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Gillard BT, Amor N, Iraizoz FA, Pauža AG, Campbell C, Greenwood MP, Alagaili AN, Murphy D. Mobilisation of jerboa kidney gene networks during dehydration and opportunistic rehydration. iScience 2023; 26:107574. [PMID: 37664605 PMCID: PMC10470305 DOI: 10.1016/j.isci.2023.107574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/30/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Desert animals have evolved systems that enable them to thrive under dry conditions. Focusing on the kidney, we have investigated the transcriptomic adaptations that enable a desert rodent, the Lesser Egyptian Jerboa (Jaculus jaculus), to withstand water deprivation and opportunistic rehydration. Analysis of the whole kidney transcriptome showed many differentially expressed genes in the Jerboa kidney, 6.4% of genes following dehydration and an even greater number (36.2%) following rehydration compared to control. Genes correlated with the rehydration condition included many ribosomal protein coding genes suggesting a concerted effort to accelerate protein synthesis when water is made available. We identify an increase in TGF-beta signaling antagonists in dehydration (e.g., GREM2). We also describe expression of multiple aquaporin and solute carrier transporters mapped to specific nephron segments. The desert adapted renal transcriptome presented here is a valuable resource to expand our understanding of osmoregulation beyond that derived from model organisms.
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Affiliation(s)
- Benjamin T. Gillard
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - Nabil Amor
- LR18ES05, Laboratory of Biodiversity, Parasitology and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Fernando Alvira Iraizoz
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - Audrys G. Pauža
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - Colin Campbell
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, Bristol, England
| | - Michael P. Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | | | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
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2
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Arfelli VC, Chang YC, Bagnoli JW, Kerbs P, Ciamponi FE, Paz LMDS, Pankivskyi S, de Matha Salone J, Maucuer A, Massirer KB, Enard W, Kuster B, Greif PA, Archangelo LF. UHMK1 is a novel splicing regulatory kinase. J Biol Chem 2023; 299:103041. [PMID: 36803961 PMCID: PMC10033318 DOI: 10.1016/j.jbc.2023.103041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/18/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif, a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3' splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division, and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 270 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on transcript expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.
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Affiliation(s)
- Vanessa C Arfelli
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Yun-Chien Chang
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Paul Kerbs
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe E Ciamponi
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Laissa M da S Paz
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Serhii Pankivskyi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Katlin B Massirer
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Philipp A Greif
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leticia Fröhlich Archangelo
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil.
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3
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Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC. An atlas of substrate specificities for the human serine/threonine kinome. Nature 2023; 613:759-766. [PMID: 36631611 PMCID: PMC9876800 DOI: 10.1038/s41586-022-05575-3] [Citation(s) in RCA: 149] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is one of the most widespread post-translational modifications in biology1,2. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes3,4. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible3. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.
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Affiliation(s)
- Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center and The Rockefeller University, New York, NY, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Junho Song
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Regev
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY, USA
| | - Katarina Liberatore
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniel M Cizin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yilun Ma
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Bert van de Kooij
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne E van Vlimmeren
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole Andrée-Busch
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Norbert F Käufer
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maxim V Dorovkov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edward R Kastenhuber
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marcus D Goncalves
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Division of Endocrinology, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin D Hopkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohamed Uduman
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Jingyi Lu
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Sean D Landry
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Bin Zhang
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Ian Cossentino
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Rune Linding
- Rewire Tx, Humboldt-Universität zu Berlin, Berlin, Germany
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Peter V Hornbeck
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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4
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Luo Y, Han S, Yan B, Ji H, Zhao L, Gladkich J, Herr I. UHMK1 Is a Novel Marker for Personalized Prediction of Pancreatic Cancer Prognosis. Front Oncol 2022; 12:834647. [PMID: 35359403 PMCID: PMC8960145 DOI: 10.3389/fonc.2022.834647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the leading causes of cancer mortality, and new therapeutic options are urgently needed. Long noncoding RNA H19 (H19) is known to promote PDAC progression, but the downstream genes of H19 are largely unknown. Five PDAC cell lines, nonmalignant pancreatic cells, TCGA, GEO-derived pancreatic tissues (malignant, n=413; nonmalignant, n=234), a pancreatic tissue array (n=96), and pancreatic tissues from our clinic (malignant, n=20; nonmalignant, n=20) were examined by a gene array, RT-qPCR, Western blotting, MTT, colony formation, wound-healing, siRNA-mediated gene silencing, bioinformatics, xenotransplantation, and immunohistochemistry assays. The cell cycle inhibitor, UHMK1, was identified to have the strongest correlation with H19. UHMK1 expression was enhanced in PDAC, and high UHMK1 expression correlated with tumor stage, and lower overall survival. siRNA-mediated UHMK1 downregulation inhibited progression signaling. siRNA-mediated downregulation of H19 or UHMK1 inhibited tumor proliferation and xenograft growth. Based on the correlation between UHMK1 expression and clinical parameters, we developed a nomogram that reliably predicts patient prognosis and overall survival. Together, we characterized UHMK1 as an H19-induced oncogene and verified it as a novel PDAC prognostic marker for overall survival.
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5
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Mikolaskova B, Jurcik M, Cipakova I, Selicky T, Jurcik J, Polakova SB, Stupenova E, Dudas A, Sivakova B, Bellova J, Barath P, Aronica L, Gregan J, Cipak L. Identification of Nrl1 Domains Responsible for Interactions with RNA-Processing Factors and Regulation of Nrl1 Function by Phosphorylation. Int J Mol Sci 2021; 22:7011. [PMID: 34209806 PMCID: PMC8268110 DOI: 10.3390/ijms22137011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 12/26/2022] Open
Abstract
Pre-mRNA splicing is a key process in the regulation of gene expression. In the fission yeast Schizosaccharomyces pombe, Nrl1 regulates splicing and expression of several genes and non-coding RNAs, and also suppresses the accumulation of R-loops. Here, we report analysis of interactions between Nrl1 and selected RNA-processing proteins and regulation of Nrl1 function by phosphorylation. Bacterial two-hybrid system (BACTH) assays revealed that the N-terminal region of Nrl1 is important for the interaction with ATP-dependent RNA helicase Mtl1 while the C-terminal region of Nrl1 is important for interactions with spliceosome components Ctr1, Ntr2, and Syf3. Consistent with this result, tandem affinity purification showed that Mtl1, but not Ctr1, Ntr2, or Syf3, co-purifies with the N-terminal region of Nrl1. Interestingly, mass-spectrometry analysis revealed that in addition to previously identified phosphorylation sites, Nrl1 is also phosphorylated on serines 86 and 112, and that Nrl1-TAP co-purifies with Cka1, the catalytic subunit of casein kinase 2. In vitro assay showed that Cka1 can phosphorylate bacterially expressed Nrl1 fragments. An analysis of non-phosphorylatable nrl1 mutants revealed defects in gene expression and splicing consistent with the notion that phosphorylation is an important regulator of Nrl1 function. Taken together, our results provide insights into two mechanisms that are involved in the regulation of the spliceosome-associated factor Nrl1, namely domain-specific interactions between Nrl1 and RNA-processing proteins and post-translational modification of Nrl1 by phosphorylation.
