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At least 19 recordsLinked to original sources
PubMed2004

Evolution of fungal sex chromosomes.

Sexual reproduction enables organisms to shuffle two parental genomes to produce recombinant progeny, and to purge the genome of deleterious mutations. Sex is conserved in virtually all organisms, from bacteria and fungi to plants and animals, and yet the mechanisms by which sexual identity are established share both conserved general features and are remarkably diverse. In animals, sexual identity is established by dimorphic sex chromosomes, whereas in fungi a specialized region of the genome, known as the mating-type locus, governs the establishment of cell type identity and differs in DNA sequence between cells of different mating-types. Recent studies on the mating-type loci of fungi and algae reveal features shared with the mammalian X and Y chromosomes, suggesting that these represent early steps in the evolution of sex chromosomes.

Animals↗
PubMed2006

Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome.

Recombination increases dramatically during meiosis to promote genetic exchange and generate recombinant progeny. Interestingly, meiotic recombination is unevenly distributed throughout genomes, and, as a consequence, genetic and physical map distances do not have a simple linear relationship. Recombination hotspots and coldspots have been described in many organisms and often reflect global features of chromosome structure. In particular, recombination frequencies are often distorted within or outside sex-determining regions of the genome. Here, we report that recombination is elevated adjacent to the mating-type locus (MAT) in the pathogenic basidiomycete Cryptococcus neoformans. Among fungi, C. neoformans has an unusually large MAT locus, and recombination is suppressed between the two >100-kilobase mating-type specific alleles. When genetic markers were introduced at defined physical distances from MAT, we found the meiotic recombination frequency to be approximately 20% between MAT and a flanking marker at 5, 10, 50, or 100 kilobases from the right border. As a result, the physical/genetic map ratio in the regions adjacent to MAT is distorted approximately 10- to 50-fold compared to the genome-wide average. Moreover, recombination frequently occurred on both sides of MAT and negative interference between crossovers was observed. MAT heterozygosity was not required for enhanced recombination, implying that this process is not due to a physical distortion from the two non-paired alleles and could also occur during same-sex mating. Sequence analysis revealed a correlation between high G + C content and these hotspot regions. We hypothesize that the presence of recombinational activators may have driven several key events during the assembly and reshaping of the MAT locus and may have played similar roles in the origins of both metabolic and biosynthetic gene clusters. Our findings suggest that during meiosis the MAT locus may be exchanged onto different genetic backgrounds and therefore have broad evolutionary implications with respect to mating-type switching in both model and pathogenic yeasts.

Base Composition↗
PubMed2006

Chromosome visualisation in filamentous fungi.

Many attempts have been made to study the chromosomes of fungi, but a major problem is that fungal nuclei are so small. Fungal chromosomes are at the lowest resolution of light microscopy; thus few attempts to visualise fungal chromosomes have been successful. Fungi examined have been mainly Ascomycotina. The number of chromosomes per nucleus, estimated by conventional light visualisation and stained with standard dyes like Giemsa or aceto-orceine, usually does not exceed ten. A method developed in the late 1980s called 'germ tube burst' enables the discharge of condensed chromosomes from the hyphal cell and their spread on the surface of a slide. This more accurate method, usually gives better resolution of chromosomes. It was used with conventional light microscopy dyes as well as in fluorescent microscopy or for in situ hybridisation. A breakthrough has been made in fungal genetics by using pulse field gel electrophoresis (PFGE). Separation of the chromosomes on the gel enables the determination of their number and estimation of genome size. It also reveals chromosome length polymorphism and the presence of supernumerary chromosomes, which are usually too small to visualise in nuclei. A combination of two methods, cytological analysis by light microscopy and PFGE, should give a tool allowing the complex analysis of fungal genomes.

Chromosomes, Fungal↗
PubMed1995

Chromosome-length polymorphism in fungi.

