1
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Drews F, Karunanithi S, Götz U, Marker S, deWijn R, Pirritano M, Rodrigues-Viana AM, Jung M, Gasparoni G, Schulz MH, Simon M. Two Piwis with Ago-like functions silence somatic genes at the chromatin level. RNA Biol 2021; 18:757-769. [PMID: 34663180 DOI: 10.1080/15476286.2021.1991114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Most sRNA biogenesis mechanisms involve either RNAse III cleavage or ping-pong amplification by different Piwi proteins harbouring slicer activity. Here, we follow the question why the mechanism of transgene-induced silencing in the ciliate Paramecium needs both Dicer activity and two Ptiwi proteins. This pathway involves primary siRNAs produced from non-translatable transgenes and secondary siRNAs from targeted endogenous loci. Our data does not indicate any signatures from ping-pong amplification but Dicer cleavage of long dsRNA. Ptiwi13 and 14 prefer different sub-cellular localizations and different preferences for primary and secondary siRNAs but do not load them mutually exclusive. Both Piwis enrich for antisense RNAs and show a general preference for uridine-rich sRNAs along the entire sRNA length. In addition, Ptiwi14-loaded siRNAs show a 5´-U signature. Our data indicates both Ptiwis and 2´-O-methylation contributing to strand selection of Dicer cleaved siRNAs. This unexpected function of the two distinct vegetative Piwis extends the increasing knowledge of the diversity of Piwi functions in diverse silencing pathways. We describe an unusual mode of action of Piwi proteins extending not only the great variety of Piwi-associated RNAi pathways but moreover raising the question whether this could have been the primordial one.
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Affiliation(s)
- Franziska Drews
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany.,Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Sivarajan Karunanithi
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe-University Hospital, Frankfurt, Germany
| | - Ulrike Götz
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Simone Marker
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Raphael deWijn
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Marcello Pirritano
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany.,Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Angela M Rodrigues-Viana
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Martin Jung
- School of Medicine, Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Gilles Gasparoni
- Genetics/Epigenetics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe-University Hospital, Frankfurt, Germany
| | - Martin Simon
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany.,Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
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2
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Clay DM, Yerlici VT, Villano DJ, Landweber LF. Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax. G3 (BETHESDA, MD.) 2019; 9:3105-3118. [PMID: 31506317 PMCID: PMC6778801 DOI: 10.1534/g3.118.200930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/28/2019] [Indexed: 01/18/2023]
Abstract
The ciliate Oxytricha trifallax contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus contains approximately 100 chromosomes of megabase scale, while the macronucleus contains 16,000 gene-sized, high ploidy "nanochromosomes." During its sexual cycle, a copy of the zygotic germline micronucleus develops into a somatic macronucleus via DNA excision and rearrangement. The rearrangement process is guided by multiple RNA-based pathways that program the epigenetic inheritance of sequences in the parental macronucleus of the subsequent generation. Here, we show that the introduction of synthetic DNA molecules homologous to a complete native nanochromosome during the rearrangement process results in either loss or heavy copy number reduction of the targeted nanochromosome in the macronucleus of the subsequent generation. This phenomenon was tested on a variety of nanochromosomes with different micronuclear structures, with deletions resulting in all cases. Deletion of the targeted nanochromosome results in the loss of expression of the targeted genes, including gene knockout phenotypes that were phenocopied using alternative knockdown approaches. Further investigation of the chromosome deletion showed that, although the full length nanochromosome was lost, remnants of the targeted chromosome remain. We were also able to detect the presence of telomeres on these remnants. The chromosome deletions and remnants are epigenetically inherited when backcrossed to wild type strains, suggesting that an undiscovered mechanism programs DNA elimination and cytoplasmically transfers to both daughter cells during conjugation. Programmed deletion of targeted chromosomes provides a novel approach to investigate genome rearrangement and expands the available strategies for gene knockout in Oxytricha trifallax.
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Affiliation(s)
- Derek M Clay
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY and
- Department of Molecular Biology, Princeton University, Princeton, NJ
| | - V Talya Yerlici
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY and
- Department of Molecular Biology, Princeton University, Princeton, NJ
| | - Danylo J Villano
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY and
| | - Laura F Landweber
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY and
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3
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Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation. Genes (Basel) 2018; 9:genes9020117. [PMID: 29466322 PMCID: PMC5852613 DOI: 10.3390/genes9020117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 12/25/2022] Open
Abstract
Genes or alleles can interact by small RNAs in a homology dependent manner meaning that short interfering (siRNAs) can act in trans at the chromatin level producing stable and heritable silencing phenotypes. Because of the puzzling data on endogenous paramutations, their impact contributing to adaptive evolution in a Lamarckian manner remains unknown. An increasing number of studies characterizes the underlying siRNA accumulation pathways using transgene experiments. Also in the ciliate Paramecium tetraurelia, we induce trans silencing on the chromatin level by injection of truncated transgenes. Here, we characterize the efficiency of this mechanism at different temperatures showing that silencing of the endogenous genes is temperature dependent. Analyzing different transgene constructs at different copy numbers, we dissected whether silencing efficiency is due to varying precursor RNAs or siRNA accumulation. Our data shows that silencing efficiency correlates with more efficient accumulation of primary siRNAs at higher temperatures rather than higher expression of precursor RNAs. Due to higher primary levels, secondary siRNAs also show temperature dependency and interestingly increase their relative proportion to primary siRNAs. Our data shows that efficient trans silencing on the chromatin level in P. tetraurelia depends on environmental parameters, thus being an important epigenetic factor limiting regulatory effects of siRNAs.