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Affiliation(s)
- Barbora Mikolaskova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Matus Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia; (S.B.P.); (E.S.)
| | - Erika Stupenova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia; (S.B.P.); (E.S.)
| | - Andrej Dudas
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia;
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
| | - Jana Bellova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
- Medirex Group Academy, n.o., Jana Bottu 2, 917 01 Trnava, Slovakia
| | - Lucia Aronica
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
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Zhang KL, Feng Z, Yang JF, Yang F, Yuan T, Zhang D, Hao GF, Fang YM, Zhang J, Wu C, Chen MX, Zhu FY. Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses. BMC PLANT BIOLOGY 2020; 20:379. [PMID: 32811430 PMCID: PMC7433366 DOI: 10.1186/s12870-020-02570-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5' and 3' splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. RESULTS To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. CONCLUSION Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Affiliation(s)
- Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Zhen Feng
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079 China
| | - Feng Yang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tian Yuan
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Di Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079 China
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Jianhua Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Mo-Xian Chen
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 PR China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
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7
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Tari M, Manceau V, de Matha Salone J, Kobayashi A, Pastré D, Maucuer A. U2AF 65 assemblies drive sequence-specific splice site recognition. EMBO Rep 2019; 20:e47604. [PMID: 31271494 PMCID: PMC6681011 DOI: 10.15252/embr.201847604] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
The essential splicing factor U2AF65 is known to help anchoring U2 snRNP at the branch site. Its C-terminal UHM domain interacts with ULM motifs of SF3b155, an U2 snRNP protein. Here, we report a cooperative binding of U2AF65 and the related protein CAPERα to the multi-ULM domain of SF3b155. In addition, we show that the RS domain of U2AF65 drives a liquid-liquid phase separation that is amplified by intronic RNA with repeated pyrimidine tracts. In cells, knockdown of either U2AF65 or CAPERα improves the inclusion of cassette exons that are preceded by such repeated pyrimidine-rich motifs. These results support a model in which liquid-like assemblies of U2AF65 and CAPERα on repetitive pyrimidine-rich RNA sequences are driven by their RS domains, and facilitate the recruitment of the multi-ULM domain of SF3b155. We anticipate that posttranslational modifications and proteins recruited in dynamical U2AF65 and CAPERα condensates may further contribute to the complex mechanisms leading to specific splice site choice that occurs in cells.
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Affiliation(s)
- Manel Tari
- SABNPUniv EvryINSERM U1204Université Paris‐SaclayEvryFrance
| | - Valérie Manceau
- Institut Necker Enfants Malades (INEM)Inserm U1151 – CNRS UMR 8253Université Paris DescartesParisFrance
- Present address:
Faculty of MedicineInstitut Necker Enfants Malades (INEM)Inserm U1151–CNRS UMR 8253University Paris DescartesSorbonne Paris CitéParisFrance
| | | | | | - David Pastré
- SABNPUniv EvryINSERM U1204Université Paris‐SaclayEvryFrance
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8
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Královicová J, Ševcíková I, Stejskalová E, Obuca M, Hiller M, Stanek D, Vorechovský I. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res 2019; 46:6166-6187. [PMID: 29788428 PMCID: PMC6093180 DOI: 10.1093/nar/gky389] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/01/2018] [Indexed: 12/27/2022] Open
Abstract
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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Affiliation(s)
- Jana Královicová
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Ševcíková
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Eva Stejskalová
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Mina Obuca
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - David Stanek
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Igor Vorechovský
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
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9
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Wei T, Weiler SME, Tóth M, Sticht C, Lutz T, Thomann S, De La Torre C, Straub B, Merker S, Ruppert T, Marquardt J, Singer S, Gretz N, Schirmacher P, Breuhahn K. YAP-dependent induction of UHMK1 supports nuclear enrichment of the oncogene MYBL2 and proliferation in liver cancer cells. Oncogene 2019; 38:5541-5550. [PMID: 30936457 DOI: 10.1038/s41388-019-0801-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/01/2019] [Accepted: 03/16/2019] [Indexed: 02/03/2023]
Abstract
The oncogene yes-associated protein (YAP) is a key modifier of liver homeostasis and regulates mitosis in hepatocytes as well as in malignantly transformed cells. However, the question of how YAP supports cell proliferation in hepatocellular carcinoma (HCC) is not well understood. Here we identified U2AF momology motif kinase 1 (UHMK1) as a direct transcriptional target of YAP and the transcription factor forkhead box M1 (FOXM1), which supports HCC cell proliferation but not migration. Indeed, UHMK1 stimulates the expression of genes that are specific for cell cycle regulation and which are known downstream effectors of YAP. By using BioID labeling and mass spectrometry, the dimerization partner, RB-like, E2F and multi-vulval class B (DREAM) complex constituent MYB proto-oncogene like 2 (MYBL2, B-MYB) was identified as a direct UHMK1 interaction partner. Like YAP, UHMK1 stimulates nuclear enrichment of MYBL2, which is associated HCC cell proliferation and the expression of the cell cycle regulators CCNB1, CCNB2, KIF20A, and MAD2L1. The association between YAP, UHMK1, MYBL2, and proliferation was confirmed in YAPS127A-transgenic mice and human HCC tissues. In summary, we provide a model by which YAP supports cell proliferation through the induction of important cell cycle regulators in a UHMK1- and MYBL2-dependent manner.
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Affiliation(s)
- Teng Wei
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Marcell Tóth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carsten Sticht
- Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Teresa Lutz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Thomann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carolina De La Torre
- Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Beate Straub
- Institute of Pathology, Johannes Gutenberg University, Mainz, Germany
| | - Sabine Merker
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jens Marquardt
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Stephan Singer
- Institute of Pathology, University Medicine Greifswald, Greifswald, Germany
| | - Norbert Gretz
- Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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10
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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11
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Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino MJ, Kielkopf CL. The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface. J Biol Chem 2018; 294:2892-2902. [PMID: 30567737 DOI: 10.1074/jbc.ra118.006764] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/10/2018] [Indexed: 01/09/2023] Open
Abstract
The transcription elongation and pre-mRNA splicing factor Tat-SF1 associates with the U2 small nuclear ribonucleoprotein (snRNP) of the spliceosome. However, the direct binding partner and underlying interactions mediating the Tat-SF1-U2 snRNP association remain unknown. Here, we identified SF3b1 as a Tat-SF1-interacting subunit of the U2 snRNP. Our 1.1 Å resolution crystal structure revealed that Tat-SF1 contains a U2AF homology motif (UHM) protein-protein interaction module. We demonstrated that Tat-SF1 preferentially and directly binds the SF3b1 subunit compared with other U2AF ligand motif (ULM)-containing splicing factors, and further established that SF3b1 association depends on the integrity of the Tat-SF1 UHM. We next compared the Tat-SF1-binding affinities for each of the five known SF3b1 ULMs and then determined the structures of representative high- and low-affinity SF3b1 ULM complexes with the Tat-SF1 UHM at 1.9 Å and 2.1 Å resolutions, respectively. These structures revealed a canonical UHM-ULM interface, comprising a Tat-SF1 binding pocket for a ULM tryptophan (SF3b1 Trp338) and electrostatic interactions with a basic ULM tail. Importantly, we found that SF3b1 regulates Tat-SF1 levels and that these two factors influence expression of overlapping representative transcripts, consistent with a functional partnership of Tat-SF1 and SF3b1. Altogether, these results define a new molecular interface of the Tat-SF1-U2 snRNP complex for gene regulation.
