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Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network.

Kaboli S, Yamakawa T, Sunada K, Takagaki T, Sasano Y, Sugiyama M, Kaneko Y, Harashima S - Nucleic Acids Res. (2014)

Bottom Line: Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis.This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome.Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan.

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Phenotypic characteristics of deletion mutants under various stress conditions. Deletion strains as well as the wild-type strain were tested for their ability to growth on YPDA medium incubated at 13°C, 30°C, and 41°C, and YPDA medium supplemented with 4%, 6% and 8% ethanol (A), 4%, 5% and 6% lactic acid, and sulfuric acid (pH2.5, pH2.4 and pH2.3) (B),0.02% SDS, 80 mM acetic acid, 36 mM formic acid, 1.8 M NaCl, 150 mM CaCl2,10 mM furfural,and 2.0 M sorbitol (C). For panel (A) and (B), each strain was plated in serial ten-fold dilutions from 2.5 × 108 cells/ml to 2.5 × 101 cells/ml, from left to right, as indicated. For panel (C), 4μl from cell suspension with concentration of 2.5 × 108 cells/ml was spotted on plate. Plates were incubated for 3 days. White and black boxes represent tolerant and sensitive phenotypes, respectively.
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Figure 5: Phenotypic characteristics of deletion mutants under various stress conditions. Deletion strains as well as the wild-type strain were tested for their ability to growth on YPDA medium incubated at 13°C, 30°C, and 41°C, and YPDA medium supplemented with 4%, 6% and 8% ethanol (A), 4%, 5% and 6% lactic acid, and sulfuric acid (pH2.5, pH2.4 and pH2.3) (B),0.02% SDS, 80 mM acetic acid, 36 mM formic acid, 1.8 M NaCl, 150 mM CaCl2,10 mM furfural,and 2.0 M sorbitol (C). For panel (A) and (B), each strain was plated in serial ten-fold dilutions from 2.5 × 108 cells/ml to 2.5 × 101 cells/ml, from left to right, as indicated. For panel (C), 4μl from cell suspension with concentration of 2.5 × 108 cells/ml was spotted on plate. Plates were incubated for 3 days. White and black boxes represent tolerant and sensitive phenotypes, respectively.

Mentions: Some of the strains displayed a sensitive or resistant phenotype under the stressful environment (Figure 5A, B and C and Supplementary Table S4) including a low-temperature-sensitive phenotype, ScΔ(Chr 10-4), ScΔ(Chr 11-1) and ScΔ(Chr 16-8); a high-temperature-sensitive phenotype, ScΔ(Chr 5-1), ScΔ(Chr 9-1), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1), ScΔ(Chr 16-5), ScΔ(Chr 16-7) and ScΔ(Chr 16-8) (Figure 5A); a high-temperature-resistant phenotype, ScΔ(Chr 4-10) and ScΔ(Chr 4-11) (Figure 5A); a ethanol-sensitive phenotype, ScΔ(Chr 5-1), ScΔ(Chr 9-4), ScΔ(Chr 9-6), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1) and ScΔ(Chr 16-8); a lactic-acid-resistant phenotype, ScΔ(Chr 3-1), ScΔ(Chr 4-1) and ScΔ(Chr 16-9) (Figure 5B) and a sulfuric acid-sensitive phenotype (all strains except for ScΔ(Chr 1-1), ScΔ(Chr 6-1) and ScΔ(Chr 7-4)) (Figure 5B). We did not find strains that were resistant to the ethanol or the sulfuric acid. Based on information in the SGD, neither of the regions deleted in the high-temperature-resistant strains, ScΔ(Chr 4-10) and ScΔ(Chr 4-11), contains the genes whose single deletion is known to cause high-temperature resistance; instead, each region contain a gene (FPR2 and STL1, respectively) whose single deletion cause heat sensitivity. This result suggests that the deletion of either of these genes in combination with another in the respective chromosomal regions caused the observed tolerant phenotype of those strains. We found that all regions deleted in the ethanol-sensitive strains, ScΔ(Chr 5-1), ScΔ(Chr 9-4), ScΔ(Chr 9-6), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1) and ScΔ(Chr 16-8), contain the genes, (CIN8, GVP36 and TED1, YVH1, RAV1, URA1 and SAC1, PIF1 and TDA6 and KRE6, respectively), whose single deletion cause ethanol sensitivity (SGD)(http://www.yeastgenome.org/). Therefore, observed sensitive phenotypes due to deletion of those regions might be conferred by deletion of respective genes. Lack of resistance to ethanol in deletion strains implies that neither of deleted regions nor genes have important role in conferring ethanol-tolerance phenotype.


Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network.

