1
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Moreno-Aguilera M, Neher AM, Mendoza MB, Dodel M, Mardakheh FK, Ortiz R, Gallego C. KIS counteracts PTBP2 and regulates alternative exon usage in neurons. eLife 2024; 13:e96048. [PMID: 38597390 PMCID: PMC11045219 DOI: 10.7554/elife.96048] [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: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024] Open
Abstract
Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here, we show that KIS, a kinase upregulated in the developmental brain, imposes a genome-wide alteration in exon usage during neuronal differentiation in mice. KIS contains a protein-recognition domain common to spliceosomal components and phosphorylates PTBP2, counteracting the role of this splicing factor in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from two co-regulators, Matrin3 and hnRNPM, and hinders the RNA-binding capability of the complex. Furthermore, KIS and PTBP2 display strong and opposing functional interactions in synaptic spine emergence and maturation. Taken together, our data uncover a post-translational control of splicing regulators that link transcriptional and alternative exon usage programs in neuronal development.
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Affiliation(s)
| | - Alba M Neher
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Mónica B Mendoza
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Martin Dodel
- Barts Cancer Institute, Queen Mary University of LondonLondonUnited Kingdom
| | - Faraz K Mardakheh
- Barts Cancer Institute, Queen Mary University of LondonLondonUnited Kingdom
| | - Raúl Ortiz
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Carme Gallego
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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2
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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3
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Kubick N, Paszkiewicz J, Bieńkowska I, Ławiński M, Horbańczuk JO, Sacharczuk M, Mickael ME. Investigation of Mutated in Colorectal Cancer (MCC) Gene Family Evolution History Indicates a Putative Role in Th17/Treg Differentiation. Int J Mol Sci 2023; 24:11940. [PMID: 37569317 PMCID: PMC10418881 DOI: 10.3390/ijms241511940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The MCC family of genes plays a role in colorectal cancer development through various immunological pathways, including the Th17/Treg axis. We have previously shown that MCC1 but not MCC2 plays a role in Treg differentiation. Our understanding of the genetic divergence patterns and evolutionary history of the MCC family in relation to its function, in general, and the Th17/Treg axis, in particular, remains incomplete. In this investigation, we explored 12 species' genomes to study the phylogenetic origin, structure, and functional specificity of this family. In vertebrates, both MCC1 and MCC2 homologs have been discovered, while invertebrates have a single MCC homolog. We found MCC homologs as early as Cnidarians and Trichoplax, suggesting that the MCC family first appeared 741 million years ago (Ma), whereas MCC divergence into the MCC1 and MCC2 families occurred at 540 Ma. In general, we did not detect significant positive selection regulating MCC evolution. Our investigation, based on MCC1 structural similarity, suggests that they may play a role in the evolutionary changes in Tregs' emergence towards complexity, including the ability to utilize calcium for differentiation through the use of the EFH calcium-binding domain. We also found that the motif NPSTGE was highly conserved in MCC1, but not in MCC2. The NPSTGE motif binds KEAP1 with high affinity, suggesting an Nrf2-mediated function for MCC1. In the case of MCC2, we found that the "modifier of rudimentary" motif is highly conserved. This motif contributes to the regulation of alternative splicing. Overall, our study sheds light on how the evolution of the MCC family is connected to its function in regulating the Th17/Treg axis.
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Affiliation(s)
- Norwin Kubick
- Department of Biology, Institute of Plant Science and Microbiology, Univeristy of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany;
| | - Justyna Paszkiewicz
- Department of Health, John Paul II University of Applied Sciences in Biala Podlaska, Sidorska 95/97, 21-500 Biała Podlaska, Poland;
| | - Irmina Bieńkowska
- Institute of Animal Biotechnology and Genetics, Polish Academy of Science, Postępu 36A, 05-552 Jastrzębiec, Poland; (I.B.); (M.Ł.); (J.O.H.)
| | - Michał Ławiński
- Institute of Animal Biotechnology and Genetics, Polish Academy of Science, Postępu 36A, 05-552 Jastrzębiec, Poland; (I.B.); (M.Ł.); (J.O.H.)
- Department of General Surgery, Gastroenterology and Oncology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Jarosław Olav Horbańczuk
- Institute of Animal Biotechnology and Genetics, Polish Academy of Science, Postępu 36A, 05-552 Jastrzębiec, Poland; (I.B.); (M.Ł.); (J.O.H.)
| | - Mariusz Sacharczuk
- Institute of Animal Biotechnology and Genetics, Polish Academy of Science, Postępu 36A, 05-552 Jastrzębiec, Poland; (I.B.); (M.Ł.); (J.O.H.)
