Structure, function, and evolution of the Cryptococcus MAT locus

Summary

Principal Investigator: Joseph Heitman
Abstract: Cryptococcus neoformans is a fungal pathogen that infects the human brain. The organism has a defined sexual cycle involving haploid and a strains, and the mating-type is linked to virulence and differentiation. Most environmental and clinical isolates are mating-type, and strains can be more virulent than congenic a strains and preferentially penetrate the CNS during co-infection with a strains by a process involving pheromone signaling similar to quorum sensing in bacteria and other fungi. strains also undergo monokaryotic fruiting and produce basidiospores via a modified sexual cycle. Thus, the structure, function, and evolution of the mating-type locus (MAT) and its links to sexual development, virulence, and ecology are of considerable interest. In studies supported by this award, in aim 1 the MAT locus was cloned, sequenced, and annotated from both mating-types and four divergent Cryptococcus species/varieties, leading to a detailed evolutionary model. In aim 2 on MAT functions, the MAT allele specific genes SXI1 and SXI2a were shown to encode homeodomain proteins that establish cell identity and enable sexual reproduction. MAT encoded genes were shown to play roles in sexual reproduction, virulence, and essential functions. In aim 3 PCR fingerprinting and a MAT locus microarray were developed and provide comparative genomic analysis approaches to elucidate MAT structure and evolution. This progress, combined with recent advances involving genome sequences, microarrays, and discovery of fertile strains and development of congenic strains, allows us to propose new hypotheses and aims. Four interrelated specific aims are proposed. Aim 1 focuses on the sequence of MAT, and extends the analysis to all molecular and mating-types. We propose to sequence MAT from species related to the Cryptococcus pathogenic species cluster;preliminary results indicate this will reveal key evolutionary events that fashioned this large gene complex. Studies to recreate and analyze the hypothesized tripolar intermediate and tetrapolar ancestor by reconfiguring the genomic location of the SXI1/2 genes are also proposed. Aim 2 focuses on the functions of MAT, including roles of pheromones and Ste3 receptor homologs in virulence via processes similar to quorum sensing. Aim 3 focuses on the structure and function of MAT-linked recombinational activators, proposed to have played key roles in MAT origins and evolution. Aim 4 will focus on the structure and evolution of the MAT locus by CGH analysis. These studies will expand understanding of this unique genomic region and its roles in virulence, and serve as a paradigm for gene cluster and sex chromosome evolution and function.
Funding Period: 2001-07-01 - 2014-11-30
more information: NIH RePORT

Top Publications

  1. pmc Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation
    Guilhem Janbon
    Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France INRA, USC2019, Paris, France
    PLoS Genet 10:e1004261. 2014
  2. pmc Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides
    Charles H Li
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Pathog 7:e1002086. 2011
  3. pmc Cryptococcus gattii: an emerging fungal pathogen infecting humans and animals
    Edmond J Byrnes
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    Microbes Infect 13:895-907. 2011
  4. pmc Profiling a killer, the development of Cryptococcus neoformans
    Lukasz Kozubowski
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    FEMS Microbiol Rev 36:78-94. 2012
  5. pmc Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts
    C A D'Souza
    The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
    MBio 2:e00342-10. 2011
  6. pmc Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
    Anke Burmester
    Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Beutenbergstrasse 11a, Jena, 07745, Germany
    Genome Biol 12:R7. 2011
  7. pmc Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex
    Andrii P Gryganskyi
    Department of Biology, Duke University, Durham, North Carolina, United States of America
    PLoS ONE 5:e15273. 2010
  8. pmc Evolution of eukaryotic microbial pathogens via covert sexual reproduction
    Joseph Heitman
    Department of Molecular Genetics and Microbiology, Center for Microbial Pathogenesis, Duke University Medical Center, Durham, NC 27710, USA
    Cell Host Microbe 8:86-99. 2010
  9. pmc Cryptococcal cell morphology affects host cell interactions and pathogenicity
    Laura H Okagaki
    Department of Microbiology, Medical School, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS Pathog 6:e1000953. 2010
  10. pmc The evolution of sex: a perspective from the fungal kingdom
    Soo Chan Lee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Microbiol Mol Biol Rev 74:298-340. 2010

