Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species.

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Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

10.1101/2020.05.21.108084 ◽

2020 ◽

Cited By ~ 1

Author(s):

Shelby J. Priest ◽

Marco A. Coelho ◽

Verónica Mixão ◽

Shelly Clancey ◽

Yitong Xu ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Mismatch Repair ◽

Dna Sequences ◽

Meiotic Recombination ◽

Genetic Recombination ◽

Species Boundaries ◽

Repair System ◽

Hybrid Progeny ◽

Dna Mismatch ◽

Species Boundary

AbstractHybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species.Author summarySeveral mechanisms enforce species boundaries by either preventing the formation of hybrids, known as pre-zygotic barriers, or preventing the viability and fecundity of hybrids, known as post-zygotic barriers. Despite these barriers, interspecific hybrids form at an appreciable frequency, such as hybrid isolates of the human fungal pathogenic species, Cryptococcus neoformans and Cryptococcus deneoformans, which are regularly isolated from both clinical and environmental sources. C. neoformans x C. deneoformans hybrids are typically highly aneuploid, sterile, and display phenotypes intermediate to those of either parent, although self-fertile isolates and transgressive phenotypes have been observed. One important mechanism known to enforce species boundaries or lead to incipient speciation is the DNA mismatch repair system, which blocks recombination between divergent DNA sequences during meiosis. The aim of this study was to determine if genetically deleting the DNA mismatch repair component Msh2 would relax the species boundary between C. neoformans and C. deneoformans. Progeny derived from C. neoformans x C. deneoformans crosses in which both parental strains lacked Msh2 had higher viability, and unlike previous studies in Saccharomyces, these Cryptococcus hybrid progeny had higher levels of aneuploidy and no observable increase in meiotic recombination at the whole-genome level.

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Poorly Repaired Mismatches in Heteroduplex DNA are Hyper-Recombinagenic in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/142.2.407 ◽

1996 ◽

Vol 142 (2) ◽

pp. 407-416 ◽

Cited By ~ 3

Author(s):

P Manivasakam ◽

Susan M Rosenberg ◽

P J Hastings

Keyword(s):

Saccharomyces Cerevisiae ◽

Mismatch Repair ◽

Genetic Markers ◽

Meiotic Recombination ◽

Repair System ◽

Normal Allele ◽

Heteroduplex Dna ◽

Mismatch Repair System ◽

Postmeiotic Segregation ◽

System Operating

Abstract In yeast meiotic recombination, alleles used as genetic markers fall into two classes as regards their fate when incorporated into heteroduplex DNA. Normal alleles are those that form heteroduplexes that are nearly always recognized and corrected by the mismatch repair system operating in meiosis. High PMS (postmeiotic segregation) alleles form heteroduplexes that are inefficiently mismatch repaired. We report that placing any of several high PMS alleles very close to normal alleles causes hyperrecombination between these markers. We propose that this hyperrecombination is caused by the high PMS allele blocking a mismatch repair tract initiated from the normal allele, thus preventing corepair of the two alleles, which would prevent formation of recombinants. The results of three point crosses involving two PMS alleles and a normal allele suggest that high PMS alleles placed between two alleles that are normally corepaired block that corepair.

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Mismatch Repair of DNA Replication Errors Contributes to Microevolution in the Pathogenic Fungus Cryptococcus neoformans

mBio ◽

10.1128/mbio.00595-17 ◽

2017 ◽

Vol 8 (3) ◽

Cited By ~ 36

Author(s):

Kylie J. Boyce ◽

Yina Wang ◽

Surbhi Verma ◽

Viplendra P. S. Shakya ◽

Chaoyang Xue ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Mismatch Repair ◽

