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Martínez-Lumbreras S, Träger LK, Mulorz MM, Payr M, Dikaya V, Hipp C, König J, Sattler M. Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs. Nat Commun 2024; 15:3888. [PMID: 38719828 PMCID: PMC11079029 DOI: 10.1038/s41467-024-48004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
PRPF40A plays an important role in the regulation of pre-mRNA splicing by mediating protein-protein interactions in the early steps of spliceosome assembly. By binding to proteins at the 5´ and 3´ splice sites, PRPF40A promotes spliceosome assembly by bridging the recognition of the splices. The PRPF40A WW domains are expected to recognize proline-rich sequences in SF1 and SF3A1 in the early spliceosome complexes E and A, respectively. Here, we combine NMR, SAXS and ITC to determine the structure of the PRPF40A tandem WW domains in solution and characterize the binding specificity and mechanism for proline-rich motifs recognition. Our structure of the PRPF40A WW tandem in complex with a high-affinity SF1 peptide reveals contributions of both WW domains, which also enables tryptophan sandwiching by two proline residues in the ligand. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A mediates intramolecular interactions with the WW tandem. Using NMR, ITC, mutational analysis in vitro, and immunoprecipitation experiments in cells, we show that the intramolecular interaction acts as an autoinhibitory filter for proof-reading of high-affinity proline-rich motifs in bona fide PRPF40A binding partners. We propose that similar autoinhibitory mechanisms are present in most WW tandem-containing proteins to enhance binding selectivity and regulation of WW/proline-rich peptide interaction networks.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Lena K Träger
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Marco Payr
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Varvara Dikaya
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Clara Hipp
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
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Klein MT, Krause BM, Neudörfl JM, Kühne R, Schmalz HG. Design and synthesis of a tetracyclic tripeptide mimetic frozen in a polyproline type II (PP2) helix conformation. Org Biomol Chem 2022; 20:9368-9377. [PMID: 36385673 DOI: 10.1039/d2ob01857h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A synthesis of the new tetracyclic scaffold ProM-19, which represents a XPP tripeptide unit frozen in a PPII helix conformation, was developed. As a key building block, N-Boc-protected ethyl (1S,3S,4R)-2-azabicyclo[2.2.1]hept-5-ene-2-carboxylate was prepared through a diastereoselective aza-Diels-Alder reaction and subsequent hydrogenolytic removal of the chiral N-1-phenylethyl substituent under temporary protection of the double bond through dihydroxylation and reconstitution by Corey-Winter olefination. The target compound Boc-[ProM-19]-OMe was then prepared via subsequent peptide coupling and Ru-catalyzed ring-closing metathesis steps employing (S)-N-Boc-allylgylcine and cis-5-vinyl-proline methyl ester as additional building blocks. In addition, Ac-[2-Cl-Phe]-[Pro]-[ProM-19]-OMe was prepared by solution phase peptide synthesis as a potential ligand for the ena-VASP EVH1 domain.
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Affiliation(s)
- Marco T Klein
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Bernhard M Krause
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Jörg-Martin Neudörfl
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Ronald Kühne
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Hans-Günther Schmalz
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
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3
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Im H, Baek H, Yang E, Kim K, Oh SK, Lee J, Kim H, Lee JM. ROS inhibits RORα degradation by decreasing its arginine methylation in liver cancer. Cancer Sci 2022; 114:187-200. [PMID: 36114756 PMCID: PMC9807526 DOI: 10.1111/cas.15595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023] Open
Abstract
Retinoic acid receptor-related orphan receptor α (RORα) is a transcription factor involved in nuclear gene expression and a known tumor suppressor. RORα was the first identified substrate of lysine methylation-dependent degradation. However, the mechanisms of other post-translational modifications (PTMs) that occur in RORα remain largely unknown, especially in liver cancer. Arginine methylation is a common PTM in arginine residues of nonhistone and histone proteins and affects substrate protein function and fate. We found an analogous amino acid disposition containing R37 at the ROR N-terminus compared to histone H3 residue, which is arginine methylated. Here, we provide evidence that R37 methylation-dependent degradation is carried out by protein arginine methyltransferase 5 (PRMT5). Further, we discovered that PRMT5 regulated the interaction between the E3 ubiquitin ligase ITCH and RORα through RORα arginine methylation. Arginine methylation-dependent ubiquitination-mediated RORα degradation reduced downstream target gene activation. H2 O2 -induced reactive oxygen species (ROS) decreased PRMT5 protein levels, consequently increasing RORα protein levels in HepG2 liver cancer cells. In addition, ROS inhibited liver cancer progression by inducing apoptosis via PRMT5-mediated RORα methylation and the ITCH axis. Our results potentiate PRMT5 as an elimination target in cancer therapy, and this additional regulatory level within ROS signaling may help identify new targets for therapeutic intervention in liver cancer.
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Affiliation(s)
- Hyuntae Im
- Department of Molecular Bioscience, College of Biomedical SciencesKangwon National UniversityChuncheonKorea
| | - Hee‐ji Baek
- Department of Biochemistry and Molecular BiologyKorea University College of MedicineSeoulKorea,BK21 Graduate Program, Department of Biomedical SciencesKorea University College of MedicineSeoulKorea
| | - Eunbi Yang
- Department of Biochemistry and Molecular BiologyKorea University College of MedicineSeoulKorea,BK21 Graduate Program, Department of Biomedical SciencesKorea University College of MedicineSeoulKorea
| | - Kyeongkyu Kim
- Gene Expression LaboratorySalk Institute for Biological StudiesLa JollaCaliforniaUSA
| | - Se Kyu Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological SciencesSeoul National UniversitySeoulKorea
| | - Jung‐Shin Lee
- Department of Molecular Bioscience, College of Biomedical SciencesKangwon National UniversityChuncheonKorea
| | - Hyunkyung Kim
- Department of Biochemistry and Molecular BiologyKorea University College of MedicineSeoulKorea,BK21 Graduate Program, Department of Biomedical SciencesKorea University College of MedicineSeoulKorea
| | - Ji Min Lee
- Graduate School of Medical Science & EngineeringKorea Advanced Institute of Science and TechnologyDaejeonKorea
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4
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Kennedy MA, Greco TM, Song B, Cristea IM. HTT-OMNI: A Web-based Platform for Huntingtin Interaction Exploration and Multi-omics Data Integration. Mol Cell Proteomics 2022; 21:100275. [PMID: 35932982 PMCID: PMC9540350 DOI: 10.1016/j.mcpro.2022.100275] [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: 05/27/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 01/18/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurological disorder that is caused by polyglutamine expansion of the huntingtin (HTT) protein. With the hope to uncover key modifiers of disease, a focus of the field of HD research has been on characterizing HTT-interacting proteins (HIPs) and the effect of the HTT polyglutamine expansion on the cellular omics landscape. However, while hundreds of studies have uncovered over 3000 potential HIPs to date, a means to interrogate these complementary interaction and omics datasets does not exist. The lack of a unified platform for exploring this breadth of potential HIPs and associated omics data represents a substantial barrier toward understanding the impact of HTT polyQ expansion and identifying interactions proximal to HD pathogenesis. Here, we describe the development of a web-based platform called HTT-OMNI (HTT OMics and Network Integration). This application facilitates the visualization and exploration of ∼3400 potential HTT interactors (from the HINT database) and their associated polyQ-dependent omics measurements, such as transcriptome and proteome abundances. Additionally, HTT-OMNI allows for the integration of user-generated datasets with existing HIPs and omic measurements. We first demonstrate the utility of HTT-OMNI for filtering existing HTT PPIs based on a variety of experimental metadata parameters, highlighting its capacity to select for HIPs detected in specific model organisms and tissues. Next, we leverage our application to visualize the relationships between HTT PPIs, genetic disease modifiers, and their multiomic landscape. Finally, we generate and analyze a previously unreported dataset of HTT PPIs, aimed at defining tissue-specific HTT interactions and the polyQ-dependent modulation of their relative stabilities in the cortex and striatum of HD mouse models.
