1
|
Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P. Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding. Chem Sci 2023; 14:8269-8278. [PMID: 37564416 PMCID: PMC10411625 DOI: 10.1039/d3sc00985h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.
Collapse
Affiliation(s)
- Stefan Schmeing
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Katrin Bigler
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jen-Yao Chang
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Joseph Openy
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Posada
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| |
Collapse
|
2
|
Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn CD, Cheng X, Jiang YX, Zhou ZH, Feigon J. Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR. J Mol Biol 2023; 435:168044. [PMID: 37330293 PMCID: PMC10988774 DOI: 10.1016/j.jmb.2023.168044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains-N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65-TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65-TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65-TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.
Collapse
Affiliation(s)
- Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yao He
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yanjiao Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Mahavir Singh
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Xinyi Cheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yi Xiao Jiang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA.
| |
Collapse
|
3
|
NMR Analysis Suggests Synergy between the RRM2 and the Carboxy-Terminal Segment of Human La Protein in the Recognition and Interaction with HCV IRES. Int J Mol Sci 2023; 24:ijms24032572. [PMID: 36768895 PMCID: PMC9916714 DOI: 10.3390/ijms24032572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
The La protein (lupus antigen) is a ubiquitous RNA-binding protein found in all human cells. It is mainly localized in the nucleus, associates with all RNA polymerase III (Pol III) transcripts, as the first factor they interact with, and modulates subsequent processing events. Export of La to the cytoplasm has been reported to stimulate the decoding of specific cellular and viral mRNAs through IRES-dependent (Internal ribosome entry site) binding and translation. Using NMR (Nuclear Magnetic Resonance) spectroscopy, we provide atomic-level-resolution structural insights on the dynamical properties of human La (hLa) protein in solution. Moreover, using a combination of NMR spectroscopy and isothermal titration calorimetry (ITC), we provide evidence about the role and ligand specificity of the C-terminal domain of the La protein (RRM2 and C-terminal region) that could mediate the recognition of HCV-IRES.
Collapse
|
4
|
Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum. Int J Biol Macromol 2022; 224:1101-1117. [DOI: 10.1016/j.ijbiomac.2022.10.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
|
5
|
Liu R, Verma N, Henderson JA, Zhan S, Shen J. Profiling MAP kinase cysteines for targeted covalent inhibitor design. RSC Med Chem 2022; 13:54-63. [PMID: 35224496 PMCID: PMC8792824 DOI: 10.1039/d1md00277e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/28/2021] [Indexed: 07/20/2023] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important therapeutic targets, and yet no inhibitors have advanced to the market. Here we applied the GPU-accelerated continuous constant pH molecular dynamics (CpHMD) to calculate the pK a's and profile the cysteine reactivities of all 14 MAPKs for assisting the targeted covalent inhibitor design. The simulations not only recapitulated but also rationalized the reactive cysteines in the front pocket of JNK1/2/3 and the extended front pocket of p38α. Interestingly, the DFG - 1 cysteine in the DFG-in conformation of ERK1/ERK2 was found somewhat reactive or unreactive; however, simulations of MKK7 showed that switching to the DFG-out conformation makes the DFG - 1 cysteine reactive, suggesting the advantage of type II covalent inhibitors. Additionally, the simulations prospectively predicted several druggable cysteine and lysine sites, including the αH head cysteine in JNK1/3 and DFG + 6 cysteine in JNK2, corroborating the chemical proteomic screening data. Given the low cost and the ability to offer physics-based rationales, we envision CpHMD simulations to complement the chemo-proteomic platform for systematic profiling cysteine reactivities for targeted covalent drug discovery.
Collapse
Affiliation(s)
- Ruibin Liu
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Neha Verma
- University of Maryland School of Pharmacy Baltimore MD USA
| | | | - Shaoqi Zhan
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Jana Shen
- University of Maryland School of Pharmacy Baltimore MD USA
| |
Collapse
|
6
|
Soubise B, Jiang Y, Douet-Guilbert N, Troadec MB. RBM22, a Key Player of Pre-mRNA Splicing and Gene Expression Regulation, Is Altered in Cancer. Cancers (Basel) 2022; 14:cancers14030643. [PMID: 35158909 PMCID: PMC8833553 DOI: 10.3390/cancers14030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/05/2023] Open
Abstract
RNA-Binding Proteins (RBP) are very diverse and cover a large number of functions in the cells. This review focuses on RBM22, a gene encoding an RBP and belonging to the RNA-Binding Motif (RBM) family of genes. RBM22 presents a Zinc Finger like and a Zinc Finger domain, an RNA-Recognition Motif (RRM), and a Proline-Rich domain with a general structure suggesting a fusion of two yeast genes during evolution: Cwc2 and Ecm2. RBM22 is mainly involved in pre-mRNA splicing, playing the essential role of maintaining the conformation of the catalytic core of the spliceosome and acting as a bridge between the catalytic core and other essential protein components of the spliceosome. RBM22 is also involved in gene regulation, and is able to bind DNA, acting as a bona fide transcription factor on a large number of target genes. Undoubtedly due to its wide scope in the regulation of gene expression, RBM22 has been associated with several pathologies and, notably, with the aggressiveness of cancer cells and with the phenotype of a myelodysplastic syndrome. Mutations, enforced expression level, and haploinsufficiency of RBM22 gene are observed in those diseases. RBM22 could represent a potential therapeutic target in specific diseases, and, notably, in cancer.
Collapse
Affiliation(s)
- Benoît Soubise
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
| | - Yan Jiang
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- Department of Hematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Nathalie Douet-Guilbert
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
| | - Marie-Bérengère Troadec
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
- Correspondence: ; Tel.: +33-2-98-01-64-55
| |
Collapse
|
7
|
Berndt N, Bippes CC, Michalk I, Bartsch T, Arndt C, Puentes-Cala E, Soto JA, Loureiro LR, Kegler A, Bachmann D, Gross JK, Gross T, Kurien BT, Scofield RH, Farris AD, James JA, Bergmann R, Schmitz M, Feldmann A, Bachmann MP. And Yet It Moves: Oxidation of the Nuclear Autoantigen La/SS-B Is the Driving Force for Nucleo-Cytoplasmic Shuttling. Int J Mol Sci 2021; 22:9699. [PMID: 34575862 PMCID: PMC8470643 DOI: 10.3390/ijms22189699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/10/2023] Open
Abstract
Decades ago, we and many other groups showed a nucleo-cytoplasmic translocation of La protein in cultured cells. This shuttling of La protein was seen after UV irradiation, virus infections, hydrogen peroxide exposure and the Fenton reaction based on iron or copper ions. All of these conditions are somehow related to oxidative stress. Unfortunately, these harsh conditions could also cause an artificial release of La protein. Even until today, the shuttling and the cytoplasmic function of La/SS-B is controversially discussed. Moreover, the driving mechanism for the shuttling of La protein remains unclear. Recently, we showed that La protein undergoes redox-dependent conformational changes. Moreover, we developed anti-La monoclonal antibodies (anti-La mAbs), which are specific for either the reduced form of La protein or the oxidized form. Using these tools, here we show that redox-dependent conformational changes are the driving force for the shuttling of La protein. Moreover, we show that translocation of La protein to the cytoplasm can be triggered in a ligand/receptor-dependent manner under physiological conditions. We show that ligands of toll-like receptors lead to a redox-dependent shuttling of La protein. The shuttling of La protein depends on the redox status of the respective cell type. Endothelial cells are usually resistant to the shuttling of La protein, while dendritic cells are highly sensitive. However, the deprivation of intracellular reducing agents in endothelial cells makes endothelial cells sensitive to a redox-dependent shuttling of La protein.
