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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.


Synthetic genetic interaction analysis for TAE2, TAE3 and TAE4 with translation related genes. There are 72 interactions that represent synthetic genetic interactions for three query genes TAE2, TAE3 and TAE4, with 59 different translation genes. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are further divided into eight functional categories. There are a number of shared interactions that highlight the interconnectivity of the network. The nodes are coloured according to functional groups. Black edges represent synthetic sick (aggravating) interactions, and the six pink thick edges represent synthetically rescue (alleviating) interactions.
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Figure 3: Synthetic genetic interaction analysis for TAE2, TAE3 and TAE4 with translation related genes. There are 72 interactions that represent synthetic genetic interactions for three query genes TAE2, TAE3 and TAE4, with 59 different translation genes. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are further divided into eight functional categories. There are a number of shared interactions that highlight the interconnectivity of the network. The nodes are coloured according to functional groups. Black edges represent synthetic sick (aggravating) interactions, and the six pink thick edges represent synthetically rescue (alleviating) interactions.

Mentions: It is generally accepted that many genes/pathways in eukaryotic cells are functionally redundant and that compensation for loss of activity is prevalent [8]. However, deletion of a second functionally related gene/pathway could result in sickness or lethality, indicating an aggravating interaction. Consequently, the sickness of double mutants can be used to investigate genetic interaction and functional relationships between genes (synthetic genetic interaction analysis) [4]. The synthetic genetic interactions of YPL009C, YIL137C and YPL183W-A with other protein biosynthesis genes were investigated by systematically examining double gene deletions for alterations in colony size [4]. If our targeted genes are involved in protein biosynthesis, it would be expected on the basis of their molecular function that they would interact genetically with other translation genes with related functions. As presented in Figure 3 and Additional file 2, YPL009C, YIL137C and YPL183W-A interacted genetically with a number of translation genes as evidenced by the sick phenotype of the double mutants. These results suggest a functional association for our target genes with the process of protein biosynthesis. Therefore, the studied genes were named TAE2 (YPL009C), TAE3 (YIL137C) and TAE4 (YPL183W-A), or translation associated elements 2-4, respectively. The largest group of genes that interacted with TAE3 and TAE4 were those involved in translation associated RNA processing, with three and seven interactions, respectively. This group included genes such RNA exonuclease YLR059C (REX2), which is involved in rRNA maturation and processing, rRNA binding protein YHR066Wp (Ssf1p), which is a constituent of the 66 S pre-ribosomal subunit, and nuclear pore complex protein YKL068Wp (Nup100p), which is involved in mRNA and rRNA export and ribosomal protein import to the nucleus. TAE4 interacted with five genes related to different small ribosomal subunit proteins including YLR441C, which codes for S1A, and YJL190C, which codes for S22A. TAE2 had a general pattern of interaction and interacted with genes with differing functions. The largest groups of genes (three) that interacted with TAE2 had five members each, with functions in amino acid biosynthesis, small ribosomal subunit proteins and regulation of translation.


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

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

Synthetic genetic interaction analysis for TAE2, TAE3 and TAE4 with translation related genes. There are 72 interactions that represent synthetic genetic interactions for three query genes TAE2, TAE3 and TAE4, with 59 different translation genes. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are further divided into eight functional categories. There are a number of shared interactions that highlight the interconnectivity of the network. The nodes are coloured according to functional groups. Black edges represent synthetic sick (aggravating) interactions, and the six pink thick edges represent synthetically rescue (alleviating) interactions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Synthetic genetic interaction analysis for TAE2, TAE3 and TAE4 with translation related genes. There are 72 interactions that represent synthetic genetic interactions for three query genes TAE2, TAE3 and TAE4, with 59 different translation genes. Genes are represented as nodes (circles) and interactions are represented as edges (lines). The interacting genes are further divided into eight functional categories. There are a number of shared interactions that highlight the interconnectivity of the network. The nodes are coloured according to functional groups. Black edges represent synthetic sick (aggravating) interactions, and the six pink thick edges represent synthetically rescue (alleviating) interactions.
Mentions: It is generally accepted that many genes/pathways in eukaryotic cells are functionally redundant and that compensation for loss of activity is prevalent [8]. However, deletion of a second functionally related gene/pathway could result in sickness or lethality, indicating an aggravating interaction. Consequently, the sickness of double mutants can be used to investigate genetic interaction and functional relationships between genes (synthetic genetic interaction analysis) [4]. The synthetic genetic interactions of YPL009C, YIL137C and YPL183W-A with other protein biosynthesis genes were investigated by systematically examining double gene deletions for alterations in colony size [4]. If our targeted genes are involved in protein biosynthesis, it would be expected on the basis of their molecular function that they would interact genetically with other translation genes with related functions. As presented in Figure 3 and Additional file 2, YPL009C, YIL137C and YPL183W-A interacted genetically with a number of translation genes as evidenced by the sick phenotype of the double mutants. These results suggest a functional association for our target genes with the process of protein biosynthesis. Therefore, the studied genes were named TAE2 (YPL009C), TAE3 (YIL137C) and TAE4 (YPL183W-A), or translation associated elements 2-4, respectively. The largest group of genes that interacted with TAE3 and TAE4 were those involved in translation associated RNA processing, with three and seven interactions, respectively. This group included genes such RNA exonuclease YLR059C (REX2), which is involved in rRNA maturation and processing, rRNA binding protein YHR066Wp (Ssf1p), which is a constituent of the 66 S pre-ribosomal subunit, and nuclear pore complex protein YKL068Wp (Nup100p), which is involved in mRNA and rRNA export and ribosomal protein import to the nucleus. TAE4 interacted with five genes related to different small ribosomal subunit proteins including YLR441C, which codes for S1A, and YJL190C, which codes for S22A. TAE2 had a general pattern of interaction and interacted with genes with differing functions. The largest groups of genes (three) that interacted with TAE2 had five members each, with functions in amino acid biosynthesis, small ribosomal subunit proteins and regulation of translation.

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.