Abstract
Previously, we identified 49 undeletable chromosomal regions harboring only non-essential genes in the genome of Saccharomyces cerevisiae. We proposed that there might be unknown synthetic lethal combinations of genes present in such undeletable regions of the genome. In this study, we chose four of the smallest undeletable chromosomal regions among the 49 and performed extensive further analyses to narrow down the gene-pairs responsible for lethality by replacing sub-regions in various combinations with a DNA module comprising the CgLEU2 marker. Although the methodology was different from previous study, interestingly the results revealed that not only the sub-regions but also the entire region was replaceable. To solve the apparent discrepancy between previous and present results, we further conducted additional analysis including investigation of suppressor mutation and mini-chromosome loss assay through the construction of mini-chromosome harboring two particular chromosomal regions with marked with URA3 marker by employing 5-FOA system. Based upon careful observation on the phenotype of colony formation on 5-FOA medium by spot test, we came to an important conclusion that particular chromosomal regions harboring only non-essential genes can be categorized into three classes, i.e., essential, non-essential and intrinsically essential. Intrinsically essential region is defined as appearance of papillae after mini-chromosome loss which implicates that the region is essential but compensatable against cell lethality. Our present study indicates that prudent and multiple approaches as performed in this study are needed to judge whether a particular chromosomal region of the S. cerevisiae genome is essential, non-essential or intrinsically essential but compensatable.
Highlights
Discovering genetic interaction networks is required for identifying novel genes and pathways and for predicting similar networks in genomes
Synthetic lethal genetic interactions have been extensively studied in S. cerevisiae using synthetic genetic array (SGA) analysis, in which a query mutation is systematically crossed with almost all Hassan et al AMB Expr (2020) 10:73 viable deletion mutants to obtain double-mutant meiotic progeny (Tong et al 2001, 2004; Giaever et al 2002)
Identification of non‐essential genes responsible for synthetic lethality of four undeletable chromosomal regions According to our previous study (Kaboli et al 2014), 49 chromosomal regions containing only non-essential genes were identified to be undeletable from the S. cerevisiae genome
Summary
Discovering genetic interaction networks is required for identifying novel genes and pathways and for predicting similar networks in genomes. 80% of the genes in S. cerevisiae are not required for cell proliferation in nutrient medium. This makes S. cerevisiae a useful experimental organism to reveal the function of non-essential genes (Winzeler et al 1999; Giaever et al 2002). The inactivation of some non-essential genes in specific combinations can have a lethal effect (Novick et al 1989; Guarente 1993). This property makes the yeast genome resistant to engineering and could be problematic for generating new strains. Numerous linked gene-pairs that form small colonies of double mutants have been overlooked in SGA (Kaboli et al 2014)
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