Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation.

UNLABELLED: The opportunistic fungal pathogen Cryptococcus neoformans causes life-threatening meningitis in immunocompromised individuals. The expression of virulence factors, including capsule and melanin, is in part regulated by the cyclic-AMP/protein kinase A (cAMP/PKA) signal transduction pathway. In this study, we investigated the influence of PKA on the composition of the intracellular proteome to obtain a comprehensive understanding of the regulation that underpins virulence. Through quantitative proteomics, enrichment and bioinformatic analyses, and an interactome study, we uncovered a pattern of PKA regulation for proteins associated with translation, the proteasome, metabolism, amino acid biosynthesis, and virulence-related functions. PKA regulation of the ubiquitin-proteasome pathway in C. neoformans showed a striking parallel with connections between PKA and protein degradation in chronic neurodegenerative disorders and other human diseases. Further investigation of proteasome function with the inhibitor bortezomib revealed an impact on capsule production as well as hypersusceptibility for strains with altered expression or activity of PKA. Parallel studies with tunicamycin also linked endoplasmic reticulum stress with capsule production and PKA. Taken together, the data suggest a model whereby expression of PKA regulatory and catalytic subunits and the activation of PKA influence proteostasis and the function of the endoplasmic reticulum to control the elaboration of the polysaccharide capsule. Overall, this study revealed both broad and conserved influences of the cAMP/PKA pathway on the proteome and identified proteostasis as a potential therapeutic target for the treatment of cryptococcosis. IMPORTANCE: Fungi cause life-threatening diseases, but very few drugs are available to effectively treat fungal infections. The pathogenic fungus Cryptococcus neoformans causes a substantial global burden of life-threatening meningitis in patients suffering from HIV/AIDS. An understanding of the mechanisms by which fungi deploy virulence factors to cause disease is critical for developing new therapeutic approaches. We employed a quantitative proteomic approach to define the changes in the protein complement that occur upon modulating the cAMP signaling pathway that regulates virulence in C. neoformans. This approach identified a conserved role for cAMP signaling in the regulation of the ubiquitin-proteasome pathway and revealed a link between this pathway and elaboration of a major virulence determinant, the polysaccharide capsule. Targeting the ubiquitin-proteasome pathway opens new therapeutic options for the treatment of cryptococcosis.

Aimless mutants of Cryptococcus neoformans: failure to disseminate.

The pathogenic fungus Cryptococcus neoformans exhibits a striking propensity to cause central nervous system (CNS) disease in people with HIV/AIDS. Given that cryptococcal infections are generally initiated by pulmonary colonization, dissemination requires that the fungus withstand phagocytic killing, cross the alveolar-capillary interface in the lung, survive in the circulatory system and breach the blood-brain barrier. We know little about the molecular mechanisms underlying dissemination, but there is a rapidly growing list of mutants that fail to cause CNS disease. These mutants reveal a remarkable diversity of functions and therefore illustrate the complexity of the cryptococcal-host interaction. The challenge now is to extend the analysis of these mutants to acquire a detailed understanding of each step in dissemination.

Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

Cryptococcus gattii recently emerged as the causative agent of cryptococcosis in healthy individuals in western North America, despite previous characterization of the fungus as a pathogen in tropical or subtropical regions. As a foundation to study the genetics of virulence in this pathogen, we sequenced the genomes of a strain (WM276) representing the predominant global molecular type (VGI) and a clinical strain (R265) of the major genotype (VGIIa) causing disease in North America. We compared these C. gattii genomes with each other and with the genomes of representative strains of the two varieties of Cryptococcus neoformans that generally cause disease in immunocompromised people. Our comparisons included chromosome alignments, analysis of gene content and gene family evolution, and comparative genome hybridization (CGH). These studies revealed that the genomes of the two representative C. gattii strains (genotypes VGI and VGIIa) are colinear for the majority of chromosomes, with some minor rearrangements. However, multiortholog phylogenetic analysis and an evaluation of gene/sequence conservation support the existence of speciation within the C. gattii complex. More extensive chromosome rearrangements were observed upon comparison of the C. 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.

Self-fertility: the genetics of sex in lonely fungi.

The genome of the fungus Aspergillus nidulans encodes both of the mating-type regulators of sexuality, thus allowing self-fertility. Pheromone signaling genes are induced during sexual development, as found in outcrossing species, but, surprisingly, the regulators do not control expression of these genes.

Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei.

