Electrophoretic karyotype of the zygomycete Absidia glauca: evidence for differences between mating types

Genotypic analysis of variability in Zygomycetes. A mini-review

Different types of molecular markers are available for use in evolutionary and population studies of microscopic fungi. These approaches have proved their merits and have been successfully applied to a wide range of fungal species belonging in the Ascomycetes and Basidiomycetes. Species in the class Zygomycetes have been rather neglected from this aspect. This review discusses the information available from investigations of the genotypic variability in this group of fungi.

Electrophoretic karyotype analysis in fungi

The resolution of chromosomal-sized DNAs by PFGE has many applications that include karyotyping, strain identification of similar species, characterization of transformed strains, building of linkage maps, and preparation of DNA for genomic analysis. Successful electrophoretic separation of chromosomes is an empiric process in which the initial concentration of intact chromosome-sized DNA and the optimization of electrophoretic parameters are the most important experimental variables. Nonetheless, inherent attributes of the genome architecture of certain species may thwart success. When a karyotype contains numerous chromosomes of the same size and/or many large (greater than 8 Mb) chromosomes, no amount of manipulation of the electrophoretic parameters will resolve individual chromosome bands using present technology. Further, fungi display a surprising amount of intraspecific variation in both chromosome number and size, making it difficult to establish a standard "reference" karyotype for many species. Although PFGE is not a panacea for bringing genetics to species that lack classical genetic systems, it often does provide a way for developing a molecular linkage map in the absence of a formal genetic system. It is far faster than parasexual analysis in the discovery of linkage relationships. For genomics projects, DNA can be recovered from pulsed field gels and used to prepare chromosome-specific libraries. Where whole genome sequencing strategies are used, chromosomes separated by PFGE provide an anchor for sequencing data. Electrophoretic karyotypes can be probed with anonymous pieces of DNA from bacterial artificial chromosome (BAC) contigs, thereby facilitating the building of physical maps. In conclusion, despite its shortcomings, the PFGE technique underlies much of our current understanding of the physical nature of the fungal genome.

Electrophoretic karyotype of two Micromucor species

Electrophoretic karyotype analysis was applied to obtain information on the organisation and intrageneric variability of the nuclear genome in three Micromucor isolates of two different species (M. isabellina and M. ramanniana). A protoplast formation protocol, conditions for the preparation of highly-intact chromosome-size DNA molecules and for the separation of DNA molecules were established. The chromosomal banding patterns revealed substantial variability among the isolates: 11 to 14 chromosomal mobility groups were resolved. The DNA in the Micromucor chromosomes were rather small; their estimated sizes were calculated to be between 2.60 and 0.4 Mb. Using Saccharomyces cerevisiae and Schizosaccharomyces pombe as size standard, the minimum total genome sizes were estimated to be between 24.19 and 24.9 Mb.

Electrophoretic karyotype analysis of Crinipellis perniciosa, the causal agent of witches' broom disease of Theobroma cacao

Pulse-field gel electrophoresis (PFGE) was used to determine the genome size and characterize karyotypic differences in isolates of the cacao biotype of Crinipellis perniciosa (C-biotype). The karyotype analysis of four isolates from Brazil revealed that this biotype could be divided into two genotypes: one presenting six chromosomal bands and the other presenting eight. The size of the chromosomes ranged from 2.7 to 5.3 Mb. The different genotypes correlate with telomere-based PCR analysis. The isolates with six chromosomal bands had two that appeared to be doublets, as shown by densitometric analysis, indicating that the haploid chromosome number for this biotype is eight. The size of the haploid genomes was estimated at approximately 30 Mb by both PFGE and Feulgen-image analysis. DNA hybridization revealed that the rDNA sequences are clustered on a single chromosome and these sequences were located on different chromosomes in an isolate dependent manner. This is the first report of genome size and chromosomal polymorphism for the C-biotype of C. perniciosa.