- Department of Pharmacodynamics, Faculty of Pharmacy, Medical University of Warsaw, l Banacha 1, 02-697 Warsaw, Poland
| | - Michel Edwar Mickael
- Institute of Animal Biotechnology and Genetics, Polish Academy of Science, Postępu 36A, 05-552 Jastrzębiec, Poland; (I.B.); (M.Ł.); (J.O.H.)
- PM Research Center, Väpnaregatan 22, 58649 Linköping, Sweden
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4
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Fernandez GJ, Ramírez-Mejía JM, Urcuqui-Inchima S. Transcriptional and post-transcriptional mechanisms that regulate the genetic program in Zika virus-infected macrophages. Int J Biochem Cell Biol 2022; 153:106312. [DOI: 10.1016/j.biocel.2022.106312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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5
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Han Z, Wu Z, Gong W, Zhou W, Chen L, Li C. Allosteric mechanism for SL RNA recognition by polypyrimidine tract binding protein RRM1: An atomistic MD simulation and network-based study. Int J Biol Macromol 2022; 221:763-772. [PMID: 36058398 DOI: 10.1016/j.ijbiomac.2022.08.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/20/2022] [Accepted: 08/27/2022] [Indexed: 12/01/2022]
Abstract
Polypyrimidine tract-binding protein (PTB), an RNA-binding protein, is involved in the regulation of diverse processes in mRNA metabolism. However, the allosteric modulation of its binding with RNA remains unclear. We explore the dynamic characteristics of PTB RNA recognition motif 1 (RRM1) in its RNA-free and wild-type/mutant RNA-bound states to understand the issues using molecular dynamics (MD) simulation, perturbation response scanning (PRS) and protein structure network (PSN) models. It is found that RNA binding strengthens RRM1 stability, while L151G mutation in α3 helix far away from the interface makes the complex unstable. The latter is caused by long-distance dynamic couplings, which makes intermolecular electrostatic and entropy energies unfavorable. The weakened couplings between interface β sheets and C-terminal parts upon mutation reveal RNA recognition is co-regulated by these regions. Interestingly, PRS analysis reveals the allostery caused by the perturbation on α3 helix has already been pre-encoded in the equilibrium dynamics of the protein structure. PSN analysis shows the details of the allosteric signal transmission, revealing the necessity of strong couplings between α3 helix and interface for maintaining the high binding affinity. This study sheds light on the mechanisms of PTB allostery and RNA recognition and can provide important information for drug design.
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Affiliation(s)
- Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhixiang Wu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Wenxue Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Lei Chen
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.
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6
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Abstract
RNA-binding proteins (RBPs) are essential factors required for the physiological function of neurons, muscle, and other tissue types. In keeping with this, a growing body of genetic, clinical, and pathological evidence indicates that RBP dysfunction and/or gene mutation leads to neurodegeneration and myopathy. Here, we summarize the current understanding of matrin 3 (MATR3), a poorly understood RBP implicated not only in ALS and frontotemporal dementia but also in distal myopathy. We begin by reviewing MATR3's functions, its regulation, and how it may be involved in both sporadic and familial neuromuscular disease. We also discuss insights gleaned from cellular and animal models of MATR3 pathogenesis, the links between MATR3 and other disease-associated RBPs, and the mechanisms underlying RBP-mediated disorders.
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Affiliation(s)
- Ahmed M. Malik
- Medical Scientist Training Program
- Neuroscience Graduate Program, and
| | - Sami J. Barmada
- Neuroscience Graduate Program, and
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
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7
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Lixa C, Mujo A, de Magalhães MTQ, Almeida FCL, Lima LMTR, Pinheiro AS. Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution. JOURNAL OF BIOMOLECULAR NMR 2018; 72:179-192. [PMID: 30535889 DOI: 10.1007/s10858-018-0217-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central β-strands, β1 and β3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the β2-β3 loop undergoes fast backbone dynamics (ps-ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI-IMS-MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding β-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer-dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.
