skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

Abstract

Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. In this study, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae. We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Lastly, phylogeneticmore » analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.« less

Authors:
 [1];  [1];  [1];  [2];  [2];  [1];  [3];  [1];  [3]; ORCiD logo [2]; ORCiD logo [1]
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. Vanderbilt Univ., Nashville, TN (United States)
  3. US Department of Agriculture, Peoria, IL (United States)
Publication Date:
Research Org.:
Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Org.:
University of Wisconsin Biotechnology Center
OSTI Identifier:
1506646
Grant/Contract Number:  
SC0018409; FC02-07ER64494
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 43; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; secondary metabolism; gene cluster; siderophore; budding yeasts; cyclodipeptide synthase

Citation Formats

Krause, David J., Kominek, Jacek, Opulente, Dana A., Shen, Xing-Xing, Zhou, Xiaofan, Langdon, Quinn K., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Kurtzman, Cletus P., Rokas, Antonis, and Hittinger, Chris Todd. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. United States: N. p., 2018. Web. doi:10.1073/pnas.1806268115.
Krause, David J., Kominek, Jacek, Opulente, Dana A., Shen, Xing-Xing, Zhou, Xiaofan, Langdon, Quinn K., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Kurtzman, Cletus P., Rokas, Antonis, & Hittinger, Chris Todd. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. United States. doi:10.1073/pnas.1806268115.
Krause, David J., Kominek, Jacek, Opulente, Dana A., Shen, Xing-Xing, Zhou, Xiaofan, Langdon, Quinn K., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Kurtzman, Cletus P., Rokas, Antonis, and Hittinger, Chris Todd. Mon . "Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts". United States. doi:10.1073/pnas.1806268115. https://www.osti.gov/servlets/purl/1506646.
@article{osti_1506646,
title = {Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts},
author = {Krause, David J. and Kominek, Jacek and Opulente, Dana A. and Shen, Xing-Xing and Zhou, Xiaofan and Langdon, Quinn K. and DeVirgilio, Jeremy and Hulfachor, Amanda Beth and Kurtzman, Cletus P. and Rokas, Antonis and Hittinger, Chris Todd},
abstractNote = {Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. In this study, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae. We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Lastly, phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.},
doi = {10.1073/pnas.1806268115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 43,
volume = 115,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 12 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: The PUL gene cluster and its phylogenetic distribution. The genome-scale cladogram was constructed using alignments of 1,037 conserved BUSCO genes with newly sequenced genomes in bold. Collapsed clades with multiple ($N$) species are shown as triangles, and the complete tree, with bootstrap values, is shown in SI Appendix,more » Fig. S1. Red filled boxes indicate pulcherrimin production has been observed in that species, and filled boxes for PUL1-4 indicate presence or absence of the corresponding PUL gene. Gene arrow diagrams show the arrangement of the four PUL genes in representative species that produce pulcherrimin. The gene table contains putative annotations for the four genes prior to this study.« less

Save / Share:

Works referenced in this record:

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching
journal, October 2016

  • Dejong, Chris A.; Chen, Gregory M.; Li, Haoxin
  • Nature Chemical Biology, Vol. 12, Issue 12
  • DOI: 10.1038/nchembio.2188

Siderophores: Structure and Function of Microbial Iron Transport Compounds
journal, November 1995


Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus
journal, July 2005


Ferrichrome Production by Lipomycetaceae
journal, May 1990


Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
journal, September 2016

  • Shen, Xing-Xing; Zhou, Xiaofan; Kominek, Jacek
  • G3: Genes|Genomes|Genetics, Vol. 6, Issue 12
  • DOI: 10.1534/g3.116.034744

Metschnikowia : half tetrads, a regicide and the fountain of youth : Metschnikowia
journal, October 2016


