DLH1 is a functional Candida albicans homologue of the meiosis-specific gene DMC1

Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi

Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.

Partner Choice in Spontaneous Mitotic Recombination in Wild Type and Homologous Recombination Mutants of Candida albicans

Candida albicans, the most common fungal pathogen, is a diploid with a genome that is rich in repeats and has high levels of heterozygosity. To study the role of different recombination pathways on direct-repeat recombination, we replaced either allele of the RAD52 gene (Chr6) with the URA-blaster cassette (hisG-URA3-hisG), measured rates of URA3 loss as resistance to 5-fluoroorotic acid (5FOA^R) and used CHEF Southern hybridization and SNP-RFLP analysis to identify recombination mechanisms and their frequency in wildtype and recombination mutants. FOA^R rates varied little across different strain backgrounds. In contrast, the type and frequency of mechanisms underlying direct repeat recombination varied greatly. For example, wildtype, rad59 and lig4 strains all displayed a bias for URA3 loss via pop-out/deletion vs. inter-homolog recombination and this bias was reduced in rad51 mutants. In addition, in rad51-derived 5FOA^R strains direct repeat recombination was associated with ectopic translocation (5%), chromosome loss/truncation (14%) and inter-homolog recombination (6%). In the absence of RAD52, URA3 loss was mostly due to chromosome loss and truncation (80–90%), and the bias of retained allele frequency points to the presence of a recessive lethal allele on Chr6B. However, a few single-strand annealing (SSA)-like events were identified and these were independent of either Rad59 or Lig4. Finally, the specific sizes of Chr6 truncations suggest that the inserted URA-blaster could represent a fragile site.

A 'parameiosis' drives depolyploidization and homologous recombination in Candida albicans

Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CCL). Here, we report that recombination rates are more than three orders of magnitude higher during CCL than during normal mitotic growth. Furthermore, two conserved ‘meiosis-specific’ factors play central roles in CCL as SPO11 mediates DNA double-strand break formation while both SPO11 and REC8 regulate chromosome stability and promote inter-homolog recombination. Unexpectedly, SPO11 also promotes DNA repair and recombination during normal mitotic divisions. These results indicate that C. albicans CCL represents a ‘parameiosis’ that blurs the conventional boundaries between mitosis and meiosis. They also reveal parallels with depolyploidization in mammalian cells and provide potential insights into the evolution of meiosis.

Mating of Candida albicans produces tetraploid products that return to the diploid state via a non-meiotic process known as concerted chromosome loss (CCL). Here, Anderson et al. show high recombination rates during CCL and identify factors that are essential for chromosome stability and recombination during CCL.

The parasexual lifestyle of Candida albicans

Candida albicans is both a prevalent human commensal and the most commonly encountered human fungal pathogen. This lifestyle is dependent on the ability of the fungus to undergo rapid genetic and epigenetic changes, often in response to specific environmental cues. A parasexual cycle in C. albicans has been defined that includes several unique properties when compared to the related model yeast, Saccharomyces cerevisiae. Novel features include strict regulation of mating via a phenotypic switch, enhanced conjugation within a sexual biofilm, and a program of concerted chromosome loss in place of a conventional meiosis. It is expected that several of these adaptations co-evolved with the ability of C. albicans to colonize the mammalian host.

Evolution of eukaryotic microbial pathogens via covert sexual reproduction

Sexual reproduction enables eukaryotic organisms to reassort genetic diversity and purge deleterious mutations, producing better-fit progeny. Sex arose early and pervades eukaryotes. Fungal and parasite pathogens once thought asexual have maintained cryptic sexual cycles, including unisexual or parasexual reproduction. As pathogens become niche and host adapted, sex appears to specialize to promote inbreeding and clonality yet maintain outcrossing potential. During self-fertile sexual modes, sex itself may generate genetic diversity de novo. 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.

Role of the homologous recombination genes RAD51 and RAD59 in the resistance of Candida albicans to UV light, radiomimetic and anti-tumor compounds and oxidizing agents

We have cloned and characterized the RAD51 and RAD59 orthologs of the pathogenic fungus Candida albicans. CaRad51 exhibited more than 50% identity with several other eukaryotes and the conserved the catalytic domain of a bacterial RecA. As compared to the parental strain, null strains of rad51 exhibited a filamentous morphology, had a decreased grow rate and exhibited a moderate sensitivity to UV light, oxidizing agents, and compounds that cause double-strand breaks (DSB), indicating a role in DNA repair. By comparison, the rad52 null had a higher percentage of filaments, a more severe growth defect and a greater sensitivity to DNA-damaging compounds. Null strains of rad59 showed a UV-sensitive phenotype but behaved similarly to the parental strain in the rest of the assays. As compared to Saccharomyces cerevisiae, C. albicans was much more resistant to bleomycin and the same was true for their respective homologous recombination (HR) mutants. These results indicate that, as described in S. cerevisiae, RAD52 plays a more prominent role than RAD51 in the repair of DSBs in C. albicans and suggest the existence of at least two Rad52-dependent HR pathways, one dependent and one independent of Rad51.