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Affiliation(s)
- Carolina Lixa
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Amanda Mujo
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Mariana T Q de Magalhães
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fabio C L Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas, Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luis Mauricio T R Lima
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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8
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Pina JM, Reynaga JM, Truong AAM, Keppetipola NM. Post-Translational Modifications in Polypyrimidine Tract Binding Proteins PTBP1 and PTBP2. Biochemistry 2018; 57:3873-3882. [PMID: 29851470 PMCID: PMC6211845 DOI: 10.1021/acs.biochem.8b00256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA binding proteins play an important role in regulating alternative pre-mRNA splicing and in turn cellular gene expression. Many of these RNA binding proteins occur as gene families with members sharing a high degree of primary structure identity and domain organization yet have tissue-specific expression patterns and regulate different sets of target exons. How highly similar members in a gene family can exert different splicing outcomes is not well understood. We conducted mass spectrometry analysis of post-translational phosphorylation and acetylation modifications for two paralogs of the polypyrimidine tract binding protein family, PTBP1 and PTBP2, to discover modifications that occur in splicing reaction mixtures and to identify discrete modifications that may direct their different splicing activities. We find that PTBP1 and PTBP2 have many distinct phosphate modifications located in the unstructured N-terminal, linker 1, and linker 2 regions. We find that the two proteins have many overlapping acetate modifications in the RNA recognition motifs (RRMs) with a few distinct sites in PTBP1 RRM2 and RRM3. Our data also reveal that lysine residues in the nuclear localization sequence of PTBP2 are acetylated. Collectively, our results highlight important differences in post-translational modifications between the paralogs and suggest a role for them in the differential splicing activity of PTBP1 and PTBP2.
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Affiliation(s)
- Jeffrey M. Pina
- Department of Chemistry and Biochemistry, California State University, Fullerton, 800 North State College Boulevard, Fullerton, California 92831, United States
| | - Janice M. Reynaga
- Department of Chemistry and Biochemistry, California State University, Fullerton, 800 North State College Boulevard, Fullerton, California 92831, United States
| | - Anthony A. M. Truong
- Department of Chemistry and Biochemistry, California State University, Fullerton, 800 North State College Boulevard, Fullerton, California 92831, United States
| | - Niroshika M. Keppetipola
- Department of Chemistry and Biochemistry, California State University, Fullerton, 800 North State College Boulevard, Fullerton, California 92831, United States
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9
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Gmeiner C, Dorn G, Allain FHT, Jeschke G, Yulikov M. Spin labelling for integrative structure modelling: a case study of the polypyrimidine-tract binding protein 1 domains in complexes with short RNAs. Phys Chem Chem Phys 2018; 19:28360-28380. [PMID: 29034946 DOI: 10.1039/c7cp05822e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A combined method, employing NMR and EPR spectroscopies, has demonstrated its strength in solving structures of protein/RNA and other types of biomolecular complexes. This method works particularly well when the large biomolecular complex consists of a limited number of rigid building blocks, such as RNA-binding protein domains (RBDs). A variety of spin labels is available for such studies, allowing for conventional as well as spectroscopically orthogonal double electron-electron resonance (DEER) measurements in EPR. In this work, we compare different types of nitroxide-based and Gd(iii)-based spin labels attached to isolated RBDs of the polypyrimidine-tract binding protein 1 (PTBP1) and to short RNA fragments. In particular, we demonstrate experiments on spectroscopically orthogonal labelled RBD/RNA complexes. For all experiments we analyse spin labelling, DEER method performance, resulting distance distributions, and their consistency with the predictions from the spin label rotamers analysis. This work provides a set of intra-domain calibration DEER data, which can serve as a basis to start structure determination of the full length PTBP1 complex with an RNA derived from encephalomycarditis virus (EMCV) internal ribosomal entry site (IRES). For a series of tested labelling sites, we discuss their particular advantages and drawbacks in such a structure determination approach.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland.
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10
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Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochem Soc Trans 2017; 44:1058-65. [PMID: 27528752 DOI: 10.1042/bst20160080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 02/04/2023]
Abstract
Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.
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11
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Uemura Y, Oshima T, Yamamoto M, Reyes CJ, Costa Cruz PH, Shibuya T, Kawahara Y. Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing. Genes Cells 2017; 22:785-798. [PMID: 28695676 DOI: 10.1111/gtc.12512] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/11/2017] [Indexed: 12/13/2022]
Abstract
Matrin3 is an RNA-binding protein that is localized in the nuclear matrix. Although various roles in RNA metabolism have been reported for Matrin3, in vivo target RNAs to which Matrin3 binds directly have not been investigated comprehensively so far. Here, we show that Matrin3 binds predominantly to intronic regions of pre-mRNAs. Photoactivatable Ribonucleoside-Enhanced Cross-linking and Immunoprecipitation (PAR-CLIP) analysis using human neuronal cells showed that Matrin3 recognized pyrimidine-rich sequences as binding motifs, including the polypyrimidine tract, a splicing regulatory element. Splicing-sensitive microarray analysis showed that depletion of Matrin3 preferentially increased the inclusion of cassette exons that were adjacent to introns that contained Matrin3-binding sites. We further found that although most of the genes targeted by polypyrimidine tract binding protein 1 (PTBP1) were also bound by Matrin3, Matrin3 could control alternative splicing in a PTBP1-independent manner, at least in part. These findings suggest that Matrin3 is a splicing regulator that targets intronic pyrimidine-rich sequences.
