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Cited by 101Fungal Infections and StudiesFungal and yeast genetics researchDNA Repair Mechanisms

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

Open access
Boyce, Kylie J., Wang, Yina, Verma, Surbhi, Shakya, Viplendra P. S., Xue, Chaoyang, Idnurm, Alexander·2017·mBio
DOI 10.1128/mbio.00595-17PMC PMC5449657
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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.

AI snapshot

Written from the paper’s full text.

TL;DR

Two clinical *Cryptococcus neoformans* isolates carried *MSH2* mutations and showed a mutator phenotype, with mutation frequencies about 200-fold higher than wild type. Deleting *MSH2*, *MLH1*, or *PMS1* increased mutation rate and enabled rapid microevolution and antifungal resistance, but only *PMS1* deletion reduced virulence.

Key findings

  • Among 11 clinical and 11 environmental *C. neoformans* var. grubii isolates, 2 clinical isolates, C23 and C45, had mutation frequencies approximately 200-fold higher than strain KN99α; both had *MSH2* mutations, and introducing wild-type *MSH2* complemented the mutator phenotype.
  • Deletion of *MSH2*, *MLH1*, or *PMS1* produced mutation frequencies approximately 200-fold higher than wild-type and complemented strains; double mutants showed no additive effects, while deletion of *MSH1*, *MSH3*, *MSH4*, or *MSH5* did not affect nuclear mutation frequency.
  • MMR mutants shifted mutation spectra: transitions rose from 40% in wild type to 75%, 100%, and 85% in *msh2Δ*, *mlh1Δ*, and *pms1Δ*; *msh2Δ* and *mlh1Δ* generated predominantly G-to-A transitions, and homopolymeric-tract mutations increased from 55% in wild type to 90%, 95%, and 95%.
  • After approximately 600 generations of passaging, *msh2Δ* and *mlh1Δ* showed phenotypic variation in stress growth and melanization; all MMR mutants showed increased spontaneous fluconazole- and amphotericin B-resistant colonies, but only *pms1Δ* showed reduced virulence and fungal load in mice.

Methods

  • Screened 11 clinical and 11 environmental *C. neoformans* var. grubii serotype A strains; measured mutation rates by spontaneous resistance to 5-FOA and 5-FU using fluctuation analysis, with the Lea-Coulson method of the median and FALCOR software.
  • Performed Ion Torrent whole-genome sequencing of C23 and C45 aligned to H99; generated MMR deletion, double-deletion, and complemented strains; sequenced *URA5* and *FUR1* from resistant mutants; tested DNA-damaging/oxidative stress sensitivity, passaged strains for approximately 600 generations, measured antifungal resistance by Etests and colony frequency, and assessed virulence/fungal burden in a murine inhalation model.
  • Used two-tailed Student’s *t* tests for most comparisons and log rank tests for murine survival, with significance thresholds as stated in the paper.

Limitations

  • The paper states that genetic reporter assays measure only mutations conferring resistance, so phenotypically silent mutations are not measured, and single-nucleotide variations in dinucleotide/trinucleotide tracts or microsatellites could not be detected.
  • The paper states that determining whether clinical *C. neoformans* populations contain a high proportion of MMR mutants requires larger sample sizes; only two clinical mutator isolates were identified here.
  • Evident from the text: C45 had an extremely high level of genetic heterogeneity, with 269,177 predicted SNPs and genome variations and 32 *MSH2* SNPs, complicating attribution of its phenotype; the virulence results also differ from a prior pooled screen, which the authors suggest may reflect competitive conditions, genetic background, or population bottlenecks.

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Integrity signals

Registry

Crossref · 10.1128/mbio.00595-17

Cites

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Statistics

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Claims the paper makes

0 of 58 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Complementation with a wild-type copy of MSH2 confirmed that the MSH2 mutations are responsible for the mutator phenotype in C23 and C45.

    “complementation confirmed that these mutations are responsible for the mutator phenotype.”
    • Also stated in: § Cryptococcus neoformans clinical isolates exhibit a mutator phenotype. · hedged
      “The introduction of a wild-type copy of MSH2 complemented the increased mutation rate phenotype of both the C23 and C45 isolates, suggesting that the mutations in MSH2 identified by next-generation DNA sequencing were responsible for the enhanced mutation rate in these clinical isolates (Fig. 1B).”
    Quote in the paperSubstantial claim
  • Findingown data

    Deletion of MMR components MSH2, MLH1, and PMS1 in C. neoformans resulted in an elevated mutation rate due to an increase in mutations in homopolymeric tracts and transitions, specifically G to A.

    “Deletion of the MMR components encoded by MSH2, MLH1, and PMS1 in C. neoformans resulted in an elevated mutation rate due to an increase in mutations in homopolymeric tracts and transitions, specifically, G to A, suggesting that MMR in C. neoformans repairs errors arising from both replication and oxidative damage.”
    Quote in the paperSubstantial claim
  • Findingown data

    Loss of MSH2, MLH1, or PMS1 in C. neoformans results in increased mutation rates.

    “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.”
    • Also stated in: § Deletion of MMR components results in an elevated mutation rate. · plain
      “The msh2Δ, mlh1Δ, and pms1Δ mutants possessed mutation frequencies approximately 200-fold higher than those of the wild-type and complemented strains (Fig. 2B and C).”
    Quote in the paperSubstantial claim
  • Findingown data

    Two clinical isolates of Cryptococcus neoformans, C23 and C45, exhibited a mutator phenotype (increased mutation rate).

    “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.”
    • Also stated in: § Cryptococcus neoformans clinical isolates exhibit a mutator phenotype. · hedged
      “In contrast, 2 of the 11 clinical isolates, C23 and C45, had an increase in the number of spontaneously resistant 5-FOA colonies indicative of an increased mutation rate (Fig. 1A).”
    Quote in the paperSubstantial claim
  • Findingown data

    Whole-genome analysis of C23 and C45 revealed mutations in MSH2 of the mismatch repair pathway.