Collapse
Affiliation(s)
- Nicole Berndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Claudia C. Bippes
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Irene Michalk
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Tabea Bartsch
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Edinson Puentes-Cala
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
- Corporación para la Investigación de la Corrosión (CIC), Piedecuesta 681011, Colombia
| | - Javier Andrés Soto
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
- Instituto de Investigación Masira, Facultad de Ciencias Médicas y de la Salud, Universidad de Santander, Cúcuta 540001, Colombia
| | - Liliana R. Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Alexandra Kegler
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Dominik Bachmann
- Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus Technische Universität Dresden, 01307 Dresden, Germany;
| | - Joanne K. Gross
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Tim Gross
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Biji T. Kurien
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - R. Hal Scofield
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - A. Darise Farris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Judith A. James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Ralf Bergmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
- Department of Biophysics and Radiobiology, Semmelweis University, 1094 Budapest, Hungary
| | - Marc Schmitz
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- National Center for Tumor Diseases (NCT), 03128 Dresden, Germany
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
| | - Michael P. Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (T.B.); (C.A.); (E.P.-C.); (J.A.S.); (L.R.L.); (A.K.); (R.B.); (A.F.)
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- National Center for Tumor Diseases (NCT), 03128 Dresden, Germany
| |
Collapse
|
8
|
Berndt N, Bippes CC, Michalk I, Bachmann D, Bachmann J, Puentes-Cala E, Bartsch T, Loureiro LR, Kegler A, Bergmann R, Gross JK, Gross T, Kurien BT, Scofield RH, Farris AD, James JA, Schmitz M, Fahmy K, Feldmann A, Arndt C, Bachmann MP. Two Be or Not Two Be: The Nuclear Autoantigen La/SS-B Is Able to Form Dimers and Oligomers in a Redox Dependent Manner. Int J Mol Sci 2021; 22:3377. [PMID: 33806091 PMCID: PMC8036718 DOI: 10.3390/ijms22073377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
According to the literature, the autoantigen La is involved in Cap-independent translation. It was proposed that one prerequisite for this function is the formation of a protein dimer. However, structural analyses argue against La protein dimers. Noteworthy to mention, these structural analyses were performed under reducing conditions. Here we describe that La protein can undergo redox-dependent structural changes. The oxidized form of La protein can form dimers, oligomers and even polymers stabilized by disulfide bridges. The primary sequence of La protein contains three cysteine residues. Only after mutation of all three cysteine residues to alanine La protein becomes insensitive to oxidation, indicating that all three cysteines are involved in redox-dependent structural changes. Biophysical analyses of the secondary structure of La protein support the redox-dependent conformational changes. Moreover, we identified monoclonal anti-La antibodies (anti-La mAbs) that react with either the reduced or oxidized form of La protein. Differential reactivities to the reduced and oxidized form of La protein were also found in anti-La sera of autoimmune patients.
Collapse
Affiliation(s)
- Nicole Berndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Claudia C. Bippes
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Irene Michalk
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Dominik Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Jennifer Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Edinson Puentes-Cala
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Corporación para la Investigación de la Corrosión (CIC), Piedecuesta 681011, Colombia
| | - Tabea Bartsch
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Liliana R. Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Alexandra Kegler
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Ralf Bergmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Department of Biophysics and Radiobiology, Semmelweis University, 1094 Budapest, Hungary
| | - Joanne K. Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Tim Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Biji T. Kurien
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - R. Hal Scofield
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - A. Darise Farris
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Judith A. James
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Marc Schmitz
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany;
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Michael P. Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| |
Collapse
|
9
|
Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021; 27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
Abstract
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding of misfolded substrates into functional conformations. The best characterized tRNA chaperone is the La protein, which interacts with nascent RNA polymerase III transcripts to promote folding and offers protection from exonucleases. More recently, certain tRNA modification enzymes have also been demonstrated to possess tRNA folding activity distinct from their catalytic activity, suggesting that they may act as tRNA chaperones. In this review, we will discuss pioneering studies relating post-transcriptional modification to tRNA stability and decay pathways, present recent advances into the mechanism by which the RNA chaperone La assists pre-tRNA maturation, and summarize emerging research directions aimed at characterizing modification enzymes as tRNA chaperones. Together, these findings shed light on the importance of tRNA folding and how tRNA chaperones, in particular, increase the fraction of nascent pre-tRNAs that adopt a folded, functional conformation.
Collapse
|
10
|
Bayfield MA, Vinayak J, Kerkhofs K, Mansouri-Noori F. La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates. RNA Biol 2021; 18:168-177. [PMID: 30777481 PMCID: PMC7928037 DOI: 10.1080/15476286.2019.1582955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
La shuttles between the nucleus and cytoplasm where it binds nascent RNA polymerase III (pol III) transcripts and mRNAs, respectively. La protects the 3' end of pol III transcribed RNA precursors, such as pre-tRNAs, through the use of a well-characterized UUU-3'OH binding mode. La proteins are also RNA chaperones, and La-dependent RNA chaperone activity is hypothesized to promote pre-tRNA maturation and translation at cellular and viral internal ribosome entry sites via binding sites distinct from those used for UUU-3'OH recognition. Since the publication of La-UUU-3'OH co-crystal structures, biochemical and genetic experiments have expanded our understanding of how La proteins use UUU-3'OH-independent binding modes to make sequence-independent contacts that can increase affinity for ligands and promote RNA remodeling. Other recent work has also expanded our understanding of how La binds mRNAs through contacts to the poly(A) tail. In this review, we focus on advances in the study of La protein-RNA complex surfaces beyond the description of the La-UUU-3'OH binding mode. We highlight recent advances in the functions of expected canonical nucleic acid interaction surfaces, a heightened appreciation of disordered C-terminal regions, and the nature of sequence-independent RNA determinants in La-RNA target binding. We further discuss how these RNA binding modes may have relevance to the function of the La-related proteins.
Collapse
Affiliation(s)
- Mark A. Bayfield
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jyotsna Vinayak
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Kyra Kerkhofs
- Department of Biology, York University, Toronto, Ontario, Canada
| | | |
Collapse
|
11
|
Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
12
|
Mattijssen S, Kozlov G, Gaidamakov S, Ranjan A, Fonseca BD, Gehring K, Maraia RJ. The isolated La-module of LARP1 mediates 3' poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1. RNA Biol 2021; 18:275-289. [PMID: 33292040 PMCID: PMC7928023 DOI: 10.1080/15476286.2020.1860376] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the LARPs in linker length and RRM subtype. The La-modules of La protein and LARP7 bind and protect nuclear RNAs with UUU-3' tails from degradation by 3' exonucleases. LARP4 is an mRNA poly(A) stabilization factor that binds poly(A) and the cytoplasmic poly(A)-binding protein PABPC1 (also known as PABP). LARP1 exhibits poly(A) length protection and mRNA stabilization similar to LARP4. Here, we show that these LARP1 activities are mediated by its La-module and dependent on a PAM2 motif that binds PABP. The isolated La-module of LARP1 is sufficient for PABP-dependent poly(A) length protection and mRNA stabilization in HEK293 cells. A point mutation in the PAM2 motif in the La-module impairs mRNA stabilization and PABP binding in vivo but does not impair oligo(A) RNA binding by the purified recombinant La-module in vitro. We characterize the unusual PAM2 sequence of LARP1 and show it may differentially affect stable and unstable mRNAs. The unique LARP1 La-module can function as an autonomous factor to confer poly(A) protection and stabilization to heterologous mRNAs.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Amitabh Ranjan
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA
| |
Collapse
|
13
|
Bachmann MP, Bartsch T, Bippes CC, Bachmann D, Puentes-Cala E, Bachmann J, Bartsch H, Arndt C, Koristka S, Loureiro LR, Kegler A, Laube M, Gross JK, Gross T, Kurien BT, Scofield RH, Farris AD, James JA, Schmitz M, Feldmann A. T Cell Mediated Conversion of a Non-Anti-La Reactive B Cell to an Autoreactive Anti-La B Cell by Somatic Hypermutation. Int J Mol Sci 2021; 22:1198. [PMID: 33530489 PMCID: PMC7865296 DOI: 10.3390/ijms22031198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Since the first description of nuclear autoantigens in the late 1960s and early 1970s, researchers, including ourselves, have found it difficult to establish monoclonal antibodies (mabs) against nuclear antigens, including the La/SS-B (Sjögrens' syndrome associated antigen B) autoantigen. To date, only a few anti-La mabs have been derived by conventional hybridoma technology; however, those anti-La mabs were not bona fide autoantibodies as they recognize either human La specific, cryptic, or post-translationally modified epitopes which are not accessible on native mouse La protein. Herein, we present a series of novel murine anti-La mabs including truly autoreactive ones. These mabs were elicited from a human La transgenic animal through adoptive transfer of T cells from non-transgenic mice immunized with human La antigen. Detailed epitope and paratope analyses experimentally confirm the hypothesis that somatic hypermutations that occur during T cell dependent maturation can lead to autoreactivity to the nuclear La/SS-B autoantigen.