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Borao S, Ayté J, Hümmer S. Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing. Int J Mol Sci 2021; 22:ijms222212444. [PMID: 34830325 PMCID: PMC8624252 DOI: 10.3390/ijms222212444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: (J.A.); (S.H.)
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Translational Molecular Pathology, Vall d’Hebron Research Institute (VHIR), CIBERONC, 08035 Barcelona, Spain
- Correspondence: (J.A.); (S.H.)
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6
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Carron J, Torricelli C, Silva JK, Coser LDO, Lima CSP, Lourenço GJ. Intronic variants of MITF (rs7623610) and CREB1 (rs10932201) genes may enhance splicing efficiency in human melanoma cell line. Mutat Res 2021; 823:111763. [PMID: 34710701 DOI: 10.1016/j.mrfmmm.2021.111763] [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: 07/27/2021] [Revised: 09/24/2021] [Accepted: 10/17/2021] [Indexed: 11/20/2022]
Abstract
We previously reported that intronic single nucleotide variations (SNVs) in MITF (c.938-325G>A, rs7623610) and CREB1 (c.303+373G>A, rs10932201) genes were associated with risk, aggressiveness, and prognosis of cutaneous melanoma (CM). In this study, we investigated the influence of the above SNVs in splicing patterns and efficiency. We constructed minigenes with wild type and variant alleles from MITF and CREB1 to assess the effect of the SNVs on splicing. The minigenes were transfected in the human melanoma cell line (SK-MEL-28). RT-PCR and DNA sequencing investigated the constructs' splicing patterns. Minigenes constructs' splicing efficiency and HNRNPA1 and SF1 splicing genes' expression were investigated by qPCR. We found that MITF and CREB1 SNVs did not alter the splicing pattern, but they influenced the splicing efficiency. MITF-A (p= 0.03) and CREB1-A (p= 0.005) variant minigenes yielded an increase of mRNA generated from the constructions. Additionally, lower mRNA levels of HNRNPA1 and SF1 were seen in the variant minigenes MITF-A (p= 0.04) and CREB1-A (p= 0.005). We described for the first time the potential importance of MITF rs7623610 and CREB1 rs10932201 SNVs in splicing efficiency and its relationship with CM.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Janet Keller Silva
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Lilian de Oliveira Coser
- Laboratory of Nerve Regeneration, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil; Department of Radiology, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.
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7
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A machine learning-based framework for modeling transcription elongation. Proc Natl Acad Sci U S A 2021; 118:2007450118. [PMID: 33526657 DOI: 10.1073/pnas.2007450118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gene expression regulation. Characterizing the transcriptional elongation dynamics can thus help us understand many essential biological processes in eukaryotic cells. However, experimentally measuring Pol II elongation rates is generally time and resource consuming. We developed PEPMAN (polymerase II elongation pausing modeling through attention-based deep neural network), a deep learning-based model that accurately predicts Pol II pausing sites based on the native elongating transcript sequencing (NET-seq) data. Through fully taking advantage of the attention mechanism, PEPMAN is able to decipher important sequence features underlying Pol II pausing. More importantly, we demonstrated that the analyses of the PEPMAN-predicted results around various types of alternative splicing sites can provide useful clues into understanding the cotranscriptional splicing events. In addition, associating the PEPMAN prediction results with different epigenetic features can help reveal important factors related to the transcription elongation process. All these results demonstrated that PEPMAN can provide a useful and effective tool for modeling transcription elongation and understanding the related biological factors from available high-throughput sequencing data.
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8
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Genetic locus responsible for diabetic phenotype in the insulin hyposecretion (ihs) mouse. PLoS One 2020; 15:e0234132. [PMID: 32502168 PMCID: PMC7274380 DOI: 10.1371/journal.pone.0234132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
Diabetic animal models have made significant contributions to understanding the etiology of diabetes and to the development of new medications. Our research group recently developed a novel diabetic mouse strain, the insulin hyposecretion (ihs)mouse. The strain involves neither obesity nor insulitis but exhibits notable pancreatic β-cell dysfunction, distinguishing it from other well-characterized animal models. In ihs mice, severe impairment of insulin secretion from pancreas has been elicited by glucose or potassium chloride stimulation. To clarify the genetic basis of impaired insulin secretion, beginning with identifying the causative gene, genetic linkage analysis was performed using [(C57BL/6 × ihs) F1 × ihs] backcross progeny. Genetic linkage analysis and quantitative trait loci analysis for blood glucose after oral glucose loading indicated that a recessively acting locus responsible for impaired glucose tolerance was mapped to a 14.9-Mb region of chromosome 18 between D18Mit233 and D18Mit235 (the ihs locus). To confirm the gene responsible for the ihs locus, a congenic strain harboring the ihs locus on the C57BL/6 genetic background was developed. Phenotypic analysis of B6.ihs-(D18Mit233-D18Mit235) mice showed significant glucose tolerance impairment and markedly lower plasma insulin levels during an oral glucose tolerance test. Whole-genome sequencing and Sanger sequencing analyses on the ihs genome detected two ihs-specific variants changing amino acids within the ihs locus; both variants in Slc25a46 and Tcerg1 were predicted to disrupt the protein function. Based on information regarding gene functions involving diabetes mellitus and insulin secretion, reverse-transcription quantitative polymerase chain reaction analysis revealed that the relative abundance of Reep2 and Sil1 transcripts from ihs islets was significantly decreased whereas that of Syt4 transcripts were significantly increased compared with those of control C57BL/6 mice. Thus, Slc25a46, Tcerg1, Syt4, Reep2 and Sil1 are potential candidate genes for the ihs locus. This will be the focus of future studies in both mice and humans.
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Bhadra M, Howell P, Dutta S, Heintz C, Mair WB. Alternative splicing in aging and longevity. Hum Genet 2019; 139:357-369. [PMID: 31834493 DOI: 10.1007/s00439-019-02094-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/24/2019] [Indexed: 12/13/2022]
Abstract
Alternative pre-mRNA splicing increases the complexity of the proteome that can be generated from the available genomic coding sequences. Dysregulation of the splicing process has been implicated in a vast repertoire of diseases. However, splicing has recently been linked to both the aging process itself and pro-longevity interventions. This review focuses on recent research towards defining RNA splicing as a new hallmark of aging. We highlight dysfunctional alternative splicing events that contribute to the aging phenotype across multiple species, along with recent efforts toward deciphering mechanistic roles for RNA splicing in the regulation of aging and longevity. Further, we discuss recent research demonstrating a direct requirement for specific splicing factors in pro-longevity interventions, and specifically how nutrient signaling pathways interface to splicing factor regulation and downstream splicing targets. Finally, we review the emerging potential of using splicing profiles as a predictor of biological age and life expectancy. Understanding the role of RNA splicing components and downstream targets altered in aging may provide opportunities to develop therapeutics and ultimately extend healthy lifespan in humans.
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Affiliation(s)
- Malini Bhadra
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Porsha Howell
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Sneha Dutta
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - William B Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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Moreno-Castro C, Prieto-Sánchez S, Sánchez-Hernández N, Hernández-Munain C, Suñé C. Role for the splicing factor TCERG1 in Cajal body integrity and snRNP assembly. J Cell Sci 2019; 132:jcs.232728. [PMID: 31636114 DOI: 10.1242/jcs.232728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/11/2019] [Indexed: 12/29/2022] Open
Abstract
Cajal bodies are nuclear organelles involved in the nuclear phase of small nuclear ribonucleoprotein (snRNP) biogenesis. In this study, we identified the splicing factor TCERG1 as a coilin-associated factor that is essential for Cajal body integrity. Knockdown of TCERG1 disrupts the localization of the components of Cajal bodies, including coilin and NOLC1, with coilin being dispersed in the nucleoplasm into numerous small foci, without affecting speckles, gems or the histone locus body. Furthermore, the depletion of TCERG1 affects the recruitment of Sm proteins to uridine-rich small nuclear RNAs (snRNAs) to form the mature core snRNP. Taken together, the results of this study suggest that TCERG1 plays an important role in Cajal body formation and snRNP biogenesis.