Dna Sequences ◽

Fungal Pathogens ◽

Fungal Infections ◽

Pathogenic Fungus ◽

Clinical Isolates ◽

Mutation Rates ◽

Mutator Phenotype ◽

Study Results

ABSTRACT The ability to adapt to a changing environment provides a selective advantage to microorganisms. In the case of many pathogens, a large change in their environment occurs when they move from a natural setting to a setting within a human host and then during the course of disease development to various locations within that host. Two clinical isolates of the human fungal pathogen Cryptococcus neoformans were identified from a collection of environmental and clinical strains that exhibited a mutator phenotype, which is a phenotype which provides the ability to change rapidly due to the accumulation of DNA mutations at high frequency. Whole-genome analysis of these strains revealed mutations in MSH2 of the mismatch repair pathway, and complementation confirmed that these mutations are responsible for the mutator phenotype. Comparison of mutation frequencies in deletion strains of eight mismatch repair pathway genes in C. neoformans showed that the loss of three of them, MSH2, MLH1, and PMS1, results in an increase in mutation rates. Increased mutation rates enable rapid microevolution to occur in these strains, generating phenotypic variations in traits associated with the ability to grow in vivo, in addition to allowing rapid generation of resistance to antifungal agents. Mutation of PMS1 reduced virulence, whereas mutation of MSH2 or MLH1 had no effect on the level of virulence. These findings thus support the hypothesis that this pathogenic fungus can take advantage of a mutator phenotype in order to cause disease but that it can do so only in specific pathways that lead to a mutator trait without a significant tradeoff in fitness. IMPORTANCE Fungi account for a large number of infections that are extremely difficult to treat; superficial fungal infections affect approximately 1.7 billion (25%) of the general population worldwide, and systemic fungal diseases result in an unacceptably high mortality rate. How fungi adapt to their hosts is not fully understood. This research investigated the role of changes to DNA sequences in adaption to the host environment and the ability to cause disease in Cryptococcus neoformans, one of the world’s most common and most deadly fungal pathogens. The study results showed that microevolutionary rates are enhanced in either clinical isolates or in gene deletion strains with msh2 mutations. This gene has similar functions in regulating the rapid emergence of antifungal drug resistance in a distant fungal relative of C. neoformans, the pathogen Candida glabrata. Thus, microevolution resulting from enhanced mutation rates may be a common contributor to fungal pathogenesis. IMPORTANCE Fungi account for a large number of infections that are extremely difficult to treat; superficial fungal infections affect approximately 1.7 billion (25%) of the general population worldwide, and systemic fungal diseases result in an unacceptably high mortality rate. How fungi adapt to their hosts is not fully understood. This research investigated the role of changes to DNA sequences in adaption to the host environment and the ability to cause disease in Cryptococcus neoformans, one of the world’s most common and most deadly fungal pathogens. The study results showed that microevolutionary rates are enhanced in either clinical isolates or in gene deletion strains with msh2 mutations. This gene has similar functions in regulating the rapid emergence of antifungal drug resistance in a distant fungal relative of C. neoformans, the pathogen Candida glabrata. Thus, microevolution resulting from enhanced mutation rates may be a common contributor to fungal pathogenesis.

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The mismatch repair system reduces meiotic homeologous recombination and stimulates recombination-dependent chromosome loss.

Molecular and Cellular Biology ◽

10.1128/mcb.16.11.6110 ◽

1996 ◽

Vol 16 (11) ◽

pp. 6110-6120 ◽

Cited By ~ 125

Author(s):

S R Chambers ◽

N Hunter ◽

E J Louis ◽

R H Borts

Keyword(s):

Mismatch Repair ◽

Genetic Recombination ◽

Sequence Divergence ◽

Chromosome Loss ◽

Repair System ◽

Closely Related Species ◽

Spore Viability ◽

Mismatch Repair System ◽

Homeologous Recombination ◽

Chromosome Iii

Efficient genetic recombination requires near-perfect homology between participating molecules. Sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. The effects of chromosomal divergence in diploids of Saccharomyces cerevisiae in which one copy of chromosome III is derived from a closely related species, Saccharomyces paradoxus, have been examined. Meiotic recombination between the diverged chromosomes is decreased by 25-fold. Spore viability is reduced with an observable increase in the number of tetrads with only two or three viable spores. Asci with only two viable spores are disomic for chromosome III, consistent with meiosis I nondisjunction of the homeologs. Asci with three viable spores are highly enriched for recombinants relative to tetrads with four viable spores. In 96% of the class with three viable spores, only one spore possesses a recombinant chromosome III, suggesting that the recombination process itself contributes to meiotic death. This phenomenon is dependent on the activities of the mismatch repair genes PMS1 and MSH2. A model of mismatch-stimulated chromosome loss is proposed to account for this observation. As expected, crossing over is increased in pms1 and msh2 mutants. Furthermore, genetic exchange in pms1 msh2 double mutants is affected to a greater extent than in either mutant alone, suggesting that the two proteins act independently to inhibit homeologous recombination. All mismatch repair-deficient strains exhibited reductions in the rate of chromosome III nondisjunction.