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Affiliation(s)
- Sarah Loerch
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Justin R Leach
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Steven W Horner
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Debanjana Maji
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Jermaine L Jenkins
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Mary J Pulvino
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Clara L Kielkopf
- From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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12
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Barbutti I, Machado-Neto JA, Arfelli VC, de Melo Campos P, Traina F, Saad STO, Archangelo LF. The U2AF homology motif kinase 1 (UHMK1) is upregulated upon hematopoietic cell differentiation. Biochim Biophys Acta Mol Basis Dis 2018; 1864:959-966. [PMID: 29307747 DOI: 10.1016/j.bbadis.2018.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/10/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023]
Abstract
UHMK1 (KIS) is a nuclear serine/threonine kinase that possesses a U2AF homology motif and phosphorylates and regulates the activity of the splicing factors SF1 and SF3b155. Mutations in these components of the spliceosome machinery have been recently implicated in leukemogenesis. The fact that UHMK1 regulates these factors suggests that UHMK1 might be involved in RNA processing and perhaps leukemogenesis. Here we analyzed UHMK1 expression in normal hematopoietic and leukemic cells as well as its function in leukemia cell line. In the normal hematopoietic compartment, markedly higher levels of transcripts were observed in differentiated lymphocytes (CD4+, CD8+ and CD19+) compared to the progenitor enriched subpopulation (CD34+) or leukemia cell lines. UHMK1 expression was upregulated in megakaryocytic-, monocytic- and granulocytic-induced differentiation of established leukemia cell lines and in erythrocytic-induced differentiation of CD34+ cells. No aberrant expression was observed in patient samples of myelodysplastic syndrome (MDS), acute myeloid (AML) or lymphoblastic (ALL) leukemia. Nonetheless, in MDS patients, increased levels of UHMK1 expression positively impacted event free and overall survival. Lentivirus mediated UHMK1 knockdown did not affect proliferation, cell cycle progression, apoptosis or migration of U937 leukemia cells, although UHMK1 silencing strikingly increased clonogenicity of these cells. Thus, our results suggest that UHMK1 plays a role in hematopoietic cell differentiation and suppression of autonomous clonal growth of leukemia cells.
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Affiliation(s)
- Isabella Barbutti
- Hematology and Transfusion Medicine Center, State University of Campinas (UNICAMP), Carlos Chagas 480, 13083-878 Campinas, SP, Brazil
| | - João Agostinho Machado-Neto
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa Cristina Arfelli
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula de Melo Campos
- Hematology and Transfusion Medicine Center, State University of Campinas (UNICAMP), Carlos Chagas 480, 13083-878 Campinas, SP, Brazil
| | - Fabiola Traina
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sara Teresinha Olalla Saad
- Hematology and Transfusion Medicine Center, State University of Campinas (UNICAMP), Carlos Chagas 480, 13083-878 Campinas, SP, Brazil
| | - Leticia Fröhlich Archangelo
- Hematology and Transfusion Medicine Center, State University of Campinas (UNICAMP), Carlos Chagas 480, 13083-878 Campinas, SP, Brazil; Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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13
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Glasser E, Agrawal AA, Jenkins JL, Kielkopf CL. Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry 2017; 56:4757-4761. [PMID: 28850223 DOI: 10.1021/acs.biochem.7b00551] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acquired point mutations of pre-mRNA splicing factors recur among cancers, leukemias, and related neoplasms. Several studies have established that somatic mutations of a U2AF1 subunit, which normally recognizes 3' splice site junctions, recur among myelodysplastic syndromes. The U2AF2 splicing factor recognizes polypyrimidine signals that precede most 3' splice sites as a heterodimer with U2AF1. In contrast with those of the well-studied U2AF1 subunit, descriptions of cancer-relevant U2AF2 mutations and their structural relationships are lacking. Here, we survey databases of cancer-associated mutations and identify recurring missense mutations in the U2AF2 gene. We determine ultra-high-resolution structures of the U2AF2 RNA recognition motifs (RRM1 and RRM2) at 1.1 Å resolution and map the structural locations of the mutated U2AF2 residues. Comparison with prior, lower-resolution structures of the tandem U2AF2 RRMs in the RNA-bound and apo states reveals clusters of cancer-associated mutations at the U2AF2 RRM-RNA or apo-RRM1-RRM2 interfaces. Although the role of U2AF2 mutations in malignant transformation remains uncertain, our results show that cancer-associated mutations correlate with functionally important surfaces of the U2AF2 splicing factor.
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Affiliation(s)
- Eliezra Glasser
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Anant A Agrawal
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
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14
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Chatrikhi R, Wang W, Gupta A, Loerch S, Maucuer A, Kielkopf CL. SF1 Phosphorylation Enhances Specific Binding to U2AF 65 and Reduces Binding to 3'-Splice-Site RNA. Biophys J 2017; 111:2570-2586. [PMID: 28002734 DOI: 10.1016/j.bpj.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 12/25/2022] Open
Abstract
Splicing factor 1 (SF1) recognizes 3' splice sites of the major class of introns as a ternary complex with U2AF65 and U2AF35 splicing factors. A conserved SPSP motif in a coiled-coil domain of SF1 is highly phosphorylated in proliferating human cells and is required for cell proliferation. The UHM kinase 1 (UHMK1), also called KIS, double-phosphorylates both serines of this SF1 motif. Here, we use isothermal titration calorimetry to demonstrate that UHMK1 phosphorylation of the SF1 SPSP motif slightly enhances specific binding of phospho-SF1 to its cognate U2AF65 protein partner. Conversely, quantitative fluorescence anisotropy RNA binding assays and isothermal titration calorimetry experiments establish that double-SPSP phosphorylation reduces phospho-SF1 and phospho-SF1-U2AF65 binding affinities for either optimal or suboptimal splice-site RNAs. Domain-substitution and mutagenesis experiments further demonstrate that arginines surrounding the phosphorylated SF1 loop are required for cooperative 3' splice site recognition by the SF1-U2AF65 complex (where cooperativity is defined as a nonadditive increase in RNA binding by the protein complex relative to the individual proteins). In the context of local, intracellular concentrations, the subtle effects of SF1 phosphorylation on its associations with U2AF65 and splice-site RNAs are likely to influence pre-mRNA splicing. However, considering roles for SF1 in pre-mRNA retention and transcriptional repression, as well as in splicing, future comprehensive investigations are needed to fully explain the requirement for SF1 SPSP phosphorylation in proliferating human cells.
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Affiliation(s)
- Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Wenhua Wang
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | - Sarah Loerch
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York
| | | | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York.
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15
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Loerch S, Kielkopf CL. Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (NEW YORK, N.Y.) 2016; 22:1795-1807. [PMID: 27852923 PMCID: PMC5113200 DOI: 10.1261/rna.057950.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.
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Affiliation(s)
- Sarah Loerch
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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16
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Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift. Proc Natl Acad Sci U S A 2016; 113:E7169-E7175. [PMID: 27799531 DOI: 10.1073/pnas.1605873113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3' splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3' splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein-RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3' splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.
