ABSTRACT
This corrects the article DOI: 10.1038/nchembio.2436.
ABSTRACT
This corrects the article DOI: 10.1038/nchembio.2436.
ABSTRACT
Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.
Subject(s)
Drug Delivery Systems , Small Molecule Libraries , Drug Evaluation, Preclinical , Gene Expression Profiling , Molecular StructureABSTRACT
The core feature of trusts-holding property for the benefit of others-is well suited to constructing a research community that treats reagents as public goods.
Subject(s)
Biomedical Research , Cooperative Behavior , Trust , Indicators and ReagentsABSTRACT
Genetic suppression occurs when the phenotypic defects caused by a mutation in a particular gene are rescued by a mutation in a second gene. To explore the principles of genetic suppression, we examined both literature-curated and unbiased experimental data, involving systematic genetic mapping and whole-genome sequencing, to generate a large-scale suppression network among yeast genes. Most suppression pairs identified novel relationships among functionally related genes, providing new insights into the functional wiring diagram of the cell. In addition to suppressor mutations, we identified frequent secondary mutations,in a subset of genes, that likely cause a delay in the onset of stationary phase, which appears to promote their enrichment within a propagating population. These findings allow us to formulate and quantify general mechanisms of genetic suppression.
Subject(s)
Gene Regulatory Networks , Genes, Fungal , Genes, Suppressor , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Suppression, Genetic , Cell Physiological Phenomena/genetics , Chromosome MappingABSTRACT
Chemical-genomic (CG) profiling of bioactive compounds is a powerful approach for drug target identification and mode of action studies. Within the last decade, research focused largely on the development and application of CG approaches in the model yeast Saccharomyces cerevisiae. The success of these methods has sparked interest in transitioning CG profiling to other biological systems to extend clinical and evolutionary relevance. Additionally, CG profiling has proven to enhance drug-synergy screens for developing combinatorial therapies. Herein, we briefly review CG profiling, focusing on emerging cross-species technologies and novel drug-synergy applications, as well as outlining needs within the field.
Subject(s)
Drug Discovery/methods , Genomics/methods , Animals , Antifungal Agents/pharmacology , Drug Synergism , Gene Expression Profiling/methods , Gene Regulatory Networks/drug effects , Humans , Mycoses/drug therapy , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/geneticsABSTRACT
Two highly modified linear tetrapeptides, padanamides A (1) and B (2), are produced by laboratory cultures of a Streptomyces sp. obtained from a marine sediment. Padanamide B is cytotoxic to Jurkat cells, and a chemical genomics analysis using Saccharomyces cerevisiae deletion mutants suggested that padanamide A inhibits cysteine and methionine biosynthesis or that these amino acids are involved in the yeast's response to the peptide.
Subject(s)
Geologic Sediments/microbiology , Oligopeptides/chemistry , Streptomyces/chemistry , Cell Survival/drug effects , Humans , Jurkat Cells , Models, Molecular , Molecular Structure , Oligopeptides/biosynthesis , Oligopeptides/pharmacology , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Streptomyces/isolation & purificationABSTRACT
Dosage suppression is a genetic interaction in which overproduction of one gene rescues a mutant phenotype of another gene. Although dosage suppression is known to map functional connections among genes, the extent to which it might illuminate global cellular functions is unclear. Here we analyze a network of interactions linking dosage suppressors to 437 essential genes in yeast. For 424 genes, we curated interactions from the literature. Analyses revealed that many dosage suppression interactions occur between functionally related genes and that the majority do not overlap with other types of genetic or physical interactions. To confirm the generality of these network properties, we experimentally identified dosage suppressors for 29 genes from pooled populations of temperature-sensitive mutant cells transformed with a high-copy molecular-barcoded open reading frame library, MoBY-ORF 2.0. We classified 87% of the 1,640 total interactions into four general types of suppression mechanisms, which provided insight into their relative frequencies. This work suggests that integrating the results of dosage suppression studies with other interaction networks could generate insights into the functional wiring diagram of a cell.
