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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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Comparative growth of the Ura− strain (BY4742), Ura+ strain (SH4233), H-mini and D-mini on YPDA, SC-Ura and 5-FOA media. Each strain was first grown overnight at 30°C on SC medium, and then washed twice with water. Aliquots of 105 cells were spotted onto YPDA, SC-Ura and 5-FOA media and incubated at 30°C for 2 days. In total, 67 H-mini strains harboring a URA3-marked mini-chromosome of either an essential or non-essential region were observed to grow on 5-FOA medium. The strains are indicated above their respective lanes. H-mini strains showing growth on 5-FOA contain deletions of non-essential regions; those showing no growth on 5-FOA contain mini-chromosomes of essential regions.
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Figure 4: Comparative growth of the Ura− strain (BY4742), Ura+ strain (SH4233), H-mini and D-mini on YPDA, SC-Ura and 5-FOA media. Each strain was first grown overnight at 30°C on SC medium, and then washed twice with water. Aliquots of 105 cells were spotted onto YPDA, SC-Ura and 5-FOA media and incubated at 30°C for 2 days. In total, 67 H-mini strains harboring a URA3-marked mini-chromosome of either an essential or non-essential region were observed to grow on 5-FOA medium. The strains are indicated above their respective lanes. H-mini strains showing growth on 5-FOA contain deletions of non-essential regions; those showing no growth on 5-FOA contain mini-chromosomes of essential regions.

Mentions: Next, the essentiality of these regions was examined by using diploids constructed by crossing each of these strains with a wild-type strain (ura3) with no split chromosomes on 5-FOA selection medium on which only Ura− clones can grow (20). In brief, haploid strains harboring the URA3-marked mini-chromosome, called ‘H-mini’, were mated with wild-type strain BY4741 to produce a resultant diploid, called D-mini. Cells of the haploid parental strain (BY4742), H-mini, and D-mini were then spotted on YPDA, SC-Ura and 5-FOA selection medium and observed for growth (Figure 4). 5-FOA is toxic to yeast cells that can synthesize the enzyme orotidine-5′-phosphate decarboxylase encoded by URA3; as a result, Ura+ cells die when plated on 5-FOA-containing media, whereas ura3 cells survive. Thus, if the lost chromosomal region in uracil auxotroph strains (H-mini) is non-essential, the H-mini strain will grow on medium containing 5-FOA, whereas it will not grow on 5-FOA selection medium if the lost region is essential. By contrast, a D-mini strain harboring a mini-chromosome comprising an essential region is expected to grow on 5-FOA selection medium even if the mini-chromosome marked with URA3 is lost, owing to the presence of an intact chromosome from the wild-type parent (Figure 4).


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)

Comparative growth of the Ura− strain (BY4742), Ura+ strain (SH4233), H-mini and D-mini on YPDA, SC-Ura and 5-FOA media. Each strain was first grown overnight at 30°C on SC medium, and then washed twice with water. Aliquots of 105 cells were spotted onto YPDA, SC-Ura and 5-FOA media and incubated at 30°C for 2 days. In total, 67 H-mini strains harboring a URA3-marked mini-chromosome of either an essential or non-essential region were observed to grow on 5-FOA medium. The strains are indicated above their respective lanes. H-mini strains showing growth on 5-FOA contain deletions of non-essential regions; those showing no growth on 5-FOA contain mini-chromosomes of essential regions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150759&req=5

Figure 4: Comparative growth of the Ura− strain (BY4742), Ura+ strain (SH4233), H-mini and D-mini on YPDA, SC-Ura and 5-FOA media. Each strain was first grown overnight at 30°C on SC medium, and then washed twice with water. Aliquots of 105 cells were spotted onto YPDA, SC-Ura and 5-FOA media and incubated at 30°C for 2 days. In total, 67 H-mini strains harboring a URA3-marked mini-chromosome of either an essential or non-essential region were observed to grow on 5-FOA medium. The strains are indicated above their respective lanes. H-mini strains showing growth on 5-FOA contain deletions of non-essential regions; those showing no growth on 5-FOA contain mini-chromosomes of essential regions.
Mentions: Next, the essentiality of these regions was examined by using diploids constructed by crossing each of these strains with a wild-type strain (ura3) with no split chromosomes on 5-FOA selection medium on which only Ura− clones can grow (20). In brief, haploid strains harboring the URA3-marked mini-chromosome, called ‘H-mini’, were mated with wild-type strain BY4741 to produce a resultant diploid, called D-mini. Cells of the haploid parental strain (BY4742), H-mini, and D-mini were then spotted on YPDA, SC-Ura and 5-FOA selection medium and observed for growth (Figure 4). 5-FOA is toxic to yeast cells that can synthesize the enzyme orotidine-5′-phosphate decarboxylase encoded by URA3; as a result, Ura+ cells die when plated on 5-FOA-containing media, whereas ura3 cells survive. Thus, if the lost chromosomal region in uracil auxotroph strains (H-mini) is non-essential, the H-mini strain will grow on medium containing 5-FOA, whereas it will not grow on 5-FOA selection medium if the lost region is essential. By contrast, a D-mini strain harboring a mini-chromosome comprising an essential region is expected to grow on 5-FOA selection medium even if the mini-chromosome marked with URA3 is lost, owing to the presence of an intact chromosome from the wild-type parent (Figure 4).

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