Fungal meiosis and parasexual reproduction--lessons from pathogenic yeast

Meiosis is an integral part of sexual reproduction in eukaryotic species. It performs the dual functions of halving the genetic content in the cell, as well as increasing genetic diversity by promoting recombination between chromosome homologs. Despite extensive studies of meiosis in model yeast, it is now apparent that both the regulation of meiosis and the machinery mediating recombination have significantly diverged, even between closely related species. To highlight this, we discuss new studies on sex in Candida species, a diverse collection of hemiascomycetes that are related to Saccharomyces cerevisiae and are important human pathogens. These provide new insights into the most conserved, as well as the most plastic, aspects of meiosis, meiotic recombination, and related parasexual processes.

The parasexual cycle in Candida albicans provides an alternative pathway to meiosis for the formation of recombinant strains

Candida albicans has an elaborate, yet efficient, mating system that promotes conjugation between diploid a and alpha strains. The product of mating is a tetraploid a/alpha cell that must undergo a reductional division to return to the diploid state. Despite the presence of several "meiosis-specific" genes in the C. albicans genome, a meiotic program has not been observed. Instead, tetraploid products of mating can be induced to undergo efficient, random chromosome loss, often producing strains that are diploid, or close to diploid, in ploidy. Using SNP and comparative genome hybridization arrays we have now analyzed the genotypes of products from the C. albicans parasexual cycle. We show that the parasexual cycle generates progeny strains with shuffled combinations of the eight C. albicans chromosomes. In addition, several isolates had undergone extensive genetic recombination between homologous chromosomes, including multiple gene conversion events. Progeny strains exhibited altered colony morphologies on laboratory media, demonstrating that the parasexual cycle generates phenotypic variants of C. albicans. In several fungi, including Saccharomyces cerevisiae and Schizosaccharomyces pombe, the conserved Spo11 protein is integral to meiotic recombination, where it is required for the formation of DNA double-strand breaks. We show that deletion of SPO11 prevented genetic recombination between homologous chromosomes during the C. albicans parasexual cycle. These findings suggest that at least one meiosis-specific gene has been re-programmed to mediate genetic recombination during the alternative parasexual life cycle of C. albicans. We discuss, in light of the long association of C. albicans with warm-blooded animals, the potential advantages of a parasexual cycle over a conventional sexual cycle.

Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex

Sexual reproduction is the dominant reproductive mode in eukaryotes but, in many taxa, it has never been observed. Molecular methods that detect evidence of sex are largely based on the genetic consequences of sexual reproduction. Here we describe a powerful new approach to directly search genomes for genes that function in meiosis. We describe a "meiosis detection toolkit", a set of meiotic genes that represent the best markers for the presence of meiosis. These genes are widely present in eukaryotes, function only in meiosis and can be isolated by degenerate PCR. The presence of most, or all, of these genes in a genome would suggest they have been maintained for meiosis and, implicitly, sexual reproduction. In contrast, their absence would be consistent with the loss of meiosis and asexuality. This approach will help to understand both meiotic gene evolution and the capacity for meiosis and sex in putative obligate asexuals.

Mating in Candida albicans and the search for a sexual cycle

Candida albicans is a normal part of the human microflora, but it is also an opportunistic fungal pathogen that causes both mucosal infections and life-threatening systemic infections. Until recently, C. albicans was thought to be asexual, existing only as an obligate diploid. However, a mating locus was identified that was homologous to those in sexually reproducing fungi, and mating of C. albicans strains was subsequently demonstrated in the laboratory. In this review, we compare and contrast the mating process in C. albicans with that of other fungi, particularly Saccharomyces cerevisiae, whose mating has been most intensively studied. Several features of the mating pathway appear unique to C. albicans, including aspects of gene regulation and cell biology, as well as the involvement of "white-opaque" switching, an alteration between two quasi-stable inheritable states. These specializations of the mating process may have evolved to promote the survival of C. albicans in the hostile environment of a mammalian host.

CaNAT1, a heterologous dominant selectable marker for transformation of Candida albicans and other pathogenic Candida species

A dominant selectable marker for Candida albicans and other Candida species, which confers resistance to nourseothricin, was characterized. In a heterologous promoter system and a recyclable cassette, the marker efficiently permitted deletion and complementation of C. albicans genes. Neither growth nor filamentous development was affected in strains expressing this marker.

