Discrepancies between recombination frequencies and physical distances in Aspergillus nidulans: implications for gene identification

Positional cloning in Cryptococcus neoformans and its application for identification and cloning of the gene encoding methylenetetrahydrofolate reductase

Cryptococcus neoformans, a basidiomycetous human pathogenic yeast, has been widely used in research fields in medical mycology as well as basic biology. Gene cloning or identification of the gene responsible for a mutation of interest is a key step for functional analysis of a particular gene. The availability therefore, of the multiple methods for cloning is desirable. In this study, we proposed a method for a mapping-based gene identification/cloning (positional cloning) method in C. neoformans. To this end, we constructed a series of tester strains, one of whose chromosomes was labeled with the URA5 gene. A heterozygous diploid constructed by crossing one of the tester strains to a mutant strain of interest loses a chromosome(s) spontaneously, which is the basis for assigning a recessive mutant gene to a particular chromosome in the mitotic mapping method. Once the gene of interest is mapped to one of the 14 chromosomes, classical genetic crosses can then be performed to determine its more precise location. The positional information thus obtained can then be used to significantly narrow down candidate genes by referring to the Cryptococcus genome database. Each candidate gene is then examined whether it would complement the mutation. We successfully applied this method to identify CNA07390 encoding methylenetetrahydrofolate reductase as the gene responsible for a methionine-requiring mutant in our mutant collection.

In Aspergillus nidulans the suppressors suaA and suaC code for release factors eRF1 and eRF3 and suaD codes for a glutamine tRNA

In Aspergillus nidulans, after extensive mutagenesis, a collection of mutants was obtained and four suppressor loci were identified genetically that could suppress mutations in putative chain termination mutations in different genes. Suppressor mutations in suaB and suaD have a similar restricted spectrum of suppression and suaB111 was previously shown to be an alteration in the anticodon of a gln tRNA. We have shown that like suaB, a suaD suppressor has a mutation in the anticodon of another gln tRNA allowing suppression of UAG mutations. Mutations in suaA and suaC had a broad spectrum of suppression. Four suaA mutations result in alterations in the coding region of the eukaryotic release factor, eRF1, and another suaA mutation has a mutation in the upstream region of eRF1 that prevents splicing of the first intron within the 5'UTR. Epitope tagging of eRF1 in this mutant results in 20% of the level of eRF1 compared to the wild-type. Two mutations in suaC result in alterations in the eukaryotic release factor, eRF3. This is the first description in Aspergillus nidulans of an alteration in eRF3 leading to suppression of chain termination mutations.

Virulence regulation of phytopathogenic fungi by pH

SIGNIFICANCE

Postharvest pathogens can start its attack process immediately after spores land on wounded tissue, whereas other pathogens can forcibly breach the unripe fruit cuticle and then remain quiescent for months until fruit ripens and then cause major losses.

RECENT ADVANCES

Postharvest fungal pathogens activate their development by secreting organic acids or ammonia that acidify or alkalinize the host ambient surroundings.

CRITICAL ISSUES

These fungal pH modulations of host environment regulate an arsenal of enzymes to increase fungal pathogenicity. This arsenal includes genes and processes that compromise host defenses, contribute to intracellular signaling, produce cell wall-degrading enzymes, regulate specific transporters, induce redox protectant systems, and generate factors needed by the pathogen to effectively cope with the hostile environment found within the host. Further, evidence is accumulating that the secreted molecules (organic acids and ammonia) are multifunctional and together with effect of the ambient pH, they activate virulence factors and simultaneously hijack the plant defense response and induce program cell death to further enhance their necrotrophic attack.

FUTURE DIRECTIONS

Global studies of the effect of secreted molecules on fruit pathogen interaction, will determine the importance of these molecules on quiescence release and the initiation of fungal colonization leading to fruit and vegetable losses.

Role of the zinc finger transcription factor SltA in morphogenesis and sterigmatocystin biosynthesis in the fungus Aspergillus nidulans