    “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.”
    • Also stated in: § Cryptococcus neoformans clinical isolates exhibit a mutator phenotype. · plain
      “MSH2, which is 1 of the 57 DNA repair genes in the C23 genome sequence, contained a sequence variation.”
    • Also stated in: § Cryptococcus neoformans clinical isolates exhibit a mutator phenotype. · plain
      “A total of 32 SNPs were present within MSH2 in isolate C45, with 21 within the coding sequence.”
    Quote in the paperSubstantial claim
  • May combine two claims. 50
  • Classified as probably not a substantial claim. 22

  • May combine two claims.

    Findingown data

    The elevated mutation rate and the types of mutations generated in the MMR mutants are not detrimental to growth and result in only minor sensitivity to stress.

    “We show that the elevated mutation rate and the types of mutations generated in the MMR mutants are not detrimental to growth and result in only minor sensitivity to stress while enabling rapid microevolution to occur.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    The elevated mutation rate of the MMR mutants was not detrimental to C. neoformans in vivo, with no decrease in colonization or virulence observed in msh2Δ and mlh1Δ mutants in a murine infection model.

    “Interestingly, the elevated mutation rate of the MMR mutants was not detrimental to C. neoformans in vivo, with no decrease in colonization or virulence observed in msh2Δ and mlh1Δ mutants in a murine infection model.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Mutation of PMS1 reduced virulence, whereas mutation of MSH2 or MLH1 had no effect on the level of virulence.

    “Mutation of PMS1 reduced virulence, whereas mutation of MSH2 or MLH1 had no effect on the level of virulence.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the wild-type strain, 100% of the transition mutations generated were T-to-C transitions; in contrast, the msh2Δ and mlh1Δ mutants generated predominately G-to-A transitions.

    “In the wild-type strain, 100% of the transition mutations generated were T-to-C transitions. In contrast, the msh2Δ and mlh1Δ mutants generated predominately G-to-A transitions (Fig. 3C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    The numbers of transition mutations in FUR1 between the strains remained equivalent, suggesting that mutations in homopolymeric tracts occur more frequently than transitions.

    “The numbers of transition mutations in FUR1 between the strains remained equivalent, suggesting that mutations in homopolymeric tracts occur more frequently than transitions.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The MMR mutants showed an excess of transition mutations, specifically G-to-A transitions in the msh2Δ and mlh1Δ mutants, and an increase in single-nucleotide deletions and insertions at homopolymeric tracts.

    “The mutants showed an excess of transition mutations, specifically, G-to-A transitions in the msh2Δ and mlh1Δ mutants, and an increase in single-nucleotide deletions and insertions at homopolymeric tracts.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    None of the missense mutations in C45 MSH2 were in highly conserved amino acids; however, the T182I substitution is located in an equivalent position that, when mutated in S. cerevisiae (L183P), resulted in a 220-fold induction of mutation rate due to a lack of structural integrity.

    “None of the missense mutations were in highly conserved amino acids; however, the T182I substitution is located in an equivalent position that, when mutated in S. cerevisiae (L183P), resulted in a 220-fold induction of mutation rate due to a lack of structural integrity (24).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [24] Lang GI, Parsons L, Gammie AE 2013 Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3 3: 1453– 1465. doi: 10.1534/g3.113.006429. 23821616 PMC3755907 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The passaged mlh1Δ and pms1Δ strains showed differences in melanization compared to the original mutants, though the differences were not as extreme as those seen with the msh2Δ strains.

    “The passaged mlh1Δ and pms1Δ strains showed differences in melanization compared to the original mutants also, though the differences were not as extreme as those seen with the msh2Δ strains (Fig. 5B).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Deletion of PMS1, but not MSH2 or MHL1, results in a reduction in C. neoformans virulence.

    “Deletion of PMS1, but not MSH2 or MHL1, results in a reduction in C. neoformans virulence.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Despite the increased mutation rate and the shift in the mutational profile, the MMR mutants did not show a decrease in viability in vitro or for the msh2Δ and mlh1Δ mutants in a mouse model of disease.

    “Despite the increased mutation rate and the shift in the mutational profile, the MMR mutants did not show a decrease in viability in vitro or for the msh2Δ and mlh1Δ mutants in a mouse model of disease.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Fluconazole-resistant strains derived from either wild-type or msh2Δ strains were not resistant to amphotericin B and vice versa.

    “Fluconazole-resistant strains derived from either wild-type or msh2Δ strains were not resistant to amphotericin B and vice versa (data not shown).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    URA5 from msh2Δ, mlh1Δ, and pms1Δ 5-FOA-resistant strains showed a reduction in the number of insertion, deletion, and transversion mutations and an increase in the number of transition mutations (from 40% in the wild type to 75%, 100%, and 85% in the mutants, respectively).

    “In comparison to the wild-type results, URA5 from msh2Δ, mlh1Δ, and pms1Δ 5-FOA-resistant strains showed a reduction in the number of insertion, deletion, and transversion mutations and an increase in the number of transition mutations (from 40% in the wild type to 75%, 100%, and 85% in the mutants, respectively) (Fig. 3B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    The increased mutation rate corresponds to approximately 1 mutation per genome per generation, in contrast to 1 mutation every few hundred generations for the wild type.

    “This corresponds to approximately 1 mutation per genome per generation in contrast to 1 mutation every few hundred generations for the wild type.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    FUR1 from msh2Δ, mlh1Δ, and pms1Δ 5-FU-resistant strains possessed a reduction in the numbers of large deletions and an increase in the numbers of deletions and insertions in homopolymeric tracts (from 55% in the wild-type strain to 90%, 95%, and 95% in the mutants, respectively).

    “In comparison to the wild-type results, FUR1 from msh2Δ, mlh1Δ, and pms1Δ 5-FU-resistant strains possessed a reduction in the numbers of large deletions and an increase in the numbers of deletions and insertions in homopolymeric tracts (from 55% in the wild-type strain to 90%, 95%, and 95% in the mutants, respectively) (Fig. 3E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The C45 isolate possessed a MIC lower than that of the wild-type strain (3.0 ± 1.0 μg/ml) and very few spontaneously arising fluconazole-resistant colonies in the zone of clearance.

    “In contrast, the C45 isolate possessed a MIC lower than that of the wild-type strain (3.0 ± 1.0 µg/ml) and very few spontaneously arising fluconazole-resistant colonies in the zone of clearance (Fig. 7A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The melanization results differed dramatically in the passaged msh2Δ strains compared to the original mutant, with each strain exhibiting a decrease in melanization, an almost complete absence of melanization, and an increase in melanization.

