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Tesnière C, Pradal M, Legras JL. Sterol uptake analysis in Saccharomyces and non-Saccharomyces wine yeast species. FEMS Yeast Res 2021; 21:6225805. [PMID: 33852000 DOI: 10.1093/femsyr/foab020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/09/2021] [Indexed: 01/18/2023] Open
Abstract
Sterols are essential components of the yeast membrane and their synthesis requires oxygen. Yet, Saccharomyces cerevisiae has developed the ability to take up sterols from the medium under anaerobiosis. Here we investigated sterol uptake efficiency and the expression of genes related to sterol import in Saccharomyces and non-Saccharomyces wine yeast species fermenting under anaerobic conditions. The sterol uptake efficiency of 39 strains was evaluated by flow cytometry (with 25-NBD Cholesterol, a fluorescent cholesterol probe introduced in the medium) and we found an important discrepancy between Saccharomyces and non-Saccharomyces wine yeast species that we correlated to a lower final cell population and a lower fermentation rate. A high uptake of sterol was observed in the various Saccharomyces strains. Spot tests performed on 13 of these strains confirmed the differences between Saccharomyces and non-Saccharomyces strains, suggesting that the presence of the sterol uptake transporters AUS1 and PDR11 could cause these discrepancies. Indeed, we could not find any homologue to these genes in the genome of Hanseniaspora uvarum, H. guillermondii, Lachancea thermotolerans, Torulaspora delbreueckii, Metschnikowia pulcherrima, or Starmarella bacillaris species. The specialization of sterol import function for post genome-duplication species may have favored growth under anaerobiosis.
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Affiliation(s)
- Catherine Tesnière
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France
| | - Jean-Luc Legras
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France.,CIRM-Levures, SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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Legrand J, Bolotin-Fukuhara M, Bourgais A, Fairhead C, Sicard D. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res 2015; 16:fov112. [PMID: 26684721 DOI: 10.1093/femsyr/fov112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.
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Affiliation(s)
- Judith Legrand
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Monique Bolotin-Fukuhara
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Aurélie Bourgais
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Cécile Fairhead
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France INRA, UMR 1083 Sciences pour l'oenologie, 34060 Montpellier Cedex 2, France
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Abstract
Introns in protein-coding genes are very rare in hemiascomycetous yeast genomes. It has been suggested that these species have experienced extensive intron loss during their evolution from the postulated intron-rich fungal ancestor. However, no intron-devoid yeast species have been identified and some of the introns remaining within the genomes of intron-poor species, such as Saccharomyces cerevisiae, appear to be beneficial during growth under stress conditions. In order to reveal the pattern of intron retention within intron-poor yeast species and better understand the mechanisms of intron evolution, we generated a comprehensive set of 250 orthologous introns in the 20 species that comprise the Saccharomycetaceae, by analyzing RNA deep-sequencing data and alignments of intron-containing genes. Analysis of these intron sets shows that intron loss is at least two orders of magnitude more frequent than intron gain. Fine mapping of intron positions shows that intron sliding is rare, and that introns are almost always removed without changing the primary sequence of the encoded protein. The latter finding is consistent with the prevailing view that homologous recombination between reverse-transcribed mature mRNAs and the corresponding genomic locus is the primary mechanism of intron loss. However, we also find evidence that loss of a small number of introns is mediated by micro-homology, and that the number of intron losses is diminished in yeast species that have lost the microhomology end joining and nonhomologous end joining machinery.
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Affiliation(s)
- Katarzyna B. Hooks
- Faculty of Life Sciences, University of Manchester, United Kingdom
- U1053 INSERM, Université de Bordeaux, France
| | - Daniela Delneri
- Faculty of Life Sciences, University of Manchester, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, United Kingdom
- *Corresponding author: E-mail:
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Iragne F, Nikolski M, Sherman D. Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomycesyeasts. FEMS Yeast Res 2008; 8:132-9. [PMID: 17714476 DOI: 10.1111/j.1567-1364.2007.00290.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Mathematical models of biological processes for the model yeast Saccharomyces cerevisiae are the subject of intensive effort and are available in increasing numbers. An open question is whether such models are informative for related yeasts of biotechnological and medical interest that will not themselves benefit from an equivalent effort. In this study, we assess a method for extrapolating reference models to other completely sequenced yeasts, using a combination of graph-theoretic analysis and reliable identification of homologous genes using Génolevures protein families. In this first assessment, we focus on subtractive modeling, identified through the correlated loss of input and output ports in metabolic pathways. We confirm that the major, highly connected, pathways of central metabolism are conserved and might be universal. In 60-80% of our results, further analysis is not required to determine whether the pathway is lost or conserved, so that our method can be systematically applied as a first step in developing species-specific models.
