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Descorps-Declère S, Richard GF. Megasatellite formation and evolution in vertebrate genes. Cell Rep 2022; 40:111347. [PMID: 36103826 DOI: 10.1016/j.celrep.2022.111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
Since formation of the first proto-eukaryotes, gene repertoire and genome complexity have significantly increased. Among genetic elements responsible for this increase are tandem repeats. Here we describe a genome-wide analysis of large tandem repeats, called megasatellites, in 58 vertebrate genomes. Two bursts occurred, one after the radiation between Agnatha and Gnathostomata fishes and the second one in therian mammals. Megasatellites are enriched in subtelomeric regions and frequently encoded in genes involved in transcription regulation, intracellular trafficking, and cell membrane metabolism, reminiscent of what is observed in fungus genomes. The presence of many introns within young megasatellites suggests that an exon-intron DNA segment is first duplicated and amplified before accumulation of mutations in intronic parts partially erases the megasatellite in such a way that it becomes detectable only in exons. Our results suggest that megasatellite formation and evolution is a dynamic and still ongoing process in vertebrate genomes.
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Affiliation(s)
- Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25 rue du Dr Roux, 75015 Paris, France.
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Natural & Synthetic Genome Instabilities, 25 rue du Dr Roux, 75015 Paris, France.
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2
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Saguez C, Viterbo D, Descorps-Declère S, Cormack BP, Dujon B, Richard GF. Functional variability in adhesion and flocculation of yeast megasatellite genes. Genetics 2022; 221:iyac042. [PMID: 35274698 PMCID: PMC9071537 DOI: 10.1093/genetics/iyac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several Candida glabrata megasatellite-containing genes and found that 2 of them were positively involved in adhesion to epithelial cells, whereas 3 genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling Candida glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230-kbp segmental duplication.
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Affiliation(s)
- Cyril Saguez
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Present address: Abolis Biotechnologies, 5 Rue Henri Desbruères, Evry 91030, France
| | - David Viterbo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris F-75015, France
| | - Brendan P Cormack
- Department of Molecular Biology & Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Bernard Dujon
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
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3
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Poggi L, Emmenegger L, Descorps-Declère S, Dumas B, Richard GF. Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations. Nucleic Acids Res 2021; 49:8120-8134. [PMID: 34233005 PMCID: PMC8373144 DOI: 10.1093/nar/gkab569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Microsatellite expansions are the cause of >20 neurological or developmental human disorders. Shortening expanded repeats using specific DNA endonucleases may be envisioned as a gene editing approach. Here, we measured the efficacy of several CRISPR-Cas nucleases to induce recombination within disease-related microsatellites, in Saccharomyces cerevisiae. Broad variations in nuclease performances were detected on all repeat tracts. Wild-type Streptococcus pyogenes Cas9 (SpCas9) was more efficient than Staphylococcus aureus Cas9 on all repeats tested, except (CAG)33. Cas12a (Cpf1) was the most efficient on GAA trinucleotide repeats, whereas GC-rich repeats were more efficiently cut by SpCas9. The main genetic factor underlying Cas efficacy was the propensity of the recognition part of the sgRNA to form a stable secondary structure, independently of its structural part. This suggests that such structures form in vivo and interfere with sgRNA metabolism. The yeast genome contains 221 natural CAG/CTG and GAA/CTT trinucleotide repeats. Deep sequencing after nuclease induction identified three of them as carrying statistically significant low frequency mutations, corresponding to SpCas9 off-target double-strand breaks.
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Affiliation(s)
- Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Sorbonne Université, Collège Doctoral, 4 Place Jussieu, F-75005 Paris, France.,Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Lisa Emmenegger
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France
| | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR3756 CNRS, F-75015 Paris, France
| | - Bruno Dumas
- Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Guy-Franck Richard
- Institut Pasteur, CNRS, UMR3525, 25 rue du Dr Roux, F-75015 Paris, France.,Sorbonne Université, Collège Doctoral, 4 Place Jussieu, F-75005 Paris, France
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Abstract
Trinucleotide repeats are a peculiar class of microsatellites whose expansions are responsible for approximately 30 human neurological or developmental disorders. The molecular mechanisms responsible for these expansions in humans are not totally understood, but experiments in model systems such as yeast, transgenic mice, and human cells have brought evidence that the mismatch repair machinery is involved in generating these expansions. The present review summarizes, in the first part, the role of mismatch repair in detecting and fixing the DNA strand slippage occurring during microsatellite replication. In the second part, key molecular differences between normal microsatellites and those that show a bias toward expansions are extensively presented. The effect of mismatch repair mutants on microsatellite expansions is detailed in model systems, and in vitro experiments on mismatched DNA substrates are described. Finally, a model presenting the possible roles of the mismatch repair machinery in microsatellite expansions is proposed.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, CNRS UMR3525, 25 rue du Docteur Roux, 75015 Paris, France
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Mosbach V, Viterbo D, Descorps-Declère S, Poggi L, Vaysse-Zinkhöfer W, Richard GF. Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal deletions. PLoS Genet 2020; 16:e1008924. [PMID: 32673314 PMCID: PMC7413560 DOI: 10.1371/journal.pgen.1008924] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/07/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Microsatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ~2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used the Streptococcus pyogenes Cas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal deletions around the repeat tract. These deletions depended on RAD50, RAD52, DNL4 and SAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in a rad50Δ strain, whereas they were impaired in a sae2Δ mutant, only on the DSB end containing most of the repeat tract. This observation demonstrates that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end. In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfere with gene conversion too. Altogether, these data show that SpCas9 may not be the best choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome. With the discovery of highly specific DNA endonucleases such as TALEN and CRISPR-Cas systems, gene editing has become an attractive approach to address genetic disorders. Myotonic dystrophy type 1 (Steinert disease) is due to a large expansion of a CTG trinucleotide repeat in the DMPK gene. At the present time, despite numerous therapeutic attempts, this dramatic neurodegenerative disorder still has no cure. In the present work, we tried to use the Cas9 endonuclease to induce a double-strand break within the expanded CTG repeat of the DMPK gene integrated in the yeast genome. Surprisingly, this break induced chromosomal deletions around the repeat tract. These deletions were local and involved non-homologous joining of the two DNA ends, or more extensive involving homologous recombination between repeated elements upstream and downstream the break. Using yeast genetics, we investigated the genetic requirements for these deletions and found that the triplet repeat tract altered the capacity of the repair machinery to faithfully repair the double-strand break. These results have implications for future gene therapy approaches in human patients.