    “In contrast, the melanization results differed dramatically in the passaged msh2Δ strains compared to the original mutant, with each strain exhibiting a decrease in melanization, an almost complete absence of melanization, and an increase in melanization (Fig. 5B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Most SNPs in C45 MSH2 resulted in silent mutations; however, 6 resulted in missense mutations (V167A, T182I, D238V, L436P, S885F, and N863D).

    “Most of these SNPs resulted in silent mutations; however, 6 (V167A, T182I, D238V, L436P, S885F, and N863D) resulted in missense mutations.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The msh2Δ, mlh1Δ, and pms1Δ mutants all showed a statistically significant increase in the frequency of amphotericin B-resistant colonies compared to the wild type, and the mutant colonies also differed in size from those seen with the wild-type and complemented strains.

    “Similarly to the rapid emergence of resistance to fluconazole, the msh2Δ, mlh1Δ, and pms1Δ mutants all showed a statistically significant increase in the frequency of amphotericin B-resistant colonies compared to the wild type, and the mutant colonies also differed in size from those seen with the wild-type and complemented strains (Fig. 6E and F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The mlh1Δ mutant displayed a higher number of spontaneously arising fluconazole-resistant colonies than the msh2Δ and pms1Δ mutants that was probably a reflection of the higher MIC.

    “The mlh1Δ mutant displayed a higher number of spontaneously arising fluconazole-resistant colonies than the msh2Δ and pms1Δ mutants that was probably a reflection of the higher MIC (Fig. 6C and D).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The increase in fluconazole resistance was also observed in the msh2Δ mlh1Δ double mutant but not in the pms1Δ mlh1Δ mutant.

    “This increase in fluconazole resistance was also observed in the msh2Δ mlh1Δ double mutant but not in the pms1Δ mlh1Δ mutant (Fig. 6A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A number of C. neoformans clinical isolates carry mutations in MMR components that give rise to a hypermutation phenotype, high levels of fluconazole resistance, and the ability to rapidly generate spontaneous fluconazole-resistant subisolates.

    “This study showed that a number of C. neoformans clinical isolates carry mutations in MMR components that give rise to a hypermutation phenotype, high levels of fluconazole resistance, and the ability to rapidly generate spontaneous fluconazole-resistant subisolates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    Although the pms1Δ mutant displays a shift in the mutational profile to more transition mutations and mutations in homopolymeric tracts, like the msh2Δ and mlh1Δ mutants, the types of transition mutations generated differ.

    “Although the pms1Δ mutant displays a shift in the mutational profile to more transition mutations and mutations in homopolymeric tracts, like the msh2Δ and mlh1Δ mutants, the types of transition mutations generated differ.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Single-base mutations arising from errors in DNA replication can generate novel traits that facilitate the ability to cause disease and provide an avenue for the pathogen to undergo microevolution during infection.

    “This suggests that single-base mutations arising from errors in DNA replication can generate novel traits that facilitate the ability to cause disease and therefore provide an avenue for the pathogen to undergo microevolution during infection.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In bacteria, replication errors are corrected by the 3′-5′ editing exonuclease activity of the ε subunit of DNA polymerase III and the mutHLS mismatch repair system.

    “In bacteria, replication errors are corrected by the 3′–5′ editing exonuclease activity of the ε subunit of DNA polymerase III and the mutHLS mismatch repair system (reviewed in reference 14).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites (reviewed in reference 14)

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Single-base-pair mutations may play an important role in the microevolution of pathogenic fungi during infection.

    “Interestingly, recent studies have also indicated that single-base-pair mutations may play an important role in the microevolution of pathogenic fungi during infection (11, 12).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [11] Chow EW, Morrow CA, Djordjevic JT, Wood IA, Fraser JA 2012 Microevolution of Cryptococcus neoformans driven by massive tandem gene amplification. Mol Biol Evol 29: 1987– 2000. doi: 10.1093/molbev/mss066. 22334577

      Not checked in the free run.

    • cites [12] Magditch DA, Liu TB, Xue C, Idnurm A 2012 DNA mutations mediate microevolution between host-adapted forms of the pathogenic fungus Cryptococcus neoformans. PLoS Pathog 8: e1002936. doi: 10.1371/journal.ppat.1002936. 23055925 PMC3464208

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    55% of clinical isolates of the fungus Candida glabrata contain a mutation in MSH2.

    “In addition, 55% of clinical isolates of the fungus Candida glabrata contain a mutation in MSH2 (21).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Healey KR, Zhao Y, Perez WB, Lockhart SR, Sobel JD, Farmakiotis D, Kontoyiannis DP, Sanglard D, Taj-Aldeen SJ, Alexander BD, Jimenez-Ortigosa C, Shor E, Perlin DS 2016 Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance. Nat Commun 7: 11128. doi: 10.1038/ncomms11128. 27020939 PMC5603725 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Microevolution in fungal pathogens has previously been attributed to changes at the chromosomal level, with evidence of gain, loss, or recombination between chromosomes leading to resistance to antifungal agents.

    “Microevolution in fungal pathogens has previously been attributed to changes at the chromosomal level, with evidence of gain, loss, or recombination between chromosomes leading to resistance to antifungal agents (1–5).”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [1] Almeida AM, Matsumoto MT, Baeza LC, de Oliveira e Silva RB, Kleiner AA, Melhem MDS, Mendes Giannini MJ, Laboratory Group on Cryptococcosis 2007 Molecular typing and antifungal susceptibility of clinical sequential isolates of Cryptococcus neoformans from Sao Paulo State, Brazil. FEMS Yeast Res 7: 152– 164. doi: 10.1111/j.1567-1364.2006.00128.x. 17311593

      Not checked in the free run.

    • cites [2] Blasi E, Brozzetti A, Francisci D, Neglia R, Cardinali G, Bistoni F, Vidotto V, Baldelli F 2001 Evidence of microevolution in a clinical case of recurrent Cryptococcus neoformans meningoencephalitis. Eur J Clin Microbiol Infect Dis 20: 535– 543. doi: 10.1007/s100960100549. 11681432

      Not checked in the free run.