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Affiliation(s)
- Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Noemí Sánchez-Hernández
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
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Hernando CE, García Hourquet M, de Leone MJ, Careno D, Iserte J, Mora Garcia S, Yanovsky MJ. A Role for Pre-mRNA-PROCESSING PROTEIN 40C in the Control of Growth, Development, and Stress Tolerance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1019. [PMID: 31456814 PMCID: PMC6700278 DOI: 10.3389/fpls.2019.01019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/22/2019] [Indexed: 05/08/2023]
Abstract
Because of their sessile nature, plants have adopted varied strategies for growing and reproducing in an ever-changing environment. Control of mRNA levels and pre-mRNA alternative splicing are key regulatory layers that contribute to adjust and synchronize plant growth and development with environmental changes. Transcription and alternative splicing are thought to be tightly linked and coordinated, at least in part, through a network of transcriptional and splicing regulatory factors that interact with the carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II. One of the proteins that has been shown to play such a role in yeast and mammals is pre-mRNA-PROCESSING PROTEIN 40 (PRP40, also known as CA150, or TCERG1). In plants, members of the PRP40 family have been identified and shown to interact with the CTD of RNA Pol II, but their biological functions remain unknown. Here, we studied the role of AtPRP40C, in Arabidopsis thaliana growth, development and stress tolerance, as well as its impact on the global regulation of gene expression programs. We found that the prp40c knockout mutants display a late-flowering phenotype under long day conditions, associated with minor alterations in red light signaling. An RNA-seq based transcriptome analysis revealed differentially expressed genes related to biotic stress responses and also differentially expressed as well as differentially spliced genes associated with abiotic stress responses. Indeed, the characterization of stress responses in prp40c mutants revealed an increased sensitivity to salt stress and an enhanced tolerance to Pseudomonas syringae pv. maculicola (Psm) infections. This constitutes the most thorough analysis of the transcriptome of a prp40 mutant in any organism, as well as the first characterization of the molecular and physiological roles of a member of the PRP40 protein family in plants. Our results suggest that PRP40C is an important factor linking the regulation of gene expression programs to the modulation of plant growth, development, and stress responses.
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12
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Pons M, Prieto S, Miguel L, Frebourg T, Campion D, Suñé C, Lecourtois M. Identification of TCERG1 as a new genetic modulator of TDP-43 production in Drosophila. Acta Neuropathol Commun 2018; 6:138. [PMID: 30541625 PMCID: PMC6292132 DOI: 10.1186/s40478-018-0639-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
TAR DNA-binding protein-43 (TDP-43) is a ubiquitously expressed DNA-/RNA-binding protein that has been linked to numerous aspects of the mRNA life cycle. Similar to many RNA-binding proteins, TDP-43 expression is tightly regulated through an autoregulatory negative feedback loop. Cell function and survival depend on the strict control of TDP-43 protein levels. TDP-43 has been identified as the major constituent of ubiquitin-positive inclusions in patients with Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). Several observations argue for a pathogenic role of elevated TDP-43 levels in these disorders. Modulation of the cycle of TDP-43 production might therefore provide a new therapeutic strategy. Using a Drosophila model mimicking key features of the TDP-43 autoregulatory feedback loop, we identified CG42724 as a genetic modulator of TDP-43 production in vivo. We found that CG42724 protein influences qualitatively and quantitatively the TDP-43 mRNA transcript pattern. CG42724 overexpression promotes the production of transcripts that can be efficiently released into the cytoplasm for protein translation. Importantly, we showed that TCERG1, the human homolog of the Drosophila CG42724 protein, also caused an increase of TDP-43 protein steady-state levels in mammalian cells. Therefore, our data suggest the possibility that targeting TCERG1 could be therapeutic in TDP-43 proteinopathies.
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13
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The HIV-1 Tat Protein Enhances Splicing at the Major Splice Donor Site. J Virol 2018; 92:JVI.01855-17. [PMID: 29743356 DOI: 10.1128/jvi.01855-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/25/2018] [Indexed: 12/23/2022] Open
Abstract
Transcription of the HIV-1 proviral DNA and subsequent processing of the primary transcript results in the production of a large set of unspliced and differentially spliced viral RNAs. The major splice donor site (5'ss) that is located in the untranslated leader of the HIV-1 transcript is used for the production of all spliced RNAs, and splicing at this site has to be tightly regulated to allow the balanced production of all viral RNAs and proteins. We demonstrate that the viral Tat protein, which is known to activate viral transcription, also stimulates splicing at the major 5'ss. As for the transcription effect, Tat requires the viral long terminal repeat promoter and the trans-acting responsive RNA hairpin for splicing regulation. These results indicate that HIV-1 transcription and splicing are tightly coupled processes through the coordinated action of the essential Tat protein.IMPORTANCE The HIV-1 proviral DNA encodes a single RNA transcript that is used as RNA genome and packaged into newly assembled virus particles. This full-length RNA is also used as mRNA for the production of structural and enzymatic proteins. Production of other essential viral proteins depends on alternative splicing of the primary transcript, which yields a large set of differentially spliced mRNAs. Optimal virus replication requires a balanced production of all viral RNAs, which means that the splicing process has to be strictly regulated. We show that the HIV-1 Tat protein, a factor that is well known for its transcription activating function, also stimulates splicing. Thus, Tat controls not only the level of the viral RNA but also the balance between spliced and unspliced RNAs.
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14
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Chiha S, Soicke A, Barone M, Müller M, Bruns J, Opitz R, Neudörfl JM, Kühne R, Schmalz HG. Design and Synthesis of Building Blocks for PPII-Helix Secondary-Structure Mimetics: A Stereoselective Entry to 4-Substituted 5-Vinylprolines. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Slim Chiha
- Department of Chemistry; University of Cologne; Greinstrasse 4 50939 Cologne Germany
| | - Arne Soicke
- Department of Chemistry; University of Cologne; Greinstrasse 4 50939 Cologne Germany
| | - Matthias Barone
- Campus BerlinBuch; Leibniz-Institut für Molekulare Pharmakologie (FMP); 13125 Berlin Germany
| | - Matthias Müller
- Campus BerlinBuch; Leibniz-Institut für Molekulare Pharmakologie (FMP); 13125 Berlin Germany
| | - Judith Bruns
- Department of Chemistry; University of Cologne; Greinstrasse 4 50939 Cologne Germany
| | - Robert Opitz
- Campus BerlinBuch; Leibniz-Institut für Molekulare Pharmakologie (FMP); 13125 Berlin Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry; University of Cologne; Greinstrasse 4 50939 Cologne Germany
| | - Ronald Kühne
- Campus BerlinBuch; Leibniz-Institut für Molekulare Pharmakologie (FMP); 13125 Berlin Germany
| | - Hans-Günther Schmalz
- Department of Chemistry; University of Cologne; Greinstrasse 4 50939 Cologne Germany
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Galganski L, Urbanek MO, Krzyzosiak WJ. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res 2017; 45:10350-10368. [PMID: 28977640 PMCID: PMC5737799 DOI: 10.1093/nar/gkx759] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
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Affiliation(s)
- Lukasz Galganski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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16
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Abstract
Pre-mRNA processing protein 40 (Prp40) is a nuclear protein that has a role in pre-mRNA splicing. Prp40 possesses two leucine-rich nuclear export signals, but little is known about the function of Prp40 in the export process. Another protein that has a role in protein export is centrin, a member of the EF-hand superfamily of Ca2+-binding proteins. Prp40 was found to be a centrin target by yeast-two-hybrid screening using both Homo sapiens centrin 2 (Hscen2) and Chlamydomonas reinhardtii centrin (Crcen). We identified a centrin-binding site within H. sapiens Prp40 homolog A (HsPrp40A), which contains a hydrophobic triad W1L4L8 that is known to be important in the interaction with centrin. This centrin-binding site is highly conserved within the first nuclear export signal consensus sequence identified in Saccharomyces cerevisiae Prp40. Here, we examine the interaction of HsPrp40A peptide (HsPrp40Ap) with both Hscen2 and Crcen by isothermal titration calorimetry. We employed the thermodynamic parameterization to estimate the polar and apolar surface area of the interface. In addition, we have defined the molecular mechanism of thermally induced unfolding and dissociation of the Crcen-HsPrp40Ap complex using two-dimensional infrared correlation spectroscopy. These complementary techniques showed for the first time, to our knowledge, that HsPrp40Ap interacts with centrin in vitro, supporting a coupled functional role for these proteins in pre-mRNA splicing.
