Genetic and transcriptomic basis of copper tolerance across natural European Drosophila melanogaster populations
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PROVIDER: PRJNA646768 | ENA |
REPOSITORIES: ENA
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Project description:Resistance to oxidative stress plays a vital role in animal physiology, where it influences both life history traits and the ability to tolerate the effects of a myriad of environmental stressors. While stress resistance has previously been shown to share a role in shaping an organism's response to traits as varied as desiccation, thermal tolerance and xenobiotic resistance, heavy metal tolerance presents a particular challenge with regards to adaptation to stress. Heavy metals contamination can result in robust and persistent selection pressure: not only is acute exposure highly toxic, but metals can accumulate in the environment over long periods, prolonging this exposure. However, many heavy metals, such as copper and zinc, are also essential micronutrients, which may constrain adaption in high copper conditions. To determine the genetic basis of copper tolerance in European Drosophila melanogaster, we phenotyped 76 inbred lines sampled from nine locations across Western Europe on copper sulphate, demonstrating that that copper tolerance is a highly variable trait. A combination of long-read nanopore sequencing and high-throughput RNA-seq analysis carried out before and after copper exposure shows that while copper tolerance is a highly heterogenous trait, affected by changes in expression across multiple loci, the greatest changes in expression a seen in the digestive tract. In addition, a large proportion of genes found differentially expressed upon copper exposure have previously shown to be regulated by a number of transcription factors with known roles in a broad range of metabolic processes, indicating that while the initial response may be tissue restricted, long term affects of copper expose are more likely to be systemic.
2020-12-31 | GSE154608 | GEO
Project description:Climate change is one of the main factors shaping the distributions and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are specially threatened by these challenging dry environments, thanks to their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern African origin and recent and fast worldwide spreading. Desiccation stress response is a complex and extensively studied trait, however the natural variation and underlying molecular and physiological mechanisms responsible for the tolerance in natural European D. melanogaster populations has never been studied. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains belonging to the cold semi-arid climates are more tolerant compared to the others, and that this tolerance can be explained by the combination of altitude and evaporation. The tolerant strains had a lower level of initial water content and lost less water during desiccation stress. We found that the reduction in the water loss happens through a decrease in the respiration rate in desiccation stress conditions, and by having a less permeable cuticle prior the stress exposure. The decreased rate of respiration in the tolerant strains is a consequence of the down-regulation of genes related to diverse metabolic processes. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. We also identified four transposable element insertions, which might be responsible for changes in gene expression. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains, and generated a list of putative mutations shaping desiccation stress response.
2020-12-31 | GSE153850 | GEO
Project description:Climate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern-central African origin and recent worldwide colonization. Desiccation stress response is a complex and extensively studied trait, however the natural variation in tolerance, and the underlying transcriptomic and physiological mechanisms are still not clear. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains from cold semi-arid climates are more tolerant compared with the ones from hot summer mediterranean climate zones. Moreover, the variance in the tolerance of the strains correlates with the interaction of altitude and evaporation. We found that the tolerant strains had a lower level of initial water content and lose less water during desiccation stress. The reduction in the water loss is probably due to the decrease in the respiration rate in desiccation stress conditions, and to the cuticular hydrocarbon composition found in tolerant strains. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. Furthermore, we identified several desiccation candidate genes unique for the tolerant strains that can be targeted by tRNA derived fragments, known to be important in post-transcriptional gene regulation in several stress responses. We also looked for transposable element insertions possibly affecting the expression of genes relevant in desiccation tolerance, however, except for four insertions, there is no clear association between the presence of the TE insertions and the tolerance level of the strains. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains and puts tRFs in the scope of desiccation related studies as possible regulators of desiccation tolerance.
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Project description:Copper tolerance and sulfite tolerance are two well-studied phenotypic traits of Saccharomyces cerevisiae. The genetic bases of these traits are derived from allelic expansion at the CUP1 locus and reciprocal translocation at the SSU1 locus, respectively. Previous work identified a negative association between sulfite and copper tolerance in S. cerevisiae wine yeasts. Here we probe the relationship between sulfite and copper tolerance and show that an increase in CUP1 copy number does not impart copper tolerance in all S. cerevisiae wine yeast. Bulk-segregant QTL analysis was used to identify variance at SSU1 as a causative factor in copper sensitivity, which was verified by reciprocal hemizygosity analysis in a strain carrying 20 copies of CUP1. Transcriptional and proteomic analysis demonstrated that SSU1 over-expression did not suppress CUP1 transcription or constrain protein production but suggested that SSU1 overexpression induced sulfur limitation during exposure to copper. Finally, an SSU1 over-expressing strain exhibited increased sensitivity to moderately elevated copper concentrations in sulfur-limited medium, demonstrating that SSU1 over-expression burdens the sulfate assimilation pathway. Over-expression of MET 3/14/16, genes upstream of H2S production in the sulfate assimilation pathway increased the production of SO2 and H2S but did not improve copper sensitivity in an SSU1 overexpressing background. We conclude that copper and sulfite tolerance are conditional traits in S. cerevisiae and provide evidence of the metabolic basis for their mutual exclusivity. These findings suggest an evolutionary basis for the extreme amplification of CUP1 observed in some yeasts.
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Project description:Copper (Cu) homeostasis has not been well-documented in filamentous fungi, especially extremophiles. Acidophilic fungus Acidomyces richmondensis MEY-1 has extremely high Cu tolerance among filamentous fungi, and the transcription factor ArAceA has been shown to be involved in this process. The ArAceA deletion mutant (ΔArAceA) exhibits specific growth defects at Cu concentrations of ≥ 10 mM. To gain genomic insight into the Cu tolerance mechanism and the role of ArAceA in Cu tolerance, we treated the ΔArAceA mutant and WT strains with or without 15 mM CuCl2 for 6 h. Transcriptional profiling analysis revealed that ΔArAceA mutant is transcriptionally more sensitive to Cu than the wild-type strain. Our findings provide insights into the molecular basis of Cu tolerance in acidophilic filamentous fungi.
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