The related fungal species Cryptococcus neoformans and Cryptococcus gattii frequently infect humans, causing life-threatening lung and brain infections. Although often considered opportunistic pathogens, these organisms can cause disease in hosts with both compromised and normal immunity. More than 1,000,000 infections occur worldwide annually, leading to >620,000 deaths comprising more than one-third of all HIV/AIDS-related deaths. A specialized genomic region, the mating type locus (MAT), governs cell identity, sexual reproduction, infectious spore production, and virulence. We previously discovered that the Cryptococcus MAT locus is a large, complex gene cluster, and we proposed to elucidate how this unusual suite of sex- and virulence-determining genes evolved from a simpler nonpathogenic ancestral state. Our comparative phylogenomic studies provide evidence that 1) the bipolar/unipolar mating system is a shared characteristic of these two Cryptococcus pathogenic species, and 2) the inbreeding bipolar/unipolar system evolved from an ancestral outbreeding tetrapolar system via gene acquisition and translocation-driven fusion. Similar transitions have occurred in other fungal pathogens of plants and animals, suggesting convergent evolution in concert with host adaptation. These studies illustrate general principles of gene cluster evolution and forces by which recombination has forged the genomes of microbial pathogens. Our studies supported by this award defined the structure, function, and evolution of the MAT locus. In the prior award period, we 1) cloned and sequenced the bipolar MAT locus from pathogenic Cryptococcus species; 2) discovered tetrapolar sexual cycles and MAT loci of closely related nonpathogenic species; and 3) found the two MAT loci of the nonpathogen Cryptococcus amylolentus lie on different chromosomes and are both centromere-linked. We hypothesize the tetrapolar-bipolar transition occurred concomitant with pathogen emergence via two steps. First, genes were recruited into two unlinked MAT loci; second, chromosomal translocation fused the MAT loci. Our recent studies reveal novel MAT features allowing us to propose new aims to test these hypotheses.
Aim 1 focuses on MAT locus structure and evolution. We will sequence genomes, define centromeres, and test the hypothesis that inter-centromeric recombination drove fusion of unlinked ancestral MAT loci and key chromosomal translocations that punctuate pathogen evolution.
Aim 2 focuses on MAT locus functions. We will address 1) mechanisms governing uniparental mitochondrial inheritance that restrict mitochondrial genome recombination and impact mitochondrial dynamics that promote replication inside macrophages and pathogenesis, and 2) roles of essential diverged ribosomal protein paralogs in development and virulence. Not only do these studies advance our understanding of the dynamic evolution of microbial genomes, but given the association with specific gene clusters and virulence, they also have direct implications for infectious disease treatment and prevention.

Public Health Relevance

The focus of this proposal is to elucidate how the mating type locus (MAT) evolved and controls development and virulence of the human fungal pathogen Cryptococcus. This eukaryotic pathogen is of worldwide impact, and infects both immunocompromised and immunocompetent individuals to cause diseases of the lung and central nervous system (pneumonia, meningoencephalitis). This results in >1,000,000 infections each year, and more than 600,000 deaths worldwide resulting in >one-third of all AIDS associated deaths. Cryptococcus has a defined sexual cycle orchestrated by MAT, a large gene cluster that governs cell identity, production of infectious spores, and virulence. This proposal focuses on the structure, functions, and evolution of MAT by comparing closely related pathogenic and nonpathogenic species. The central hypothesis is that recombination between repetitive sequences in centromeres drives genome evolution of eukaryotic microbial pathogens, including key events involving transitions from sexual outcrossing to inbreeding. These investigations will inform our understanding of how eukaryotic microbes evolve and cause human infection, providing insights to advance treatment and prevention.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI050113-15
Application #
9601622
Study Section
Pathogenic Eukaryotes Study Section (PTHE)
Program Officer
Love, Dona
Project Start
2002-06-15
Project End
2019-11-30
Budget Start
2018-12-01
Budget End
2019-11-30
Support Year
15
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Duke University
Department
Genetics
Type
Schools of Medicine
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Jung, Kwang-Woo; Lee, Kyung-Tae; Averette, Anna F et al. (2018) Evolutionarily Conserved and Divergent Roles of Unfolded Protein Response (UPR) in the Pathogenic Cryptococcus Species Complex. Sci Rep 8:8132
Gryganskyi, Andrii P; Golan, Jacob; Dolatabadi, Somayeh et al. (2018) Phylogenetic and Phylogenomic Definition of Rhizopus Species. G3 (Bethesda) 8:2007-2018
Fu, Ci; Donadio, Nicholas; Cardenas, Maria E et al. (2018) Dissecting the Roles of the Calcineurin Pathway in Unisexual Reproduction, Stress Responses, and Virulence in Cryptococcus deneoformans. Genetics 208:639-653
Yadav, Vikas; Sun, Sheng; Billmyre, R Blake et al. (2018) RNAi is a critical determinant of centromere evolution in closely related fungi. Proc Natl Acad Sci U S A 115:3108-3113
Garcia-Hermoso, Dea; Criscuolo, Alexis; Lee, Soo Chan et al. (2018) Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing. MBio 9:
Persinoti, Gabriela F; Martinez, Diego A; Li, Wenjun et al. (2018) Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. Genetics 208:1657-1669
Wang, Liuyang; Pittman, Kelly J; Barker, Jeffrey R et al. (2018) An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 24:308-323.e6
Fu, Ci; Heitman, Joseph (2017) PRM1 and KAR5 function in cell-cell fusion and karyogamy to drive distinct bisexual and unisexual cycles in the Cryptococcus pathogenic species complex. PLoS Genet 13:e1007113
Desjardins, Christopher A; Giamberardino, Charles; Sykes, Sean M et al. (2017) Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans. Genome Res 27:1207-1219
Calo, Silvia; Nicolás, Francisco E; Lee, Soo Chan et al. (2017) A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides. PLoS Genet 13:e1006686

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