    • cites [3] Fries BC, Casadevall A 1998 Serial isolates of Cryptococcus neoformans from patients with AIDS differ in virulence for mice. J Infect Dis 178: 1761– 1766. 9815230

      Not checked in the free run.

    • cites [4] Ormerod KL, Morrow CA, Chow EW, Lee IR, Arras SD, Schirra HJ, Cox GM, Fries BC, Fraser JA 2013 Comparative genomics of serial isolates of Cryptococcus neoformans reveals gene associated with carbon utilization and virulence. G3 3: 675– 686. doi: 10.1534/g3.113.005660. 23550133 PMC3618354

      Not checked in the free run.

    • cites [5] Sullivan D, Haynes K, Moran G, Shanley D, Coleman D 1996 Persistence, replacement, and microevolution of Cryptococcus neoformans strains in recurrent meningitis in AIDS patients. J Clin Microbiol 34: 1739– 1744. 8784580 PMC229105

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In bacteria, mutators found in nature carry defects in a component of the MMR.

    “In bacteria, mutators found in nature carry defects in a component of the MMR (20).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [20] Denamur E, Matic I 2006 Evolution of mutation rates in bacteria. Mol Microbiol 60: 820– 827. doi: 10.1111/j.1365-2958.2006.05150.x. 16677295

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The findings support the hypothesis that C. neoformans can take advantage of a mutator phenotype to cause disease but only in specific pathways that lead to a mutator trait without a significant tradeoff in fitness.

    “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.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    S. cerevisiae MSH2, MLH1, and PMS1 MMR mutants exhibit a mutator phenotype in which the rate of spontaneous mutation is elevated.

    “The S. cerevisiae MSH2, MLH1, and PMS1 MMR mutants exhibit a mutator phenotype in which the rate of spontaneous mutation is elevated (15).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [15] Kunkel TA 2011 Balancing eukaryotic replication asymmetry with replication fidelity. Curr Opin Chem Biol 15: 620– 626. doi: 10.1016/j.cbpa.2011.07.025. 21862387 PMC3189284

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Pathogens can retain a larger-than-expected proportion of mutators in their populations.

    “Pathogens can retain a larger-than-expected proportion of mutators, i.e., cells with a greater-than-normal mutation frequency, in their populations (17–19).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [17] Canfield GS, Schwingel JM, Foley MH, Vore KL, Boonanantanasarn K, Gill AL, Sutton MD, Gill SR 2013 Evolution in fast forward: a potential role for mutators in accelerating Staphylococcus aureus pathoadaptation. J Bacteriol 195: 615– 628. doi: 10.1128/JB.00733-12. 23204459 PMC3554003

      Not checked in the free run.

    • cites [18] LeClerc JE, Li B, Payne WL, Cebula TA 1996 High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274: 1208– 1211. doi: 10.1126/science.274.5290.1208. 8895473

      Not checked in the free run.

    • cites [19] Oliver A, Cantón R, Campo P, Baquero F, Blázquez J 2000 High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251– 1254. doi: 10.1126/science.288.5469.1251. 10818002

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    In S. cerevisiae, only MSH2, MSH3, MSH6, MLH1, and PMS1 are required for mismatch repair of nuclear DNA, with MSH3 and MSH6 playing partially redundant roles.

    “The S. cerevisiae genome encodes six MutS homologues (MSH1 to MSH6) and four MutL homologues (MLH1 to MLH3 and PMS1); however, only MSH2, MSH3, MSH6, MLH1, and PMS1 are required for mismatch repair of nuclear DNA, with MSH3 and MSH6 playing partially redundant roles (reviewed in reference 15).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites (reviewed in reference 15)

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The resulting uracil in DNA is typically removed by the homologue of the Ung1 uracil DNA N-glycosylase of the base excision repair (BER) pathway.

    “The resulting uracil in DNA is typically removed by the homologue of the Ung1 uracil DNA N-glycosylase of the base excision repair (BER) pathway (30).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [30] Boiteux S, Jinks-Robertson S 2013 DNA repair mechanisms and the bypass of DNA damage in Saccharomyces cerevisiae. Genetics 193: 1025– 1064. doi: 10.1534/genetics.112.145219. 23547164 PMC3606085

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Minor or no phenotypes are expected on ROS as oxidative damage is mainly repaired by the base excision repair (BER) pathway, although MMR has been shown to play a role in repairing oxidation of guanine to 8-oxo-7,8-dihydroguanine (8-oxoG).

    “Minor or no phenotypes are expected on ROS as oxidative damage is mainly repaired by the base excision repair (BER) pathway, although MMR has been shown to play a role in repairing oxidation of guanine to 8-oxo-7,8-dihydroguanine (8-oxoG) (27).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [27] Kanvah S, Joseph J, Schuster GB, Barnett RN, Cleveland CL, Landman U 2010 Oxidation of DNA: damage to nucleobases. Acc Chem Res 43: 280– 287. doi: 10.1021/ar900175a. 19938827 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    G-to-A transitions, followed by G-to-T transversions, are the most commonly observed mutations arising from oxidative damage to DNA but can also be generated through misincorporation of dUTP instead of dTTP during replication or deamination of cytosine.

    “G-to-A transitions, followed by G-to-T transversions, are the most commonly observed mutations arising from oxidative damage to DNA but can also be generated through misincorporation of dUTP instead of dTTP during replication or deamination of cytosine (29).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [29] Wang D, Kreutzer DA, Essigmann JM 1998 Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat Res 400: 99– 115. doi: 10.1016/S0027-5107(98)00066-9. 9685598

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    Rates of phenotypically silent mutations are not measured, as evidenced by the frequent deletion of nucleotides in the (T)14 homopolymer of FUR1 in the 5-FU-resistant msh2Δ, mlh1Δ, and pms1Δ isolates, in combination with mutations in the (C)7 and (A)6 homopolymers, as the (T)14 homopolymer falls within an intron and is therefore silent.

    “Rates of phenotypically silent mutations are not measured, as evidenced by the frequent deletion of nucleotides in the (T)14 homopolymer of FUR1 in the 5-FU-resistant msh2Δ, mlh1Δ, and pms1Δ isolates, in combination with mutations in the (C)7 and (A)6 homopolymers, as the (T)14 homopolymer falls within an intron and is therefore silent (Fig. 3D).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    A lack of repair of guanine oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG) can also result in an increased number of G-to-A transitions (depending on the sequence context) but normally results in an abundance of G-to-T transversions.

