A variegated position effect in Aspergillus nidulans

Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism

Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.

Asexual sporulation in Aspergillus nidulans

The formation of mitotically derived spores, called conidia, is a common reproductive mode in filamentous fungi, particularly among the large fungal class Ascomycetes. Asexual sporulation strategies are nearly as varied as fungal species; however, the formation of conidiophores, specialized multicellular reproductive structures, by the filamentous fungus Aspergillus nidulans has emerged as the leading model for understanding the mechanisms that control fungal sporulation. Initiation of A. nidulans conidiophore formation can occur either as a programmed event in the life cycle in response to intrinsic signals or to environmental stresses such as nutrient deprivation. In either case, a development-specific set of transcription factors is activated and these control the expression of each other as well as genes required for conidiophore morphogenesis. Recent progress has identified many of the earliest-acting genes needed for initiating conidiophore development and shown that there are at least two antagonistic signaling pathways that control this process. One pathway is modulated by a heterotrimeric G protein that when activated stimulates growth and represses both asexual and sexual sporulation as well as production of the toxic secondary metabolite, sterigmatocystin. The second pathway apparently requires an extracellular signal to induce sporulation-specific events and to direct the inactivation of the first pathway, removing developmental repression. A working model is presented in which the regulatory interactions between these two pathways during the fungal life cycle determine whether cells grow or develop.

Chromosome rearrangements in Neurospora and other filamentous fungi

Knowledge of fungal chromosome rearrangements comes primarily from N. crassa, but important information has also been obtained from A. nidulans and S. macrospora. Rearrangements have been identified in other Sordaria species and in Cochliobolus, Coprinus, Magnaporthe, Podospora, and Ustilago. In Neurospora, heterozygosity for most chromosome rearrangements is signaled by the appearance of unpigmented deficiency ascospores, with frequencies and ascus types that are characteristic of the type of rearrangement. Summary information is provided on each of 355 rearrangements analyzed in N. crassa. These include 262 reciprocal translocations, 31 insertional translocations, 27 quasiterminal translocations, 6 pericentric inversions, 1 intrachromosomal transposition, and numerous complex or cryptic rearrangements. Breakpoints are distributed more or less randomly among the seven chromosomes. Sixty of the rearrangements have readily detected mutant phenotypes, of which half are allelic with known genes. Constitutive mutations at certain positively regulated loci involve rearrangements having one breakpoint in an upstream regulatory region. Of 11 rearrangements that have one breakpoint in or near the NOR, most appear genetically to be terminal but are in fact physically reciprocal. Partial diploid strains can be obtained as recombinant progeny from crosses heterozygous for insertional or quasiterminal rearrangements. Duplications produced in this way precisely define segments that cover more than two thirds of the genome. Duplication-producing rearrangements have many uses, including precise genetic mapping by duplication coverage and alignment of physical and genetic maps. Typically, fertility is greatly reduced in crosses parented by a duplication strain. The finding that genes within the duplicated segment have undergone RIP mutation in some of the surviving progeny suggests that RIP may be responsible for the infertility. Meiotically generated recessive-lethal segmental deficiencies can be rescued in heterokaryons. New rearrangements are found in 10% or more of strains in which transforming DNA has been stably integrated. Electrophoretic separation of rearranged chromosomal DNAs has found useful applications. Synaptic adjustment occurs in inversion heterozygotes, leading progressively to nonhomologous association of synaptonemal complex lateral elements, transforming loop pairing into linear pairing. Transvection has been demonstrated in Neurospora. Beginnings have been made in constructing effective balancers. Experience has increased our understanding of several phenomena that may complicate analysis. With some rearrangements, nondisjunction of centromeres from reciprocal translocation quadrivalents results in 3:1 segregation and produces asci with four deficiency ascospores that occupy diagnostic positions in linear asci. Three-to-one segregation is most frequent when breakpoints are near centromeres. With some rearrangements, inviable deficiency ascospores become pigmented. Diagnosis must then depend on ascospore viability. In crosses between highly inbred strains, analysis may be handicapped by random ascospore abortion. This is minimized by using noninbred strains as testers.