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17
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Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol 2016; 72:497-511. [PMID: 27050129 PMCID: PMC4822562 DOI: 10.1107/s2059798316001248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
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Affiliation(s)
- Galina A. Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Eigen Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Carol L. Farr
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott A. Lesley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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18
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Post-Translational Modifications and RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:297-317. [PMID: 27256391 DOI: 10.1007/978-3-319-29073-7_12] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins affect cellular metabolic programs through development and in response to cellular stimuli. Though much work has been done to elucidate the roles of a handful of RNA-binding proteins and their effect on RNA metabolism, the progress of studies to understand the effects of post-translational modifications of this class of proteins is far from complete. This chapter summarizes the work that has been done to identify the consequence of post-translational modifications to some RNA-binding proteins. The effects of these modifications have been shown to increase the panoply of functions that a given RNA-binding protein can assume. We will survey the experimental methods that are used to identify the presence of several protein modifications and methods that attempt to discern the consequence of these modifications.
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19
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Denisov S, Bazykin G, Favorov A, Mironov A, Gelfand M. Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals. PLoS One 2015; 10:e0144388. [PMID: 26642327 PMCID: PMC4671708 DOI: 10.1371/journal.pone.0144388] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/17/2015] [Indexed: 12/26/2022] Open
Abstract
Splice sites (SSs)--short nucleotide sequences flanking introns--are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.
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Affiliation(s)
- Stepan Denisov
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
| | - Georgii Bazykin
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Favorov
- Division of Oncology Biostatistics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, United States of America
- Laboratory of System Biology and Computational Genetics, Department of Computational System Biology, N. I. Vavilov Institute of General Genetics, Moscow, Russia
- Laboratory of Bioinformatics, State Research Institute of Genetics and Selection of Industrial Microorganism (GosNIIGenetika), Moscow, Russia
| | - Andrey Mironov
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Gelfand
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
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20
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Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
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Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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21
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Crisci A, Raleff F, Bagdiul I, Raabe M, Urlaub H, Rain JC, Krämer A. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. Nucleic Acids Res 2015; 43:10456-73. [PMID: 26420826 PMCID: PMC4666396 DOI: 10.1093/nar/gkv952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/10/2015] [Indexed: 02/03/2023] Open
Abstract
Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions.
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Affiliation(s)
- Angela Crisci
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Flore Raleff
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Monika Raabe
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | | | - Angela Krämer
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
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22
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Lipp JJ, Marvin MC, Shokat KM, Guthrie C. SR protein kinases promote splicing of nonconsensus introns. Nat Struct Mol Biol 2015; 22:611-7. [PMID: 26167880 DOI: 10.1038/nsmb.3057] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/04/2015] [Indexed: 01/01/2023]
Abstract
Phosphorylation of the spliceosome is essential for RNA splicing, yet how and to what extent kinase signaling affects splicing have not been defined on a genome-wide basis. Using a chemical genetic approach, we show in Schizosaccharomyces pombe that the SR protein kinase Dsk1 is required for efficient splicing of introns with suboptimal splice sites. Systematic substrate mapping in fission yeast and human cells revealed that SRPKs target evolutionarily conserved spliceosomal proteins, including the branchpoint-binding protein Bpb1 (SF1 in humans), by using an RXXSP consensus motif for substrate recognition. Phosphorylation of SF1 increases SF1 binding to introns with nonconsensus splice sites in vitro, and mutation of such sites to consensus relieves the requirement for Dsk1 and phosphorylated Bpb1 in vivo. Modulation of splicing efficiency through kinase signaling pathways may allow tuning of gene expression in response to environmental and developmental cues.
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Affiliation(s)
- Jesse J Lipp
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
| | - Michael C Marvin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
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23
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Abstract
Ribonucleoprotein complexes involved in pre-mRNA splicing and mRNA decay are often regulated by phosphorylation of RNA-binding proteins. Cells use phosphorylation-dependent signaling pathways to turn on and off gene expression. Not much is known about how phosphorylation-dependent signals transmitted by exogenous factors or cell cycle checkpoints regulate RNA-mediated gene expression at the atomic level. Several human diseases are linked to an altered phosphorylation state of an RNA binding protein. Understanding the structural response to the phosphorylation "signal" and its effect on ribonucleoprotein assembly provides mechanistic understanding, as well as new information for the design of novel drugs. In this review, I highlight recent structural studies that reveal the mechanisms by which phosphorylation can regulate protein-protein and protein-RNA interactions in ribonucleoprotein complexes.
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Affiliation(s)
- Roopa Thapar
- BioSciences
at Rice, Biochemistry
and Cell Biology, Rice University, Houston, Texas 77251-1892, United States
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24
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Ishizuka A, Hasegawa Y, Ishida K, Yanaka K, Nakagawa S. Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Genes Cells 2015; 19:704-21. [PMID: 25145264 PMCID: PMC4255692 DOI: 10.1111/gtc.12169] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 06/28/2014] [Indexed: 12/19/2022]
Abstract
Gomafu/MIAT/Rncr2 is a long noncoding RNA that has been proposed to control retinal cell specification, stem cell differentiation and alternative splicing of schizophrenia-related genes. However, how Gomafu controls these biological processes at the molecular level has remained largely unknown. In this study, we identified the RNA-binding protein Celf3 as a novel Gomafu-associating protein. Knockdown of Celf3 led to the down-regulation of Gomafu, and cross-link RNA precipitation analysis confirmed specific binding between Celf3 and Gomafu. In the neuroblastoma cell line Neuro2A, Celf3 formed novel nuclear bodies (named CS bodies) that colocalized with SF1, another Gomafu-binding protein. Gomafu, however, was not enriched in the CS bodies; instead, it formed distinct nuclear bodies in separate regions in the nucleus. These observations suggest that Gomafu indirectly modulates the function of the splicing factors SF1 and Celf3 by sequestering these proteins into separate nuclear bodies.
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Affiliation(s)
- Akira Ishizuka
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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25
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Loerch S, Maucuer A, Manceau V, Green MR, Kielkopf CL. Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. J Biol Chem 2014; 289:17325-37. [PMID: 24795046 DOI: 10.1074/jbc.m114.558825] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
U2AF homology motifs (UHMs) mediate protein-protein interactions with U2AF ligand motifs (ULMs) of pre-mRNA splicing factors. The UHM-containing alternative splicing factor CAPERα regulates splicing of tumor-promoting VEGF isoforms, yet the molecular target of the CAPERα UHM is unknown. Here we present structures of the CAPERα UHM bound to a representative SF3b155 ULM at 1.7 Å resolution and, for comparison, in the absence of ligand at 2.2 Å resolution. The prototypical UHM/ULM interactions authenticate CAPERα as a bona fide member of the UHM family of proteins. We identify SF3b155 as the relevant ULM-containing partner of full-length CAPERα in human cell extracts. Isothermal titration calorimetry comparisons of the purified CAPERα UHM binding known ULM-containing proteins demonstrate that high affinity interactions depend on the presence of an intact, intrinsically unstructured SF3b155 domain containing seven ULM-like motifs. The interplay among bound CAPERα molecules gives rise to the appearance of two high affinity sites in the SF3b155 ULM-containing domain. In conjunction with the previously identified, UHM/ULM-mediated complexes of U2AF(65) and SPF45 with SF3b155, this work demonstrates the capacity of SF3b155 to offer a platform for coordinated recruitment of UHM-containing splicing factors.