Potassium, a widely accepted macronutrient, is vital for many physiological processes such as regulation of cell volume, maintenance of intracellular pH, synthesis of proteins and activation of enzymes in filamentous fungi. Another cation, calcium, plays an essential role in many signaling processes from lower to higher eukaryotes. Imbalance in the intracellular ionic levels of potassium or calcium causes adverse effects on cell growth, morphology and development, and eventually death. Previous studies on the adaptation of Aspergillus nidulans to salt and osmotic stress conditions have revealed the role of SltA, a C₂H₂ zinc finger transcription factor in cation homeostasis. SltA is highly conserved in the Ascomycota phylum with no identifiable homolog in S. cerevisiae and other yeast-like fungi, and prevents toxicity by the cations Na⁺, K⁺, Li⁺, Cs⁺ and Mg²⁺, but not by Ca²⁺. However its role in morphology and biosynthesis of natural products such as mycotoxins remained unknown. This study shows the first characterization of the role of calcium and SltA fungal homologs in morphogenesis using the model system A. nidulans. Addition of potassium to sltA deletion mutants resulted in decreased levels of sterigmatocystin production. A similar phenotype was observed for both types of mutants in veA1 and veA⁺ genetic background. Expression of the sterigmatocystin genes aflR and stcU was strongly reduced in sltA deletion mutant when K⁺ was added. Additionally, increased concentrations of K⁺ drastically reduced sexual and asexual development, as well as radial growth in deletion sltA colonies. This reduction was accompanied by lower expression of the morphology related genes nsdD, steA and brlA. Interestingly, addition of calcium was able to stimulate asexual and sexual development and remediate the deletion sltA phenotype, including defects in morphology and toxin production.

Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ∼52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.

The mode of reproduction in natural populations of ascomycetous fungus, Emericella nidulans, from Israel

The mode of reproduction of the soil ascomycetous fungus Emericella nidulans of Israeli populations was studied using 15 microsatellite (simple sequence repeats or SSR) trinucleotide markers. The study was performed in three canyons: two located in the northern part of Israel (Mount Carmel and western Upper Galilee) and one in the southern Negev desert. In each canyon, E. nidulans strains were isolated from the opposite slopes and (in the desert canyon) the valley bottom. Testing the reproductive structure of the populations indicated the presence of sexuality in the northern population and predominant clonality in the desert population. The predominantly clonal character of the desert population of E. nidulans was explained by the assumption that for relevant multilocus systems of a fungus, only several haplotypes can survive in the rather constant, extremely stressful desert conditions. Additionally, the very low density of E. nidulans populations in the soil of the desert canyon, which reduces the probability of finding a sexual partner, might favour predominant clonality via selfing. Increasing sexuality in E. nidulans populations on the north-facing slopes of the northern canyons may be a result of biotic stress (pressure of competitive fungal species), due to the more mild ecological conditions in these canyons.

Analysis of a novel calcium auxotrophy in Aspergillus nidulans

In Aspergillus nidulans a combination of null mutations in halA, encoding a protein kinase, and sltA, encoding a zinc-finger transcription factor having no yeast homologues, results in an elevated calcium requirement (‘calcium auxotrophy’) without impairing net calcium uptake. sltA⁻ (±halA⁻) mutations result in hypertrophy of the vacuolar system. In halA⁻sltA⁻ (and sltA⁻) strains, transcript levels for pmcA and pmcB, encoding vacuolar Ca²⁺-ATPase homologues, are highly elevated, suggesting a regulatory relationship between vacuolar membrane area and certain vacuolar membrane ATPase levels. Deletion of both pmcA and pmcB strongly suppresses the ‘calcium auxotrophy’. Therefore the ‘calcium auxotrophy’ possibly results from excessive vacuolar calcium sequestration, causing cytosolic calcium deprivation. Null mutations in nhaA, homologous to Saccharomyces cerevisiaeNHA1, encoding a plasma membrane Na⁺/H⁺ antiporter effluxing Na⁺ and K⁺, and a non-null mutation in trkB, homologous to S. cerevisiaeTRK1, encoding a plasma membrane high affinity K⁺ transporter, also suppress the calcium auxotrophy.

Microsatellite Diversity in Natural Populations of Ascomycetous Fungus, Emericella Nidulans, from Different Climatic-Edaphic Conditions in Israel

The genetic divergence of Israeli populations of the soil ascomycetous fungusEmericella nidulanswas studied on regional and local scales using fifteen microsatellite (SSR) markers. The study was performed in the framework of the "Evolution Canyon" research program at the Institute of Evolution, University of Haifa, in three "Evolution Canyons" (ECs): EC I (Mt. Carmel), EC II (western Upper Galilee), and EC III (the southern Negev desert). The first two canyons (EC I and EC II) are located in the northern part of Israel at a distance of 38 km apart; EC III is located southward at a distance of nearly 350 km from the northern ECs. In each canyon,E. nidulansstrains were isolated from opposite slopes and, in EC III, from the valley bottom. All three EC populations ofE. nidulanswere found to be genetically distinct. The estimated genetic divergences correspond to geographical distances and ecological differences between the three studied canyons. On a regional scale, simple sequence repeat (SSR) polymorphism tends to increase with severity of ecological conditions. In general, both environmental parameters (soil moisture and temperature) and genetic factors (predicted number of repeats in SSR markers, distance from marker to centromere, codon evolutionary chronologies, and hydrophobic vs. hydrophilic character of encoded amino acid) influenced genetic diversity ofE. nidulanspopulations.

