Unisexual Reproduction in Cryptococcus: Evolutionary Implications, Virulence and RNA Silencing

<p>Sexual development enables microbial pathogens to purge deleterious mutations from the genome and drives genetic diversity in the population. <italic>Cryptococcus neoformans</italic> is a human fungal pathogen with a defined sexual cycle. Nutrient-limiting conditions and pheromones induce a dimorphic transition from unicellular yeast to multicellular hyphae and the production of infectious spores. <italic>C. neoformans</italic> has a defined <bold>a</bold>&ndash;&alpha; opposite sexual cycle (bisexual reproduction); however, >99% of clinical and environmental isolates are of the &alpha; mating type. Interestingly, &alpha; cells can undergo &alpha;&ndash;&alpha; unisexual reproduction, even involving genotypically identical cells. A central question is why would cells mate with themselves given that sex is costly and typically serves to admix pre-existing genetic diversity from genetically divergent parents? Sexual reproduction generates abundant spores that following inhalation, they penetrate deep into the alveoli of the lung, germinate, and establish a pulmonary infection growing as budding yeast. Therefore sex has been linked with virulence; however, hyphal development has been previously associated with reduced virulence and thus the roles of morphogenesis in virulence have not been extensively analyzed. To further understand the role of unisexual reproduction in <italic>C. neoformans</italic> we will investigate the evolutionary implications of &alpha;&ndash;&alpha; mating, explore its role in pathogenesis, and we will dissect the signaling pathway that regulates sexual development.</p><p>We isolated &alpha;&ndash;&alpha; unisexual reproduction progeny from the hyperfilamentous strain XL280 and subjected to a variety of phenotypic and genotypic assays (including whole genome sequencing and CGH). We found that unisexual and bisexual reproduction frequently generates phenotypic and genotypic diversity de novo, including aneuploidy. Aneuploidy was responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments, such as the mammalian host.</p><p>Interestingly aneuploidy strains that were fluconazole resistant were as virulent as the WT parental strain XL280. Although XL280 belongs to the serotype D lineage that exhibits limited pathogenicity, in further studies we found that is hypervirulent in the murine model. It can grow inside the lung of the host, establishing a pulmonary infection, and then disseminates to the brain to cause cryptococcal meningoencephalitis. Surprisingly, this hyperfilamentous strain triggers an immune response polarized towards Th2-type immunity, which is characterized by less protective immunity and is usually observed in the highly virulent sibling species <italic>C. gattii</italic>, responsible for the Pacific Northwest outbreak. These studies: 1) provide a technological advance that will facilitate analysis of virulence genes and attributes in <italic>C. neoformans</italic> var. <italic>neoformans</italic> (serotype D), and 2) reveal the virulence potential of serotype D that is broader and more dynamic than previously appreciated.</p><p>Bisexual and unisexual reproduction are governed by shared components of the conserved pheromone-sensing Cpk1 MAPK signal transduction cascade and by Mat2, the major transcriptional regulator of the pathway. However, the downstream targets of the pathway are largely unknown, and homology-based approaches have failed to yield downstream transcriptional regulators or other targets. To address this question we applied an insertional mutagenesis via <italic>Agrobacterium tumefaciens</italic> transkingdom DNA delivery to identify mutants with unisexual reproduction defects. In addition to elements known to be involved in sexual development (Crg1, Ste7, Mat2, and Znf2), three key regulators of sexual development were identified by our screen: Znf3, Spo11, and Ubc5. Spo11 and Ubc5 promote sporulation during both bisexual and unisexual reproduction. Genetic and phenotypic analyses provide further evidence implicating both genes in the regulation of meiosis. Phenotypic analysis of sexual development showed that Znf3 is required for hyphal development during unisexual reproduction and also plays a central role during bisexual reproduction. Znf3 governs cell fusion and pheromone production through a pathway parallel to and independent of the pheromone signaling cascade. Surprisingly, Znf3 participates in transposon silencing during unisexual reproduction and may serve as a link between RNAi silencing and sexual development. In further studies we found that Znf3 is required for sex- and mitotic-induced (SIS and MIS). SIS is less efficient in <italic>znf3</italic> unilateral matings and is abolished in <italic>znf3</italic> x <italic>znf3</italic> bilateral matings, similar to the phenotypes of <italic>rdp1</italic> mutants (the RNA-dependent RNA-polymerase of RNAi pathway). Znf3 is also required for transgene-induced mitotic silencing; <italic>znf3</italic> mutations abrogate silencing of repetitive transgenes during vegetative growth. Znf3 tagged with mCherry is localized in the cytoplasm in bright, distinct foci. Co-localization of Znf3 with the P-body marker Dcp1-GFP further supports the hypothesis that Znf3 is a novel element of the RNAi pathway and operates to defend the genome during sexual development and vegetative growth. In concussion our studies provide further understanding of unisexual reproduction as an evolutionary successful strategy.</p>Dissertatio

RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops

Telomeres- repeated, noncoding nucleotide motifs and associated proteins that are found at the ends of eukaryotic chromosomes—mediate genome stability and determine cellular lifespan. Telomeric-repeat-containing RNA (TERRA) is a class of long noncoding RNAs (lncRNAs) that are transcribed from chromosome ends; these RNAs in turn regulate telomeric chromatin structure and telomere maintenance through the telomere-extending enzyme telomerase and homology-directed DNA repair. The mechanisms by which TERRA is recruited to chromosome ends remain poorly defined. Here we develop a reporter system with which to dissect the underlying mechanisms, and show that the UUAGGG repeats of TERRA are both necessary and sufficient to target TERRA to chromosome ends. TERRA preferentially associates with short telomeres through the formation of telomeric DNA–RNA hybrid (R-loop) structures that can form in trans. Telomere association and R-loop formation trigger telomere fragility and are promoted by the recombinase RAD51 and its interacting partner BRCA2, but counteracted by the RNA-surveillance factors RNaseH1 and TRF1. RAD51 physically interacts with TERRA and catalyses R-loop formation with TERRA in vitro, suggesting a direct involvement of this DNA recombinase in the recruitment of TERRA by strand invasion. Together, our findings reveal a RAD51-dependent pathway that governs TERRA-mediated R-loop formation after transcription, providing a mechanism for the recruitment of lncRNAs to new loci in trans

Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans

Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individuals with compromised immunity, such as HIV/AIDS patients, causing life-threatening meningoencephalitis. C. neoformans has a defined a-α opposite sexual cycle; however, >99% of isolates are of the α mating type. Interestingly, α cells can undergo α-α unisexual reproduction, even involving genotypically identical cells. A central question is: Why would cells mate with themselves given that sex is costly and typically serves to admix preexisting genetic diversity from genetically divergent parents? In this study, we demonstrate that α-α unisexual reproduction frequently generates phenotypic diversity, and the majority of these variant progeny are aneuploid. Aneuploidy is responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Phenotypic/genotypic changes were not observed following asexual mitotic reproduction. Aneuploidy was also detected in progeny from a-α opposite-sex congenic mating; thus, both homothallic and heterothallic sexual reproduction can generate phenotypic diversity de novo. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments

Transcription Factors Mat2 and Znf2 Operate Cellular Circuits Orchestrating Opposite- and Same-Sex Mating in Cryptococcus neoformans

Cryptococcus neoformans is a human fungal pathogen that undergoes a dimorphic transition from a unicellular yeast to multicellular hyphae during opposite sex (mating) and unisexual reproduction (same-sex mating). Opposite- and same-sex mating are induced by similar environmental conditions and involve many shared components, including the conserved pheromone sensing Cpk1 MAPK signal transduction cascade that governs the dimorphic switch in C. neoformans. However, the homeodomain cell identity proteins Sxi1α/Sxi2a encoded by the mating type locus that are essential for completion of sexual reproduction following cell–cell fusion during opposite-sex mating are dispensable for same-sex mating. Therefore, identification of downstream targets of the Cpk1 MAPK pathway holds the key to understanding molecular mechanisms governing the two distinct developmental fates. Thus far, homology-based approaches failed to identify downstream transcription factors which may therefore be species-specific. Here, we applied insertional mutagenesis via Agrobacterium-mediated transformation and transcription analysis using whole genome microarrays to identify factors involved in C. neoformans differentiation. Two transcription factors, Mat2 and Znf2, were identified as key regulators of hyphal growth during same- and opposite-sex mating. Mat2 is an HMG domain factor, and Znf2 is a zinc finger protein; neither is encoded by the mating type locus. Genetic, phenotypic, and transcriptional analyses of Mat2 and Znf2 provide evidence that Mat2 is a downstream transcription factor of the Cpk1 MAPK pathway whereas Znf2 functions as a more terminal hyphal morphogenesis determinant. Although the components of the MAPK pathway including Mat2 are not required for virulence in animal models, Znf2, as a hyphal morphology determinant, is a negative regulator of virulence. Further characterization of these elements and their target circuits will reveal genes controlling biological processes central to fungal development and virulence

A practical qPCR approach to detect TERRA, the elusive telomeric repeat-containing RNA