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17
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Miller NJ, Schick K, Timchenko N, Harrison E, Roesler WJ. The Glutamine-Alanine Repeat Domain of TCERG1 is Required for the Inhibition of the Growth Arrest Activity of C/EBPα. J Cell Biochem 2016; 117:612-20. [PMID: 26264132 DOI: 10.1002/jcb.25309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/07/2015] [Indexed: 11/12/2022]
Abstract
TCERG1 was characterized previously as a repressor of the transcription factor C/EBPα through a mechanism that involved relocalization of TCERG1 from nuclear speckles to pericentromeric regions. The inhibitory activity as well as the relocalization activity has been demonstrated to lie in the amino terminal half of the protein, which contains several discrete motifs including an imperfect glutamine-alanine (QA) repeat. In the present study, we showed that deletion of this domain completely abrogated the ability of TCERG1 to inhibit the growth arrest activity of C/EBPα. Moreover, the QA repeat deletion mutant of TCERG1 lost the ability to be relocalized from nuclear speckles to pericentromeric regions, and caused an increase in the average size of individual speckles. We also showed that deletion of the QA repeat abrogated the complex formation between TCERG1 and C/EBPα. Examination of mutants with varying numbers of QA repeats indicated that a minimal number of repeats are required for inhibitory activity as well as relocalization ability. These data contribute to our overall understanding of how TCERG1 can have gene-specific effects in addition to its more general roles in coordinating transcription elongation and splicing.
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Affiliation(s)
- Nicholas J Miller
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kaitlyn Schick
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Emmett Harrison
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - William J Roesler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
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18
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Transcriptional Elongation Regulator 1 Affects Transcription and Splicing of Genes Associated with Cellular Morphology and Cytoskeleton Dynamics and Is Required for Neurite Outgrowth in Neuroblastoma Cells and Primary Neuronal Cultures. Mol Neurobiol 2016; 54:7808-7823. [PMID: 27844289 DOI: 10.1007/s12035-016-0284-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022]
Abstract
TCERG1 is a highly conserved human protein implicated in interactions with the transcriptional and splicing machinery that is associated with neurodegenerative disorders. Biochemical, neuropathological, and genetic evidence suggests an important role for TCERG1 in Huntington's disease (HD) pathogenesis. At present, the molecular mechanism underlying TCERG1-mediated neuronal effects is unknown. Here, we show that TCERG1 depletion led to widespread alterations in mRNA processing that affected different types of alternative transcriptional or splicing events, indicating that TCERG1 plays a broad role in the regulation of alternative splicing. We observed considerable changes in the transcription and alternative splicing patterns of genes involved in cytoskeleton dynamics and neurite outgrowth. Accordingly, TCERG1 depletion in the neuroblastoma SH-SY5Y cell line and primary mouse neurons affected morphogenesis and resulted in reduced dendritic outgrowth, with a major effect on dendrite ramification and branching complexity. These defects could be rescued by ectopic expression of TCERG1. Our results indicate that TCERG1 affects expression of multiple mRNAs involved in neuron projection development, whose misregulation may be involved in TCERG1-linked neurological disorders.
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Abstract
Introns inserted within introns are commonly referred to as twintrons, however the original definition for twintron implied that splicing of the external member of the twintron could only proceed upon splicing of the internal member. This review examines the various types of twintron-like arrangements that have been reported and assigns them to either nested or twintron categories that are subdivided further into subtypes based on differences of their mode of splicing. Twintron-like arrangements evolved independently by fortuitous events among different types of introns but once formed they offer opportunities for the evolution of new regulatory strategies and/or novel genetic elements.
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Affiliation(s)
- Mohamed Hafez
- a Department of Biochemistry ; Faculty of Medicine; University of Montreal ; Montréal , QC Canada.,b Department of Botany and Microbiology ; Faculty of Science; Suez University ; Suez , Egypt
| | - Georg Hausner
- c Department of Microbiology ; University of Manitoba ; Winnipeg , MB Canada
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20
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Hollander D, Naftelberg S, Lev-Maor G, Kornblihtt AR, Ast G. How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing? Trends Genet 2016; 32:596-606. [PMID: 27507607 DOI: 10.1016/j.tig.2016.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/19/2022]
Abstract
The splice sites (SSs) delimiting an intron are brought together in the earliest step of spliceosome assembly yet it remains obscure how SS pairing occurs, especially when introns are thousands of nucleotides long. Splicing occurs in vivo in mammals within minutes regardless of intron length, implying that SS pairing can instantly follow transcription. Also, factors required for SS pairing, such as the U1 small nuclear ribonucleoprotein (snRNP) and U2AF65, associate with RNA polymerase II (RNAPII), while nucleosomes preferentially bind exonic sequences and associate with U2 snRNP. Based on recent publications, we assume that the 5' SS-bound U1 snRNP can remain tethered to RNAPII until complete synthesis of the downstream intron and exon. An additional U1 snRNP then binds the downstream 5' SS, whereas the RNAPII-associated U2AF65 binds the upstream 3' SS to facilitate SS pairing along with exon definition. Next, the nucleosome-associated U2 snRNP binds the branch site to advance splicing complex assembly. This may explain how RNAPII and chromatin are involved in spliceosome assembly and how introns lengthened during evolution with a relatively minimal compromise in splicing.
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Affiliation(s)
- Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Shiran Naftelberg
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.
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21
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Sánchez-Hernández N, Boireau S, Schmidt U, Muñoz-Cobo JP, Hernández-Munain C, Bertrand E, Suñé C. The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing. RNA (NEW YORK, N.Y.) 2016; 22:571-582. [PMID: 26873599 PMCID: PMC4793212 DOI: 10.1261/rna.052795.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 06/05/2023]
Abstract
Coupling between transcription and RNA processing is key for gene regulation. Using live-cell photobleaching techniques, we investigated the factor TCERG1, which coordinates transcriptional elongation with splicing. We demonstrate that TCERG1 is highly mobile in the nucleoplasm and that this mobility is slightly decreased when it is associated with speckles. Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) but not α-amanitin treatment reduced the mobility of TCERG1, which suggests interaction with paused transcription elongation complexes. We found that TCERG1 mobility is rapid at the transcription site (TS) of a reporter that splices post-transcriptionally and that TCERG1 is recruited to the active TS independent of the CTD of RNAPII, thus excluding phosphorylated CTD as a requirement for recruiting this factor to the TS. Importantly, the mobility of TCERG1 is reduced when the reporter splices cotranscriptionally, which suggests that TCERG1 forms new macromolecular complexes when splicing occurs cotranscriptionally. In this condition, spliceostatin A has no effect, indicating that TCERG1 rapidly binds and dissociates from stalled spliceosomal complexes and that the mobility properties of TCERG1 do not depend on events occurring after the initial spliceosome formation. Taken together, these data suggest that TCERG1 binds independently to elongation and splicing complexes, thus performing their coupling by transient interactions rather than by stable association with one or the other complexes. This finding has conceptual implications for understanding the coupling between transcription and RNA processing.