Collapse
Affiliation(s)
- Michael P. Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tabea Bartsch
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Claudia C. Bippes
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (H.B.); (M.S.)
| | - Dominik Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Edinson Puentes-Cala
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
- Corporación para la Investigación de la Corrosión (CIC), Piedecuesta, Santander 681011, Colombia
| | - Jennifer Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Holger Bartsch
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (H.B.); (M.S.)
| | - Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Stefanie Koristka
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Liliana R. Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Alexandra Kegler
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Markus Laube
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| | - Joanne K. Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Tim Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Biji T. Kurien
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - R. Hal Scofield
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - A. Darise Farris
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Judith A. James
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Marc Schmitz
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (H.B.); (M.S.)
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 03128 Dresden, Germany; (T.B.); (E.P.-C.); (C.A.); (S.K.); (L.R.L.); (A.K.); (M.L.); (A.F.)
| |
Collapse
|
14
|
Kaliatsi EG, Argyriou AI, Bouras G, Apostolidi M, Konstantinidou P, Shaukat AN, Spyroulias GA, Stathopoulos C. Functional and Structural Aspects of La Protein Overexpression in Lung Cancer. J Mol Biol 2020; 432:166712. [PMID: 33197462 DOI: 10.1016/j.jmb.2020.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
La is an abundant phosphoprotein that protects polymerase III transcripts from 3'-5' exonucleolytic degradation and facilitates their folding. Consisting of the evolutionary conserved La motif (LAM) and two consecutive RNA Recognition Motifs (RRMs), La was also found to bind additional RNA transcripts or RNA domains like internal ribosome entry site (IRES), through sequence-independent binding modes which are poorly understood. Although it has been reported overexpressed in certain cancer types and depletion of its expression sensitizes cancer cells to certain chemotherapeutic agents, its role in cancer remains essentially uncharacterized. Herein, we study the effects of La overexpression in A549 lung adenocarcinoma cells, which leads to increased cell proliferation and motility. Expression profiling of several transcription and translation factors indicated that La overexpression leads to downregulation of global translation through hypophosphorylation of 4E-BPs and upregulation of IRES-mediated translation. Moreover, analysis of La localization after nutrition deprivation of the transfected cells showed a normal distribution in the nucleus and nucleoli. Although the RNA binding capacity of La has been primarily linked to the synergy between the conserved LAM and RRM1 domains which act as a module, we show that recombinant stand-alone LAM can specifically bind a pre-tRNA ligand, based on binding experiments combined with NMR analysis. We propose that LAM RNA binding properties could support the expanding and diverse RNA ligand repertoire of La, thus promoting its modulatory role, both under normal and pathogenic conditions like cancer.
Collapse
Affiliation(s)
- Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Georgios Bouras
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | | | | | | |
Collapse
|
15
|
Basu R, Eichhorn CD, Cheng R, Peterson RD, Feigon J. Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins. RNA Biol 2020; 18:1181-1192. [PMID: 33131423 DOI: 10.1080/15476286.2020.1836891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein complex that maintains the telomeric DNA at eukaryotic chromosome ends. p65 is important for the ordered assembly of telomerase RNA (TER) with telomerase reverse transcriptase. Unexpectedly, Schizosaccharomyces pombe Pof8 was recently identified as a LARP7 protein and a core component of fission yeast telomerase essential for biogenesis. LARP7 proteins have a conserved N-terminal La motif and RRM1 (La module) and C-terminal RRM2 with specific RNA substrate recognition attributed to RRM2, first structurally characterized in p65 as an atypical RRM named xRRM. Here we present the X-ray crystal structure and NMR studies of S. pombe Pof8 RRM2. Sequence and structure comparison of Pof8 RRM2 to p65 and human Larp7 xRRMs reveals conserved features for RNA binding with the main variability in the length of the non-canonical helix α3. This study shows that Pof8 has conserved xRRM features, providing insight into TER recognition and the defining characteristics of the xRRM.
Collapse
Affiliation(s)
- Ritwika Basu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ryan Cheng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert D Peterson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| |
Collapse
|
16
|
Abstract
RNA-binding proteins are important regulators of RNA metabolism and are of critical importance in all steps of the gene expression cascade. The role of aberrantly expressed RBPs in human disease is an exciting research field and the potential application of RBPs as a therapeutic target or a diagnostic marker represents a fast-growing area of research.Aberrant overexpression of the human RNA-binding protein La has been found in various cancer entities including lung, cervical, head and neck, and chronic myelogenous leukaemia. Cancer-associated La protein supports tumour-promoting processes such as proliferation, mobility, invasiveness and tumour growth. Moreover, the La protein maintains the survival of cancer cells by supporting an anti-apoptotic state that may cause resistance to chemotherapeutic therapy.The human La protein represents a multifunctional post-translationally modified RNA-binding protein with RNA chaperone activity that promotes processing of non-coding precursor RNAs but also stimulates the translation of selective messenger RNAs encoding tumour-promoting and anti-apoptotic factors. In our model, La facilitates the expression of those factors and helps cancer cells to cope with cellular stress. In contrast to oncogenes, able to initiate tumorigenesis, we postulate that the aberrantly elevated expression of the human La protein contributes to the non-oncogenic addiction of cancer cells. In this review, we summarize the current understanding about the implications of the RNA-binding protein La in cancer progression and therapeutic resistance. The concept of exploiting the RBP La as a cancer drug target will be discussed.
Collapse
Affiliation(s)
- Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| |
Collapse
|
17
|
Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
Collapse
Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| |
Collapse
|
18
|
Affiliation(s)
- Gábor Erdős
- Department of Biochemistry, MTA‐ELTE Momentum Bioinformatics Research Group ELTE Eötvös Loránd University Budapest Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, MTA‐ELTE Momentum Bioinformatics Research Group ELTE Eötvös Loránd University Budapest Hungary
| |
Collapse
|
19
|
Dock-Bregeon AC, Lewis KA, Conte MR. The La-related proteins: structures and interactions of a versatile superfamily of RNA-binding proteins. RNA Biol 2019; 18:178-193. [PMID: 31752575 DOI: 10.1080/15476286.2019.1695712] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The La-related proteins (LaRPs) are an ancient superfamily of RNA-binding proteins orchestrating the major fates of RNA, from processing and maturation to regulation of mRNA translation. LaRPs are instrumental in modulating complex assemblies where the RNA is bound, folded, processed, escorted and presented to the functional effectors often through recruitment of protein partners. This intricate web of protein-RNA and protein-protein interactions is enabled by the modular nature of the LaRPs, comprising several structured domains connected by flexible linkers, and other sequences lacking recognizable folded motifs. Recent structures, together with biochemical and biophysical studies, have provided insights into how each LaRP family has evolved unique mechanisms of RNA recognition, not only through the conserved RNA-binding unit, the La-module, but also mediated by other family-specific motifs. Furthermore, in a series of unexpected twists and turns, they have revealed that the dynamic and conformational interplay of multi-structured domains and disordered regions operate in unison to achieve RNA substrate discrimination. This review proposes a perspective of our current knowledge of the structure-function relationship of the LaRP superfamily.