The biology of mating in Candida albicans

Candida albicans has maintained an elaborate--but largely hidden--mating apparatus, which shares some features with the closely related 'model' yeast Saccharomyces cerevisiae, but which also has some important differences. The differences are particularly noteworthy, as they could indicate the strategies that allow C. albicans to survive and mate in the hostile environment of a mammalian host. Indeed, some features of C. albicans mating seem to be intimately connected to its host.

The Arabidopsis homologue of Xrcc3 plays an essential role in meiosis

The eukaryotic RecA homologue Rad51 is a key factor in homologous recombination and recombinational repair. Rad51-like proteins have been identified from yeast (Rad55, Rad57 and Dmc1) to vertebrates (Rad51B, Rad51C, Rad51D, Xrcc2, Xrcc3 and Dmc1). These Rad51-like proteins are all members of the genetic recombination and DNA damage repair pathways. The sequenced genome of Arabidopsis thaliana encodes putative homologues of all six vertebrate Rad51-like proteins. We have identified and characterized an Arabidopsis mutant defective for one of these, AtXRCC3, the homologue of XRCC3. atxrcc3 plants are sterile, while they have normal vegetative development. Cytological observation shows that the atxrcc3 mutation does not affect homologous chromosome synapsis, but leads to chromosome fragmentation after pachytene, thus disrupting both male and female gametogenesis. This study shows an essential role for AtXrcc3 in meiosis in plants and possibly in other higher eukaryotes. Furthermore, atxrcc3 cells and plants are hypersensitive to DNA-damaging treatments, supporting the involvement of this Arabidopsis Rad51-like protein in recombinational repair.

Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains

The human pathogenic fungus Candida albicans has traditionally been classified as a diploid, asexual organism. However, mating-competent forms of the organism were recently described that produced tetraploid mating products. In principle, the C.albicans life cycle could be completed via a sexual process, via a parasexual mechanism, or by both mechanisms. Here we describe conditions in which growth of a tetraploid strain of C.albicans on Saccharomyces cerevisiae 'pre-sporulation' medium induced efficient, random chromosome loss in the tetraploid. The products of chromosome loss were often strains that were diploid, or very close to diploid, in DNA content. If they inherited the appropriate MTL (mating-type like) loci, these diploid products were themselves mating competent. Thus, an efficient parasexual cycle can be performed in C.albicans, one that leads to the reassortment of genetic material in this organism. We show that this parasexual cycle-consisting of mating followed by chromosome loss-can be used in the laboratory for simple genetic manipulations in C.albicans.

White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating

Discovered over a decade ago, white-opaque switching in the human fungal pathogen Candida albicans is an alternation between two quasistable, heritable transcriptional states. Here, we show that white-opaque switching and sexual mating are both controlled by mating type locus homeodomain proteins and that opaque cells mate approximately 10(6) times more efficiently than do white cells. These results show that opaque cells are a mating-competent form of C. albicans and that this pathogen undergoes a white-to-opaque switch as a critical step in the mating process. As white cells are generally more robust in a mammalian host than are opaque cells, this strategy allows the organism to survive the rigors of life within a mammalian host, yet generate mating-competent cells.

Genomic evidence for a complete sexual cycle in Candida albicans

Candida albicans is a diploid fungus that has become a medically important opportunistic pathogen in immunocompromised individuals. We have sequenced the C. albicans genome to 10.4-fold coverage and performed a comparative genomic analysis between C. albicans and Saccharomyces cerevisiae with the objective of assessing whether Candida possesses a genetic repertoire that could support a complete sexual cycle. Analyzing over 500 genes important for sexual differentiation in S. cerevisiae, we find many homologues of genes that are implicated in the initiation of meiosis, chromosome recombination, and the formation of synaptonemal complexes. However, others are striking in their absence. C. albicans seems to have homologues of all of the elements of a functional pheromone response pathway involved in mating in S. cerevisiae but lacks many homologues of S. cerevisiae genes for meiosis. Other meiotic gene homologues in organisms ranging from filamentous fungi to Drosophila melanogaster and Caenorhabditis elegans were also found in the C. albicans genome, suggesting potential alternative mechanisms of genetic exchange.

Transcriptional control of cell type and morphogenesis in Candida albicans

Candida albicans has a number of transcriptional regulatory circuits that control aspects of cell type and cell morphogenesis. Recent work has uncovered a cryptic mating-type locus, and a variety of transcription factors that are important in regulation of the transition from yeast growth to hyphal growth. In some cases, the signalling pathways regulating these transcription factors are becoming defined. Analysis of phenotypic switching implicates internal factors, as well as external signals, in control of cellular morphogenesis.