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Affiliation(s)
- Noemí Sánchez-Hernández
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Ute Schmidt
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Juan Pablo Muñoz-Cobo
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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22
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Becerra S, Andrés-León E, Prieto-Sánchez S, Hernández-Munain C, Suñé C. Prp40 and early events in splice site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:17-32. [PMID: 26494226 DOI: 10.1002/wrna.1312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/18/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
The alternative splicing (AS) of precursor messenger RNA (pre-mRNA) is a tightly regulated process through which introns are removed to leave the resulting exons in the mRNA appropriately aligned and ligated. The AS of pre-mRNA is a key mechanism for increasing the complexity of proteins encoded in the genome. In humans, more than 90% of genes undergo AS, underscoring the importance of this process in RNA biogenesis. As such, AS misregulation underlies multiple human diseases. The splicing reaction is catalyzed by the spliceosome, a highly dynamic complex that assembles at or near the intron/exon boundaries and undergoes sequential conformational and compositional changes during splicing. The initial recognition of splice sites defines the exons that are going to be removed, which is a critical step in the highly regulated splicing process. Although the available lines of evidence are increasing, the molecular mechanisms governing AS, including the initial interactions occurring at intron/exon boundaries, and the factors that modulate these critical connections by functioning as a scaffold for active-site RNAs or proteins, remain poorly understood. In this review, we summarize the major hallmarks of the initial steps in the splicing process and the role of auxiliary factors that contribute to the assembly of the spliceosomal complex. We also discuss the role of the essential yeast Prp40 protein and its mammalian homologs in the specificity of this pre-mRNA processing event. In addition, we provide the first exhaustive phylogenetic analysis of the molecular evolution of Prp40 family members. WIREs RNA 2016, 7:17-32. doi: 10.1002/wrna.1312 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soraya Becerra
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
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23
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Functional Consequences for Apoptosis by Transcription Elongation Regulator 1 (TCERG1)-Mediated Bcl-x and Fas/CD95 Alternative Splicing. PLoS One 2015; 10:e0139812. [PMID: 26462236 PMCID: PMC4604205 DOI: 10.1371/journal.pone.0139812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/17/2015] [Indexed: 11/19/2022] Open
Abstract
Here, we present evidence for a specific role of the splicing-related factor TCERG1 in regulating apoptosis in live cells by modulating the alternative splicing of the apoptotic genes Bcl-x and Fas. We show that TCERG1 modulates Bcl-x alternative splicing during apoptosis and its activity in Bcl-x alternative splicing correlates with the induction of apoptosis, as determined by assessing dead cells, sub-G1-phase cells, annexin-V binding, cell viability, and cleavage of caspase-3 and PARP-1. Furthermore, the effect of TCERG1 on apoptosis involved changes in mitochondrial membrane permeabilization. We also found that depletion of TCERG1 reduces the expression of the activated form of the pro-apoptotic mitochondrial membrane protein Bak, which remains inactive by heterodimerizing with Bcl-xL, preventing the initial step of cytochrome c release in Bak-mediated mitochondrial apoptosis. In addition, we provide evidence that TCERG1 also participates in the death receptor-mediated apoptosis pathway. Interestingly, TCERG1 also modulates Fas/CD95 alternative splicing. We propose that TCERG1 sensitizes a cell to apoptotic agents, thus promoting apoptosis by regulating the alternative splicing of both the Bcl-x and Fas/CD95 genes. Our findings may provide a new link between the control of alternative splicing and the molecular events leading to apoptosis.
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24
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Crisci A, Raleff F, Bagdiul I, Raabe M, Urlaub H, Rain JC, Krämer A. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. Nucleic Acids Res 2015; 43:10456-73. [PMID: 26420826 PMCID: PMC4666396 DOI: 10.1093/nar/gkv952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/10/2015] [Indexed: 02/03/2023] Open
Abstract
Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions.
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Affiliation(s)
- Angela Crisci
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Flore Raleff
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Monika Raabe
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | | | - Angela Krämer
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
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25
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Reuter C, Opitz R, Soicke A, Dohmen S, Barone M, Chiha S, Klein MT, Neudörfl JM, Kühne R, Schmalz HG. Design and Stereoselective Synthesis of ProM-2: A Spirocyclic Diproline Mimetic with Polyproline Type II (PPII) Helix Conformation. Chemistry 2015; 21:8464-70. [DOI: 10.1002/chem.201406493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/11/2015] [Indexed: 11/08/2022]
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26
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Kralovicova J, Knut M, Cross NCP, Vorechovsky I. Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins. Nucleic Acids Res 2015; 43:3747-63. [PMID: 25779042 PMCID: PMC4402522 DOI: 10.1093/nar/gkv194] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/24/2015] [Indexed: 01/05/2023] Open
Abstract
The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3′ splice site (3′ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3′ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3′UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream. Although most differentially used exons were responsive to both U2AF subunits and their inclusion correlated with U2AF levels, a small number of transcripts exhibited distinct responses to U2AF35a and U2AF35b, supporting the existence of isoform-specific interactions. These results provide new insights into function of U2AF and U2AF35 in alternative RNA processing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Marcin Knut
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Nicholas C P Cross
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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27
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Becerra S, Montes M, Hernández-Munain C, Suñé C. Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo. RNA (NEW YORK, N.Y.) 2015; 21:438-57. [PMID: 25605964 PMCID: PMC4338339 DOI: 10.1261/rna.047258.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The first stable complex formed during the assembly of spliceosomes onto pre-mRNA substrates in mammals includes U1 snRNP, which recognizes the 5' splice site, and the splicing factors SF1 and U2AF, which bind the branch point sequence, polypyrimidine tract, and 3' splice site. The 5' and 3' splice site complexes are thought to be joined together by protein-protein interactions mediated by factors that ensure the fidelity of the initial splice site recognition. In this study, we identified and characterized PRPF40B, a putative mammalian ortholog of the U1 snRNP-associated yeast splicing factor Prp40. PRPF40B is highly enriched in speckles with a behavior similar to splicing factors. We demonstrated that PRPF40B interacts directly with SF1 and associates with U2AF(65). Accordingly, PRPF40B colocalizes with these splicing factors in the cell nucleus. Splicing assays with reporter minigenes revealed that PRPF40B modulates alternative splice site selection. In the case of Fas regulation of alternative splicing, weak 5' and 3' splice sites and exonic sequences are required for PRPF40B function. Placing our data in a functional context, we also show that PRPF40B depletion increased Fas/CD95 receptor number and cell apoptosis, which suggests the ability of PRPF40B to alter the alternative splicing of key apoptotic genes to regulate cell survival.
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Affiliation(s)
| | | | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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Satoh T, Katano-Toki A, Tomaru T, Yoshino S, Ishizuka T, Horiguchi K, Nakajima Y, Ishii S, Ozawa A, Shibusawa N, Hashimoto K, Mori M, Yamada M. Coordinated regulation of transcription and alternative splicing by the thyroid hormone receptor and its associating coregulators. Biochem Biophys Res Commun 2014; 451:24-9. [PMID: 25019984 DOI: 10.1016/j.bbrc.2014.07.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 12/17/2022]
Abstract
Emerging evidence has indicated that the transcription and processing of precursor mRNA (pre-mRNA) are functionally coupled to modulate gene expression. In collaboration with coregulators, several steroid hormone receptors have previously been shown to directly affect alternative pre-mRNA splicing coupled to hormone-induced gene transcription; however, the roles of the thyroid hormone receptor (TR) and its coregulators in alternative splicing coordinated with transcription remain unknown. In the present study, we constructed a luciferase reporter and CD44 alternative splicing (AS) minigene driven by a minimal promoter carrying 2 copies of the palindromic thyroid hormone-response element. We then examined whether TR could modulate pre-mRNA processing coupled to triiodothyronine (T3)-induced gene transcription using luciferase reporter and splicing minigene assays in HeLa cells. In the presence of cotransfected TRβ1, T3 increased luciferase activities along with the inclusion of the CD44 variable exons 4 and 5 in a dose- and time-dependent manner. In contrast, cotransfected TRβ1 did not affect the exon-inclusion of the CD44 minigene driven by the cytomegalovirus promoter. T3-induced two-exon inclusion was significantly increased by the cotransfection of the TR-associated protein, 150-kDa, a subunit of the TRAP/Mediator complex that has recently been shown to function as a splicing factor. In contrast, T3-induced two-exon inclusion was significantly decreased by cotransfection of the polypyrimidine tract-binding protein-associated splicing factor, which was previously shown to function as a corepressor of TR. These results demonstrated that liganded TR in cooperation with its associating cofactors could modulate alternative pre-mRNA splicing coupled to gene transcription.
