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Donovan PD, Holland LM, Lombardi L, Coughlan AY, Higgins DG, Wolfe KH, Butler G. TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida. PLoS Genet 2018; 14:e1007429. [PMID: 29852014 PMCID: PMC5997356 DOI: 10.1371/journal.pgen.1007429] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/12/2018] [Accepted: 05/18/2018] [Indexed: 11/30/2022] Open
Abstract
Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants, marine protists and fungi. We find that riboswitches are widespread in the budding yeasts (Saccharomycotina), and they are most common in homologs of DUR31, originally described as a spermidine transporter. We show that DUR31 (an ortholog of N. crassa gene NCU01977) encodes a thiamin transporter in Candida species. Using an RFP/riboswitch expression system, we show that the functional elements of the riboswitch are contained within the native intron of DUR31 from Candida parapsilosis, and that the riboswitch regulates splicing in a thiamin-dependent manner when RFP is constitutively expressed. The DUR31 gene has been lost from Saccharomyces, and may have been displaced by an alternative thiamin transporter. TPP riboswitches are also present in other putative transporters in yeasts and filamentous fungi. However, they are rare in thiamin biosynthesis genes THI4 and THI5 in the Saccharomycotina, and have been lost from all genes in the sequenced species in the family Saccharomycetaceae, including S. cerevisiae. Thiamin, or Vitamin B1, is an essential requirement in all living organisms because it is a co-factor for many enzymes in metabolism. Unlike animals, many yeasts can synthesize thiamin, or they can import it from the environment. Expression of thiamin biosynthesis genes and of thiamin transporters is strictly regulated in response to the presence of thiamin. In many filamentous fungi, expression of thiamin biosynthesis genes is regulated by TPP riboswitches, RNA regulatory elements that are located within messenger RNA. TPP riboswitches are rare in yeasts. However, we find that TPP riboswitches are conserved in an ancient thiamin transporter, found in filamentous fungi, yeasts and other related organisms. There appears to be a high turnover of thiamin transporters in fungi, and there has been a gradual loss of TPP riboswitches in yeasts.
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Affiliation(s)
- Paul D. Donovan
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Linda M. Holland
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lisa Lombardi
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Y. Coughlan
- School of Medicine and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Desmond G. Higgins
- School of Medicine and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth H. Wolfe
- School of Medicine and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Geraldine Butler
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- * E-mail:
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Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res 2017; 24:251-260. [PMID: 28338834 PMCID: PMC5499648 DOI: 10.1093/dnares/dsx002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/21/2017] [Indexed: 11/14/2022] Open
Abstract
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.
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Affiliation(s)
- Abdel Belkorchia
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | | | - Valérie Polonais
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Nicolas Parisot
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Frédéric Delbac
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Jean-François Brugère
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | | | - Eric Peyretaillade
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
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Drory Retwitzer M, Kifer I, Sengupta S, Yakhini Z, Barash D. An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PLoS One 2015; 10:e0134262. [PMID: 26230932 PMCID: PMC4521916 DOI: 10.1371/journal.pone.0134262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 11/22/2022] Open
Abstract
Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additional eukaryotic riboswitches since more than 20 riboswitch classes have been found in prokaryotes but only one class has been found in eukaryotes. Moreover, this single known class of eukaryotic riboswitch, namely the TPP riboswitch class, has been found in bacteria, archaea, fungi and plants but not in animals. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods such as a combination of BLAST and pattern matching techniques that incorporate base-pairing considerations. None of these approaches perform energy minimization structure predictions. There is a clear motivation to develop new bioinformatics methods, aside of the ongoing advances in covariance models, that will sample the sequence search space more flexibly using structural guidance while retaining the computational efficiency of sequence-based methods. We present a new energy minimization approach that transforms structure-based search into a sequence-based search, thereby enabling the utilization of well established sequence-based search utilities such as BLAST and FASTA. The transformation to sequence space is obtained by using an extended inverse RNA folding problem solver with sequence and structure constraints, available within RNAfbinv. Examples in applying the new method are presented for the purine and preQ1 riboswitches. The method is described in detail along with its findings in prokaryotes. Potential uses in finding novel eukaryotic riboswitches and optimizing pre-designed synthetic riboswitches based on ligand simulations are discussed. The method components are freely available for use.
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Affiliation(s)
| | - Ilona Kifer
- Agilent Laboratories, Tel Aviv, Israel; Microsoft R&D Center, Herzliya, Israel
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
| | - Zohar Yakhini
- Agilent Laboratories, Tel Aviv, Israel; Laboratory of Computational Biology, Computer Science Department, Israel Institute of Technology, Haifa, 32000, Israel
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, 84105, Israel
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Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:66. [PMID: 24834124 PMCID: PMC4022394 DOI: 10.1186/1754-6834-7-66] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/19/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant. RESULTS The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. CONCLUSIONS The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.
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Affiliation(s)
- Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
- Yeast Genetics, Leibniz Institute of Plant Research (IPK), Corrensstrasse 3, Gatersleben 06466, Germany
| | - Claude Gaillardin
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Małgorzata Czernicka
- Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, Krakow 31-425, Poland
| | - Pascal Durrens
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Tiphaine Martin
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Erik Böer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Jose A Cruz
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Emmanuel Talla
- Aix-Marseille Université, CNRS UMR 7283, Laboratoire de Chimie Bactérienne, F-13402 Marseille, Cedex 20, France
| | - Christian Marck
- CEA, Saclay Biology and Technologies Institute (iBiTec-S), Gif-sur-Yvette F-91191, France
| | - André Goffeau
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 5/15, Louvain-la-Neuve 1349, Belgium
| | - Valérie Barbe
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Philippe Baret
- Université Catholique de Louvain, Earth and Life Institute (ELI), Louvain-la-Neuve 1348, Belgium
| | - Keith Baronian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | | | - Rüdiger Bode
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorffstraße 4, Greifswald D-17487, Germany
| | - Serge Casaregola
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Laurence Despons
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR CNRS 8621, F- Orsay CEDEX 91405, France
| | - Martin Giersberg
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Przemysław Piotr Gierski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Urs Hähnel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Dagmara Jankowska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Claire Jubin
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry F-91000, France
- Université d’Evry, Bd François Mitterand, Evry F-91025, France
| | - Paul Jung
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Ingrid Lafontaine
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | | | - Marc Lemaire
- Université Lyon 1, CNRS UMR 5240, Villeurbanne F-69621, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Guillaume Morel
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Guy-Franck Richard
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Jan Riechen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Christine Sacerdot
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
- Present address: École Normale Supérieure, Institut de Biologie de l’ENS (IBENS), 46 rue d’Ulm, Paris F-75005, France
| | - Anasua Sarkar
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Guilhem Savel
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | | | - David J Sherman
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | | | - Agnès Thierry
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Anke Trautwein-Schult
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Benoit Vacherie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Eric Westhof
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Sebastian Worch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Bernard Dujon
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry F-91000, France
- Université d’Evry, Bd François Mitterand, Evry F-91025, France
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Cécile Neuvéglise
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
- INRA Institut Micalis UMR 1319, AgroParisTech, BIMLip, Avenue de Bretignières, Bât. CBAI, Thiverval-Grignon 78850, France
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