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Affiliation(s)
- Yuri Uemura
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takuya Oshima
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Munetaka Yamamoto
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Charles Jourdan Reyes
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
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12
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Loerch S, Kielkopf CL. Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (NEW YORK, N.Y.) 2016; 22:1795-1807. [PMID: 27852923 PMCID: PMC5113200 DOI: 10.1261/rna.057950.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.
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Affiliation(s)
- Sarah Loerch
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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13
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Falk S, Finogenova K, Melko M, Benda C, Lykke-Andersen S, Jensen TH, Conti E. Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. Nat Commun 2016; 7:13573. [PMID: 27905398 PMCID: PMC5146272 DOI: 10.1038/ncomms13573] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/13/2016] [Indexed: 01/24/2023] Open
Abstract
The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 Å resolution. On the basis of the structure, we identify a proline-rich segment within the splicing factor SAP145 with strong similarity to ZCCHC8. We show that this segment of SAP145 not only binds the RRM region of another splicing factor SAP49 but also the RRM of RBM7. These dual interactions of RBM7 with the exosome and the spliceosome suggest a model whereby NEXT might recruit the exosome to degrade intronic RNAs. RBM7 and ZCCHC8 are two core subunits of the Nuclear Exosome Targeting complex, which regulates the degradation of selected non-coding RNAs in human cells. Here, the authors use structural and biochemical methods to show how ZCCHC8 recruits RBM7 in the complex, leaving the RNA binding site accessible and revealing possible implications for splicing.
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Affiliation(s)
- Sebastian Falk
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Ksenia Finogenova
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mireille Melko
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, 8000C Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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14
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Kuwasako K, Nameki N, Tsuda K, Takahashi M, Sato A, Tochio N, Inoue M, Terada T, Kigawa T, Kobayashi N, Shirouzu M, Ito T, Sakamoto T, Wakamatsu K, Güntert P, Takahashi S, Yokoyama S, Muto Y. Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment. Protein Sci 2016; 26:280-291. [PMID: 27862552 PMCID: PMC5275738 DOI: 10.1002/pro.3080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 01/17/2023]
Abstract
The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods. Chemical shift mapping showed that the SF3b145 fragment spanning residues 598–631 interacts with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of β1‐α1‐β2‐β3‐α2‐β4. Furthermore, a docking model based on NOESY measurements suggests that residues 607–616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via α1, consequently exhibiting a helix–helix interaction in almost antiparallel. This mode of interaction was confirmed by a mutational analysis using GST pull‐down assays. Comparison with structures of all RRM domains when complexed with a peptide found that this helix–helix interaction is unique to SF3b49 RRM1. Additionally, all amino acid residues involved in the interaction are well conserved among eukaryotes, suggesting evolutionary conservation of this interaction mode between SF3b49 RRM1 and SF3b145. PDB Code(s): 5GVQ
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Affiliation(s)
- Kanako Kuwasako
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo, 202-8585, Japan.,RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Nobukazu Nameki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kengo Tsuda
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mari Takahashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Atsuko Sato
- Department of Chemical & Biological Sciences, Japan Women's University, Mejirodai, Bunkyo, Tokyo, 112-8681, Japan
| | - Naoya Tochio
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Makoto Inoue
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takuhiro Ito
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kaori Wakamatsu
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt, Max-von-Laue-Str, Frankfurt am Main, 60438, Germany
| | - Seizo Takahashi
- Department of Chemical & Biological Sciences, Japan Women's University, Mejirodai, Bunkyo, Tokyo, 112-8681, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yutaka Muto
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo, 202-8585, Japan.,RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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15
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Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. eLife 2016; 5. [PMID: 27882870 PMCID: PMC5122456 DOI: 10.7554/elife.19743] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest. DOI:http://dx.doi.org/10.7554/eLife.19743.001
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, Phoenix, United States
| | - Darryl Chui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
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16
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Keppetipola NM, Yeom KH, Hernandez AL, Bui T, Sharma S, Black DL. Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2. RNA (NEW YORK, N.Y.) 2016; 22:1172-1180. [PMID: 27288314 PMCID: PMC4931110 DOI: 10.1261/rna.057505.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Most human genes generate multiple protein isoforms through alternative pre-mRNA splicing, but the mechanisms controlling alternative splicing choices by RNA binding proteins are not well understood. These proteins can have multiple paralogs expressed in different cell types and exhibiting different splicing activities on target exons. We examined the paralogous polypyrimidine tract binding proteins PTBP1 and PTBP2 to understand how PTBP1 can exhibit greater splicing repression activity on certain exons. Using both an in vivo coexpression assay and an in vitro splicing assay, we show that PTBP1 is more repressive than PTBP2 per unit protein on a target exon. Constructing chimeras of PTBP1 and 2 to determine amino acid features that contribute to their differential activity, we find that multiple segments of PTBP1 increase the repressive activity of PTBP2. Notably, when either RRM1 of PTBP2 or the linker peptide separating RRM2 and RRM3 are replaced with the equivalent PTBP1 sequences, the resulting chimeras are highly active for splicing repression. These segments are distinct from the known region of interaction for the PTBP1 cofactors Raver1 and Matrin3 in RRM2. We find that RRM2 of PTBP1 also increases the repression activity of an otherwise PTBP2 sequence, and that this is potentially explained by stronger binding by Raver1. These results indicate that multiple features over the length of the two proteins affect their ability to repress an exon.