Molecular mechanisms of chromosomal rearrangement in fungi

Both sexual and asexual fungi undergo chromosomal rearrangements, which are the main cause of karyotype variability among the populations. Different recombination processes can produce chromosomal reorganizations, both during mitosis and meiosis, but other mechanisms operate to limit the extent of the rearrangements; some of these mechanisms, such as the RIP (repeat-induced point mutations) of Neurospora crassa, have been well established for sexual fungi. In laboratory strains, treatments such as mutation and transformation enhance the appearance of chromosomal rearrangements. Different DNA sequences present in fungal genomes are able to promote these reorganizations; some of these sequences are involved in well-regulated processes (e.g., site-specific recombination) but most of them act simply as substrates for recombination events leading to DNA rearrangements. In Penicillium chrysogenum we have found that short specific DNA sequences are involved in tandem reiterations leading to amplification of the cluster of the penicillin biosynthesis genes. In some cases, specific chromosomal rearrangements have been associated with particular phenotypes (as occurs in adaptive-like mutants of Candida albicans and Candida stellatoidea), and they may play a role in genetic variability for environmental adaptation.

Radiation-induced chromosomal rearrangement as an aid to analysis of the genetic constitution of Phaffia rhodozyma

Electrophoretic karyotypes of 80 auxotrophic and morphological mutants obtained from two Phaffia rhodozyma strains (ATCC 24203 and ATCC 24229) by gamma-radiation were investigated. Contour-clamped homogeneous gel electrophoresis separation of the chromosomal size DNAs revealed 29 new chromosomal patterns after mutagen treatment. No correlation was found between a given type of chromosomal aberration and any phenotypic character. However, analysis of the chromosomal rearrangements proved to be useful for a more exact determination of chromosome number and genome size. The total genome size of ATCC 24229 was found to be 19.3 Mb, with nine chromosomes, while analysis of the mutant derivatives of ATCC 24203 suggested the presence of 11 chromosomes, with an estimated total genome size of 22.2 Mb. The advantages of the analysis of mutant electrophoretic karyotypes for genome characterization are discussed.

High copy number integration into the ribosomal DNA of the yeast Phaffia rhodozyma

This report describes a transformation system leading to stable high copy number integration into the ribosomal DNA (rDNA) of the astaxanthin-producing yeast Phaffia rhodozyma. A plasmid was constructed that contains the transposon Tn5 encoded kanamycin resistance gene (KmR) fused in frame to the 5'-terminal portion of the Phaffia actin gene. This marker, driven by the Phaffia actin promoter, confers resistance to G418 (Geneticin). The plasmid also contains a rDNA portion that comprises the 18S rDNA and promotes high copy integration leading to stable Phaffia transformants that maintained the plasmid at high copy number after 15 generations of non-selective growth. Phaffia, strain CBS 6938, was found to contain the rDNA units in clusters distributed over three chromosomes with a total copy number of 61. Phaffia transformants were shown to have over 50 copies of pGB-Ph9 integrated in tandem in chromosomes that contain rDNA loci. The chromosomal shifts that occur as a result of these integrations as shown by pulsed field electrophoresis strongly suggest that Phaffia is haploid.

Molecular karyotype of the phytopathogenic fungus Sclerotinia sclerotiorum

Molecular techniques have been used to characterize different field isolates of Sclerotinia sclerotiorum, an ubiquitous phytopathogen. Chromosomal DNA resolved by pulsed-field gel electrophoresis (PFGE) revealed that S. sclerotiorum contains at least 16 chromosomes ranging from 1.5 Mb to 4.0 Mb. The size of the haploid genome was estimated to be 43.5 Mb. Six field isolates with different levels of virulence on sunflower germlings or green beans were differentiated by random amplification of polymorphic DNA (RAPD), and analysed by clamped homogeneous electric field electrophoresis. This analysis revealed few chromosome-length polymorphisms among these strains. Chromosomal DNA hybridization indicated that the endopolygalacturonase-encoding pg1 gene is localized on the smallest chromosome of all the strains, whereas the ribosomal DNA mapped to different-sized chromosomes. The less-aggressive strain was characterized by the presence of a supernumary small band, presumably consisting of dsRNA. In contrast to numerous other phytopathogenic fungi, this study reveals a strong karyotypic stability among the strains of S. sclerotiorum which may be preserved by the sexual mode of reproduction of this species

