Saccharomycetes

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Paul M. Harrison - One of the best experts on this subject based on the ideXlab platform.

  • Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution.
    PeerJ, 2020
    Co-Authors: Paul M. Harrison
    Abstract:

    Prions are self-propagating alternative states of protein domains. They are linked to both diseases and functional protein roles in eukaryotes. Prion-forming domains in Saccharomyces cerevisiae are typically domains with high intrinsic protein disorder (i.e., that remain unfolded in the cell during at least some part of their functioning), that are converted to self-replicating amyloid forms. S. cerevisiae is a member of the fungal class Saccharomycetes, during the evolution of which a large population of prion-like domains has appeared. It is still unclear what principles might govern the molecular evolution of prion-forming domains, and intrinsically disordered domains generally. Here, it is discovered that in a set of such prion-forming domains some evolve in the fungal class Saccharomycetes in such a way as to absorb general mutation biases across millions of years, whereas others do not, indicating a spectrum of selection pressures on composition and sequence. Thus, if the bias-absorbing prion formers are conserving a prion-forming capability, then this capability is not interfered with by the absorption of bias changes over the duration of evolutionary epochs. Evidence is discovered for selective constraint against the occurrence of lysine residues (which likely disrupt prion formation) in S. cerevisiae prion-forming domains as they evolve across Saccharomycetes. These results provide a case study of the absorption of mutational trends by compositionally biased domains, and suggest methodology for assessing selection pressures on the composition of intrinsically disordered regions.

  • Conservation of Prion-Like Composition and Sequence in Prion-Formers and Prion-Like Proteins of Saccharomyces cerevisiae
    Frontiers in Molecular Biosciences, 2019
    Co-Authors: Ting-yi Su, Paul M. Harrison
    Abstract:

    Prions in eukaryotes have been linked to diseases, evolutionary capacitance, large-scale genetic control, and long-term memory formation. Prion formation and propagation have been studied extensively in the budding yeast Saccharomyces cerevisiae. Here, we have analysed the conservation of sequence and of prion-like composition for prion-forming proteins and for other prion-like proteins from S. cerevisiae, across three evolutionary levels. We discover that prion-like status is well-conserved for about half the set of prion-formers at the Saccharomycetes level, and that prion-forming domains evolve more quickly as sequences than other prion-like domains do. Such increased mutation rates may be linked to the acquisition of functional roles for prion-forming domains during the evolutionary epoch of Saccharomycetes. Domain scores for prion-like composition in S. cerevisiae are strongly correlated with scores for such composition weighted evolutionarily over the dozens of fungal species examined, indicating conservation of such prion-like status. Examples of notable prion-like proteins that are highly conserved both in sequence and prion-like composition are discussed.

Ting-yi Su - One of the best experts on this subject based on the ideXlab platform.

  • Conservation of Prion-Like Composition and Sequence in Prion-Formers and Prion-Like Proteins of Saccharomyces cerevisiae
    Frontiers in Molecular Biosciences, 2019
    Co-Authors: Ting-yi Su, Paul M. Harrison
    Abstract:

    Prions in eukaryotes have been linked to diseases, evolutionary capacitance, large-scale genetic control, and long-term memory formation. Prion formation and propagation have been studied extensively in the budding yeast Saccharomyces cerevisiae. Here, we have analysed the conservation of sequence and of prion-like composition for prion-forming proteins and for other prion-like proteins from S. cerevisiae, across three evolutionary levels. We discover that prion-like status is well-conserved for about half the set of prion-formers at the Saccharomycetes level, and that prion-forming domains evolve more quickly as sequences than other prion-like domains do. Such increased mutation rates may be linked to the acquisition of functional roles for prion-forming domains during the evolutionary epoch of Saccharomycetes. Domain scores for prion-like composition in S. cerevisiae are strongly correlated with scores for such composition weighted evolutionarily over the dozens of fungal species examined, indicating conservation of such prion-like status. Examples of notable prion-like proteins that are highly conserved both in sequence and prion-like composition are discussed.

Waldl, Maria Of Theoretical Chemistry, Faculty Of Chemistry, University Of Vienna) - One of the best experts on this subject based on the ideXlab platform.

  • TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
    'MDPI AG', 2018
    Co-Authors: Waldl, Maria Of Theoretical Chemistry, Faculty Of Chemistry, University Of Vienna), Thiel, Bernhard Of Theoretical Chemistry, Faculty Of Chemistry, University Of Vienna), Ochsenreiter, Roman Of Theoretical Chemistry, Faculty Of Chemistry, University Of Vienna), Holzenleiter, Alexander Group, Fakultät Cb Hochschule Mittweida), De Araujo Oliveira, João De Ciência Da Computação, Instituto De Ciências Ex, Walter, Maria De Ciência Da Computação, Instituto De Ciências Ex, Stadler, Peter Of Theoretical Chemistry, Faculty Of Chemistry, University Of Vienna)
    Abstract:

    The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.© 2018 by the author

G. I. Naumov - One of the best experts on this subject based on the ideXlab platform.

  • Massive isolation and identification of Saccharomyces paradoxus yeasts from plant phyllosphere
    Microbiology, 2007
    Co-Authors: A. M. Glushakova, Yu. V. Ivannikova, E. S. Naumova, I. Yu. Chernov, G. I. Naumov
    Abstract:

    Year-round studies of epiphytic yeast communities revealed that the number of ascosporogenous yeasts of the genus Saccharomyces inhabiting living and decaying leaves of some plants increased considerably in certain short periods (at the beginning of summer and in winter). Massive isolation of Saccharomycetes was performed from 11 plant species; earlier, these yeasts had been revealed mainly in sugar-rich substrates. The isolates were identified as Saccharomyces paradoxus based on their physiological properties and RELP analysis of 5.8S-ITS. Possible reasons for short-term increases in the number of Saccharomycetes in plant phyllosphere are discussed.

  • Massive isolation and identification of Saccharomyces paradoxus yeasts from plant phyllosphere
    Mikrobiologiia, 2007
    Co-Authors: A. M. Glushakova, E. S. Naumova, Iu V Ivannikova, I Iu Chernov, G. I. Naumov
    Abstract:

    Year-round studies of epiphytic yeast communities revealed that the number of ascosporogenous yeasts of the genus Saccharomyces inhabiting living and decaying leaves of some plants increased considerably in certain short periods (at the beginning of summer and in winter). Massive isolation of Saccharomycetes was performed from 11 plant species; earlier, these yeasts had been revealed mainly in sugar-rich substrates. The isolates were identified as Saccharomyces paradoxus based on their physiological properties and the lengths of restriction fragments of 5.8S-ITS rDNA. Possible reasons for short-term increases in the number of Saccharomycetes in plant phyllosphere are discussed.

Peter F. Stadler - One of the best experts on this subject based on the ideXlab platform.

  • TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.
    Genes, 2018
    Co-Authors: Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor De Araujo Oliveira, Maria Emilia M. T. Walter, Michael T. Wolfinger, Peter F. Stadler
    Abstract:

    The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.