Collapse
Affiliation(s)
| | - Karen A Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| |
Collapse
|
20
|
Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S. RRMdb-an evolutionary-oriented database of RNA recognition motif sequences. Database (Oxford) 2019; 2019:5289646. [PMID: 30649297 PMCID: PMC6334006 DOI: 10.1093/database/bay148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/24/2018] [Accepted: 12/20/2018] [Indexed: 11/14/2022]
Abstract
RNA-recognition motif (RRM) is an RNA-interacting protein domain that plays an important role in the processes of RNA metabolism such as the splicing, editing, export, degradation, and regulation of translation. Here, we present the RNA-recognition motif database (RRMdb), which affords rapid identification and annotation of RRM domains in a given protein sequence. The RRMdb database is compiled from ~57 000 collected representative RRM domain sequences, classified into 415 families. Whenever possible, the families are associated with the available literature and structural data. Moreover, the RRM families are organized into a network of sequence similarities that allows for the assessment of the evolutionary relationships between them.
Collapse
Affiliation(s)
- Martyna Nowacka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elzbieta Jankowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Tomasz Jarzynka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| |
Collapse
|
21
|
Marrella SA, Brown KA, Mansouri-Noori F, Porat J, Wilson DJ, Bayfield MA. An interdomain bridge influences RNA binding of the human La protein. J Biol Chem 2018; 294:1529-1540. [PMID: 30530494 DOI: 10.1074/jbc.ra118.003995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
La proteins are RNA chaperones that perform various functions depending on distinct RNA-binding modes and their subcellular localization. In the nucleus, they help process UUU-3'OH-tailed nascent RNA polymerase III transcripts, such as pre-tRNAs, whereas in the cytoplasm they contribute to translation of poly(A)-tailed mRNAs. La accumulation in the nucleus and cytoplasm is controlled by several trafficking elements, including a canonical nuclear localization signal in the extreme C terminus and a nuclear retention element (NRE) in the RNA recognition motif 2 (RRM2) domain. Previous findings indicate that cytoplasmic export of La due to mutation of the NRE can be suppressed by mutations in RRM1, but the mechanism by which the RRM1 and RRM2 domains functionally cooperate is poorly understood. In this work, we use electromobility shift assays (EMSA) to show that mutations in the NRE and RRM1 affect binding of human La to pre-tRNAs but not UUU-3'OH or poly(A) sequences, and we present compensatory mutagenesis data supporting a direct interaction between the RRM1 and RRM2 domains. Moreover, we use collision-induced unfolding and time-resolved hydrogen-deuterium exchange MS analyses to study the conformational dynamics that occur when this interaction is intact or disrupted. Our results suggest that the intracellular distribution of La may be linked to its RNA-binding modes and provide the first evidence for a direct protein-protein interdomain interaction in La proteins.
Collapse
Affiliation(s)
- Stefano A Marrella
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Kerene A Brown
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Farnaz Mansouri-Noori
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jennifer Porat
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada.
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
| |
Collapse
|
22
|
Eichhorn CD, Yang Y, Repeta L, Feigon J. Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7. Proc Natl Acad Sci U S A 2018; 115:E6457-E6466. [PMID: 29946027 PMCID: PMC6048529 DOI: 10.1073/pnas.1806276115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The La and the La-related protein (LARP) superfamily is a diverse class of RNA binding proteins involved in RNA processing, folding, and function. Larp7 binds to the abundant long noncoding 7SK RNA and is required for 7SK ribonucleoprotein (RNP) assembly and function. The 7SK RNP sequesters a pool of the positive transcription elongation factor b (P-TEFb) in an inactive state; on release, P-TEFb phosphorylates RNA Polymerase II to stimulate transcription elongation. Despite its essential role in transcription, limited structural information is available for the 7SK RNP, particularly for protein-RNA interactions. Larp7 contains an N-terminal La module that binds UUU-3'OH and a C-terminal atypical RNA recognition motif (xRRM) required for specific binding to 7SK and P-TEFb assembly. Deletion of the xRRM is linked to gastric cancer in humans. We report the 2.2-Å X-ray crystal structure of the human La-related protein group 7 (hLarp7) xRRM bound to the 7SK stem-loop 4, revealing a unique binding interface. Contributions of observed interactions to binding affinity were investigated by mutagenesis and isothermal titration calorimetry. NMR 13C spin relaxation data and comparison of free xRRM, RNA, and xRRM-RNA structures show that the xRRM is preordered to bind a flexible loop 4. Combining structures of the hLarp7 La module and the xRRM-7SK complex presented here, we propose a structural model for Larp7 binding to the 7SK 3' end and mechanism for 7SK RNP assembly. This work provides insight into how this domain contributes to 7SK recognition and assembly of the core 7SK RNP.
Collapse
Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Lucas Repeta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| |
Collapse
|
23
|
Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M. Crystal structure of human Acinus RNA recognition motif domain. PeerJ 2018; 6:e5163. [PMID: 30042883 PMCID: PMC6057467 DOI: 10.7717/peerj.5163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
Acinus is an abundant nuclear protein involved in apoptosis and splicing. It has been implicated in inducing apoptotic chromatin condensation and DNA fragmentation during programmed cell death. Acinus undergoes activation by proteolytic cleavage that produces a truncated p17 form that comprises only the RNA recognition motif (RRM) domain. We have determined the crystal structure of the human Acinus RRM domain (AcRRM) at 1.65 Å resolution. It shows a classical four-stranded antiparallel β-sheet fold with two flanking α-helices and an additional, non-classical α-helix at the C-terminus, which harbors the caspase-3 target sequence that is cleaved during Acinus activation. In the structure, the C-terminal α-helix partially occludes the potential ligand binding surface of the β-sheet and hypothetically shields it from non-sequence specific interactions with RNA. Based on the comparison with other RRM-RNA complex structures, it is likely that the C-terminal α-helix changes its conformation with respect to the RRM core in order to enable RNA binding by Acinus.
Collapse
Affiliation(s)
- Humberto Fernandes
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Katarzyna Grudziaz
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Martyna Nowacka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| |
Collapse
|
24
|
Dahlin JL, Cuellar M, Singh G, Nelson KM, Strasser J, Rappe T, Xia Y, Veglia G, Walters MA. ALARM NMR for HTS triage and chemical probe validation. ACTA ACUST UNITED AC 2018; 10:91-117. [PMID: 30034947 DOI: 10.1002/cpch.35] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nonspecific target engagement by test compounds and purported chemical probes is a significant source of assay interference and promiscuous bioactivity in high-throughput screening (HTS) and chemical biology. Most counter-screens for thiol-reactive compounds utilize mass spectrometry or fluorescence detection, and non-proteinaceous reporters like glutathione that may not always approximate the reactivity of protein side-chains. By contrast, a La assay to detect reactive molecules by nuclear magnetic resonance (ALARM NMR) is an industry-developed protein-based [1H-13C]-heteronuclear multiple quantum coherence (HMQC) NMR counter-screen to identify nonspecific protein interactions by test compounds by reporting their tendencies to modulate the human La antigen conformation. This Current Protocol is a users-guide to the production of the 13C-labeled La antigen reporter protein, the reaction of test compounds with this reporter protein, as well as the collection and analysis of characteristic NMR spectra. Combined with other assay interference counter-screens, this assay will enhance chemical biology by helping researchers better prioritize chemical matter and which will increase the number of tractable HTS screening actives and aid in the development of better chemical probes.