The examination of fungal chromosomes by pulsed-field gel electrophoresis has revealed that length polymorphism is widespread in both sexual and asexual species. This review summarizes characteristics of fungal chromosome-length polymorphism and possible mitotic and meiotic mechanisms of chromosome length change. Most fungal chromosome-length polymorphisms are currently uncharacterized with respect to content and origin. However, it is clear that long tandem repeats, such as tracts of rRNA genes, are frequently variable in length and that other chromosomal rearrangements are suppressed during normal mitotic growth. Dispensable chromosomes and dispensable chromosome regions, which have been well documented for some fungi, also contribute to the variability of the fungal karyotype. For sexual species, meiotic recombination increases the overall karyotypic variability in a population while suppressing genetic translocations. The range of karyotypes observed in fungi indicates that many karyotypic changes may be genetically neutral, at least under some conditions. In addition, new linkage combinations of genes may also be advantageous in allowing adaptation of fungi to new environments.

Chromosomes, Fungal↗
PubMed1997

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.

Chromosome Aberrations↗
PubMed1999

Chromosomes, karyotype analysis, chromosome rearrangements in fungi.

In this review the organization of fungal chromosomes and the methods used for karyotype analysis are briefly summarized. The role of chromosome rearrangement, supernumerary chromosomes and repeated DNA sequences in the genetic change of fungi is evaluated.

Chromosomes, Fungal↗
PubMed1976

The similarities of ribosomal and basic chromosomal proteins from fungi.

We have compared the physical and chemical properties of yeast and fungal ribosomal proteins with those of higher eukaryotic histones. We have found that acidic urea gel electrophoresis, sodium dodecyl sulfate gel electrophoresis or chromatography on carboxymethylcellulose columns failed to distinguish ribosomal proteins from histones. The majority of the ribosomal proteins did not adsorb to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. Histones quantitatively adsorbed to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. A small number of fungal acid-soluble nuclear proteins, which coelectrophoresed with histones, were identified in a presumed nucleolar and nuclear membrane fraction. This fraction contained large amounts of RNA and small amounts of DNA. It is suggested that contamination of yeast and fungal chromosome preparations by a small number of ribosomal proteins can occur. Furthermore, several commonly employed criteria did not distinguish contaminating ribosomal proteins from authentic histones.

Binding Sites↗
PubMed1996

The Use of Rare-Cutting Endonucleases in Electrophoretic Karyotyping of Fungal Genomes

A method for the fast and reliable restriction analysis of intact fungal chromosomes is presented. For this purpose rare-cutting restriction enzymes of pro- and eukaryotic origin were used. Restriction fragments were separated on pulsed-field gels. Complete inactivation of proteinases remaining from chromosome preparations was crucial in this attempt. Rare-cutting restriction enzymes were employed to demonstrate the applicability of this procedure to the analysis of complex fungal genomes. This includes the localization of genes on discrete chromosomal fragments,the identification of telomeric restriction fragments, and the analysis of fungal transformants.

Journal Article↗
PubMed1993

Genomic mismatch scanning: a new approach to genetic linkage mapping.

Genomic mismatch scanning (GMS) is a new method of genetic linkage analysis that does not require conventional polymorphic markers or gel electrophoresis. GMS is ideally suited to affected-relative-pair mapping. DNA fragments from all regions of identity-by-descent between two relatives are isolated based on their ability to form extensive mismatch-free hybrid molecules. The genomic origin of this selected pool of DNA fragments is then mapped in a single hybridization step. Here we demonstrate the practicality of GMS in a model organism, Saccharomyces cerevisiae. GMS is likely to be applicable to other organisms, including humans, and may be of particular value in mapping complex genetic traits.

Chromosome Mapping↗
PubMed1997

Regulated system for heterologous gene expression in Penicillium chrysogenum.

