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Genes required for survival in microgravity revealed by genome-wide yeast deletion collections cultured during spaceflight.

Nislow C, Lee AY, Allen PL, Giaever G, Smith A, Gebbia M, Stodieck LS, Hammond JS, Birdsall HH, Hammond TG - Biomed Res Int (2015)

Bottom Line: Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses.The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported.We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.

ABSTRACT
Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses. However, the more subtle biological effects of spaceflight on cells and organisms are difficult to measure in a systematic, unbiased manner. Here we test the utility of the molecularly barcoded yeast deletion collection to provide a quantitative assessment of the effects of microgravity on a model organism. We developed robust hardware to screen, in parallel, the complete collection of ~4800 homozygous and ~5900 heterozygous (including ~1100 single-copy deletions of essential genes) yeast deletion strains, each carrying unique DNA that acts as strain identifiers. We compared strain fitness for the homozygous and heterozygous yeast deletion collections grown in spaceflight and ground, as well as plus and minus hyperosmolar sodium chloride, providing a second additive stressor. The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported. We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

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Biological processes enriched amongst genes associated with flight-specific fitness defects at different time points in the homozygous deletion series. Each node represents a significantly enriched gene ontology (GO) biological process (hypergeometric test P ≤ 0.01). A circle node indicates enrichment at 14 generations compared to 7 generations (the first time point), a square node indicates enrichment at 21 generations compared to 7 generations, and a diamond node indicates enrichment at both 14 generations and 21 generations (see Methods). Node size is proportional to the significance of enrichment [−log10(P)]. Node color indicates processes that share genes (see Methods) and summary labels are shown for nodes of the same color. Edges indicate ≥ 50% gene overlap between connected processes; width is proportional to the degree of overlap. Each bar plot provides fitness defect (FD) scores for genes that contribute to the enrichment of processes with the same node color as the plot border. Specifically, the length of a bar is proportional to the log2(abundance7G/abundance14G/21G), where abundanceyG represents the abundance of the corresponding gene deletion strain at y generations (see Methods). An “x” on the bar indicates that the abundance of the strain lowers to background level at later time point.
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fig2: Biological processes enriched amongst genes associated with flight-specific fitness defects at different time points in the homozygous deletion series. Each node represents a significantly enriched gene ontology (GO) biological process (hypergeometric test P ≤ 0.01). A circle node indicates enrichment at 14 generations compared to 7 generations (the first time point), a square node indicates enrichment at 21 generations compared to 7 generations, and a diamond node indicates enrichment at both 14 generations and 21 generations (see Methods). Node size is proportional to the significance of enrichment [−log10(P)]. Node color indicates processes that share genes (see Methods) and summary labels are shown for nodes of the same color. Edges indicate ≥ 50% gene overlap between connected processes; width is proportional to the degree of overlap. Each bar plot provides fitness defect (FD) scores for genes that contribute to the enrichment of processes with the same node color as the plot border. Specifically, the length of a bar is proportional to the log2(abundance7G/abundance14G/21G), where abundanceyG represents the abundance of the corresponding gene deletion strain at y generations (see Methods). An “x” on the bar indicates that the abundance of the strain lowers to background level at later time point.

Mentions: We visualized GO enrichment results with enrichment maps shown in Figures 2 and 3 that were generated using an approach similar to the Enrichment Map Cytoscape Plugin v1.1 [23, 24]. In contrast to the plugin, the nodes in each map were clustered with MCL (inflation = 2), using the overlap coefficient computed by the plugin as the similarity metric (coefficients less than 0.5 were set to zero). Nodes in the same cluster were assigned the same node color, and a cluster label was determined based on common themes in the processes within the cluster. Moreover, the size of a node was made to be proportional to the significance with which the corresponding process is enriched [−log10(P)]. Each bar plot summarizes the genes that contribute the most to the enrichment of processes with the same node color as the plot border. Specifically, a plot shows the flight-associated genes that are annotated to the largest number of relevant processes (if more than 10 genes, only the top 10 are shown). For each gene, the bar length is proportional to a fitness defect measure (i.e., log2ratio).