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Affiliation(s)
| | | | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Paris, France
| | - Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
| | - Wilhelm Vaysse-Zinkhöfer
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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7
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Abstract
Cells can repair a double-strand break (DSB) by homologous recombination if a homologous sequence is provided as a template. This can be achieved by classical gene conversion (with or without crossover) or by single-strand annealing (SSA) between two direct repeat sequences flanking the DSB. To initiate SSA, single-stranded regions are needed adjacent to the break, extending up to the direct repeats in such a way that complementary strands can anneal to each other to repair the DSB. In the present protocol, we describe a GFP reporter assay in Saccharomyces cerevisiae allowing for the quantification of nuclease efficacy at inducing a DSB, by monitoring the reconstitution of a functional GFP gene whose expression can be rapidly quantified by flow cytometry.
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Affiliation(s)
- Lucie Poggi
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
- Collège Doctoral, Sorbonne Université, Paris, France.
- Biologics Research, Sanofi R&D, Vitry sur Seine, France.
| | - Bruno Dumas
- Biologics Research, Sanofi R&D, Vitry sur Seine, France
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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Abstract
Trinucleotide repeats are a peculiar class of microsatellites involved in many neurological as well as developmental disorders. Their propensity to generate very large expansions over time is supposedly due to their capacity to form specific secondary structures, such as imperfect hairpins, triple helices, or G-quadruplexes. These unusual structures were proposed to trigger expansions in vivo. Here, I review known technical issues linked to these structures, such as slippage during polymerase chain reaction and aberrant migration of long trinucleotide repeats during agarose gel electrophoresis. Our current understanding of interactions between trinucleotide repeat secondary structures and the mismatch-repair machinery is also quickly reviewed, and critical questions relevant to these interactions are addressed.
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Affiliation(s)
- Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS UMR3525, Paris, France.
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9
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Viterbo D, Marchal A, Mosbach V, Poggi L, Vaysse-Zinkhöfer W, Richard GF. A fast, sensitive and cost-effective method for nucleic acid detection using non-radioactive probes. Biol Methods Protoc 2018; 3:bpy006. [PMID: 32161800 PMCID: PMC6994052 DOI: 10.1093/biomethods/bpy006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/01/2018] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular biology procedure. Here, we describe a new method, based on commonly used laboratory solutions, for nucleic acid hybridization and detection with digoxigenin-labeled DNA probes. The protocol described is faster, more sensitive and much cheaper than a standard protocol using commercial solutions. Comparison with a classical radioactive detection method shows that the latter exhibits less background and shows a greater linear response. Hence, the proposed protocol may be routinely performed for qualitative detection of nucleic acid, but when precise signal quantitation needs to be obtained, radioactive probe hybridization associated to phosphorimaging technology is more reliable.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France
| | - Astrid Marchal
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France
| | - Valentine Mosbach
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France
| | - Lucie Poggi
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France.,Collège Doctoral, Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France.,Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Wilhelm Vaysse-Zinkhöfer
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France.,Biologics Research, Sanofi R&D, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, 25 rue du Dr Roux, F-75015 Paris, France.,CNRS, UMR3525, F-75015 Paris, France
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Nguyen JHG, Viterbo D, Anand RP, Verra L, Sloan L, Richard GF, Freudenreich CH. Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nucleic Acids Res 2017; 45:4519-4531. [PMID: 28175398 PMCID: PMC5416882 DOI: 10.1093/nar/gkx088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/31/2017] [Indexed: 12/25/2022] Open
Abstract
Trinucleotide repeats are a source of genome instability, causing replication fork stalling, chromosome fragility, and impaired repair. Specialized helicases play an important role in unwinding DNA structures to maintain genome stability. The Srs2 helicase unwinds DNA hairpins, facilitates replication, and prevents repeat instability and fragility. However, since Srs2 is a multifunctional protein with helicase activity and the ability to displace Rad51 recombinase, it was unclear which functions were required for its various protective roles. Here, using SRS2 separation-of-function alleles, we show that in the absence of Srs2 recruitment to PCNA or in helicase-deficient mutants, breakage at a CAG/CTG repeat increases. We conclude that Srs2 interaction with PCNA allows the helicase activity to unwind fork-blocking CAG/CTG hairpin structures to prevent breaks. Independently of PCNA binding, Srs2 also displaces Rad51 from nascent strands to prevent recombination-dependent repeat expansions and contractions. By 2D gel electrophoresis, we detect two different kinds of structured intermediates or joint molecules (JMs). Some JMs are Rad51-independent and exhibit properties of reversed forks, including being processed by the Exo1 nuclease. In addition, in a helicase-deficient mutant, Rad51-dependent JMs are detected, probably corresponding to recombination between sisters. These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions.
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Affiliation(s)
| | - David Viterbo
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
| | - Ranjith P Anand
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Lauren Verra
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Laura Sloan
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Guy-Franck Richard
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
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Viterbo D, Michoud G, Mosbach V, Dujon B, Richard GF. Replication stalling and heteroduplex formation within CAG/CTG trinucleotide repeats by mismatch repair. DNA Repair (Amst) 2016; 42:94-106. [DOI: 10.1016/j.dnarep.2016.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/01/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
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Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF. Genome-wide replication landscape of Candida glabrata. BMC Biol 2015; 13:69. [PMID: 26329162 PMCID: PMC4556013 DOI: 10.1186/s12915-015-0177-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/05/2015] [Indexed: 11/25/2022] Open
Abstract
Background The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. Results We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus. Conclusions Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphane Descorps-Declère
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France.
| | - Cyril Saguez
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
| | - Axel Cournac
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Martial Marbouty
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Thomas Rolland
- Present address: Institut Pasteur, Unité de Génétique Humaine et Fonctions Cognitives, Département des Neurosciences, F-75015, Paris, France.
| | - Laurence Ma
- Institut Pasteur, Plate-forme Génomique, Département Génomes & Génétique, F-75015, Paris, France.
| | - Christiane Bouchier
- Institut Pasteur, Plate-forme Génomique, Département Génomes & Génétique, F-75015, Paris, France.
| | - Ivan Moszer
- Present address: Plate-forme Bio-informatique/Biostatistique, Institut de Neurosciences Translationnelles IHU-A-ICM, Hôpital Pitié-Salpêtrière, 47-83 bd de l'Hôpital, 75561, Paris, Cedex 13, France.