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Affiliation(s)
- Sarah Loerch
- From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and
| | - Alexandre Maucuer
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Valérie Manceau
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Michael R Green
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Clara L Kielkopf
- From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and
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26
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Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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27
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Archangelo LF, Greif PA, Maucuer A, Manceau V, Koneru N, Bigarella CL, Niemann F, dos Santos MT, Kobarg J, Bohlander SK, Saad STO. The CATS (FAM64A) protein is a substrate of the Kinase Interacting Stathmin (KIS). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1269-79. [PMID: 23419774 DOI: 10.1016/j.bbamcr.2013.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 01/21/2013] [Accepted: 02/08/2013] [Indexed: 12/22/2022]
Abstract
The CATS protein (also known as FAM64A and RCS1) was first identified as a novel CALM (PICALM) interactor that influences the subcellular localization of the leukemogenic fusion protein CALM/AF10. CATS is highly expressed in cancer cell lines in a cell cycle dependent manner and is induced by mitogens. CATS is considered a marker for proliferation, known to control the metaphase-to-anaphase transition during the cell division. Using CATS as a bait in a yeast two-hybrid screen we identified the Kinase Interacting Stathmin (KIS or UHMK1) protein as a CATS interacting partner. The interaction between CATS and KIS was confirmed by GST pull-down, co-immunoprecipitation and co-localization experiments. Using kinase assay we showed that CATS is a substrate of KIS and mapped the phosphorylation site to CATS serine 131 (S131). Protein expression analysis revealed that KIS levels changed in a cell cycle-dependent manner and in the opposite direction to CATS levels. In a reporter gene assay KIS was able to enhance the transcriptional repressor activity of CATS, independent of CATS phophorylation at S131. Moreover, we showed that CATS and KIS antagonize the transactivation capacity of CALM/AF10.In summary, our results show that CATS interacts with and is a substrate for KIS, suggesting that KIS regulates CATS function.
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28
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Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL. Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure 2012; 21:197-208. [PMID: 23273425 DOI: 10.1016/j.str.2012.10.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 11/15/2022]
Abstract
The essential splicing factors U2AF⁶⁵ and SF1 cooperatively bind consensus sequences at the 3' end of introns. Phosphorylation of SF1 on a highly conserved "SPSP" motif enhances its interaction with U2AF⁶⁵ and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF⁶⁵/3' splice site complex. Crystal structures of the phosphorylated (P)SF1 domain bound to the C-terminal domain of U2AF⁶⁵ at 2.29 Å resolution and of the unphosphorylated SF1 domain at 2.48 Å resolution demonstrate that phosphorylation induces a disorder-to-order transition within a previously unknown SF1/U2AF⁶⁵ interface. We find by small-angle X-ray scattering that the local folding of the SPSP motif transduces into global conformational changes in the nearly full-length (P)SF1/U2AF⁶⁵/3' splice site assembly. We further determine that SPSP phosphorylation and the SF1/U2AF⁶⁵ interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors.
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Affiliation(s)
- Wenhua Wang
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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29
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Zhang Y, Madl T, Bagdiul I, Kern T, Kang HS, Zou P, Mäusbacher N, Sieber SA, Krämer A, Sattler M. Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition. Nucleic Acids Res 2012; 41:1343-54. [PMID: 23175611 PMCID: PMC3553976 DOI: 10.1093/nar/gks1097] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recognition of the 3'-splice site is a key step in pre-mRNA splicing and accomplished by a dynamic complex comprising splicing factor 1 (SF1) and the U2 snRNP auxiliary factor 65-kDa subunit (U2AF65). Both proteins mediate protein-protein and protein-RNA interactions for cooperative RNA-binding during spliceosome assembly. Here, we report the solution structure of a novel helix-hairpin domain in the N-terminal region of SF1 (SF1(NTD)). The nuclear magnetic resonance- and small-angle X-ray scattering-derived structure of a complex of the SF1(NTD) with the C-terminal U2AF homology motif domain of U2AF65 (U2AF65(UHM)) reveals that, in addition to the known U2AF65(UHM)-SF1 interaction, the helix-hairpin domain forms a secondary, hydrophobic interface with U2AF65(UHM), which locks the orientation of the two subunits. Mutational analysis shows that the helix hairpin is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. We further show that tandem serine phosphorylation of a conserved Ser80-Pro81-Ser82-Pro83 motif rigidifies a long unstructured linker in the SF1 helix hairpin. Phosphorylation does not significantly alter the overall conformations of SF1, SF1-U2AF65 or the SF1-U2AF65-RNA complexes, but slightly enhances RNA binding. Our results indicate that the helix-hairpin domain of SF1 is required for cooperative 3'-splice site recognition presumably by stabilizing a unique quaternary arrangement of the SF1-U2AF65-RNA complex.
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Affiliation(s)
- Yun Zhang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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30
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Manceau V, Kremmer E, Nabel EG, Maucuer A. The protein kinase KIS impacts gene expression during development and fear conditioning in adult mice. PLoS One 2012; 7:e43946. [PMID: 22937132 PMCID: PMC3427225 DOI: 10.1371/journal.pone.0043946] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/27/2012] [Indexed: 11/18/2022] Open
Abstract
The brain-enriched protein kinase KIS (product of the gene UHMK1) has been shown to phosphorylate the human splicing factor SF1 in vitro. This phosphorylation in turn favors the formation of a U2AF65-SF1-RNA complex which occurs at the 3′ end of introns at an early stage of spliceosome assembly. Here, we analyzed the effects of KIS knockout on mouse SF1 phosphorylation, physiology, adult behavior, and gene expression in the neonate brain. We found SF1 isoforms are differently expressed in KIS-ko mouse brains and fibroblasts. Re-expression of KIS in fibroblasts restores a wild type distribution of SF1 isoforms, confirming the link between KIS and SF1. Microarray analysis of transcripts in the neonate brain revealed a subtle down-regulation of brain specific genes including cys-loop ligand-gated ion channels and metabolic enzymes. Q-PCR analyses confirmed these defects and point to an increase of pre-mRNA over mRNA ratios, likely due to changes in splicing efficiency. While performing similarly in prepulse inhibition and most other behavioral tests, KIS-ko mice differ in spontaneous activity and contextual fear conditioning. This difference suggests that disregulation of gene expression due to KIS inactivation affects specific brain functions.