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Affiliation(s)
- Tetsurou Satoh
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan.
| | - Akiko Katano-Toki
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takuya Tomaru
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Satoshi Yoshino
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takahiro Ishizuka
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Horiguchi
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yasuyo Nakajima
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Sumiyasu Ishii
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Atsushi Ozawa
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Nobuyuki Shibusawa
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Koshi Hashimoto
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Masatomo Mori
- Kitakanto Molecular Novel Research Institute for Obesity and Metabolism, Midori, Japan
| | - Masanobu Yamada
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
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29
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Meinel DM, Burkert-Kautzsch C, Kieser A, O'Duibhir E, Siebert M, Mayer A, Cramer P, Söding J, Holstege FCP, Sträßer K. Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genet 2013; 9:e1003914. [PMID: 24244187 PMCID: PMC3828145 DOI: 10.1371/journal.pgen.1003914] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/09/2013] [Indexed: 12/31/2022] Open
Abstract
Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.
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Affiliation(s)
- Dominik M. Meinel
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Cornelia Burkert-Kautzsch
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Anja Kieser
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthias Siebert
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Andreas Mayer
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Patrick Cramer
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Johannes Söding
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Frank C. P. Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Katja Sträßer
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Munich, Germany
- * E-mail:
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30
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Affiliation(s)
- Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich,
Germany
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry,
Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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31
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Zhu S, Wang G, Liu B, Wang Y. Modeling exon expression using histone modifications. PLoS One 2013; 8:e67448. [PMID: 23825663 PMCID: PMC3692485 DOI: 10.1371/journal.pone.0067448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/17/2013] [Indexed: 12/22/2022] Open
Abstract
Histones undergo numerous covalent modifications that play important roles in regulating gene expression. Previous investigations have focused on the effects of histone modifications on gene promoters, whereas efforts to unravel their effects on transcribed regions have lagged behind. To elucidate the effects of histone modification on transcribed regions, we constructed a quantitative model, which we suggest can predict the variation of gene expression more faithfully than the model constructed on promoters. Moreover, motivated by the fact that exon spicing is functionally coupled to transcription, we also devised a quantitative model to predict alternative exon expression using histone modifications on exons. This model was found to be general across different exon types and even cell types. Furthermore, an interaction network linking histone modifications to alternative exon expression was constructed using partial correlations. The network indicated that gene expression and specific histone modifications (H3K36me3 and H4K20me1) could directly influence the exon expression, while other modifications could act in an additive way to account for the stability and robustness. In addition, our results suggest that combinations of histone modifications contribute to exon splicing in a redundant and cumulative fashion. To conclude, this study provides a better understanding of the effects of histone modifications on gene transcribed regions.
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Affiliation(s)
- Shijia Zhu
- Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guohua Wang
- Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Bo Liu
- Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yadong Wang
- Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
- * E-mail:
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32
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Pushpa K, Kumar GA, Subramaniam K. PUF-8 and TCER-1 are essential for normal levels of multiple mRNAs in the C. elegans germline. Development 2013; 140:1312-20. [PMID: 23444359 PMCID: PMC3585663 DOI: 10.1242/dev.087833] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
PUF family proteins are well-conserved regulators of cell proliferation in different developmental processes. They regulate target mRNAs by promoting degradation or by influencing translation through interaction with the translation initiation machinery. Here we show that Caenorhabditis elegans PUF-8 functions redundantly with the nuclear protein TCER-1 in the post-transcriptional maintenance of at least six germline mRNAs. The levels of spliced mRNAs in the puf-8(-) tcer-1(-) double mutant are only 10-30% of the wild type, whereas the unspliced forms increase by ∼2- to 3-fold compared with the wild type. These two proteins colocalise at the inner nuclear periphery, and their absence leads to reduced germ cell proliferation and to sterility. A yeast two-hybrid screen of 31 components of the nuclear pore complex and mRNA processing machineries identified seven proteins involved in mRNA export as potential partners of PUF-8. One of these, the nuclear cap-binding protein NCBP-2, colocalises with PUF-8 in the nucleus. A 50 amino acid N-terminal domain of PUF-8 is essential for interaction with NCBP-2 and for PUF-8 to function redundantly with TCER-1. These results reveal two important unexpected aspects of PUF proteins: that, in addition to the C-terminal PUF domain, the N-terminal domain is crucial for PUF function, and that PUF proteins have a novel role in mRNA maintenance. We propose that PUF proteins, in addition to their known cytoplasmic roles, participate in nuclear processing and/or export of mRNAs.
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Affiliation(s)
- Kumari Pushpa
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
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Abstract
The type I interferon system genes IKBKE and IFIH1 are associated with the risk of systemic lupus erythematosus (SLE). To identify the sequence variants that are able to account for the disease association, we resequenced the genes IKBKE and IFIH1. Eighty-six single-nucleotide variants (SNVs) with potentially functional effect or differences in allele frequencies between patients and controls determined by sequencing were further genotyped in 1140 SLE patients and 2060 controls. In addition, 108 imputed sequence variants in IKBKE and IFIH1 were included in the association analysis. Ten IKBKE SNVs and three IFIH1 SNVs were associated with SLE. The SNVs rs1539241 and rs12142086 tagged two independent association signals in IKBKE, and the haplotype carrying their risk alleles showed an odds ratio of 1.68 (P-value=1.0 × 10(-5)). The risk allele of rs12142086 affects the binding of splicing factor 1 in vitro and could thus influence its transcriptional regulatory function. Two independent association signals were also detected in IFIH1, which were tagged by a low-frequency SNV rs78456138 and a missense SNV rs3747517. Their joint effect is protective against SLE (odds ratio=0.56; P-value=6.6 × 10(-3)). In conclusion, we have identified new SLE-associated sequence variants in IKBKE and IFIH1, and proposed functional hypotheses for the association signals.
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34
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Liu J, Fan S, Lee CJ, Greenleaf AL, Zhou P. Specific interaction of the transcription elongation regulator TCERG1 with RNA polymerase II requires simultaneous phosphorylation at Ser2, Ser5, and Ser7 within the carboxyl-terminal domain repeat. J Biol Chem 2013; 288:10890-901. [PMID: 23436654 DOI: 10.1074/jbc.m113.460238] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human transcription elongation regulator TCERG1 physically couples transcription elongation and splicing events by interacting with splicing factors through its N-terminal WW domains and the hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II through its C-terminal FF domains. Here, we report biochemical and structural characterization of the C-terminal three FF domains (FF4-6) of TCERG1, revealing a rigid integral domain structure of the tandem FF repeat that interacts with the hyperphosphorylated CTD (PCTD). Although FF4 and FF5 adopt a classical FF domain fold containing three orthogonally packed α helices and a 310 helix, FF6 contains an additional insertion helix between α1 and α2. The formation of the integral tandem FF4-6 repeat is achieved by merging the last helix of the preceding FF domain and the first helix of the following FF domain and by direct interactions between neighboring FF domains. Using peptide column binding assays and NMR titrations, we show that binding of the FF4-6 tandem repeat to the PCTD requires simultaneous phosphorylation at Ser(2), Ser(5), and Ser(7) positions within two consecutive Y(1)S(2)P(3)T(4)S(5)P(6)S(7) heptad repeats. Such a sequence-specific PCTD recognition is achieved through CTD-docking sites on FF4 and FF5 of TCERG1 but not FF6. Our study presents the first example of a nuclear factor requiring all three phospho-Ser marks within the heptad repeat of the CTD for high affinity binding and provides a molecular interpretation for the biochemical connection between the Ser(7) phosphorylation enrichment in the CTD of the transcribing RNA polymerase II over introns and co-transcriptional splicing events.