Collapse
Affiliation(s)
- Jayme L Dahlin
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Gurpreet Singh
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn M Nelson
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Jessica Strasser
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Todd Rappe
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
25
|
Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
Collapse
Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
| |
Collapse
|
26
|
García-Mauriño SM, Díaz-Quintana A, Rivero-Rodríguez F, Cruz-Gallardo I, Grüttner C, Hernández-Vellisca M, Díaz-Moreno I. A putative RNA binding protein from Plasmodium vivax apicoplast. FEBS Open Bio 2017; 8:177-188. [PMID: 29435408 PMCID: PMC5794462 DOI: 10.1002/2211-5463.12351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/03/2017] [Accepted: 11/14/2017] [Indexed: 01/30/2023] Open
Abstract
Malaria is caused by Apicomplexa protozoans from the Plasmodium genus entering the bloodstream of humans and animals through the bite of the female mosquitoes. The annotation of the Plasmodium vivax genome revealed a putative RNA binding protein (apiRBP) that was predicted to be trafficked into the apicoplast, a plastid organelle unique to Apicomplexa protozoans. Although a 3D structural model of the apiRBP corresponds to a noncanonical RNA recognition motif with an additional C‐terminal α‐helix (α3), preliminary protein production trials were nevertheless unsuccessful. Theoretical solvation analysis of the apiRBP model highlighted an exposed hydrophobic region clustering α3. Hence, we used a C‐terminal GFP‐fused chimera to stabilize the highly insoluble apiRBP and determined its ability to bind U‐rich stretches of RNA. The affinity of apiRBP toward such RNAs is highly dependent on ionic strength, suggesting that the apiRBP–RNA complex is driven by electrostatic interactions. Altogether, apiRBP represents an attractive tool for apicoplast transcriptional studies and for antimalarial drug design.
Collapse
Affiliation(s)
- Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Francisco Rivero-Rodríguez
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | | | - Christian Grüttner
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Marian Hernández-Vellisca
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| |
Collapse
|
27
|
Franco-Echevarría E, González-Polo N, Zorrilla S, Martínez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sánchez M, Calvo O, González B, Pérez-Cañadillas JM. The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Nucleic Acids Res 2017; 45:10293-10305. [PMID: 28973465 PMCID: PMC5737872 DOI: 10.1093/nar/gkx685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022] Open
Abstract
Transcription termination of non-coding RNAs is regulated in yeast by a complex of three RNA binding proteins: Nrd1, Nab3 and Sen1. Nrd1 is central in this process by interacting with Rbp1 of RNA polymerase II, Trf4 of TRAMP and GUAA/G terminator sequences. We lack structural data for the last of these binding events. We determined the structures of Nrd1 RNA binding domain and its complexes with three GUAA-containing RNAs, characterized RNA binding energetics and tested rationally designed mutants in vivo. The Nrd1 structure shows an RRM domain fused with a second α/β domain that we name split domain (SD), because it is formed by two non-consecutive segments at each side of the RRM. The GUAA interacts with both domains and with a pocket of water molecules, trapped between the two stacking adenines and the SD. Comprehensive binding studies demonstrate for the first time that Nrd1 has a slight preference for GUAA over GUAG and genetic and functional studies suggest that Nrd1 RNA binding domain might play further roles in non-coding RNAs transcription termination.
Collapse
Affiliation(s)
- Elsa Franco-Echevarría
- Departament of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Silvia Zorrilla
- Department of Cellular and Molecular Biology, Biological Research Center, CSIC
| | - Santiago Martínez-Lumbreras
- Department of Chemistry, King's College London.,Department of Biological Physical Chemistry, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | - Clara M Santiveri
- Spectroscopy and Nuclear Magnetic Resonance Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre
| | - Ramón Campos-Olivas
- Spectroscopy and Nuclear Magnetic Resonance Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca
| | - Beatriz González
- Departament of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | - José Manuel Pérez-Cañadillas
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| |
Collapse
|
28
|
Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| |
Collapse
|
29
|
Platelet phosphorylated TDP-43: an exploratory study for a peripheral surrogate biomarker development for Alzheimer's disease. Future Sci OA 2017; 3:FSO238. [PMID: 29134122 PMCID: PMC5674277 DOI: 10.4155/fsoa-2017-0090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/28/2017] [Indexed: 12/13/2022] Open
Abstract
Aim: Alzheimer's disease (AD) and other forms of dementia create a noncurable disease population in world's societies. To develop a blood-based biomarker is important so that the remedial or disease-altering therapeutic intervention for AD patients would be available at the early stage. Materials & methods: TDP-43 levels were analyzed in postmortem brain tissue and platelets of AD and control subjects. Results: We observed an increased TDP-43 (<60%) in postmortem AD brain regions and similar trends were also observed in patient's platelets. Conclusion: Platelet TDP-43 could be used as a surrogate biomarker that is measurable, reproducible and sensitive for screening the patients with some early clinical signs of AD and can be used to monitor disease prognosis. In this study, we explore to identify an Alzheimer's disease (AD)-selective phospho-specific antibody that recognizes the diseased form of TDP-43 protein in patient's blood-derived platelets. Our results suggest that selective antiphosphorylated TDP-43 antibody discriminates AD from non-demented controls and patients with amyotrophic lateral sclerosis. Therefore, platelet screening with a selective antibody could potentially be a useful tool for diagnostic purposes for AD.
Collapse
|
30
|
Zhang J, Gonzalez LE, Hall TMT. Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Nucleic Acids Res 2017; 45:2829-2837. [PMID: 27789691 PMCID: PMC5389651 DOI: 10.1093/nar/gkw961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/13/2016] [Indexed: 01/23/2023] Open
Abstract
The RNA recognition motif (RRM) is the most abundant RNA-binding domain in eukaryotes, and it plays versatile roles in RNA metabolism. Despite its abundance, diversity of RRM structure and function is generated by variations on a conserved core. Yeast Nop15 is an RRM protein that is essential for large ribosomal subunit biogenesis. We determined a 2.0 Å crystal structure of Nop15 that reveals a C-terminal α-helical region obscures its canonical RNA-binding surface. Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible, but essential for tight RNA binding. Moreover, comparison with a recently reported cryo-electron microscopy structure indicates that dramatic rearrangement of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize the base of its stem-loop target RNA and extends a newly-formed α helix to the distal loop where it forms protein interactions.
Collapse
Affiliation(s)
- Jun Zhang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, MD F3-05, Research Triangle Park, NC 27709, USA
| | - Lauren E Gonzalez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, MD F3-05, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, MD F3-05, Research Triangle Park, NC 27709, USA
| |
Collapse
|
31
|
Brown KA, Sharifi S, Hussain R, Donaldson L, Bayfield MA, Wilson DJ. Distinct Dynamic Modes Enable the Engagement of Dissimilar Ligands in a Promiscuous Atypical RNA Recognition Motif. Biochemistry 2016; 55:7141-7150. [PMID: 27959512 DOI: 10.1021/acs.biochem.6b00995] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes. In particular, binding of the single-stranded RNA induces helical "unwinding" in a region of the CTD previously hypothesized to play an important role in La and La-related protein-associated RNA remodeling, while the same region becomes less dynamic upon engagement with the double-stranded HCV RNA. Binding of double-stranded RNA also involves less penetration into the RRM2 binding pocket and more engagement with the unstructured C-terminus of the La CTD. The complementarity between TRESI-HDX and Δδ nuclear magnetic resonance measurements for ligand binding analysis is also explored.
Collapse
Affiliation(s)
- Kerene A Brown
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
| | - Samel Sharifi
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Rawaa Hussain
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Logan Donaldson
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
| |
Collapse
|
32
|
Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
Collapse
Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| |
Collapse
|
33
|
Martino L, Salisbury NJH, Brown P, Kelly G, Atkinson RA, Conte MR. (1)H, (15)N and (13)C chemical shift assignments of the La motif and RRM1 from human LARP6. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:337-40. [PMID: 25896032 PMCID: PMC4568005 DOI: 10.1007/s12104-015-9605-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
We report here the nearly complete (1)H, (15)N and (13)C resonance assignment of the La motif and RNA recognition motif 1 of human LARP6, an RNA binding protein involved in regulating collagen synthesis.
