Quantitative intrachromosomal changes arising at mitosis in Aspergillus nidulans

Phenotypic instability in fungi

Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.

Cytological characterization of an Aspergillus Nidulans mutant from a strain with chromosomic duplication

A development mutant, named V103, was obtained spontaneously from the A strain of A. nidulans. The A strain contains a duplicated segment of chromosome I that has undergone translocation to chromosome II (I II). It is mitotically unstable and generates phenotypically deteriorated types, some with enhanced stability. The deteriorated variants of A. nidulans show abnormal development, exhibiting slower colony growth, variations in colony pigmentation and changes in conidiophore structure. The alterations observed in the conidiophore include fewer metulae and phialides, further elongation and ramification of these structures, delayed nuclear migration and the presence of secondary conidiophores.

Genetic analysis of an unequal chromosomal translocation in Aspergillus nidulans

Translocation T(III–VIII) in Aspergillus nidulans has been analysed by the detection of meiotic linkage between markers previously located separately on linkage groups III and VIII. The breakage points have been mapped by the detection of linkage between the crinkled type and genetic markers in the region of the break. A segment from linkage group III, approximately 43 units long and including the markers moC96, sC12, sA1 and cnxH3, has been translocated into linkage group VIII. The breakage point is between su6proA and moC96 and the attachment point is close to cha in linkage group VIII. It seems probable that the segment has been inserted into linkage group VIII.

Electrophoretic characterization of Aspergillus nidulans strains with chromosomal duplications

Pulsed-field gel electrophoresis was used to characterize strains of Aspergillus nidulans with a chromosomal duplication Dp(I-II). Morphologically deteriorated and improved variants of these strains were also analyzed. The electrophoretic karyotype demonstrated that in two duplicated strains (A and B) the 4.2 Mb band, which corresponds to chromosome II, was absent and a new band was observed. Hybridization studies using the uapA (chromosome I) and wA (chromosome II) genes demonstrated that the new band corresponded to chromosome II plus the duplicated segment of chromosome I. The size of the chromosomal duplication was approximately 1.0 Mb. Analysis of the chromosomal bands of a morphologically improved strain showed that the duplicated segment of chromosome I was completely lost. The morphologically deteriorated variants V9 and V17 had the same karyotype as the duplicated strains. However, the deteriorated variant V5 lost part of chromosome I and had a rearrangement involving chromosome V. This rearrangement may have resulted from the mutagenic treatment used to obtain the genetic markers. Pulsed-field gel electrophoresis was found to be an excellent tool for locating chromosomal rearrangements.

A simple method for the detection of recombinogenic substances in filamentous fungi

Several tests are available for detecting mutagenic and recombinogenic products in fungi. Since fungi are eukaryotic, these tests permit the detection of substances that produce chromosomal aberrations, or that are recombinogenic. We have developed a new method for testing substances that affect fungal stability using a duplication strain of Aspergillus nidulans and circular statistics for data analysis. The fungus was inoculated on the center of Petri dishes and the substance to be tested was applied to a defined area of the dish. Position of resulting sectors was measured by an angle and the data were analyzed by the Rayleigh test. Extensive testing with different compounds showed this method to be rapid and efficient for screening recombinogenic substances.

sodVIC is an alpha-COP-related gene which is essential for establishing and maintaining polarized growth in Aspergillus nidulans

Strains of Aspergillus nidulans carrying the conditional-lethal mutation sodVIC1 (stabilization of disomy) are defective in nuclear division and hyphal extension. The mutation affects both the establishment and maintenance of polar growth, since mutant spores do not germinate at restrictive temperature and preexisting hyphae stop growing upon upshift. The defect is reversible within the first 3-4 h at restrictive temperature but longer periods of incubation are lethal due to cell lysis and morphological abnormalities. There is no evidence for a specific cell cycle lesion, suggesting the existence of a feedback mechanism whereby hyphal extension is coordinated with nuclear partitioning. The sodVIC gene has been cloned from a chromosome VI-specific cosmid library and its product exhibits strong homology to the alpha-COP subunit of the coatomer complex involved in the secretory pathway in yeast and higher organisms. Molecular disruption of the gene is lethal, indicating that SodVIC is essential for growth in A. nidulans.

Characterization of an Aspergillus nidulans mutant with abnormal distribution of nuclei in hyphae, metulae, phialides and conidia

The V10 deteriorated variant of Aspergillus nidulans has hyphae, metulae, phialides and conidia with abnormal nuclear distributions. The alterations observed were: increase in the number of nuclei in hyphae, metulae and phialides, presence of anucleate, uninucleate and multinucleate conidia, abnormal vegetative growth and defection conidiation. When 0.5 M NaCl was added to the medium, an increase in the number of conidia was observed but their morphology and number of nuclei were not modified. The gene responsible for these alterations was named anuA1. The anuA1 gene is located on linkage group VII and is possibly involved in nuclear migration to hyphae, metulae, phialides and conidia.