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4
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Götz U, Marker S, Cheaib M, Andresen K, Shrestha S, Durai DA, Nordström KJ, Schulz MH, Simon M. Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. Nucleic Acids Res 2016; 44:5908-23. [PMID: 27085807 PMCID: PMC4937312 DOI: 10.1093/nar/gkw267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/04/2016] [Indexed: 12/13/2022] Open
Abstract
Across kingdoms, RNA interference (RNAi) has been shown to control gene expression at the transcriptional- or the post-transcriptional level. Here, we describe a mechanism which involves both aspects: truncated transgenes, which fail to produce intact mRNA, induce siRNA accumulation and silencing of homologous loci in trans in the ciliate Paramecium. We show that silencing is achieved by co-transcriptional silencing, associated with repressive histone marks at the endogenous gene. This is accompanied by secondary siRNA accumulation, strictly limited to the open reading frame of the remote locus. Our data shows that in this mechanism, heterochromatic marks depend on a variety of RNAi components. These include RDR3 and PTIWI14 as well as a second set of components, which are also involved in post-transcriptional silencing: RDR2, PTIWI13, DCR1 and CID2. Our data indicates differential processing of nascent un-spliced and long, spliced transcripts thus suggesting a hitherto-unrecognized functional interaction between post-transcriptional and co-transcriptional RNAi. Both sets of RNAi components are required for efficient trans-acting RNAi at the chromatin level and our data indicates similar mechanisms contributing to genome wide regulation of gene expression by epigenetic mechanisms.
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Affiliation(s)
- Ulrike Götz
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Simone Marker
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Miriam Cheaib
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Karsten Andresen
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Simon Shrestha
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Dilip A Durai
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Karl J Nordström
- Department for Genetics, Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Martin Simon
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
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5
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Maliszewska-Olejniczak K, Gruchota J, Gromadka R, Denby Wilkes C, Arnaiz O, Mathy N, Duharcourt S, Bétermier M, Nowak JK. TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements. PLoS Genet 2015; 11:e1005383. [PMID: 26177014 PMCID: PMC4503560 DOI: 10.1371/journal.pgen.1005383] [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: 12/16/2014] [Accepted: 06/22/2015] [Indexed: 02/07/2023] Open
Abstract
Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs) in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline) nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs). Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium, and establishes for the first time a specific role of TFIIS in non-coding transcription in eukaryotes. Paramecium tetraurelia provides an excellent model for studying the mechanisms involved in the production of non-coding transcripts and their mode of action. Different types of non-coding RNAs (ncRNAs) were shown to be implicated in the programmed DNA elimination process that occurs in this organism. At each sexual cycle, during development of the somatic nucleus from the germline nucleus, the genome is massively rearranged through the reproducible elimination of germline-specific sequences including thousands of short, single copy, non-coding Internal Eliminated Sequences (IES). Here, we demonstrate, using RNA interference, that the TFIIS4 gene encoding a development-specific homolog of RNA polymerase II elongation factor TFIIS, is indispensable for ncRNA synthesis in the new somatic nucleus. TFIIS4 depletion impairs the assembly of a functional somatic genome and affects excision of a large fraction of IESs, which leads to strong lethality in the sexual progeny. We propose that TFIIS4-dependent ncRNAs provide an important component of the molecular machinery that is responsible for developmental genome remodeling in Paramecium.
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Affiliation(s)
| | - Julita Gruchota
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France
| | - Nathalie Mathy
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France
| | - Sandra Duharcourt
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mireille Bétermier
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, Gif-sur-Yvette, France
| | - Jacek K. Nowak
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
- * E-mail:
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6
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Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S. Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia. Nucleic Acids Res 2015; 43:1818-33. [PMID: 25593325 PMCID: PMC4330347 DOI: 10.1093/nar/gku1331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In various organisms, an efficient RNAi response can be triggered by feeding cells with bacteria producing double-stranded RNA (dsRNA) against an endogenous gene. However, the detailed mechanisms and natural functions of this pathway are not well understood in most cases. Here, we studied siRNA biogenesis from exogenous RNA and its genetic overlap with endogenous RNAi in the ciliate Paramecium tetraurelia by high-throughput sequencing. Using wild-type and mutant strains deficient for dsRNA feeding we found that high levels of primary siRNAs of both strands are processed from the ingested dsRNA trigger by the Dicer Dcr1, the RNA-dependent RNA polymerases Rdr1 and Rdr2 and other factors. We further show that this induces the synthesis of secondary siRNAs spreading along the entire endogenous mRNA, demonstrating the occurrence of both 3′-to-5′ and 5′-to-3′ transitivity for the first time in the SAR clade of eukaryotes (Stramenopiles, Alveolates, Rhizaria). Secondary siRNAs depend on Rdr2 and show a strong antisense bias; they are produced at much lower levels than primary siRNAs and hardly contribute to RNAi efficiency. We further provide evidence that the Paramecium RNAi machinery also processes single-stranded RNAs from its bacterial food, broadening the possible natural functions of exogenously induced RNAi in this organism.
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Affiliation(s)
- Quentin Carradec
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France UPMC, IFD, Sorbonne Universités, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ulrike Götz
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Olivier Arnaiz
- Centre de Génétique Moléculaire, CNRS UPR3404, 91198 Gif-sur-Yvette cedex, France
| | - Juliette Pouch
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Martin Simon
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Eric Meyer
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Simone Marker
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
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7
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Arambasic M, Sandoval PY, Hoehener C, Singh A, Swart EC, Nowacki M. Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium. PLoS One 2014; 9:e112899. [PMID: 25397898 PMCID: PMC4232520 DOI: 10.1371/journal.pone.0112899] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 10/16/2014] [Indexed: 01/25/2023] Open
Abstract
The epigenetic influence of maternal cells on the development of their progeny has long been studied in various eukaryotes. Multicellular organisms usually provide their zygotes not only with nutrients but also with functional elements required for proper development, such as coding and non-coding RNAs. These maternally deposited RNAs exhibit a variety of functions, from regulating gene expression to assuring genome integrity. In ciliates, such as Paramecium these RNAs participate in the programming of large-scale genome reorganization during development, distinguishing germline-limited DNA, which is excised, from somatic-destined DNA. Only a handful of proteins playing roles in this process have been identified so far, including typical RNAi-derived factors such as Dicer-like and Piwi proteins. Here we report and characterize two novel proteins, Pdsg1 and Pdsg2 (Paramecium protein involved in Development of the Somatic Genome 1 and 2), involved in Paramecium genome reorganization. We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny. Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs) and chromatin modification patterns during development. Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.
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Affiliation(s)
| | | | | | - Aditi Singh
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
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8
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Swart EC, Wilkes CD, Sandoval PY, Arambasic M, Sperling L, Nowacki M. Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion. Nucleic Acids Res 2014; 42:8970-83. [PMID: 25016527 PMCID: PMC4132734 DOI: 10.1093/nar/gku619] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control.