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
| | - Romain Koszul
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
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13
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Richard GF. Shortening trinucleotide repeats using highly specific endonucleases: a possible approach to gene therapy? Trends Genet 2015; 31:177-86. [PMID: 25743488 DOI: 10.1016/j.tig.2015.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
Abstract
Trinucleotide repeat expansions are involved in more than two dozen neurological and developmental disorders. Conventional therapeutic approaches aimed at regulating the expression level of affected genes, which rely on drugs, oligonucleotides, and/or transgenes, have met with only limited success so far. An alternative approach is to shorten repeats to non-pathological lengths using highly specific nucleases. Here, I review early experiments using meganucleases, zinc-finger nucleases (ZFN), and transcription-activator like effector nucleases (TALENs) to contract trinucleotide repeats, and discuss the possibility of using CRISPR-Cas nucleases to the same end. Although this is a nascent field, I explore the possibility of designing nucleases and effectively delivering them in the context of gene therapy.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Department Genomes and Genetics, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3525, 25 Rue du Dr Roux, 75015 Paris, France
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Richard GF, Viterbo D, Khanna V, Mosbach V, Castelain L, Dujon B. Highly specific contractions of a single CAG/CTG trinucleotide repeat by TALEN in yeast. PLoS One 2014; 9:e95611. [PMID: 24748175 PMCID: PMC3991675 DOI: 10.1371/journal.pone.0095611] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/28/2014] [Indexed: 12/22/2022] Open
Abstract
Trinucleotide repeat expansions are responsible for more than two dozens severe neurological disorders in humans. A double-strand break between two short CAG/CTG trinucleotide repeats was formerly shown to induce a high frequency of repeat contractions in yeast. Here, using a dedicated TALEN, we show that induction of a double-strand break into a CAG/CTG trinucleotide repeat in heterozygous yeast diploid cells results in gene conversion of the repeat tract with near 100% efficacy, deleting the repeat tract. Induction of the same TALEN in homozygous yeast diploids leads to contractions of both repeats to a final length of 3–13 triplets, with 100% efficacy in cells that survived the double-strand breaks. Whole-genome sequencing of surviving yeast cells shows that the TALEN does not increase mutation rate. No other CAG/CTG repeat of the yeast genome showed any length alteration or mutation. No large genomic rearrangement such as aneuploidy, segmental duplication or translocation was detected. It is the first demonstration that induction of a TALEN in an eukaryotic cell leads to shortening of trinucleotide repeat tracts to lengths below pathological thresholds in humans, with 100% efficacy and very high specificity.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
- * E-mail:
| | - David Viterbo
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Varun Khanna
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Valentine Mosbach
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Lauriane Castelain
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
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Marbouty M, Ermont C, Dujon B, Richard GF, Koszul R. Purification of G1 daughter cells from different Saccharomycetes species through an optimized centrifugal elutriation procedure. Yeast 2014; 31:159-66. [PMID: 24604765 DOI: 10.1002/yea.3005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 01/31/2023] Open
Abstract
Centrifugal elutriation discriminates cells according to their sedimentation coefficients, generating homogeneous samples well suited for genomic comparative approaches. It can, for instance, isolate G1 daughter cells from a Saccharomyces cerevisiae unsynchronized population, alleviating ageing and cell-cycle biases when conducting genome-wide/single-cell studies. The present report describes a straightforward and robust procedure to determine whether a cell population of virtually any yeast species can be efficiently elutriated, while offering solutions to optimize success. This approach was used to characterize elutriation parameters and S-phase progression of four yeast species (S. cerevisiae, Candida glabrata, Lachancea kluyveri and Pichia sorbitophila) and could theoretically be applied to any culture of single, individual cells.
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Affiliation(s)
- Martial Marbouty
- Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, F-75015, Paris, France; CNRS, UMR3525, F-75015, Paris, France
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16
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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. Biotechnol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nguyen J, Anand R, Richard GF, Freudenreich C. Srs2 functions needed to replicate CAG/CTG hairpins and prevent repeat instability. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.741.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (Bethesda) 2012; 2:299-311. [PMID: 22384408 PMCID: PMC3284337 DOI: 10.1534/g3.111.000745] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/16/2011] [Indexed: 12/19/2022]
Abstract
Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
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Affiliation(s)
| | - Laurence Despons
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Tiphaine Martin
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Pascal Durrens
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Serge Casarégola
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Neuvéglise
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR CNRS 8621, F-91405 Orsay CEDEX, France
| | - Christian Marck
- Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, F-91191 Gif-sur-Yvette CEDEX, France
| | - José A. Cruz
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | | | - Valérie Kugler
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Christine Sacerdot
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Zlatyo Uzunov
- Sofia University St. Kliment Ohridski, Faculty of Biology, Department of General and Applied Microbiology, 1164, Sofia, Bulgaria
| | - Agnes Thierry
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Stéphanie Weiss
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | | | | | - Noemie Jacques
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Paul Jung
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Marc Lemaire
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne; CNRS, UMR5240 Microbiologie, Adaptation et Pathogénie; INSA de Lyon, F-69621, Villeurbanne, France
| | - Sandrine Mallet
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guillaume Morel
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guy-Franck Richard
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Anasua Sarkar
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | - Guilhem Savel
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | | | - Marie-Line Seret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Emmanuel Talla
- Université de la Méditerranée, Laboratoire de Chimie Bactérienne, CNRS-UPR9043, 31 chemin Joseph Aiguier, F-13402 Marseille CEDEX 20, France
| | - Gaelle Samson
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claire Jubin
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Julie Poulain
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Benoît Vacherie
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Valérie Barbe
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Eric Pelletier
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - David J. Sherman
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Eric Westhof
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Jean Weissenbach
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Philippe V. Baret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Patrick Wincker
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claude Gaillardin
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Bernard Dujon
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
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Abstract
Megasatellites are a new family of long tandem repeats, recently discovered in the yeast Candida glabrata. Compared to shorter tandem repeats, such as minisatellites, megasatellite motifs range in size from 135 to more than 300 bp, and allow calculation of evolutionary distances between individual motifs. Using divergence based on nucleotide substitutions among similar motifs, we determined the smallest distance between two motifs, allowing their subsequent clustering. Motifs belonging to the same cluster are recurrently found in different megasatellites located on different chromosomes, showing transfer of genetic information between megasatellites. In comparison, evolution of the few similar tandem repeats in Saccharomyces cerevisiae FLO genes mainly involves subtelomeric homologous recombination. We estimated selective constraints acting on megasatellite motifs and their host genes, and found that motifs are under strong purifying selection. Surprisingly, motifs inserted within pseudogenes are also under purifying selection, whereas the pseudogenes themselves evolve neutrally. We propose that megasatellite motifs propagate by a combination of three different molecular mechanisms: (i) gene duplication, (ii) ectopic homologous recombination and (iii) transfer of motifs from one megasatellite to another one. These mechanisms actively cooperate to create new megasatellites, that may play an important role in the adaptation of Candida glabrata to its human host.