Relationships between sexual processes and parasitic interactions in the host–pathogen systemAbsidia glauca–Parasitella parasitica

Parasitella parasitica is a facultative parasite of many Mucorales including Absidia glauca. The infection process includes the formation of a plasmatic continuum between host and parasite, which allows the invasion of the host by nuclei of the parasite. This process gives rise to interspecies recombinants. Auxotrophic A. glauca mutants are complemented by the transfer of genes from the parasite to the host. At the molecular level, we could show that plasmid-coded genes are also transferred. The successful formation of infection structures is mating-type dependent. Parasitella parasitica exclusively infects hosts belonging to the complementary mating type. The formation of infection structures is correlated with the ability to synthesise the sex pheromone trisporic acid, which is produced in mixed cultures by compatible combinations between host and parasite. Normally, trisporic acid is formed by a cooperative biosynthesis involving both mating types. Trisporic acid seems to be involved also in mediating the recognition between P. parasitica and A. glauca. To test the hypothesis of direct hormonal correlations between sex and parasitism, we have isolated one of the key enzymes for trisporic acid synthesis, dihydromethyltrisporic acid dehydrogenase, sequenced the N-termini of some proteolytic cleavage products, and have started to isolate the corresponding gene. Key words: mycoparasitism, zygomycetes, trisporic acid, Absidia glauca, Parasitella parasitica, Mucor.

Variability in genome organization of the zygomycete Parasitella parasitica

In addition to conventional methods for the identification of fungi, molecular techniques at the DNA level are increasingly being employed. In order to check the validity of such experimental approaches, we have analyzed the well-defined species Parasitella parasitica, which belongs to the family Mucoraceae (Mucorales, Zygometes). The seven strains of this species, which are available from international strain collections, were analyzed by several molecular methods: restriction fragment length polymorphism analysis (RFLP), the random primer-dependent polymerase chain reaction (RAPD-PCR), and electrophoretic karyotyping. Unexpectedly, these strains are highly diverse at the molecular level. By these techniques they can be divided consistently into two different groups. Nevertheless, all seven strains belong to a single species. They show no morphological differences and sexual spores (zygospores) were found in all possible combinations either within or between the two groups. Southern-blot analysis of genomic DNA of all P. parasitica strains with RAPD-PCR-derived labelled probes shows the existence of repetitive elements characteristic for only one group of P. parasitica. In addition, chromosome sizes, which were separated by rotating-field electrophoresis, were highly divergent, and ranged from 3 to 6.5 Mb in one group and between 2 and 4.5 Mb in the other. The RAPD-PCR patterns also discriminate both groups of P. parasitica. However, they are very similar if strains of a single group are compared. Therefore, we propose that the determination of fungal species by molecular techniques should be vetted at least by morphological and physiological parameters and, whenever possible, by mating experiments.

Electrophoretic karyotype of Mucor circinelloides

Contour-clamped homogeneous electric field (CHEF) gel electrophoresis was used to separate chromosomal size DNA molecules of two Mucor circinelloides strains. Electrophoretic karyotypes revealed the presence of eight distinct bands for the M. circinelloides f. lusitanicus strain, and four, presumably multiple, bands for the M. circinelloides f. gryseo-cyanus strain. The approximate sizes of the resolved chromosomal DNA bands ranged from 2.3 to 8.1 Mb, giving estimated genome sizes of 38.7 and 32.6 Mb, respectively. Hybridisation techniques were used to assign the leuA gene to a chromosome.

An electrophoretic karyotype of the cultivated mushroom--Agaricus bisporus

Thirteen chromosomal-sized DNA bands of the cultivated mushroom Agaricus bisporus have been resolved using the method of clamped homogeneous electric field (CHEF) electrophoresis. Using chromosome size standards from Schizosaccharomyces pombe, Saccharomyces cerevisiae and Candida albicans, the estimated size of the chromosomal DNAs ranged from 3.5 to 1.2 megabase pairs (Mb). By Southern hybridization with homologous gene probes, the chromosomal location of cellulase and laccase genes have been mapped. In addition, rDNA has been assigned to chromosomal bands using a heterologous gene probe. Genomic rearrangement is suggested in the commercial heterokaryon, as indicated by the presence of non-comigrating homologous chromosomes, identified by a number of probes for particular DNA sequences.