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Affiliation(s)
- Estienne C Swart
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Cyril Denby Wilkes
- CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Pamela Y Sandoval
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Miroslav Arambasic
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Linda Sperling
- CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
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9
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Marker S, Carradec Q, Tanty V, Arnaiz O, Meyer E. A forward genetic screen reveals essential and non-essential RNAi factors in Paramecium tetraurelia. Nucleic Acids Res 2014; 42:7268-80. [PMID: 24860163 PMCID: PMC4066745 DOI: 10.1093/nar/gku223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In most eukaryotes, small RNA-mediated gene silencing pathways form complex interacting networks. In the ciliate Paramecium tetraurelia, at least two RNA interference (RNAi) mechanisms coexist, involving distinct but overlapping sets of protein factors and producing different types of short interfering RNAs (siRNAs). One is specifically triggered by high-copy transgenes, and the other by feeding cells with double-stranded RNA (dsRNA)-producing bacteria. In this study, we designed a forward genetic screen for mutants deficient in dsRNA-induced silencing, and a powerful method to identify the relevant mutations by whole-genome sequencing. We present a set of 47 mutant alleles for five genes, revealing two previously unknown RNAi factors: a novel Paramecium-specific protein (Pds1) and a Cid1-like nucleotidyl transferase. Analyses of allelic diversity distinguish non-essential and essential genes and suggest that the screen is saturated for non-essential, single-copy genes. We show that non-essential genes are specifically involved in dsRNA-induced RNAi while essential ones are also involved in transgene-induced RNAi. One of the latter, the RNA-dependent RNA polymerase RDR2, is further shown to be required for all known types of siRNAs, as well as for sexual reproduction. These results open the way for the dissection of the genetic complexity, interconnection, mechanisms and natural functions of RNAi pathways in P. tetraurelia.
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Affiliation(s)
- Simone Marker
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
| | - Quentin Carradec
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France Sorbonne Universités, UPMC Univ., IFD, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Véronique Tanty
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
| | - Olivier Arnaiz
- CNRS UPR3404 Centre de Génétique Moléculaire, Gif-sur-Yvette F-91198 cedex, France; Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Eric Meyer
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
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10
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Sandoval PY, Swart EC, Arambasic M, Nowacki M. Functional diversification of Dicer-like proteins and small RNAs required for genome sculpting. Dev Cell 2014; 28:174-88. [PMID: 24439910 DOI: 10.1016/j.devcel.2013.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/04/2013] [Accepted: 12/17/2013] [Indexed: 12/15/2022]
Abstract
In eukaryotes, small RNAs (sRNAs) have key roles in development, gene expression regulation, and genome integrity maintenance. In ciliates, such as Paramecium, sRNAs form the heart of an epigenetic system that has evolved from core eukaryotic gene silencing components to selectively target DNA for deletion. In Paramecium, somatic genome development from the germline genome accurately eliminates the bulk of typically gene-interrupting, noncoding DNA. We have discovered an sRNA class (internal eliminated sequence [IES] sRNAs [iesRNAs]), arising later during Paramecium development, which originates from and precisely delineates germline DNA (IESs) and complements the initial sRNAs ("scan" RNAs [scnRNAs]) in targeting DNA for elimination. We show that whole-genome duplications have facilitated successive differentiations of Paramecium Dicer-like proteins, leading to cooperation between Dcl2 and Dcl3 to produce scnRNAs and to the production of iesRNAs by Dcl5. These innovations highlight the ability of sRNA systems to acquire capabilities, including those in genome development and integrity.
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Affiliation(s)
- Pamela Y Sandoval
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern 3012, Switzerland
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern 3012, Switzerland
| | - Miroslav Arambasic
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern 3012, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern 3012, Switzerland.
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11
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Abstract
Research using ciliates revealed early examples of epigenetic phenomena and continues to provide novel findings. These protozoans maintain separate germline and somatic nuclei that carry transcriptionally silent and active genomes, respectively. Examining the differences in chromatin within distinct nuclei of Tetrahymena identified histone variants and established that transcriptional regulators act by modifying histones. Formation of somatic nuclei requires both transcriptional activation of silent chromatin and large-scale DNA elimination. This somatic genome remodeling is directed by homologous RNAs, acting with an RNA interference (RNAi)-related machinery. Furthermore, the content of the parental somatic genome provides a homologous template to guide this genome restructuring. The mechanisms regulating ciliate DNA rearrangements reveal the surprising power of homologous RNAs to remodel the genome and transmit information transgenerationally.
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Affiliation(s)
- Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri 63130
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12
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Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet 2011; 12:367-89. [PMID: 21801022 DOI: 10.1146/annurev-genom-082410-101420] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha's somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells.
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Affiliation(s)
- Mariusz Nowacki
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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13
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Bouhouche K, Gout JF, Kapusta A, Bétermier M, Meyer E. Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. Nucleic Acids Res 2011; 39:4249-64. [PMID: 21216825 PMCID: PMC3105430 DOI: 10.1093/nar/gkq1283] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins of the Argonaute family are small RNA carriers that guide regulatory complexes to their targets. The family comprises two major subclades. Members of the Ago subclade, which are present in most eukaryotic phyla, bind different classes of small RNAs and regulate gene expression at both transcriptional and post-transcriptional levels. Piwi subclade members appear to have been lost in plants and fungi and were mostly studied in metazoa, where they bind piRNAs and have essential roles in sexual reproduction. Their presence in ciliates, unicellular organisms harbouring both germline micronuclei and somatic macronuclei, offers an interesting perspective on the evolution of their functions. Here, we report phylogenetic and functional analyses of the 15 Piwi genes from Paramecium tetraurelia. We show that four constitutively expressed proteins are involved in siRNA pathways that mediate gene silencing throughout the life cycle. Two other proteins, specifically expressed during meiosis, are required for accumulation of scnRNAs during sexual reproduction and for programmed genome rearrangements during development of the somatic macronucleus. Our results indicate that Paramecium Piwi proteins have evolved to perform both vegetative and sexual functions through mechanisms ranging from post-transcriptional mRNA cleavage to epigenetic regulation of genome rearrangements.