The penicillin gene cluster is amplified in tandem repeats linked by conserved hexanucleotide sequences

The penicillin biosynthetic genes (pcbAB, pcbC, penDE) of Penicillium chrysogenum AS-P-78 were located in a 106.5-kb DNA region that is amplified in tandem repeats (five or six copies) linked by conserved TTTACA sequences. The wild-type strains P. chrysogenum NRRL 1951 and Penicillium notatum ATCC 9478 (Fleming's isolate) contain a single copy of the 106.5-kb region. This region was bordered by the same TTTACA hexanucleotide found between tandem repeats in strain AS-P-78. A penicillin overproducer strain, P. chrysogenum E1, contains a large number of copies in tandem of a 57.9-kb DNA fragment, linked by the same hexanucleotide or its reverse complementary TGTAAA sequence. The deletion mutant P. chrysogenum npe10 showed a deletion of 57.9 kb that corresponds exactly to the DNA fragment that is amplified in E1. The conserved hexanucleotide sequence was reconstituted at the deletion site. The amplification has occurred within a single chromosome (chromosome I). The tandem reiteration and deletion appear to arise by mutation-induced site-specific recombination at the conserved hexanucleotide sequences.

Large amplification of a 35-kb DNA fragment carrying two penicillin biosynthetic genes in high penicillin producing strains of Penicillium chrysogenum

The isopenicillin N synthase (pcbC) and acyl-CoA:6-APA acyltransferase (penDE) genes of Penicillium chrysogenum were located in a 19.5-kb DNA fragment that had been previously cloned in phage vector EMBL3. This 19.5-kb DNA fragment was mapped with several endonucleases, and the pcbC and penDE genes were located by hybridization with probes corresponding to internal fragments of each gene. A low penicillin producing strain (P. chrysogenum Wis 54-1255) and two high producing strains (AS-P-78 and P2) showed hybridizing fragments of identical sizes in their chromosomes. Dot-blot hybridization of serial dilutions of the total DNA of the three strains showed that the intensity of all the hybridizing bands was much higher in strains AS-P-78 and P2 than in Wis 54-1255. Hybridization of total DNA digestions with probes corresponding to fragments which mapped upstream or downstream of the pcbC-penDE region revealed that a fragment of at least 35 kb DNA has been amplified 9 to 14 fold in the high penicillin producing strains. The amplified region did not include the previously cloned pyrG gene that encodes OMP-decarboxylase, an enzyme involved in pyrimidine biosynthesis.

Effect of the bncA gene on the instability of Aspergillus nidulans

The presence of a gene designatedbncAwhich produces binucleate and trinucleate conidia inA. nidulansalters the instability of disomics, diploids, and strains with chromosome duplication. In disomics, the genebncAincreases instability. In duplicate and diploid strains, thebncAgene reduces instability by acting as a partial stabilizer. In the strain with chromosome duplication, thebncAgene produces increased percentages of bi- and trinucleate conidia, a fact that may be interpreted to be due to the larger conidial volume of this strain or to the combined effect ofbncAand of the strain, which normally already exhibits a small amount of binucleate conidia.

Mitotic recombination in stable and unstable chromosome III disomics of Aspergillus nidulans

Approximately 2% of the haploid breakdown sectors of heterozygous chromosome III disomics of Aspergillus nidulans are the result of recombination between the homologous chromosomes. The exchanges are concentrated between the two mutations spanning the centromere. Comparisons are made between disomics hemizygous for the sodIII A1 mutation (Upshall et al. 1979) which are stable when grown at 37 degrees C, and disomics carrying the wild type allele of the sodIII A1 locus, which are unstable under all conditions. It is shown that neither temperature nor the sodIII A1 mutation affect the frequency or pattern of recombination between the homologues.