The validity of the Aspergillus nidulans linkage map

The Aspergillus nidulans linkage map is reviewed as a background to physical mapping by cosmid cross-hybridization and genome sequencing. DNA-based methods depend on contiguity, so that the resulting maps are only as good as the weakest link, whereas each new marker added to a linkage map can provide independent confirmation of the positions of its neighbors. For all eight chromosomes of A. nidulans a reliable framework has been provided by analysis of mitotic crossing over, in many cases substantiated by the study of translocation disomics. Building on this framework, there is a backbone of loci linked by reliable three-point meiotic mapping and a second set of less precisely mapped loci. The result is a map with a high degree of self-consistency although some areas of uncertainty or conflict are also noted.

An intragenic map of the brlA locus of Aspergillus nidulans

We have constructed an intragenic map for the Aspergillus nidulans brlA gene, mutants in which are distinguishable by visual criteria only. Most of the leaky phenotype mutants map near the right (3') end. The gene shows distinct recombinational polarity consistent with recombination initiation at the promoter (centromere-proximal) end of the gene. brlA12 and brlA20 mutants gave abnormal DNA restriction patterns consistent with the III; VIII and VI; VIII translocations, respectively, determined by haploidization.

X-ray-induced specific locus mutations in the ad-3 region of two-component heterokaryons of Neurospora crassa. I. Modification of the heterozygous effects of multilocus deletions covering the ad-3A or ad-3B loci

The basis for the reduced growth rates of heterokaryons between strains carrying nonallelic combinations of gene/point mutations (ad-3R) and multilocus deletion mutations (ad-3IR) has been investigated by a simple genetic test. The growth rates of forced 2-component heterokaryons (dikaryons) between multilocus deletion mutations were compared with forced 3-component heterokaryons (trikaryons) containing an ad-3AR ad-3BR double mutant as their third component. Since the third component has no genetic damage at other loci immediately adjacent to the ad-3A or ad-3B locus, the growth rate on minimal medium depends on the functional activity of the unaltered (and presumed "wild-type") ad-3A and ad-3B loci in the first two components. In many cases, the requirements of the original dikaryons have been satisfied by the addition of unaltered genes (in the third component), and these trikaryons grow at wild-type rate on minimal medium. Those trikaryons growing at less than wild-type rate were shown to be adenine-requiring, and wild-type growth rate was obtained with the addition of low levels of adenine to the medium. Such tests in the present experiments have shown that ad-3IR mutations result not only in inactivation of the ad-3 loci by multilocus deletion but also, in many cases, in partial gene inactivation by an unknown mechanisms at other loci in the immediately adjacent regions. The heterozygous effects observed in our present experiments with multilocus deletions in Neurospora can be explained either by a spreading-type position effect of the type found by others in Drosophila, mice, Oenothera and Aspergillus or by undetected genetic damage ("cryptic mutations") in the immediately adjacent genetic regions. An attempt will be made to distinguish between these two alternative hypotheses with techniques for DNA cloning and sequencing in future experiments.

Isolation and physical characterization of three essential conidiation genes from Aspergillus nidulans

We cloned and characterized three genes from Aspergillus nidulans, designated brlA, abaA, and wetA, whose activities are required to complete different stages of conidiophore development. Inactivation of these genes causes major abnormalities in conidiophore morphology and prevents expression of many unrelated, developmentally regulated genes, without affecting the expression of nonregulated genes. The three genes code for poly(A)+ RNAs that begin to accumulate at different times during conidiation. The brlA- and abaA-encoded RNAs accumulate specifically in cells of the conidiophore. The wetA-encoded RNA accumulates in mature conidia. Inactivation of the brlA gene prevents expression of the abaA and wetA genes, whereas inactivation of the abaA gene prevents expression of the wetA gene. Our results confirm genetic predictions as to the temporal and spatial patterns of expression of these genes and demonstrate that these patterns are specified at the level of RNA accumulation.

