Limits...
Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae.

North M, Steffen J, Loguinov AV, Zimmerman GR, Vulpe CD, Eide DJ - PLoS Genet. (2012)

Bottom Line: Our studies also indicated the critical role of macroautophagy in low zinc growth.Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis.Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutritional Science and Toxicology, University of California Berkeley, Berkeley, California, USA.

ABSTRACT
Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors. To discover genes and processes in yeast that are required for growth when zinc is limiting, we used genome-wide functional profiling. Mixed pools of ∼4,600 deletion mutants were inoculated into zinc-replete and zinc-limiting media. These cells were grown for several generations, and the prevalence of each mutant in the pool was then determined by microarray analysis. As a result, we identified more than 400 different genes required for optimal growth under zinc-limiting conditions. Among these were several targets of the Zap1 zinc-responsive transcription factor. Their importance is consistent with their up-regulation by Zap1 in low zinc. We also identified genes that implicate Zap1-independent processes as important. These include endoplasmic reticulum function, oxidative stress resistance, vesicular trafficking, peroxisome biogenesis, and chromatin modification. Our studies also indicated the critical role of macroautophagy in low zinc growth. Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis. Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency.

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Related in: MedlinePlus

Fitness data for all significantly affected sensitive strains identified from this study were mapped onto the S. cerevisiae BioGRID interaction dataset using Cytoscape.The fitness scores (the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2) of these sensitive strains were then used to identify and create a smaller sub-network (283 genes) containing the sensitive genes and the non-sensitive and essential genes that link them through known genetic and physical interactions. The sub-network was then assessed for significant overrepresentation of Gene Ontology (GO) Cellular Component categories. These categories were visualized as a linked network. Node color of categories indicates the significance of representation (white = not identified as significant) and node size indicates the number of genes identified present in each category. Edge arrows indicate hierarchy of GO terms. For clarity, only GO Cellular Component categories with a p-value<0.0005 are shown. A separate GO enrichment assessment identified overrepresentation of all GO categories in the sub-network. This analysis was used to generate visual representations of the GO processes and cellular components identified showing the genes involved in these processes. In these cases, node color indicates the sensitivity of each deletion strain in our study (fitness score). The edge color defines the interaction type between nodes (from the BioGRID database).
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pgen-1002699-g003: Fitness data for all significantly affected sensitive strains identified from this study were mapped onto the S. cerevisiae BioGRID interaction dataset using Cytoscape.The fitness scores (the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2) of these sensitive strains were then used to identify and create a smaller sub-network (283 genes) containing the sensitive genes and the non-sensitive and essential genes that link them through known genetic and physical interactions. The sub-network was then assessed for significant overrepresentation of Gene Ontology (GO) Cellular Component categories. These categories were visualized as a linked network. Node color of categories indicates the significance of representation (white = not identified as significant) and node size indicates the number of genes identified present in each category. Edge arrows indicate hierarchy of GO terms. For clarity, only GO Cellular Component categories with a p-value<0.0005 are shown. A separate GO enrichment assessment identified overrepresentation of all GO categories in the sub-network. This analysis was used to generate visual representations of the GO processes and cellular components identified showing the genes involved in these processes. In these cases, node color indicates the sensitivity of each deletion strain in our study (fitness score). The edge color defines the interaction type between nodes (from the BioGRID database).

Mentions: To provide further insight into the biological processes required for the tolerance of zinc limitation, we performed a network mapping analysis. Fitness data for all sensitive strains identified in this study were mapped onto the BioGRID S. cerevisiae functional interaction data set. Fitness scores for each mutant, i.e. the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2, were then used to identify a sub-network within the BioGRID network enriched for genes that have sensitive fitness data associated with them, and so may identify cellular processes or protein complexes affected by zinc limitation. Mutants sensitive to low zinc were then assessed for significant overrepresentation of GO categories, which can be visualized in many different ways (Figure 3). Cellular components identified included the endoplasmic reticulum, the peroxisome, the Golgi apparatus, and histone deacetylase complexes.


Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae.