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Affiliation(s)
- Khaled Bouhouche
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris, France
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14
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Marker S, Le Mouël A, Meyer E, Simon M. Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia. Nucleic Acids Res 2010; 38:4092-107. [PMID: 20200046 PMCID: PMC2896523 DOI: 10.1093/nar/gkq131] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/13/2010] [Accepted: 02/15/2010] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway. They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response. We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing. In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA). Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs. In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes. Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family. While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens. These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth.
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Affiliation(s)
- Simone Marker
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Anne Le Mouël
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Eric Meyer
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Martin Simon
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
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15
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Nishiyama N, Mikami K, Ochiai T, Yamauchi K. The presence of chimeric DNA consisting of 5' regions of the hemoglobin and nucleosome assembly protein-1 genes in Paramecium caudatum macronuclear genomic DNA. Zoolog Sci 2009; 26:259-65. [PMID: 19798919 DOI: 10.2108/zsj.26.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We detected an unexpected small-sized DNA fragment during polymerase chain reaction (PCR) analysis of the heterogeneity of a macronuclear intergenic region of Paramecium caudatum. Southern blotting of total genomic DNA with the PCR product as a probe indicated that the small-sized DNA fragment constituted part of the macronuclear genome. Sequencing revealed that the PCR product was a chimeric DNA structure that may be generated by tail-to-tail fusion of the 5' region of the hemoglobin (hb) gene to most of the nucleosome assembly protein-1 (nap-1) gene. Short tandem repeats consisting of tetra- and tri-nucleotides exist at the putative cleavage sites in the hb and nap-1 genes, respectively. This feature differs from those found at the boundaries of TA-internal eliminated sequences in the P. aurelia complex and at transposable elements in other species. This suggests that the chimeric DNA is generated by a novel mechanism. Although the chimeric DNA contains the hb and nap-1 promoters, transcripts corresponding to the chimeric DNA were not detected by reverse transcription (RT)-PCR analysis during vegetative cell growth. Possible roles of chimeric DNA are discussed.
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Affiliation(s)
- Norihito Nishiyama
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
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16
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Nowacki M, Landweber LF. Epigenetic inheritance in ciliates. Curr Opin Microbiol 2009; 12:638-43. [PMID: 19879799 DOI: 10.1016/j.mib.2009.09.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 09/10/2009] [Indexed: 01/12/2023]
Abstract
2009 marks not only the 200th anniversary of Darwin's birth but also publication of the first scientific evolutionary theory, Lamarck's Philosophie Zoologique. While Lamarck embraced the notion of the inheritance of acquired characters, he did not invent it (Burkhardt, 1984). New phenomena discovered recently offer molecular pathways for the transmission of several acquired characters. Ciliates have long provided model systems to study phenomena that bypass traditional modes of inheritance. RNA, normally thought of as a conduit in gene expression, displays a novel mode of action in ciliated protozoa. For example, maternal RNA templates provide both an organizing guide for DNA rearrangements in Oxytricha and a template that can transmit spontaneous mutations that may arise during somatic growth to the next generation, providing two such mechanisms of so-called Lamarckian inheritance. This suggests that the somatic ciliate genome is really an 'epigenome', formed through templates and signals arising from the previous generation. This review will discuss these new biological roles for RNA, including non-coding 'template' RNA molecules. The evolutionary consequences of viable mechanisms in ciliates to transmit acquired characters may create an additional store of heritable variation that contributes to the cosmopolitan success of this diverse lineage of microbial eukaryotes.
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Affiliation(s)
- Mariusz Nowacki
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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17
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Duharcourt S, Lepère G, Meyer E. Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts. Trends Genet 2009; 25:344-50. [PMID: 19596481 DOI: 10.1016/j.tig.2009.05.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 11/24/2022]
Abstract
Several classes of non-protein-coding RNAs have recently been identified as epigenetic regulators of developmental genome rearrangements in ciliates, providing an interesting insight into the role of genome-wide transcription. In these unicellular eukaryotes, extensive rearrangements of the germline genome occur during the development of a new somatic macronucleus from the germline micronucleus. Rearrangement patterns are not dictated by the germline sequence, but reproduce the pre-existing rearrangements of the maternal somatic genome, implying a homology-dependent global comparison of germline and somatic genomes. We review recent evidence showing that this is achieved by a natural genomic subtraction, computed by pairing interactions between meiosis-specific, germline scnRNAs (small RNAs that resemble metazoan piRNAs) and longer non-coding transcripts from the somatic genome. We focus on current models for the RNA-based mechanisms enabling the cell to recognize the germline sequences to be eliminated from the somatic genome and to maintain an epigenetic memory of rearrangement patterns across sexual generations.
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Affiliation(s)
- Sandra Duharcourt
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, 75005 Paris, France.
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18
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Lepère G, Nowacki M, Serrano V, Gout JF, Guglielmi G, Duharcourt S, Meyer E. Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia. Nucleic Acids Res 2008; 37:903-15. [PMID: 19103667 PMCID: PMC2647294 DOI: 10.1093/nar/gkn1018] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Distinct small RNA pathways are involved in the two types of homology-dependent effects described in Paramecium tetraurelia, as shown by a functional analysis of Dicer and Dicer-like genes and by the sequencing of small RNAs. The siRNAs that mediate post-transcriptional gene silencing when cells are fed with double-stranded RNA (dsRNA) were found to comprise two subclasses. DCR1-dependent cleavage of the inducing dsRNA generates approximately 23-nt primary siRNAs from both strands, while a different subclass of approximately 24-nt RNAs, characterized by a short untemplated poly-A tail, is strictly antisense to the targeted mRNA, suggestive of secondary siRNAs that depend on an RNA-dependent RNA polymerase. An entirely distinct pathway is responsible for homology-dependent regulation of developmental genome rearrangements after sexual reproduction. During early meiosis, the DCL2 and DCL3 genes are required for the production of a highly complex population of approximately 25-nt scnRNAs from all types of germline sequences, including both strands of exons, introns, intergenic regions, transposons and Internal Eliminated Sequences. A prominent 5'-UNG signature, and a minor fraction showing the complementary signature at positions 21-23, indicate that scnRNAs are cleaved from dsRNA precursors as duplexes with 2-nt 3' overhangs at both ends, followed by preferential stabilization of the 5'-UNG strand.