Research Grants

Detail Information

Publications54

  1. pmc Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation
    Guilhem Janbon
    Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France INRA, USC2019, Paris, France
    PLoS Genet 10:e1004261. 2014
    ..The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence. ..
  2. pmc Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides
    Charles H Li
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Pathog 7:e1002086. 2011
    ..circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex...
  3. pmc Cryptococcus gattii: an emerging fungal pathogen infecting humans and animals
    Edmond J Byrnes
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    Microbes Infect 13:895-907. 2011
    ..Infections in patients and animals can be severe and often fatal if untreated. We review the molecular epidemiology, population structure, clinical manifestations, and ecological niche of this emerging pathogen...
  4. pmc Profiling a killer, the development of Cryptococcus neoformans
    Lukasz Kozubowski
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    FEMS Microbiol Rev 36:78-94. 2012
    ..Recent studies have led to the emergence of many intriguing questions and hypotheses. In this review, we describe and discuss the most interesting aspects of C. neoformans development and address their impact on pathogenicity...
  5. pmc Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts
    C A D'Souza
    The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
    MBio 2:e00342-10. 2011
    ..gattii and the C. neoformans genomes. Finally, CGH revealed considerable variation in clinical and environmental isolates as well as changes in chromosome copy numbers in C. gattii isolates displaying fluconazole heteroresistance...
  6. pmc Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
    Anke Burmester
    Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Beutenbergstrasse 11a, Jena, 07745, Germany
    Genome Biol 12:R7. 2011
    ....
  7. pmc Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex
    Andrii P Gryganskyi
    Department of Biology, Duke University, Durham, North Carolina, United States of America
    PLoS ONE 5:e15273. 2010
    ..oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species...
  8. pmc Evolution of eukaryotic microbial pathogens via covert sexual reproduction
    Joseph Heitman
    Department of Molecular Genetics and Microbiology, Center for Microbial Pathogenesis, Duke University Medical Center, Durham, NC 27710, USA
    Cell Host Microbe 8:86-99. 2010
    ..Mating-type loci govern fungal sexual identity; how parasites establish sexual identity is unknown. Comparing and contrasting fungal and parasite sex promises to reveal how microbial pathogens evolved and are evolving...
  9. pmc Cryptococcal cell morphology affects host cell interactions and pathogenicity
    Laura H Okagaki
    Department of Microbiology, Medical School, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS Pathog 6:e1000953. 2010
    ..neoformans evades host phagocytosis to allow survival of a subset of the population at early stages of infection. Thus, morphological changes play unique and specialized roles during infection...
  10. pmc The evolution of sex: a perspective from the fungal kingdom
    Soo Chan Lee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Microbiol Mol Biol Rev 74:298-340. 2010
    ....
  11. pmc The mating type locus (MAT) and sexual reproduction of Cryptococcus heveanensis: insights into the evolution of sex and sex-determining chromosomal regions in fungi
    Banu Metin
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Genet 6:e1000961. 2010
    ..These studies provide insight into convergent processes that independently punctuated evolution of sex-determining loci and sex chromosomes in fungi, plants, and animals...
  12. pmc Is sex necessary?
    Sheng Sun
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    BMC Biol 9:56. 2011
    ..However, presumed asexual species may also be cryptically sexual, as revealed by other recent studies...
  13. pmc A diverse population of Cryptococcus gattii molecular type VGIII in southern Californian HIV/AIDS patients
    Edmond J Byrnes
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Pathog 7:e1002205. 2011
    ..gattii molecular types influencing infection of immunocompetent (VGI/VGII) vs. immunocompromised (VGIII/VGIV) hosts...
  14. pmc Sex in fungi
    Min Ni
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Annu Rev Genet 45:405-30. 2011
    ..As robust and diverse genetic models, fungi provide insights into the molecular nature of sex, sexual specification, and evolution to advance our understanding of sexual reproduction and its impact throughout the eukaryotic tree of life...
  15. pmc Ordered kinetochore assembly in the human-pathogenic basidiomycetous yeast Cryptococcus neoformans
    Lukasz Kozubowski
    Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
    MBio 4:e00614-13. 2013
    ..Taken together, the results of this study demonstrate that kinetochore dynamics in C. neoformans is reminiscent of that of metazoans and shed new light on the evolution of mitosis in eukaryotes...
  16. pmc Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans
    Min Ni
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Biol 11:e1001653. 2013
    ....