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Mismatch repair, genetic stability and tumour avoidance

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1995.0014 ◽

1995 ◽

Vol 347 (1319) ◽

pp. 89-95 ◽

Cited By ~ 33

Keyword(s):

Mismatch Repair ◽

Dna Sequences ◽

Dna Ligase ◽

Cytotoxic Action ◽

Repair System ◽

Base Pairs ◽

Mismatch Correction ◽

Nuclear Extracts ◽

Mutation Avoidance

Escherischia coli methyl-directed mismatch repair eliminates premutagenic lesions that arise via DNA biosynthetic errors; components of the repair system also block ectopic recombination between diverged DNA sequences. A mismatch-dependent, methyl-directed excision reaction that accounts for function of the system in replication fidelity has been reconstituted in a purified system dependent on ten activities. The reaction displays a broad specificity for mismatched base pairs and is characterized by an unusual bidirectional excision capability. Human cell nuclear extracts support strand-specific mismatch correction in a reaction that is similar to bacterial repair, with respect to both mismatch specificity and unusual features of mechanism. Like the bacterial system, the human pathway also functions in mutation avoidance because several classes of mutator human cells are deficient in the reaction. These include an alkylation-tolerance cell line that is resistant to the cytotoxic action of N -methyl- N' -nitro-nitrosoguanidine, as well as hypermutable RER+ tumour cells such as those associated with hereditary non-polyposis colon cancer. In vitro experiments indicate that the human repair reaction is dependent on at least six activities, excluding DNA ligase, and that distinct defects in the system can lead to the RER+ phenotype.

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Control of large chromosomal duplications in Escherichia coli by the mismatch repair system.

Genetics ◽

10.1093/genetics/129.2.327 ◽

1991 ◽

Vol 129 (2) ◽

pp. 327-332 ◽

Cited By ~ 12

Author(s):

M A Petit ◽

J Dimpfl ◽

M Radman ◽

H Echols

Keyword(s):

Escherichia Coli ◽

Mismatch Repair ◽

Dna Sequences ◽

Chromosomal Rearrangements ◽

Point Mutations ◽

Repair System ◽

E Coli ◽

Mismatch Repair System ◽

Mismatch Recognition ◽

Homeologous Recombination

Abstract Excessive recombination between repeated, interspersed, and diverged DNA sequences is a potential source of genomic instability. We have investigated the possibility that a mechanism exists to suppress genetic exchange between these quasi-homologous (homeologous) sequences. We examined the role of the general mismatch repair system of Escherichia coli because previous work has shown that the mismatch repair pathway functions as a barrier to interspecies recombination between E. coli and Salmonella typhimurium. The formation of large duplications by homeologous recombination in E. coli was increased some tenfold by mutations in the mutL and mutS genes that encode the mismatch recognition proteins. These findings indicate that the mismatch recognition proteins act to prevent excessive intrachromosomal exchanges. We conclude that mismatch repair proteins serve as general controllers of the fidelity of genetic inheritance, acting to suppress chromosomal rearrangements as well as point mutations.

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The evolutionary history and molecular systematics of the Musteloidea

10.1093/oso/9780198759805.003.0002 ◽

2018 ◽

Author(s):

Klaus-Peter Koepfli ◽

Jerry W. Dragoo ◽

Xiaoming Wang

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Evolutionary History ◽

Molecular Data ◽

Morphological Data ◽

Species Boundaries ◽

Extant Species ◽

Taxonomic History ◽

History Of ◽

A New Species

This chapter provides a review of the evolutionary and taxonomic history of the Musteloidea, which is the most species-rich superfamily of the Carnivora, containing approximately 30% of the extant species in the order. An up-to-date summary of knowledge on the evolutionary and taxonomic history and phylogenetic relationships of the Mephitidae, Ailuridae, Procyonidae and Mustelidae is provided. Multilocus DNA sequences have made a large impact on the understanding of phylogenetic relationships among the Musteloidea. Molecular data have revealed distinct families (Ailuridae and Mephitidae) within the Musteloidea and have illuminated new relationships based on tempo and patterns of evolution within the Procyonidae. Morphological data in conjunction with molecular data have been used to elucidate species boundaries within certain musteloid genera and have led to the discovery of a new species. Research studies published during the last 30 years have enriched and transformed our understanding of the evolution of musteloid biodiversity.