Two-way selection of mutants and revertants to chloroneb resistance in Aspergillus nidulans

5 mutants of Aspergillus nidulans, selected for resistance to chloroneb, were also partially dependent on it. The resistance of these mutants to chloroneb was about 20-150 times higher than that of the original strain. The resistance marker was due to a mutation in a single gene, located in linkage group III, and behaved as a recessive character. This genetic marker was distal in relation to galAl with a recombination frequency of about 30-35%. The different levels of resistance were attributed to mutations at different sites in the same locus. Both stable and unstable sectors were obtained from resistant strains inoculated on chloroneb-free medium. The emergence of stable sectors was due to back mutation, suppressor mutation or another mutation, which allows growth to the full extent in the absence of the drug. The unstable sectors showed better growth when compared with the resistant strain, kept their resistance and produced both resistant and non-resistant secondary sectors. This procedure of 2-way selection of mutants and revertants to chloroneb resistance could be useful for studying forward and back mutation in A. nidulans.

The ability of ionizing radiations of different LET to induce chromosomal deletions in Aspergillus nidulans

Conidia, derived from a strain of Aspergillus nidulans known to carry a specific chromosomal duplication, were irradiated. The duplicated segment had genetic markers, which, when eliminated from the genome, allowed the easy detection of deletion mutants. Survival curves derived following 15 MeV electron and gamma-ray irradiation were characterised by the presence of an appreciable shoulder, whilst 50 kvp X-rays gave a much smaller shoulder. Irradiation with beta-particles and alpha-particles gave rise to exponential survival curves. The RBE values for these radiations, based on the D37 value were for gamma-rays, 1.0, 15 MeV electrons 1.0, 50 kvp X-rays 1.9, beta-particles 2.1 and alpha-particles 3.4. With the exception of gamma-rays the radiations described were compared with respect to their ability to induce chromosomal deletions. When the number of deletants amongst survivors was plotted against dose, a linear relationship was found for electrons, X-rays and beta-particles. The response recorded for alpha-particles was essentially linear but with a biphasic component. The RBE values for the radiations, based on a value of unity for 15 MeV electrons were as follows: X-rays 1.3, beta-particles 0.8, alpha-particles above 7.5 krad 2.3 and below 7.5 krad 3.5. When these same data were re-plotted with number of deletants amongst survivors against log survival, electrons appeared the most efficient radiation at producing deletants amongst survivors, with an "m value" of 283 X 10(-5). Tritiated water was least efficient, the corresponding value being 182 X 10(-5). The number of deletants per 10(4) conidia plated, when plotted against dose yielded a curve which increased to a peak and then decreased linearly for all radiations. The peaks for electrons, X-rays and alpha-particles each had a value of about 14 deletants per 10(4) conidia plated and the peaks roughly corresponded with the point at which the survival curve became exponential and was clearly indicative of the accumulation of sub-lethal damage. However, for beta-particles the peak had a value of 7 deletants per 10(4) conidia plated. A non-DNA target has been implicated for cellular death following beta-particle irradiation.

Reversion in variants from a duplication strain of Aspergillus nidulans

Strains of Aspergillus nidulans with a chromosome segment in duplicate, one in normal position and one translocated to another chromosome, are unstable at mitosis. In addition to variants which result from deletions in either of the duplicate segments, which usually have improved morphology, they produce variants with deteriorated morphology. Three deteriorated variants reverted frequently to parental type morphology, both spontaneously and after ultra-violet treatment. Of six reversions analysed genetically, five were due to suppressors and one was probably due to back mutation. The suppressors segregated as single genes and were not linked to the mutation which they suppress. The instability of these so-called "deteriorate"variants is discussed in relation to mitotic instability phenomena in A. nidulans.

The effects of coumarin on the frequency of deletions in a duplication strain of Aspergillus nidulans

Strains of A. nidulans with a chromosome segment in duplicate show instability resulting from deletions in either of the duplicate segments. In Dp (I, II) strains, with the terminal segment of IR attached terminally to IIR, spontaneous deletions occur most frequently, though not exclusively, from the translocated segment. Coumarin, at concentrations which did not affect viability viability or growth rate, enhanced the instability of Dp (I, II) strains by selectively increasing only the deletion class of highest spontaneous frequency. This selective action is interpreted tentatively as due to inhibition of the repair of a particular class of DNA lesion occurring spontaneously in the attachment region of Dp (I, II) strains.

Resistance and mitotic instability to chloroneb and 1,4-oxathiin in Aspergillus nidulans

Mutants resistant to two fungicides, chloroneb (1,4-dichloro-2,5-dimethoxybenzene) and vitavax (2,3-dihydro-5-carboxanilido-6-methyl-1,4-oxathiin) were spontaneously obtained from a strain of Aspergillus nidulans with frequencies of 12.5 and 1.1 respectively, in 10(8) conidia. One chloroneb-resistant mutant (Chl 1) segregated as a single gene and was mapped in linkage group IV. It also caused a partial dependence of the strain on the fungicide and was semi-dominant. The mutant resistant to vitavax (Vit 1) also segregated as a single gene and was dominant. Both fungicides altered the instability of diploid and duplication strains. Chloroneb mainly increased haploidization, and vitavax reduced the mitotic recombination in diploids. Chloroneb increased the instability of duplication strains, and vitavax reduced such instability. The possible mode of action of such fungicides affecting stability is discussed.

