Genotoxic Assays for Measuring P450 Activation of Chemical Mutagens

This review discusses using yeast as a model organism for studying the biological effects of P450-mediated metabolism of xenobiotics. We discuss the challenges of testing the safety of thousands of chemicals currently introduced into the market place, the limitations of the animal systems, the advantages of model organisms, and the humanization of the yeast cells by expressing human cytochrome P450 (CYP) genes. We discuss strategies in utilizing multiple genetic endpoints in screening chemicals and yeast strains that facilitate phenotyping CYP polymorphisms. In particular, we discuss yeast mutants that facilitate xenobiotic import and retention and particular DNA repair mutants that can facilitate in measuring genotoxic endpoints and elucidating genotoxic mechanisms. New directions in toxicogenetics suggest that particular DNA damaging agents may interact with chromatin and perturb gene silencing, which may also generate genetic instabilities. By introducing human CYP genes into yeast strains, new strategies can be explored for high-throughput testing of xenobiotics and identifying potent DNA damaging agents

Cellular Responses to Aflatoxin-Associated DNA Adducts

Aflatoxin B1 (AFB1) is the most potent known hepatocarcinogen. The signature p53 mutation (p53 249ser) that is found in AFB1-associated liver cancer suggests that AFB1 is a potent genotoxin. AFB1 is not genotoxic per se but is metabolically activated by cytochrome P450 enzymes that convert the promutagen into a highly reactive epoxide, which primarily reacts with the N7 group of guanine, forming 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N7-dG). While this primary adduct is unstable, the subsequent trans-8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy aflatoxin B1 (AFB1-Fapy)-derived adducts are stable and are mutagenic. Studies have revealed that nucleotide excision repair (NER), base excision repair (BER), recombinational repair, and DNA replication bypass are all involved in conferring AFB1 resistance. To minimize the genotoxicity of AFB1, pathways function to detoxify the metabolically active intermediate, excise resulting DNA adducts, bypass unrepaired adducts, and repair secondary DNA breaks. How these repair pathways functionally cooperate to minimize AFB1-associated genetic instability phenotypes is not well understood. Insights can be gained from epidemiological research and model organisms. Gene profiling and next-generation sequencing are facilitating how pathways and tissue-specific differences are induced. This review will encompass studies concerning human genetic susceptibility to AFB1 and pathways that repair and tolerate AFB1-associated DNA damage

Checkpoint Control of DNA Repair in Yeast

Budding yeast has been a model organism for understanding how DNA damage is repaired and how cells minimize genetic instability caused by arresting or delaying the cell cycle at well-defined checkpoints. However, many DNA damage insults are tolerated by mechanisms that can both be error-prone and error-free. The mechanisms that tolerate DNA damage and promote cell division are less well-understood. This review summarizes current information known about the checkpoint response to agents that elicit both the G2/M checkpoint and the intra-S phase checkpoint and how cells adapt to unrepaired DNA damage. Tolerance to particular bulky DNA adducts and radiomimetic agents are discussed, as well as possible mechanisms that may control phosphatases that deactivate phosphorylated proteins

Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants

MEC1, the essential yeast homolog of the human ATR/ATM genes, controls the S-phase checkpoint and prevents replication fork collapse at slow zones of DNA replication. The viability of hypomorphic mec1-21 is reduced in the rad52 mutant, defective in homologous recombination, suggesting that replication generates recombinogenic lesions. We previously observed a 6-, 10- and 30-fold higher rate of spontaneous sister chromatid exchange (SCE), heteroallelic recombination and translocations, respectively, in mec1-21 mutants compared to wild-type. Here we report that the hyper-recombination phenotype correlates with lower deoxyribonucleoside triphosphate (dNTP) levels, compared to wild-type. By introducing a dun1 mutation, thus eliminating inducible expression of ribonucleotide reductase in mec1-21, rates of spontaneous SCE increased 15-fold above wild-type. All the hyper-recombination phenotypes were reduced by SML1 deletions, which increase dNTP levels. Measurements of dNTP pools indicated that, compared to wild-type, there was a significant decrease in dNTP levels in mec1-21, dun1 and mec1-21 dun1, while the dNTP levels of mec1-21 sml1, mec1-21 dun1 sml1 and sml1 mutants were ∼2-fold higher. Interestingly, higher dNTP levels in mec1-21 dun1 sml1 correlate with ∼2-fold higher rate of spontaneous mutagenesis, compared to mec1-21 dun1. We suggest that higher dNTP levels in specific checkpoint mutants suppress the formation of recombinogenic lesions

Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant

Inverted repeats (IRs) and trinucleotide repeats (TNRs) that have the potential to form secondary structures in vivo are known to cause genome rearrangements. Expansions of TNRs in humans are associated with several neurological disorders. Both IRs and TNRs stimulate spontaneous unequal sister-chromatid exchange (SCE) in yeast. Secondary structure-associated SCE events occur via double-strand break repair. Here we show that the rate of spontaneous IR-stimulated unequal SCE events in yeast is significantly reduced in strains with mutations in the mismatch repair genes MSH2 or MSH3, but unaffected by a mutation in the nucleotide excision-repair gene RAD1. Non-IR-associated unequal SCE events are increased in both MMR- and rad1-mutant cells; however, SCE events for both IR- and non-IR-containing substrates occur at a higher level in the exo1 background. Our results suggest that spontaneous SCE occurs by a template switching mechanism. Like IRs, TNRs have been shown to generate double-strand breaks (DSBs) in yeast. TNR expansions in mice are MSH2-dependent. Since IR-mediated SCE events are reduced in msh2 cells, we propose that TNR expansion mutations arise when DSBs are repaired using the sister or the homolog as a template

Aflatoxin B1-Associated DNA Adducts Stall S Phase and Stimulate Rad51 foci in Saccharomyces cerevisiae

AFB1 is a potent recombinagen in budding yeast. AFB1 exposure induces RAD51 expression and triggers Rad53 activation in yeast cells that express human CYP1A2. It was unknown, however, when and if Rad51 foci appear. Herein, we show that Rad53 activation correlates with cell-cycle delay in yeast and the subsequent formation of Rad51 foci. In contrast to cells exposed to X-rays, in which Rad51 foci appear exclusively in G2 cells, Rad51 foci in AFB1-exposed cells can appear as soon as cells enter S phase. Although rad51 and rad4 mutants are mildly sensitive to AFB1, chronic exposure of the NER deficient rad4 cells to AFB1 leads to increased lag times, while rad4 rad51 double mutants exhibit synergistic sensitivity and do not grow when exposed to 50 μM AFB1. We suggest RAD51 functions to facilitate DNA replication after replication fork stalling or collapse in AFB1-exposed cells

ENSO-driven energy budget perturbations in observations and CMIP models

Various observation-based datasets are employed to robustly quantify changes in ocean heat content (OHC), anomalous ocean–atmosphere energy exchanges and atmospheric energy transports during El Niño-Southern Oscillation (ENSO). These results are used as a benchmark to evaluate the energy pathways during ENSO as simulated by coupled climate model runs from the CMIP3 and CMIP5 archives. The models are able to qualitatively reproduce observed patterns of ENSO-related energy budget variability to some degree, but key aspects are seriously biased. Area-averaged tropical Pacific OHC variability associated with ENSO is greatly underestimated by all models because of strongly biased responses of net radiation at top-of-the-atmosphere to ENSO. The latter are related to biases of mean convective activity in the models and project on surface energy fluxes in the eastern Pacific Intertropical Convergence Zone region. Moreover, models underestimate horizontal and vertical OHC redistribution in association with the generally too weak Bjerknes feedback, leading to a modeled ENSO affecting a too shallow layer of the Pacific. Vertical links between SST and OHC variability are too weak even in models driven with observed winds, indicating shortcomings of the ocean models. Furthermore, modeled teleconnections as measured by tropical Atlantic OHC variability are too weak and the tropical zonal mean ENSO signal is strongly underestimated or even completely missing in most of the considered models. Results suggest that attempts to infer insight about climate sensitivity from ENSO-related variability are likely to be hampered by biases in ENSO in CMIP simulations that do not bear a clear link to future changes