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Affiliation(s)
- Thomas Rolland
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Department Genomes and Genetics, Paris, France
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20
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Thierry A, Dujon B, Richard GF. Megasatellites: a new class of large tandem repeats discovered in the pathogenic yeast Candida glabrata. Cell Mol Life Sci 2009; 67:671-6. [DOI: 10.1007/s00018-009-0216-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 11/29/2022]
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Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E. Comparative genomics of protoploid Saccharomycetaceae. Genome Res 2009; 19:1696-709. [PMID: 19525356 DOI: 10.1101/gr.091546.109] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
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Affiliation(s)
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- Université de Strasbourg, CNRS UMR, France.
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22
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Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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23
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Thierry A, Bouchier C, Dujon B, Richard GF. Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata. Nucleic Acids Res 2008; 36:5970-82. [PMID: 18812401 PMCID: PMC2566889 DOI: 10.1093/nar/gkn594] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Minisatellites are DNA tandem repeats that are found in all sequenced genomes. In the yeast Saccharomyces cerevisiae, they are frequently encountered in genes encoding cell wall proteins. Minisatellites present in the completely sequenced genome of the pathogenic yeast Candida glabrata were similarly analyzed, and two new types of minisatellites were discovered: minisatellites that are composed of two different intermingled repeats (called compound minisatellites), and minisatellites containing unusually long repeated motifs (126–429 bp). These long repeat minisatellites may reach unusual length for such elements (up to 10 kb). Due to these peculiar properties, they have been named ‘megasatellites’. They are found essentially in genes involved in cell–cell adhesion, and could therefore be involved in the ability of this opportunistic pathogen to colonize the human host. In addition to megasatellites, found in large paralogous gene families, there are 93 minisatellites with simple shorter motifs, comparable to those found in S. cerevisiae. Most of the time, these minisatellites are not conserved between C. glabrata and S. cerevisiae, although their host genes are well conserved, raising the question of an active mechanism creating minisatellites de novo in hemiascomycetes.
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Affiliation(s)
- Agnès Thierry
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, F-75015 Paris, France
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24
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Coïc E, Richard GF, Haber JE. Saccharomyces cerevisiae donor preference during mating-type switching is dependent on chromosome architecture and organization. Genetics 2006; 173:1197-206. [PMID: 16624909 PMCID: PMC1526691 DOI: 10.1534/genetics.106.055392] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces mating-type (MAT) switching occurs by gene conversion using one of two donors, HMLalpha and HMRa, located near the ends of the same chromosome. MATa cells preferentially choose HMLalpha, a decision that depends on the recombination enhancer (RE) that controls recombination along the left arm of chromosome III (III-L). When RE is inactive, the two chromosome arms constitute separate domains inaccessible to each other; thus HMRa, located on the same arm as MAT, becomes the default donor. Activation of RE increases HMLalpha usage, even when RE is moved 50 kb closer to the centromere. If MAT is inserted into the same domain as HML, RE plays little or no role in activating HML, thus ruling out any role for RE in remodeling the silent chromatin of HML in regulating donor preference. When the donors MAT and RE are moved to chromosome V, RE increases HML usage, but the inaccessibility of HML without RE apparently depends on other chromosome III-specific sequences. Similar conclusions were reached when RE was placed adjacent to leu2 or arg4 sequences engaged in spontaneous recombination. We propose that RE's targets are anchor sites that tether chromosome III-L in MATalpha cells thus reducing its mobility in the nucleus.
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Affiliation(s)
- Eric Coïc
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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25
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Abstract
Minisatellites are DNA tandem repeats exhibiting size polymorphism among individuals of a population. This polymorphism is generated by two different mechanisms, both in human and yeast cells, "replication slippage" during S-phase DNA synthesis and "repair slippage" associated to meiotic gene conversion. The Saccharomyces cerevisiae genome contains numerous natural minisatellites. They are located on all chromosomes without any obvious distribution bias. Minisatellites found in protein-coding genes have longer repeat units and on the average more repeat units than minisatellites in noncoding regions. They show an excess of cytosines on the coding strand, as compared to guanines (negative GC skew). They are always multiples of three, encode serine- and threonine-rich amino acid repeats, and are found preferably within genes encoding cell wall proteins, suggesting that they are positively selected in this particular class of genes. Genome-wide, there is no statistically significant association between minisatellites and meiotic recombination hot spots. In addition, minisatellites that are located in the vicinity of a meiotic hot spot are not more polymorphic than minisatellites located far from any hot spot. This suggests that minisatellites, in S. cerevisiae, evolve probably by strand slippage during replication or mitotic recombination. Finally, evolution of minisatellites among hemiascomycetous yeasts shows that even though many minisatellite-containing genes are conserved, most of the time the minisatellite itself is not conserved. The diversity of minisatellite sequences found in orthologous genes of different species suggests that minisatellites are differentially acquired and lost during evolution of hemiascomycetous yeasts at a pace faster than the genes containing them.