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Blanco M, Núñez L, Tarrío N, Canto E, Becerra M, González-Siso MI, Cerdán ME. An approach to the hypoxic and oxidative stress responses inKluyveromyces lactisby analysis of mRNA levels. FEMS Yeast Res 2007; 7:702-14. [PMID: 17425672 DOI: 10.1111/j.1567-1364.2007.00233.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Genome duplication, after the divergence of Saccharomyces cerevisiae from Kluyveromyces lactis along evolution, has been proposed as a mechanism of yeast evolution from strict aerobics, such as Candida albicans, to facultatives/fermentatives, such as S. cerevisiae. This feature, together with the preponderance of respiration and the use of the pentose phosphate pathway in glucose utilization, makes K. lactis a model yeast for studies related to carbon and oxygen metabolism. In this work, and based on the knowledge of the sequence of the genome of K. lactis, obtained by the Génolevures project, we have constructed DNA arrays from K. lactis including a limited amount of selected probes. They are related to the aerobiosis-hypoxia adaptation and to the oxidative stress response, and have been used to test changes in mRNA levels in response to hypoxia and oxidative stress generated by H(2)O(2). The study was carried out in both wild-type and rag2 mutant K. lactis strains in which glycolysis is blocked at the phosphoglucose isomerase step. This approach is the first analysis carried out in K. lactis for the majority of the genes selected.
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Affiliation(s)
- Moisés Blanco
- Department of Molecular and Cell Biology, University of A Coruña, A Coruña, Spain
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Suleau A, Gourdon P, Reitz-Ausseur J, Casaregola S. Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains. EUKARYOTIC CELL 2006; 5:1360-70. [PMID: 16896219 PMCID: PMC1539144 DOI: 10.1128/ec.00087-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Accepted: 05/17/2006] [Indexed: 11/20/2022]
Abstract
Genome-wide analysis of transcriptional regulation is generally carried out on well-characterized reference laboratory strains; hence, the characteristics of industrial isolates are therefore overlooked. In a previous study on the major cheese yeast Kluyveromyces lactis, we have shown that the reference strain and an industrial strain used in cheese making display a differential gene expression when grown on a single carbon source. Here, we have used more controlled conditions, i.e., growth in a fermentor with pH and oxygen maintained constant, to study how these two isolates grown in glucose reacted to an addition of lactose. The observed differences between sugar consumption and the production of various metabolites, ethanol, acetate, and glycerol, correlated with the response were monitored by the analysis of the expression of 482 genes. Extensive differences in gene expression between the strains were revealed in sugar transport, glucose repression, ethanol metabolism, and amino acid import. These differences were partly due to repression by glucose and another, yet-unknown regulation mechanism. Our results bring to light a new type of K. lactis strain with respect to hexose transport gene content and repression by glucose. We found that a combination of point mutations and variation in gene regulation generates a biodiversity within the K. lactis species that was not anticipated. In contrast to S. cerevisiae, in which there is a massive increase in the number of sugar transporter and fermentation genes, in K. lactis, interstrain diversity in adaptation to a changing environment is based on small changes at the level of key genes and cell growth control.
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Affiliation(s)
- Audrey Suleau
- Laboratoire de Microbiologie et Génétique Moléculaire, INRA UMR1238, CNRS/INA-PG UMR 2585, 78850 Thiverval-Grignon, France
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Bussereau F, Casaregola S, Lafay JF, Bolotin-Fukuhara M. TheKluyveromyces lactisrepertoire of transcriptional regulators. FEMS Yeast Res 2006; 6:325-35. [PMID: 16630273 DOI: 10.1111/j.1567-1364.2006.00028.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
We have exploited the recently obtained complete genome sequence of Kluyveromyces lactis to compare the repertoire of transcriptional regulators between K. lactis and Saccharomyces cerevisiae. Looking for similarities with the S. cerevisiae proteins of this functional class, we observed a reduction in gene number, which is not randomly distributed among the different DNA-binding classes, the zinc binuclear cluster class (Zn(II)2Cys6), specific to ascomycetes, being one of the most affected. However, when one examines the number of proteins that, in the K. lactis genome, possess the different DNA-binding signatures, it is not reduced compared to S. cerevisiae. This indicates that transactivator proteins have strongly diverged between the two species and cannot be recognized any more, and/or that each genome has developed a specific set of regulators to adapt the cell to its specific niches. These two aspects are discussed on the basis of available data.
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Affiliation(s)
- Françoise Bussereau
- Institut de Génétique et Microbiologie, UMR 8621 CNRS, Université Paris-Sud, Orsay, France
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