Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Habig, Michael; Lorrain, Cécile; Feurtey, Alice; Komluski, Jovan; Stukenbrock, Eva H.

doi:10.1038/s41467-021-26108-y

Cited by 59 publications

(67 citation statements)

References 85 publications

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“…By correlating mutations with epigenetic modifications, it was found that H3K27me3 affects mutations by inducing replication stress. However, H3K27me3 modifications only affect local mutation rates, and not structural variations in nucleic acid sequences on a large scale ( Habig et al, 2021 ).…”

Section: Mechanisms Of Adaptationmentioning

confidence: 99%

Microbial Adaptation to Enhance Stress Tolerance

et al. 2022

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Microbial cell factories have been widely used in the production of various chemicals. Although synthetic biology is useful in improving the cell factories, adaptation is still widely applied to enhance its complex properties. Adaptation is an important strategy for enhancing stress tolerance in microbial cell factories. Adaptation involves gradual modifications of microorganisms in a stressful environment to enhance their tolerance. During adaptation, microorganisms use different mechanisms to enhance non-preferred substrate utilization and stress tolerance, thereby improving their ability to adapt for growth and survival. In this paper, the progress on the effects of adaptation on microbial substrate utilization capacity and environmental stress tolerance are reviewed, and the mechanisms involved in enhancing microbial adaptive capacity are discussed.

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Section: Mechanisms Of Adaptationmentioning

confidence: 99%

Microbial Adaptation to Enhance Stress Tolerance

et al. 2022

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“…Point mutations can lead to heterokaryosis where both wild type and fungicide resistant nuclei coexist ( Miao et al, 2021 ). Interestingly, the rates at which mutations occur in some fungi have been observed to be environment-dependent ( Lamb et al, 2008 ), e.g., increase with higher temperatures ( Habig et al, 2021 ) and freezing ( Stoycheva et al, 2007 ). Higher mutation rates could be just a by-product of stress-induced malfunctions or of adaptive significance.…”

Section: Nuclear Genotype Heterogeneity and Dynamicsmentioning

confidence: 99%

A Nuclei-Based Conceptual Model of (Eco)evolutionary Dynamics in Fungal Heterokaryons

Lakovic

Rillig

2022

Front. Microbiol.

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Filamentous fungi are characterised by specific features, such as multinuclearity, coexistence of genetically different nuclei and nuclear movement across the mycelial network. These attributes make them an interesting, yet rather underappreciated, system for studying (eco)evolutionary dynamics. This is especially noticeable among theoretical studies, where rather few consider nuclei and their role in (eco)evolutionary dynamics. To encourage such theoretical approaches, we here provide an overview of existing research on nuclear genotype heterogeneity (NGH) and its sources, such as mutations and vegetative non-self-fusion. We then discuss the resulting intra-mycelial nuclear dynamics and the potential consequences for fitness and adaptation. Finally, we formulate a nuclei-based conceptual framework, which considers three levels of selection: a single nucleus, a subpopulation of nuclei and the mycelium. We compare this framework to other concepts, for example those that consider only the mycelium as the level of selection, and outline the benefits of our approach for studying (eco)evolutionary dynamics. Our concept should serve as a baseline for modelling approaches, such as individual-based simulations, which will contribute greatly to our understanding of multilevel selection and (eco)evolutionary dynamics in filamentous fungi.

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“…Interactions between DNA repair and histone modifications are predicted to evolve if they promote repair in regions prone to deleterious mutations, such as coding regions of essential genes (Lynch 2010; Martincorena and Luscombe 2013; Lynch et al 2016). Associations between histone modifications and mutation rates have been observed across diverse organisms (Habig et al 2021; de la Peña et al 2022; Yang et al 2021; Yan et al 2021; Monroe et al 2022; Makova and Hardison 2015; Schuster-Böckler and Lehner 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Associations between histone modifications and mutation rates have been observed across diverse organisms (Habig et al, 2021; de la Peña et al, 2022; Yang et al, 2021; Yan et al, 2021; Monroe et al, 2022; Makova and Hardison, 2015; Schuster-Böckler and Lehner, 2012). That the localization of DNA repair proteins can drive such mutation biases has been well-established in humans (Supek and Lehner, 2015, 2017, 2019; Katju et al, 2022a; Foster et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

The H3K4me1 histone mark recruits DNA repair to functionally constrained genomic regions in plants

Quiroz

Zhao

Carbonell‐Bejerano

et al. 2022

Preprint

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Mutation is the ultimate source of genetic variation in natural populations and crops. To study mechanisms determining mutation rate variation within plant genomes, we analyzed 43,483 de novo germline single base substitutions in 1,504 fast neutron mutation lines of the model rice cultivar Kitaake (Oryza sativa ssp japonica) (from Li et al. 2017). We find that, like previously observed for de novo germline mutations in Arabidopsis. thaliana, mutation rates are significantly lower in genomic regions marked by H3K4me1, a histone modification found in the gene bodies of actively expressed genes in plants. We also observed conservation in rice for PDS5C, a cohesion cofactor involved in the homology-directed repair pathway that in A. thaliana binds to H3K4me1 via its Tudor domain. By examining existing ChIP-seq data for PDS5C in A. thaliana, we find that it localizes to genome regions marked by H3K4me1: regions of low mutation rates, coding regions, essential genes, constitutively expressed genes, and genes under stronger purifying selection, mirroring mutation biases observed in rice as well. We searched the A. thaliana proteome for genes containing similar Tudor domains and found that they are significantly enriched for DNA repair functions (p<1×10-11), including the mismatch repair MSH6 gene (in both rice and A. thaliana ), suggesting the potential for multiple DNA repair pathways to specifically target gene bodies and essential genes through H3K4me1 reading. These findings inspire further research to characterize mechanisms that localize DNA repair via histone interactions, leading to hypomutation in functionally constrained regions and potentially tuning the evolutionary trajectories of plant genomes.

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Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Cited by 59 publications

References 85 publications

Microbial Adaptation to Enhance Stress Tolerance

Microbial Adaptation to Enhance Stress Tolerance

A Nuclei-Based Conceptual Model of (Eco)evolutionary Dynamics in Fungal Heterokaryons

The H3K4me1 histone mark recruits DNA repair to functionally constrained genomic regions in plants

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