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Functional and Evolutionary Characterization of a Secondary Metabolite Gene Cluster in Budding Yeasts

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Functional and Evolutionary Characterization of a Secondary Metabolite Gene Cluster in Budding Yeasts Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts David J. Krausea,b,c,d, Jacek Komineka,b,c,d, Dana A. Opulentea,b,c,d, Xing-Xing Shene, Xiaofan Zhoue, Quinn K. Langdona,b,c, Jeremy DeVirgiliof, Amanda Beth Hulfachora,b,c, Cletus P. Kurtzmanf,1, Antonis Rokase, and Chris Todd Hittingera,b,c,d,2 aLaboratory of Genetics, Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI 53706; bWisconsin Energy Institute, University of Wisconsin–Madison, Madison, WI 53706; cJ. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI 53706; dDOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI 53706; eDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235; and fMycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604 Edited by Jasper Rine, University of California, Berkeley, CA, and approved September 19, 2018 (received for review April 11, 2018) Secondary metabolites are key in how organisms from all domains role of pulcherrimin is not well understood, but several studies of life interact with their environment and each other. The iron- have shown it to mediate interspecific antagonistic interactions, binding molecule pulcherrimin was described a century ago, but possibly due to its ability to sequester ferric iron from the growth the genes responsible for its production in budding yeasts have medium (14–16). The ability to sequester free iron from the remained uncharacterized. Here, we used phylogenomic foot- environment from competitors could be counterproductive if the printing on 90 genomes across the budding yeast subphylum producer species were also unable to utilize the pulcherrimin- Saccharomycotina to identify the gene cluster associated with bound iron, raising the possibility that pulcherrimin producers pulcherrimin production. Using targeted gene replacements in can also reutilize the compound as a siderophore. Pulcherrimin Kluyveromyces lactis, we characterized the four genes that make may not be the only secondary metabolite produced by budding up the cluster, which likely encode two pulcherriminic acid bio- yeasts; there is evidence for ferrichrome production by some synthesis enzymes, a pulcherrimin transporter, and a transcription Lipomyces and Dipodascopsis spp. (17), but the genes responsible factor involved in both biosynthesis and transport. The require- for production of both secondary metabolites in yeasts are un- ment of a functional putative transporter to utilize extracellular known. Biochemical work in the pulcherrimin-producing bacte- pulcherrimin-complexed iron demonstrates that pulcherriminic rium Bacillus subtilis has characterized a two-step biosynthetic acid is a siderophore, a chelator that binds iron outside the cell pathway: Two leucine molecules are cyclized via a CDPS, and for subsequent uptake. Surprisingly, we identified homologs of the resulting diketopiperazine is oxidized by a cytochrome P450 oxidase to generate pulcherriminic acid (PA), which can then the putative transporter and transcription factor genes in multiple – yeast genera that lacked the biosynthesis genes and could not spontaneously bind iron to form pulcherrimin (18 20). The make pulcherrimin, including the model yeast Saccharomyces cer- formation of diketopiperazines, such as the cyclo-Leu-Leu pre- evisiae. We deleted these previously uncharacterized genes and cursor to PA, is often catalyzed by biochemical pathways con- showed they are also required for pulcherrimin utilization in S. taining NRPS or CDPS proteins (21). Thus, the absence of known homologs of these genes in budding yeasts raises the cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Phylogenetic analy- ses of this gene cluster suggest that pulcherrimin biosynthesis and Significance utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many Evolutionary and comparative genomics, combined with reverse lineages, mirroring other microbial public goods systems that lead genetics, have the power to identify and characterize new bi- to the rise of cheater organisms. ology. Here, we use these approaches in several nontraditional model species of budding yeasts to characterize a budding yeast secondary metabolism | gene cluster | siderophore | budding yeasts | secondary metabolite gene cluster, a set of genes responsible cyclodipeptide synthase for production and reutilization of the siderophore pulcherrimin. We also use this information to assign roles in pulcherrimin Saccharomyces he production