Evidence for mating of the "asexual" yeast Candida albicans in a mammalian host

Since its classification nearly 80 years ago, the human pathogen Candida albicans has been designated as an asexual yeast. In this report, we describe the construction of C. albicans strains that were subtly altered at the mating-type-like (MTL) locus, a cluster of genes that resembles the mating-type loci of other fungi. These derivatives were capable of mating after inoculation into a mammalian host. C. albicans is a diploid organism, but most of the mating products isolated from a mouse host were tetrasomic for the two chromosomes that could be rigorously monitored and, overall, exhibited substantially higher than 2n DNA content. These observations demonstrated that C. albicans can recombine sexually.

Identification of a mating type-like locus in the asexual pathogenic yeast Candida albicans

Candida albicans, the most prevalent fungal pathogen in humans, is thought to lack a sexual cycle. A set of C. albicans genes has been identified that corresponds to the master sexual cycle regulators a1, alpha1, and alpha2 of the Saccharomyces cerevisiae mating-type (MAT) locus. The C. albicans genes are arranged in a way that suggests that these genes are part of a mating type-like locus that is similar to the mating-type loci of other fungi. In addition to the transcriptional regulators a1, alpha1, and alpha2, the C. albicans mating type-like locus contains several genes not seen in other fungal MAT loci, including those encoding proteins similar to poly(A) polymerases, oxysterol binding proteins, and phosphatidylinositol kinases.

Formation of azole-resistant Candida albicans by mutation of sterol 14-demethylase P450

The sterol 14-demethylase P450 (CYP51) of a fluconazole-resistant isolate of Candida albicans, DUMC136, showed reduced susceptibility to this azole but with little change in its catalytic activity. Twelve nucleotide substitutions, resulting in four amino acid changes, were identified in the DUMC136 CYP51 gene in comparison with a reported CYP51 sequence from a wild-type, fluconazole-susceptible C. albicans strain. Seven of these substitutions, including all of those causing amino acid changes, were located within a region covering one of the putative substrate recognition sites of the enzyme (SRS-1). Polymorphisms within this region were observed in several C. albicans isolates, and some were found to be CYP51 heterozygotes. Among the amino acid changes occurring in this region, only an alteration of Y132 was common among these fluconazole-resistant isolates, which suggests the importance of this residue to the fluconazole resistance of the target enzyme. DUMC136 and another fluconazole-resistant isolate were homozygotes with respect to CYP51, although the typical wild-type, fluconazole-susceptible C. albicans was a CYP51 heterozygote. These findings suggest that part of the fluconazole-resistant phenotype of C. albicans DUMC136 was acquired through a mutation-prone area of CYP51, an area which might promote the formation of fluconazole-resistant CYP51, along with a mechanism(s) which allows the formation of a homozygote of this altered CYP51 in this diploid pathogenic yeast.

Application of mating type gene technology to problems in fungal biology

In ascomycetes, the single mating type locus (MAT) controls sexual development. This locus is structurally unusual because the two alternate forms ("alleles") are completely dissimilar sequences, encoding different transcription factors, yet they occupy the same chromosomal position. Recently developed procedures allow efficient cloning of MAT genes from a wide array of filamentous ascomycetes, thereby providing MAT-based technology for application to several ongoing issues in fungal biology. This article first outlines the basic nature of MAT genes, then addresses the following topics: efficient cloning of MAT genes; the unusual molecular characteristics of these genes; phylogenetics using MAT; the issues of why some fungi are self-sterile, others self-fertile, and yet others asexual; the long-standing mystery of possible mating type switching in filamentous fungi; and finally the evolutionary origins of pathogenic capability.

Nonfilamentous C. albicans mutants are avirulent

Candida albicans and Saccharomyces cerevisiae switch from a yeast to a filamentous form. In Saccharomyces, this switch is controlled by two regulatory proteins, Ste12p and Phd1p. Single-mutant strains, ste12/ste12 or phd1/phd1, are partially defective, whereas the ste12/ste12 phd1/phd1 double mutant is completely defective in filamentous growth and is noninvasive. The equivalent cph1/cph1 efg1/efg1 double mutant in Candida (Cph1p is the Ste12p homolog and Efg1p is the Phd1p homolog) is also defective in filamentous growth, unable to form hyphae or pseudohyphae in response to many stimuli, including serum or macrophages. This Candida cph1/cph1 efg1/efg1 double mutant, locked in the yeast form, is avirulent in a mouse model.