID: 19674106 DOI: 10.1111/j.1742-4658.2009.07217.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
SR protein kinases (SRPKs) phosphorylate Ser/Arg dipeptide-containing proteins that play crucial roles in a broad spectrum of basic cellular processes. Phosphorylation by SRPKs constitutes a major way of regulating such cellular mechanisms. In the past, we have shown that SRPK1a interacts with the nuclear matrix protein scaffold attachment factor B1 (SAFB1) via its unique N-terminal domain, which differentiates it from SRPK1. In this study, we show that SAFB1 inhibits the activity of both SRPK1a and SRPK1 in vitro and that its RE-rich region is redundant for the observed inhibition. We demonstrate that kinase activity inhibition is caused by direct binding of SAFB1 to SRPK1a and SRPK1, and we also present evidence for the in vitro binding of SAFB2 to the two kinases, albeit with different affinity. Moreover, we show that both SR protein kinases can form complexes with both scaffold attachment factors B in living cells and that this interaction is capable of inhibiting their activity, depending on the tenacity of the complex formed. Finally, we present data demonstrating that SRPK/SAFB complexes are present in the nucleus of HeLa cells and that the enzymatic activity of the nuclear matrixlocalized SRPK1 is repressed. These results suggest a new role for SAFB proteins as regulators of SRPK activity and underline the importance of the assembly of transient intranuclear complexes in cellular regulation.
Collapse
Affiliation(s)
- Dora Tsianou
- Department of Medicine, University of Thessaly, Mezourlo, 41110 Larissa, Greece
| | | | | | | | | | | |
Collapse
|
38
|
Liu S, Kang K, Zhang J, Ouyang Q, Zhou Z, Tian S, Xing M. A novel Physarum polycephalum SR protein kinase specifically phosphorylates the RS domain of the human SR protein, ASF/SF2. Acta Biochim Biophys Sin (Shanghai) 2009; 41:657-67. [PMID: 19657567 DOI: 10.1093/abbs/gmp054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A 1591-bp cDNA of a serine-rich protein kinase (SRPK)-like protein has been identified in Physarum polycephalum (GenBank accession No. DQ140379). The cDNA contains two repeat sequences at bp 1-153 and bp 395-547. The encoding sequence is 56% homologous to human SRPK1 and is named Physarum SRPK (PSRPK). Consistent with other SRPKs, the consensus motifs of PSRPK are within the two conserved domains (CDs). However, divergent motifs between the N-terminal and CDs are much shorter than the corresponding sequences of other SRPKs. To study the structure and function of this protein, we performed co-expression experiment in Escherichia coli and in vitro phosphorylation assay to investigate the phosphorylation effect of recombinant PSRPK on the human SR protein, ASF/SF2. Western blot analysis showed that PSRPK could phosphorylate ASF/SF2 in E. coli cells. Autoradiographic examination showed that both recombinant PSRPK and a truncated form of PSRPK with a 28-aa deletion at the N-terminus could phosphorylate ASF/SF2 and a truncated form of ASF/SF2 that contains the RS domain. However, these two forms of PSRPK could not phosphorylate a truncated form ASF/SF2 that lacks the RS domain. A truncated form of PSRPK that lacks either of CDs does not have any phosphorylation activity. These results indicated that, like other SRPKs, the phosphorylation site in PSRPK is located within the RS domain of the SR protein and that its phosphorylation activity is closely associated with the two CDs. This study on the structure and function of PSRPK demonstrates that it is a new member of the SRPK family.