Telomeres, the heterochromatic structures that protect the ends of the chromosomes, are transcribed into a class of long non-coding RNAs, telomeric repeat-containing RNAs (TERRA), whose transcriptional regulation and functions are not well understood. The identification of TERRA adds a novel level of structural and functional complexity at telomeres, opening up a new field of research. TERRA molecules are expressed at several chromosome ends with transcription starting from the subtelomeric DNA proceeding into the telomeric tracts. TERRA is heterogeneous in length and its expression is regulated during the cell cycle and upon telomere damage. Little is known about the mechanisms of regulation at the level of transcription and post transcription by RNA stability. Furthermore, it remains to be determined to what extent the regulation at different chromosome ends may differ. We present an overview on the methodology of how RT-qPCR and primer pairs that are specific for different subtelomeric sequences can be used to detect and quantify TERRA expressed from different chromosome ends. (C) 2016 The Authors. Published by Elsevier Inc

Genetic circuits that govern bisexual and unisexual reproduction in Cryptococcus neoformans.

Cryptococcus neoformans is a human fungal pathogen with a defined sexual cycle. Nutrient-limiting conditions and pheromones induce a dimorphic transition from unicellular yeast to multicellular hyphae and the production of infectious spores. Sexual reproduction involves cells of either opposite (bisexual) or one (unisexual) mating type. Bisexual and unisexual reproduction are governed by shared components of the conserved pheromone-sensing Cpk1 MAPK signal transduction cascade and by Mat2, the major transcriptional regulator of the pathway. However, the downstream targets of the pathway are largely unknown, and homology-based approaches have failed to yield downstream transcriptional regulators or other targets. In this study, we applied insertional mutagenesis via Agrobacterium tumefaciens transkingdom DNA delivery to identify mutants with unisexual reproduction defects. In addition to elements known to be involved in sexual development (Crg1, Ste7, Mat2, and Znf2), three key regulators of sexual development were identified by our screen: Znf3, Spo11, and Ubc5. Spo11 and Ubc5 promote sporulation during both bisexual and unisexual reproduction. Genetic and phenotypic analyses provide further evidence implicating both genes in the regulation of meiosis. Phenotypic analysis of sexual development showed that Znf3 is required for hyphal development during unisexual reproduction and also plays a central role during bisexual reproduction. Znf3 promotes cell fusion and pheromone production through a pathway parallel to and independent of the pheromone signaling cascade. Surprisingly, Znf3 participates in transposon silencing during unisexual reproduction and may serve as a link between RNAi silencing and sexual development. Our studies illustrate the power of unbiased genetic screens to reveal both novel and conserved circuits that operate sexual reproduction

Phenotypic analysis of insertion mutants altered in unisexual reproduction.

<p>Nourseothricin (NAT)-resistant <i>Agrobacterium</i> transconjugant mutants of XL280α were grown on V8 solid agar for 14 days in the dark at room temperature to examine hyphal development during sexual reproduction by light microscopy. (<b>A</b>) The wild type strain XL280α undergoes robust hyphal growth during unisexual reproduction. The most extreme mutant phenotypes include no hyphal development, short hyphae, or hyperfilamentous strains. The scale bar represents 100 µm. (<b>B</b>) The progeny of wild type strain XL280α are organized in four long chains of spores that emerge from the surface of the basidium. Sporulation was severely impaired in several insertion mutants. The scale bar represents 10 µm.</p

X-irradiation-induced DSBs partially rescue the spore survival defect of <i>spo11</i>Δ mutants during bisexual and unisexual reproduction.

<p>Cultures were incubated on V8 medium for six days for unisexual reproduction and four days for bisexual reproduction. Plates were irradiated at the designated dose and incubated in the dark for two days to allow spore production. A total of 30 spores were isolated from each culture.</p>a<p>Viable CFU determined from vegetative growth on solid media independently for XL280α, <i>spo11</i>Δ, <i>ubc5</i>Δ, and JEC21α. The viable CFU for each strain at the same dose was similar with minor differences. Here we present the viability of XL280α as reference.</p

Deletion of <i>ZNF3</i> impairs hyphal development during bisexual and unisexual reproduction.

<p>(<b>A</b>) XL280α, two mutants with independent insertions in <i>ZNF3</i> (II-12, II-147), and two independent <i>znf3</i>Δ deletion mutants (MF01, MF38) were incubated on V8 medium in the dark at room temperature for 10 days and hyphal formation during unisexual reproduction was assessed by microscopy. (<b>B</b>) Bisexual wild type crosses (JEC21α×JEC20<b>a</b> and XL280α×JEC20<b>a</b>), unilateral mutant crosses (α <i>znf3</i>Δ×WT<b>a</b> and WTα×<b>a </b><i>znf3</i>Δ), and bilateral mutant crosses (α <i>znf3</i>Δ×<b>a </b><i>znf3</i>Δ) were conducted on V8 medium in the dark at room temperature for 7 days and photographed. The scale bar represents 100 µm.</p