Collapse
Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Nicholas J H Salisbury
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paul Brown
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.
| |
Collapse
|
34
|
Argyriou AI, Chasapis CT, Apostolidi M, Konstantinidou P, Stathopoulos C, Bentrop D, Spyroulias GA. Backbone and side chain NMR assignment, along with the secondary structure prediction of RRM2 domain of La protein from a lower eukaryote exhibiting identical structural organization with its human homolog. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:219-222. [PMID: 25281001 DOI: 10.1007/s12104-014-9578-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/26/2014] [Indexed: 06/03/2023]
Abstract
The La protein (Lupus antigen), a key mediator during biogenesis of RNA polymerase III transcripts, contains a characteristic La motif and one or two RNA recognition motif (RRM) domains, depending on the organism of origin. The RRM1 domain is conserved in higher eukaryotes and located in the N-terminal region, whereas the C-terminal RRM2 domain is absent in most lower eukaryotes and its specific role remains, so far, uncharacterized. Here, we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of RRM2 of La protein from Dictyostelium discoideum. Interestingly, the La protein in this lower eukaryote, exhibits high homology to its human counterpart. Moreover, it contains two RRM domains, instead of one, raising questions on its evolutionary origin and the putative role of RRM2 in vivo. We also provide its secondary structure as predicted by the TALOS+ online tool.
Collapse
|
35
|
Abstract
RRM-containing proteins are involved in most of the RNA metabolism steps. Their functions are closely related to their mode of RNA recognition, which has been studied by structural biologists for more than 20 years. In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. We show that multiple variations of their canonical fold can be used to adapt to different single-stranded sequences with a large range of affinities. Furthermore, we describe the consequences on RNA binding of the different structural arrangements found in tandem RRMs and higher order RNPs. Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. Finally, we show how structural and cellular biology can benefit from each other and pave a way for understanding, defining, and predicting a code of RNA recognition by the RRMs.
Collapse
|
36
|
Martino L, Pennell S, Kelly G, Busi B, Brown P, Atkinson RA, Salisbury NJH, Ooi ZH, See KW, Smerdon SJ, Alfano C, Bui TTT, Conte MR. Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module. Nucleic Acids Res 2015; 43:645-60. [PMID: 25488812 PMCID: PMC4288179 DOI: 10.1093/nar/gku1287] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023] Open
Abstract
The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3' UUUOH sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5' UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs.
Collapse
Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Simon Pennell
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Baptiste Busi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biology, École Normale Supérieure de Lyon, CEDEX 07, France
| | - Paul Brown
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Nicholas J H Salisbury
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Zi-Hao Ooi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Kang-Wei See
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Stephen J Smerdon
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Caterina Alfano
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| |
Collapse
|
37
|
Kuehnert J, Sommer G, Zierk AW, Fedarovich A, Brock A, Fedarovich D, Heise T. Novel RNA chaperone domain of RNA-binding protein La is regulated by AKT phosphorylation. Nucleic Acids Res 2015; 43:581-94. [PMID: 25520193 PMCID: PMC4288197 DOI: 10.1093/nar/gku1309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 01/13/2023] Open
Abstract
The cellular function of the cancer-associated RNA-binding protein La has been linked to translation of viral and cellular mRNAs. Recently, we have shown that the human La protein stimulates IRES-mediated translation of the cooperative oncogene CCND1 in cervical cancer cells. However, there is little known about the underlying molecular mechanism by which La stimulates CCND1 IRES-mediated translation, and we propose that its RNA chaperone activity is required. Herein, we show that La binds close to the CCND1 start codon and demonstrate that La's RNA chaperone activity can change the folding of its binding site. We map the RNA chaperone domain (RCD) within the C-terminal region of La in close proximity to a novel AKT phosphorylation site (T389). Phosphorylation at T389 by AKT-1 strongly impairs its RNA chaperone activity. Furthermore, we demonstrate that the RCD as well as T389 is required to stimulate CCND1 IRES-mediated translation in cells. In summary, we provide a model whereby a novel interplay between RNA-binding, RNA chaperoning and AKT phosphorylation of La protein regulates CCND1 IRES-mediated translation.
Collapse
Affiliation(s)
- Julia Kuehnert
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gunhild Sommer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Avery W Zierk
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alena Fedarovich
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alexander Brock
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Dzmitry Fedarovich
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tilman Heise
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| |
Collapse
|
38
|
Xu B, Zhang J, Strom J, Lee S, Chen QM. Myocardial ischemic reperfusion induces de novo Nrf2 protein translation. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1638-47. [PMID: 24915518 DOI: 10.1016/j.bbadis.2014.06.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022]
Abstract
Nrf2 is a bZIP transcription factor regulating the expression of antioxidant and detoxification genes. We have found that Nrf2 knockout mice have an increased infarction size in response to regional ischemic reperfusion and have a reduced degree of cardiac protection by means of ischemic preconditioning. With cycles of brief ischemia and reperfusion (5'I/5'R) that induce cardiac protection in wild type mice, an elevated Nrf2 protein was observed without prior increases of Nrf2 mRNA. When an mRNA species is being translated into a protein, it is occupied by multiple ribosomes. The level of ribosome-associated Nrf2 mRNA increased following cycles of 5'I/5'R, supporting de novo Nrf2 protein translation. A dicistronic reporter assay indicated a role of the 5' untranslated region (5' UTR) of Nrf2 mRNA in oxidative stress induced Nrf2 protein translation in isolated cardiomyocytes. Western blot analyses after isolation of proteins binding to biotinylated Nrf2 5' UTR from the myocardium or cultured cardiomyocytes demonstrated that cycles of 5'I/5'R or oxidants caused an increased association of La protein with Nrf2 5' UTR. Ribonucleoprotein complex immunoprecipitation assays confirmed such association indeed occurring in vivo. Knocking down La using siRNA was able to prevent Nrf2 protein elevation by oxidants in cultured cardiomyocytes and by cycles of 5'I/5'R in the myocardium. Our data point out a novel mechanism of cardiac protection by de novo Nrf2 protein translation involving interaction of La protein with 5' UTR of Nrf2 mRNA in cardiomyocytes.
Collapse
Affiliation(s)
- Beibei Xu
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ 85724, USA
| | - Jack Zhang
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ 85724, USA
| | - Joshua Strom
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ 85724, USA
| | - Sang Lee
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ 85724, USA
| | - Qin M Chen
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ 85724, USA.
| |
Collapse
|
39
|
Apostolidi M, Vourtsis DJ, Chasapis CT, Stathopoulos C, Bentrop D, Spyroulias GA. ¹H, ¹⁵N, ¹³C assignment and secondary structure determination of two domains of La protein from D. discoideum. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:47-51. [PMID: 23239108 DOI: 10.1007/s12104-012-9450-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/04/2012] [Indexed: 06/01/2023]
Abstract
Biosynthesis of RNA polymerase III transcripts requires binding of the La protein at their 3' end. La is an abundant nuclear RNA-binding protein which protects the nascent transcripts from 3' exonuclease degradation. Here, we report the high yield expression and preliminary structural analysis through NMR spectroscopy of two recombinant RNA binding domains (La motif and NRRM) from the La protein of Dictyostelium discoideum. Both recombinant protein constructs were well-folded and allowed for an almost complete sequence-specific assignment of the (15)N and (13)C labeled domains and their secondary structure prediction using PECAN online tool.
Collapse
Affiliation(s)
- Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504, Patras, Greece
| | | | | | | | | | | |
Collapse
|
40
|
Wang I, Hennig J, Jagtap PKA, Sonntag M, Valcárcel J, Sattler M. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1. Nucleic Acids Res 2014; 42:5949-66. [PMID: 24682828 PMCID: PMC4027183 DOI: 10.1093/nar/gku193] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.