Collapse
Affiliation(s)
- Shide Liu
- Shenzhen Key Laboratory of Microbial and Genetic Engineering, College of Life Science Shenzhen University, Shenzhen, China
| | | | | | | | | | | | | |
Collapse
|
39
|
Jang SW, Liu X, Fu H, Rees H, Yepes M, Levey A, Ye K. Interaction of Akt-phosphorylated SRPK2 with 14-3-3 mediates cell cycle and cell death in neurons. J Biol Chem 2009; 284:24512-25. [PMID: 19592491 DOI: 10.1074/jbc.m109.026237] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Terminally differentiated neurons are unable to reenter the cell cycle. Aberrant cell cycle activation provokes neuronal cell death, whereas cell cycle inhibition elevates neuronal survival. However, the molecular mechanism regulating the cell cycle and cell death in mature neurons remains elusive. Here we show that SRPK2, a protein kinase specific for the serine/arginine (SR) family of splicing factors, triggers cell cycle progression in neurons and induces apoptosis through regulation of nuclear cyclin D1. Akt phosphorylates SRPK2 on Thr-492 and promotes its nuclear translocation leading to cyclin D1 up-regulation, cell cycle reentry, and neuronal apoptosis. In addition, SRPK2 phosphorylates SC35 and, thus, inactivates p53, resulting in cyclin D1 up-regulation. 14-3-3 binding to SRPK2, regulated by Akt phosphorylation, inhibits these events. We find that SRPK2 is phosphorylated in ischemia-attacked brain, correlating with the observed increase in cyclin D1 levels. Hence, phosphatidylinositol 3-kinase/Akt mediates the cell cycle and cell death machinery in the nervous system through phosphorylation of SRPK2.
Collapse
Affiliation(s)
- Sung-Wuk Jang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
Jang SW, Yang SJ, Ehlén A, Dong S, Khoury H, Chen J, Persson JL, Ye K. Serine/arginine protein-specific kinase 2 promotes leukemia cell proliferation by phosphorylating acinus and regulating cyclin A1. Cancer Res 2008; 68:4559-70. [PMID: 18559500 DOI: 10.1158/0008-5472.can-08-0021] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Serine/arginine (SR) protein-specific kinase (SRPK), a family of cell cycle-regulated protein kinases, phosphorylate SR domain-containing proteins in nuclear speckles and mediate the pre-mRNA splicing. However, the physiologic roles of this event in cell cycle are incompletely understood. Here, we show that SRPK2 binds and phosphorylates acinus, an SR protein essential for RNA splicing, and redistributes it from the nuclear speckles to the nucleoplasm, resulting in cyclin A1 but not A2 up-regulation. Acinus S422D, an SRPK2 phosphorylation mimetic, enhances cyclin A1 transcription, whereas acinus S422A, an unphosphorylatable mutant, blocks the stimulatory effect of SRPK2. Ablation of acinus or SRPK2 abrogates cyclin A1 expression in leukemia cells and arrest cells at G(1) phase. Overexpression of acinus or SRPK2 increases leukemia cell proliferation. Furthermore, both SRPK2 and acinus are overexpressed in some human acute myelogenous leukemia patients and correlate with elevated cyclin A1 expression levels, fitting with the oncogenic activity of cyclin A1 in leukemia. Thus, our findings establish a molecular mechanism by which SR splicing machinery regulates cell cycle and contributes to leukemia tumorigenesis.
Collapse
Affiliation(s)
- Sung-Wuk Jang
- Department of Pathology and Laboratory Medicine and Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
CDK13, a new potential human immunodeficiency virus type 1 inhibitory factor regulating viral mRNA splicing. J Virol 2008; 82:7155-66. [PMID: 18480452 DOI: 10.1128/jvi.02543-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) Tat is a 14-kDa viral protein that acts as a potent transactivator by binding to the transactivation-responsive region, a structured RNA element located at the 5' end of all HIV-1 transcripts. Tat transactivates viral gene expression by inducing the phosphorylation of the C-terminal domain of RNA polymerase II through several Tat-activated kinases and by recruiting chromatin-remodeling complexes and histone-modifying enzymes to the HIV-1 long terminal repeat. Histone acetyltransferases, including p300 and hGCN5, not only acetylate histones but also acetylate Tat at lysine positions 50 and 51 in the arginine-rich motif. Acetylated Tat at positions 50 and 51 interacts with a specialized protein module, the bromodomain, and recruits novel factors having this particular domain, such as P/CAF and SWI/SNF. In addition to having its effect on transcription, Tat has been shown to be involved in splicing. In this study, we demonstrate that Tat interacts with cyclin-dependent kinase 13 (CDK13) both in vivo and in vitro. We also found that CDK13 increases HIV-1 mRNA splicing and favors the production of the doubly spliced protein Nef. In addition, we demonstrate that CDK13 acts as a possible restriction factor, in that its overexpression decreases the production of the viral proteins Gag and Env and subsequently suppresses virus production. Using small interfering RNA against CDK13, we show that silencing of CDK13 leads to a significant increase in virus production. Finally, we demonstrate that CDK13 mediates its effect on splicing through the phosphorylation of ASF/SF2.