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Affiliation(s)
- Valérie Manceau
- INSERM, UMR-S 839, Paris, France
- Université Pierre et Marie Curie, Paris, France
- Institut du Fer à Moulin, Paris, France
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, München, Germany
| | - Elizabeth G. Nabel
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexandre Maucuer
- INSERM, UMR-S 839, Paris, France
- Université Pierre et Marie Curie, Paris, France
- Institut du Fer à Moulin, Paris, France
- * E-mail:
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31
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Gupta A, Kielkopf CL. Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:486-90. [PMID: 21505248 PMCID: PMC3080157 DOI: 10.1107/s1744309111004623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 02/07/2011] [Indexed: 11/11/2022]
Abstract
Pre-mRNA splicing is an essential source of genetic diversity in eukaryotic organisms. In the early stages of splicing, splicing factor 1 (SF1) recognizes the pre-mRNA splice site as a complex with its partner, U2 auxiliary factor 65 kDa subunit (U2AF(65)). A central `mystery' domain of SF1 (SF1md) lacks detectable homology with known structures, yet is the region of highest phylogenetic sequence conservation among SF1 homologues. Here, steps towards determining the SF1md structure are described. Firstly, SF1md was expressed and purified. The presence of regular secondary structure was verified using circular dichroism spectroscopy and the SF1md protein was then crystallized. A native data set was collected and processed to 2.5 Å resolution. The SF1md crystals belonged to space group C2 and have most probable solvent contents of 64, 52 or 39% with three, four or five molecules per asymmetric unit, respectively. Mutually perpendicular peaks on the κ = 180° section of the self-rotation function support the presence of four molecules in the asymmetric unit.
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Affiliation(s)
- Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Clara L. Kielkopf
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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32
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Gupta A, Jenkins JL, Kielkopf CL. RNA induces conformational changes in the SF1/U2AF65 splicing factor complex. J Mol Biol 2011; 405:1128-38. [PMID: 21146534 PMCID: PMC3037027 DOI: 10.1016/j.jmb.2010.11.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/02/2010] [Accepted: 11/27/2010] [Indexed: 10/18/2022]
Abstract
Spliceosomes assemble on pre-mRNA splice sites through a series of dynamic ribonucleoprotein complexes, yet the nature of the conformational changes remains unclear. Splicing factor 1 (SF1) and U2 auxiliary factor (U2AF(65)) cooperatively recognize the 3' splice site during the initial stages of pre-mRNA splicing. Here, we used small-angle X-ray scattering to compare the molecular dimensions and ab initio shape restorations of SF1 and U2AF(65) splicing factors, as well as the SF1/U2AF(65) complex in the absence and presence of AdML (adenovirus major late) splice site RNAs. The molecular dimensions of the SF1/U2AF(65)/RNA complex substantially contracted by 15 Å in the maximum dimension, relative to the SF1/U2AF(65) complex in the absence of RNA ligand. In contrast, no detectable changes were observed for the isolated SF1 and U2AF(65) splicing factors or their individual complexes with RNA, although slight differences in the shapes of their molecular envelopes were apparent. We propose that the conformational changes that are induced by assembly of the SF1/U2AF(65)/RNA complex serve to position the pre-mRNA splice site optimally for subsequent stages of splicing.
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Affiliation(s)
- Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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O'Hayre M, Salanga CL, Kipps TJ, Messmer D, Dorrestein PC, Handel TM. Elucidating the CXCL12/CXCR4 signaling network in chronic lymphocytic leukemia through phosphoproteomics analysis. PLoS One 2010; 5:e11716. [PMID: 20661426 PMCID: PMC2908618 DOI: 10.1371/journal.pone.0011716] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 06/29/2010] [Indexed: 01/07/2023] Open
Abstract
Background Chronic Lymphocytic Leukemia (CLL) pathogenesis has been linked to the prolonged survival and/or apoptotic resistance of leukemic B cells in vivo, and is thought to be due to enhanced survival signaling responses to environmental factors that protect CLL cells from spontaneous and chemotherapy-induced death. Although normally associated with cell migration, the chemokine, CXCL12, is one of the factors known to support the survival of CLL cells. Thus, the signaling pathways activated by CXCL12 and its receptor, CXCR4, were investigated as components of these pathways and may represent targets that if inhibited, could render resistant CLL cells more susceptible to chemotherapy. Methodology/Principal Findings To determine the downstream signaling targets that contribute to the survival effects of CXCL12 in CLL, we took a phosphoproteomics approach to identify and compare phosphopeptides in unstimulated and CXCL12-stimulated primary CLL cells. While some of the survival pathways activated by CXCL12 in CLL are known, including Akt and ERK1/2, this approach enabled the identification of additional signaling targets and novel phosphoproteins that could have implications in CLL disease and therapy. In addition to the phosphoproteomics results, we provide evidence from western blot validation that the tumor suppressor, programmed cell death factor 4 (PDCD4), is a previously unidentified phosphorylation target of CXCL12 signaling in all CLL cells probed. Additionally, heat shock protein 27 (HSP27), which mediates anti-apoptotic signaling and has previously been linked to chemotherapeutic resistance, was detected in a subset (∼25%) of CLL patients cells examined. Conclusions/Significance Since PDCD4 and HSP27 have previously been associated with cancer and regulation of cell growth and apoptosis, these proteins may have novel implications in CLL cell survival and represent potential therapeutic targets. PDCD4 also represents a previously unknown signaling target of chemokine receptors; therefore, these observations increase our understanding of alternative pathways to migration that may be activated or inhibited by chemokines in the context of cancer cell survival.
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MESH Headings
- Blotting, Western
- Cell Movement/physiology
- Cells, Cultured
- Chemokine CXCL12/genetics
- Chemokine CXCL12/metabolism
- Flow Cytometry
- HSP27 Heat-Shock Proteins/genetics
- HSP27 Heat-Shock Proteins/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mass Spectrometry
- Models, Biological
- Phosphorylation
- Proteomics/methods
- Receptors, CXCR4/genetics
- Receptors, CXCR4/metabolism
- Signal Transduction/genetics
- Signal Transduction/physiology
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Affiliation(s)
- Morgan O'Hayre
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Catherina L. Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Thomas J. Kipps
- Rebecca and John Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Davorka Messmer
- Rebecca and John Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Francone VP, Ifrim MF, Rajagopal C, Leddy CJ, Wang Y, Carson JH, Mains RE, Eipper BA. Signaling from the secretory granule to the nucleus: Uhmk1 and PAM. Mol Endocrinol 2010; 24:1543-58. [PMID: 20573687 DOI: 10.1210/me.2009-0381] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neurons and endocrine cells package peptides in secretory granules (large dense-core vesicles) for storage and stimulated release. Studies of peptidylglycine alpha-amidating monooxygenase (PAM), an essential secretory granule membrane enzyme, revealed a pathway that can relay information from secretory granules to the nucleus, resulting in alterations in gene expression. The cytosolic domain (CD) of PAM, a type 1 membrane enzyme essential for the production of amidated peptides, is basally phosphorylated by U2AF homology motif kinase 1 (Uhmk1) and other Ser/Thr kinases. Proopiomelanocortin processing in AtT-20 corticotrope tumor cells was increased when Uhmk1 expression was reduced. Uhmk1 was concentrated in the nucleus, but cycled rapidly between nucleus and cytosol. Endoproteolytic cleavage of PAM releases a soluble CD fragment that localizes to the nucleus. Localization of PAM-CD to the nucleus was decreased when PAM-CD with phosphomimetic mutations was examined and when active Uhmk1 was simultaneously overexpressed. Membrane-tethering Uhmk1 did not eliminate its ability to exclude PAM-CD from the nucleus, suggesting that cytosolic Uhmk1 could cause this response. Microarray analysis demonstrated the ability of PAM to increase expression of a small subset of genes, including aquaporin 1 (Aqp1) in AtT-20 cells. Aqp1 mRNA levels were higher in wild-type mice than in mice heterozygous for PAM, indicating that a similar relationship occurs in vivo. Expression of PAM-CD also increased Aqp1 levels whereas expression of Uhmk1 diminished Aqp1 expression. The outlines of a pathway that ties secretory granule metabolism to the transcriptome are thus apparent.
