PHENOXIGEN

A systems approach linking genotype and environment to phenotype: oxidative stress response mechanisms in fission yeast

 Partecipanti

Mappa

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 Obiettivo del progetto (Objective)

'Cellular protection against oxidative damage is relevant to ageing and numerous complex diseases. We plan to use fission yeast as a model organism to gain a systems-level understanding of the oxidative stress response and obtain insights into the interplay of variable genotype, phenotype, and environment. To this end, the four participants will pursue a range of multi-disciplinary and complementing approaches that will be integrated with innovative computational methods for a unified view of a complete regulatory system. We will create a genetically and phenotypically diverse library of yeast strains from crosses of three independent parental strains with distinct stress sensitivities. The parental and segregant strains will be genotyped and phenotyped (in stressed and unstressed cells) using state-of-the-art sequencing, tiling array, and proteomics approaches, thus providing a rich basis for genome-wide association studies and computational modelling. Genetic, functional genomic, and proteomic approaches, along with computational methods, will be applied in parallel to develop protein and gene interaction networks that will further support the modelling efforts. Predictions based on the modelling will be validated with targeted wet-lab experiments to test and refine the mathematical models. Intimate inter-dependency between experimental and bioinformatic approaches based on close collaboration among participants with different expertise will be vital to develop successful models predicting the regulatory response to oxidative stress. The relative simplicity of yeast cells, which can be grown under tightly controlled conditions and with defined genetic and environmental perturbations, promises a thorough and deep understanding of the oxidative stress response system. Concepts developed in the proposed study will provide a valuable framework for research into more complex systems such as response networks and association studies in human cells.'

Introduzione (Teaser)

An organism's genotype defines its cellular phenotype and the response to environmental conditions. Based on this, a large European consortium worked to unveil the complex interplay between genetic variability and the response to oxidative stress.

Descrizione progetto (Article)

Oxidative stress is caused by an excess of reactive oxygen species (ROS), which essentially induce damage to DNA and other cellular components. ROS are generated as metabolic by-products of aerobically growing cells and after exposure to environmental agents such as ultraviolet (UV) radiation.

The generation of antioxidant responses is central to the cell's viability and response impairment in humans is responsible for ageing, cancer, atherosclerosis, Alzheimer's disease and Parkinson's disease. Accumulating evidence indicates that the response to oxidative stress is mediated through activation of a mitogen-activated protein kinase (MAPK) cascade, through expression of survival genes by the AP1-like transcription factor Pap1, and additionally in yeast through the action of the Prr1 regulator.

Understanding the mechanisms involved in the regulation of oxidative stress was the subject of the EU-funded PHENOXIGEN project. To this end, the consortium used fission yeast as a model organism and aimed to associate genetic factors to phenotype.

Alongside a detailed description of the cellular stress response, partners addressed fundamental biological questions regarding the natural genetic variability that affects the oxidative stress response. Given the established complexity of regulatory networks, the consortium undertook a genome-wide association analysis of specific molecular and cellular traits.

Scientists monitored the ability of over 170 genetically diverse yeast strains to respond to oxidative stress through continuous growth assays and measurement of various molecular properties, including RNA and protein expression. Mapping of these traits onto the yeast genome by quantitative trait locus (QTL) analysis revealed a hotspot region of 713 genes implicated in the response to oxidative stress.

The PHENOXIGEN consortium generated important insight into the role of genetic variability in shaping cellular responses to oxidative stress. This knowledge, coupled with the identification of regulatory networks implicated in the eukaryotic stress response, may be exploited to understand the nature of various complex diseases.