Electrophoretic karyotyping of the lignin-degrading basidiomycete Phanerochaete chrysosporium

Electrophoretic karyotyping of the two most widely studied strains of Phanerochaete chrysosporium, BKMF-1767 and ME-446, has been determined using transverse alternating field electrophoresis. The genomic DNA of BKMF-1767 was resolved into 10 chromosomes ranging in size from 1.8-5.0 Mb, amounting to a total genome size of about 29 Mb. The genomic DNA of strain ME-446, on the other hand, was resolved into 11 chromosomes, amounting to a total genome size of about 32 Mb. Lignin peroxidase genes have been localized to five chromosomes in strain BKMF-1767 and to four chromosomes in strain ME-446.

Transfer of genetic information from the mycoparasite Parasitella parasitica to its host Absidia glauca

The infection of the model organism Absidia glauca by P. parasitica is accompanied by the fusion of both mycelia. By two lines of evidence we were able to show that this process is associated with the transfer of genes. First, auxotrophically labelled A. glauca mutants are efficiently complemented as a consequence of transfer of the parasite's genetic material. Second, for a plasmid-coded dominant marker (neomycin resistance), which is expressed in either organism, we proved the presence of plasmid DNA in recombinant recipients by molecular analysis at the DNA level. We propose the term para-recombinants for describing recombinant inter-generic chimaerae, which are generated as a consequence of mycoparasitism.

Rapid identification and differentiation of yeasts by DNA and PCR fingerprinting

We have used the techniques of DNA fingerprinting and polymerase chain reaction (PCR) with probes specific for hypervariable repetitive DNA sequences (mini- and microsatellite DNAs) to analyze 36 yeast strains belonging to 10 species and 2 genera. Using (GTG)5, (GACA)4, phage M13 DNA and the M13 sequence GAGGGTGGCGGTTCT as probes and primers, respectively, we obtained DNA polymorphisms which allowed us to discriminate 23 biotechnologically important strains of the yeast Saccaromyces cerevisiae and to distinguish them from strains of S. pastorianus, S. bayanus and S. willianus. Our results demonstrate that both DNA and PCR fingerprinting are suitable tools for an easy, fast and reliable molecular typing of yeasts. The DNA fingerprinting method seems to be more sensitive than PCR fingerprinting with respect to the individualization of strains. Nevertheless, using the PCR fingerprinting technique we were able to unambigously discriminate between genotypes of different species. Therefore, PCR fingerprinting might become a useful tool in the classification of yeasts on the basis of phylogenetic relatedness.

The SEG1 element: a new DNA region promoting stable mitotic segregation of plasmids in the zygomycete Absidia glauca

A series of new vectors for the model zygomycete Absidia glauca was constructed on the basis of the structural neomycin resistance (Neor) gene controlled by the promoter of the gene for elongation factor 1 (TEF). In order to select for transformed colonies with a stable Neor phenotype, spores from primary transformants were pooled and grown for two sporulation cycles under non-selective conditions. Southern blot analysis of DNA from single spore isolates originating from independent transformant pools allowed the identification of two autonomously replicating plasmids. Retransformation of Escherichia coli and restriction analysis of the two plasmids provided evidence for spontaneous in vivo insertion of a new DNA element (SEG1) from the A. glauca genome. The inserted regions in both plasmids are essentially identical and do not represent repetitive DNA. Compared with other autonomously replicating vectors, these SEG1-containing plasmids are mitotically extremely stable and are passed on to the vegetative spore progeny of a retransformed A. glauca strain. We assume that SEG1 contains structural elements involved in partitioning and stable segregation of plasmids. For the construction of stable transformants of A. glauca, the SEG1 element may be regarded as a major breakthrough, because stabilization of transformed genetic traits by integration is difficult to achieve in all mucoraceous fungi and all known replicating plasmids are mitotically unstable.