Race-cultivar specialization during the interaction of the basidiomycete smut pathogen Ustilago hordei with its barley host was described in the 1940s. Subsequent genetic analyses revealed the presence of dominant avirulence genes in the pathogen that conform to the gene-for-gene theory. This pathosystem therefore presents an opportunity for the molecular genetic characterization of fungal genes controlling avirulence. We performed a cross between U. hordei strains to obtain 54 progeny segregating for three dominant avirulence genes on three differential barley cultivars. Bulked segregant analysis was used to identify RAPD and AFLP markers tightly linked to the avirulence gene UhAvr1. The UhAvr1 gene is located in an area containing repetitive DNA and this region is undetectable in cosmid libraries prepared from the avirulent parental strain. PCR and hybridization probes developed from the linked markers were therefore used to identify cosmid clones from the virulent (Uhavr1) parent. By walking on Uhavr1-linked cosmid clones, a nonrepetitive, nearby probe was found that recognized five overlapping BAC clones spanning 170 kb from the UhAvr1 parent. A contig of the clones in the UhAvr1 region was constructed and selected probes were used for RFLP analysis of the segregating population. This approach genetically defined an approximately 80-kb region that carries the UhAvr1 gene and provided cloned sequences for subsequent genetic analysis. UhAvr1 represents the first avirulence gene cloned from a basidiomycete plant pathogen.

Castles and cuitlacoche: the first international Ustilago conference.

The first international Ustilago conference was held in Marburg, Germany from August 22 to 25, 2002. The meeting focused on molecular genetic and cell biology research with Ustilago maydis, the causative agent of common smut of maize. This fungus has emerged as a useful experimental organism for studying the biology of basidiomycete fungi, with a particular emphasis on the interaction of the fungus with the host plant. Thus presentations at the meeting covered the range of current research topics including DNA recombination and repair, mating and sexual development, phytopathology, cell biology, the cell cycle, signaling, and genomics. The meeting also highlighted historical aspects of U. maydis research with presentations by pioneers in the field including Robin Holiday (recombination), Yigal Koltin (killer phenomenon) and Peter Day (plant pathology).

The ukb1 gene encodes a putative protein kinase required for bud site selection and pathogenicity in Ustilago maydis.

Morphogenesis and pathogenesis are closely associated aspects of the life cycle of the fungal pathogen Ustilago maydis. In this fungus, the dimorphic switch from budding to filamentous growth coincides with the transition from non-pathogenic to pathogenic growth on maize. We have cloned and characterized the ukb1 gene that encodes a putative serine/threonine protein kinase with a role in budding and filamentous growth. Mutants defective in ukb1 were altered in bud site selection and produced lateral buds at a greater frequency than wild-type cells. Dikaryotic cells defective in ukb1 were capable of colonizing host tissue and growing with a filamentous morphology in planta. However, the mutants were incapable of inducing tumor formation and they failed to complete sexual development. In addition, the ukb1 gene influenced the ability of colonies to form aerial mycelia in response to environmental stimuli. Overall, the discovery of ukb1 reinforces the connection between morphogenesis and pathogenesis in U. maydis.

Induction of phenylalanine ammonia-lyase activity by tryptophan in Ustilago maydis.

To understand the regulation of phenylalanine ammonia-lyase (PAL) activity in the corn smut fungus, Ustilago maydis, we examined the effects of different media, metabolic effectors (including aromatic amino acids), and environmental factors on induction and repression of PAL activity. PAL was detected only in cell extracts and not in the culture medium. U. maydis PAL is constitutively produced at a low level in all media tested but its regulation can be influenced by aromatic amino acids. L-Tryptophan (0.3 mM) induces PAL activity 3- to 5-fold but tryptophan analogs and tryptophan-related metabolites do not. The enzyme is most readily induced during the early stationary phase of growth and the induced activity remains relatively constant during stationary stage. No induction or inhibition of PAL activity was observed as a function of culture temperature, pH or light. PAL induction was repressed by glucose but not by its reaction product, t-cinnamic acid. Induction did not require de novo protein synthesis, suggesting that some form of post-translational protein modification or a metabolic effect may be involved. This study shows that the regulation of U. maydis PAL is very different from the patterns known for plants and other fungi.

Cloning and disruption of a phenylalanine ammonia-lyase gene from Ustilago maydis.