Kaboli S, Yamakawa T, Sunada K, Takagaki T, Sasano Y, Sugiyama M, Kaneko Y, Harashima S - Nucleic Acids Res. (2014)

Phenotypic characteristics of deletion mutants under various stress conditions. Deletion strains as well as the wild-type strain were tested for their ability to growth on YPDA medium incubated at 13°C, 30°C, and 41°C, and YPDA medium supplemented with 4%, 6% and 8% ethanol (A), 4%, 5% and 6% lactic acid, and sulfuric acid (pH2.5, pH2.4 and pH2.3) (B),0.02% SDS, 80 mM acetic acid, 36 mM formic acid, 1.8 M NaCl, 150 mM CaCl2,10 mM furfural,and 2.0 M sorbitol (C). For panel (A) and (B), each strain was plated in serial ten-fold dilutions from 2.5 × 108 cells/ml to 2.5 × 101 cells/ml, from left to right, as indicated. For panel (C), 4μl from cell suspension with concentration of 2.5 × 108 cells/ml was spotted on plate. Plates were incubated for 3 days. White and black boxes represent tolerant and sensitive phenotypes, respectively.
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Related In: Results  -  Collection

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Figure 5: Phenotypic characteristics of deletion mutants under various stress conditions. Deletion strains as well as the wild-type strain were tested for their ability to growth on YPDA medium incubated at 13°C, 30°C, and 41°C, and YPDA medium supplemented with 4%, 6% and 8% ethanol (A), 4%, 5% and 6% lactic acid, and sulfuric acid (pH2.5, pH2.4 and pH2.3) (B),0.02% SDS, 80 mM acetic acid, 36 mM formic acid, 1.8 M NaCl, 150 mM CaCl2,10 mM furfural,and 2.0 M sorbitol (C). For panel (A) and (B), each strain was plated in serial ten-fold dilutions from 2.5 × 108 cells/ml to 2.5 × 101 cells/ml, from left to right, as indicated. For panel (C), 4μl from cell suspension with concentration of 2.5 × 108 cells/ml was spotted on plate. Plates were incubated for 3 days. White and black boxes represent tolerant and sensitive phenotypes, respectively.
Mentions: Some of the strains displayed a sensitive or resistant phenotype under the stressful environment (Figure 5A, B and C and Supplementary Table S4) including a low-temperature-sensitive phenotype, ScΔ(Chr 10-4), ScΔ(Chr 11-1) and ScΔ(Chr 16-8); a high-temperature-sensitive phenotype, ScΔ(Chr 5-1), ScΔ(Chr 9-1), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1), ScΔ(Chr 16-5), ScΔ(Chr 16-7) and ScΔ(Chr 16-8) (Figure 5A); a high-temperature-resistant phenotype, ScΔ(Chr 4-10) and ScΔ(Chr 4-11) (Figure 5A); a ethanol-sensitive phenotype, ScΔ(Chr 5-1), ScΔ(Chr 9-4), ScΔ(Chr 9-6), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1) and ScΔ(Chr 16-8); a lactic-acid-resistant phenotype, ScΔ(Chr 3-1), ScΔ(Chr 4-1) and ScΔ(Chr 16-9) (Figure 5B) and a sulfuric acid-sensitive phenotype (all strains except for ScΔ(Chr 1-1), ScΔ(Chr 6-1) and ScΔ(Chr 7-4)) (Figure 5B). We did not find strains that were resistant to the ethanol or the sulfuric acid. Based on information in the SGD, neither of the regions deleted in the high-temperature-resistant strains, ScΔ(Chr 4-10) and ScΔ(Chr 4-11), contains the genes whose single deletion is known to cause high-temperature resistance; instead, each region contain a gene (FPR2 and STL1, respectively) whose single deletion cause heat sensitivity. This result suggests that the deletion of either of these genes in combination with another in the respective chromosomal regions caused the observed tolerant phenotype of those strains. We found that all regions deleted in the ethanol-sensitive strains, ScΔ(Chr 5-1), ScΔ(Chr 9-4), ScΔ(Chr 9-6), ScΔ(Chr 10-4), ScΔ(Chr 11-1), ScΔ(Chr 13-1) and ScΔ(Chr 16-8), contain the genes, (CIN8, GVP36 and TED1, YVH1, RAV1, URA1 and SAC1, PIF1 and TDA6 and KRE6, respectively), whose single deletion cause ethanol sensitivity (SGD)(http://www.yeastgenome.org/). Therefore, observed sensitive phenotypes due to deletion of those regions might be conferred by deletion of respective genes. Lack of resistance to ethanol in deletion strains implies that neither of deleted regions nor genes have important role in conferring ethanol-tolerance phenotype.

Bottom Line: Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis.This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome.Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan.

Show MeSH
Related in: MedlinePlus