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Affiliation(s)
- Guy-Franck Richard
- Unité de Génétique Moléculaire des Levures, Université Pierre et Marie Curie, Institut Pasteur, 75724 Paris Cedex 15, France.
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26
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Loeillet S, Palancade B, Cartron M, Thierry A, Richard GF, Dujon B, Doye V, Nicolas A. Genetic network interactions among replication, repair and nuclear pore deficiencies in yeast. DNA Repair (Amst) 2005; 4:459-68. [PMID: 15725626 DOI: 10.1016/j.dnarep.2004.11.010] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 11/25/2004] [Indexed: 10/25/2022]
Abstract
The yeast RAD27 gene encodes a functional homolog of the mammalian FEN1 protein, a structure-specific endo/exonuclease which plays an important role in DNA replication and repair. Previous genetic interaction studies, including a synthetic genetic array (SGA) analysis, showed that the survival of rad27Delta cells requires several DNA metabolic processes, in particular those mediated by all members of the Rad52-dependent recombinational repair pathway. Here, we report the results of our SGA analysis of the collection of non-essential yeast genes against the rad27Delta mutation, which resulted in the identification of a novel synthetic lethal interaction conferred by mutations affecting the Nup84 nuclear pore subcomplex (nup133Delta, nup120Delta and nup84Delta). Additional screens showed that all Rad52 group genes are required for the survival of the nup133Delta and nup120Delta mutants, which are defective in nuclear pore distribution and mRNA export, but not of the nup133DeltaN mutant, which is solely defective in pore distribution. This requirement for the DNA double-strand break (DSB) repair pathway is consistent with the observation that, like rad27Delta, the nup133Delta, nup120Delta and nup84Delta mutants are sensitive to methyl methanesulfonate (MMS). Furthermore, nup133Delta cells exhibit an increased number of spontaneous DNA repair foci containing Rad52. Altogether, these data suggest that the pathological interactions between the rad27Delta and specific nupDelta mutations result from the accumulation of unrepaired DNA damages.
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Affiliation(s)
- Sophie Loeillet
- Institut Curie, Section de Recherche, UMR144 Centre National de la Recherche Scientifique, Génétique Moléculaire de la Recombinaison, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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27
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Richard GF, Kerrest A, Lafontaine I, Dujon B. Comparative Genomics of Hemiascomycete Yeasts: Genes Involved in DNA Replication, Repair, and Recombination. Mol Biol Evol 2005; 22:1011-23. [PMID: 15647519 DOI: 10.1093/molbev/msi083] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Among genes conserved from bacteria to mammals are those involved in replicating and repairing DNA. Following the complete sequencing of four hemiascomycetous yeast species during the course of the Genolevures 2 project, we have studied the conservation of 106 genes involved in replication, repair, and recombination in Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica and compared them with their Saccharomyces cerevisiae orthologues. We found that proteins belonging to the replication fork and to the nucleotide excision repair pathway were-on the average-more conserved than proteins involved in the checkpoint response to DNA damage or in meiotic recombination. The meiotic recombination proteins Spo11p and Mre11p-Rad50p, involved in making meiotic double-strand breaks (DSBs), are conserved as is Mus81p, involved in resolving meiotic recombination intermediates. Interestingly, genes found in organisms in which DSB-repair is required for proper synapsis during meiosis are also found in C. glabrata, K. lactis, and D. hansenii but not in Y. lipolytica, suggesting that two modes of meiotic recombination have been selected during evolution of the hemiascomycetous yeasts. In addition, we found that SGS1 and TOP1, respectively, a DEAD/DEAH helicase and a type I topoisomerase, are duplicated in C. glabrata and that SRS2, a helicase involved in homologous recombination, is tandemly duplicated in K. lactis. Phylogenetic analyses show that the duplicated SGS1 gene evolved faster than the original gene, probably leading to a specialization of function of the duplicated copy.
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Affiliation(s)
- Guy-Franck Richard
- Unité de Génétique Moléculaire des Levures, URA 2171 CNRS, UFR 927 Université Pierre et Marie Curie, Institut Pasteur, Paris cedex, France.
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28
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Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B. Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol 2004; 5:R72. [PMID: 15345056 PMCID: PMC522879 DOI: 10.1186/gb-2004-5-9-r72] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2004] [Revised: 07/13/2004] [Accepted: 07/26/2004] [Indexed: 03/24/2023] Open
Abstract
We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.
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Affiliation(s)
- Jeanne Boyer
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Gwenaël Badis
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Unité de Génétique des Interactions Macromoléculaires (URA2171 CNRS), Department of Structure and Dynamics of Genomes, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris-Cedex 15, France
| | - Cécile Fairhead
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Emmanuel Talla
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- CNRS-Laboratoire de Chimie Bactérienne, 31 Chemin Joseph Aiguier, 13402 Marseille-Cedex 20, France
| | - Florence Hantraye
- Unité de Génétique des Interactions Macromoléculaires (URA2171 CNRS), Department of Structure and Dynamics of Genomes, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris-Cedex 15, France
| | - Emmanuelle Fabre
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Gilles Fischer
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Christophe Hennequin
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Laboratoire de Parasitologie, Faculté de Médecine St-Antoine, 27 rue de Chaligny, 75012 Paris, France
| | - Romain Koszul
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Ingrid Lafontaine
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | | | - Miria Ricchetti
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Unité de Génétique et Biochimie du Développement, Institut Pasteur, 25 rue du Dr Roux 75724 Paris-Cedex 15, France
| | - Guy-Franck Richard
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Agnès Thierry
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Bernard Dujon
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
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29
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Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature 2004; 430:35-44. [PMID: 15229592 DOI: 10.1038/nature02579] [Citation(s) in RCA: 1187] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/19/2004] [Indexed: 11/09/2022]
Abstract
Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
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Affiliation(s)
- Bernard Dujon
- Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie.