Genes required for survival in microgravity revealed by genome-wide yeast deletion collections cultured during spaceflight.

Nislow C, Lee AY, Allen PL, Giaever G, Smith A, Gebbia M, Stodieck LS, Hammond JS, Birdsall HH, Hammond TG - Biomed Res Int (2015)

Biological processes enriched amongst genes associated with flight-specific fitness defects at different time points in the homozygous deletion series. Each node represents a significantly enriched gene ontology (GO) biological process (hypergeometric test P ≤ 0.01). A circle node indicates enrichment at 14 generations compared to 7 generations (the first time point), a square node indicates enrichment at 21 generations compared to 7 generations, and a diamond node indicates enrichment at both 14 generations and 21 generations (see Methods). Node size is proportional to the significance of enrichment [−log10(P)]. Node color indicates processes that share genes (see Methods) and summary labels are shown for nodes of the same color. Edges indicate ≥ 50% gene overlap between connected processes; width is proportional to the degree of overlap. Each bar plot provides fitness defect (FD) scores for genes that contribute to the enrichment of processes with the same node color as the plot border. Specifically, the length of a bar is proportional to the log2(abundance7G/abundance14G/21G), where abundanceyG represents the abundance of the corresponding gene deletion strain at y generations (see Methods). An “x” on the bar indicates that the abundance of the strain lowers to background level at later time point.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4309212&req=5

fig2: Biological processes enriched amongst genes associated with flight-specific fitness defects at different time points in the homozygous deletion series. Each node represents a significantly enriched gene ontology (GO) biological process (hypergeometric test P ≤ 0.01). A circle node indicates enrichment at 14 generations compared to 7 generations (the first time point), a square node indicates enrichment at 21 generations compared to 7 generations, and a diamond node indicates enrichment at both 14 generations and 21 generations (see Methods). Node size is proportional to the significance of enrichment [−log10(P)]. Node color indicates processes that share genes (see Methods) and summary labels are shown for nodes of the same color. Edges indicate ≥ 50% gene overlap between connected processes; width is proportional to the degree of overlap. Each bar plot provides fitness defect (FD) scores for genes that contribute to the enrichment of processes with the same node color as the plot border. Specifically, the length of a bar is proportional to the log2(abundance7G/abundance14G/21G), where abundanceyG represents the abundance of the corresponding gene deletion strain at y generations (see Methods). An “x” on the bar indicates that the abundance of the strain lowers to background level at later time point.
Mentions: We visualized GO enrichment results with enrichment maps shown in Figures 2 and 3 that were generated using an approach similar to the Enrichment Map Cytoscape Plugin v1.1 [23, 24]. In contrast to the plugin, the nodes in each map were clustered with MCL (inflation = 2), using the overlap coefficient computed by the plugin as the similarity metric (coefficients less than 0.5 were set to zero). Nodes in the same cluster were assigned the same node color, and a cluster label was determined based on common themes in the processes within the cluster. Moreover, the size of a node was made to be proportional to the significance with which the corresponding process is enriched [−log10(P)]. Each bar plot summarizes the genes that contribute the most to the enrichment of processes with the same node color as the plot border. Specifically, a plot shows the flight-associated genes that are annotated to the largest number of relevant processes (if more than 10 genes, only the top 10 are shown). For each gene, the bar length is proportional to a fitness defect measure (i.e., log2ratio).

Bottom Line: Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses.The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported.We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.

ABSTRACT
Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses. However, the more subtle biological effects of spaceflight on cells and organisms are difficult to measure in a systematic, unbiased manner. Here we test the utility of the molecularly barcoded yeast deletion collection to provide a quantitative assessment of the effects of microgravity on a model organism. We developed robust hardware to screen, in parallel, the complete collection of ~4800 homozygous and ~5900 heterozygous (including ~1100 single-copy deletions of essential genes) yeast deletion strains, each carrying unique DNA that acts as strain identifiers. We compared strain fitness for the homozygous and heterozygous yeast deletion collections grown in spaceflight and ground, as well as plus and minus hyperosmolar sodium chloride, providing a second additive stressor. The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported. We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

Show MeSH
Related in: MedlinePlus