    “A lack of repair of guanine oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG) can also result in an increased number of G-to-A transitions (depending on the sequence context) but normally results in an abundance of G-to-T transversions”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [27] Kanvah S, Joseph J, Schuster GB, Barnett RN, Cleveland CL, Landman U 2010 Oxidation of DNA: damage to nucleobases. Acc Chem Res 43: 280– 287. doi: 10.1021/ar900175a. 19938827 source

      Not checked in the free run.

    • cites [29] Wang D, Kreutzer DA, Essigmann JM 1998 Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat Res 400: 99– 115. doi: 10.1016/S0027-5107(98)00066-9. 9685598

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A similar shift in mutational profile is observed in S. cerevisiae msh2Δ mutants, in which an equivalent shift to transitions is observed and a large number of single nucleotide variations (−1 to +1) occur within homopolymeric tracts.

    “A similar shift in mutational profile is also observed in S. cerevisiae msh2Δ mutants, in which an equivalent shift to transitions is observed and a large number of single nucleotide variations (−1 to +1) occur within homopolymeric tracts (24, 25).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [24] Lang GI, Parsons L, Gammie AE 2013 Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3 3: 1453– 1465. doi: 10.1534/g3.113.006429. 23821616 PMC3755907 source

      Not checked in the free run.

    • cites [25] Serero A, Jubin C, Loeillet S, Legoix-Né P, Nicolas AG 2014 Mutational landscape of yeast mutator strains. Proc Natl Acad Sci U S A 111: 1897– 1902. doi: 10.1073/pnas.1314423111. 24449905 PMC3918763

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationnone given

    The majority of mutations are likely to occur in noncoding DNA or to be silent, and only a minute fraction would be deleterious.

    “The majority of mutations are likely to occur in noncoding DNA or to be silent, and it is expected that only a minute fraction would be deleterious.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premiseown data

    FUR1 contains homopolymeric tracts: (C)7 at +81 to +87, (A)6 at +460 to +465, and (T)14 at +941 to +954.

    “Unlike URA5, FUR1 contains a number of homopolymeric tracts: (C)7 at +81 to +87, (A)6 at +460 to +465, and (T)14 at +941 to +954 (Fig. 3D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Mutations of the URA5 and FUR1 genes in C. neoformans are the most common cause of resistance to 5-FOA and 5-FU, respectively.

    “Mutations of the URA5 and FUR1 genes in C. neoformans are the most common cause of resistance to 5-FOA and 5-FU, respectively (12, 26).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [12] Magditch DA, Liu TB, Xue C, Idnurm A 2012 DNA mutations mediate microevolution between host-adapted forms of the pathogenic fungus Cryptococcus neoformans. PLoS Pathog 8: e1002936. doi: 10.1371/journal.ppat.1002936. 23055925 PMC3464208

      Not checked in the free run.

    • cites [26] Kwon-Chung KJ, Varma A, Edman JC, Bennett JE 1992 Selection of ura5 and ura3 mutants from the two varieties of Cryptococcus neoformans on 5-fluoroorotic acid medium. J Med Vet Mycol 30: 61– 69. doi: 10.1080/02681219280000081. 1573522

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In S. cerevisiae, single nucleotide variations are also detected within dinucleotide/trinucleotide tracts (microsatellites).

    “In S. cerevisiae, single nucleotide variations are also detected within dinucleotide/trinucleotide tracts (microsatellites) (24, 25).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [24] Lang GI, Parsons L, Gammie AE 2013 Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3 3: 1453– 1465. doi: 10.1534/g3.113.006429. 23821616 PMC3755907 source

      Not checked in the free run.

    • cites [25] Serero A, Jubin C, Loeillet S, Legoix-Né P, Nicolas AG 2014 Mutational landscape of yeast mutator strains. Proc Natl Acad Sci U S A 111: 1897– 1902. doi: 10.1073/pnas.1314423111. 24449905 PMC3918763

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Equivalent levels of mice colonization and infection were observed between the wild type and the msh2Δ mutant in a standard C. glabrata virulence assay.

    “Similarly to C. neoformans, equivalent levels of mice colonization and infection were also observed between the wild type and the msh2Δ mutant in a standard C. glabrata virulence assay (21).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Healey KR, Zhao Y, Perez WB, Lockhart SR, Sobel JD, Farmakiotis D, Kontoyiannis DP, Sanglard D, Taj-Aldeen SJ, Alexander BD, Jimenez-Ortigosa C, Shor E, Perlin DS 2016 Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance. Nat Commun 7: 11128. doi: 10.1038/ncomms11128. 27020939 PMC5603725 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The mutational profile and phenotype of the pms1Δ mutant differ from those of the msh2Δ and mlh1Δ mutants, and this may relate to the reason that the pms1Δ mutant strain shows attenuation of virulence whereas the other two mutants do not.

    “It is interesting that the mutational profile and phenotype of the pms1Δ mutant differ from those of the msh2Δ and mlh1Δ mutants, and this may relate to the reason that the pms1Δ mutant strain shows attenuation of virulence whereas the other two mutants do not.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    One of the three clonal subpopulations causing the outbreak consisted of two distinct groups: a group of less-virulent strains containing a frameshift mutation in MSH2 and a group of highly virulent outbreak strains in which the MSH2 mutation is hypothesized to have reverted.

    “One of the three clonal subpopulations causing the outbreak consisted of two distinct groups: a group of less-virulent strains containing a frameshift mutation in MSH2 and a group of highly virulent outbreak strains in which the MSH2 mutation is hypothesized to have reverted (34).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [34] Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J 2014 Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution. mBio 5: e01494-14. doi: 10.1128/mBio.01494-14. 25073643 PMC4128362

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    A transient mutator provides a scenario by which mutators can benefit temporarily from elevated mutation frequencies for adaptation and yet can reduce the risk of accumulating deleterious mutations.