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Affiliation(s)
- Gersende Lepère
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, CNRS, UMR8541, 46 rue d'Ulm, 75005 Paris, France
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19
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Lepère G, Bétermier M, Meyer E, Duharcourt S. Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev 2008; 22:1501-12. [PMID: 18519642 PMCID: PMC2418586 DOI: 10.1101/gad.473008] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/28/2008] [Indexed: 12/22/2022]
Abstract
The germline genome of ciliates is extensively rearranged during the development of a new somatic macronucleus from the germline micronucleus, after sexual events. In Paramecium tetraurelia, single-copy internal eliminated sequences (IESs) are precisely excised from coding sequences and intergenic regions. For a subset of IESs, introduction of the IES sequence into the maternal macronucleus specifically inhibits excision of the homologous IES in the developing zygotic macronucleus, suggesting that epigenetic regulation of excision involves a global comparison of germline and somatic genomes. ScanRNAs (scnRNAs) produced during micronuclear meiosis by a developmentally regulated RNAi pathway have been proposed to mediate this transnuclear cross-talk. In this study, microinjection experiments provide direct evidence that 25-nucleotide (nt) scnRNAs promote IES excision. We further show that noncoding RNAs are produced from the somatic maternal genome, both during vegetative growth and during sexual events. Maternal inhibition of IES excision is abolished when maternal somatic transcripts containing an IES are targeted for degradation by a distinct RNAi pathway involving 23-nt siRNAs. The results strongly support a scnRNA/macronuclear RNA scanning model in which a natural genomic subtraction, occurring during meiosis between deletion-inducing scnRNAs and antagonistic transcripts from the maternal macronucleus, regulates rearrangements of the zygotic genome.
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Affiliation(s)
- Gersende Lepère
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Mireille Bétermier
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Eric Meyer
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
| | - Sandra Duharcourt
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, Centre 75005 Paris, France
- Centre National de la Recherche Scientifique, UMR 8541, 75005 Paris, France
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20
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Howard-Till RA, Yao MC. Induction of gene silencing by hairpin RNA expression in Tetrahymena thermophila reveals a second small RNA pathway. Mol Cell Biol 2006; 26:8731-42. [PMID: 17000759 PMCID: PMC1636817 DOI: 10.1128/mcb.01430-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unlike in other eukaryotes, in which it causes gene silencing, RNA interference (RNAi) has been linked to programmed DNA deletion in the ciliate Tetrahymena thermophila. Here we have developed an efficient method to inducibly express double-stranded RNA hairpins and demonstrated that they cause gene silencing through targeted mRNA degradation in all phases of the life cycle, including growth, starvation, and mating. This technique offers a new tool for gene silencing in this model organism. Induction of RNA hairpins causes dramatic upregulation of Dicer and Argonaute family genes, revealing a system capable of rapidly responding to double-stranded RNA. These hairpins are processed into 23- to 24-nucleotide (nt) small RNAs, which are distinctly different from the 28- to 30-nt small RNAs known to be associated with DNA deletion. Thus, two different small RNA pathways appear to be responsible for gene silencing and DNA deletion. Surprisingly, expression of the RNA hairpin also causes targeted DNA deletion during conjugation, although at low efficiencies, which suggests a possible crossover of these two molecular paths.
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Affiliation(s)
- Rachel A Howard-Till
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 98109, USA
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21
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Amar L, Dubrana K. Epigenetic control of chromosome breakage at the 5' end of Paramecium tetraurelia gene A. EUKARYOTIC CELL 2005; 3:1136-46. [PMID: 15470241 PMCID: PMC522615 DOI: 10.1128/ec.3.5.1136-1146.2004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Macronuclei and micronuclei of ciliates have related genomes, with macronuclei developing from zygotic micronuclei through programmed DNA rearrangements. While Paramecium tetraurelia wild-type strain 51 and mutant strain d48 have the same micronuclear genome, qualitative differences between their macronuclear genomes have been described, demonstrating that programmed DNA rearrangements could be epigenetically controlled in ciliates. Macronuclear chromosomes end downstream of gene A (A51 Mac ends) and at the 5' end of gene A (Ad48 Mac ends) in strains 51 and d48, respectively. To gain further insight into the process of chromosome end formation, we performed an extensive analysis of locus A rearrangement in strains d48 and 51, in strain d12, which harbors a gene A deletion, and in interstrain cross progeny. We show that (i) allele Ad12 harbors a deletion of >16 kb, (ii) A51 Mac ends distribute over four rather than three DNA regions, (iii) strains d48 and 51 display only quantitative differences (rare Ad48 and A51 Mac ends do form in strains 51 and d48, respectively), (iv) the level of A51 Mac ends is severalfold enhanced in d12- and d48-derived progeny, and (v) this level inversely correlates with the level of Ad48 Mac ends in the d48 parent. Together, these data lead to a model in which the formation of Ad48 Mac ends is epigenetically controlled by a d48 factor(s). We propose that the d48 factor(s) may be derived from RNA molecules transcribed from the Ad48 Mac ends and encompassing the truncated A gene and telomeric repeats.
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Affiliation(s)
- Laurence Amar
- UMR 8080, IBAIC, Bat 444, 91405 Orsay Cedex, France.
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22
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Froissard M, Keller AM, Dedieu JC, Cohen J. Novel secretory vesicle proteins essential for membrane fusion display extracellular-matrix domains. Traffic 2005; 5:493-502. [PMID: 15180826 DOI: 10.1111/j.1600-0854.2004.00194.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Exocytotic mutants can be obtained in Paramecium that affect the organization of the fusion machinery, visible by electron microscopy. The site of action of the genes in the plasma membrane, cytosol or secretory compartment can easily be determined in such mutants. Functional complementation cloning of exocytotic mutants specifically affected in the secretory compartment, nd2-1 and nd169-1, reported here, and the previously studied nd7-1, led to the discovery of a set of novel proteins that display PSI and EGF domains, normally found in extracellular matrix proteins and involved in transmembrane signaling. The structure of one of these proteins, Nd2p, and of the product of a paralog found in the genome Nd22p, corresponds to that of type I membrane receptors, generally involved in protein and vesicle sorting. Our characterization suggests that the proteins we have identified are required to indicate the presence of a mature secretory vesicle to the plasma membrane, to prepare the machinery for fusion. We propose to name this novel subclass of receptors VEMIF, for Vesicular Extracellular-Matrix-like proteins Involved in preparing membrane Fusion.
