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Chemical-genetic profile analysis of five inhibitory compounds in yeast.

Alamgir M, Erukova V, Jessulat M, Azizi A, Golshani A - BMC Chem Biol (2010)

Bottom Line: Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays.Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions.We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1 S 5B6, ON, Canada. ashkan_golshani@carleton.ca.

ABSTRACT

Background: Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s).

Results: Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. These compounds target the process of protein biosynthesis. More than 70,000 strains were analyzed from the array of gene deletion mutant yeast strains. As expected, the overall profiles of the tested compounds were similar, with deletions for genes involved in protein biosynthesis being the major category followed by metabolism. This implies that novel genes involved in protein biosynthesis could be identified from these profiles. Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays.

Conclusion: Chemical-genetic profiles provide insight into the molecular mechanism(s) of the examined compounds by elucidating their potential primary and secondary cellular target sites. Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions. We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

No MeSH data available.


Overexpression of TAE2 and TAE4 suppresses the sensitivity of numerous translation genes to drug treatments. Overexpression of TAE2 and TAE4 suppresses the phenotype of a number of translation gene deletion strains against neomycin and/or streptomycin treatments. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are divided into functional categories and colored accordingly. (A) TAE2 over-expression rescued 20 gene deletions with a variety of functions. (B) TAE4 over-expression rescued 18 gene deletions, the majority of which are 40 S subunit proteins (nine genes) or function as translation-associated RNA processing proteins (five genes). Blue letters represent genes that are rescued by the overexpression of both TAE2 and TAE4.
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Figure 4: Overexpression of TAE2 and TAE4 suppresses the sensitivity of numerous translation genes to drug treatments. Overexpression of TAE2 and TAE4 suppresses the phenotype of a number of translation gene deletion strains against neomycin and/or streptomycin treatments. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are divided into functional categories and colored accordingly. (A) TAE2 over-expression rescued 20 gene deletions with a variety of functions. (B) TAE4 over-expression rescued 18 gene deletions, the majority of which are 40 S subunit proteins (nine genes) or function as translation-associated RNA processing proteins (five genes). Blue letters represent genes that are rescued by the overexpression of both TAE2 and TAE4.

Mentions: Overexpression of a gene often compensates for a phenotypic consequence caused by the absence of a functionally related gene [38,39]. Therefore, one approach to studying protein function would be to investigate whether its overexpression can compensate for the absence of proteins with known functions. This approach was used to investigate further the biological activity of the gene products for TAE2 and TAE4 by investigating whether their overexpression could reverse the phenotypic consequences caused by the absence of other translation genes (phenotypic suppression analysis). For an unknown reason our multiple attempts to isolate an overexpression plasmid for TAE3 from the yeast gene overexpression library were unsuccessful. Consequently, TAE3 was omitted from this part of the investigation. Reduced growth was used as the target phenotypic consequence for gene deletion strains cultured in the presence of neomycin and streptomycin. As indicated in Figure 4 (and Additional file 3), we observed that the growth defects in the presence of neomycin and/or streptomycin for a number of deletion strains for translation genes were compensated by the overexpression of TAE2 (Figure 4A) or TAE4 (Figure 4B). In agreement with the synthetic genetic interactions described previously, the two main functional categories that TAE4 overexpression rescued included genes involved in translation related RNA processing and 40 S ribosomal structure maintenance. For example, TAE4 overexpression rescued the sensitivity to drugs of deletion strains for the pre rRNA processing gene YGR159C (NSR1) and the 40 S ribosomal subunit protein S28 gene YGR118W (RPS23A). These observations can be explained by a role for TAE4 in 40 S biogenesis, which is in agreement with the synthetic sick and synthetic rescue interactions observed for TAE4.


Chemical-genetic profile analysis of five inhibitory compounds in yeast.

Alamgir M, Erukova V, Jessulat M, Azizi A, Golshani A - BMC Chem Biol (2010)

Overexpression of TAE2 and TAE4 suppresses the sensitivity of numerous translation genes to drug treatments. Overexpression of TAE2 and TAE4 suppresses the phenotype of a number of translation gene deletion strains against neomycin and/or streptomycin treatments. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are divided into functional categories and colored accordingly. (A) TAE2 over-expression rescued 20 gene deletions with a variety of functions. (B) TAE4 over-expression rescued 18 gene deletions, the majority of which are 40 S subunit proteins (nine genes) or function as translation-associated RNA processing proteins (five genes). Blue letters represent genes that are rescued by the overexpression of both TAE2 and TAE4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2925817&req=5

Figure 4: Overexpression of TAE2 and TAE4 suppresses the sensitivity of numerous translation genes to drug treatments. Overexpression of TAE2 and TAE4 suppresses the phenotype of a number of translation gene deletion strains against neomycin and/or streptomycin treatments. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are divided into functional categories and colored accordingly. (A) TAE2 over-expression rescued 20 gene deletions with a variety of functions. (B) TAE4 over-expression rescued 18 gene deletions, the majority of which are 40 S subunit proteins (nine genes) or function as translation-associated RNA processing proteins (five genes). Blue letters represent genes that are rescued by the overexpression of both TAE2 and TAE4.
Mentions: Overexpression of a gene often compensates for a phenotypic consequence caused by the absence of a functionally related gene [38,39]. Therefore, one approach to studying protein function would be to investigate whether its overexpression can compensate for the absence of proteins with known functions. This approach was used to investigate further the biological activity of the gene products for TAE2 and TAE4 by investigating whether their overexpression could reverse the phenotypic consequences caused by the absence of other translation genes (phenotypic suppression analysis). For an unknown reason our multiple attempts to isolate an overexpression plasmid for TAE3 from the yeast gene overexpression library were unsuccessful. Consequently, TAE3 was omitted from this part of the investigation. Reduced growth was used as the target phenotypic consequence for gene deletion strains cultured in the presence of neomycin and streptomycin. As indicated in Figure 4 (and Additional file 3), we observed that the growth defects in the presence of neomycin and/or streptomycin for a number of deletion strains for translation genes were compensated by the overexpression of TAE2 (Figure 4A) or TAE4 (Figure 4B). In agreement with the synthetic genetic interactions described previously, the two main functional categories that TAE4 overexpression rescued included genes involved in translation related RNA processing and 40 S ribosomal structure maintenance. For example, TAE4 overexpression rescued the sensitivity to drugs of deletion strains for the pre rRNA processing gene YGR159C (NSR1) and the 40 S ribosomal subunit protein S28 gene YGR118W (RPS23A). These observations can be explained by a role for TAE4 in 40 S biogenesis, which is in agreement with the synthetic sick and synthetic rescue interactions observed for TAE4.

Bottom Line: Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays.Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions.We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1 S 5B6, ON, Canada. ashkan_golshani@carleton.ca.

ABSTRACT

Background: Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s).

Results: Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. These compounds target the process of protein biosynthesis. More than 70,000 strains were analyzed from the array of gene deletion mutant yeast strains. As expected, the overall profiles of the tested compounds were similar, with deletions for genes involved in protein biosynthesis being the major category followed by metabolism. This implies that novel genes involved in protein biosynthesis could be identified from these profiles. Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays.

Conclusion: Chemical-genetic profiles provide insight into the molecular mechanism(s) of the examined compounds by elucidating their potential primary and secondary cellular target sites. Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions. We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

No MeSH data available.