    “A transient mutator provides a scenario by which mutators can benefit temporarily from elevated mutation frequencies for adaptation and yet can reduce the risk of accumulating deleterious mutations.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    These disomic chromosomes allow the rapid emergence of fluconazole resistance; however, the disomic chromosomes are lost when fluconazole is removed, presumably due to reduced fitness as evidenced by reduced proliferation and virulence.

    “These disomic chromosomes allow the rapid emergence of fluconazole resistance; however, the disomic chromosomes are lost when fluconazole is removed, presumably due to reduced fitness as evidenced by reduced proliferation and virulence (10).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [10] Sionov E, Lee H, Chang YC, Kwon-Chung KJ 2010 Cryptococcus neoformans overcomes stress of azole drugs by formation of disomy in specific multiple chromosomes. PLoS Pathog 6: e10000848. doi: 10.1371/journal.ppat.1000848. PMC2848560 20368972 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The animal models and procedures used have been approved by the IACUC at Rutgers University (protocol 15041D0518).

    “The animal models and procedures used have been approved by the IACUC at Rutgers University (protocol 15041D0518).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Deletion of MSH2 and PMS1 in C. albicans resulted in resistant colonies arising in the inhibition ellipse of fluconazole Etests, although the rate was not as high as that observed in C. neoformans or C. glabrata.

    “Likewise, deletion of MSH2 and PMS1 in C. albicans also resulted in resistant colonies arising in the inhibition ellipse of fluconazole Etests, although the rate was not as high as that observed in C. neoformans or C. glabrata (as expected due to the diploid state of C. albicans) (36).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [36] Legrand M, Chan CL, Jauert PA, Kirkpatrick DT 2008 Analysis of base excision and nucleotide excision repair in Candida albicans. Microbiology 154: 2446– 2456. doi: 10.1099/mic.0.2008/017616-0. 18667577

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Fifty-five percent of C. glabrata clinical isolates recovered from patients are msh2 mutants.

    “Fifty-five percent of C. glabrata clinical isolates recovered from patients are msh2 mutants (other components of the MMR pathway were not sequenced) (21).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Healey KR, Zhao Y, Perez WB, Lockhart SR, Sobel JD, Farmakiotis D, Kontoyiannis DP, Sanglard D, Taj-Aldeen SJ, Alexander BD, Jimenez-Ortigosa C, Shor E, Perlin DS 2016 Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance. Nat Commun 7: 11128. doi: 10.1038/ncomms11128. 27020939 PMC5603725 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The original analysis of these mutants showed they had increased proliferation in vivo.

    “This is in contrast to the original analysis of these mutants, which showed they had increased proliferation in vivo (13).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [13] Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM 2008 Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell 135: 174– 188. doi: 10.1016/j.cell.2008.07.046. 18854164 PMC2628477 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Deletions of MSH2 in C. glabrata result in high levels of spontaneous antifungal resistance in vitro, in addition to an increase in the occurrence of resistance to caspofungin arising during in vivo growth.

    “Deletions of MSH2 in C. glabrata also result in high levels of spontaneous antifungal resistance in vitro, in addition to an increase in the occurrence of resistance to caspofungin arising during in vivo growth (21).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Healey KR, Zhao Y, Perez WB, Lockhart SR, Sobel JD, Farmakiotis D, Kontoyiannis DP, Sanglard D, Taj-Aldeen SJ, Alexander BD, Jimenez-Ortigosa C, Shor E, Perlin DS 2016 Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance. Nat Commun 7: 11128. doi: 10.1038/ncomms11128. 27020939 PMC5603725 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    An increase in proliferation would be observed only in a strain with lower virulence than that seen in the KN99 background, when the mutants are in a competitive environment, or when a small number of cells are inoculated, effectively creating a population bottleneck.

    “It is possible that an increase in proliferation would be observed only in a strain with lower virulence than that seen in the KN99 background, when the mutants are in a competitive environment, or when a small number of cells are inoculated, effectively creating a population bottleneck.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Mutations in MSH2 provide the pathogen with an opportunity for the rapid evolution of resistance to antifungal drugs and could be a cause of patient relapse.

    “Mutations in MSH2 provide the pathogen with an opportunity for the rapid evolution of resistance to antifungal drugs and could be a cause of patient relapse.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The bacterial pathogens Staphylococcus aureus, Escherichia coli, and Salmonella enterica retain a larger-than-expected proportion of mutator cells in their populations with defects in components of MMR, and 20% of Pseudomonas aeruginosa isolates from cystic fibrosis patients are mutators compared to 0% of environmental isolates.

    “In addition, the bacterial pathogens Staphylococcus aureus, Eschericha coli, and Salmonella enterica retain a larger-than-expected proportion of mutator cells in their populations with defects in components of MMR, and 20% of Pseudomonas aeruginosa isolates from cystic fibrosis patients are mutators compared to 0% of environmental isolates (17–20).”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [17] Canfield GS, Schwingel JM, Foley MH, Vore KL, Boonanantanasarn K, Gill AL, Sutton MD, Gill SR 2013 Evolution in fast forward: a potential role for mutators in accelerating Staphylococcus aureus pathoadaptation. J Bacteriol 195: 615– 628. doi: 10.1128/JB.00733-12. 23204459 PMC3554003

      Not checked in the free run.

    • cites [18] LeClerc JE, Li B, Payne WL, Cebula TA 1996 High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274: 1208– 1211. doi: 10.1126/science.274.5290.1208. 8895473

      Not checked in the free run.

    • cites [19] Oliver A, Cantón R, Campo P, Baquero F, Blázquez J 2000 High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251– 1254. doi: 10.1126/science.288.5469.1251. 10818002

      Not checked in the free run.

    • cites [20] Denamur E, Matic I 2006 Evolution of mutation rates in bacteria. Mol Microbiol 60: 820– 827. doi: 10.1111/j.1365-2958.2006.05150.x. 16677295

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    All gene replacements were confirmed by PCR.

    “All gene replacements were confirmed by PCR.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Antifungal resistance in C. neoformans is often associated with changes in karyotype.

    “Antifungal resistance in C. neoformans is often associated with changes in karyotype (reviewed in reference 6).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [6] Morrow CA, Fraser JA 2013 Ploidy variation as an adaptive mechanism in human pathogenic fungi. Semin Cell Dev Biol 24: 339– 346. doi: 10.1016/j.semcdb.2013.01.008. 23380396

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    MSH2 mutations are present in a higher percentage in fluconazole-resistant clinical isolates than in susceptible strains in C. glabrata.