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Affiliation(s)
- Victor P Francone
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
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35
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Sette C. Post-translational regulation of star proteins and effects on their biological functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 693:54-66. [PMID: 21189685 DOI: 10.1007/978-1-4419-7005-3_4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
STAR (Signal Transduction and Activation of RNA) proteins owed their name to the presence in their structure ofa RNA-binding domain and several hallmarks of their involvement in signal transduction pathways. In many members of the family, the STAR RNA-binding domain (also named GSG, an acronym for GRP33/Sam68/ GLD-1) is flanked by regulatory regions containing proline-rich sequences, which serve as docking sites for proteins containing SH3 and WW domains and also a tyrosine-rich region at the C-terminus, which can mediateprotein-protein interactions with partners through SH2 domains. These regulatory regions contain consensus sequences for additional modifications, including serine/threonine phosphorylation, methylation, acetylation and sumoylation. Since their initial description, evidence has been gathered in different cell types and model organisms that STAR proteins can indeed integrate signals from external and internal cues with changes in transcription and processing of target RNAs. The most striking example of the high versatility of STAR proteins is provided by Sam68 (KHDRBS1), whose function, subcellular localization and affinity for RNA are strongly modulated by several signaling pathways through specific modifications. Moreover, the recent development of genetic knockout models has unveiled the physiological function of some STAR proteins, pointing to a crucial role of their post-translational modifications in the biological processes regulated by these RNA-binding proteins. This chapter offers an overview of the most updated literature on the regulation of STAR proteins by post-translational modifications and illustrates examples of how signal transduction pathways can modulate their activity and affect biological processes.
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Affiliation(s)
- Claudio Sette
- Department of Public Health and Cell Biology, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy.
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36
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Bristow GC, Lane TA, Walker M, Chen L, Sei Y, Hyde TM, Kleinman JE, Harrison PJ, Eastwood SL. Expression of kinase interacting with stathmin (KIS, UHMK1) in human brain and lymphoblasts: Effects of schizophrenia and genotype. Brain Res 2009; 1301:197-206. [PMID: 19747464 DOI: 10.1016/j.brainres.2009.08.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 08/25/2009] [Accepted: 08/26/2009] [Indexed: 12/26/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within the gene encoding the serine/threonine kinase KIS (Kinase Interacting with Stathmin, also known as UHMK1) have recently been associated with schizophrenia. As none of the disease associated SNPs are coding, they may confer susceptibility by altering some facet of KIS expression. Here we have characterised the cellular distribution of KIS in human brain using in situ hybridisation and immunohistochemistry, and quantified KIS protein and mRNA in two large brain series to determine if KIS expression is altered in schizophrenia or bipolar disorder or in relation to a schizophrenia-associated SNP (rs7513662). Post-mortem tissue from the superior temporal gyrus of schizophrenia and control subjects, and also dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum from schizophrenia, bipolar disorder, and control subjects were used. KIS expression was measured by quantitative PCR (mRNA) and immunoautoradiography (protein), and was also quantified by immunoblot in lymphoblast cell lines derived from schizophrenia and control subjects. Our results demonstrate that KIS is expressed in neurons, and its encoded protein is localised to the nucleus and cytoplasm. No difference in KIS expression was found between diagnostic groups, or in the lymphoblast cell lines, and no effect of rs7513662 genotype on KIS expression was found. Hence, these data do not provide support for the hypothesis that altered expression is the mechanism by which genetic variation of KIS may increase susceptibility to schizophrenia, nor evidence that KIS expression is altered in the disease itself, at least in terms of the parameters studied here.
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Affiliation(s)
- Greg C Bristow
- University Department of Psychiatry, Warneford Hospital, Oxford, UK
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37
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Prigge JR, Iverson SV, Siders AM, Schmidt EE. Interactome for auxiliary splicing factor U2AF(65) suggests diverse roles. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:487-92. [PMID: 19540372 DOI: 10.1016/j.bbagrm.2009.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/10/2009] [Accepted: 06/15/2009] [Indexed: 12/17/2022]
Abstract
U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) is an essential component of the splicing machinery that is composed of two protein subunits, the 35 kDa U2AF(35) (U2AF1) and the 65 kDa U2AF(65) (U2AF2). U2AF interacts with various splicing factors within this machinery. Here we expand the list of mammalian splicing factors that are known to interact with U2AF(65) as well as the list of nuclear proteins not known to participate in splicing that interact with U2AF(65). Using a yeast two-hybrid system, we found fourteen U2AF(65)-interacting proteins. The validity of the screen was confirmed by identification of five known U2AF(65)-interacting proteins, including its heterodimeric partner, U2AF(35). In addition to binding these known partners, we found previously unrecognized U2AF(65) interactions with four splicing-related proteins (DDX39, SFRS3, SFRS18, SNRPA), two zinc finger proteins (ZFP809 and ZC3H11A), a U2AF(65) homolog (RBM39), and two other regulatory proteins (DAXX and SERBP1). We report which regions of U2AF(65) each of these proteins interacts with and we discuss their potential roles in regulation of pre-mRNA splicing, 3'-end mRNA processing, and U2AF(65) sub-nuclear localization. These findings suggest expanded roles for U2AF(65) in both splicing and non-splicing functions.
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Affiliation(s)
- Justin R Prigge
- Department of Veterinary Molecular Biology, Montana State University, Molecular Biosciences, 960 Technology Blvd., Bozeman, MT 59718, USA
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38
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Cambray S, Pedraza N, Rafel M, Garí E, Aldea M, Gallego C. Protein kinase KIS localizes to RNA granules and enhances local translation. Mol Cell Biol 2009; 29:726-35. [PMID: 19015237 PMCID: PMC2630681 DOI: 10.1128/mcb.01180-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 08/22/2008] [Accepted: 11/10/2008] [Indexed: 01/11/2023] Open
Abstract
The regulation of mRNA transport is a fundamental process for cytoplasmic sorting of transcripts and spatially controlled translational derepression once properly localized. There is growing evidence that translation is locally modulated as a result of specific synaptic inputs. However, the underlying molecular mechanisms that regulate this translational process are just emerging. We show that KIS, a serine/threonine kinase functionally related to microtubule dynamics and axon development, interacts with three proteins found in RNA granules: KIF3A, NonO, and eEF1A. KIS localizes to RNA granules and colocalizes with the KIF3A kinesin and the beta-actin mRNA in cultured cortical neurons. In addition, KIS is found associated with KIF3A and 10 RNP-transported mRNAs in brain extracts. The results of knockdown experiments indicate that KIS is required for normal neurite outgrowth. More important, the kinase activity of KIS stimulates 3' untranslated region-dependent local translation in neuritic projections. We propose that KIS is a component of the molecular device that modulates translation in RNA-transporting granules as a result of local signals.