  17. pmc Molecular and genetic evidence for a tetrapolar mating system in the basidiomycetous yeast Kwoniella mangrovensis and two novel sibling species
    Marco A Guerreiro
    Centro de Recursos Microbiológicos CREM, Departamento de Ciências da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
    Eukaryot Cell 12:746-60. 2013
    ....
  18. pmc Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis
    Anastasia Gioti
    Science for Life Laboratory, Translational Immunology Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
    MBio 4:e00572-12. 2013
    ..We further present evidence that M. sympodialis may have the capacity to undergo sexual reproduction and present a model for a pseudobipolar mating system that allows limited recombination between two linked MAT loci...
  19. pmc Should Y stay or should Y go: the evolution of non-recombining sex chromosomes
    Sheng Sun
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    Bioessays 34:938-42. 2012
    ..We also discuss potential insights gained on the evolution of sex-determining chromosomes by studying simpler sex-determining chromosomal regions of unicellular and multicellular microorganisms...
  20. pmc Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction
    Sheng Sun
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Genet 8:e1002810. 2012
    ..We discuss the implications of these findings with regards to the possible functional and evolutionary importance of gene conversion within the C. neoformans MAT locus and, more generally, in fungi...
  21. pmc Discovery of a modified tetrapolar sexual cycle in Cryptococcus amylolentus and the evolution of MAT in the Cryptococcus species complex
    Keisha Findley
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Genet 8:e1002528. 2012
    ....
  22. pmc Know your enemy: how to build and vanquish a global fungal scourge
    Xuying Wang
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mycopathologia 173:295-301. 2012
    ..With more than 250 participants, this meeting was the largest gathering of the Cryptococcus international community in the 24-year history. Here, we review the advances presented and the current state of knowledge in the field...
  23. pmc Transcription factors Mat2 and Znf2 operate cellular circuits orchestrating opposite- and same-sex mating in Cryptococcus neoformans
    Xiaorong Lin
    Department of Biology, Texas A and M University, College Station, Texas, United States of America
    PLoS Genet 6:e1000953. 2010
    ..Further characterization of these elements and their target circuits will reveal genes controlling biological processes central to fungal development and virulence...
  24. pmc Evolution of the sex-related locus and genomic features shared in microsporidia and fungi
    Soo Chan Lee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS ONE 5:e10539. 2010
    ..Recent phylogenetic studies and gene order analysis suggest that microsporidia share a particularly close evolutionary relationship with the zygomycetes...
  25. pmc Transitions in sexuality: recapitulation of an ancestral tri- and tetrapolar mating system in Cryptococcus neoformans
    Yen Ping Hsueh
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Eukaryot Cell 7:1847-55. 2008
    ....
  26. pmc Impact of mating type, serotype, and ploidy on the virulence of Cryptococcus neoformans
    Xiaorong Lin
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Infect Immun 76:2923-38. 2008
    ..This study provides insights into the impact of ploidy, mating type, and serotype on virulence and the impact of hybridization on the fitness and virulence of a eukaryotic microbial pathogen...
  27. pmc Amt2 permease is required to induce ammonium-responsive invasive growth and mating in Cryptococcus neoformans
    Julian C Rutherford
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham NC 27710, USA
    Eukaryot Cell 7:237-46. 2008
    ..We propose that Amt2 may be a new fungal ammonium sensor and an element of the signaling cascades that govern the mating of C. neoformans in response to environmental nutritional cues...
  28. ncbi The human fungal pathogen Cryptococcus can complete its sexual cycle during a pathogenic association with plants
    Chaoyang Xue
    Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
    Cell Host Microbe 1:263-73. 2007
    ..These findings reveal that Cryptococcus can parasitically interact with plants to complete its sexual cycle, which may impact an understanding of the origin and evolution of both plant and animal fungal pathogens in nature...
  29. pmc alpha AD alpha hybrids of Cryptococcus neoformans: evidence of same-sex mating in nature and hybrid fitness
    Xiaorong Lin
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
    PLoS Genet 3:1975-90. 2007
    ..These findings provide insights on the origins, genetic mechanisms, and fitness impact of unisexual hybridization in the Cryptococcus population...
  30. pmc Many globally isolated AD hybrid strains of Cryptococcus neoformans originated in Africa
    Anastasia P Litvintseva
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Pathog 3:e114. 2007
    ....
  31. pmc Cryptococcus neoformans mates on pigeon guano: implications for the realized ecological niche and globalization
    Kirsten Nielsen
    Department of Molecular Genetics and Microbiology, Research Drive, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 6:949-59. 2007
