Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Funding Information: This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number DE-SC0018409; the National Science Foundation (under grant Nos. DBI-2305612 to K.T.D., DEB-2110403 to C.T.H., and DEB-2110404 to A.R.); and the National Institute of Food and Agriculture, United States Department of Agriculture, Hatch project 7005101. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in the Rokas lab is also supported by the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Welcome Fund. Publisher Copyright: © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.publishersversionpublishe

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

Funding Information: We want to thank Barbara Roberts from the NCBI Taxonomy Team for providing the update of the current fungal names in NCBI Taxonomic database. Masako Takashima is supported by the Institution for Fermentation, Osaka (IFO). Heide-Marie Daniel is supported by the Belgian Science Policy Office grant C5/00/BCCM. Chris Todd Hittinger is supported by the National Science Foundation under Grant Nos. DEB-1442148 and DEB-2110403, the USDA National Institute of Food and Agriculture (Hatch Project 1020204), in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE–SC0018409, and an H.I. Romnes Faculty Fellowship, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in Antonis Rokas’s lab is supported by grants from the National Science Foundation (DEB-1442113 and DEB-2110404), the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. Antonis Rokas acknowledges support from a Klaus Tschira Guest Professorship from the Heidelberg Institute for Theoretical Studies and from a Visiting Research Fellowship from Merton College of the University of Oxford. Marc-André Lachance acknowledges lifelong financial support from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Carlos A. Rosa is supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – Brazil, process numbers 408733/2021-7 and 406564/2022-1); Fundação do Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG, process numberAPQ-01525-14). Teun Boekhout is supported by the Distinguished Scientist Fellow Program of King Saud University, Ryadh, Saudi Arabia. Publisher Copyright: © 2023 Westerdijk Fungal Biodiversity Institute.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.publishersversionpublishe

The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence

Funding: This work was funded by the European Research Council [http://erc.europa.eu/], AJPB (STRIFE Advanced Grant; C-2009-AdG-249793). The work was also supported by: the Wellcome Trust [www.wellcome.ac.uk], AJPB (080088, 097377); the UK Biotechnology and Biological Research Council [www.bbsrc.ac.uk], AJPB (BB/F00513X/1, BB/K017365/1); the CNPq-Brazil [http://cnpq.br], GMA (Science without Borders fellowship 202976/2014-9); and the National Centre for the Replacement, Refinement and Reduction of Animals in Research [www.nc3rs.org.uk], DMM (NC/K000306/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We thank Dr. Elizabeth Johnson (Mycology Reference Laboratory, Bristol) for providing strains, and the Aberdeen Proteomics facility for the biotyping of S. cerevisiae clinical isolates, and to Euroscarf for providing S. cerevisiae strains and plasmids. We are grateful to our Microscopy Facility in the Institute of Medical Sciences for their expert help with the electron microscopy, and to our friends in the Aberdeen Fungal Group for insightful discussions.Peer reviewedPublisher PD

Into the wild: new yeast genomes from natural environments and new tools for their analysis

This is a pre-copyedited, author-produced version of an article accepted for publication in FEMS Yeast Research following peer review. The version of record "D Libkind, D Peris, F A Cubillos, J L Steenwyk, D A Opulente, Q K Langdon, A Rokas, C T Hittinger, Into the wild: new yeast genomes from natural environments and new tools for their analysis, FEMS Yeast Research, Volume 20, Issue 2, March 2020, foaa008" is available online at: https://doi.org/10.1093/femsyr/foaa008Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.DL has been funded through CONICET (PIP11220130100392CO) and Universidad Nacional del Comahue (B199). Research in AR's lab has been funded through a National Science Foundation grant (DEB-1442113); JLS and AR have also received funding by the Howard Hughes Medical Institute through the James H. Gilliam Fellowships for Advanced Study program. CTH has been funded through the National Science Foundation (DEB-1442148), USDA National Institute of Food and Agriculture (Hatch Project 1020204), and DOE Great Lakes Bioenergy Research Center (DE-SC0018409). CTH is a Pew Scholar in the Biomedical Sciences and a H. I. Romnes Faculty Fellow, supported by the Pew Charitable Trusts and Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation, respectively. DP is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 747775).Peer reviewe

Nonlinear fitness consequences of variation in expression level of a eukaryotic gene

Levels of gene expression show considerable variation in eukaryotes, but no fine-scale maps have been made of the fitness consequences of such variation in controlled genetic backgrounds and environments. To address this, we assayed fitness at many levels of up- and down-regulated expression of a single essential gene, LCB2, involved in sphingolipid synthesis in budding yeast Saccharomyces cerevisiae. Reduced LCB2 expression rapidly decreases cellular fitness, yet increased expression has little effect. The wild-type expression level is therefore perched on the edge of a nonlinear fitness cliff. LCB2 is upregulated when cells are exposed to osmotic stress; consistent with this, the entire fitness curve is shifted upward to higher expression under osmotic stress, illustrating the selective force behind gene regulation. Expression levels of LCB2 are lower in wild yeast strains than in the experimental lab strain, suggesting that higher levels in the lab strain may be idiosyncratic. Reports indicate that the effect sizes of alleles contributing to variation in complex phenotypes differ among environments and genetic backgrounds; our results suggest that such differences may be explained as simple shifts in the position of nonlinear fitness curves