How Do Yeast and Other Fungi Recognize and Respond to Genome Perturbations?

Skoneczna, Adrianna; Król, Kamil; Skoneczny, Marek

doi:10.1007/978-3-030-00683-9_3

Cited by 3 publications

(3 citation statements)

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“…In the wild type, upregulated proteins also included the adenylosuccinate lyase CF317_004119-T1 and the M20_dimer domain-containing protein (Carboxypeptidase S) CF317_006825-T1, both implicated in amino acid (alanine, aspartate and glutamate) metabolism (KEGG pathway pae00250), and the plasma membrane ATPase CF317_002664-T1, partaking in oxidative phosphorylation ( Table 2 ). Also in the wild type, the casein kinase I 1 CF317_004827-T1 and the histone H2A CF317_001633-T1, both involved in DNA repair ( Skoneczna et al, 2018 ), were found in the LSSMG-exposed secretome at levels 1.7- and 1.6-fold higher than in the unexposed one. The two downregulated proteins were protein CF317_008131-T1, homolog of the arabinan endo-1,5-alpha-L-arabinosidase from Aspergillus wentii DTO 134E9 , and protein CF317_002949-T1, homolog of the feruloyl esterase A0A177BY00_9PLEO from Paraphaeosphaeria sporulosa , both with a predicted extracellular localization and reportedly involved in polysaccharide degradation ( Tesei et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos

et al. 2021

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Black fungi are a group of melanotic microfungi characterized by remarkable polyextremotolerance. Due to a broad ecological plasticity and adaptations at the cellular level, it is predicted that they may survive in a variety of extreme environments, including harsh niches on Earth and Mars, and in outer space. However, the molecular mechanisms aiding survival, especially in space, are yet to be fully elucidated. Based on these premises, the rock-inhabiting black fungus Knufia chersonesos (Wt) and its non-melanized mutant (Mut) were exposed to simulated microgravity—one of the prevalent features characterizing space conditions—by growing the cultures in high-aspect-ratio vessels (HARVs). Qualitative and quantitative proteomic analyses were performed on the mycelia and supernatant of culture medium (secretome) to assess alterations in cell physiology in response to low-shear simulated microgravity (LSSMG) and to ultimately evaluate the role of cell-wall melanization in stress survival. Differential expression was observed for proteins involved in carbohydrate and lipid metabolic processes, transport, and ribosome biogenesis and translation via ribosomal translational machinery. However, no evidence of significant activation of stress components or starvation response was detected, except for the scytalone dehydratase, enzyme involved in the synthesis of dihydroxynaphthalene (DNH) melanin, which was found to be upregulated in the secretome of the wild type and downregulated in the mutant. Differences in protein modulation were observed between K. chersonesos Wt and Mut, with several proteins being downregulated under LSSMG in the Mut when compared to the Wt. Lastly, no major morphological alterations were observed following exposure to LSSMG. Similarly, the strains’ survivability was not negatively affected. This study is the first to characterize the response to simulated microgravity in black fungi, which might have implications on future astrobiological missions.

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Section: Resultsmentioning

confidence: 99%

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos

et al. 2021

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“…To further characterize Rad52- and Rad51-dependent processes activated in response to replication impediments that arise in psf1-100 cells, we tested the involvement of the template switch (TS), reviewed in [ 86 ], or break-induced replication (BIR), reviewed in [ 87 ]. These processes enable completion of DNA replication after replication fork stalling or in the presence of DNA replication impediments [ 88 ]. TS uses the newly created sister chromatid as a template for DNA synthesis and requires Ubc13-Mms2-Rad5-dependent polyubiquitylation of the proliferating cell nuclear antigen (PCNA) [ 86 , 89 , 90 ].…”

Section: Resultsmentioning

confidence: 99%

Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase—Pol ε Interaction

Denkiewicz-Kruk

Jedrychowska

Endo

et al. 2020

IJMS

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The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.

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“…The recombinases Rad52 and Rad51 are two major players in HR [94,95]. The most important function of Rad52 is the promotion of Rad51 filament formation on RPA-coated ssDNA.…”

Section: Resultsmentioning

confidence: 99%

Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism

et al. 2019

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Faithful replication and repair of DNA lesions ensure genome maintenance. During replication in eukaryotic cells, DNA is unwound by the CMG helicase complex, which is composed of three major components: the Cdc45 protein, Mcm2-7, and the GINS complex. The CMG in complex with DNA polymerase epsilon (CMG-E) participates in the establishment and progression of the replisome. Impaired functioning of the CMG-E was shown to induce genomic instability and promote the development of various diseases. Therefore, CMG-E components play important roles as caretakers of the genome. In Saccharomyces cerevisiae, the GINS complex is composed of the Psf1, Psf2, Psf3, and Sld5 essential subunits. The Psf1-1 mutant form fails to interact with Psf3, resulting in impaired replisome assembly and chromosome replication. Here, we show increased instability of repeat tracts (mononucleotide, dinucleotide, trinucleotide and longer) in yeast psf1-1 mutants. To identify the mechanisms underlying this effect, we analyzed repeated sequence instability using derivatives of psf1-1 strains lacking genes involved in translesion synthesis, recombination, or mismatch repair. Among these derivatives, deletion of RAD52, RAD51, MMS2, POL32, or PIF1 significantly decreased DNA repeat instability. These results, together with the observed increased amounts of single-stranded DNA regions and Rfa1 foci suggest that recombinational mechanisms make important contributions to repeat tract instability in psf1-1 cells. We propose that defective functioning of the CMG-E complex in psf1-1 cells impairs the progression of DNA replication what increases the contribution of repair mechanisms such as template switch and break-induced replication. These processes require sequence homology search which in case of a repeated DNA tract may result in misalignment leading to its expansion or contraction.

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How Do Yeast and Other Fungi Recognize and Respond to Genome Perturbations?

Cited by 3 publications

References 297 publications

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos

Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase—Pol ε Interaction

Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism

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