    ..gattii. Based on these studies, we hypothesize that an ancestral Cryptococcus strain gained the ability to sexually reproduce in pigeon guano and then swept the globe...
  32. pmc Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii
    James A Fraser
    Department of Molecular Genetics and Microbiology, 322 CARL Building, Research Drive, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 6:622-9. 2007
    ....
  33. pmc Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation
    Xiaorong Lin
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Genet 2:e187. 2006
    ..Further characterization of these QTL regions will reveal additional quantitative trait genes controlling biological processes central to fungal development and pathogenicity...
  34. pmc Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome
    Yen Ping Hsueh
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Genet 2:e184. 2006
    ..Our findings suggest that during meiosis the MAT locus may be exchanged onto different genetic backgrounds and therefore have broad evolutionary implications with respect to mating-type switching in both model and pathogenic yeasts...
  35. ncbi Yeast diversity sampling on the San Juan Islands reveals no evidence for the spread of the Vancouver Island Cryptococcus gattii outbreak to this locale
    James A Fraser
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    FEMS Yeast Res 6:620-4. 2006
    ....
  36. pmc Magnificent seven: roles of G protein-coupled receptors in extracellular sensing in fungi
    Chaoyang Xue
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    FEMS Microbiol Rev 32:1010-32. 2008
    ..We also emphasize the utility of yeast as a discovery tool for systemic studies of GPCRs from other organisms...
  37. pmc Orchestration of sexual reproduction and virulence by the fungal mating-type locus
    Yen Ping Hsueh
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States
    Curr Opin Microbiol 11:517-24. 2008
    ....
  38. pmc Microsporidia evolved from ancestral sexual fungi
    Soo Chan Lee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Curr Biol 18:1675-9. 2008
    ..These findings support the hypothesis that microsporidia are true fungi that descended from a zygomycete ancestor and suggest microsporidia may have an extant sexual cycle...
  39. pmc Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex
    Marianela Rodriguez-Carres
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS ONE 5:e9620. 2010
    ..depauperata. We therefore propose that chromosomal rearrangements appear to be a major force driving speciation and sexual divergence in these closely related pathogenic and saprobic species...
  40. pmc Organization and evolutionary trajectory of the mating type (MAT) locus in dermatophyte and dimorphic fungal pathogens
    Wenjun Li
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Eukaryot Cell 9:46-58. 2010
    ..These studies further support a foundation to develop molecular and genetic tools for dermatophyte and dimorphic human fungal pathogens...
  41. pmc Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    Geraldine Butler
    UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Nature 459:657-62. 2009
    ..Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes...
  42. pmc Mechanistic plasticity of sexual reproduction and meiosis in the Candida pathogenic species complex
    Jennifer L Reedy
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Curr Biol 19:891-9. 2009
    ....
  43. pmc Molecular evidence that the range of the Vancouver Island outbreak of Cryptococcus gattii infection has expanded into the Pacific Northwest in the United States
    Edmond J Byrnes
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    J Infect Dis 199:1081-6. 2009
    ..Multilocus sequence typing demonstrates the spread of C. gattii VGIIa and VGIIb from Vancouver Island to the Pacific Northwest. Clinical strains recovered in Oregon represent a unique VGIIc genotype...
  44. pmc Diploids in the Cryptococcus neoformans serotype A population homozygous for the alpha mating type originate via unisexual mating
    Xiaorong Lin
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Pathog 5:e1000283. 2009
    ..Our findings underscore the importance of same-sex mating in shaping the current population structure of this important human pathogenic fungus, with implications for mechanisms of selfing and inbreeding in other microbial pathogens...
  45. pmc Signalling pathways in the pathogenesis of Cryptococcus
    Lukasz Kozubowski
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Cell Microbiol 11:370-80. 2009
    ....
  46. pmc Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales
    Keisha Findley
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Eukaryot Cell 8:353-61. 2009
    ....
  47. pmc G protein-coupled receptor Gpr4 senses amino acids and activates the cAMP-PKA pathway in Cryptococcus neoformans
    Chaoyang Xue
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Biol Cell 17:667-79. 2006
    ..Activation of the cAMP-PKA pathway by glucose and amino acids represents a nutrient coincidence detection system shared in other pathogenic fungi...

Research Grants30

  1. Moving Beyond Diversity by Revealing Biological Functions of Uncultured Bacteria
    JEFFREY SCOTT MCLEAN; Fiscal Year: 2013
    ..This new approach will provide a deeper understanding of disease progression and allow for the subsequent development of novel therapeutic approaches to battle these diseases. ..