Collapse
|
42
|
Mathew R, Hartmuth K, Möhlmann S, Urlaub H, Ficner R, Lührmann R. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nat Struct Mol Biol 2008; 15:435-43. [PMID: 18425142 DOI: 10.1038/nsmb.1415] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Accepted: 03/10/2008] [Indexed: 11/09/2022]
Abstract
Several protein kinases, including SRPK1 and SRPK2, have been implicated in spliceosome assembly and catalytic activation. However, little is known about their targets. Here we show that SRPK1 is predominantly associated with U1 small nuclear ribonucleoprotein (snRNP), whereas SRPK2 associates with the U4/U6-U5 tri-snRNP. RNAi-mediated depletion in HeLa cells showed that SRPK2 is essential for cell viability, and it is required for spliceosomal B complex formation. SRPK2 knock down results in hypophosphorylation of the arginine-serine (RS) domain-containing human PRP28 protein (PRP28, also known as DDX23), and destabilizes PRP28 association with the tri-snRNP. Immunodepletion of PRP28 from HeLa cell nuclear extract and complementation studies revealed that PRP28 phosphorylation is required for its stable association with the tri-snRNP and for tri-snRNP integration into the B complex. Our results demonstrate a role for SRPK2 in splicing and reveal a previously unknown function for PRP28 in spliceosome assembly.
Collapse
Affiliation(s)
- Rebecca Mathew
- Department of Cellular Biochemistry MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | | | | | | | | | | |
Collapse
|
43
|
Yomoda JI, Muraki M, Kataoka N, Hosoya T, Suzuki M, Hagiwara M, Kimura H. Combination of Clk family kinase and SRp75 modulates alternative splicing of Adenovirus E1A. Genes Cells 2008; 13:233-44. [DOI: 10.1111/j.1365-2443.2008.01163.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
44
|
Skotheim RI, Nees M. Alternative splicing in cancer: Noise, functional, or systematic? Int J Biochem Cell Biol 2007; 39:1432-49. [PMID: 17416541 DOI: 10.1016/j.biocel.2007.02.016] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/13/2007] [Accepted: 02/22/2007] [Indexed: 12/22/2022]
Abstract
Pre-messenger RNA splicing is a fine-tuned process that generates multiple functional variants from individual genes. Various cell types and developmental stages regulate alternative splicing patterns differently in their generation of specific gene functions. In cancers, splicing is significantly altered, and understanding the underlying mechanisms and patterns in cancer will shed new light onto cancer biology. Cancer-specific transcript variants are promising biomarkers and targets for diagnostic, prognostic, and treatment purposes. In this review, we explore how alternative splicing cannot simply be considered as noise or an innocent bystander, but is actively regulated or deregulated in cancers. A special focus will be on aspects of cell biology and biochemistry of alternative splicing in cancer cells, addressing differences in splicing mechanisms between normal and malignant cells. The systems biology of splicing is only now applied to the field of cancer research. We explore functional annotations for some of the most intensely spliced gene classes, and provide a literature mining and clustering that reflects the most intensely investigated genes. A few well-established cancer-specific splice events, such as the CD44 antigen, are used to illustrate the potential behind the exploration of the mechanisms of their regulation. Accordingly, we describe the functional connection between the regulatory machinery (i.e., the spliceosome and its accessory proteins) and their global impact on qualitative transcript variation that are only now emerging from the use of genomic technologies such as microarrays. These studies are expected to open an entirely new level of genetic information that is currently still poorly understood.