Effects of ethidium bromide in diploid and duplication strains of Aspergillus nidulans

Unstable duplication and diploid strains of Aspergillus nidulans were treated with ethidium bromide, and it was shown that this drug reduces the number of sectors produced by such strains. The mechanisms which could be responsible for the partial stabilization of the strains are discussed and it is suggested that a similar mechanism is responsible for the production of sectors in both strains. It is also suggested that ethidium bromide could be useful for the reduction of instability of industrial strains.

The genetic instability and mutagenic interaction of chromosomal duplications present together in haploid strains of Aspergillus nidulans

Previous work has shown that strains of Aspergillus nidulans with a chromosome segment in duplicate (one in normal position, one translocated to another chromosome) are unstable. Deletions occur from either duplicate segment. The present work has shown that when a chromosome I duplication and a chromosome III duplication are together in a haploid, deletions from the intact III duplication generally precede deletions from particular sections of the I duplication. Furthermore, the III duplication can enhance to some (but not major) extent the frequency of deletions from the I duplication. After the III duplication becomes reduced in size as a result of the loss of chromosomal material from the translocated duplicate III segment, such a reduced III duplication can greatly enhance the frequency of deletions from the I duplication. In other words, a III duplication of reduced size can promote far more deletions from the I duplication than the intact III duplication. The major increase in the deletional instability of the I duplication as promoted by the reduced III duplication is confined to the translocated duplicate I segment. The reduced III duplication can induce deletions from a section of the translocated duplicate I segment in accord with a temporal programme, and it appears that a particular region of the I duplication is far more under the mutagenic influence of the reduced III duplication than another region. Moreover, there is indication that there is a differential effect of two generally different genetic backgrounds on the susceptibility of duplication-regions to deletion. Possible mechanisms involved in such chromosomal instability are proposed. A manner in which genetic instability may be related to development is also proposed.

The effects of temperature on genetic instability in Aspergillus nidulans

Previous work has shown that strains of Aspergillus nidulans with a chromosome segment in duplicate (one in normal position, one translocated to another chromosome) are unstable. Deletions occur from either duplicate segment. The present work has shown that most deletions occur from the translocated duplicate segment. Furthermore, it has been found that the overall frequency of deletions from a duplication is dependent upon the temperature of growth. The overall frequency of deletions from a chromosome III duplication is greatly enhanced by low temperatures, while the overall frequency of deletions from a chromosome I duplication is markedly enhanced by high temperatures. A temperature of 39.5 degrees C appears to enhance to overall frequency of deletions from the I duplication to the greatest extent. With regard to the non-translocated duplicate I segment, an increase in temperature progressively enhances the frequency of those deletions to which it is subject to far more deletions during a particular period of growth than during any other period, and at 42 degrees C, a section of the III duplication is subject to far more deletions during a given period of growth than during any other period. Comparisons with other cases of genetic instability are made and common underlying connections are proposed.

Genetic control of chromosome instability in Aspergillus nidulans as a mean for gene amplification in eukaryotic microorganisms

A haploid strain of Aspergillus nidulans carrying I-II duplication homozygous for the leaky mutation adE20 shows impreved growth on minimal medium. The duplication, though more stable than disomics, still shows instability. Several methods were used for detecting genetic control of improved stability. (a) visual selection, using a duplicated strain which is very unstable due to UV sensitivity, (adE20, biAl/dp yA2; uvsB). One stable strain showed a deletion (or a lethal mutation?) DISTAL TO BIA on the segment at the original position (on chromosome I). This deletion reduces crossing over frequency between the two homologous segments. As the deletion of the non-translocated segment (yelow sectors) must be preceded by crossing over, the above reduces the frequency of yellow sectors. A deletion of the translocated segment (green sectors) results in non-viability due to the deletion, and such sectors do not appear. The net result is a stable duplication involving only 12 C.O. units carrying the gene in concern. (b) Suppressors of UV sensitivity (su-uvsB) were attempted using the above uvs duplicated strain. Phenotypic revertants were easily obtained, but all were back mutations at the uvsB locus. (c) Mutations for UV resistance higher than that of the wild type were not obtained, in spite of the strong selective pressure inserted. (d) Recombination deficient mutations (rec), six altogether, all uvs+, did not have any effect on stability.

