Abstract
BackgroundChemical-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).ResultsColony 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.ConclusionChemical-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.
Highlights
Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action
Drug sensitivity screens The entire collection of the haploid yeast gene deletion array (~4700) was screened for increased sensitivity to the bioactive compounds cycloheximide, 3-amino1,2,4-triazole (3-AT), paromomycin, streptomycin and neomycin
Cycloheximide is a glutarimide antibiotic that binds to the 60 S ribosomal subunit and inhibits translation elongation [19]. 3-AT is a competitive inhibitor of imidazole glycerol phosphate dehydratase, an enzyme involved in the biosynthesis of the amino acid histidine [20], and causes amino acid starvation [21]
Summary
Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. The inactivity of a second functionally overlapping pathway, in this case using a chemical treatment, can cause a “double hit” effect and result in a phenotypic consequence that can be scored as a reduction in the rate of growth, or a sick/sensitive phenotype [4,9]. Such chemical-genetic profile analyses can be used to study cellular target sites of various bioactive compounds [9], pharmaceuticals [10] and herbal extracts [11] whose mechanisms of action are unknown
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