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30
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Picardeau M, Le Dantec C, Richard GF, Saint Girons I. The spirochetal chpK-chromosomal toxin-antitoxin locus induces growth inhibition of yeast and mycobacteria. FEMS Microbiol Lett 2004; 229:277-81. [PMID: 14680711 DOI: 10.1016/s0378-1097(03)00848-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Toxin-antitoxin systems encoded by bacterial plasmids and chromosomes typically consist of a toxin that inhibits growth of the host cell and a specific antitoxin. In this report, the chpK gene from the chromosomal toxin-antitoxin locus of the spirochete Leptospira interrogans was studied in both prokaryotic and eukaryotic systems. Cloning of the the spirochetal chpK gene into a mycobacterial expressing vector led to dramatic reductions of transformation efficiency in both Mycobacterium smegmatis and Mycobacterium bovis BCG. However, few mycobacterial transformants were obtained. This result could be due to plasmid structural modifications leading to disruption of chpK expression, suggesting that L. interrogans ChpK is highly toxic for mycobacteria. Presence of the L. interrogans chpK gene was also found to inhibit cell growth of the yeast Saccharomyces cerevisiae. These results show that ChpK possesses a broad activity against both prokaryotes and eukaryotes, suggesting that the cellular target of the toxin is conserved in these organisms.
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Affiliation(s)
- Mathieu Picardeau
- Unité de Bactériologie Moléculaire et Médicale, Institut Pasteur, 28 rue du docteur Roux, 75724 Paris15, France.
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31
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Abstract
We have analyzed all di-, tri-, and tetranucleotide repeats in the partially sequenced genomes of 13 hemiascomycetous yeast species, and compared their sequences, lengths, and distributions to those observed in the genome of Saccharomyces cerevisiae. We found that most of the 13 species exhibit a unique distribution of microsatellites, not correlated to the base composition of their genome. Species close to S. cerevisiae exhibit a similar distribution, while species more distantly related show a more divergent distribution. We propose that de novo formation and continuous loss of microsatellites are active processes generating new DNA sequences. We also show that hemiascomycete-specific genes encoding transcription factors contain trinucleotide repeats more frequently than expected from their average frequency distribution. These transcription factors might play an important role in the speciation process, by regulating gene expression through DNA-protein or protein-protein interactions mediated by stretches of charged amino acids encoded by trinucleotide repeats.
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Affiliation(s)
- Alain Malpertuy
- Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université Pierre et Marie Curie), Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris cedex 15, France
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32
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Abstract
Trinucleotide repeats are involved in several neurological disorders in humans. DNA sequences containing CAG/CTG repeats are prone to slippage during replication and double-strand break repair. The effects of trinucleotide repeats on transcription and on nuclear export were analyzed in vivo in yeast. Transcription of a CAG/CTG trinucleotide repeat in the 3'-untranslated region of a URA3 reporter gene leads to transcription of messenger RNAs several kilobases longer than the expected size. These long mRNAs form more readily when CAG rather than CTG repeats are transcribed. CAG- or CUG-containing transcripts show a non-homogeneous cellular localization. We propose that long mRNAs result from transcription slippage, and discuss the possible implications for human diseases.
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Affiliation(s)
- Emmanuelle Fabre
- Unité de Génétique Moléculaire des Levures (URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie) Institut Pasteur, 25 rue du Dr Roux, 75724 Paris cedex 15, France.
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33
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Abstract
The instability of simple tandem repeats, such as human minisatellite loci, has been suggested to arise by gene conversions. In Saccharomyces cerevisiae, a double-strand break (DSB) was created by the HO endonuclease so that DNA polymerases associated with gap repair must traverse an artificial minisatellite of perfect 36-bp repeats or a yeast Y' minisatellite containing diverged 36-bp repeats. Gene conversions are frequently accompanied by changes in repeat number when the template contains perfect repeats. When the ends of the DSB have nonhomologous tails of 47 and 70 nucleotides that must be removed before repair DNA synthesis can begin, 16% of gene conversions had rearrangements, most of which were contractions, almost always in the recipient locus. When efficient removal of nonhomologous tails was prevented in rad1 and msh2 strains, repair was reduced 10-fold, but among survivors there was a 10-fold reduction in contractions. Half the remaining events were expansions. A similar decrease in the contraction rate was observed when the template was modified so that DSB ends were homologous to the template; and here, too, half of the remaining rearrangements were expansions. In this case, efficient repair does not require RAD1 and MSH2, consistent with our previous observations. In addition, without nonhomologous DSB ends, msh2 and rad1 mutations did not affect the frequency or the distribution of rearrangements. We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences.
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Affiliation(s)
- F Pâques
- Rosenstiel Center and Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
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34
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Hennequin C, Thierry A, Richard GF, Lecointre G, Nguyen HV, Gaillardin C, Dujon B. Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J Clin Microbiol 2001; 39:551-9. [PMID: 11158105 PMCID: PMC87774 DOI: 10.1128/jcm.39.2.551-559.2001] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since Saccharomyces cerevisiae appears to be an emerging pathogen, there is a need for a valuable molecular marker able to distinguish among strains. In this work, we investigated the potential value of microsatellite length polymorphism with a panel of 91 isolates, including 41 clinical isolates, 14 laboratory strains, and 28 strains with industrial relevance. Testing seven polymorphic regions (five trinucleotide repeats and two dinucleotide repeats) in a subgroup of 58 unrelated strains identified a total of 69 alleles (6 to 13 per locus) giving 52 different patterns with a discriminatory power of 99.03%. We found a cluster of clinical isolates sharing their genotype with a bakery strain, suggesting a digestive colonization following ingestion of this strain with diet. With the exception of this cluster of isolates and isolates collected from the same patient or from patients treated with Saccharomyces boulardii, all clinical isolates gave different and unique patterns. The genotypes are stable, and the method is reproducible. The possibility to make the method portable is of great interest for further studies using this technique. This work shows the possibility to readily identify S. boulardii (a strain increasingly isolated from invasive infections) using a unique and specific microsatellite allele.
