A genetic map of Phycomyces blakesleeanus

Identification of the ergC gene involved in polyene drug sensitivity in the Mucorales species Phycomyces blakesleeanus

BACKGROUND

A strain of Phycomyces blakesleeanus (Mucorales, Mucoromycota) that was previously isolated after ultraviolet mutagenesis has altered responses to polyene antifungal drugs, sterol profiles, and phototropism of its sporangia. In this study, the genetic basis for these changes was sought.

METHODS AND RESULTS

Two base pair substitutions were identified in the mutant within a P. blakelesleeanus gene that is homologous to others characterized from fungi, such as the Saccharomyces cerevisiae ERG3 gene, encoding sterol Δ5,6-desaturase. The polyene resistance and growth reduction phenotypes co-segregated with mutations in the gene in genetic crosses. The P. blakelesleeanus wild type ergC gene complemented a S. cerevisiae deletion strain of ERG3.

CONCLUSIONS

This gene discovery may contribute towards better antifungal use in treating mucormycoses diseases caused by related species in the order Mucorales.

Fungal Sex: The Mucoromycota

Although at the level of resolution of genes and molecules most information about mating in fungi is from a single lineage, the Dikarya, many fundamental discoveries about mating in fungi have been made in the earlier branches of the fungi. These are nonmonophyletic groups that were once classified into the chytrids and zygomycetes. Few species in these lineages offer the potential of genetic tractability, thereby hampering the ability to identify the genes that underlie those fundamental insights. Research performed during the past decade has now established the genes required for mating type determination and pheromone synthesis in some species in the phylum Mucoromycota, especially in the order Mucorales. These findings provide striking parallels with the evolution of mating systems in the Dikarya fungi. Other discoveries in the Mucorales provide the first examples of sex-cell type identity being driven directly by a gene that confers mating type, a trait considered more of relevance to animal sex determination but difficult to investigate in animals. Despite these discoveries, there remains much to be gleaned about mating systems from these fungi.

A new genetic linkage map of the zygomycete fungus Phycomyces blakesleeanus

Phycomyces blakesleeanus is a member of the subphylum Mucoromycotina. A genetic map was constructed from 121 progeny of a cross between two wild type isolates of P. blakesleeanus with 134 markers. The markers were mostly PCR-RFLPs. Markers were located on 46 scaffolds of the genome sequence, covering more than 97% of the genome. Analysis of the alleles in the progeny revealed nine or 12 linkage groups, depending on the log of the odds (LOD) score, across 1583.4 cM at LOD 5. The linkage groups were overlaid on previous mapping data from crosses between mutants, aided by new identification of the mutations in primary metabolism mutant strains. The molecular marker map, the phenotype map and the genome sequence are overall congruent, with some exceptions. The new genetic map provides a genome-wide estimate for recombination, with the average of 33.2 kb per cM. This frequency is one piece of evidence for meiosis during zygospore development in Mucoromycotina species. At the same time as meiosis, transmission of non-recombinant chromosomes is also evident in the mating process in Phycomyces. The new map provides scaffold ordering for the genome sequence and a platform upon which to identify the genes in mutants that are affected in traits of interest, such as carotene biosynthesis, phototropism or gravitropism, using positional cloning.

Functional analysis of the Phycomyces carRA gene encoding the enzymes phytoene synthase and lycopene cyclase

Phycomyces carRA gene encodes a protein with two domains. Domain R is characterized by red carR mutants that accumulate lycopene. Domain A is characterized by white carA mutants that do not accumulate significant amounts of carotenoids. The carRA-encoded protein was identified as the lycopene cyclase and phytoene synthase enzyme by sequence homology with other proteins. However, no direct data showing the function of this protein have been reported so far. Different Mucor circinelloides mutants altered at the phytoene synthase, the lycopene cyclase or both activities were transformed with the Phycomyces carRA gene. Fully transcribed carRA mRNA molecules were detected by Northern assays in the transformants and the correct processing of the carRA messenger was verified by RT-PCR. These results showed that Phycomyces carRA gene was correctly expressed in Mucor. Carotenoids analysis in these transformants showed the presence of ß-carotene, absent in the untransformed strains, providing functional evidence that the Phycomyces carRA gene complements the M. circinelloides mutations. Co-transformation of the carRA cDNA in E. coli with different combinations of the carotenoid structural genes from Erwinia uredovora was also performed. Newly formed carotenoids were accumulated showing that the Phycomyces CarRA protein does contain lycopene cyclase and phytoene synthase activities. The heterologous expression of the carRA gene and the functional complementation of the mentioned activities are not very efficient in E. coli. However, the simultaneous presence of both carRA and carB gene products from Phycomyces increases the efficiency of these enzymes, presumably due to an interaction mechanism.

Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides

Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (-) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (-) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex.

Two origins for the gene encoding alpha-isopropylmalate synthase in fungi

BACKGROUND

The biosynthesis of leucine is a biochemical pathway common to prokaryotes, plants and fungi, but absent from humans and animals. The pathway is a proposed target for antimicrobial therapy.

METHODOLOGY/PRINCIPAL FINDINGS

Here we identified the leuA gene encoding alpha-isopropylmalate synthase in the zygomycete fungus Phycomyces blakesleeanus using a genetic mapping approach with crosses between wild type and leucine auxotrophic strains. To confirm the function of the gene, Phycomyces leuA was used to complement the auxotrophic phenotype exhibited by mutation of the leu3+ gene of the ascomycete fungus Schizosaccharomyces pombe. Phylogenetic analysis revealed that the leuA gene in Phycomyces, other zygomycetes, and the chytrids is more closely related to homologs in plants and photosynthetic bacteria than ascomycetes or basidiomycetes, and suggests that the Dikarya have acquired the gene more recently.

CONCLUSIONS/SIGNIFICANCE

The identification of leuA in Phycomyces adds to the growing body of evidence that some primary metabolic pathways or parts of them have arisen multiple times during the evolution of fungi, probably through horizontal gene transfer events.

New Mutants of Phycomyces blakesleeanus for (beta)-Carotene Production

The accumulation of (beta)-carotene by the zygomycete Phycomyces blakesleeanus is increased by mutations in the carS gene. The treatment of spores of carS mutants with N-methyl-N(prm1)-nitro-N-nitrosoguanidine led to the isolation, at very low frequencies, of mutants that produced higher levels of (beta)-carotene. Strain S556 produced about 9 mg of (beta)-carotene per g of dry mass when it was grown on minimal agar. Crosses involving strain S556 separated the original carS mutation from a new, unlinked mutation, carF. The carF segregants produced approximately as much carotene as did carS mutants, but they were unique in their ability to produce zygospores on mating and in their response to agents that increase carotenogenesis in the wild type. The carotene contents of carF segregants and carF carS double mutants were increased by sexual interaction and by dimethyl phthalate but were not increased by light or retinol. Mixed opposite-sex cultures of carF carS mutants contained up to 33 mg of (beta)-carotene per g of dry mass. Another strain, S444, produced more (beta)-carotene than did S556 but was marred by slow growth, defective morphology, and bizarre genetic behavior. In all the strains tested, the carotene concentration was minimal during the early growth phase and became higher and constant for several days in older mycelia.

Protein-DNA interactions in the promoter region of the Phycomyces carB and carRA genes correlate with the kinetics of their mRNA accumulation in response to light

Carotene biosynthesis in Phycomyces is photoinducible and carried out by phytoene dehydrogenase (encoded by carB) and a bifunctional enzyme possessing lycopene cyclase and phytoene synthase activities (carRA). A light pulse followed by periods of darkness produced similar biphasic responses in the expression of the carB and carRA genes, indicating their coordinated regulation. Specific binding complexes were formed between the carB-carRA intergenic region and protein extracts from wild type mycelia grown in the dark or 8min after irradiation. These two conditions correspond to the points at which the expression of both genes is minimal, suggesting that these binding complexes are involved in the down-regulation of photocarotenogenesis in Phycomyces. Protein extracts from carotene mutants failed to form the dark retardation complex, suggesting a role of these genes in the regulation of photocarotenogenesis. In contrast, protein extracts from phototropic mutants formed dark retardation complexes identical to that of the wild type.

