Limits...
Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast.

Ruotolo R, Marchini G, Ottonello S - Genome Biol. (2008)

Bottom Line: A strikingly differential effect was observed for a large set of deletions, the majority of which centered on the ESCRT (endosomal sorting complexes required for transport) and retromer complexes, which - by affecting transporter downregulation and intracellular protein traffic - cause cadmium sensitivity but nickel resistance.The data show that a previously underestimated variety of pathways are involved in cadmium and nickel tolerance in eukaryotic cells.However, many conserved pathways centered on membrane transporters and protein traffic affect cell viability with a surprisingly high degree of metal specificity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Viale G.P. Usberti 23/A, University of Parma, I-43100 Parma, Italy.

ABSTRACT

Background: The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other metals.

Results: A number of novel genes and pathways that affect multimetal as well as metal-specific tolerance were discovered. Although the vacuole emerged as a major hot spot for metal detoxification, we also identified a number of pathways that play a more general, less direct role in promoting cell survival under stress conditions (for example, mRNA decay, nucleocytoplasmic transport, and iron acquisition) as well as proteins that are more proximally related to metal damage prevention or repair. Most prominent among the latter are various nutrient transporters previously not associated with metal toxicity. A strikingly differential effect was observed for a large set of deletions, the majority of which centered on the ESCRT (endosomal sorting complexes required for transport) and retromer complexes, which - by affecting transporter downregulation and intracellular protein traffic - cause cadmium sensitivity but nickel resistance.

Conclusion: The data show that a previously underestimated variety of pathways are involved in cadmium and nickel tolerance in eukaryotic cells. As revealed by comparison with five additional metals, there is a good correlation between the chemical properties and the cellular toxicity signatures of various metals. However, many conserved pathways centered on membrane transporters and protein traffic affect cell viability with a surprisingly high degree of metal specificity.

Show MeSH

Related in: MedlinePlus

Interaction subnetworks among gene products whose disruption causes cadmium/nickel sensitivity. Physical (110) and genetic (105) interactions were identified computationally using the Network Visualization System Osprey [103]. Gene products are represented as nodes, shown as filled circles colored according to their Gene Ontology (GO) classification; interactions are represented as node-connecting edges, shown as lines, colored according to the type of experimental approach utilized to document interaction as specified in the BioGRID database [22] and in the Osprey reference manual. The nine identified subnetworks (a minimum of three interacting gene products sharing at least one GO biologic process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods') are encircled and associated with a general function descriptor. Thirteen interacting gene products whose interaction or functional similarity features do not satisfy the above criterion are shown outside encircled subnetworks; genes without any reported interaction (or linked via essential genes, not addressed in this study) are shown at the bottom. Individual subnetworks were subjected to independent verification by serial dilution growth assays carried on at least two untagged strains of the opposite mating type (see 'Materials and methods'). sn., subnetwork.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2643938&req=5

Figure 2: Interaction subnetworks among gene products whose disruption causes cadmium/nickel sensitivity. Physical (110) and genetic (105) interactions were identified computationally using the Network Visualization System Osprey [103]. Gene products are represented as nodes, shown as filled circles colored according to their Gene Ontology (GO) classification; interactions are represented as node-connecting edges, shown as lines, colored according to the type of experimental approach utilized to document interaction as specified in the BioGRID database [22] and in the Osprey reference manual. The nine identified subnetworks (a minimum of three interacting gene products sharing at least one GO biologic process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods') are encircled and associated with a general function descriptor. Thirteen interacting gene products whose interaction or functional similarity features do not satisfy the above criterion are shown outside encircled subnetworks; genes without any reported interaction (or linked via essential genes, not addressed in this study) are shown at the bottom. Individual subnetworks were subjected to independent verification by serial dilution growth assays carried on at least two untagged strains of the opposite mating type (see 'Materials and methods'). sn., subnetwork.

Mentions: To gain a more detailed understanding of metal toxicity-modulating pathways and the way in which they are interconnected, we set out to analyze genome phenotyping data in the framework of the known yeast interactome [22-24]. The 79 genes that when mutated cause sensitivity to both cadmium and nickel were initially addressed. As shown in Figure 2, 52 of these genes were identified as part of nine functional subnetworks (a minimum of three gene products sharing at least one GO biological process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods', below, for details on this analysis). Seventeen of the remaining genes could be traced to a particular subnetwork but did not pass the above criterion, whereas the other ten remained as 'solitary' entries. Metal sensitivity phenotypes for at least two deletion mutants randomly sampled from each subnetwork were confirmed by independent serial dilution assays carried out on untagged strains of the opposite mating type (data not shown).


Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast.

