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Evolutionary Significance of Fungal Hypermutators: Lessons Learned from Clinical Strains and Implications for Fungal Plant Pathogens. mSphere 2022; 7:e0008722. [PMID: 35638358 PMCID: PMC9241500 DOI: 10.1128/msphere.00087-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid evolution of fungal pathogens poses a serious threat to medicine and agriculture. The mutation rate determines the pace of evolution of a fungal pathogen. Hypermutator fungal strains have an elevated mutation rate owing to certain defects such as those in the DNA mismatch repair system. Studies in Saccharomyces cerevisiae show that hypermutators expedite evolution by generating beneficial alleles at a faster pace than the wild-type strains. However, an accumulation of deleterious alleles in a hypermutator may reduce its fitness. The balance between fitness cost and mutation benefit determines the prevalence of hypermutators in a population. This balance is affected by a complex interaction of ploidy, mode of reproduction, population size, and recent population history. Studies in human fungal pathogens like Aspergillus fumigatus, Candida albicans, Candida glabrata, Cryptococcus deuterogattii, and Cryptococcus neoformans have highlighted the importance of hypermutators in host adaptation and development of antifungal resistance. However, a critical examination of hypermutator biology, experimental evolution studies, and epidemiological studies suggests that hypermutators may impact evolutionary investigations. This review aims to integrate the knowledge about biology, experimental evolution, and dynamics of fungal hypermutators to critically examine the evolutionary role of hypermutators in fungal pathogen populations and project implications of hypermutators in the evolution of fungal plant pathogen populations. Understanding the factors determining the emergence and evolution of fungal hypermutators can open a novel avenue of managing rapidly evolving fungal pathogens in medicine and agriculture.
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Saakian DB, Cheong KH. Weak mixed phase in the mutator model. Phys Rev E 2021; 103:032113. [PMID: 33862733 DOI: 10.1103/physreve.103.032113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/10/2021] [Indexed: 11/07/2022]
Abstract
We consider the mutator model with unidirected transitions from the wild type to the mutator type, with different fitness functions for the wild types and mutator types. We calculate both the fraction of mutator types in the population and the surpluses, i.e., the mean number of mutations in the regular part of genomes for the wild type and mutator type, which have never been derived exactly. We identify the phase structure. Beside the mixed (ordinary evolution phase with finite fraction of wild types at large genome length) and the mutator phase (the absolute majority is mutators), we find another new phase as well-it has the mean fitness of the mixed phase but an exponentially small (in genome length) fraction of wild types. We identify the phase transition point and discuss its implications.
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Affiliation(s)
- David B Saakian
- Laboratory of Applied Physics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Kang Hao Cheong
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, S487372 Singapore
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Otto SP. Selective Interference and the Evolution of Sex. J Hered 2020; 112:9-18. [DOI: 10.1093/jhered/esaa026] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/14/2022] Open
Abstract
AbstractSelection acts upon genes linked together on chromosomes. This physical connection reduces the efficiency by which selection can act because, in the absence of sex, alleles must rise and fall together in frequency with the genome in which they are found. This selective interference underlies such phenomena as clonal interference and Muller’s Ratchet and is broadly termed Hill-Robertson interference. In this review, I examine the potential for selective interference to account for the evolution and maintenance of sex, discussing the positive and negative evidence from both theoretical and empirical studies, and highlight the gaps that remain.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, Canada
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Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nat Commun 2020; 11:3105. [PMID: 32561723 PMCID: PMC7305214 DOI: 10.1038/s41467-020-16932-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics. The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.
