Saccharomycetaceae

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Kenneth H. Wolfe - One of the best experts on this subject based on the ideXlab platform.

  • The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae
    FEMS yeast research, 2019
    Co-Authors: Alexander P Douglass, Kevin P. Byrne, Kenneth H. Wolfe
    Abstract:

    The yeast family Pichiaceae, also known as the 'methylotrophs clade', is a relatively little studied group of yeasts despite its economic and clinical relevance. To explore the genome evolution and synteny relationships within this family, we developed the Methylotroph Gene Order Browser (MGOB, http://mgob.ucd.ie) similar to our previous gene order browsers for other yeast families. The dataset contains genome sequences from nine Pichiaceae species, including our recent reference sequence of Pichia kudriavzevii. As an example, we demonstrate the conservation of synteny around the MOX1 locus among species both containing and lacking the MOX1 gene for methanol assimilation. We found ancient clusters of genes that are conserved as adjacent between Pichiaceae and Saccharomycetaceae. Surprisingly, we found evidence that the locations of some centromeres have been conserved among Pichiaceae species, and between Pichiaceae and Saccharomycetaceae, even though the centromeres fall into different structural categories-point centromeres, inverted repeats and retrotransposon cluster centromeres.

  • The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats.
    Yeast (Chichester England), 2019
    Co-Authors: Aisling Y. Coughlan, Kenneth H. Wolfe
    Abstract:

    Point centromeres, found in some ascomycete yeasts such Saccharomyces cerevisiae, are very different in structure from the centromeres of other eukaryotes. They are tiny and nonrepetitive and contain only two short conserved sequence motifs. Until recently, point centromeres were thought to have a single evolutionary origin, in the budding yeast family Saccharomycetaceae. Most yeasts outside this family have centromeres that are many kilobases in size. Some have centromeres consisting of a large inverted repeat sequence, others have centromeric clusters of retrotransposons, and a third group including Candida albicans has centromeres with no conserved sequence features. It was recently reported that Scheffersomyces stipitis has point centromeres with a strongly conserved 125-bp core sequence, which is unexpected because S. stipitis is only distantly related to the known point-centromere species. We show here that the 125-bp core sequence is actually part of the long terminal repeat (LTR) of the Ty5-like retrotransposon Tps5, which forms a cluster in the centromeric region of each S. stipitis chromosome. Thus, the LTR of a centromere-associated retrotransposon confers centromere-like mitotic stability when cloned into a plasmid. The centromeric regions of S. stipitis contain three types of Tps5 element (Tps5a, Tps5b, and Tps5c) and a noncoding nonautonomous large retrotransposon derivative.

  • TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.
    PLOS Genetics, 2018
    Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine Butler
    Abstract:

    Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants, marine protists and fungi. We find that riboswitches are widespread in the budding yeasts (Saccharomycotina), and they are most common in homologs of DUR31, originally described as a spermidine transporter. We show that DUR31 (an ortholog of N. crassa gene NCU01977) encodes a thiamin transporter in Candida species. Using an RFP/riboswitch expression system, we show that the functional elements of the riboswitch are contained within the native intron of DUR31 from Candida parapsilosis, and that the riboswitch regulates splicing in a thiamin-dependent manner when RFP is constitutively expressed. The DUR31 gene has been lost from Saccharomyces, and may have been displaced by an alternative thiamin transporter. TPP riboswitches are also present in other putative transporters in yeasts and filamentous fungi. However, they are rare in thiamin biosynthesis genes THI4 and THI5 in the Saccharomycotina, and have been lost from all genes in the sequenced species in the family Saccharomycetaceae, including S. cerevisiae.

  • Thi7 orthologs in the Saccharomycotina.
    2018
    Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine Butler
    Abstract:

    Thi7 orthologs were identified as shown in S1 Fig, and the tree is rooted using paralogous genes. The amino acid sequences of predicted Thi7 homologs were aligned using Muscle (v3.8.31, [48]), and a phylogenetic tree was constructed using RAxML [49]. Branch support is indicated using bootstrap values (from 100. Only values >50 are shown). Protein accession numbers are shown, or where unavailable, contig names are shown. A possible HGT event in Brettanomyces is highlighted in a box. The species are colored using the format in Fig 5 (Saccharomycetaceae (dark blue), Saccharomycodaceae (sea green), Phaffomycetaceae (cyan), Yarrowia (red), Debaryomycetaceae/Metschnikowiaceae (yellow), Pichiaceae (orange).