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Affiliation(s)
- C Hennequin
- Service de Parasitologie-Mycologie et Médecine des Voyages, CHU Amiens, F-80054 Amiens, France.
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Richard GF, Pâques F. Mini- and microsatellite expansions: the recombination connection. EMBO Rep 2000; 1:122-6. [PMID: 11265750 PMCID: PMC1084263 DOI: 10.1093/embo-reports/kvd031] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2000] [Revised: 06/21/2000] [Accepted: 06/28/2000] [Indexed: 11/14/2022] Open
Abstract
It is widely accepted that the large trinucleotide repeat expansions observed in many neurological diseases occur during replication. However, genetic recombination has emerged as a major source of instability for tandem repeats, including minisatellites, and recent studies raise the possibility that it may also be responsible for trinucleotide repeat expansions. We will review data connecting tandem repeat rearrangements and recombination in humans and in eukaryotic model organisms, and discuss the possible role of recombination in trinucleotide repeat expansions in human neurological disorders.
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Affiliation(s)
- G F Richard
- Unité de Génétique Moléculaire des Levures, URA 2171 CNRS, Paris, France.
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Abstract
Recombination induced by double-strand breaks (DSBs) in yeast leads to a higher proportion of expansions to contractions than does replication-associated tract length changes. Expansions are apparently dependent on the property of the repeat array to form hairpins, since DSB repair of a CAA(87) repeat induces only contractions of the repeat sequence. DSB-repair efficiency is reduced by 40% when DNA synthesis must traverse a CAG(98) array, as compared with a CAA(87) array. These data indicate that repair- associated DNA synthesis is inhibited by secondary structures formed by CAG(98) and that these structures promote repeat expansions during DSB repair. Overexpression of Mre11p or Rad50p suppresses the inhibition of DSB repair by CAG(98) and significantly increases the average size of expansions found at the recipient locus. Both effects are dependent on the integrity of the Mre11p-Rad50p-Xrs2p complex. The Mre11 complex thus appears to be directly involved in removing CAG or CTG hairpins that arise frequently during DNA synthesis accompanying gene conversion of these trinucleotide repeats.
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Affiliation(s)
- G F Richard
- Rosenstiel Center and Department of Biology, MS029, Brandeis University, Waltham, MA 02454-9110, USA
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Abstract
Microsatellites are direct tandem DNA repeats found in all genomes. A particular class of microsatellites, called trinucleotide repeats, is responsible for a number of neurological disorders in humans. We review here our current state of knowledge on trinucleotide repeat instability, and discuss the molecular mechanisms that may be involved in trinucleotide repeat expansions leading to fatal diseases in humans. We also present original data on microsatellite distribution in several microbial genomes, and on the use of microsatellites as physical markers to accurately and easily genotype yeast strains.
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Affiliation(s)
- G F Richard
- Unité de génétique moléculaire des levures, URA1300 CNRS, UFR927, université Pierre et Marie Curie, Institut Pasteur, Paris, France
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Richard GF, Dujon B, Haber JE. Double-strand break repair can lead to high frequencies of deletions within short CAG/CTG trinucleotide repeats. Mol Gen Genet 1999; 261:871-82. [PMID: 10394925 DOI: 10.1007/s004380050031] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Trinucleotide repeats undergo contractions and expansions in humans, leading in some cases to fatal neurological disorders. The mechanism responsible for these large size variations is unknown, but replication-slippage events are often suggested as a possible source of instability. We constructed a genetic screen that allowed us to detect spontaneous expansions/contractions of a short trinucleotide repeat in yeast. We show that deletion of RAD27, a gene involved in the processing of Okazaki fragments, increases the frequency of contractions tenfold. Repair of a chromosomal double-strand break (DSB) using a trinucleotide repeat-containing template induces rearrangements of the repeat with a frequency 60 times higher than the natural rate of instability of the same repeat. Our data suggest that both gene conversion and single-strand annealing are major sources of trinucleotide repeat rearrangements.
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Affiliation(s)
- G F Richard
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454-9110, USA
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Abstract
The yeast genome exhibits a variety of trinucleotide repeat arrays within protein-coding genes and intergenic regions. In the first situation, repeats are often not random relative to the translational frame, resulting preferably in long stretches of the two acidic amino acids or of their corresponding amine forms. Interestingly, the longest trinucleotide repeats are often found in genes encoding nuclearly located proteins. Repeats tend to be more frequent in long genes, but less frequent among members of gene families compared to unique genes. In the latter case, repeat arrays often differ in length or composition between the gene homologs, indicating their instability.
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Affiliation(s)
- G F Richard
- Unité de Génétique moléculaire des Levures (UMR1300 CNRS and UFR927 Univ. P. M. Curie, Paris), Institut Pasteur
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Abstract
The mitochondrial gene coding for the large rRNA contains a self-splicing optional group-I intron (Sc-LSU.1) in some Saccharomyces cerevisiae strains. Although the mechanisms of splicing have been extensively studied, little is known about the possible interactions of this intron with other mitochondrial molecules such as proteins. Using glycerol gradients, we have compared the sedimentation coefficients of mitochondrial transcripts containing the Sc-LSU.1 intron in native yeast extracts and in purified RNA preparations. By comparing extracts from rho+ and rho- cells we have found that at least three RNA species containing the Sc-LSU.1 intron (4.5 kb, 2.7 kb and 1.2 kb respectively) are associated in vivo with a multimolecular complex of sedimentation coefficient 50S made up of nuclearly encoded proteins. Another RNA species of 2.7 kb, which may correspond to a cleavage at the dodecamer sequence of the intron, is not associated with the same particle. The possibility that the 50S particle corresponds to the mitochondrial ribosome or its precursor form(s) is discussed.