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Chavhan YD, Ali SI, Dey S. Larger Numbers Can Impede Adaptation in Asexual Populations despite Entailing Greater Genetic Variation. Evol Biol 2019. [DOI: 10.1007/s11692-018-9467-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Baumgartner M, Roffler S, Wicker T, Pernthaler J. Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment. ISME JOURNAL 2017; 11:2258-2266. [PMID: 28585936 DOI: 10.1038/ismej.2017.87] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/21/2017] [Indexed: 12/16/2022]
Abstract
Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism. Bacteria were propagated in serial batch culture in a nutrient-restricted environment either with or without a bacterivorous flagellate. Strains isolated after 26 growth cycles of the predator-prey co-cultures formed as much total biomass as the ancestor at ancestral growth conditions, albeit largely reallocated to cell aggregates. A ~273 kbp genome fragment was lost in three strains that had independently evolved with predators. These strains had significantly higher growth yield on substrate-restricted media than others that were isolated from the same treatment before the excision event. Under predation pressure, the isolates with the deletion outcompeted both, the ancestor and the strains evolved without predators even at rich growth conditions. At the same time, genome reduction led to a growth disadvantage in the presence of benzoate due to the loss of the respective degradation pathway, suggesting that niche constriction might be the price for the bidirectional optimization.
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Affiliation(s)
- Michael Baumgartner
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
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Skelly DA, Magwene PM, Meeks B, Murphy HA. Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains. Proc Biol Sci 2017; 284:20162672. [PMID: 28404772 PMCID: PMC5394658 DOI: 10.1098/rspb.2016.2672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/17/2017] [Indexed: 11/12/2022] Open
Abstract
Natural selection has the potential to act on all phenotypes, including genomic mutation rate. Classic evolutionary theory predicts that in asexual populations, mutator alleles, which cause high mutation rates, can fix due to linkage with beneficial mutations. This phenomenon has been demonstrated experimentally and may explain the frequency of mutators found in bacterial pathogens. By contrast, in sexual populations, recombination decouples mutator alleles from beneficial mutations, preventing mutator fixation. In the facultatively sexual yeast Saccharomyces cerevisiae, segregating alleles of MLH1 and PMS1 have been shown to be incompatible, causing a high mutation rate when combined. These alleles had never been found together naturally, but were recently discovered in a cluster of clinical isolates. Here we report that the incompatible mutator allele combination only marginally elevates mutation rate in these clinical strains. Genomic and phylogenetic analyses provide no evidence of a historically elevated mutation rate. We conclude that the effect of the mutator alleles is dampened by background genetic modifiers. Thus, the relationship between mutation rate and microbial pathogenicity may be more complex than once thought. Our findings provide rare observational evidence that supports evolutionary theory suggesting that sexual organisms are unlikely to harbour alleles that increase their genomic mutation rate.
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Affiliation(s)
| | | | - Brianna Meeks
- Department of Biology, The College of William and Mary, Williamsburg, VA, USA
| | - Helen A Murphy
- Department of Biology, The College of William and Mary, Williamsburg, VA, USA
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Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E. Mismatch Repair Incompatibilities in Diverse Yeast Populations. Genetics 2017; 205:1459-1471. [PMID: 28193730 PMCID: PMC5378106 DOI: 10.1534/genetics.116.199513] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
An elevated mutation rate can provide cells with a source of mutations to adapt to changing environments. We identified a negative epistatic interaction involving naturally occurring variants in the MLH1 and PMS1 mismatch repair (MMR) genes of Saccharomyces cerevisiae We hypothesized that this MMR incompatibility, created through mating between divergent S. cerevisiae, yields mutator progeny that can rapidly but transiently adapt to an environmental stress. Here we analyzed the MLH1 and PMS1 genes across 1010 S. cerevisiae natural isolates spanning a wide range of ecological sources (tree exudates, Drosophila, fruits, and various fermentation and clinical isolates) and geographical sources (Europe, America, Africa, and Asia). We identified one homozygous clinical isolate and 18 heterozygous isolates containing the incompatible MMR genotype. The MLH1-PMS1 gene combination isolated from the homozygous clinical isolate conferred a mutator phenotype when expressed in the S288c laboratory background. Using a novel reporter to measure mutation rates, we showed that the overall mutation rate in the homozygous incompatible background was similar to that seen in compatible strains, indicating the presence of suppressor mutations in the clinical isolate that lowered its mutation rate. This observation and the identification of 18 heterozygous isolates, which can lead to MMR incompatible genotypes in the offspring, are consistent with an elevated mutation rate rapidly but transiently facilitating adaptation. To avoid long-term fitness costs, the incompatibility is apparently buffered by mating or by acquiring suppressors. These observations highlight effective strategies in eukaryotes to avoid long-term fitness costs associated with elevated mutation rates.