The enzyme L-phenylalanine ammonia-lyase (PAL) catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid and ammonia. This enzyme is universally present in higher plants and it catalyzes the starting reaction for a central pathway that generates hundreds of different phenylpropanoid metabolites. Genes encoding PAL have been identified in fungi, but the role of the enzyme has not been determined. We cloned and characterized a gene that encodes PAL from the phytopathogenic fungus Ustilago maydis and we constructed fungal strains carrying a null mutation in the gene. These mutants behaved like wild-type strains in terms of growth, mating, and pathogenicity. These results indicate that PAL does not play a major role in the life cycle of U. maydis under laboratory conditions.

The hgl1 gene is required for dimorphism and teliospore formation in the fungal pathogen Ustilago maydis.

The fungal pathogen Ustilago maydis causes a dramatic disease in maize involving the induction of tumours and the formation of masses of black teliospores. In this fungus, mating between haploid, budding cells results in the formation of the infectious, filamentous cell type that invades host tissue. Mating and filamentous growth are governed by the mating-type loci and by cAMP signalling, perhaps in response to signals from maize. To dissect the involvement of cAMP signalling further, the constitutive filamentous phenotype of a mutant with a defect in the catalytic subunit of protein kinase A was used to isolate suppressor mutations that restore budding growth. One such mutation identified the hgl1 gene, which is shown to be required for both the switch between budding and filamentous growth and teliospore formation during infection. In addition, the hgl1 gene product may be a target of phosphorylation by protein kinase A, and transcript levels for the gene are elevated during mating. Thus, the hgl1 gene provides a connection between mating, cAMP signalling and two important aspects of virulence: filamentous growth and the formation of teliospores.

The cAMP signal transduction pathway mediates resistance to dicarboximide and aromatic hydrocarbon fungicides in Ustilago maydis.

The cAMP signal transduction pathway mediates the switch between yeast-like and filamentous growth and influences both sexual development and pathogenicity in the smut fungus Ustilago maydis. Signaling via cAMP may also play a role in fungicide resistance in U. maydis. In particular, the adr1 gene, which encodes the catalytic subunit of the U. maydis cAMP-dependent protein kinase (PKA), is implicated in resistance to the dicarboximide and aromatic hydrocarbon fungicides. In this study, we examined the sensitivity of PKA to vinclozolin and could not demonstrate direct inhibition of protein kinase activity. However, we did find that mutants with disruptions in the ubc1 gene, which encodes the regulatory subunit of PKA, were resistant to both vinclozolin and chloroneb. We also found that these fungicides altered the morphology of both wild-type and ubc1 mutant cells. In addition, strains that are defective in ubc1 display osmotic sensitivity, a property often associated with vinclozolin and chloroneb resistance in other fungi.

The mating-type and pathogenicity locus of the fungus Ustilago hordei spans a 500-kb region.

The fungal pathogen Ustilago hordei causes the covered smut disease of barley and oats. Mating and pathogenicity in this fungus are controlled by the MAT locus, which contains two distinct gene complexes, a and b. In this study, we tagged the a and b regions with the recognition sequence for the restriction enzyme I-SceI and determined that the distance between the complexes is 500 kb in a MAT-1 strain and 430 kb in a MAT-2 strain. Characterization of the organization of the known genes within the a and b gene complexes provided evidence for nonhomology and sequence inversion between MAT-1 and MAT-2. Antibiotic-resistance markers also were used to tag the a gene complex in MAT-1 strains (phleomycin) and the b gene complex in MAT-2 strains (hygromycin). Crosses were performed with these strains and progeny resistant to both antibiotics were recovered at a very low frequency, suggesting that recombination is suppressed within the MAT region. Overall, the chromosome homologues carrying the MAT locus of U. hordei share features with primitive sex chromosomes, with the added twist that the MAT locus also controls pathogenicity.

Identification of a cAMP-dependent protein kinase catalytic subunit required for virulence and morphogenesis in Ustilago maydis.

Ustilago maydis, a fungal pathogen of maize, alternates between budding and filamentous growth in response to mating and other environmental signals. Defects in components of the cAMP signaling pathway affect this morphological transition and reveal an association of budding growth with elevated cAMP levels and filamentous growth with low cAMP levels. We have identified two genes, adr1 and uka1, encoding catalytic subunits of cAMP-dependent protein kinase (PKA). Disruption of adr1 resulted in a constitutively filamentous growth phenotype similar to that of mutants deficient in adenylyl cyclase. Importantly, adr1 is required for pathogenicity and is responsible for the majority of PKA activity in fungal cells. In contrast, uka1 has little influence on pathogenicity, and deletion of the uka1 gene does not affect cell morphology. These results provide compelling evidence that regulated PKA activity is crucial during infectious development of U. maydis.