Phenotypes of mutations in the 5'-UTR of a limiting transcription factor in Aspergillus nidulans can be accounted for by translational inhibition and leaky scanning

The uaY gene encodes the transcriptional activator of purine catabolism genes in Aspergillus nidulans. uaY12 results in strongly defective growth on purines as nitrogen sources and in strongly diminished transcription of UaY-regulated genes. This mutation introduces an ATG codon 64 bp upstream of the uaY ATG, generating a 68-codon open reading frame (uORFA), overlapping with the uaY ORF. uaY12 revertants fall into three categories: i. The majority eliminate the aberrant ATG. The growth and transcriptional phenotypes of these revertants are identical to those of the wild type. i. Two revertants create a stop codon in frame with the uaY12 aberrant ATG, shortening the length of the uORFA, thus uORFA no longer overlaps the uaY ORF. The latter are partial suppressors of the uaY12 mutation, while chain termination suppressors, in turn, suppress this novel phenotype. iii. Two partial suppressors are unlinked to uaY. These two mutations result in a pleiotropic phenotype usually associated with ribosomal proteins. We hypothesize that uORFA strongly diminishes translation of the uaY ORF and that revertants negate this effect by a number of different mechanisms. The first-AUG rule and the phenomena of translational inhibition and leaky scanning provide a coherent explanation of the results presented in this article.

Ras GTPase-activating protein regulation of actin cytoskeleton and hyphal polarity in Aspergillus nidulans

Aspergillus nidulans gapA1, a mutation leading to compact, fluffy colonies and delayed polarity establishment, maps to a gene encoding a Ras GTPase-activating protein. Domain organization and phylogenetic analyses strongly indicate that GapA regulates one or more "true" Ras proteins. A gapADelta strain is viable. gapA colonies are more compact than gapA1 colonies and show reduced conidiation. gapADelta strains have abnormal conidiophores, characterized by the absence of one of the two layers of sterigmata seen in the wild type. gapA transcript levels are very low in conidia but increase during germination and reach their maximum at a time coincident with germ tube emergence. Elevated levels persist in hyphae. In germinating conidiospores, gapADelta disrupts the normal coupling of isotropic growth, polarity establishment, and mitosis, resulting in a highly heterogeneous cell population, including malformed germlings and a class of giant cells with no germ tubes and a multitude of nuclei. Unlike wild-type conidia, gapADelta conidia germinate without a carbon source. Giant multinucleated spores and carbon source-independent germination have been reported in strains carrying a rasA dominant active allele, indicating that GapA downregulates RasA. gapADelta cells show a polarity maintenance defect characterized by apical swelling and subapical branching. The strongly polarized wild-type F-actin distribution is lost in gapADelta cells. As GapA-green fluorescent protein shows cortical localization with strong predominance at the hyphal tips, we propose that GapA-mediated downregulation of Ras signaling at the plasma membrane of these tips is involved in the polarization of the actin cytoskeleton that is required for hyphal growth and, possibly, for asexual morphogenesis.

Identification of a mitotic recombination hotspot on chromosome III of the asexual fungus Aspergillus niger and its possible correlation with [corrected] elevated basal transcription

Genetic recombination is an important tool in strain breeding in many organisms. We studied the possibilities of mitotic recombination in strain breeding of the asexual fungus Aspergillus niger. By identifying genes that complemented mapped auxotrophic mutations, the physical map was compared to the genetic map of chromosome III using the genome sequence. In a program to construct a chromosome III-specific marker strain by selecting mitotic crossing-over in diploids, a mitotic recombination hotspot was identified. Analysis of the mitotic recombination hotspot revealed some physical features, elevated basal transcription and a possible correlation with purine stretches.

Genetic linkage map and expression analysis of genes expressed in the lamellae of the edible basidiomycete Pleurotus ostreatus

Pleurotus ostreatus is an industrially cultivated basidiomycete with nutritional and environmental applications. Its genome contains 35 Mbp organized in 11 chromosomes. There is currently available a genetic linkage map based predominantly on anonymous molecular markers complemented with the mapping of QTLs controlling growth rate and industrial productivity. To increase the saturation of the existing linkage maps, we have identified and mapped 82 genes expressed in the lamellae. Their manual annotation revealed that 34.1% of the lamellae-expressed and 71.5% of the lamellae-specific genes correspond to previously unknown sequences or to hypothetical proteins without a clearly established function. Furthermore, the expression pattern of some genes provides an experimental basis for studying gene regulation during the change from vegetative to reproductive growth. Finally, the identification of various differentially regulated genes involved in protein metabolism suggests the relevance of these processes in fruit body formation and maturation.