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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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Construction of a segmental chromosomal deletion in chromosomes II, III, IV, V and IX. (A) Illustration of each target chromosome, deleted region and hybridization probe location. Deleted regions are shown as black dotted lines on the left, right and internal side of each chromosome. Probes 1, 2, 3, 4, 5 and 6 correspond to coordinate number between 768 247–768 628 of chromosomes II, 17 312–17 705 of chromosome III, 1 517 154–1 517 535 of chromosome IV, 26 785–27 159 of chromosome V, 277 726–278 122 and 37 397–37 878 of chromosome IX, respectively. The length of each deleted region is indicated. The blue box, green box, red box, yellow circle and black circle represent the CgHIS3 marker, CgLEU2 marker, probe, artificial CEN4 and natural CEN sequence, respectively. (B) PFGE and Southern hybridization showing karyotype analysis of the parental haploid and transformant clones carrying segmental deletion on chromosomes II, III, IV, V and IX. For all chromosomes, probes were prepared by PCR amplification of a 400-bp internal sequence of the target region.
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Figure 2: Construction of a segmental chromosomal deletion in chromosomes II, III, IV, V and IX. (A) Illustration of each target chromosome, deleted region and hybridization probe location. Deleted regions are shown as black dotted lines on the left, right and internal side of each chromosome. Probes 1, 2, 3, 4, 5 and 6 correspond to coordinate number between 768 247–768 628 of chromosomes II, 17 312–17 705 of chromosome III, 1 517 154–1 517 535 of chromosome IV, 26 785–27 159 of chromosome V, 277 726–278 122 and 37 397–37 878 of chromosome IX, respectively. The length of each deleted region is indicated. The blue box, green box, red box, yellow circle and black circle represent the CgHIS3 marker, CgLEU2 marker, probe, artificial CEN4 and natural CEN sequence, respectively. (B) PFGE and Southern hybridization showing karyotype analysis of the parental haploid and transformant clones carrying segmental deletion on chromosomes II, III, IV, V and IX. For all chromosomes, probes were prepared by PCR amplification of a 400-bp internal sequence of the target region.

Mentions: We found that 33 (blue boxes in Figure 1) of the 110 regions harboring only non-essential genes could be deleted (Figure 1 and Table 2). Example results of the karyotype analysis of some transformants are shown in Figure 2. A deletion in the right terminal region of chromosome II (Chr 2-9) of 68 kb, in the left terminal region of chromosome III (Chr 3-1) of 19 kb, in the right terminal region of chromosome IV (Chr 4-11) of 29 kb, in the left terminal region of chromosome V (Chr 5-1) of 39 kb, in an internal region of chromosome IX (Chr 9-4) of 15 kb, and in the left terminal region of chromosome IX (Chr 9-1) of 56 kb are shown (Figure 2A). Figure 2B shows that the hybridization signal of all probes designed to hybridize with the deleted regions were detected, as expected, for the respective 813-, 316-, 1532-, 577-, 440- and 440-kb intact chromosomes. However, hybridization signals were absent for transformants harboring the expected deletions (lanes 2, 4, 6, 8, 10 and 12). These results indicate that a 68-kb region of chromosome II, 19-kb region of chromosome III, 29-kb region of chromosome IV, 39-kb region of chromosome V, 15-kb region of chromosome IX and 56-kb region of chromosome IX harboring, respectively, 38, 20, 19, 23, 11 and 35 genes were successfully deleted by a single transformation. Similar results were obtained for the other 27 regions identified as deletable by PCD (data not shown). The remaining 77 regions (red boxes in Figure 1) could not be deleted by PCD (Figure 1 and Table 2).


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)

Construction of a segmental chromosomal deletion in chromosomes II, III, IV, V and IX. (A) Illustration of each target chromosome, deleted region and hybridization probe location. Deleted regions are shown as black dotted lines on the left, right and internal side of each chromosome. Probes 1, 2, 3, 4, 5 and 6 correspond to coordinate number between 768 247–768 628 of chromosomes II, 17 312–17 705 of chromosome III, 1 517 154–1 517 535 of chromosome IV, 26 785–27 159 of chromosome V, 277 726–278 122 and 37 397–37 878 of chromosome IX, respectively. The length of each deleted region is indicated. The blue box, green box, red box, yellow circle and black circle represent the CgHIS3 marker, CgLEU2 marker, probe, artificial CEN4 and natural CEN sequence, respectively. (B) PFGE and Southern hybridization showing karyotype analysis of the parental haploid and transformant clones carrying segmental deletion on chromosomes II, III, IV, V and IX. For all chromosomes, probes were prepared by PCR amplification of a 400-bp internal sequence of the target region.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Construction of a segmental chromosomal deletion in chromosomes II, III, IV, V and IX. (A) Illustration of each target chromosome, deleted region and hybridization probe location. Deleted regions are shown as black dotted lines on the left, right and internal side of each chromosome. Probes 1, 2, 3, 4, 5 and 6 correspond to coordinate number between 768 247–768 628 of chromosomes II, 17 312–17 705 of chromosome III, 1 517 154–1 517 535 of chromosome IV, 26 785–27 159 of chromosome V, 277 726–278 122 and 37 397–37 878 of chromosome IX, respectively. The length of each deleted region is indicated. The blue box, green box, red box, yellow circle and black circle represent the CgHIS3 marker, CgLEU2 marker, probe, artificial CEN4 and natural CEN sequence, respectively. (B) PFGE and Southern hybridization showing karyotype analysis of the parental haploid and transformant clones carrying segmental deletion on chromosomes II, III, IV, V and IX. For all chromosomes, probes were prepared by PCR amplification of a 400-bp internal sequence of the target region.
Mentions: We found that 33 (blue boxes in Figure 1) of the 110 regions harboring only non-essential genes could be deleted (Figure 1 and Table 2). Example results of the karyotype analysis of some transformants are shown in Figure 2. A deletion in the right terminal region of chromosome II (Chr 2-9) of 68 kb, in the left terminal region of chromosome III (Chr 3-1) of 19 kb, in the right terminal region of chromosome IV (Chr 4-11) of 29 kb, in the left terminal region of chromosome V (Chr 5-1) of 39 kb, in an internal region of chromosome IX (Chr 9-4) of 15 kb, and in the left terminal region of chromosome IX (Chr 9-1) of 56 kb are shown (Figure 2A). Figure 2B shows that the hybridization signal of all probes designed to hybridize with the deleted regions were detected, as expected, for the respective 813-, 316-, 1532-, 577-, 440- and 440-kb intact chromosomes. However, hybridization signals were absent for transformants harboring the expected deletions (lanes 2, 4, 6, 8, 10 and 12). These results indicate that a 68-kb region of chromosome II, 19-kb region of chromosome III, 29-kb region of chromosome IV, 39-kb region of chromosome V, 15-kb region of chromosome IX and 56-kb region of chromosome IX harboring, respectively, 38, 20, 19, 23, 11 and 35 genes were successfully deleted by a single transformation. Similar results were obtained for the other 27 regions identified as deletable by PCD (data not shown). The remaining 77 regions (red boxes in Figure 1) could not be deleted by PCD (Figure 1 and Table 2).

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