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Affiliation(s)
- Marine Froissard
- Centre de Génétique Moléulaire, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
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23
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Garnier O, Serrano V, Duharcourt S, Meyer E. RNA-mediated programming of developmental genome rearrangements in Paramecium tetraurelia. Mol Cell Biol 2004; 24:7370-9. [PMID: 15314149 PMCID: PMC506981 DOI: 10.1128/mcb.24.17.7370-7379.2004] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The germ line genome of ciliates is extensively rearranged during development of the somatic macronucleus. Numerous sequences are eliminated, while others are amplified to a high ploidy level. In the Paramecium aurelia group of species, transformation of the maternal macronucleus with transgenes at high copy numbers can induce the deletion of homologous genes in sexual progeny, when a new macronucleus develops from the wild-type germ line. We show that this trans-nuclear effect correlates with homology-dependent silencing of maternal genes before autogamy and with the accumulation of approximately 22- to 23-nucleotide (nt) RNA molecules. The same effects are induced by feeding cells before meiosis with bacteria containing double-stranded RNA, suggesting that small interfering RNA-like molecules can target deletions. Furthermore, experimentally induced macronuclear deletions are spontaneously reproduced in subsequent sexual generations, and reintroduction of the missing gene into the variant macronucleus restores developmental amplification in sexual progeny. We discuss the possible roles of the approximately 22- to 23-nt RNAs in the targeting of deletions and the implications for the RNA-mediated genome-scanning process that is thought to determine developmentally regulated rearrangements in ciliates.
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Affiliation(s)
- Olivier Garnier
- Laboratoire de Génétique Moléculaire, CNRS UMR 8541, Ecole Normale Supérieure, 46, rue d'Ulm, 75005 Paris, France
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24
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Yano J, Rachochy V, Van Houten JL. Glycosyl phosphatidylinositol-anchored proteins in chemosensory signaling: antisense manipulation of Paramecium tetraurelia PIG-A gene expression. EUKARYOTIC CELL 2004; 2:1211-9. [PMID: 14665456 PMCID: PMC326658 DOI: 10.1128/ec.2.6.1211-1219.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glycosyl phosphatidylinositol (GPI)-anchored proteins are peripheral membrane proteins tethered to the cell through a lipid anchor. GPI-anchored proteins serve many functions in cellular physiology and cell signaling. The PIG-A gene codes for one of the enzymes of a complex that catalyzes the first step in anchor synthesis, and we have cloned the Paramecium tetraurelia pPIG-A gene using homology PCR. To understand the function of pPIG-A and the significance of GPI-anchored proteins in Paramecium, we reduced the mRNA for pPIG-A in transformed cells using an expression vector that transcribed antisense mRNA. The amount of transcript is reduced to approximately 0.3% of the mRNA in control-transformed cells. Compared to control cells, cells transformed with the antisense pPIG-A vector show reduced synthesis of GPI anchor intermediates catalyzed in their endoplasmic reticula and a very few GPI-anchored proteins among the peripheral proteins that can be recovered from their surfaces. They also show specific defects in chemoresponse to glutamate and folate. Other cellular functions, such as growth and mating, seem to be normal.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Western
- Chemoreceptor Cells/drug effects
- Chemoreceptor Cells/metabolism
- Cloning, Molecular
- Conserved Sequence
- Gene Expression/drug effects
- Genes, Protozoan
- Glycosylphosphatidylinositols/genetics
- Glycosylphosphatidylinositols/metabolism
- Molecular Sequence Data
- Oligonucleotides, Antisense/pharmacology
- Paramecium tetraurelia/chemistry
- Paramecium tetraurelia/metabolism
- Protein Structure, Tertiary
- Protozoan Proteins/chemistry
- RNA, Antisense/metabolism
- RNA, Messenger/drug effects
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transformation, Genetic
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Affiliation(s)
- Junji Yano
- Department of Biology, University of Vermont, Burlington, Vermont 05405, USA
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25
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Le Mouël A, Butler A, Caron F, Meyer E. Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia. EUKARYOTIC CELL 2004; 2:1076-90. [PMID: 14555491 PMCID: PMC219357 DOI: 10.1128/ec.2.5.1076-1090.2003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The chromosomes of ciliates are fragmented at reproducible sites during the development of the polyploid somatic macronucleus, but the mechanisms involved appear to be quite diverse in different species. In Paramecium aurelia, the process is imprecise and results in de novo telomere addition at locally heterogeneous positions. To search for possible determinants of chromosome fragmentation, we have studied an approximately 21-kb fragmentation region from the germ line genome of P. primaurelia. The mapping and sequencing of alternative macronuclear versions of the region show that two distinct multicopy elements, a minisatellite and a degenerate transposon copy, are eliminated by an imprecise mechanism leading either to chromosome fragmentation and the formation of new telomeres or to the rejoining of flanking sequences. Heterogeneous internal deletions occur between short direct repeats containing TA dinucleotides. The complex rearrangement patterns produced vary slightly among genetically identical cell lines, show non-Mendelian inheritance during sexual reproduction, and can be experimentally modified by transformation of the maternal macronucleus with homologous sequences. These results suggest that chromosome fragmentation in Paramecium is the consequence of imprecise DNA elimination events that are distinct from the precise excision of single-copy internal eliminated sequences and that target multicopy germ line sequences by homology-dependent epigenetic mechanisms.
