Functional Toxicogenomic Profiling Expands Insight into Modulators of Formaldehyde Toxicity in Yeast

Abstract

Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. Accordingly, occupational and environmental exposure to FA is prevalent worldwide. Various adverse effects, including nasopharyngeal, sinonasal, and lymphohematopoietic cancers, have been linked to FA exposure, prompting designation of FA as a human carcinogen by U.S. and international scientific entities. Although the mechanism(s) of FA toxicity have been well studied, additional insight is needed in regard to the genetic requirements for FA tolerance. In this study, a functional toxicogenomics approach was utilized in the model eukaryotic yeast Saccharomyces cerevisiae to identify genes and cellular processes modulating the cellular toxicity of FA. Our results demonstrate mutant strains deficient in multiple DNA repair pathways–including homologous recombination, single strand annealing, and postreplication repair–were sensitive to FA, indicating FA may cause various forms of DNA damage in yeast. The SKI complex and its associated factors, which regulate mRNA degradation by the exosome, were also required for FA tolerance, suggesting FA may have unappreciated effects on RNA stability. Furthermore, various strains involved in osmoregulation and stress response were sensitive to FA. Together, our results are generally consistent with FA-mediated damage to both DNA and RNA. Considering DNA repair and RNA degradation pathways are evolutionarily conserved from yeast to humans, mechanisms of FA toxicity identified in yeast may be relevant to human disease and genetic susceptibility.

An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity

“…Of the 16 remaining genes from the human DDR screen, 9 also conferred formaldehyde sensitivity in our yeast deletion strain screen and mapped to comparable functional pathways: HR, DSB repair, DNA replication, DNA damage checkpoints, and cell cycle regulation (Table 1). Although deletion of RAD57 did not sensitize cells to formaldehyde in our yeast screen, a comparable screen done in diploid yeast demonstrated that RAD57 was required for formaldehyde tolerance (22). Together, these results identify several important functional pathways that strongly modulate formaldehyde toxicity across different functional pathways and eukaryotic species.…”

“…The genotoxicity and ubiquitous nature of formaldehyde exposure have driven efforts to better understand the cellular pathways that mitigate formaldehyde toxicity. Specific cellular processes reported to promote cell survival include Nucleotide Excision Repair (NER) (20–22), proteasomal degradation (23), metalloproteases (24,25), the Fanconi Anemia pathway (26–29), and Homologous Recombination (HR) (20,22,30,31). We and others have also shown that formaldehyde can perturb the cell cycle and alter gene expression (21,30,32–35).…”

The Identification of Genetic Determinants of Methanol Tolerance in Yeast Suggests Differences in Methanol and Ethanol Toxicity Mechanisms and Candidates for Improved Methanol Tolerance Engineering

“…The main feature that clearly distinguishes methanol from ethanol tolerance determinants relates with DNA repair mechanisms presumably required for overcoming methanol-induced stress. Among the eight RAD genes (a designation due to the sensitivity of the corresponding mutants to exposure to X-rays [ 46 ]) exclusively present in the methanol dataset and involved in several mechanisms of DNA repair, such as recombinational repair and double-strand break repair [ 47 , 48 ] are genes, previously identified as formaldehyde tolerance determinants: the RAD18 , RAD27 , RAD5 , RAD51 , and RAD57 [ 16 ]. The mechanisms proposed to be required for formaldehyde tolerance involve homologous recombination and nucleotide excision repair; while homologous recombination is considered the preferred mechanism to repair damage due to chronic exposure to formaldehyde, nucleotide excision repair is the preferred mechanism to repair acute exposure [ 17 ].…”

“…Results suggest that the major cellular targets for methanol and formaldehyde toxicity are membrane structure and proteins, respectively [ 14 ], and that the response to methanol also includes the up-regulation, at different levels and depending on the yeast strain, of genes of mitochondrial and peroxisomal metabolism, alcohol and formate dehydrogenation, glutathione metabolism, at different levels, [ 15 ]. The screening of the same yeast deletion mutant collection used in our study was carried out for the identification of formaldehyde tolerance determinants [ 16 , 17 ]. Among them, DNA repair mechanisms were found to underlie formaldehyde tolerance, consistent with the alkylating activity of this compound [ 16 , 17 ].…”

“…The screening of the same yeast deletion mutant collection used in our study was carried out for the identification of formaldehyde tolerance determinants [ 16 , 17 ]. Among them, DNA repair mechanisms were found to underlie formaldehyde tolerance, consistent with the alkylating activity of this compound [ 16 , 17 ]. Concerning formic acid, produced in the last step of methanol detoxification in yeast [ 14 ], another chemogenomic analysis performed in our lab, indicates an enrichment of tolerance genes involved in intracellular trafficking and protein synthesis, cell wall and cytoskeleton organization, carbohydrate metabolism, lipid, amino acid and vitamin metabolism, response to stress, chromatin remodeling, transcription, and internal pH homeostasis [ 18 ].…”