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Affiliation(s)
- Niroshika M Keppetipola
- California State University Fullerton, Department of Chemistry and Biochemistry, Fullerton, California 92831, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Adrian L Hernandez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Tessa Bui
- California State University Fullerton, Department of Chemistry and Biochemistry, Fullerton, California 92831, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
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17
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Coelho MB, Attig J, Ule J, Smith CWJ. Matrin3: connecting gene expression with the nuclear matrix. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:303-15. [PMID: 26813864 DOI: 10.1002/wrna.1336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 01/06/2023]
Abstract
As indicated by its name, Matrin3 was discovered as a component of the nuclear matrix, an insoluble fibrogranular network that structurally organizes the nucleus. Matrin3 possesses both DNA- and RNA-binding domains and, consistent with this, has been shown to function at a number of stages in the life cycle of messenger RNAs. These numerous activities indicate that Matrin3, and indeed the nuclear matrix, do not just provide a structural framework for nuclear activities but also play direct functional roles in these activities. Here, we review the structure, functions, and molecular interactions of Matrin3 and of Matrin3-related proteins, and the pathologies that can arise upon mutation of Matrin3. WIREs RNA 2016, 7:303-315. doi: 10.1002/wrna.1336 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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18
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Ge Z, Quek BL, Beemon KL, Hogg JR. Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. eLife 2016; 5. [PMID: 26744779 PMCID: PMC4764554 DOI: 10.7554/elife.11155] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/07/2016] [Indexed: 12/26/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing long 3'UTRs to perform dual roles in mRNA quality control and gene expression regulation. However, expansion of vertebrate 3'UTR functions has required a physical expansion of 3'UTR lengths, complicating the process of detecting nonsense mutations. We show that the polypyrimidine tract binding protein 1 (PTBP1) shields specific retroviral and cellular transcripts from NMD. When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs. PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression. Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD. DOI:http://dx.doi.org/10.7554/eLife.11155.001 Genes are used as templates to create molecules of messenger RNA (mRNA) that contain all the information needed to make a protein. This information begins with a 'start site' and ends with a 'stop site.' The regions of the mRNA outside of the start and stop sites are called untranslated regions. Not all mRNAs are correctly made, and cells combat this problem by detecting and destroying faulty mRNAs before they are translated into protein. One way cells do this is by recognizing and destroying mRNAs that include long untranslated regions, which can indicate that the mRNA might have a stop site too early in its sequence. A key problem with this mechanism, however, is that long untranslated regions also serve important roles in the cell: for example, by determining where and when mRNA molecules are read to make protein. How then do mRNAs with long but important untranslated regions escape detection and degradation? Ge et al. have now investigated this question using an approach that allows a 'handle' to be attached to particular RNA molecules. This allows the RNA and any proteins bound to it to be purified away from all other RNAs and proteins in the cell, and the proteins can then be identified by a technique called mass spectrometry. Ge at al. found that mRNAs can recruit a protein called PTBP1 to part of the RNA sequence near the stop site. This prevents an RNA decay protein recognizing and triggering the degradation of the mRNA, even if the mRNA has a long untranslated region. Thus, PTBP1 plays a crucial role in protecting human RNAs with long untranslated regions from destruction by the nonsense-mediated decay pathway. Some viral RNAs are also able to evade decay, and so Ge et al. hypothesize that the virus stole this method for maintaining its RNAs from host cells. A future goal is to understand whether this system works the same way in all cell types or protects different RNAs in different cells. DOI:http://dx.doi.org/10.7554/eLife.11155.002
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Affiliation(s)
- Zhiyun Ge
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Bao Lin Quek
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Karen L Beemon
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
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19
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Piazzi M, Williamson A, Lee CF, Pearson S, Lacaud G, Kouskoff V, McCubrey JA, Cocco L, Whetton AD. Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood. Oncotarget 2015; 6:10924-39. [PMID: 25890499 PMCID: PMC4484429 DOI: 10.18632/oncotarget.3454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQ(TM)) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia.