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ROLE OF DNA SEQUENCES IN GENETIC RECOMBINATION IN THE ISO-1-CYTOCHROME c GENE OF YEAST. I. DISCREPANCIES BETWEEN PHYSICAL DISTANCES AND GENETIC DISTANCES DETERMINED BY FIVE MAPPING PROCEDURES

Genetics ◽

10.1093/genetics/79.3.397 ◽

1975 ◽

Vol 79 (3) ◽

pp. 397-418

Author(s):

Carol W Moore ◽

Fred Sherman

Keyword(s):

Ultraviolet Light ◽

Dna Sequences ◽

Meiotic Recombination ◽

Genetic Recombination ◽

Genetic Distances ◽

Nucleotide Sequences ◽

X Rays ◽

Recombination Rates ◽

Near Ultraviolet ◽

X Irradiation

ABSTRACT Recombination rates have been examined in two-point crosses of various defined cyc1 mutants using five mapping methods. Nucleotide sequences of mutant codons were identified in previous studies from alterations in functional iso-1-cytochromes c produced by intragenic revertants. Heteroallelic diploids were analyzed for rates of mitotic recombination that occurred spontaneously and that were induced with X-rays, ultraviolet light and the near-ultraviolet light emitted by sunlamps, as well as rates of meiotic recombination that occur after sporulation. Frequencies of both mitotic and meiotic recombination do not necessarily correspond with physical distances separating altered nucleotides. The most extreme discrepancy involved two adjacent intervals of thirteen base pairs which differed approximately thirtyfold in their spontaneous and X-ray-induced recombination rates. Marked disproportions between genetic and physical distances appear to be due to the interaction of the two nucleotide sequences in the heteroallelic combination and not to the sequences of the mutant codons alone. Recombination values that were obtained by all five methods could not be used to establish the correct order of mutant sites. Relationships of the recombination rates for the various pairwise crosses are different after mitosis from those after meiosis, suggesting that these two recombinational processes are to some extent different in their dependence on particular nucleotide configurations. On the other hand, the relationships of the rates induced by UV-, sunlamp- and X-irradiation were identical or very similar. In addition to the intrinsic properties of the alleles affecting frequencies of mitotic and meiotic recombination rates, two- to threefold variations in recombination rates could be attributed to genetic backgrounds.

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ROLE OF DNA SEQUENCES IN GENETIC RECOMBINATION IN THE ISO-1-CYTOCHROME c GENE OF YEAST. II. COMPARISON OF MUTANTS ALTERED AT THE SAME AND NEARBY BASE PAIRS

Genetics ◽

10.1093/genetics/85.1.1 ◽

1977 ◽

Vol 85 (1) ◽

pp. 1-22

Author(s):

Carol W Moore ◽

Fred Sherman

Keyword(s):

Cytochrome C ◽

Dna Sequences ◽

Meiotic Recombination ◽

Base Pair ◽

Genetic Recombination ◽

Initiation Codon ◽

Recombination Rates ◽

Base Pairs ◽

Yeast Saccharomyces Cerevisiae ◽

X Ray

ABSTRACT X-ray-induced mitotic recombination rates and spontaneous meiotic recombination rates have been determined in two-point crosses of various defined cyc1 mutants of the yeast Saccharomyces cerevisiae. All but one of the 17 cyc1 mutants chosen for this study contained either the addition, deletion or substitution of single base-pairs located within a defined segment of the gene that corresponds to the 11 amino acid residues at the amino terminus of iso-1-cytochrome c; approximately half of these mutants had alterations of the AUG initiation codon, some at the same base pair. Up to 66-fold differences in X-ray-induced recombination rates were observed when the same cyc1 mutant was crossed to cyc1 mutants having different alterations in the AUG initiation codon; over a ten-fold difference was observed in series of homologous crosses involving mutants with different changes at the same base-pair. Recombination rates that were associated with specific cyc1 mutants co-segregated with the particular alleles following meiosis, and comparable recombination patterns were also observed for independently isolated, identical mutations. With the mutants used in this study, the frequencies of meiotic recombination did not differ as markedly, suggesting a dissimilar dependence on specific DNA sequences for these two modes of recombination. These disproportionalities of recombination rates suggest that the nature of the mismatched bases influences the recombination process, but not in a way that can be simply interpreted.

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