Circular extrachromosomal DNA codes for a surface protein in the (+) mating type of the zygomycete Absidia glauca

A small protein with a molecular mass of 15 kDa, which is specifically found on the hyphal surface of a (+) mating-type strain of the model zygomycete Absidia glauca, was purified to electrophoretic homogeneity and partially sequenced. The corresponding gene was cloned by means of an oligonucleotide probe deduced from the protein sequence. It could be localized on an extrachromosomal circular DNA element with a total length of 1250 bp. Electron microscopic analysis of A. glauca DNA showed that small extrachromosomal DNAs with varying length are a common feature of this zygomycete. There are no indications of additional chromosomal copies of the gene for this surface protein, and the plasmid is absent from DNA preparations of the (-) mating type. The copy number ranges around three per haploid genome, and a single transcript with a length of 400 bp, coding for the surface protein, could be found by employing a hybridization probe which spans the complete fungal plasmid. This is the first report of naturally occurring extrachromosomal DNA in a Mucor-like fungus, and the only example where an integral protein of the cell wall is encoded by a plasmid.

Chromosomal and genetic analysis of the electrophoretic karyotype of Trichoderma reesei: mapping of the cellulase and xylanase genes

An electrophoretic karyotype has been established for Trichoderma reesei strain QM6a, and several of its derivatives, by pulsed-field gel electrophoresis. All strains examined appear to have seven chromosomes with a total genome size of approximately 33 megabases (Mb). The sizes of the chromosomal bands in strain QM6a are approximately 6.2, 6.0, 5.1, 4.2 (doublet), 3.6 and 3.2 Mb. Genes encoding the cellulase complex and xylanases of T. reesei have been mapped, as have several other genes.

Electrophoretic karyotyping of wild-type and mutant Trichoderma longibrachiatum (reesei) strains

An electrophoretic karyotype of Trichoderma longibrachiatum (reesei) was obtained using contour-clamped homogeneous electric field (CHEF) gel electrophoresis. Seven chromosomal DNA bands were separated in the wild-type T. longibrachiatum strain QM6a. The sizes of the chromosomal DNA bands ranged from 2.8 to 6.9 Mb, giving an estimated total genome size of about 33 Mb. The electrophoretic karyotype of the strain QM6a was compared to three hyper-celluloytic mutant strains, QM9414, RutC30 and VTT-D-79125. The chromosome pattern of the mutant QM9414 was quite similar to that of the wild-type QM6a except that the smallest chromosome differed somewhat in size. The VTT-D-79125 and RutC30 strains, which have undergone several mutagenesis steps, showed striking differences in their karyotype compared to the initial parent. The chromosomal DNA bands were identified using the previously characterized T. longibrachiatum genes (egl1, egl2, cbh1, cbh2, pgk1, rDNA) and random clones isolated from a genomic library. In all strains the cellulase genes cbh1, cbh2 and egl2 were located in the same linkage group (chromosome II in the wild-type), while the main endoglucanase, egl1, hybridized to another chromosomal DNA band (chromosome VI in the wild-type).

Electrophoretic karyotype of cellulolytic Penicillium janthinellum strains

The genome of the cellulolytic fungus Penicillium janthinellum BIOURGE was resolved completely by rotating field electrophoresis. The gel pattern revealed 8-10 different chromosomes. On the basis of data for yeast chromosome size standards from Schizosaccharomyces pombe and Saccharomyces cerevisiae, chromosome sizes in the range from 2.0 to 8 mb were estimated. By Southern hybridization with heterologous probes, the chromosomal locations of rDNA, the elongation factor EF1, actin and ubiquitin have all been mapped. In addition, first results with heterologous and homologous probes for cellulolytic genes from Trichoderma reesei and P. janthinellum are presented. In contrast to the other probes, signals obtained with cellulase genes are clearly distributed over several chromosomes.