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Affiliation(s)
- Manuela Piazzi
- Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy
| | - Andrew Williamson
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Chia-Fang Lee
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Stella Pearson
- Stem Cell Research Group, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Georges Lacaud
- Stem Cell Biology Group Paterson Institute for Cancer Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Valerie Kouskoff
- Stem Cell Research Group, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - James A. McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Lucio Cocco
- Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy
| | - Anthony D. Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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20
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Frege T, Uversky VN. Intrinsically disordered proteins in the nucleus of human cells. Biochem Biophys Rep 2015; 1:33-51. [PMID: 29124132 PMCID: PMC5668563 DOI: 10.1016/j.bbrep.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the disordered nuclear proteins.
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Affiliation(s)
- Telma Frege
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- GenomeNext LLC, 175 South 3rd Street, Suite 200, Columbus OH 43215, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer׳s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Correspondence to: Department of Molecular, Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC07, Tampa, FL 33612, USA. Tel.: +1 813 974 5816; fax: +1 813 974 7357.
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21
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Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CWJ. Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J 2015; 34:653-68. [PMID: 25599992 PMCID: PMC4365034 DOI: 10.15252/embj.201489852] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolás Bellora
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain INIBIOMA CONICET-UNComahue, Bariloche, Argentina
| | - Julian König
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge, UK Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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22
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Afroz T, Skrisovska L, Belloc E, Guillén-Boixet J, Méndez R, Allain FHT. A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins. Genes Dev 2014; 28:1498-514. [PMID: 24990967 PMCID: PMC4083092 DOI: 10.1101/gad.241133.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
How CPEB RNA-binding proteins regulate cytoplasmic polyadenylation and translation is poorly understood. Allain and colleagues report the structures of the tandem RNA recognition motifs (RRMs) of two human paralogs (CPEB1 and CPEB4) in their free and RNA-bound states. Structural and functional studies reveal how RNA binding by CPEB proteins leads to an optimal positioning of the N-terminal and zinc-binding domains at the 3′ UTR, which favors the nucleation of ribonucleoprotein complexes for translation regulation. This study provides the molecular basis for the translational regulatory circuit established by CPEB proteins. Cytoplasmic changes in polyA tail length is a key mechanism of translational control and is implicated in germline development, synaptic plasticity, cellular proliferation, senescence, and cancer progression. The presence of a U-rich cytoplasmic polyadenylation element (CPE) in the 3′ untranslated regions (UTRs) of the responding mRNAs gives them the selectivity to be regulated by the CPE-binding (CPEB) family of proteins, which recognizes RNA via the tandem RNA recognition motifs (RRMs). Here we report the solution structures of the tandem RRMs of two human paralogs (CPEB1 and CPEB4) in their free and RNA-bound states. The structures reveal an unprecedented arrangement of RRMs in the free state that undergo an original closure motion upon RNA binding that ensures high fidelity. Structural and functional characterization of the ZZ domain (zinc-binding domain) of CPEB1 suggests a role in both protein–protein and protein–RNA interactions. Together with functional studies, the structures reveal how RNA binding by CPEB proteins leads to an optimal positioning of the N-terminal and ZZ domains at the 3′ UTR, which favors the nucleation of the functional ribonucleoprotein complexes for translation regulation.
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Affiliation(s)
- Tariq Afroz
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
| | - Lenka Skrisovska
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
| | - Eulàlia Belloc
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | | | - Raúl Méndez
- Institute for Research in Biomedicine, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
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23
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Tripsianes K, Friberg A, Barrandon C, Brooks M, van Tilbeurgh H, Seraphin B, Sattler M. A novel protein-protein interaction in the RES (REtention and Splicing) complex. J Biol Chem 2014; 289:28640-50. [PMID: 25160624 PMCID: PMC4192513 DOI: 10.1074/jbc.m114.592311] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp232 in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions.
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Affiliation(s)
- Konstantinos Tripsianes
- From the Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic,
| | - Anders Friberg
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Charlotte Barrandon
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Mark Brooks
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Herman van Tilbeurgh
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Bertrand Seraphin
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France, the Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104, Institut National de Santé et de Recherche Médicale (INSERM) U964, Université de Strasbourg, 67404 Illkirch, France
| | - Michael Sattler
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany,
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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25
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Joshi A, Esteve V, Buckroyd AN, Blatter M, Allain FHT, Curry S. Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB). PeerJ 2014; 2:e305. [PMID: 24688880 PMCID: PMC3961105 DOI: 10.7717/peerj.305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/14/2014] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposite sides that face away from each other. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.