Isolation and physical characterization of three essential conidiation genes from Aspergillus nidulans

We cloned and characterized three genes from Aspergillus nidulans, designated brlA, abaA, and wetA, whose activities are required to complete different stages of conidiophore development. Inactivation of these genes causes major abnormalities in conidiophore morphology and prevents expression of many unrelated, developmentally regulated genes, without affecting the expression of nonregulated genes. The three genes code for poly(A)+ RNAs that begin to accumulate at different times during conidiation. The brlA- and abaA-encoded RNAs accumulate specifically in cells of the conidiophore. The wetA-encoded RNA accumulates in mature conidia. Inactivation of the brlA gene prevents expression of the abaA and wetA genes, whereas inactivation of the abaA gene prevents expression of the wetA gene. Our results confirm genetic predictions as to the temporal and spatial patterns of expression of these genes and demonstrate that these patterns are specified at the level of RNA accumulation.

Genetic and environmental modification of gene expression in the brlA12 variegated position effect mutant of Aspergillus nidulans

ThebrlA12variegated position effect mutant is particularly suited for tests of environmental and genetic influences on variegation, but out of a large number of substances added to the medium, only salts at high concentrations and methylamine significantly increased expression of this gene. Medium shifting experiments showed thatbrlA12activity could be switched on late, but once active, was rarely switched off again during conidiation. SeparatebrlA12clones in heterokaryons were activated independently. SomebrlA12-specific suppressor mutants, including those at loci giving almost complete suppression, have been studied. One class of suppressors also confers inability to utilize galactose as carbon source and comparison with other, pre-existing mutants showed that thebrlA12phenotype was either suppressed or enhanced by mutants with complex phenotypes involving galactose utilization, molybdate resistance, acid phosphatase production and sulphur metabolism. Tests for the involvement of DNA methylation inbrlA12expression gave negative results.

Developmental regulation of the Aspergillus nidulans trpC gene

We have cloned the trifunctional trpC gene from Aspergillus nidulans by hybrid phage lambda complementation of an Escherichia coli trpC mutant lacking phosphoribosylanthranilate isomerase activity. Four different phages sharing a 4.3-kilobase region were obtained. Plasmid subclones containing this region also complemented the E. coli trpC mutant. We determined that a 1.8-kilobase DNA fragment was minimally required for complementation. The fragment hybridized with two poly(A)+ RNAs, 3.0 and 3.2 kilobases in length. We infer that these transcripts are Aspergillus trpC mRNAs and that the entire Aspergillus trpC gene is not required for complementation in E. coli. Levels of both trpC transcripts in poly(A)+ RNA are regulated by growth medium composition. They were highest when cells were grown in minimal medium containing nitrate as the nitrogen source and lowest when cells were grown in medium containing yeast extract. The concentrations of the transcripts are also regulated during conidiophore development. Conidiating cultures grown on medium containing yeast extract had significantly higher levels of both transcripts than did hyphae grown in minimal medium containing nitrate. Levels of the transcripts in mature spores were equivalent to those found in hyphae grown in minimal medium containing nitrate. Results from nutritional experiments with an A. nidulans trpC mutant suggest that developmental regulation of trpC mRNA levels may be related to a high requirement for tryptophan or a compound derived from tryptophan during conidiation.

Organization of a gene cluster expressed specifically in the asexual spores of A. nidulans

We have investigated the organization and regulation of a 13.3 kb region of the Aspergillus nidulans genome that is preferentially expressed during conidiophore development. This cloned DNA segment codes for six polysomal poly(A)RNAs present in dormant asexual spores (conidia) at from 8 to 50 copies per cell. The genes encoding these RNAs occur once per haploid genome, are separate and distinct, appear to be colinear with their mature RNA products and are present in both polarities. Two of the genes have short regions of homology near their 5' ends, but otherwise the segment is internally unique. All of the RNAs are absent from or present at very low levels in wild-type somatic cells (Hyphae) and developing cultures of asporogenous mutant strains. In synchronously conidiating wild-type cultures, each of the RNAs can first be detected at a time coinciding with the appearance of mature spores. Thus this region comprises a cluster of tightly linked, discrete genes, which are all expressed at the same time, but not to the same extent, in a single differentiating cell type.