Collapse
Affiliation(s)
- Iren Wang
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Miriam Sonntag
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| |
Collapse
|
41
|
Law MJ, Lee DS, Lee CS, Anglim PP, Haworth IS, Laird-Offringa IA. The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA. Nucleic Acids Res 2013; 41:7092-100. [PMID: 23703211 PMCID: PMC3737524 DOI: 10.1093/nar/gkt326] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Previous kinetic investigations of the N-terminal RNA Recognition Motif (RRM) domain of spliceosomal A protein of the U1 small nuclear ribonucleoprotein particle (U1A) interacting with its RNA target U1 hairpin II (U1hpII) provided experimental evidence for a ‘lure and lock’ model of binding. The final step of locking has been proposed to involve conformational changes in an α-helix immediately C-terminal to the RRM domain (helix C), which occludes the RNA binding surface in the unbound protein. Helix C must shift its position to accommodate RNA binding in the RNA–protein complex. This results in a new hydrophobic core, an intraprotein hydrogen bond and a quadruple stacking interaction between U1A and U1hpII. Here, we used a surface plasmon resonance-based biosensor to gain mechanistic insight into the role of helix C in mediating the interaction with U1hpII. Truncation, removal or disruption of the helix exposes the RNA-binding surface, resulting in an increase in the association rate, while simultaneously reducing the ability of the complex to lock, reflected in a loss of complex stability. Disruption of the quadruple stacking interaction has minor kinetic effects when compared with removal of the intraprotein hydrogen bonds. These data provide new insights into the mechanism whereby sequences C-terminal to an RRM can influence RNA binding.
Collapse
Affiliation(s)
- Michael J Law
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | | | | |
Collapse
|
42
|
Jiang J, Miracco EJ, Hong K, Eckert B, Chan H, Cash DD, Min B, Zhou ZH, Collins K, Feigon J. The architecture of Tetrahymena telomerase holoenzyme. Nature 2013; 496:187-92. [PMID: 23552895 PMCID: PMC3817743 DOI: 10.1038/nature12062] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/08/2013] [Indexed: 01/15/2023]
Abstract
Telomerase adds telomeric repeats to chromosome ends using an internal RNA template and a specialized telomerase reverse transcriptase (TERT), thereby maintaining genome integrity. Little is known about the physical relationships among protein and RNA subunits within a biologically functional holoenzyme. Here we describe the architecture of Tetrahymena thermophila telomerase holoenzyme determined by electron microscopy. Six of the seven proteins and the TERT-binding regions of telomerase RNA (TER) have been localized by affinity labelling. Fitting with high-resolution structures reveals the organization of TERT, TER and p65 in the ribonucleoprotein (RNP) catalytic core. p50 has an unanticipated role as a hub between the RNP catalytic core, p75-p19-p45 subcomplex, and the DNA-binding Teb1. A complete in vitro holoenzyme reconstitution assigns function to these interactions in processive telomeric repeat synthesis. These studies provide the first view of the extensive network of subunit associations necessary for telomerase holoenzyme assembly and physiological function.
Collapse
Affiliation(s)
- Jiansen Jiang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Singh M, Choi CP, Feigon J. xRRM: a new class of RRM found in the telomerase La family protein p65. RNA Biol 2013; 10:353-9. [PMID: 23328630 DOI: 10.4161/rna.23608] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genuine La and La-related proteins group 7 (LARP7) bind to the non-coding RNAs transcribed by RNA polymerase III (RNAPIII), which end in UUU-3'OH. The La motif and RRM1 of these proteins (the La module) cooperate to bind the UUU-3'OH, protecting the RNA from degradation, while other domains may be important for RNA folding or other functions. Among the RNAPIII transcripts is ciliate telomerase RNA (TER). p65, a member of the LARP7 family, is an integral Tetrahymena thermophila telomerase holoenzyme protein required for TER biogenesis and telomerase RNP assembly. p65, together with TER and telomerase reverse transcriptase (TERT), form the Tetrahymena telomerase RNP catalytic core. p65 has an N-terminal domain followed by a La module and a C-terminal domain, which binds to the TER stem 4. We recently showed that the p65 C-terminal domain harbors a cryptic, atypical RRM, which uses a unique mode of single- and double-strand RNA binding and is required for telomerase RNP catalytic core assembly. This domain, which we named xRRM, appears to be present in and unique to genuine La and LARP7 proteins. Here we review the structure of the xRRM, discuss how this domain could recognize diverse substrates of La and LARP7 proteins and discuss the functional implications of the xRRM as an RNP chaperone.
Collapse
Affiliation(s)
- Mahavir Singh
- Department of Chemistry and Biochemistry and the Molecular Biology Institute; University of California; Los Angeles, CA USA
| | | | | |
Collapse
|
44
|
Singh M, Wang Z, Koo BK, Patel A, Cascio D, Collins K, Feigon J. Structural basis for telomerase RNA recognition and RNP assembly by the holoenzyme La family protein p65. Mol Cell 2012; 47:16-26. [PMID: 22705372 PMCID: PMC3398246 DOI: 10.1016/j.molcel.2012.05.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 03/02/2012] [Accepted: 05/10/2012] [Indexed: 02/07/2023]
Abstract
Telomerase is a ribonucleoprotein complex essential for maintenance of telomere DNA at linear chromosome ends. The catalytic core of Tetrahymena telomerase comprises a ternary complex of telomerase RNA (TER), telomerase reverse transcriptase (TERT), and the essential La family protein p65. NMR and crystal structures of p65 C-terminal domain and its complex with stem IV of TER reveal that RNA recognition is achieved by a combination of single- and double-stranded RNA binding, which induces a 105° bend in TER. The domain is a cryptic, atypical RNA recognition motif with a disordered C-terminal extension that forms an α helix in the complex necessary for hierarchical assembly of TERT with p65-TER. This work provides the first structural insight into biogenesis and assembly of TER with a telomerase-specific protein. Additionally, our studies define a structurally homologous domain (xRRM) in genuine La and LARP7 proteins and suggest a general mode of RNA binding for biogenesis of their diverse RNA targets.
Collapse
Affiliation(s)
- Mahavir Singh
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Zhonghua Wang
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Bon-Kyung Koo
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Anooj Patel
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720-3200, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| |
Collapse
|
45
|
Zhang J, Dinh TN, Kappeler K, Tsaprailis G, Chen QM. La autoantigen mediates oxidant induced de novo Nrf2 protein translation. Mol Cell Proteomics 2012; 11:M111.015032. [PMID: 22207702 PMCID: PMC3433904 DOI: 10.1074/mcp.m111.015032] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/25/2011] [Indexed: 01/20/2023] Open
Abstract
Nrf2 gene encodes a transcription factor that regulates the expression of a cluster of antioxidant and detoxification genes. Recent works from our laboratory indicate that oxidative stress causes rapid de novo synthesis of Nrf2 protein. We have found that 5' Untranslated Region (5'UTR) of Nrf2 allows the mRNA to undergo an Internal Ribosomal Entry Site (IRES) mediated protein translation. Using liquid chromatography tandem MS, we have discovered that La/SSB protein bound to Nrf2 5'UTR in response to oxidative stress. In vitro RNA binding and in vivo ribonucleoprotein immunoprecipitation showed H(2)O(2) dose and time dependent increases of La/SSB binding to Nrf2 5'UTR. La/SSB protein translocated from the nuclei to cytoplasm and distributed in the perinuclear space in cells treated with H(2)O(2). Isolation of ribosomal fractions indicated that oxidants caused an association of La/SSB with ribosomes. Physical interaction of La/SSB with representative proteins from the small or large subunits of ribosomes was found to increase in cells responding to H(2)O(2) treatment. Knocking down La/SSB gene with siRNA prevented Nrf2 protein elevation or Nrf2 5'UTR activation by oxidants. In contrast, overexpression of La/SSB gene was able to enhance Nrf2 5'UTR activation and Nrf2 protein increase. Our data suggest that oxidants cause nuclear export of La/SSB protein and subsequent association of La/SSB with Nrf2 5'UTR and ribosomes. These events contribute to de novo Nrf2 protein translation because of oxidative stress.