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Affiliation(s)
- Serafí Cambray
- Departament de Ciències Mèdiques Bàsiques, IRBLLEIDA, Universitat de Lleida, Lleida, Catalonia, Spain
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39
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Corsini L, Hothorn M, Stier G, Rybin V, Scheffzek K, Gibson TJ, Sattler M. Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. J Biol Chem 2008; 284:630-639. [PMID: 18974054 DOI: 10.1074/jbc.m805395200] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PUF60 is an essential splicing factor functionally related and homologous to U2AF(65). Its C-terminal domain belongs to the family of U2AF (U2 auxiliary factor) homology motifs (UHM), a subgroup of RNA recognition motifs that bind to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Here, we show that the Puf60 UHM is mainly monomeric in physiological buffer, whereas its dimerization is induced upon the addition of SDS. The crystal structure of PUF60-UHM at 2.2 angstroms resolution, NMR data, and mutational analysis reveal that the dimer interface is mediated by electrostatic interactions involving a flexible loop. Using glutathione S-transferase pulldown experiments, isothermal titration calorimetry, and NMR titrations, we find that Puf60-UHM binds to ULM sequences in the splicing factors SF1, U2AF65, and SF3b155. Compared with U2AF65-UHM, Puf60-UHM has distinct binding preferences to ULMs in the N terminus of SF3b155. Our data suggest that the functional cooperativity between U2AF65 and Puf60 may involve simultaneous interactions of the two proteins with SF3b155.
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Affiliation(s)
- Lorenzo Corsini
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Hothorn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Gunter Stier
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Vladimir Rybin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Klaus Scheffzek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany.
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40
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Manceau V, Kielkopf CL, Sobel A, Maucuer A. Different requirements of the kinase and UHM domains of KIS for its nuclear localization and binding to splicing factors. J Mol Biol 2008; 381:748-62. [PMID: 18588901 DOI: 10.1016/j.jmb.2008.06.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/07/2008] [Accepted: 06/10/2008] [Indexed: 11/29/2022]
Abstract
The protein kinase KIS is made by the juxtaposition of a unique kinase domain and a C-terminal domain with a U2AF homology motif (UHM), a sequence motif for protein interaction initially identified in the heterodimeric pre-mRNA splicing factor U2AF. This domain of KIS is closely related to the C-terminal UHM domain of the U2AF large subunit, U2AF(65). KIS phosphorylates the splicing factor SF1, which in turn enhances SF1 binding to U2AF(65) and the 3' splice site, an event known to take place at an early step of spliceosome assembly. Here, the analysis of the subcellular localization of mutated forms of KIS indicates that the kinase domain of KIS is the necessary domain for its nuclear localization. As in the case of U2AF(65), the UHM-containing C-terminal domain of KIS is required for binding to the splicing factors SF1 and SF3b155. The efficiency of KIS binding to SF1 and SF3b155 is similar to that of U2AF(65) in pull-down assays. These results further support the functional link of KIS with splicing factors. Interestingly, when compared to other UHM-containing proteins, KIS presents a different specificity for the UHM docking sites that are present in the N-terminal region of SF3b155, thus providing a new insight into the variety of interactions mediated by UHM domains.
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Affiliation(s)
- Valérie Manceau
- Institut National de la Santé et de la Recherche Médicale, UMR839, 17, rue du Fer à Moulin, F-75005 Paris, France
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Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 2007; 18:88-103. [PMID: 18032728 DOI: 10.1101/gr.6818908] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5' splice site (5'ss), the branch site (BS), and the polypyrimdine tract/3'splice site (PPT-3'ss). To study the evolution of these splicing signals, we have conducted a systematic comparative analysis of these signals in over 1.2 million introns from 22 eukaryotes. Our analyses suggest that all these signals have dramatically evolved: The PPT is weak among most fungi, intermediate in plants and protozoans, and strongest in metazoans. Within metazoans it shows a gradual strengthening from Caenorhabditis elegans to human. The 5'ss and the BS were found to be degenerate among most organisms, but highly conserved among some fungi. A maximum parsimony-based algorithm for reconstructing ancestral position-specific scoring matrices suggested that the ancestral 5'ss and BS were degenerate, as in metazoans. To shed light on the evolutionary variation in splicing signals, we have analyzed the evolutionary changes in the factors that bind these signals. Our analysis reveals coevolution of splicing signals and their corresponding splicing factors: The strength of the PPT is correlated to changes in key residues in its corresponding splicing factor U2AF2; limited correlation was found between changes in the 5'ss and U1 snRNA that binds it; but not between the BS and U2 snRNA. Thus, although the basic ability of eukaryotes to splice introns has remained conserved throughout evolution, the splicing signals and their corresponding splicing factors have considerably evolved, uniquely shaping the splicing mechanisms of different organisms.
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Affiliation(s)
- Schraga H Schwartz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
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42
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Villén J, Beausoleil SA, Gerber SA, Gygi SP. Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A 2007; 104:1488-93. [PMID: 17242355 PMCID: PMC1785252 DOI: 10.1073/pnas.0609836104] [Citation(s) in RCA: 631] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation is a complex network of signaling and regulatory events that affects virtually every cellular process. Our understanding of the nature of this network as a whole remains limited, largely because of an array of technical challenges in the isolation and high-throughput sequencing of phosphorylated species. In the present work, we demonstrate that a combination of tandem phosphopeptide enrichment methods, high performance MS, and optimized database search/data filtering strategies is a powerful tool for surveying the phosphoproteome. Using our integrated analytical platform, we report the identification of 5,635 nonredundant phosphorylation sites from 2,328 proteins from mouse liver. From this list of sites, we extracted both novel and known motifs for specific Ser/Thr kinases including a "dipolar" motif. We also found that C-terminal phosphorylation was more frequent than at any other location and that the distribution of potential kinases for these sites was unique. Finally, we identified double phosphorylation motifs that may be involved in ordered phosphorylation.
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Affiliation(s)
- Judit Villén
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | - Scott A. Gerber
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- To whom correspondence should be addressed at:
240 Longwood Avenue, Harvard Medical School, Boston, MA 02115. E-mail:
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43
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Garrey SM, Voelker R, Berglund JA. An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding. J Biol Chem 2006; 281:27443-53. [PMID: 16861232 DOI: 10.1074/jbc.m603137200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The highly conserved branch point sequence (BPS) of UACUAAC in Saccharomyces cerevisiae is initially recognized by the branch point-binding protein (BBP). Using systematic evolution of ligands by exponential enrichment we have determined that yeast BBP binds the branch point sequence UACUAAC with highest affinity and prefers an additional adenosine downstream of the BPS. Furthermore, we also found that a stem-loop upstream of the BPS enhances binding both to an artificially designed RNA (30-fold effect) and to an RNA from a yeast intron (3-fold effect). The zinc knuckles of BBP are partially responsible for the enhanced binding to the stem-loop but do not appear to have a significant role in the binding of BBP to single-strand RNA substrates. C-terminal deletions of BBP reveal that the linker regions between the two zinc knuckles and between the N-terminal RNA binding domains (KH and QUA2 domains) and the first zinc knuckle are important for binding to RNA. The lack of involvement of the second highly conserved zinc knuckle in RNA binding suggests that this zinc knuckle plays a different role in RNA processing than enhancing the binding of BBP to the BPS.
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Affiliation(s)
- Stephen M Garrey
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
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