    “MSH2 mutations are present in a higher percentage in fluconazole-resistant clinical isolates than in susceptible strains in C. glabrata (21).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Healey KR, Zhao Y, Perez WB, Lockhart SR, Sobel JD, Farmakiotis D, Kontoyiannis DP, Sanglard D, Taj-Aldeen SJ, Alexander BD, Jimenez-Ortigosa C, Shor E, Perlin DS 2016 Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance. Nat Commun 7: 11128. doi: 10.1038/ncomms11128. 27020939 PMC5603725 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The range of transitions generated in the pms1Δ mutant may result in more deleterious mutations than in msh2Δ and mlh1Δ mutants, as a greater range of codons can be mutated and as C-to-T transitions also result in premature stops, unlike G-to-A transitions.

    “The range of transitions generated in the pms1Δ mutant may result in more deleterious mutations than in msh2Δ and mlh1Δ mutants, as a greater range of codons can be mutated and as C-to-T transitions also result in premature stops, unlike G-to-A transitions.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Pms1 is playing a role in addition to that of the MutLα heterodimer in nuclear mismatch repair, possibly through interaction with PCNA.

    “This suggests that Pms1 is playing a role in addition to that of the MutLα heterodimer in nuclear mismatch repair, possibly through interaction with the PCNA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Rather than having a direct impact on the virulence composition of isolates, MMR mutations are more likely to be a significant factor in allowing outbreaks to occur via the generation of hypervirulent strains from less-virulent ancestors and by allowing recurrence of cryptococcal meningitis through the generation of antifungal resistance.

    “Rather than having a direct impact on the virulence composition of isolates, MMR mutations are more likely to be a significant factor in allowing outbreaks to occur via the generation of hypervirulent strains from less-virulent ancestors and by allowing recurrence of cryptococcal meningitis through the generation of antifungal resistance.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    MMR is more efficient at repairing lagging-strand errors generated by DNA polymerase ∂ (Pol3) as the MutSα/β complex is directed to the 5′ ends of Okazaki fragments and is tethered to PCNA, a DNA clamp that acts as a processivity factor for DNA polymerase ∂ (Pol3).

    “MMR is more efficient at repairing lagging-strand errors generated by DNA polymerase ∂ (Pol3) as the MutSα/β complex is directed to the 5′ ends of Okazaki fragments and is tethered to the proliferating cell nuclear antigen (PCNA), a DNA clamp that acts as a processivity factor for DNA polymerase ∂ (Pol3) (31–33).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [31] Pavlov YI, Mian IM, Kunkel TA 2003 Evidence for preferential mismatch repair of lagging strand DNA replication errors in yeast. Curr Biol 13: 744– 748. doi: 10.1016/S0960-9822(03)00284-7. 12725731

      Not checked in the free run.

    • cites [32] Fortune JM, Pavlov YI, Welch CM, Johansson E, Burgers PMJ, Kunkel TA 2005 Saccharomyces cerevisiae DNA polymerase delta: high fidelity for base substitutions but lower fidelity for single- and multi-base deletions. J Biol Chem 280: 29980– 29987. doi: 10.1074/jbc.M505236200. 15964835

      Not checked in the free run.

    • cites [33] Lujan SA, Williams JS, Pursell ZF, Abdulovic-Cui AA, Clark AB, Nick McElhinny SA, Kunkel TA 2012 Mismatch repair balances leading and lagging strand DNA replication fidelity. PLoS Genet 8: e1003016. doi: 10.1371/journal.pgen.1003016. 23071460 PMC3469411

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In the original experiment, 48 pooled mutants were simultaneously inoculated into mice to allow large-scale screening and a less virulent genetic background was used.

    “In that experiment, however, 48 pooled mutants were simultaneously inoculated into mice to allow large-scale screening and a less virulent genetic background was used.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [13] Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM 2008 Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell 135: 174– 188. doi: 10.1016/j.cell.2008.07.046. 18854164 PMC2628477 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Mutations in MMR components provide C. neoformans with an additional mechanism enabling microevolution to occur and this has implications for the development of antifungal resistance.

    “What is clear is that mutations in MMR components provide C. neoformans with an additional mechanism enabling microevolution to occur and that this has implications for the development of antifungal resistance.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Mutations resulted in measurable phenotypic change, suggesting that those arising in the msh2Δ and mlh1Δ mutants provide a powerful mode of rapid microevolution in C. neoformans.

    “Mutations resulted in measurable phenotypic change, suggesting that those arising in the msh2Δ and mlh1Δ mutants provide a powerful mode of rapid microevolution in C. neoformans.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The majority of mutations are generated by errors during lagging-strand synthesis by DNA polymerase ∂ (Pol3), which shows inefficient proofreading and lower fidelity than DNA polymerase ε (Pol2).

    “However, the majority of mutations are generated by errors during lagging-strand synthesis by DNA polymerase ∂ (Pol3), which shows inefficient proofreading and, consequently, lower fidelity than that seen with DNA polymerase ε (Pol2) (31).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] Pavlov YI, Mian IM, Kunkel TA 2003 Evidence for preferential mismatch repair of lagging strand DNA replication errors in yeast. Curr Biol 13: 744– 748. doi: 10.1016/S0960-9822(03)00284-7. 12725731

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The msh2Δ, mlh1Δ, and pms1Δ strains were backcrossed twice to a MATa congenic parent to remove unwanted melanin and mating differences known to exist in their background.

    “These three strains were backcrossed twice to a MATa congenic parent to remove unwanted melanin and mating differences known to exist in their background (13, 37) to create strains AISVCN195, AISVCN196, and AISVCN198.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [13] Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM 2008 Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell 135: 174– 188. doi: 10.1016/j.cell.2008.07.046. 18854164 PMC2628477 source

      Not checked in the free run.

    • cites [37] Janbon G, Ormerod KL, Paulet D, Byrnes EJ III, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuveglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA 2014 Analysis of the genome and transcri

      Not checked in the free run.

67 of 67

  • The paper relies on this without support.

    The ability to adapt to a changing environment provides a selective advantage to microorganisms.