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Affiliation(s)
- G F Richard
- Département des Biotechnologies, (URA 1300 du CNRS and UFR927 Université P. M. Curie), Institut Pasteur, Paris, France
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Abstract
Systematic sequencing of the genome of Saccharomyces cerevisiae has demonstrated the existence of many novel genes, whose functions need to be studied. Entire chromosome sequences also offer the possibility to examine functional properties of the genome at a higher hierarchical level than the genes themselves. We used ordered DNA fragments of chromosome XI to systematically probe yeast DNA and total RNA extracted from MAT a, MAT alpha and diploid cells grown under three different conditions. Taking into account transcript sizes and uniqueness of probes, we attributed 94 transcripts to sequence-predicted open reading frames (ORFs) or tRNA genes; another 83 being tentatively assigned. The remaining 187 ORFs on chromosome XI do not correspond to transcripts detected under our conditions. More than 80% of transcripts are constitutively expressed, others are regulated by medium composition or cell type, the most frequent regulations being determined by carbon source (glycerol/glucose) or rich versus synthetic medium. Moreover, we show that transcript levels and regulation patterns are not statistically different between ORFs of unknown function, which constitute ca. 40% of the total, and previously identified genes (ca. 30%) or their structural homologues.
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Affiliation(s)
- G F Richard
- Unité de Génétique Moléculaire des Levures URA1149 du CNRS and UFR927U. P.M. Curie, Institut Pasteur, Paris, France
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Abstract
We have examined the distribution of trinucleotide repeats in the yeast genome. Perfect and imperfect repeats, ranging from four to 130 triplets were recognized and the repartition of different triplet combinations was found to differ between Open Reading Frames and Intergenic Regions. Examination of different laboratory strains, revealed polymorphic size variations for all perfect repeats studied, compared to an absence of variation for the imperfect ones. Size variations were found discrete in the range of 6-18 triplets, each strain showing one allelic form for a given repeat array. The distribution and stability of trinucleotide repeats in the yeast genome resembles that of humans and may provide an experimental approach to study the mechanisms of their expansion.
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Affiliation(s)
- G F Richard
- Unité de Génétique Moléculaire des Levures (URA1149 du CNRS and UFR927, Univ. P. & M. Curie), Institut Pasteur, Paris, France
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Dujon B, Alexandraki D, André B, Ansorge W, Baladron V, Ballesta JP, Banrevi A, Bolle PA, Bolotin-Fukuhara M, Bossier P, Bou G, Boyer J, Bultrago MJ, Cheret G, Colleaux L, Dalgnan-Fornler B, del Rey F, Dlon C, Domdey H, Düsterhoft A, Düsterhus S, Entlan KD, Erfle H, Esteban PF, Feldmann H, Fernandes L, Robo GM, Fritz C, Fukuhara H, Gabel C, Gaillon L, Carcia-Cantalejo JM, Garcia-Ramirez JJ, Gent NE, Ghazvini M, Goffeau A, Gonzaléz A, Grothues D, Guerreiro P, Hegemann J, Hewitt N, Hilger F, Hollenberg CP, Horaitis O, Indge KJ, Jacquier A, James CM, Jauniaux C, Jimenez A, Keuchel H, Kirchrath L, Kleine K, Kötter P, Legrain P, Liebl S, Louis EJ, Maia e Silva A, Marck C, Monnier AL, Möstl D, Müller S, Obermaier B, Oliver SG, Pallier C, Pascolo S, Pfeiffer F, Philippsen P, Planta RJ, Pohl FM, Pohl TM, Pöhlmann R, Portetelle D, Purnelle B, Puzos V, Ramezani Rad M, Rasmussen SW, Remacha M, Revuelta JL, Richard GF, Rieger M, Rodrigues-Pousada C, Rose M, Rupp T, Santos MA, Schwager C, Sensen C, Skala J, Soares H, Sor F, Stegemann J, Tettelin H, Thierry A, Tzermia M, Urrestarazu LA, van Dyck L, Van Vliet-Reedijk JC, Valens M, Vandenbo M, Vilela C, Vissers S, von Wettstein D, Voss H, Wiemann S, Xu G, Zimmermann J, Haasemann M, Becker I, Mewes HW. Complete DNA sequence of yeast chromosome XI. Nature 1994; 369:371-8. [PMID: 8196765 DOI: 10.1038/369371a0] [Citation(s) in RCA: 308] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.
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Affiliation(s)
- B Dujon
- Unité de Génétique Moléculaire des Levures (URA 1149 du CNRS and UFR927 University P.M. Curie), Départment de Biologie Moléculaire, Insitut Pasteur, Paris, France
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Boyer J, Pascolo S, Richard GF, Dujon B. Sequence of a 7.8 kb segment on the left arm of yeast chromosome XI reveals four open reading frames, including the CAP1 gene, an intron-containing gene and a gene encoding a homolog to the mammalian UOG-1 gene. Yeast 1993; 9:279-87. [PMID: 8488728 DOI: 10.1002/yea.320090307] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We report here the DNA sequence of a segment of chromosome XI of Saccharomyces cerevisiae extending over 7.8 kb. The segment contains four long open reading frames, YKL150, YKL153, YKL155 and YKL156, YKL155 corresponds to the CAP1 gene. YKL153 contains an intron and shows an extremely biased codon usage suggestive of a highly expressed protein. YKL156 is a homolog to UOG-1, an open reading frame associated with the cDNA clone of the mammalian growth/differentiation factor 1. YKL150 reveals common motifs to both the RNA polymerase II elongation factor of Drosophila melanogaster and to the yeast PPR2 gene product.
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Affiliation(s)
- J Boyer
- Unité de Génétique Moléculaire des Levures (URA 1149 du CNRS), Institut Pasteur, Paris, France
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Colleaux L, Richard GF, Thierry A, Dujon B. Sequence of a segment of yeast chromosome XI identifies a new mitochondrial carrier, a new member of the G protein family, and a protein with the PAAKK motif of the H1 histones. Yeast 1992; 8:325-36. [PMID: 1514329 DOI: 10.1002/yea.320080410] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have entirely sequenced an 8.3 kb segment localized on the left arm of chromosome XI of Saccharomyces cerevisiae. Five new open reading frames have been uncovered. One of them encodes a new mitochondrial carrier protein which is dispensable for growth on glycerol medium. Another could be a new member of the G protein family. A third possesses the PAAKK motif common to H1 histones.
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Affiliation(s)
- L Colleaux
- Unité de Génétique Moléculaire des Levures (URA 1149 du CNRS), Institut Pasteur, Paris, France
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