Photobiology in the Zygomycota: multiple photoreceptor genes for complex responses to light

Light is an environmental signal that modulates many aspects of the biology of zygomycete fungi. Light regulation has been investigated in the zygomycetes Phycomyces blakesleeanus, Mucor circinelloides and Pilobolus crystallinus. Examples of light regulation include the phototropism of the fruiting bodies, the regulation of the development of reproductive structures, and the activation of the biosynthesis of β-carotene. In fungi blue light is perceived by proteins homologous to WC-1, a Neurospora crassa photoreceptor and Zn finger protein that interacts with WC-2 to form a photoresponsive transcription factor complex. Unlike ascomycete and basidiomycete fungi that usually have one wc-1 and one wc-2 gene, several studies have uncovered an unexpected multitude of genes similar to wc-1 and wc-2 in the genomes of several zygomycete fungi. Some of these genes are required for fungal photoresponses, but the function of many of them remains unknown. The presence of multiple wc-1 genes confirms previous suggestions of multiple blue-light photoreceptors in Phycomyces.

Phycomyces MADB interacts with MADA to form the primary photoreceptor complex for fungal phototropism

The fungus Phycomyces blakesleeanus reacts to environmental signals, including light, gravity, touch, and the presence of nearby objects, by changing the speed and direction of growth of its fruiting body (sporangiophore). Phototropism, growth toward light, shares many features in fungi and plants but the molecular mechanisms remain to be fully elucidated. Phycomyces mutants with altered phototropism were isolated approximately 40 years ago and found to have mutations in the mad genes. All of the responses to light in Phycomyces require the products of the madA and madB genes. We showed that madA encodes a protein similar to the Neurospora blue-light photoreceptor, zinc-finger protein WC-1. We show here that madB encodes a protein similar to the Neurospora zinc-finger protein WC-2. MADA and MADB interact to form a complex in yeast 2-hybrid assays and when coexpressed in E. coli, providing evidence that phototropism and other responses to light are mediated by a photoresponsive transcription factor complex. The Phycomyces genome contains 3 genes similar to wc-1, and 4 genes similar to wc-2, many of which are regulated by light in a madA or madB dependent manner. We did not detect any interactions between additional WC proteins in yeast 2-hybrid assays, which suggest that MADA and MADB form the major photoreceptor complex in Phycomyces. However, the presence of multiple wc genes in Phycomyces may enable perception across a broad range of light intensities, and may provide specialized photoreceptors for distinct photoresponses.

Influence of parental strains on the germination ofPhycomyces blakesleeanuszygospores

Phycomyces blakesleeanuswild-type NRRL1555( − ), the standard strain, when crossed with UBC21( + ), another wild type, gives zygospores that germinate in 50–60 days. By backcrossing to UBC21 and selecting for shorter dormancy we have isolated a ( − ) strain, A803, and a ( + ) strain A804, which when crossed give zygospores that germinate in 32 days, the shortest dormancy period found inPhycomyces.The same result was obtained when A803 was crossed with UBC21. Zygospore dormancy decreased as the parental strains became more isogenic with UBC21, but the number of zygospores giving germsporangia with viable germspores also decreased to zero in the third backcross. The existence of germspore-killer alleles in the strain UBC21 is postulated. The strains of shortest dormancy can be used as helper strains (Orejaset al.1985) in sexual crosses. Tetrad analysis of the cross NRRL1554 × S102, a two-factor cross, showed 90% of reciprocal ditypes plus tetratypes in the progeny, indicating that the ( + ) wild-type strain NRRL1554, when crossed with the standard strain, gives regular meiosis and, contrary to current beliefs, may be used inPhycomycesgenetic analysis.

Phycomyces and the biology of light and color

Phycomyces has been in the laboratories for about 140 years, sometimes following trends and fashions, but often anticipating them. Researchers have been attracted by the sensitive and precise responses of Phycomyces to light and other stimuli, coupled with easy manipulations and good adaptation to laboratory life. It is a simple prototype of the many organisms that use light as a source of information but not as a significant source of energy. Growth, development, genetics, and carotene production have been other subjects of pioneering research. Phycomyces was the second organism, after us, known to require a vitamin. It was one of the first organisms in the research on spontaneous mutants and the second, after Drosophila, in which mutations were induced artificially. It was used to coin the concept and the name of heterokaryosis. Phycomyces heterokaryons offer unique experimental possibilities, for instance in the study of gene function in vivo and the causes of cell death. An overall impression of parsimony and combinatorial gene usage arises from the genetic analysis of the complex functions of this fungus. The main subjects of recent attention have been the various reactions to light, gravitropism, and some aspects of metabolism, particularly the production of carotene. Interest in Phycomyces is slacking because of the repeated failures at transforming it stably with exogenous DNA.