    “The ability to adapt to a changing environment provides a selective advantage to microorganisms.”

  • The paper relies on this without support.

    An essential prerequisite for all groups of microbial pathogens is the ability to change rapidly during infection to adapt to the hostile environment of the host.

    “An essential prerequisite for all groups of microbial pathogens is the ability to change rapidly during infection to adapt to the hostile environment of the host.”

  • The paper relies on this without support.

    Errors generated during DNA replication are corrected by two sequential repair systems, namely, the DNA polymerase 3′–5′ exonuclease activity system and the mismatch repair (MMR) system.

    “Errors generated during DNA replication are corrected by the action of two sequential repair systems, namely, the DNA polymerase 3′–5′ exonuclease activity system and the mismatch repair (MMR) system.”

  • The paper relies on this without support.

    Possession of sequential repair mechanisms enables a multiplicative effect, increasing the fidelity of DNA replication by a factor of 10^4 to 10^5.

    “Possession of sequential repair mechanisms enables a multiplicative effect, increasing the fidelity of DNA replication by a factor of 104 to 105.”

  • The paper relies on this without support.

    The MMR system is structurally and functionally conserved in eukaryotes.

    “This system is structurally and functionally conserved in eukaryotes.”

  • The paper relies on this without support.

    Microevolution during the course of infection can select for a small proportion of the microbe population that has gained novel traits that facilitate the ability to cause disease.

    “Microevolution during the course of infection can select for a small proportion of the microbe population that has gained novel traits that facilitate the ability to cause disease.”

  • The paper relies on this without support.

    G-to-A transitions also occur by the deamination of methylated cytosine to thymine.

    “G-to-A transitions also occur by the deamination of methylated cytosine to thymine.”

  • The paper relies on this without support.

    Retaining a proportion of mutator cells in a microbial population provides a selective advantage in vivo.

    “In other microbial populations, retaining a proportion of mutator cells in the population is thought to provide a selective advantage in vivo.”
8 of 8

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Hypermutator phenotypes resulting from mutations in the DNA mismatch repair gene MSH2 have been suggested to enable fast adaptation to drugs in Cryptococcus neoformans and C. glabrata.

    “Similarly, hypermutator phenotypes resulting from mutations in the DNA mismatch repair gene MSH2, have been suggested to enable fast adaptation to drugs in Cryptococcus neoformans and C. glabrata [134,135].”

    From Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens (2018) · cites this paper as [134]

  • These mutations result in an ~200-fold higher mutation rate than in standard laboratory strains and preferentially affect genes containing homopolymer runs.

    “These mutations result in an ~200-fold higher mutation rate than in standard laboratory strains30 and preferentially affect genes containing homopolymer runs33.”

    From Treatment strategies for cryptococcal infection: challenges, advances and future outlook (2021) · cites this paper as [30]

  • A subset of Cryptococcus isolates have been identified as hypermutator strains, which contain mutations in core genes in the DNA mismatch repair pathway, most notably MSH2.

    “a subset of Cryptococcus isolates have been identified as hypermutator strains30,31, which contain mutations in core genes in the DNA mismatch repair pathway, most notably MSH2 (refs30,32,33)”

    From Treatment strategies for cryptococcal infection: challenges, advances and future outlook (2021) · cites this paper as [30]

  • Hypermutator phenotypes can also result from mutations in other genes, such as MSL1 and PMS1.

    “However, hypermutator phenotypes can also result from mutations in other genes, such as MSL1 and PMS1 (ref.30).”

    From Treatment strategies for cryptococcal infection: challenges, advances and future outlook (2021) · cites this paper as [30]

  • Hypermutator isolates derived from both the clinic and the laboratory lead to the rapid emergence of resistance to drugs such as rapamycin, FK506, flucytosine, fluconazole and even amphotericin B.

    “hypermutator isolates derived from both the clinic and the laboratory lead to the rapid emergence of resistance to drugs such as rapamycin, FK506 (ref.33), flucytosine32, fluconazole and even amphotericin B30.”

    From Treatment strategies for cryptococcal infection: challenges, advances and future outlook (2021) · cites this paper as [30]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • FUR1 homopolymer is labeled both (C)6 and (C)7

    Minor

    The text identifies the C-rich FUR1 tract as (C)7, whereas the Fig. 3F caption refers to an insertion in a (C)6 tract.

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Related

Authors
Boyce, K. J., Wang, Y., Verma, S., Shakya, V. P. S., Xue, C., & Idnurm, A.
Affiliations
  • The University of Melbourne (AU)
  • Rutgers, The State University of New Jersey (US)
  • University of Utah (US)
Corresponding author
  • Boyce, Kylie J.
  • Idnurm, Alexander
ORCID
Venue
mBio
Publisher
American Society for Microbiology
Published
2017-07-05
Volume
8
Issue
3
ISSN
  • 2150-7511 (ISSN-L)
  • 2161-2129
DOI
10.1128/mbio.00595-17
PMC
PMC5449657
OpenAlex
W2620457249
Semantic Scholar
691fde701218756c441e2b188ccfb46bc853127c
Cited by
101
References
41
Citations by year
2026: 8 · 2025: 8 · 2024: 9 · 2023: 7 · 2022: 11 · 2021: 13 · 2020: 9 · 2019: 18 · 2018: 11 · 2017: 7
FWCI
9.61
Type
journal article
Language
en
Open access
Licence
Locations
  • mBio (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • RMIT Research Repository (RMIT University Library) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
  • HHS | National Institutes of Health (AI123315-01A1)
  • Australian Research Council (FT130100146)
Topics
  • Health Sciences › Medicine › Epidemiology › Fungal Infections and Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Keywords
Cryptococcus neoformans, DNA mismatch repair, mutator phenotype, MSH2, MLH1, PMS1, mutation rate, microevolution, virulence, antifungal resistance, host adaptation, fungal pathogenesis, clinical isolates, Candida glabrata
MeSH terms
Antifungal Agents, Cryptococcosis, Cryptococcus neoformans, DNA Damage, DNA Repair, DNA Replication, Genes, Fungal, Humans, Mutation, Phenotype, Virulence, Genome, Fungal, Evolution, Molecular, Drug Resistance, Fungal, DNA Mismatch Repair

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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