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Affiliation(s)
- Amar Joshi
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vicent Esteve
- Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | - Adrian N Buckroyd
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Markus Blatter
- Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | | | - Stephen Curry
- Department of Life Sciences, Imperial College, London, United Kingdom
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26
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Edge C, Gooding C, Smith CWJ. Dissecting domains necessary for activation and repression of splicing by Muscleblind-like protein 1. BMC Mol Biol 2013; 14:29. [PMID: 24373687 PMCID: PMC3880588 DOI: 10.1186/1471-2199-14-29] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/16/2013] [Indexed: 01/06/2023] Open
Abstract
Background Alternative splicing contributes to the diversity of the proteome, and provides the cell with an important additional layer of regulation of gene expression. Among the many RNA binding proteins that regulate alternative splicing pathways are the Muscleblind-like (MBNL) proteins. MBNL proteins bind YGCY motifs in RNA via four CCCH zinc fingers arranged in two tandem arrays, and play a crucial role in the transition from embryonic to adult muscle splicing patterns, deregulation of which leads to Myotonic Dystrophy. Like many other RNA binding proteins, MBNL proteins can act as both activators or repressors of different splicing events. Results We used targeted point mutations to interfere with the RNA binding of MBNL1 zinc fingers individually and in combination. The effects of the mutations were tested in assays for splicing repression and activation, including overexpression, complementation of siRNA-mediated knockdown, and artificial tethering using MS2 coat protein. Mutations were tested in the context of both full length MBNL1 as well as a series of truncation mutants. Individual mutations within full length MBNL1 had little effect, but mutations in ZF1 and 2 combined were more detrimental than those in ZF 3 and 4, upon splicing activation, repression and RNA binding. Activation and repression both required linker sequences between ZF2 and 3, but activation was more sensitive to loss of linker sequences. Conclusions Our results highlight the importance of RNA binding by MBNL ZF domains 1 and 2 for splicing regulatory activity, even when the protein is artificially recruited to its regulatory location on target RNAs. However, RNA binding is not sufficient for activity; additional regions between ZF 2 and 3 are also essential. Activation and repression show differential sensitivity to truncation of this linker region, suggesting interactions with different sets of cofactors for the two types of activity.
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Affiliation(s)
| | | | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
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27
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New insights into functional roles of the polypyrimidine tract-binding protein. Int J Mol Sci 2013; 14:22906-32. [PMID: 24264039 PMCID: PMC3856098 DOI: 10.3390/ijms141122906] [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: 09/22/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022] Open
Abstract
Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, PTB can interact with selected RNA targets, structural elements and proteins. There is increasing evidence that PTB and its paralog PTBP2 play a major role as repressors of alternatively spliced exons, whose transcription is tissue-regulated. In addition to alternative splicing, PTB is involved in almost all steps of mRNA metabolism, including polyadenylation, mRNA stability and initiation of protein translation. Furthermore, it is well established that PTB recruitment in internal ribosome entry site (IRES) activates the translation of picornaviral and cellular proteins. Detailed studies of the structural properties of PTB have contributed to our understanding of the mechanism of RNA binding by RNA Recognition Motif (RRM) domains. In the present review, we will describe the structural properties of PTB, its paralogs and co-factors, the role in post-transcriptional regulation and actions in cell differentiation and pathogenesis. Defining the multifunctional roles of PTB will contribute to the understanding of key regulatory events in gene expression.
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28
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Edwards JM, Long J, de Moor CH, Emsley J, Searle MS. Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1. Nucleic Acids Res 2013; 41:7153-66. [PMID: 23748565 PMCID: PMC3737555 DOI: 10.1093/nar/gkt470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5'-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ∼ 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3' or 5' terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5' to 3' orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing.
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Affiliation(s)
- John M Edwards
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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29
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Shah S, Butler NM, Hannapel DJ, Rao AG. Mapping and characterization of the interaction interface between two polypyrimidine-tract binding proteins and a nova-type protein of Solanum tuberosum. PLoS One 2013; 8:e64783. [PMID: 23717658 PMCID: PMC3663837 DOI: 10.1371/journal.pone.0064783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/18/2013] [Indexed: 11/21/2022] Open
Abstract
Polypyrimidine tract-binding (PTB) proteins are RNA-binding proteins that generally contain four RNA recognition motifs (RRMs). In potato, six cDNAs encoding full-length PTB proteins have been identified. In the present study Nova1-like protein, designated StNova1, was identified as a potential interacting partner of the StPTB proteins via yeast two-hybrid screening. Nova protein is a RNA-binding protein that contains three K-homology (KH) domains. In humans, these proteins are involved in regulation of neuronal RNA metabolism but the role of Nova-like proteins in plants is poorly understood. We have validated this interaction and mapped the protein binding region on StNova1 and StPTB1 and −6 using a novel domain interaction phage display (DIPP) technique. The interaction between the two RNA-binding proteins StPTB1/6 and StNova1 is mediated through linker regions that are distinctly separated from the RRMs. Furthermore, using a random 21-mer phage-peptide library, we have identified a number of peptides with the consensus sequence motif [S/G][V/I][L/V]G that recognize the StPTB proteins. One over-represented peptide that recognizes StPTB6 contains the GVLGPWP sequence that is similar to the GIGGRYP sequence in the glycine-rich linker region between the KH2 and KH3 domains of StNova1. We show, through site-specific mutations, the importance of glycine and proline residues in StNova1-StPTB interactions.