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Affiliation(s)
- Anne Le Mouël
- Laboratoire de Génétique Moléculaire, CNRS UMR 8541, Ecole Normale Supérieure, 75005 Paris, France
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26
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Plattner H, Kissmehl R. Dense-core secretory vesicle docking and exocytotic membrane fusion in Paramecium cells. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1641:183-93. [PMID: 12914959 DOI: 10.1016/s0167-4889(03)00092-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Work with Paramecium has contributed to the actual understanding of certain aspects of exocytosis regulation, including membrane fusion. The system is faster and more synchronous than any other dense-core vesicle system described and its highly regular design facilitates correlation of functional and ultrastructural (freeze-fracture) features. From early times on, several crucial aspects of exocytosis regulation have been found in Paramecium cells, e.g. genetically controlled microdomains (with distinct ultrastructure) for organelle docking and membrane fusion, involvement of calmodulin in establishing such microdomains, priming by ATP, occurrence of focal fusion with active participation of integral and peripheral proteins, decay of a population of integral proteins ("rosettes", mandatory for fusion capacity) into subunits and their lateral dispersal during fusion, etc. The size of rosette particles and their dispersal upon focal fusion would be directly compatible with proteolipid V(0) subunits of a V-ATPase, much better than the size predicted for oligomeric SNARE pins (SCAMPs are unknown from Paramecium at this time). However, there are some restrictions for a straightforward interpretation of ultrastructural results. The rather pointed, nipple-like tip of the trichocyst membrane could accommodate only one (or very few) potential V(0) counterpart(s), while the overlaying domain of the cell membrane contains numerous rosette particles. Particle size is compatible with V(0), but larger than that assumed for the SNARE complexes. When membrane fusion is induced in the presence of antibodies against cell surface components, focal fusion is seen to occur with dispersing rosette particles but without dispersal of their subunits and without pore expansion. Clearly, this is required for completing fusion and pore expansion. After cloning SNARE and V(0) components in Paramecium (with increasing details becoming rapidly available), we may soon be able to address the question more directly, whether any of these components or some new ones to be detected, serve exocytotic and/or any other membrane fusions in Paramecium.
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Affiliation(s)
- Helmut Plattner
- Fachbereich Biologie, Universität Konstanz, P.O. Box 5560, 78457, Konstanz, Germany.
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Durand-Dubief M, Kohl L, Bastin P. Efficiency and specificity of RNA interference generated by intra- and intermolecular double stranded RNA in Trypanosoma brucei. Mol Biochem Parasitol 2003; 129:11-21. [PMID: 12798502 DOI: 10.1016/s0166-6851(03)00071-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In many eukaryotes, double-stranded (ds) RNA leads to specific degradation of RNA of cognate sequence, a process termed RNA interference (RNAi). Here we used the protozoan Trypanosoma brucei as a model to investigate efficiency and specificity of RNAi generated by expression of long dsRNA of PFRA and PFRC genes, which code for flagellar proteins required for cell motility. Consequences of RNAi were monitored at all three levels: target RNA expression, protein expression and phenotype observation, using population or individual cell analysis. Expression of PFRA dsRNA from an inverted repeat was extremely efficient, knocking down PFRA RNA and PFRA protein, and producing a severe paralysis phenotype. Silencing by expression of PFRA dsRNA using a dual facing promoter system was also very efficient, producing a clear phenotype, although low amounts of PFRA RNA and PFRA protein were detected. Expression via the dual facing promoters of PAR2 dsRNA (83% overall identity with PFRA, including nine blocks of >20 nt total identity) did not produce significant reduction of total amounts of PFRA RNA or PFRA protein. However, individual cell analysis by immunofluorescence revealed that 10-60% cells (depending on subclones) exhibited lower PFRA amounts in their flagellum, producing a reduced-motility phenotype.
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Affiliation(s)
- Mickaël Durand-Dubief
- Unité INSERM U565 & CNRS UMR8646, Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris Cedex 05, France
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Plattner H, Kissmehl R. Molecular Aspects of Membrane Trafficking in Paramecium. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 232:185-216. [PMID: 14711119 DOI: 10.1016/s0074-7696(03)32005-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Results achieved in the molecular biology of Paramecium have shed new light on its elaborate membrane trafficking system. Paramecium disposes not only of the standard routes (endoplasmic reticulum --> Golgi --> lysosomes or secretory vesicles; endo- and phagosomes --> lysosomes/digesting vacuoles), but also of some unique features, e.g. and elaborate phagocytic route with the cytoproct and membrane recycling to the cytopharynx, as well as the osmoregulatory system with multiple membrane fusion sites. Exocytosis sites for trichocysts (dense-core secretory vesicles), parasomal sacs (coated pits), and terminal cisternae (early endosomes) display additional regularly arranged predetermined fusion/fission sites, which now can be discussed on a molecular basis. Considering the regular, repetitive arrangements of membrane components, availability of mutants for complementation studies, sensitivity to gene silencing, and so on, Paramecium continues to be a valuable model system for analyzing membrane interactions. This review intends to set a new baseline for ongoing work along these lines.
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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Haynes WJ, Kung C, Saimi Y, Preston RR. An exchanger-like protein underlies the large Mg2+ current in Paramecium. Proc Natl Acad Sci U S A 2002; 99:15717-22. [PMID: 12422021 PMCID: PMC137782 DOI: 10.1073/pnas.242603999] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There are very few molecules known to transport Mg(2+) in eukaryotes. The membrane of Paramecium tetraurelia passes a large Mg(2+)-selective current and exhibits a corresponding backward swimming behavior. Both are missing in a group of mutants called eccentric. By sorting an indexed WT genomic library through microinjection into the macronucleus, we have isolated a DNA fragment that complements the eccentric mutations. The Mg(2+) currents and behavior are restored fully in the transformed cells. Surprisingly, the conceptually translated protein is not homologous to any known ion channel but instead has some similarity to K(+)-dependent Na(+)Ca(2+) exchangers. Exchangers are either electrically silent or only pass very small and slow currents compared with ion-channel currents. In light of recent ion-channel crystal structures and considering the need to have narrow ion-selective filters, we speculate on how an exchanger might evolve to show channel-like activities in special circumstances. The significance of finding the molecular basis of a Mg(2+)-specific pathway is also discussed.
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Affiliation(s)
- W John Haynes
- Laboratory of Molecular Biology and Department of Genetics, University of Wisconsin, Madison 53706, USA.