A system for regulated heterologous gene expression in the filamentous fungus Penicillium chrysogenum was established. This is the first heterologous expression system to be developed for this organism. Expression of a recombinant fungal xylanase gene (xylp) and the cDNA for the human tear lipocalin (LCNI) was achieved by placing the encoding sequences under the control of the repressible acid phosphatase gene (phoA) promoter of P. chrysogenum. Secreted recombinant proteins were detected in the growth media of transformed P. chrysogenum cells by means of bioassays, zymogramography, and Western blotting. Levels of transcription and amounts of recombinant proteins secreted varied among transformants, mainly due to the copy number and the integration site of the expression vector on the fungal chromosome.

Carrier Proteins↗
PubMed2003

Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions.

A new measure for gene prediction in eukaryotes is presented. The measure is based on the Discrete Fourier Transform (DFT) phase at a frequency of 1/3, computed for the four binary sequences for A, T, C, and G. Analysis of all the experimental genes of S. cerevisiae revealed distribution of the phase in a bell-like curve around a central value, in all four nucleotides, whereas the distribution of the phase in the noncoding regions was found to be close to uniform. Similar findings were obtained for other organisms. Several measures based on the phase property are proposed. The measures are computed by clockwise rotation of the vectors, obtained by DFT for each analysis frame, by an angle equal to the corresponding central value. In protein coding regions, this rotation is assumed to closely align all vectors in the complex plane, thereby amplifying the magnitude of the vector sum. In noncoding regions, this operation does not significantly change this magnitude. Computing the measures with one chromosome and applying them on sequences of others reveals improved performance compared with other algorithms that use the 1/3 frequency feature, especially in short exons. The phase property is also used to find the reading frame of the sequence.

Chromosomes, Fungal↗
PubMed1989

Use of yeast artificial chromosome clones for mapping and walking within human chromosome segment 18q21.3.

Well-characterized large genomic clones obtained from yeast artificial chromosome (YAC) libraries provide the framework to localize genes and approach genetic disease. We developed universally applicable approaches to establish authenticity, localize and orient internal genes, map restriction sites, and rescue the distal ends of large human genomic DNA inserts. We selected human chromosome segment 18q21.3 as a model system. Molecular cloning of this segment was initiated by characterizing three plasminogen activator inhibitor type 2 (PAI-2) clones [290, 180, and 60 kilobases (kb)] isolated from a YAC library. Comparison of YAC and bacteriophage lambda genomic DNA clones confirmed the fidelity of the PAI-2 locus. Detailed rare cutting restriction maps were generated by ramped contour-clamped homogeneous electric field electrophoresis. The PAI-2 locus was located and oriented within the YACs, which span a distance 70 kb 5' to 220 kb 3' of PAI-2. Moreover, both left and right ends of the YAC genomic DNA inserts were rescued by amplifying circularized cloning sites with an inverted form of the polymerase chain reaction. These unique terminal genomic DNA fragments were used to rescreen the YAC library and isolate overlapping clones that extend the map. These approaches will enable neighboring loci to be definitively linked and establish the feasibility of using YAC technology to clone and map chromosomal segments.

Base Sequence↗
PubMed1989

Cloning of human telomeres by complementation in yeast.

Telomeres confer stability on chromosomes by protecting them from degradation and recombination and by allowing complete replication of the end. They are genetically important as they define the ends of the linkage map. Telomeres of lower eukaryotes contain short repeats consisting of a G-rich and a C-rich strand, the G-rich strand running 5'-3' towards the telomere and extending at the end. Telomeres of human chromosomes share characteristics with those of lower eukaryotes including sequence similarity as detected by cross-hybridization. Telomeric repeats from many organisms can provide telomere function in yeast. Here we describe a modified yeast artificial chromosome (YAC) vector with only one telomere which we used to clone human telomeres by complementation in yeast. YACs containing human telomeres were identified by hydridization to an oligonucleotide of the trypanosome telomeric repeat. A subcloned human fragment from one such YAC is immediately subtelomeric on at least one human chromosome.

Animals↗