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Affiliation(s)
- Shweta Shah
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Nathaniel M. Butler
- Plant Biology Major, Iowa State University, Ames, Iowa, United States of America
| | - David J. Hannapel
- Plant Biology Major, Iowa State University, Ames, Iowa, United States of America
| | - A. Gururaj Rao
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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30
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Gooding C, Edge C, Lorenz M, Coelho MB, Winters M, Kaminski CF, Cherny D, Eperon IC, Smith CWJ. MBNL1 and PTB cooperate to repress splicing of Tpm1 exon 3. Nucleic Acids Res 2013; 41:4765-82. [PMID: 23511971 PMCID: PMC3643581 DOI: 10.1093/nar/gkt168] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Exon 3 of the rat α-tropomyosin (Tpm1) gene is repressed in smooth muscle cells, allowing inclusion of the mutually exclusive partner exon 2. Two key types of elements affect repression of exon 3 splicing: binding sites for polypyrimidine tract-binding protein (PTB) and additional negative regulatory elements consisting of clusters of UGC or CUG motifs. Here, we show that the UGC clusters are bound by muscleblind-like proteins (MBNL), which act as repressors of Tpm1 exon 3. We show that the N-terminal region of MBNL1, containing its four CCCH zinc-finger domains, is sufficient to mediate repression. The same region of MBNL1 can make a direct protein-to-protein interaction with PTB, and RNA binding by MBNL promotes this interaction, apparently by inducing a conformational change in MBNL. Moreover, single molecule analysis showed that MBNL-binding sites increase the binding of PTB to its own sites. Our data suggest that the smooth muscle splicing of Tpm1 is mediated by allosteric assembly of an RNA–protein complex minimally comprising PTB, MBNL and their cognate RNA-binding sites.
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Affiliation(s)
- Clare Gooding
- Department of Biochemistry, University of Cambridge, CB2 1QW, UK
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31
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Abstract
PTB (polypyrimidine tract-binding protein) is an abundant and widely expressed RNA-binding protein with four RRM (RNA recognition motif) domains. PTB is involved in numerous post-transcriptional steps in gene expression in both the nucleus and cytoplasm, but has been best characterized as a regulatory repressor of some ASEs (alternative splicing events), and as an activator of translation driven by IRESs (internal ribosome entry segments). We have used a variety of approaches to characterize the activities of PTB and its molecular interactions with RNA substrates and protein partners. Using splice-sensitive microarrays we found that PTB acts not only as a splicing repressor but also as an activator, and that these two activities are determined by the location at which PTB binds relative to target exons. We have identified minimal splicing repressor and activator domains, and have determined high resolution structures of the second RRM domain of PTB binding to peptide motifs from the co-repressor protein Raver1. Using single-molecule techniques we have determined the stoichiometry of PTB binding to a regulated splicing substrate in whole nuclear extracts. Finally, we have used tethered hydroxyl radical probing to determine the locations on viral IRESs at which each of the four RRM domains bind. We are now combining tethered probing with single molecule analyses to gain a detailed understanding of how PTB interacts with pre-mRNA substrates to effect either repression or activation of splicing.
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32
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Keppetipola N, Sharma S, Li Q, Black DL. Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol 2012; 47:360-78. [PMID: 22655688 DOI: 10.3109/10409238.2012.691456] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alternative splicing patterns are regulated by RNA binding proteins that assemble onto each pre-mRNA to form a complex RNP structure. The polypyrimidine tract binding protein, PTB, has served as an informative model for understanding how RNA binding proteins affect spliceosome assembly and how changes in the expression of these proteins can control complex programs of splicing in tissues. In this review, we describe the mechanisms of splicing regulation by PTB and its function, along with its paralog PTBP2, in neuronal development.
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Affiliation(s)
- Niroshika Keppetipola
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
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