Escape from mating-type incompatibility in bisexual (A + a) Neurospora heterokaryons

In Neurospora crassa, strains of opposite mating type generally do not form stable heterokaryons because the mating type locus acts as a heterokaryon incompatibility locus. However, when one A and one a strain, having complementing auxotrophic mutants, are placed together on minimal medium, growth may occur, although the growth is generally slow. In this study, escape from such slow growth to that at a wild type or near-wild type rate was observed. The escape cultures are stable heterokaryons, mostly having lost the mating type allele function from one component nucleus, so that the nuclear types are heterokaryon compatible. Either A or a mating type can be lost. This loss of function has been attributed to deletion since only one nuclear type could be recovered in all heterokaryons except one, but deletion spanning adjacent loci has been directly demonstrated in a minority of cases. Alternatively when one component strain is tol and the other tol+ (tol being a recessive mutant suppressing the heterokaryon incompatibility associated with mating type), escape may occur by the deletion or mutation of tol+, also resulting in heterokaryon compatibility. An induction mechanism for escape is speculated upon.

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.

A variegated position effect in Aspergillus nidulans

In mutants at the ‘bristle’ locus ofAspergillus nidulansthe conidiophore remains as a stiff hypha rather than developing a vesicle, sterigmata and conidia. ThebrlA12 allele of this locus has a variegated phenotype, and genetic analysis has shown that this is associated with a translocation which has a breakpoint in the map interval adjacent to thebristlelocus.

The mutant phenotype is partially repaired on high-salt medium at low pH, and can also be repaired by suppressors, one of which has been mapped at a locus unlinked tobrlA12.

The mutant provides proof that variegation is due to instability of gene expression and not to mutability sincebrlA12 is genetically stable and can be propagated from either conidia or sterile conidiophores, the structures formed at the two extremes of variegation, and the resulting colonies in both cases are identical to the original strain.

It has been shown by mitotic recombination that the translocation associated with the variegated mutant is a ‘simple translocation’ in which the distal half of linkage group VIII is attached to the end of linkage group III. This terminal attachment site does not appear to be damaged in any genetically detectable way.

Mitotic non-conformity in Aspergillus: successive and transposable genetic changes

Strains ofAspergillus nidulanswith, a duplicate chromosome segment are mitotically unstable; in addition to phenotypically improved variants, arising following deletions in either duplicate segment, they give morphologically deteriorated types, some with, enhanced stability. In one isolate, deterioration and increased instability were determined by mutation in a duplicate segment; a more stable derivative no longer had this mutation but had one in another linkage group. Another variant, too unstable for analysis, gave derivatives whose single, new mutations were in different linkage groups. It is proposed that deterioration and increased instability result from tandem duplications on either duplicate segment; transposition of these to non-duplicated regions reduces instability. Another 17 variants had a single new mutation each; mutations, possibly clustered, occurred in all linkage groups. In these strains perhaps transposition preceded analysis. Deteriorated variants gave lineages of types with morphological changes caused by further, superimposed mutations. This continued instability is explained as interaction, in fidelity of replication, of non-homologous chromosome segments.

Instability inA. nidulansstems from chromosome imbalance. As imbalance is known or suspected in other cases of instability it may be possible to show common mechanisms for apparently diverse phenomena.

Mitotic non-conformity in Aspergillus nidulans: the production of hypodiploid and hypohaploid nuclei

Strains ofAspergillus nidulanswith a chromosome segment additional to the normal complement are vegetatively unstable. Previous work suggested that the deletions occurring at mitosis were confined to the unbalanced segments. It has been shown now that deletions, while probably always involving a duplicate segment, may extend beyond it to produce hypohaploids and hypodiploids, respectively, from unbalanced haploid and unbalanced diploid parents.

Hypoploids have been proposed tentatively as an explanation for some cases of phenotypic variegation; on this basis it is possible to account for some of the diverse phenomena shown by, for example, position-effect variegation.

A system generating spontaneous intrachromosomal changes at mitosis in Aspergillus nidulans

Previous studies had shown that haploid strains ofAspergillus nidulanswhich have a chromosome segment in duplicate are unstable at mitosis. Through the study of various haploid and diploid strains, with and without translocations and with balanced and unbalanced genomes, it has been shown: (1) that imbalance of chromosome segments is responsible for instability, and (2) that the chromosomal deletions produced are confined solely or largely to the segments which provoke instability.

The term ‘mitotic non-conformity’ has been proposed for this instability phenomenon. An explanation for it has been sought in terms of attachment sites, limited in number and specific for chromosome segments, at which replication is initiated.