North M, Steffen J, Loguinov AV, Zimmerman GR, Vulpe CD, Eide DJ - PLoS Genet. (2012)

Fitness data for all significantly affected sensitive strains identified from this study were mapped onto the S. cerevisiae BioGRID interaction dataset using Cytoscape.The fitness scores (the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2) of these sensitive strains were then used to identify and create a smaller sub-network (283 genes) containing the sensitive genes and the non-sensitive and essential genes that link them through known genetic and physical interactions. The sub-network was then assessed for significant overrepresentation of Gene Ontology (GO) Cellular Component categories. These categories were visualized as a linked network. Node color of categories indicates the significance of representation (white = not identified as significant) and node size indicates the number of genes identified present in each category. Edge arrows indicate hierarchy of GO terms. For clarity, only GO Cellular Component categories with a p-value<0.0005 are shown. A separate GO enrichment assessment identified overrepresentation of all GO categories in the sub-network. This analysis was used to generate visual representations of the GO processes and cellular components identified showing the genes involved in these processes. In these cases, node color indicates the sensitivity of each deletion strain in our study (fitness score). The edge color defines the interaction type between nodes (from the BioGRID database).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369956&req=5

pgen-1002699-g003: Fitness data for all significantly affected sensitive strains identified from this study were mapped onto the S. cerevisiae BioGRID interaction dataset using Cytoscape.The fitness scores (the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2) of these sensitive strains were then used to identify and create a smaller sub-network (283 genes) containing the sensitive genes and the non-sensitive and essential genes that link them through known genetic and physical interactions. The sub-network was then assessed for significant overrepresentation of Gene Ontology (GO) Cellular Component categories. These categories were visualized as a linked network. Node color of categories indicates the significance of representation (white = not identified as significant) and node size indicates the number of genes identified present in each category. Edge arrows indicate hierarchy of GO terms. For clarity, only GO Cellular Component categories with a p-value<0.0005 are shown. A separate GO enrichment assessment identified overrepresentation of all GO categories in the sub-network. This analysis was used to generate visual representations of the GO processes and cellular components identified showing the genes involved in these processes. In these cases, node color indicates the sensitivity of each deletion strain in our study (fitness score). The edge color defines the interaction type between nodes (from the BioGRID database).
Mentions: To provide further insight into the biological processes required for the tolerance of zinc limitation, we performed a network mapping analysis. Fitness data for all sensitive strains identified in this study were mapped onto the BioGRID S. cerevisiae functional interaction data set. Fitness scores for each mutant, i.e. the difference in the mean of the log2 hybridization signal between LZM+1 µM ZnCl2 and LZM+100 µM ZnCl2, were then used to identify a sub-network within the BioGRID network enriched for genes that have sensitive fitness data associated with them, and so may identify cellular processes or protein complexes affected by zinc limitation. Mutants sensitive to low zinc were then assessed for significant overrepresentation of GO categories, which can be visualized in many different ways (Figure 3). Cellular components identified included the endoplasmic reticulum, the peroxisome, the Golgi apparatus, and histone deacetylase complexes.

Bottom Line: Our studies also indicated the critical role of macroautophagy in low zinc growth.Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis.Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutritional Science and Toxicology, University of California Berkeley, Berkeley, California, USA.

ABSTRACT
Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors. To discover genes and processes in yeast that are required for growth when zinc is limiting, we used genome-wide functional profiling. Mixed pools of ∼4,600 deletion mutants were inoculated into zinc-replete and zinc-limiting media. These cells were grown for several generations, and the prevalence of each mutant in the pool was then determined by microarray analysis. As a result, we identified more than 400 different genes required for optimal growth under zinc-limiting conditions. Among these were several targets of the Zap1 zinc-responsive transcription factor. Their importance is consistent with their up-regulation by Zap1 in low zinc. We also identified genes that implicate Zap1-independent processes as important. These include endoplasmic reticulum function, oxidative stress resistance, vesicular trafficking, peroxisome biogenesis, and chromatin modification. Our studies also indicated the critical role of macroautophagy in low zinc growth. Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis. Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency.

Show MeSH
Related in: MedlinePlus