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Canto T, Cillo F, Palukaitis P. Generation of siRNAs by T-DNA sequences does not require active transcription or homology to sequences in the plant. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:1137-46. [PMID: 12423019 DOI: 10.1094/mpmi.2002.15.11.1137] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Delivery into plants of T-DNAs containing promoter, terminator, or coding sequences generated small interfering RNAs (siRNAs) specific to each type of sequence. When both promoter and transcribed sequences were simultaneously present in the T-DNA, accumulation of siRNAs to transcribed sequences was favored over accumulation of siRNAs to the nontranscribed upstream promoter sequences. The generation of specific siRNA sequences occurred even in the absence of T-DNA homology to sequences in the plant. Delivery of T-DNA, with homology to the transgene limited to the nontranscribed cauliflower mosaic virus 35S promoter (35SP) and the transcribed nopaline synthase transcription termination (NosT)signal sequences, into transgenic plants expressing the green fluorescent protein (GFP), generated siRNAs in infiltrated tissues to both 35SP (35SsiRNAs) and NosT (NosTsiRNAs), but not to the GFP sequence (GFPsiRNAs). In infiltrated tissues, the 35SsiRNAs failed to trigger the transcriptional silencing of the transgene, accumulation of 35SsiRNAs could be prevented by the potyviral HC-Pro, and the NosTsiRNAs required an initial amplification to trigger efficient transgene silencing, which is mediated by transcripts from the exogenous T-DNA, and not from the transgene. In upper leaves, silencing correlated with the presence of GFPsiRNAs and the absence of 35SsiRNAs, confirming that its spread was posttranscriptionally mediated by the transgene mRNA.
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Affiliation(s)
- Tomas Canto
- Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Kissmehl R, Froissard M, Plattner H, Momayezi M, Cohen J. NSF regulates membrane traffic along multiple pathways inParamecium. J Cell Sci 2002; 115:3935-46. [PMID: 12244131 DOI: 10.1242/jcs.00079] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-ethylmaleimide (NEM)-sensitive factor (NSF), a regulator of soluble NSF attachment protein receptors (SNAREs), is required for vesicular transport in many eukaryotic cells. In the ciliated protozoon Paramecium, complex but well-defined transport routes exist, constitutive and regulated exocytosis, endocytosis, phagocytosis and a fluid excretory pathway through contractile vacuoles, that can all be studied independently at the whole cell level. To unravel the role of NSF and of the SNARE machinery in this complex traffic, we looked for NSF genes in Paramecium, starting from a partial sequence found in a pilot random sequencing project. We found two very similar genes, PtNSF1 and PtNSF2, which both seem to be expressed. Peptide-specific antibodies (Abs) recognize PtNSF as a 84 kDa band. PtNSF gene silencing results in decreasing phagocytotic activity,while stimulated exocytosis of dense core-vesicles (trichocysts), once firmly attached at the cell membrane, persists. Ultrastructural analysis of silenced cells shows deformation or disappearance of structures involved in membrane traffic. Aggregates of numerous small, smooth vesicles intermingled with branches of ER occur in the cytoplasm and are most intensely labeled with anti-NSF Ab-gold. Furthermore, elongated vesicles of ∼30 nm diameter can be seen attached at cortical calcium storage compartments, the alveolar sacs,whose unknown biogenesis may thus be revealed. Involvement of PtNSF in some low frequency fusion events was visualized in non-silenced cells by immuno-fluorescence, after cautious permeabilization in the presence of ATP-γ-S and NEM. Our data document that PtNSF is involved in distinct pathways of vesicle traffic in Paramecium and that actual sensitivity to silencing is widely different, apparently dependent on the turnover of membrane-to-membrane attachment formation.
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Affiliation(s)
- Roland Kissmehl
- University of Konstanz, Department of Biology, PO Box 5560, 78457 Konstanz, Germany.
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Dupuis-Williams P, Fleury-Aubusson A, de Loubresse NG, Geoffroy H, Vayssié L, Galvani A, Espigat A, Rossier J. Functional role of epsilon-tubulin in the assembly of the centriolar microtubule scaffold. J Cell Biol 2002; 158:1183-93. [PMID: 12356863 PMCID: PMC2173240 DOI: 10.1083/jcb.200205028] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2002] [Revised: 08/09/2002] [Accepted: 08/20/2002] [Indexed: 11/26/2022] Open
Abstract
Centrioles and basal bodies fascinate by their spectacular architecture, featuring an arrangement of nine microtubule triplets into an axial symmetry, whose biogenesis relies on yet elusive mechanisms. However, the recent discovery of new tubulins, such as delta-, epsilon-, or eta-tubulin, could constitute a breakthrough for deciphering the assembly steps of this unconventional microtubule scaffold. Here, we report the functional analysis in vivo of epsilon-tubulin, based on gene silencing in Paramecium, which demonstrates that this protein, which localizes at the basal bodies, is essential for the assembly and anchorage of the centriolar microtubules.
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Affiliation(s)
- Pascale Dupuis-Williams
- Laboratoire de Neurobiologie, UMR 7637 Centre National de la Recherche Scientifique, 75005 Paris, France.
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Froissard M, Kissmehl R, Dedieu JC, Gulik-Krzywicki T, Plattner H, Cohen J. N-ethylmaleimide-sensitive factor is required to organize functional exocytotic microdomains in paramecium. Genetics 2002; 161:643-50. [PMID: 12072461 PMCID: PMC1462129 DOI: 10.1093/genetics/161.2.643] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In exocytosis, secretory granules contact plasma membrane at sites where microdomains can be observed, which are sometimes marked by intramembranous particle arrays. Such arrays are particularly obvious when membrane fusion is frozen at a subterminal stage, e.g., in neuromuscular junctions and ciliate exocytotic sites. In Paramecium, a genetic approach has shown that the "rosettes" of intramembranous particles are essential for stimulated exocytosis of secretory granules, the trichocysts. The identification of two genes encoding the N-ethylmaleimide-sensitive factor (NSF), a chaperone ATPase involved in organelle docking, prompted us to analyze its potential role in trichocyst exocytosis using a gene-silencing strategy. Here we show that NSF deprivation strongly interferes with rosette assembly but does not disturb the functioning of exocytotic sites already formed. We conclude that rosette organization involves ubiquitous partners of the fusion machinery and discuss where NSF could intervene in this mechanism.
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Affiliation(s)
- Marine Froissard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France
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Abstract
RNA interference can be induced very efficiently by feeding the ciliate Paramecium with bacteria engineered to express double-stranded RNA, opening the possibility of large-scale functional screening in this unicell.
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