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Affiliation(s)
- Duyen T Bui
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Anne Friedrich
- Université de Strasbourg, Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie, Unité Mixte de Recherche, 7156, F-67000 Strasbourg, France
| | - Najla Al-Sweel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice, 06107 Nice, France
| | - Joseph Schacherer
- Université de Strasbourg, Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie, Unité Mixte de Recherche, 7156, F-67000 Strasbourg, France
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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Abstract
We propose a modification of the Crow-Kimura and Eigen models of biological molecular evolution to include a mutator gene that causes both an increase in the mutation rate and a change in the fitness landscape. This mutator effect relates to a wide range of biomedical problems. There are three possible phases: mutator phase, mixed phase and non-selective phase. We calculate the phase structure, the mean fitness and the fraction of the mutator allele in the population, which can be applied to describe cancer development and RNA viruses. We find that depending on the genome length, either the normal or the mutator allele dominates in the mixed phase. We analytically solve the model for a general fitness function. We conclude that the random fitness landscape is an appropriate choice for describing the observed mutator phenomenon in the case of a small fraction of mutators. It is shown that the increase in the mutation rates in the regular and the mutator parts of the genome should be set independently; only some combinations of these increases can push the complex biomedical system to the non-selective phase, potentially related to the eradication of tumors.
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Bui DT, Dine E, Anderson JB, Aquadro CF, Alani EE. A Genetic Incompatibility Accelerates Adaptation in Yeast. PLoS Genet 2015; 11:e1005407. [PMID: 26230253 PMCID: PMC4521705 DOI: 10.1371/journal.pgen.1005407] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/01/2015] [Indexed: 12/21/2022] Open
Abstract
During mismatch repair (MMR) MSH proteins bind to mismatches that form as the result of DNA replication errors and recruit MLH factors such as Mlh1-Pms1 to initiate excision and repair steps. Previously, we identified a negative epistatic interaction involving naturally occurring polymorphisms in the MLH1 and PMS1 genes of baker’s yeast. Here we hypothesize that a mutagenic state resulting from this negative epistatic interaction increases the likelihood of obtaining beneficial mutations that can promote adaptation to stress conditions. We tested this by stressing yeast strains bearing mutagenic (incompatible) and non-mutagenic (compatible) mismatch repair genotypes. Our data show that incompatible populations adapted more rapidly and without an apparent fitness cost to high salt stress. The fitness advantage of incompatible populations was rapid but disappeared over time. The fitness gains in both compatible and incompatible strains were due primarily to mutations in PMR1 that appeared earlier in incompatible evolving populations. These data demonstrate a rapid and reversible role (by mating) for genetic incompatibilities in accelerating adaptation in eukaryotes. They also provide an approach to link experimental studies to observational population genomics. In nature, bacterial populations with high mutation rates can adapt faster to new environments by acquiring beneficial mutations. However, such populations also accumulate harmful mutations that reduce their fitness. We show that the model eukaryote baker’s yeast can use a similar mutator strategy to adapt to new environments. The mutator state that we observed resulted from an incompatibility involving two genes, MLH1 and PMS1, that work together to remove DNA replication errors through a spellchecking mismatch repair mechanism. This incompatibility can occur through mating between baker’s yeast from different genetic backgrounds, yielding mutator offspring containing an MLH1-PMS1 combination not present in either parent. Interestingly, these offspring adapted more rapidly to stress, compared to the parental strains, and did so without an overall loss in fitness. DNA sequencing analyses of baker’s yeast strains from across the globe support the presence of incompatible hybrid yeast strains in nature. These observations provide a powerful model to understand how the segregation of defects in DNA mismatch repair can serve as an effective strategy to enable eukaryotes to adapt to changing environments.