CESM1(WACCM) Stratospheric Aerosol Geoengineering Large Ensemble Project

This paper describes the Stratospheric Aerosol Geoengineering Large Ensemble (GLENS) project, which promotes the use of a unique model dataset, performed with the Community Earth System Model, with the Whole Atmosphere Community Climate Model as its atmospheric component [CESM1(WACCM)], to investigate global and regional impacts of geoengineering. The performed simulations were designed to achieve multiple simultaneous climate goals, by strategically placing sulfur injections at four different locations in the stratosphere, unlike many earlier studies that targeted globally averaged surface temperature by placing injections in regions at or around the equator. This advanced approach reduces some of the previously found adverse effects of stratospheric aerosol geoengineering, including uneven cooling between the poles and the equator and shifts in tropical precipitation. The 20-member ensemble increases the ability to distinguish between forced changes and changes due to climate variability in global and regional climate variables in the coupled atmosphere, land, sea ice, and ocean system. We invite the broader community to perform in-depth analyses of climate-related impacts and to identify processes that lead to changes in the climate system as the result of a strategic application of stratospheric aerosol geoengineering

Msh2 Blocks an Alternative Mechanism for Non-Homologous Tail Removal during Single-Strand Annealing in Saccharomyces cerevisiae

Chromosomal translocations are frequently observed in cells exposed to agents that cause DNA double-strand breaks (DSBs), such as ionizing radiation and chemotherapeutic drugs, and are often associated with tumors in mammals. Recently, translocation formation in the budding yeast, Saccharomyces cerevisiae, has been found to occur at high frequencies following the creation of multiple DSBs adjacent to repetitive sequences on non-homologous chromosomes. The genetic control of translocation formation and the chromosome complements of the clones that contain translocations suggest that translocation formation occurs by single-strand annealing (SSA). Among the factors important for translocation formation by SSA is the central mismatch repair (MMR) and homologous recombination (HR) factor, Msh2. Here we describe the effects of several msh2 missense mutations on translocation formation that suggest that Msh2 has separable functions in stabilizing annealed single strands, and removing non-homologous sequences from their ends. Additionally, interactions between the msh2 alleles and a null allele of RAD1, which encodes a subunit of a nuclease critical for the removal of non-homologous tails suggest that Msh2 blocks an alternative mechanism for removing these sequences. These results suggest that Msh2 plays multiple roles in the formation of chromosomal translocations following acute levels of DNA damage

CESM1(WACCM) Stratospheric Aerosol Geoengineering Large Ensemble Project

This paper describes the Stratospheric Aerosol Geoengineering Large Ensemble (GLENS) project, which promotes the use of a unique model dataset, performed with the Community Earth System Model, with the Whole Atmosphere Community Climate Model as its atmospheric component [CESM1(WACCM)], to investigate global and regional impacts of geoengineering. The performed simulations were designed to achieve multiple simultaneous climate goals, by strategically placing sulfur injections at four different locations in the stratosphere, unlike many earlier studies that targeted globally averaged surface temperature by placing injections in regions at or around the equator. This advanced approach reduces some of the previously found adverse effects of stratospheric aerosol geoengineering, including uneven cooling between the poles and the equator and shifts in tropical precipitation. The 20-member ensemble increases the ability to distinguish between forced changes and changes due to climate variability in global and regional climate variables in the coupled atmosphere, land, sea ice, and ocean system. We invite the broader community to perform in-depth analyses of climate-related impacts and to identify processes that lead to changes in the climate system as the result of a strategic application of stratospheric aerosol geoengineering