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Boehm V, Britto-Borges T, Steckelberg AL, Singh KK, Gerbracht JV, Gueney E, Blazquez L, Altmüller J, Dieterich C, Gehring NH. Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity. Mol Cell 2018; 72:482-495.e7. [DOI: 10.1016/j.molcel.2018.08.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/24/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022]
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Serpeloni M, Jiménez-Ruiz E, Vidal NM, Kroeber C, Andenmatten N, Lemgruber L, Mörking P, Pall GS, Meissner M, Ávila AR. UAP56 is a conserved crucial component of a divergent mRNA export pathway in Toxoplasma gondii. Mol Microbiol 2016; 102:672-689. [PMID: 27542978 PMCID: PMC5118106 DOI: 10.1111/mmi.13485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 01/28/2023]
Abstract
Nucleo‐cytoplasmic RNA export is an essential post‐transcriptional step to control gene expression in eukaryotic cells and is poorly understood in apicomplexan parasites. With the exception of UAP56, a component of TREX (Transcription Export) complex, other components of mRNA export machinery are not well conserved in divergent supergroups. Here, we use Toxoplasma gondii as a model system to functionally characterize TgUAP56 and its potential interaction factors. We demonstrate that TgUAP56 is crucial for mRNA export and that functional interference leads to significant accumulation of mRNA in the nucleus. It was necessary to employ bioinformatics and phylogenetic analysis to identify orthologs related to mRNA export, which show a remarkable low level of conservation in T. gondii. We adapted a conditional Cas9/CRISPR system to carry out a genetic screen to verify if these factors were involved in mRNA export in T. gondii. Only the disruption of TgRRM_1330 caused accumulation of mRNA in the nucleus as found with TgUAP56. This protein is potentially a divergent partner of TgUAP56, and provides insight into a divergent mRNA export pathway in apicomplexans.
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Affiliation(s)
- Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil.,Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil.,College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Elena Jiménez-Ruiz
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Constanze Kroeber
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Nicole Andenmatten
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | | | - Gurman S Pall
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
| | - Markus Meissner
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity & Inflammation, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, UK
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Gromadzka AM, Steckelberg AL, Singh KK, Hofmann K, Gehring NH. A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs. Nucleic Acids Res 2016; 44:2348-61. [PMID: 26773052 PMCID: PMC4797287 DOI: 10.1093/nar/gkw009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/04/2016] [Indexed: 02/05/2023] Open
Abstract
The export of messenger RNAs (mRNAs) is the final of several nuclear posttranscriptional steps of gene expression. The formation of export-competent mRNPs involves the recruitment of export factors that are assumed to facilitate transport of the mature mRNAs. Using in vitro splicing assays, we show that a core set of export factors, including ALYREF, UAP56 and DDX39, readily associate with the spliced RNAs in an EJC (exon junction complex)- and cap-dependent manner. In order to elucidate how ALYREF and other export adaptors mediate mRNA export, we conducted a computational analysis and discovered four short, conserved, linear motifs present in RNA-binding proteins. We show that mutation in one of the new motifs (WxHD) in an unstructured region of ALYREF reduced RNA binding and abolished the interaction with eIF4A3 and CBP80. Additionally, the mutation impaired proper localization to nuclear speckles and export of a spliced reporter mRNA. Our results reveal important details of the orchestrated recruitment of export factors during the formation of export competent mRNPs.
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Affiliation(s)
| | | | - Kusum K Singh
- Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
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In vitro translation of mRNAs that are in their native ribonucleoprotein complexes. Biochem J 2015; 472:111-9. [PMID: 26349537 DOI: 10.1042/bj20150772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/08/2015] [Indexed: 11/17/2022]
Abstract
mRNA is bound to a complex network of hundreds of RNA-binding proteins (RBPs) which constitute the mature ribonucleoprotein (mRNP). Such a complex particle is initially scaffolded in the nucleus and stays associated throughout mRNA's journey to the cytoplasm, where it participates in translation. However, due to the size, complexity and variability of the mRNP, it remains technically challenging to assess its impact on translation. By designing a novel in vitro translational assay, we have been able to compare the translational efficiency of reporter mRNAs that are, or are not, associated with their cognate RBPs. This showed the strong impact of these RBPs on translational efficiency, and revealed intrinsic variations according to the structure of both the mRNA and its nuclear history, e.g. the use of intron-containing mRNA constructs showed that splicing strongly enhanced translation. The present study shows that nuclear and cytoplasmic gene expression steps in vitro are coupled in eukaryotes and this is determined from the very birth of the mRNA in the nucleus by a network of hundreds of RBPs.
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Steckelberg AL, Altmueller J, Dieterich C, Gehring NH. CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes. Nucleic Acids Res 2015; 43:4687-700. [PMID: 25870412 PMCID: PMC4482076 DOI: 10.1093/nar/gkv320] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/27/2015] [Indexed: 11/17/2022] Open
Abstract
In metazoan cells, spliced mRNAs are marked by the exon junction complex (EJC), a multi-protein complex that serves as a key regulator of post-transcriptional mRNA metabolism. Deposition of EJCs on mRNA is intimately linked to the splicing process. The spliceosomal protein CWC22 directly binds the core EJC-protein eIF4A3, guides it to the spliceosome and initiates EJC assembly. In addition, CWC22 is involved in the splicing process itself, but the molecular details of its dual function remain elusive. Here we analyze the mechanisms, by which CWC22 co-regulates pre-mRNA splicing and EJC assembly. We show that the core of CWC22 is sufficient to mediate both pre-mRNA splicing and EJC assembly. Nonetheless, both processes can be functionally uncoupled with an eIF4A3-binding deficient mutant of CWC22, which impedes EJC assembly. A C-terminal domain of CWC22 strongly enhances its spliceosomal interaction and likely regulates its function. High-throughput RNA-sequencing identifies global defects of pre-mRNA splicing and downregulation of diverse gene expression pathways in CWC22-depleted cells. We propose a model, in which CWC22 represents an integral component of the spliceosome and orchestrates pre-mRNA splicing and eIF4A3 binding to achieve global assembly of exon junction complexes.
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Affiliation(s)
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, D-50931 Cologne, Germany Institute of Human Genetics, University of Cologne, D-50931 Cologne, Germany
| | - Christoph Dieterich
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, D-50931 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
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Abstract
In eukaryotes, many RNA species are transcribed, processed in the nucleus, and exported to the cytoplasm, where they are destined to function or to be further matured. Some RNAs are even reimported to the nucleus. In addition, many RNAs are localized at specific nuclear bodies before their export and/or after their nuclear reimport. To understand how RNAs are transported, Xenopus oocytes are extremely useful cells, thanks to their large size. RNA transport can be easily examined by microinjecting radioactively or fluorescently labeled RNAs into Xenopus oocytes. Mammalian cultured cells are sometimes useful by virtue of RNA-FISH technique. Here, we describe methods to analyze RNA localization and export using these cells.
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Affiliation(s)
| | - Asako McCloskey
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Mutsuhito Ohno
- Institute for Virus Research, Kyoto University, Kyoto, Japan
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