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Affiliation(s)
- Jiangxin Liu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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35
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Lee KM, Tarn WY. Coupling pre-mRNA processing to transcription on the RNA factory assembly line. RNA Biol 2013; 10:380-90. [PMID: 23392244 DOI: 10.4161/rna.23697] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It has been well-documented that nuclear processing of primary transcripts of RNA polymerase II occurs co-transcriptionally and is functionally coupled to transcription. Moreover, increasing evidence indicates that transcription influences pre-mRNA splicing and even several post-splicing RNA processing events. In this review, we discuss the issues of how RNA polymerase II modulates co-transcriptional RNA processing events via its carboxyl terminal domain, and the protein domains involved in coupling of transcription and RNA processing events. In addition, we describe how transcription influences the expression or stability of mRNAs through the formation of distinct mRNP complexes. Finally, we delineate emerging findings that chromatin modifications function in the regulation of RNA processing steps, especially splicing, in addition to transcription. Overall, we provide a comprehensive view that transcription could integrate different control systems, from epigenetic to post-transcriptional control, for efficient gene expression.
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Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences; Academia Sinica; Taipei, Taiwan
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36
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Schor IE, Gómez Acuña LI, Kornblihtt AR. Coupling between transcription and alternative splicing. Cancer Treat Res 2013; 158:1-24. [PMID: 24222352 DOI: 10.1007/978-3-642-31659-3_1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The scenario of alternative splicing regulation is far more complex than the classical picture of a pre-mRNA being processed post-transcriptionally in more than one way. Introns are efficiently removed while transcripts are still being synthesized, supporting the idea of a co-transcriptional regulation of alternative splicing. Evidence of a functional coupling between splicing and transcription has recently emerged as it was observed that properties of one process may affect the outcome of the other. Co-transcriptionality is thought to improve splicing efficiency and kinetics by directing the nascent pre-mRNA into proper spliceosome assembly and favoring splicing factor recruitment. Two models have been proposed to explain the coupling of transcription and alternative splicing: in the recruitment model, promoters and pol II status affect the recruitment to the transcribing gene of splicing factors or bifunctional factors acting on both transcription and splicing; in the kinetic model, differences in the elongation rate of pol II would determine the timing in which splicing sites are presented, and thus the outcome of alternative splicing decisions. In the later model, chromatin structure has emerged as a key regulator. Although definitive evidence for transcriptionally coupled alternative splicing alterations in tumor development or cancer pathogenesis is still missing, many alternative splicing events altered in cancer might be subject to transcription-splicing coupling regulation.
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Affiliation(s)
- Ignacio E Schor
- Laboratorio de Fisiologia y Biologia Molecular, Departmento de Fisiologia, Biologia Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, PAB. II, 20 Piso, Buenos Aires, 1428, Argentina
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37
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Antebi A. Regulation of longevity by the reproductive system. Exp Gerontol 2012; 48:596-602. [PMID: 23063987 DOI: 10.1016/j.exger.2012.09.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/06/2012] [Accepted: 09/20/2012] [Indexed: 01/04/2023]
Abstract
Pioneering work in model organisms reveals that the reproductive system is involved not only in propagation of the species but also regulates organismal metabolism and longevity. In C. elegans, prevention of germline stem cell proliferation results in a 60% extension of lifespan, termed gonadal longevity. Gonadal longevity relies on the transcriptional activities of steroid nuclear receptor DAF-12, the FOXO transcription factor homolog DAF-16, the FOXA transcription factor homolog PHA-4, and the HNF-4-like nuclear receptor NHR-80. These transcription factors work in an integrated transcriptional network to regulate fatty acid lipolysis, autophagy, stress resistance and other processes, which altogether enhance homeostasis and extend life. Because the reproductive system also regulates longevity in other species, studies in C. elegans may shed light on ancient mechanisms governing reproduction and survival.
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Affiliation(s)
- Adam Antebi
- Max Planck Institute for Biology of Ageing, Gleueler Str. 50a, D-50931 Cologne, Germany.
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38
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Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW. Alternative splicing in plants--coming of age. TRENDS IN PLANT SCIENCE 2012; 17:616-23. [PMID: 22743067 PMCID: PMC3466422 DOI: 10.1016/j.tplants.2012.06.001] [Citation(s) in RCA: 336] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/30/2012] [Accepted: 06/02/2012] [Indexed: 05/18/2023]
Abstract
More than 60% of intron-containing genes undergo alternative splicing (AS) in plants. This number will increase when AS in different tissues, developmental stages, and environmental conditions are explored. Although the functional impact of AS on protein complexity is still understudied in plants, recent examples demonstrate its importance in regulating plant processes. AS also regulates transcript levels and the link with nonsense-mediated decay and generation of unproductive mRNAs illustrate the need for both transcriptional and AS data in gene expression analyses. AS has influenced the evolution of the complex networks of regulation of gene expression and variation in AS contributed to adaptation of plants to their environment and therefore will impact strategies for improving plant and crop phenotypes.
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Affiliation(s)
- Naeem H. Syed
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - John W.S. Brown
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
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39
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Rindt H, Yen PF, Thebeau CN, Peterson TS, Weisman GA, Lorson CL. Replacement of huntingtin exon 1 by trans-splicing. Cell Mol Life Sci 2012; 69:4191-204. [PMID: 22814437 DOI: 10.1007/s00018-012-1083-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 06/07/2012] [Accepted: 07/03/2012] [Indexed: 02/06/2023]
Abstract
Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder caused by polyglutamine expansion in the amino-terminus of huntingtin (HTT). HD offers unique opportunities for promising RNA-based therapeutic approaches aimed at reducing mutant HTT expression, since the HD mutation is considered to be a "gain-of-function" mutation. Allele-specific strategies that preserve expression from the wild-type allele and reduce the levels of mutant protein would be of particular interest. Here, we have conducted proof-of-concept studies to demonstrate that spliceosome-mediated trans-splicing is a viable molecular strategy to specifically repair the HTT allele. We employed a dual plasmid transfection system consisting of a pre-mRNA trans-splicing module (PTM) containing HTT exon 1 and a HTT minigene to demonstrate that HTT exon 1 can be replaced in trans. We detected the presence of the trans-spliced RNA in which PTM exon 1 was correctly joined to minigene exons 2 and 3. Furthermore, exon 1 from the PTM was trans-spliced to the endogenous HTT pre-mRNA in cultured cells as well as disease-relevant models, including HD patient fibroblasts and primary neurons from a previously described HD mouse model. These results suggest that the repeat expansion of HTT can be repaired successfully not only in the context of synthetic minigenes but also within the context of HD neurons. Therefore, pre-mRNA trans-splicing may be a promising approach for the treatment of HD and other dominant genetic disorders.
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Affiliation(s)
- Hansjörg Rindt
- Department of Veterinary Pathobiology, Life Sciences Center, University of Missouri, Room 471G, Columbia, MO 65211, USA
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40
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David CJ, Manley JL. The RNA polymerase C-terminal domain: a new role in spliceosome assembly. Transcription 2012; 2:221-5. [PMID: 22231118 DOI: 10.4161/trns.2.5.17272] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Work over the last two decades has provided a wealth of data indicating that the RNA polymerase II transcriptional machinery can play an important role in facilitating the splicing of its transcripts. In particular, the C-terminal domain of the RNA polymerase II large subunit (CTD) is central in the coupling of transcription and splicing. While this has long been assumed to involve physical interactions between splicing factors and the CTD, few functional connections between the CTD and such factors have been established. We recently used a biochemical approach to identify a splicing factor that interacts directly with the CTD to activate splicing and, in doing so, may play a role in the process of spliceosome assembly.