Collapse
Affiliation(s)
- Rolf I Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
| | | |
Collapse
|
45
|
Abstract
Par 6 acts as a scaffold protein to facilitate atypical protein kinase C-mediated phosphorylation of cytoplasmic protein complexes, leading to epithelial and neuronal cell polarization. In addition to its location in the cytoplasm, Par 6 is localized to the nucleus. However, its organization and potential functions in the nucleus have not been examined. Using an affinity-purified Par 6 antibody and a chimera of Par 6 and green fluorescent protein, we show that Par 6 localizes precisely to nuclear speckles, but not to other nuclear structures, and displays characteristics of speckle proteins. We show that Par 6 colocalizes in the nucleus with Tax, a transcriptional activator of the human T-cell leukemia virus type 1 long terminal repeat, but multiple lines of evidence show that Par 6 is not directly involved in known functions of speckle proteins, including general transcription, splicing, or mRNA transport. Significantly, however, the structure of nuclear speckles is lost when Par 6 levels are reduced by Par 6-specific small interfering RNA. Therefore, we hypothesize that Par 6 in the nucleus acts as a scaffolding protein in nuclear speckle complexes, similar to its role in the cytoplasm.
Collapse
Affiliation(s)
- Erin G Cline
- Department of Biological Sciences, The James A Clark Center, Stanford University, Stanford, CA 94305-5430, USA
| | | |
Collapse
|
46
|
Chen HH, Wong YH, Geneviere AM, Fann MJ. CDK13/CDC2L5 interacts with L-type cyclins and regulates alternative splicing. Biochem Biophys Res Commun 2007; 354:735-40. [PMID: 17261272 DOI: 10.1016/j.bbrc.2007.01.049] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Accepted: 01/09/2007] [Indexed: 11/29/2022]
Abstract
Due to the strong sequence homology it has been suggested that CDC2L5 and CDK12 belong to a high molecular weight subfamily of CDC2 family with PITAI/VRE motifs [F. Marques, J.L. Moreau, G. Peaucellier, J.C. Lozano, P. Schatt, A. Picard, I. Callebaut, E. Perret, A.M. Geneviere, A new subfamily of high molecular mass CDC2-related kinases with PITAI/VRE motifs, Biochem. Biophys. Res. Commun. 279 (2000) 832-837]. Recently, we reported that CDK12 interacts with L-type cyclins and is involved in alternative splicing regulation [H.-H. Chen, Y.-C. Wang, M.-J. Fann, Identification and characterization of the CDK12/Cyclin L1 complex involved in alternative splicing regulation, Mol. Cel. Biol. 26 (2006) 2736-2745]. Here, we provide evidence that CDC2L5 also interacts with L-type cyclins and thus rename it as cyclin-dependent kinase 13 (CDK13). The kinase domain of CDK13 is sufficient to bind the cyclin domains of L-type cyclins. Moreover, CDK13 and L-type cyclins modulate each other's subcellular localization. When CDK13 and an E1a minigene reporter construct were over-expressed in HEK293T cells, CDK13 alters the splicing pattern of E1a transcripts in a dose-dependent manner. Similar to effects of CDK12, effects of CDK13 on splicing pattern are counteracted by SF2/ASF and SC35. These findings strengthen CDK12 and CDK13 as a subfamily of cyclin-dependent kinases that regulate alternative splicing.