Collapse
Affiliation(s)
- Jack Zhang
- From the ‡Department of Pharmacology, University of Arizona, College of Medicine, 1501 N. Campbell Ave, Tucson, Arizona 85724
| | - Thai Nho Dinh
- From the ‡Department of Pharmacology, University of Arizona, College of Medicine, 1501 N. Campbell Ave, Tucson, Arizona 85724
| | - Kyle Kappeler
- From the ‡Department of Pharmacology, University of Arizona, College of Medicine, 1501 N. Campbell Ave, Tucson, Arizona 85724
| | - George Tsaprailis
- §Center for Toxicology, College of Pharmacy, 1703 E. Mabel St Tucson, Arizona 85721
| | - Qin M. Chen
- From the ‡Department of Pharmacology, University of Arizona, College of Medicine, 1501 N. Campbell Ave, Tucson, Arizona 85724
| |
Collapse
|
46
|
Abstract
INTRODUCTION The design of target-specific covalent inhibitors is conceptually attractive because of increased biochemical efficiency through covalency and increased duration of action that outlasts the pharmacokinetics of the agent. Although many covalent inhibitors have been approved or are in advanced clinical trials to treat indications such as cancer and hepatitis C, there is a general tendency to avoid them as drug candidates because of concerns regarding immune-mediated toxicity that can arise from indiscriminate reactivity with off-target proteins. AREAS COVERED The review examines potential reason(s) for the excellent safety record of marketed covalent agents and advanced clinical candidates for emerging therapeutic targets. A significant emphasis is placed on proteomic techniques and chemical/biochemical reactivity assays that aim to provide a systematic rank ordering of pharmacologic selectivity relative to off-target protein reactivity of covalent inhibitors. EXPERT OPINION While tactics to examine selective covalent modification of the pharmacologic target are broadly applicable in drug discovery, it is unclear whether the output from such studies can prospectively predict idiosyncratic immune-mediated drug toxicity. Opinions regarding an acceptable threshold of protein reactivity/body burden for a toxic electrophile and a non-toxic electrophilic covalent drug have not been defined. Increasing confidence in proteomic and chemical/biochemical reactivity screens will require a retrospective side-by-side profiling of marketed covalent drugs and electrophiles known to cause deleterious toxic effects via non-selective covalent binding.
Collapse
Affiliation(s)
- Amit S Kalgutkar
- Pharmacokinetics, Dynamics, and Metabolism Department, Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA.
| | | |
Collapse
|
47
|
Naeeni AR, Conte MR, Bayfield MA. RNA chaperone activity of human La protein is mediated by variant RNA recognition motif. J Biol Chem 2012; 287:5472-82. [PMID: 22203678 PMCID: PMC3285324 DOI: 10.1074/jbc.m111.276071] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 12/23/2011] [Indexed: 02/05/2023] Open
Abstract
La proteins are conserved factors in eukaryotes that bind and protect the 3' trailers of pre-tRNAs from exonuclease digestion via sequence-specific recognition of UUU-3'OH. La has also been hypothesized to assist pre-tRNAs in attaining their native fold through RNA chaperone activity. In addition to binding polymerase III transcripts, human La has also been shown to enhance the translation of several internal ribosome entry sites and upstream ORF-containing mRNA targets, also potentially through RNA chaperone activity. Using in vitro FRET-based assays, we show that human and Schizosaccharomyces pombe La proteins harbor RNA chaperone activity by enhancing RNA strand annealing and strand dissociation. We use various RNA substrates and La mutants to show that UUU-3'OH-dependent La-RNA binding is not required for this function, and we map RNA chaperone activity to its RRM1 motif including a noncanonical α3-helix. We validate the importance of this α3-helix by appending it to the RRM of the unrelated U1A protein and show that this fusion protein acquires significant strand annealing activity. Finally, we show that residues required for La-mediated RNA chaperone activity in vitro are required for La-dependent rescue of tRNA-mediated suppression via a mutated suppressor tRNA in vivo. This work delineates the structural elements required for La-mediated RNA chaperone activity and provides a basis for understanding how La can enhance the folding of its various RNA targets.
Collapse
Affiliation(s)
- Amir R. Naeeni
- From the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada and
| | - Maria R. Conte
- the Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Mark A. Bayfield
- From the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada and
| |
Collapse
|
48
|
Martino L, Pennell S, Kelly G, Bui TTT, Kotik-Kogan O, Smerdon SJ, Drake AF, Curry S, Conte MR. Analysis of the interaction with the hepatitis C virus mRNA reveals an alternative mode of RNA recognition by the human La protein. Nucleic Acids Res 2012; 40:1381-94. [PMID: 22009680 PMCID: PMC3273827 DOI: 10.1093/nar/gkr890] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/29/2011] [Accepted: 10/01/2011] [Indexed: 12/31/2022] Open
Abstract
Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain IV of the hepatitis C virus (HCV) RNA, which is associated with viral translation stimulation. By systematic biophysical investigations, we have found that La binds to domain IV using an RNA recognition that is quite distinct from its mode of binding to RNAs with a 3' UUU(OH) trailer: although the La motif and first RNA recognition motif (RRM1) are sufficient for high-affinity binding to 3' oligoU, recognition of HCV domain IV requires the La motif and RRM1 to work in concert with the atypical RRM2 which has not previously been shown to have a significant role in RNA binding. This new mode of binding does not appear sequence specific, but recognizes structural features of the RNA, in particular a double-stranded stem flanked by single-stranded extensions. These findings pave the way for a better understanding of the role of La in viral translation initiation.
Collapse
Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Simon Pennell
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Geoff Kelly
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Tam T. T. Bui
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Olga Kotik-Kogan
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Stephen J. Smerdon
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Alex F. Drake
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Stephen Curry
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| |
Collapse
|
49
|
Generation of single-chain bispecific green fluorescent protein fusion antibodies for imaging of antibody-induced T cell synapses. Anal Biochem 2012; 423:261-8. [PMID: 22274538 DOI: 10.1016/j.ab.2011.12.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 11/07/2011] [Accepted: 12/28/2011] [Indexed: 01/09/2023]
Abstract
There is growing interest in the development of novel single-chain bispecific antibodies for retargeting of immune effector T cells to tumor cells. Until today, functional fusion constructs consisting of a single-chain bispecific antibody and a fluorescent protein were not reported. Such molecules could be useful for an in vivo visualization of this retargeting process. Recently, we established two novel single-chain bispecific antibodies. One is capable of retargeting T cells to CD33, and the other is capable of retargeting T cells to the prostate stem cell antigen (PSCA). CD33 is an attractive immunotarget on the surface of tumor cells from patients with acute myeloid leukemia (AML). The PSCA is a potential target on prostate cancer cells. Flanking the reading frame encoding the green fluorescent protein (GFP) with a recently described novel helical linker element allowed us to establish novel single-chain bispecific fusion antibodies. These fluorescent fusion antibodies were useful to efficiently retarget T cells to the respective tumor cells and visualize the formation of immune synapses between effector and target cells.
Collapse
|
50
|
Wang L, Zhang K, Wu L, Liu S, Zhang H, Zhou Q, Tong L, Sun F, Fan Z. Structural Insights into the Substrate Specificity of Human Granzyme H: The Functional Roles of a Novel RKR Motif. THE JOURNAL OF IMMUNOLOGY 2011; 188:765-73. [DOI: 10.4049/jimmunol.1101381] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|