of secondary metabolites is found in organisms utilization for two previously uncharacterized cerevisiae Tfrom all domains of life (1–3). Fungi are particularly well genes. The evolution of this gene cluster in budding known for their production of secondary metabolites, whose yeasts suggests an ecological role for pulcherrimin akin to other functions can include antibiotics, virulence factors, pigments, microbial public goods systems. toxins, quorum-sensing molecules, and siderophores (chelators Author contributions: D.J.K., C.P.K., A.R., and C.T.H. designed research; D.J.K., D.A.O., and produced by organisms to capture extracellular iron) (3, 4). Q.K.L. performed research; D.J.K., J.K., D.A.O., Q.K.L., J.D., and A.B.H. contributed new These molecules are generally synthesized by proteins encoded reagents/analytic tools; D.J.K., J.K., X.-X.S., and X.Z. analyzed data; and D.J.K. and C.T.H. in gene clusters, typically containing a synthase protein belonging wrote the paper. to one of several families: a nonribosomal peptide synthetase The authors declare no conflict of interest. (NRPS), polyketide synthase (PKS), terpene cyclase, dimethy- This article is a PNAS Direct Submission. lallyl tryptophan synthetase, or cyclodipeptide synthase (CDPS) Published under the PNAS license. – (2, 5 7). The absence of known genes encoding any of these Data deposition: Genome assemblies for Zygotorulaspora mrakii, Zygotorulaspora florentina, functions in sequenced budding yeast genomes has precluded an Kluyveromyces nonfermentans,andKomagataella pseudopastoris can be found under Na- understanding of secondary metabolism in the budding yeast tional Center for Biotechnology Information (NCBI) accession nos. PPHZ00000000, subphylum Saccharomycotina (8). PPJY00000000, PPKX00000000, and QYLQ00000000. The pigment pulcherrimin has long been known to be syn- 1Deceased November 27, 2017. thesized by a small number of budding yeast species, including 2To whom correspondence should be addressed. Email: [email protected]. various Metschnikowia spp. and some Kluyveromyces spp. (9–12). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. Pulcherrimin is a red iron-containing pigment composed of two 1073/pnas.1806268115/-/DCSupplemental. cyclized and modified leucine molecules (13). The ecological Published online October 8, 2018. 11030–11035 | PNAS | October 23, 2018 | vol. 115 | no. 43 www.pnas.org/cgi/doi/10.1073/pnas.1806268115 Downloaded by guest on September 28, 2021 possibilities of highly divergent homologs or novel biochemical homologs of this protein and found significant hits (e < 0.001) in pathways for pulcherrimin production. the genomes of several Kluyveromyces spp., Candida auris, and Here, we use a comparative genomic approach to identify a Metschnikowia fructicola. putative gene cluster involved in pulcherrimin production. Using Among these species, we also found conservation of three targeted gene replacements in Kluyveromyces lactis, we charac- genes surrounding the cytochrome P450 oxidase homolog, terize this four-gene cluster, finding genes responsible for the hereafter termed the PUL (PULcherrimin) gene cluster, with biosynthesis and reutilization of pulcherrimin. We also find that genes labeled PUL1-4 (Fig. 1 and SI Appendix, Fig. S1). In ad- several species, including Saccharomyces cerevisiae, contain a dition to K. lactis (10), Kluyveromyces aestuarii and M. fructicola partial gene cluster comprised of only the two utilization genes. had been described as producing pulcherrimin (11, 12). We se- Using targeted gene replacements in S. cerevisiae, we assign quenced the genomes of two more budding yeast species: one functions and standard names to these previously uncharacterized previously described as producing an unknown red pigment, genes. Finally, we infer that the gene cluster was ancestral to all Zygotorulaspora mrakii (26), from which we identified a PUL budding yeasts, but repeated gene loss led to its patchy species gene cluster; one from the other recognized species of this genus, distribution, as well as to the rise of cheater organisms that exploit Zygotorulaspora florentina, a nonpigmented strain that did not the public good of pulcherrimin without the cost of production. contain a complete PUL cluster. Thus, in each of the three genera, Kluyveromyces, Metschnikowia, and Zygotorulaspora,we Results found that red-pigmented species always have complete PUL A Secondary Metabolite Gene Cluster Is Responsible for Production of clusters, whereas species lacking the complete PUL cluster were the Siderophore Pulcherrimin. Pulcherrimin biosynthesis in B. never pigmented (Fig. 1). A handful of species have complete subtilis
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