A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

Lu, Hongzhong; Kerkhoven, Eduard J.; Nielsen, Jakob Skov

doi:10.3390/biom12111632

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…Torulaspora indica reveals high antagonistic activity againt fungal phathogens that cause plant diseases; thus, it has potential to be effective biocontrol agent ( Konsue et al 2020 , Limtong et al 2020 ). The metabolic functionalities of genera, including Kluyveromyces , Lachancea and Ogataea , have been mapped ( Lertwattanasaku et al 2015 , Nanda et al 2020 , Kosaka et al 2022 , Lu et al 2022 ).…”

Section: Resultsmentioning

confidence: 99%

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Groenewald

Hittinger

Bensch

et al. 2023

Studies in Mycology

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The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.

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Section: Resultsmentioning

confidence: 99%

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Groenewald

Hittinger

Bensch

et al. 2023

Studies in Mycology

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“…Genome-wide computational models of yeast metabolism describe the salient features of yeast growth, which are simply modeled as an increase in total biomass 69,70 . These models excel in describing steady-state situations; however, because of their nature, they cannot provide an appropriate framework for the integration of metabolism with macromolecular synthesis, cell cycle, and division.…”

Section: Discussionmentioning

confidence: 99%

A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations

Vanoni,

Palumbo,

Papa

et al. 2023

Preprint

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SummaryFor unicellular organisms, the reproduction rate and growth are crucial determinants of fitness and, therefore, essential functional manifestations of the organism genotype. Using the budding yeastSaccharomyces cerevisiaeas a model organism, we integrated metabolism, which provides energy and building blocks for growth, with cell mass growth and cell cycle progression into a low-granularity, multiscale (from cell to population) computational model. This model predicted that cells with constitutive respiration do not modulate cell size according to the growth conditions. We experimentally validated the model predictions using mutants with defects in the upper part of glycolysis or glucose transport. Plugging in molecular details of cellular subsystems allowed us to refine predictions from the cellular to the molecular level. Our hybrid multiscale modeling approach provides a framework for structuring molecular knowledge and predicting cell phenotypes under various genetic and environmental conditions.

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“… 13 This pan-genome then serves as the basis for draft model reconstruction using tools like KBase 28 and CarveMe. 29 For instance, the pan-genome models of Propionibacterium , 30 Escherichia , 31 and yeast 32 , 33 have been reconstructed from their respective pan-genomes to investigate diverse and shared metabolic traits within a genus and understand strain-specific adaptations. However, this approach often necessitates extensive manual curation to address gaps and ensure model consistency.…”

Section: Introductionmentioning

confidence: 99%

Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models

Palanikumar,

Sinha,

Raman

2024

iScience

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A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

Cited by 6 publications

References 39 publications

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations

Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models

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