Blue-light receptor requirement for gravitropism, autochemotropism and ethylene response in Phycomyces

Light, gravity and ethylene represent for plants and fungi important environment cues for spatial orientation and growth regulation. Coordination of the frequently conflicting stimuli requires signal-integration sites, which, however, remain largely unidentified. The genetic and physiological basis for signal integration was investigated with a set of phototropism mutants (genotype mad) of the UV- and blue-light-sensitive fungus Phycomyces blakesleeanus, which responds also to gravity, ethylene and nearby obstacles (autochemotropism or avoidance response). Both, class 1 and class 2 mutants display a reduced sensitivity to visible light. Class 1 mutants with defects in genes madA, B, C, I have preserved their sensitivity to gravity and ethylene, whereas class 2 mutants with defects in genes madD,E,F,G,J have lost it. We found that the phototropic sensitivity of class 1 mutants is affected roughly to the same extent in far UV and blue light. In contrast, the sensitivity loss of class 2 mutants is restricted mainly to the near-UV and the blue-light region, whereas the sensitivity to far UV is only mildly affected. This behavior of the class 2 mutants indicates that different photoreceptors mediate phototropism in far-UV and in near-UV/ blue light. The photogravitropic action spectra for two class 2 mutants with defects in genes madF and madJ display distortions between 342 and 530 nm and a bathochromic shift relative to the action spectrum of the wild type. These features indicate that the madF and madJ mutants are affected at the level of the blue-light photoreceptor system. As an implication we infer that an intact near-UV/blue-light photoreceptor system is required even in darkness for negative gravitropism, the ethylene response and autochemotropism. In Phycomyces, signal integration occurs, at least in part, at the level of the near-UV/blue-light photoreceptor system.

Genetic characterization of two phototropism mutants of Phycomyces with defects in the genes madI and madJ

Two Phycomyces genes, madI and madJ, which are involved in phototropism, were characterized by recombination and complementation analyses. The madI gene was located on linkage group IV of the genetic map of Phycomyces, 27 map units away from the gene carA. Complementation and recombination studies involving the genes madD, madE, madF, and madG, in combination with previous genetic studies, show that the recently isolated mad-407 mutation defines a novel behavioural gene, madJ, of Phycomyces. A regulatory role of the madJ gene product in the light-sensory transduction pathway is suggested.

Isolation and characterization of phototropism mutants of Phycomyces insensitive to ultraviolet light

Phototropism mutants of the zygomycete fungus Phycomyces blakesleeanus were isolated on the basis of their loss of responsivity to UV light. Four of these mutants had retained a partial sensitivity to near-UV and to blue light. Gravitropism and the avoidance response were unaffected in these mutants. One mutant, A909, had lost most of its sensitivity to near-UV and blue light while the sensitivity to far-UV light was only slightly affected. Additionally, the gravitropic and the avoidance responses were significantly reduced in A909. A complementation analysis of the five strains of Phycomyces with known phototropism mutants indicated that strains A896, A897, and A898 were defective in the madA gene, and that A905 was affected in the madC gene. In strain A909 the input, as well as the output, of the transduction chain is affected.

Isolation, characterization and mapping of pyrimidine auxotrophs of Phycomyces blakesleeanus

A total of seven pyrimidine auxotrophs of Phycomyces were isolated from among 5-fluoroorotate acid (5-FOA)-resistant mutants. They were classified by complementation into two groups. A representative mutant strain belonging to one group was deficient in orotate phosphoribosyl transferase (OPRTase; EC 2.4.2.10) activity; the mutant strain belonging to the second group was deficient in orotidine-5'-monophosphate decarboxylase (OMPdecase; EC 4.1.1.23). These mutants are defective in the genes pyrF and pyrG respectively. The results from random spore analysis, tetrad analysis, and gene-centromere distances showed that these two markers are located in linkage group VI, with pyrG being a proximal marker and pyrF a distal one.