  • Evolution of Mating in the Saccharomycotina
    Annual Review of Microbiology, 2017
    Co-Authors: Kenneth H. Wolfe, Geraldine Butler
    Abstract:

    The fungal phylum Ascomycota comprises three subphyla: Saccharomycotina, Pezizomycotina, and Taphrinomycotina. In many Saccharomycotina species, cell identity is determined by genes at the MAT (mating-type) locus; mating occurs between MATa and MATα cells. Some species can switch between MATa and MATα mating types. Switching in the Saccharomycotina originated in the common ancestor of the Saccharomycetaceae, Pichiaceae, and Metschnikowiaceae families, as a flip/flop mechanism that inverted a section of chromosome. Switching was subsequently lost in the Metschnikowiaceae, including Candida albicans, but became more complex in the Saccharomycetaceae when the mechanism changed from inversion to copy-and-paste between HML/HMR and MAT. Based on their phylogenetic closeness and the similarity of their MTL (mating-type like) loci, some Metschnikowia species may provide useful models for the sexual cycles of Candida species. Conservation of synteny demonstrates that, despite changes in its gene content, a single ...

Jure Piškur - One of the best experts on this subject based on the ideXlab platform.

  • why when and how did yeast evolve alcoholic fermentation
    Fems Yeast Research, 2014
    Co-Authors: Sofia Dashko, Nerve Zhou, Concetta Compagno, Jure Piškur
    Abstract:

    The origin of modern fruits brought to microbial communities an abundant source of rich food based on simple sugars. Yeasts, especially Saccharomyces cerevisiae, usually become the predominant group in these niches. One of the most prominent and unique features and likely a winning trait of these yeasts is their ability to rapidly convert sugars to ethanol at both anaerobic and aerobic conditions. Why, when, and how did yeasts remodel their carbon metabolism to be able to accumulate ethanol under aerobic conditions and at the expense of decreasing biomass production? We hereby review the recent data on the carbon metabolism in Saccharomycetaceae species and attempt to reconstruct the ancient environment, which could promote the evolution of alcoholic fermentation. We speculate that the first step toward the so-called fermentative lifestyle was the exploration of anaerobic niches resulting in an increased metabolic capacity to degrade sugar to ethanol. The strengthened glycolytic flow had in parallel a beneficial effect on the microbial competition outcome and later evolved as a “new” tool promoting the yeast competition ability under aerobic conditions. The basic aerobic alcoholic fermentation ability was subsequently “upgraded” in several lineages by evolving additional regulatory steps, such as glucose repression in the S. cerevisiae clade, to achieve a more precise metabolic control.

  • Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication
    PloS one, 2013
    Co-Authors: Arne Hagman, Concetta Compagno, Torbjörn Säll, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker’s yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined.

  • Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication
    'Public Library of Science (PLoS)', 2013
    Co-Authors: Arne Hagman, Concetta Compagno, T. S&#228, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker's yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined

  • Yeast ‘‘Make-Accumulate-Consume’ ’ Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication
    2013
    Co-Authors: Arne Hagman, Concetta Compagno, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker’s yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiatin

  • Phylogenetic relationship among yeast.
    2013
    Co-Authors: Arne Hagman, Concetta Compagno, Torbjörn Säll, Jure Piškur
    Abstract:

    A schematic phylogenetic relationship, based on the phylogenetic tree from Kurtzman and Robnett (2003) [16], covering twelve genera of Saccharomycetaceae and all employed species. Note that alternative models to explain the phylogenetic relationship between the Lachancea, Kluyveromyces and Eremothecium genera have been proposed [23] but here we follow the tree in ref. 15. Several evolutionary events, which are relevant for the modern traits, are shown. Note that the relative timing of some events, especially those which left a clear finger-print in the modern genomes (green arrows) is relatively precise, such as WGD [10], the horizontal transfer of a bacterial »anaerobic« DHODase (encoded by URA1) [19], complete rewiring of the respiration related promoters (RGE stands for Rapid Growth Elements) [3], and the loss of respiratory Complex I [9], while the timing of more complex traits (red arrows), such as the capability for anaerobic growth [12], [13] and petite positivity [13], might be less precise.

Kevin P. Byrne - One of the best experts on this subject based on the ideXlab platform.

  • The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae
    FEMS yeast research, 2019
    Co-Authors: Alexander P Douglass, Kevin P. Byrne, Kenneth H. Wolfe
    Abstract:

    The yeast family Pichiaceae, also known as the 'methylotrophs clade', is a relatively little studied group of yeasts despite its economic and clinical relevance. To explore the genome evolution and synteny relationships within this family, we developed the Methylotroph Gene Order Browser (MGOB, http://mgob.ucd.ie) similar to our previous gene order browsers for other yeast families. The dataset contains genome sequences from nine Pichiaceae species, including our recent reference sequence of Pichia kudriavzevii. As an example, we demonstrate the conservation of synteny around the MOX1 locus among species both containing and lacking the MOX1 gene for methanol assimilation. We found ancient clusters of genes that are conserved as adjacent between Pichiaceae and Saccharomycetaceae. Surprisingly, we found evidence that the locations of some centromeres have been conserved among Pichiaceae species, and between Pichiaceae and Saccharomycetaceae, even though the centromeres fall into different structural categories-point centromeres, inverted repeats and retrotransposon cluster centromeres.