Ruotolo R, Marchini G, Ottonello S - Genome Biol. (2008)

Interaction subnetworks among gene products whose disruption causes cadmium/nickel sensitivity. Physical (110) and genetic (105) interactions were identified computationally using the Network Visualization System Osprey [103]. Gene products are represented as nodes, shown as filled circles colored according to their Gene Ontology (GO) classification; interactions are represented as node-connecting edges, shown as lines, colored according to the type of experimental approach utilized to document interaction as specified in the BioGRID database [22] and in the Osprey reference manual. The nine identified subnetworks (a minimum of three interacting gene products sharing at least one GO biologic process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods') are encircled and associated with a general function descriptor. Thirteen interacting gene products whose interaction or functional similarity features do not satisfy the above criterion are shown outside encircled subnetworks; genes without any reported interaction (or linked via essential genes, not addressed in this study) are shown at the bottom. Individual subnetworks were subjected to independent verification by serial dilution growth assays carried on at least two untagged strains of the opposite mating type (see 'Materials and methods'). sn., subnetwork.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2643938&req=5

Figure 2: Interaction subnetworks among gene products whose disruption causes cadmium/nickel sensitivity. Physical (110) and genetic (105) interactions were identified computationally using the Network Visualization System Osprey [103]. Gene products are represented as nodes, shown as filled circles colored according to their Gene Ontology (GO) classification; interactions are represented as node-connecting edges, shown as lines, colored according to the type of experimental approach utilized to document interaction as specified in the BioGRID database [22] and in the Osprey reference manual. The nine identified subnetworks (a minimum of three interacting gene products sharing at least one GO biologic process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods') are encircled and associated with a general function descriptor. Thirteen interacting gene products whose interaction or functional similarity features do not satisfy the above criterion are shown outside encircled subnetworks; genes without any reported interaction (or linked via essential genes, not addressed in this study) are shown at the bottom. Individual subnetworks were subjected to independent verification by serial dilution growth assays carried on at least two untagged strains of the opposite mating type (see 'Materials and methods'). sn., subnetwork.
Mentions: To gain a more detailed understanding of metal toxicity-modulating pathways and the way in which they are interconnected, we set out to analyze genome phenotyping data in the framework of the known yeast interactome [22-24]. The 79 genes that when mutated cause sensitivity to both cadmium and nickel were initially addressed. As shown in Figure 2, 52 of these genes were identified as part of nine functional subnetworks (a minimum of three gene products sharing at least one GO biological process annotation and connected by at least two physical or genetic interactions; see 'Materials and methods', below, for details on this analysis). Seventeen of the remaining genes could be traced to a particular subnetwork but did not pass the above criterion, whereas the other ten remained as 'solitary' entries. Metal sensitivity phenotypes for at least two deletion mutants randomly sampled from each subnetwork were confirmed by independent serial dilution assays carried out on untagged strains of the opposite mating type (data not shown).

Bottom Line: A strikingly differential effect was observed for a large set of deletions, the majority of which centered on the ESCRT (endosomal sorting complexes required for transport) and retromer complexes, which - by affecting transporter downregulation and intracellular protein traffic - cause cadmium sensitivity but nickel resistance.The data show that a previously underestimated variety of pathways are involved in cadmium and nickel tolerance in eukaryotic cells.However, many conserved pathways centered on membrane transporters and protein traffic affect cell viability with a surprisingly high degree of metal specificity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Viale G.P. Usberti 23/A, University of Parma, I-43100 Parma, Italy.

ABSTRACT

Background: The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other metals.

Results: A number of novel genes and pathways that affect multimetal as well as metal-specific tolerance were discovered. Although the vacuole emerged as a major hot spot for metal detoxification, we also identified a number of pathways that play a more general, less direct role in promoting cell survival under stress conditions (for example, mRNA decay, nucleocytoplasmic transport, and iron acquisition) as well as proteins that are more proximally related to metal damage prevention or repair. Most prominent among the latter are various nutrient transporters previously not associated with metal toxicity. A strikingly differential effect was observed for a large set of deletions, the majority of which centered on the ESCRT (endosomal sorting complexes required for transport) and retromer complexes, which - by affecting transporter downregulation and intracellular protein traffic - cause cadmium sensitivity but nickel resistance.

Conclusion: The data show that a previously underestimated variety of pathways are involved in cadmium and nickel tolerance in eukaryotic cells. As revealed by comparison with five additional metals, there is a good correlation between the chemical properties and the cellular toxicity signatures of various metals. However, many conserved pathways centered on membrane transporters and protein traffic affect cell viability with a surprisingly high degree of metal specificity.

Show MeSH
Related in: MedlinePlus