Heterologous transformation of Mucor circinelloides with the Phycomyces blakesleeanus leu1 gene

The leu1 gene of Phycomyces blakesleeanus was isolated within a HindIII-HindIII genomic DNA fragment by heterologous hybridization screening of a cosmid library, making use of the Mucor circinelloides leuA gene as a probe. The complete nucleotide sequence of this fragment reveals a single 2070 bp ORF with no introns, which presents at least 68% homology with that of the leuA gene. The P. blakesleeanus leu1 gene has also been expressed in the M. circinelloides mutant R7B (leu-), which was used to isolate the leuA gene by complementation. The homology with other known sequences shows that the leu1 gene encodes the P. blakesleeanus alpha-IPM (isopropylmalate) isomerase.

Isolation and molecular analysis of the orotidine-5'-phosphate decarboxylase gene (pyrG) of Phycomyces blakesleeanus

The pyrG gene of Phycomyces was isolated from a Phycomyces genomic library, constructed in the cosmid pHS255, by hybridization with a 170 bp fragment of the pyrG gene of Aspergillus niger. This fragment includes a consensus sequence found in almost all species in which the orotidine-5'-phosphate decarboxylase (OMPdecase) gene has been sequenced. The complete nucleotide sequence of the cloned pyrG gene from Phycomyces was determined and the transcription start sites mapped. In the predicted amino acid sequence there are regions of strong homology to the equivalent genes of Saccharomyces cerevisiae, A. niger, Schizophyllum commune and Homo sapiens. Analysis of the sequence revealed the presence of two introns. The precise length and location of these introns was determined by sequencing the pyrG cDNA and comparing it with the genomic clone. Non-coding flanking regions showed obvious homology to the consensus TATA and CAAT boxes, and the polyadenylation signal "AATAAA". The pyrG gene is the second Phycomyces gene that has been cloned and analysed. This is the first time that introns have been reported in Phycomyces.

A new gene (madI) involved in the phototropic response of Phycomyces

Only eight genes are known to be involved in the phototropic response of Phycomyces (madA-H). Mutants affected in these genes have played a major role in the analysis of photosensory transduction processes in this system. A set of new mutants isolated by Alvarez et al. (1989) that are unable to bend towards dim unilateral blue light were studied by complementation and recombination. Two of these mutants have mutations in madE, one has a mutation in madF and one is a double madE madF mutant. The three remaining mutants tested did not complement each other and showed positive complementation with strains carrying mutations in the genes madA, madB, and madC, indicating that they carried mutations in a new gene designated madI. Recombination analysis showed that madI is unlinked to madA, madB and madC.

Electrophoretic analysis of proteins from Phycomyces mutants with abnormal tropisms

Certain phototropism mutants of Phycomyces blakesleeanus show defective bending responses (tropisms) to stimuli besides light, such as gravity, wind, and barriers. These so-called "stiff" mutants are affected in four genes (madD to madG). Using two-dimensional gel electrophoresis, we have analyzed polypeptides from microsomal and soluble fractions obtained from the wild type, four single mutants, and six double mutants affected in all pairwise combinations of the four genes. Consistent differences in spot patterns for madE and madF mutants were found in microsomal fractions but not in soluble fractions. In madE mutants, two spots designated E1 (52 kDa, pI 6.65) and E2 (50 kDa, pI 6.65) were altered. E1 appeared denser in the wild type than in the madE mutants, while the reverse was true for E2. The spots E1 and E2 are probably under regulatory control by madE, perhaps involving posttranslational modification. A protein spot, F1 (53 kDa, pI 6.1), was present on the wild-type gels but absent from all gels for madF mutants. The F1 polypeptide probably represents the madF gene product.

Mapping of the rib5 gene in Saccharomyces cerevisiae using UV light as an enhancer of rad52-mediated chromosome loss

Rib5 mutants of S. cerevisiae are blocked at the end of the riboflavin biosynthetic pathway. Using UV light to increase rad52-mediated chromosome loss, we have assigned the rib5 mutation to chromosome II. Tetrad analysis of crosses between rib5 and other markers on chromosome II shows that the RIB5 gene is located on the right arm of this chromosome, closely linked to HIS7.