  • Clade- and species-specific features of genome evolution in the Saccharomycetaceae
    FEMS Yeast Research, 2015
    Co-Authors: Kenneth H. Wolfe, David Armisén, Estelle Proux-wéra, Sean S. Oheigeartaigh, Haleema Azam, Jonathan L. Gordon, Kevin P. Byrne
    Abstract:

    Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm-for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components.

Concetta Compagno - One of the best experts on this subject based on the ideXlab platform.

  • why when and how did yeast evolve alcoholic fermentation
    Fems Yeast Research, 2014
    Co-Authors: Sofia Dashko, Nerve Zhou, Concetta Compagno, Jure Piškur
    Abstract:

    The origin of modern fruits brought to microbial communities an abundant source of rich food based on simple sugars. Yeasts, especially Saccharomyces cerevisiae, usually become the predominant group in these niches. One of the most prominent and unique features and likely a winning trait of these yeasts is their ability to rapidly convert sugars to ethanol at both anaerobic and aerobic conditions. Why, when, and how did yeasts remodel their carbon metabolism to be able to accumulate ethanol under aerobic conditions and at the expense of decreasing biomass production? We hereby review the recent data on the carbon metabolism in Saccharomycetaceae species and attempt to reconstruct the ancient environment, which could promote the evolution of alcoholic fermentation. We speculate that the first step toward the so-called fermentative lifestyle was the exploration of anaerobic niches resulting in an increased metabolic capacity to degrade sugar to ethanol. The strengthened glycolytic flow had in parallel a beneficial effect on the microbial competition outcome and later evolved as a “new” tool promoting the yeast competition ability under aerobic conditions. The basic aerobic alcoholic fermentation ability was subsequently “upgraded” in several lineages by evolving additional regulatory steps, such as glucose repression in the S. cerevisiae clade, to achieve a more precise metabolic control.

  • Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication
    PloS one, 2013
    Co-Authors: Arne Hagman, Concetta Compagno, Torbjörn Säll, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker’s yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined.

  • Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication
    'Public Library of Science (PLoS)', 2013
    Co-Authors: Arne Hagman, Concetta Compagno, T. S&#228, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker's yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined

  • Yeast ‘‘Make-Accumulate-Consume’ ’ Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication
    2013
    Co-Authors: Arne Hagman, Concetta Compagno, Jure Piškur
    Abstract:

    When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker’s yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiatin

  • Phylogenetic relationship among yeast.
    2013
    Co-Authors: Arne Hagman, Concetta Compagno, Torbjörn Säll, Jure Piškur
    Abstract:

    A schematic phylogenetic relationship, based on the phylogenetic tree from Kurtzman and Robnett (2003) [16], covering twelve genera of Saccharomycetaceae and all employed species. Note that alternative models to explain the phylogenetic relationship between the Lachancea, Kluyveromyces and Eremothecium genera have been proposed [23] but here we follow the tree in ref. 15. Several evolutionary events, which are relevant for the modern traits, are shown. Note that the relative timing of some events, especially those which left a clear finger-print in the modern genomes (green arrows) is relatively precise, such as WGD [10], the horizontal transfer of a bacterial »anaerobic« DHODase (encoded by URA1) [19], complete rewiring of the respiration related promoters (RGE stands for Rapid Growth Elements) [3], and the loss of respiratory Complex I [9], while the timing of more complex traits (red arrows), such as the capability for anaerobic growth [12], [13] and petite positivity [13], might be less precise.

Frédérique Favier - One of the best experts on this subject based on the ideXlab platform.

  • Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones
    PLoS ONE, 2016
    Co-Authors: Mathieu Schwartz, Claude Didierjean, Arnaud Hecker, Jean-michel Girardet, Mélanie Morel-rouhier, Eric Gelhaye, Frédérique Favier
    Abstract:

    Glutathionyl-hydroquinone reductases (GHRs) belong to the recently characterized Xi-class of glutathione transferases (GSTXs) according to unique structural properties and are present in all but animal kingdoms. The GHR ScECM4 from the yeast Saccharomyces cerevisiae has been studied since 1997 when it was found to be potentially involved in cell-wall biosyn-thesis. Up to now and in spite of biological studies made on this enzyme, its physiological role remains challenging. The work here reports its crystallographic study. In addition to exhibiting the general GSTX structural features, ScECM4 shows extensions including a huge loop which contributes to the quaternary assembly. These structural extensions are probably specific to Saccharomycetaceae. Soaking of ScECM4 crystals with GS-menadione results in a structure where glutathione forms a mixed disulfide bond with the cysteine 46. Solution studies confirm that ScECM4 has reductase activity for GS-menadione in presence of glutathione. Moreover, the high resolution structures allowed us to propose new roles of conserved residues of the active site to assist the cysteine 46 during the catalytic act.