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Affiliation(s)
- Duyen T. Bui
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Elliot Dine
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - James B. Anderson
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Eric E. Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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11
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Experimental evolution and the dynamics of genomic mutation rate modifiers. Heredity (Edinb) 2014; 113:375-80. [PMID: 24849169 DOI: 10.1038/hdy.2014.49] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/11/2014] [Accepted: 04/15/2014] [Indexed: 01/01/2023] Open
Abstract
Because genes that affect mutation rates are themselves subject to mutation, mutation rates can be influenced by natural selection and other evolutionary forces. The population genetics of mutation rate modifier alleles has been a subject of theoretical interest for many decades. Here, we review experimental contributions to our understanding of mutation rate modifier dynamics. Numerous evolution experiments have shown that mutator alleles (modifiers that elevate the genomic mutation rate) can readily rise to high frequencies via genetic hitchhiking in non-recombining microbial populations. Whereas these results certainly provide an explanatory framework for observations of sporadically high mutation rates in pathogenic microbes and in cancer lineages, it is nonetheless true that most natural populations have very low mutation rates. This raises the interesting question of how mutator hitchhiking is suppressed or its phenotypic effect reversed in natural populations. Very little experimental work has addressed this question; with this in mind, we identify some promising areas for future experimental investigation.
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12
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Raynes Y, Halstead AL, Sniegowski PD. The effect of population bottlenecks on mutation rate evolution in asexual populations. J Evol Biol 2013; 27:161-9. [PMID: 24330404 DOI: 10.1111/jeb.12284] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 01/20/2023]
Abstract
In the absence of recombination, a mutator allele can spread through a population by hitchhiking with beneficial mutations that appear in its genetic background. Theoretical studies over the past decade have shown that the survival and fixation probability of beneficial mutations can be severely reduced by population size bottlenecks. Here, we use computational modelling and evolution experiments with the yeast S. cerevisiae to examine whether population bottlenecks can affect mutator dynamics in adapting asexual populations. In simulation, we show that population bottlenecks can inhibit mutator hitchhiking with beneficial mutations and are most effective at lower beneficial mutation supply rates. We then subjected experimental populations of yeast propagated at the same effective population size to three different bottleneck regimes and observed that the speed of mutator hitchhiking was significantly slower at smaller bottlenecks, consistent with our theoretical expectations. Our results, thus, suggest that bottlenecks can be an important factor in mutation rate evolution and can in certain circumstances act to stabilize or, at least, delay the progressive elevation of mutation rates in asexual populations. Additionally, our findings provide the first experimental support for the theoretically postulated effect of population bottlenecks on beneficial mutations and demonstrate the usefulness of studying mutator frequency dynamics for understanding the underlying dynamics of fitness-affecting mutations.
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Affiliation(s)
- Y Raynes
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - A L Halstead
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - P D Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Dennehy JJ, Duffy S, O'Keefe KJ, Edwards SV, Turner PE. Frequent Coinfection Reduces RNA Virus Population Genetic Diversity. J Hered 2013; 104:704-12. [DOI: 10.1093/jhered/est038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Jain K, Nagar A. Fixation of mutators in asexual populations: the role of genetic drift and epistasis. Evolution 2013; 67:1143-54. [PMID: 23550762 DOI: 10.1111/evo.12005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the evolutionary dynamics of an asexual population of nonmutators and mutators on a class of epistatic fitness landscapes. We consider the situation in which all mutations are deleterious and mutators are produced from nonmutators continually at a constant rate. We find that in an infinitely large population, a minimum nonmutator-to-mutator conversion rate is required to fix the mutators but an arbitrarily small conversion rate results in the fixation of mutators in a finite population. We calculate analytical expressions for the mutator fraction at mutation-selection balance and fixation time for mutators in a finite population when the difference between the mutation rate for mutator and nonmutator is smaller (regime I) and larger (regime II) than the selection coefficient. Our main result is that in regime I, the mutator fraction and the fixation time are independent of epistasis but in regime II, mutators are rarer and take longer to fix when the decrease in fitness with the number of deleterious mutations occurs at an accelerating rate (synergistic epistasis) than at a diminishing rate (antagonistic epistasis). Our analytical results are compared with numerics and their implications are discussed.
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Affiliation(s)
- Kavita Jain
- Theoretical Sciences Unit and Evolutionary and Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India.
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