Collapse
Affiliation(s)
- Hung-Hsi Chen
- Institute of Neuroscience, National Yang-Ming University, Taipei 11221, Taiwan, ROC
| | | | | | | |
Collapse
|
47
|
Lopato S, Borisjuk L, Milligan AS, Shirley N, Bazanova N, Parsley K, Langridge P. Systematic identification of factors involved in post-transcriptional processes in wheat grain. PLANT MOLECULAR BIOLOGY 2006; 62:637-53. [PMID: 16941218 DOI: 10.1007/s11103-006-9046-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 07/06/2006] [Indexed: 05/11/2023]
Abstract
Post-transcriptional processing of primary transcripts can significantly affect both the quantity and the structure of mature mRNAs and the corresponding protein products. It is an important mechanism of gene regulation in animals, yeast and plants. Here we have investigated the interactive networks of pre-mRNA processing factors in the developing grain of wheat (Triticum aestivum), one of the world's major food staples. As a first step we isolated a homologue of the plant specific AtRSZ33 splicing factor, which has been shown to be involved in the early stages of embryo development in Arabidopsis. Real-time PCR showed that the wheat gene, designated TaRSZ38, is expressed mainly in young, developing organs (flowers, root, stem), and expression peaks in immature grain. In situ hybridization and immunodetection revealed preferential abundance of TaRSZ38 in mitotically active tissues of the major storage organ of the grain, the endosperm. The protein encoded by TaRSZ38 was subsequently used as a starting bait in a two-hybrid screen to identify additional factors in grain that are involved in pre-mRNA processing. Most of the identified proteins showed high homology to known splicing factors and splicing related proteins, supporting a role for TaRSZ38 in spliceosome formation and 5' site selection. Several clones were selected as baits in further yeast two-hybrid screens. In total, cDNAs for 16 proteins were isolated. Among these proteins, TaRSZ22, TaSRp30, TaU1-70K, and the large and small subunits of TaU2AF, are wheat homologues of known plant splicing factors. Several, additional proteins are novel for plants and show homology to known pre-mRNA splicing, splicing related and mRNA export factors from yeast and mammals.
Collapse
Affiliation(s)
- Sergiy Lopato
- Australian Centre for Plant Functional Genomics, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia.
| | | | | | | | | | | | | |
Collapse
|
48
|
Fukuhara T, Hosoya T, Shimizu S, Sumi K, Oshiro T, Yoshinaka Y, Suzuki M, Yamamoto N, Herzenberg LA, Herzenberg LA, Hagiwara M. Utilization of host SR protein kinases and RNA-splicing machinery during viral replication. Proc Natl Acad Sci U S A 2006; 103:11329-33. [PMID: 16840555 PMCID: PMC1544086 DOI: 10.1073/pnas.0604616103] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Although the viral genome is often quite small, it encodes a broad series of proteins. The virus takes advantage of the host-RNA-processing machinery to provide the alternative splicing capability necessary for the expression of this proteomic diversity. Serine-arginine-rich (SR) proteins and the kinases that activate them are central to this alternative splicing machinery. In studies reported here, we use the HIV genome as a model. We show that HIV expression decreases overall SR protein/activity. However, we also show that HIV expression is significantly increased (20-fold) when one of the SR proteins, SRp75 is phosphorylated by SR protein kinase (SRPK)2. Thus, inhibitors of SRPK2 and perhaps of functionally related kinases, such as SRPK1, could be useful antiviral agents. Here, we develop this hypothesis and show that HIV expression down-regulates SR proteins in Flp-In293 cells, resulting in only low-level HIV expression in these cells. However, increasing SRPK2 function up-regulates HIV expression. In addition, we introduce SR protein phosphorylation inhibitor 340 (SRPIN340), which preferentially inhibits SRPK1 and SRPK2 and down-regulates SRp75. Although an isonicotinamide compound, SPRIN340 (or its derivatives) remain to be optimized for better specificity and lower cytotoxicity, we show here that SRPIN340 suppresses propagation of Sindbis virus in plaque assay and variably suppresses HIV production. Thus, we show that SRPK, a well known kinase in the cellular RNA-processing machinery, is used by at least some viruses for propagation and hence suggest that SRPIN340 or its derivatives may be useful for curbing viral diseases.