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Affiliation(s)
- Charles J David
- Department of Biological Sciences, Columbia University, New York, USA
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41
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Montes M, Becerra S, Sánchez-Álvarez M, Suñé C. Functional coupling of transcription and splicing. Gene 2012; 501:104-17. [DOI: 10.1016/j.gene.2012.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 01/13/2023]
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42
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Sánchez-Hernández N, Ruiz L, Sánchez-Álvarez M, Montes M, Macias MJ, Hernández-Munain C, Suñé C. The FF4 and FF5 domains of transcription elongation regulator 1 (TCERG1) target proteins to the periphery of speckles. J Biol Chem 2012; 287:17789-17800. [PMID: 22453921 DOI: 10.1074/jbc.m111.304782] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transcription elongation regulator 1 (TCERG1) is a human factor implicated in interactions with the spliceosome as a coupler of transcription and splicing. The protein is highly concentrated at the interface between speckles (the compartments enriched in splicing factors) and nearby transcription sites. Here, we identified the FF4 and FF5 domains of TCERG1 as the amino acid sequences required to direct this protein to the periphery of nuclear speckles, where coordinated transcription/RNA processing events occur. Consistent with our localization data, we observed that the FF4 and FF5 pair is required to fold in solution, thus suggesting that the pair forms a functional unit. When added to heterologous proteins, the FF4-FF5 pair is capable of targeting the resulting fusion protein to speckles. This represents, to our knowledge, the first description of a targeting signal for the localization of proteins to sites peripheral to speckled domains. Moreover, this "speckle periphery-targeting signal" contributes to the regulation of alternative splicing decisions of a reporter pre-mRNA in vivo.
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Affiliation(s)
- Noemí Sánchez-Hernández
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18100 Armilla, Spain
| | - Lidia Ruiz
- Structural and Computational Biology Programme, Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
| | - Miguel Sánchez-Álvarez
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18100 Armilla, Spain
| | - Marta Montes
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18100 Armilla, Spain
| | - Maria J Macias
- Structural and Computational Biology Programme, Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Cristina Hernández-Munain
- Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18100 Armilla, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18100 Armilla, Spain.
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Seredenina T, Luthi-Carter R. What have we learned from gene expression profiles in Huntington's disease? Neurobiol Dis 2012; 45:83-98. [DOI: 10.1016/j.nbd.2011.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/24/2011] [Accepted: 07/01/2011] [Indexed: 12/22/2022] Open
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TCERG1 regulates alternative splicing of the Bcl-x gene by modulating the rate of RNA polymerase II transcription. Mol Cell Biol 2011; 32:751-62. [PMID: 22158966 DOI: 10.1128/mcb.06255-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Complex functional coupling exists between transcriptional elongation and pre-mRNA alternative splicing. Pausing sites and changes in the rate of transcription by RNA polymerase II (RNAPII) may therefore have fundamental impacts in the regulation of alternative splicing. Here, we show that the elongation and splicing-related factor TCERG1 regulates alternative splicing of the apoptosis gene Bcl-x in a promoter-dependent manner. TCERG1 promotes the splicing of the short isoform of Bcl-x (Bcl-x(s)) through the SB1 regulatory element located in the first half of exon 2. Consistent with these results, we show that TCERG1 associates with the Bcl-x pre-mRNA. A transcription profile analysis revealed that the RNA sequences required for the effect of TCERG1 on Bcl-x alternative splicing coincide with a putative polymerase pause site. Furthermore, TCERG1 modifies the impact of a slow polymerase on Bcl-x alternative splicing. In support of a role for an elongation mechanism in the transcriptional control of Bcl-x alternative splicing, we found that TCERG1 modifies the amount of pre-mRNAs generated at distal regions of the endogenous Bcl-x. Most importantly, TCERG1 affects the rate of RNAPII transcription of endogenous human Bcl-x. We propose that TCERG1 modulates the elongation rate of RNAPII to relieve pausing, thereby activating the proapoptotic Bcl-x(S) 5' splice site.
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45
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Moazed B, Banman SL, Wilkinson GA, Roesler WJ. TCERG1 inhibits C/EBPα through a mechanism that does not involve sequestration of C/EBPα at pericentromeric heterochromatin. J Cell Biochem 2011; 112:2317-26. [PMID: 21503969 DOI: 10.1002/jcb.23154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Transcriptional elongation regulator 1 (TCERG1) is a nuclear protein that participates in multiple events that include regulating the elongation of RNA polymerase II and coordinating transcription and pre-mRNA processing. More recently, we showed that TCERG1 is also a specific inhibitor of the transcription factor CCAAT enhancer binding protein α (C/EBPα). Interestingly, the inhibition of C/EBPα by TCERG1 is associated with the relocalization of TCERG1 from the nuclear speckle compartment to the pericentromeric regions where C/EBPα resides. In the present study, we examined additional aspects of C/EBPα-induced redistribution of TCERG1. Using several mutants of C/EBPα, we showed that C/EBPα does not need to be transcriptionally competent or have anti-proliferative activity to induce TCERG1 relocalization. Moreover, our results show that C/EBPα does not need to be localized to the pericentromeric region in order to relocalize TCERG1. This conclusion was illustrated through the use of a V296A mutant of C/EBPα, which is incapable of binding to the pericentromeric regions of heterochromatin and thus takes on a dispersed appearance in the nucleus. This mutant retained the ability to redistribute TCERG1, however in this case the redistribution was from the nuclear speckle pattern to the dispersed phenotype of C/EBPα V296A. Moreover, we showed that TCERG1 was still able to inhibit the activity of the V296A mutant. While we previously hypothesized that TCERG1 might inhibit C/EBPα by keeping it sequestered at the pericentromeric regions, our new findings indicate that TCERG1 can inhibit C/EBPα activity regardless of the latter's location in the nucleus.
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Affiliation(s)
- Banafsheh Moazed
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
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46
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Görnemann J, Barrandon C, Hujer K, Rutz B, Rigaut G, Kotovic KM, Faux C, Neugebauer KM, Séraphin B. Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain. RNA (NEW YORK, N.Y.) 2011; 17:2119-29. [PMID: 22020974 PMCID: PMC3222125 DOI: 10.1261/rna.02646811] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Complex cellular functions involve large networks of interactions. Pre-mRNA splicing and transcription are thought to be coupled by the C-terminal domain (CTD) of the large subunit of RNA polymerase II (Pol II). In yeast, the U1 snRNP subunit Prp40 was proposed to mediate cotranscriptional recruitment of early splicing factors through binding of its WW domains to the Pol II CTD. Here we investigate the role of Prp40 in splicing with an emphasis on the role of the WW domains, which might confer protein-protein interactions among the splicing and transcriptional machineries. Affinity purification revealed that Prp40 and Snu71 form a stable heterodimer that stably associates with the U1 snRNP only in the presence of Nam8, a known regulator of 5' splice site recognition. However, the Prp40 WW domains were dispensable for yeast viability. In their absence, no defect in splicing in vivo, U1 or U2 snRNP recruitment in vivo, or early splicing complex assembly in vitro was detected. We conclude that the WW domains of Prp40 do not mediate essential coupling between U1 snRNP and Pol II. Instead, delays in cotranscriptional U5 snRNP and Prp19 recruitment and altered spliceosome formation in vitro suggest that Prp40 WW domains assist in late steps of spliceosome assembly.
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Affiliation(s)
- Janina Görnemann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Katja Hujer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | | | - Kimberly M. Kotovic
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Céline Faux
- CGM, CNRS, 91198 Gif sur Yvette Cedex, France
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, 67404 Illkirch, France
| | - Karla M. Neugebauer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Corresponding authors.E-mail E-mail .
| | - Bertrand Séraphin
- CGM, CNRS, 91198 Gif sur Yvette Cedex, France
- EMBL, D-69117 Heidelberg, Germany
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, 67404 Illkirch, France
- Corresponding authors.E-mail E-mail .
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011; 50:12201-4. [DOI: 10.1002/anie.201106177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 01/23/2023]
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48
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Reuter C, Huy P, Neudörfl JM, Kühne R, Schmalz HG. Exercises in Pyrrolidine Chemistry: Gram Scale Synthesis of a Pro-Pro Dipeptide Mimetic with a Polyproline Type II Helix Conformation. Chemistry 2011; 17:12037-44. [DOI: 10.1002/chem.201101704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Indexed: 01/29/2023]
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50
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Fidan Z, Younis A, Schmieder P, Volkmer R. Chemical synthesis of the third WW domain of TCERG 1 by native chemical ligation. J Pept Sci 2011; 17:644-9. [DOI: 10.1002/psc.1383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/20/2011] [Accepted: 04/20/2011] [Indexed: 12/30/2022]
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