Likelihood-Based Tests of Topologies in Phylogenetics
journal, December 2000


Regularization and variable selection via the elastic net
journal, April 2005


Iron uptake in fungi: A system for every source
journal, July 2006


Pulcherrimin, The Pigment of Candida Pulcherrima
journal, July 1953

  • Kluyver, A. J.; van der Walt, J. P.; van Triet, A. J.
  • Proceedings of the National Academy of Sciences, Vol. 39, Issue 7
  • DOI: 10.1073/pnas.39.7.583

Isolation and Characterization of New Metschnikowia pulcherrima Strains as Producers of the Antimicrobial Pigment Pulcherrimin
journal, June 2009

  • Türkel, Sezai; Ener, Beyza
  • Zeitschrift für Naturforschung C, Vol. 64, Issue 5-6
  • DOI: 10.1515/znc-2009-5-618

SMURF: Genomic mapping of fungal secondary metabolite clusters
journal, September 2010

  • Khaldi, Nora; Seifuddin, Fayaz T.; Turner, Geoff
  • Fungal Genetics and Biology, Vol. 47, Issue 9
  • DOI: 10.1016/j.fgb.2010.06.003

A global genetic interaction network maps a wiring diagram of cellular function
journal, September 2016


Biosynthesis of pulcherriminic acid
journal, August 1965


Metschnikowia Strains Isolated from Botrytized Grapes Antagonize Fungal and Bacterial Growth by Iron Depletion
journal, August 2006


Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts
journal, May 2010


Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics
journal, January 2007

  • Donadio, Stefano; Monciardini, Paolo; Sosio, Margherita
  • Natural Product Reports, Vol. 24, Issue 5
  • DOI: 10.1039/b514050c

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
journal, April 2017

  • Blin, Kai; Wolf, Thomas; Chevrette, Marc G.
  • Nucleic Acids Research, Vol. 45, Issue W1
  • DOI: 10.1093/nar/gkx319

Ergosterol biosynthesis inSaccharomyces cerevisiae: Mutants deficient in the early steps of the pathway
journal, January 1977

  • Karst, Francis; Lacroute, Fran�ois
  • MGG Molecular & General Genetics, Vol. 154, Issue 3
  • DOI: 10.1007/BF00571282

The Prisoner's Dilemma and polymorphism in yeast SUC genes
journal, February 2004

  • Greig, Duncan; Travisano, Michael
  • Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 271, Issue suppl_3
  • DOI: 10.1098/rsbl.2003.0083

The Evolution of Fungal Metabolic Pathways
journal, December 2014


Tentative biosynthetic pathways of some microbial diketopiperazines
journal, August 2013

  • Gu, Binbin; He, Shan; Yan, Xiaojun
  • Applied Microbiology and Biotechnology, Vol. 97, Issue 19
  • DOI: 10.1007/s00253-013-5175-4

Regulation and Role of Fungal Secondary Metabolites
journal, November 2016


Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships
journal, January 2010


Kluyveromyces aestuarii, a potential environmental quality indicator yeast for mangroves in the State of Rio de Janeiro, Brazil
journal, January 2011


Fungal secondary metabolism — from biochemistry to genomics
journal, December 2005

  • Keller, Nancy P.; Turner, Geoffrey; Bennett, Joan W.
  • Nature Reviews Microbiology, Vol. 3, Issue 12, p. 937-947
  • DOI: 10.1038/nrmicro1286

Combinatorial biosynthesis of reduced polyketides
journal, December 2005

  • Weissman, Kira J.; Leadlay, Peter F.
  • Nature Reviews Microbiology, Vol. 3, Issue 12
  • DOI: 10.1038/nrmicro1287

Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog
journal, February 2011

  • Bonnefond, L.; Arai, T.; Sakaguchi, Y.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
  • DOI: 10.1073/pnas.1019480108

High-resolution DNA-binding specificity analysis of yeast transcription factors
journal, January 2009

