Global Analysis of Furfural-Induced Genomic Instability Using a Yeast Model

Abstract

Furfural is an important renewable precursor for multiple commercial chemicals and fuels; a main inhibitor existing in cellulosic hydrolysate, which is used for bioethanol fermentation; and a potential carcinogen, as well. Using a genetic system in Saccharomyces cerevisiae that allows detection of crossover events, we observed that the frequency of mitotic recombination was elevated by 1.5- to 40-fold when cells were treated with 0.1 g/liter to 20 g/liter furfural. Analysis of the gene conversion tracts associated with crossover events suggested that most furfural-induced recombination resulted from repair of DNA double-strand breaks (DSBs) that occurred in the G1 phase. Furfural was incapable of breaking DNA directly in vitro but could trigger DSBs in vivo related to reactive oxygen species accumulation. By whole-genome single nucleotide polymorphism (SNP) microarray and sequencing, furfural-induced genomic alterations that range from single base substitutions, loss of heterozygosity, and chromosomal rearrangements to aneuploidy were explored. At the whole-genome level, furfural-induced events were evenly distributed across 16 chromosomes but were enriched in high-GC-content regions. Point mutations, particularly the C-to-T/G-to-A transitions, were significantly elevated in furfural-treated cells compared to wild-type cells. This study provided multiple novel insights into the global effects of furfural on genomic stability. IMPORTANCE Whether and how furfural affects genome integrity have not been clarified. Using a Saccharomyces cerevisiae model, we found that furfural exposure leads to in vivo DSBs and elevation in mitotic recombination by orders of magnitude. Gross chromosomal rearrangements and aneuploidy events also occurred at a higher frequency in furfural-treated cells. In a genome-wide analysis, we show that the patterns of mitotic recombination and point mutations differed dramatically in furfural-treated cells and wild-type cells.

Heat shock drives genomic instability and phenotypic variations in yeast

“…The frequency of aneuploidy events (6.3 × 10 –2 per genome per division) was even higher than that of LOH events. By contrast, LOH events occur at a much higher rate than aneuploidy events in wild-type cells under normal conditions (O'Connell et al 2015 ; Qi et al 2019a , b ). Interestingly, we found that heat shock produced more trisomic chromosomes than monosomic chromosomes in yeast, and the opposite result was found in carbendazim-treated cells (spindle assembly inhibition leads to failure in pulling the chromatid into cells).…”

“…Our recent studies used the diploid S. cerevisiae strains produced by crossing two heterozygous haploid strains to determine genomic instability caused by DNA replication stress (Zheng et al 2016 ; Sui et al 2020 ), oxidative stress (Qi et al 2019a , b ; Zhang et al 2019 ), and small molecular compounds (Qi et al 2019a , b ; Sheng et al 2019 ). The abundant single nucleotide polymorphisms (SNPs) between the two homologs in the diploid strains allow for the identification of genetic events across the yeast genome at high resolution through SNP microarray and genome sequencing (Guo et al 2017 ; Yin et al 2017 ; Zheng and Petes 2018 ).…”

Origin, Regulation, and Fitness Effect of Chromosomal Rearrangements in the Yeast Saccharomyces cerevisiae

“…Similarly, chromosomal rearrangement can result from mutations of genes (such as SOD1 and TSA2 ) involved in the anti-oxidative systems [ 58 , 107 ] and intracellular ROS accumulation induced by extracellular stressors. Qi et al [ 108 ] found that exposure to furfural, a major inhibitor existing in the cellulosic hydrolysate used for bioethanol fermentation, led to enhanced rates of chromosomal rearrangements in yeast cells. Although furfural cannot cleave DNA directly, the authors observed frequent in vivo DNA breaks due to accumulation of intracellular ROS [ 108 ].…”

“…Qi et al [ 108 ] found that exposure to furfural, a major inhibitor existing in the cellulosic hydrolysate used for bioethanol fermentation, led to enhanced rates of chromosomal rearrangements in yeast cells. Although furfural cannot cleave DNA directly, the authors observed frequent in vivo DNA breaks due to accumulation of intracellular ROS [ 108 ]. It is likely that prolonged exposure of yeast cells to the recombinogenic agent under industrial conditions could quickly lead to loss of selected desirable traits of industrial yeast strains.…”

Shift of Volatile Organic Compounds (VOCs) in Gluten-Free Hemp-Enriched Sourdough Bread: A Metabolomic Approach

“…HSF breads accounted for about 20% less furfural than standard breads. Furfural has a leading role in the aroma of bakery products [23], but it was recently investigated as a potential carcinogen [69,70]. The concentration of octadienal dimethyl (Z) naturally occurring in raw hemp seeds, significantly increased in HSF bread as effect of S. cerevisiae fermentation.…”