Dual sets of chimeric alleles identify specificity sequences for the bE and bW mating and pathogenicity genes of Ustilago maydis.

The b mating-type locus of the fungal plant pathogen Ustilago maydis encodes two multiallelic gene products, bE and bW, that control the formation and maintenance of the infectious cell type. Dimerization via the N-terminal regions of bE and bW proteins encoded by alleles of different specificities establishes a homeodomain-containing transcription factor. The bE and bW products encoded by alleles of like specificities fail to dimerize. We constructed sets of chimeric alleles for the bE1 and bE2 genes and for the bW1 and bW2 genes to identify sequences that control specificity. The mating behavior of strains carrying chimeric alleles identified three classes of specificity: b2 (class I), specificity different from either parental type (class II), and b1 (class III). Crosses between strains carrying bE and bW chimeric alleles identified two short blocks of amino acids that influence specificity and that are located in the N-terminal variable regions of the b proteins. Comparisons of pairs of chimeric alleles encoding polypeptides differing in specificity and differing at single amino acid positions identified 16 codon positions that influence the interaction between bE and bW. Fifteen of these positions lie within the blocks of amino acids identified by crosses between the strains carrying chimeric alleles. Overall, this work provides insight into the organization of the regions that control recognition.

The Ustilago maydis regulatory subunit of a cAMP-dependent protein kinase is required for gall formation in maize.

In the plant, filamentous growth is required for pathogenicity of the corn smut pathogen Ustilago maydis. Earlier, we identified a role for the cAMP signal transduction pathway in the switch between budding and filamentous growth for this fungus. A gene designated ubc1 (for Ustilago bypass of cyclase) was found to be required for filamentous growth and to encode the regulatory subunit of a cAMP-dependent protein kinase (PKA). Here, we show that ubc1 is important for the virulence of the pathogen. Specifically, ubc1 mutants are able to colonize maize plants and, like the wild-type pathogen, cause localized symptoms in association with the presence of hyphae. However, in contrast to plants infected with wild-type cells that often developed galls from initially chlorotic tissue, plants infected with the ubc1 mutant did not produce galls. These data suggest that PKA regulation is critical for the transition from saprophytic to pathogenic growth and from vegetative to reproductive development. Plate mating assays in which exogenous cAMP was applied suggested that the cAMP and b mating-type morphogenetic pathways may be coordinated.

Mating type in filamentous fungi.

Mating type genes regulate sexual compatibility and sexual reproduction in fungi. This review focuses on recent molecular analyses of well-characterized mating systems from representative ascomycete (Neurospora crassa, Podospora anserina) and basidiomycete (Ustilago maydis, Coprinus cinereus, Schizophyllum commune) fungi. These mating systems include many conserved components, such as gene regulatory polypeptides and pheromone/receptor signal transduction cascades, as well as conserved processes, like self-nonself recognition and controlled nuclear migration. The components' structures and their genetic arrangements in the mating system vary greatly in different fungi. Although similar components and processes are also found in ascomycete yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe), the filamentous systems exhibit properties not encountered in yeast. Mating type genes act within, and control the development of, spatially differentiated fruiting bodies. The complex mating systems of basidiomycetes, unlike ascomycete systems, involve novel one-to-many specificity in both pheromone-receptor and homeodomain protein interactions.

The pheromone cell signaling components of the Ustilago a mating-type loci determine intercompatibility between species.

The MAT region of Ustilago hordei, a bipolar barley pathogen, harbors distinct mating functions (a and b loci). Here, we show that the b locus is essential for mating and pathogenicity, and can induce pathogenicity when introduced into a strain carrying a b locus of opposite specificity. Transformation experiments using components of the a1 locus and analysis of resulting dual mating phenotypes revealed that this locus harbors a pheromone receptor gene (Uhpra1) and a pheromone gene (Uhmfa1). These U. hordei a1 genes, when introduced by transformation, are necessary and sufficient to make U. maydis, a tetrapolar corn pathogen, intercompatible with U. hordei MAT-2, but not MAT-1, strains. U. hordei strains transformed with the U. maydis a1 locus also become intercompatible with U. maydis a2, but not a1, strains. The interspecies hybrids produced dikaryotic hyphae but were not fully virulent on either corn or barley. Partial, natural intercompatibility was shown to exist between the sugarcane smut U. scitaminea and both U. hordei and U. maydis. These results show that the signal transduction pathway for mating responses is conserved between different smut species. We conclude that, apart from intraspecies compatibility, the Ustilago a locus also dictates intercompatibility in this group of fungi.