  • Zhu, C.; Byers, K. J. R. P.; McCord, R. P.
  • Genome Research, Vol. 19, Issue 4
  • DOI: 10.1101/gr.090233.108

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations
journal, November 2012

  • Cordero, O. X.; Ventouras, L. -A.; DeLong, E. F.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 49
  • DOI: 10.1073/pnas.1213344109

Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities
journal, September 2017


Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species
journal, March 2015

  • Sylvester, Kayla; Wang, Qi-Ming; James, Brielle
  • FEMS Yeast Research, Vol. 15, Issue 3
  • DOI: 10.1093/femsyr/fov002

An Approximately Unbiased Test of Phylogenetic Tree Selection
journal, May 2002


Cyclodipeptide synthases are a family of tRNA-dependent peptide bond–forming enzymes
journal, May 2009

  • Gondry, Muriel; Sauguet, Ludovic; Belin, Pascal
  • Nature Chemical Biology, Vol. 5, Issue 6
  • DOI: 10.1038/nchembio.175

Genomics and the making of yeast biodiversity
journal, December 2015

  • Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan
  • Current Opinion in Genetics & Development, Vol. 35
  • DOI: 10.1016/j.gde.2015.10.008

Fungal metabolic gene clusters—caravans traveling across genomes and environments
journal, March 2015


The sirodesmin biosynthetic gene cluster of the plant pathogenic fungus Leptosphaeria maculans
journal, July 2004


Biosynthesis of Nonribosomal Peptides
journal, October 2004


Horizontal gene transfer in fungi
journal, December 2011


The genetics of a putative social trait in natural populations of yeast
journal, October 2014

  • Bozdag, G. O.; Greig, D.
  • Molecular Ecology, Vol. 23, Issue 20
  • DOI: 10.1111/mec.12904

Efficient gene targeting inKluyveromyces lactis
journal, July 2004

  • Kooistra, Rolf; Hooykaas, Paul J. J.; Steensma, H. Yde
  • Yeast, Vol. 21, Issue 9
  • DOI: 10.1002/yea.1131

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network
journal, March 2017

  • Usaj, Matej; Tan, Yizhao; Wang, Wen
  • G3: Genes|Genomes|Genetics, Vol. 7, Issue 5
  • DOI: 10.1534/g3.117.040220

Gene duplication and the adaptive evolution of a classic genetic switch
journal, October 2007

  • Hittinger, Chris Todd; Carroll, Sean B.
  • Nature, Vol. 449, Issue 7163
  • DOI: 10.1038/nature06151

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118
journal, September 2009

  • Novo, M.; Bigey, F.; Beyne, E.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
  • DOI: 10.1073/pnas.0904673106

Antimicrobial activity of Metschnikowia pulcherrima on wine yeasts
journal, February 2014

  • Oro, L.; Ciani, M.; Comitini, F.
  • Journal of Applied Microbiology, Vol. 116, Issue 5
  • DOI: 10.1111/jam.12446

Zygosaccharomyces mrakii nova species: A new yeast from silage
journal, January 1958


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea
journal, January 2015


    Works referencing / citing this record:

    Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm
    journal, June 2019

    • Arnaouteli, Sofia; Matoz-Fernandez, D. A.; Porter, Michael
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
    • DOI: 10.1073/pnas.1903982116

    Fungal evolution: major ecological adaptations and evolutionary transitions
    journal, April 2019

    • Naranjo‐Ortiz, Miguel A.; Gabaldón, Toni
    • Biological Reviews
    • DOI: 10.1111/brv.12510

    Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm
    journal, June 2019

    • Arnaouteli, Sofia; Matoz-Fernandez, D. A.; Porter, Michael
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
    • DOI: 10.1073/pnas.1903982116

    Fungal evolution: major ecological adaptations and evolutionary transitions
    journal, April 2019

    • Naranjo‐Ortiz, Miguel A.; Gabaldón, Toni
    • Biological Reviews
    • DOI: 10.1111/brv.12510

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.