Do the tightly linked structural genes for nitrate and nitrite reductases in Aspergillus nidulans form an operon? Evidence from an insertional translocation which separates them

Previous work (Rand and Arst, 1977) led to the proposal that the nis-5 mutation results in a new low activity promoter for niiA, the structural gene for nitrite reductase in Aspergillus nidulans. Expression of niiA via this promoter differs from expression of niiA via its normal promoter/initiator in that expression by the new promoter is not subject to nitrate induction or ammonium repression. nis-5 reduces but does not abolish niiA expression mediated by the normal promoter/initiator. In this work we show that nis-5 is associated with and is probably identical to a non-reciprocal translocation in which a considerable portion of the centromere proximal region of the right arm of linkage group II is inserted into linkage group VIII between niiA and niaD, the tightly linked, probably contiguous structural genes for nitrate reductase. This implies that niiA, along with its normal promots yet unidentified by its normal role. Further, it indicates that niiA is transcribed from the niaD-proximal side. As niiA and niaD are separated by a large number of unrelated genes in nis-5 strains, we can safely conclude that expression of niiA does not occur solely by synthesis of a messenger which carries a niaD as well as a niiA transcript. Clearly, niiA and niaD do not form an operon for which a di- (or poly-) cistronic messenger by the only transcript. This is consistent with other experimental evidence which shows that the syntheses of nitrate and nitrite reductases are not coordinately regulated. Nevertheless, all of these data would also be consistent with a model in which niiA and niaD form an operon-type structure having overlapping transcripts, one being di- (or poly-) cistronic and including both niiA and niaD and another being monocistronic for niiA. The reduced niiA expression mediated by the normal promoter/initiator in nis-5 strains could be a consequence of the functioning or positioning of the new linkage group II niiA promoter. An alternative, but not mutually exclusive, explanation would be that the insertional translocation prevents synthesis of a niiA niaD dicistronic transcript so that only that component of niiA expression which is due to a monocistronic niiA messenger can be induced by nitrate (and nitrite) in nis-5 strains. The apparently low activity of the new linkage group II promoter in comparison to the normal niiA promoter/initiator might betoken considerable efficiency of the latter rather than any particular lack of efficiency of the former. In addition, this work has involved extensive new mapping in linkage group II, including both mitotic mapping of the centromere and meiotic mapping of previously unlocated markers. A series of crosses in cluding genotype combinations both heterozygous and homozygous for nis-5 has been used to map the break-points and orientation of the translocation. As one break-point is closer to the centromere of linkage group II than the most centromere proximal identified gene on the same (i.e...

A LIGHT-MICROSCOPIC STUDY OF SOME TRANSLOCATIONS IN ASPERGILLUS NIDULANS

A cytological investigation of the ascomycete, Aspergillus nidulans (Eidam) Winter, was undertaken to test the feasibility of using simple light-microscopial techniques to study chromosome aberrations for the correlation of chromosomes and linkage groups in this genetically well analysed fungus. Pachytene chromosome analysis was not possible, because the chromosomes are very small, do not spread well when squashed, and show very little structural detail. Some catenations were seen at first metaphase in translocation heterozygotes either as dense masses or, more rarely, as open rings. Lagging chromosomes were also seen at low frequency in both first and second anaphase and telophase in translocation but not in control material. The limited evidence from the study shows that meiotic chromosome behaviour in Aspergillus nidulans heterozygous for reciprocal translocations is probably similar to that in some higher organisms. However, the species is not suitable for detailed cytological analysis, at least by the techniques employed.

Altered instability due to genetic changes in a duplication strain of Aspergillus nidulans

Strains ofAspergillus nidulanswith a duplicate segment are mitotically unstable; they produce phenotypically improved variants following deletions in either duplicate segment, and morphologically deteriorated types. The number of variants produced is characteristic of each duplication strain under the same conditions. After ultraviolet treatment two variants, one more stable and the other less stable than the original strain, were selected. Genetic analysis showed that the increased instability in the less stable variant was due to a translocation involving linkage groups V and VIII. The increased stability of the more stable variant was due to a recessive factor (stf–1) located in linkage group VIII. In the homozygous condition this factor also reduces the number of sectors in a diploid strain. The possible genetic mechanisms explaining the instability alterations are discussed.