Collapse
Affiliation(s)
- Takeshi Fukuhara
- *Laboratory of Gene Expression, School of Biomedical Science
- Department of Functional Genomics, Medical Research Institute
| | - Takamitsu Hosoya
- Division of Regeneration and Advanced Medical Science, Graduate School of Medicine, Gifu University, Gifu 501-1193, Japan
| | - Saki Shimizu
- Molecular Virology, Graduate School, and
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; and
| | - Kengo Sumi
- Division of Regeneration and Advanced Medical Science, Graduate School of Medicine, Gifu University, Gifu 501-1193, Japan
| | - Takako Oshiro
- *Laboratory of Gene Expression, School of Biomedical Science
- Department of Functional Genomics, Medical Research Institute
| | - Yoshiyuki Yoshinaka
- **Human Gene Sciences Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masaaki Suzuki
- Division of Regeneration and Advanced Medical Science, Graduate School of Medicine, Gifu University, Gifu 501-1193, Japan
| | - Naoki Yamamoto
- Molecular Virology, Graduate School, and
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; and
| | - Leonore A. Herzenberg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5318
| | - Leonard A. Herzenberg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5318
- To whom correspondence may be addressed. E-mail:
or
| | - Masatoshi Hagiwara
- *Laboratory of Gene Expression, School of Biomedical Science
- Department of Functional Genomics, Medical Research Institute
- To whom correspondence may be addressed. E-mail:
or
| |
Collapse
|
49
|
Hayes GM, Carrigan PE, Beck AM, Miller LJ. Targeting the RNA Splicing Machinery as a Novel Treatment Strategy for Pancreatic Carcinoma. Cancer Res 2006; 66:3819-27. [PMID: 16585209 DOI: 10.1158/0008-5472.can-05-4065] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aberrant patterns of pre-mRNA splicing have been established for many human malignancies, yet the mechanisms responsible for these tumor-specific changes remain undefined and represent a promising area for therapeutic intervention. Using immunohistochemistry, we have localized the expression of a central splicing regulator, serine-arginine protein kinase 1 (SRPK1), to the ductular epithelial cells within human pancreas and have further shown its increased expression in tumors of the pancreas, breast, and colon. Small interfering RNA-mediated down-regulation of SRPK1 in pancreatic tumor cell lines resulted in a dose-dependent decrease in proliferative capacity and increase in apoptotic potential. Coordinately, the disruption of SRPK1 expression resulted in enhanced sensitivity of tumor cells to killing by gemcitabine and/or cisplatin. A dose-dependent reduction in the phosphorylation status of specific SR proteins was detected following the down-regulation of SRPK1 and is likely responsible for the observed alterations in expression of proteins associated with apoptosis and multidrug resistance. These data support SRPK1 as a new, potential target for the treatment of pancreatic ductular cancer that at present remains largely unresponsive to conventional therapies. Furthermore, these results support the development of innovative therapies that target not only specific splice variants arising during tumorigenesis but also the splice regulatory machinery that itself may be abnormal in malignant cells.
Collapse
Affiliation(s)
- Gregory M Hayes
- Mayo Clinic Cancer Center and Department of Molecular Pharmacology and Experimental Therapeutics, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA
| | | | | | | |
Collapse
|
50
|
Ding JH, Zhong XY, Hagopian JC, Cruz MM, Ghosh G, Feramisco J, Adams JA, Fu XD. Regulated cellular partitioning of SR protein-specific kinases in mammalian cells. Mol Biol Cell 2005; 17:876-85. [PMID: 16319169 PMCID: PMC1356596 DOI: 10.1091/mbc.e05-10-0963] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Reversible phosphorylation of the SR family of splicing factors plays an important role in pre-mRNA processing in the nucleus. Interestingly, the SRPK family of kinases specific for SR proteins is localized in the cytoplasm, which is critical for nuclear import of SR proteins in a phosphorylation-dependent manner. Here, we report molecular dissection of the mechanism involved in partitioning SRPKs in the cytoplasm. Common among all SRPKs, the bipartite kinase catalytic core is separated by a unique spacer sequence. The spacers in mammalian SRPK1 and SRPK2 share little sequence homology, but they function interchangeably in restricting the kinases in the cytoplasm. Removal of the spacer in SRPK1 had little effect on the kinase activity, but it caused a quantitative translocation of the kinase to the nucleus and consequently induced aggregation of splicing factors in the nucleus. Rather than carrying a nuclear export signal as suggested previously, we found multiple redundant signals in the spacer that act together to anchor the kinase in the cytoplasm. Interestingly, a cell cycle signal induced nuclear translocation of the kinase at the G2/M boundary. These findings suggest that SRPKs may play an important role in linking signaling to RNA metabolism in higher eukaryotic cells.
Collapse
Affiliation(s)
- Jian-Hua Ding
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | | | | | | | | | | | | | | |
Collapse
|