On the genetic mechanisms of nutrient-dependent lifespan and reproduction
Dietary restriction (DR), a moderate reduction in nutrient intake, improves health or extends lifespan across many species. Moreover, recent insights have shown that also the effects of specific nutrients are of importance for the beneficial effects of DR rather than intake alone. However, we still lack much insight through what mechanisms the lifespan increase through diet changes is exactly mediated. To further increase our understanding of the genetic mechanisms of nutrient-dependent lifespan, in Chapter 2, 3, 4, and 5 I employed different methods of genetic interventions (i.e. a genetic knockout, natural genetic variation and experimental evolution) using the model species Drosophila melanogaster and Podospora anserina. To test whether the genetic interventions affected the diet response, a broad range of diets was applied, thereby taking the recent insights of nutritional geometry into account. Furthermore, the response of the fly’s whole-genome transcription to different dietary treatments were assessed in Chapter 6 and 7 to identify and potentially disentangle genetic mechanisms for lifespan from those for reproduction. Chapter 2 addressed the effects of a triple knockout in the insulin-IGF signalling (IIS) pathway, namely for three genes encoding insulin-like peptides in Drosophila (dilp2-3,5). The mutant showed a strong elevation of lifespan that was irrespective of food type, but also a strong reduction of the female fly fecundity. In addition, this assay also revealed that the same knockout can yield different interpretations for its function in the fly’s diet response, which was strongly dependent per diet dimension under consideration (i.e. varying yeast, sugar, or its ratio in the diet). This observation set the stage for other experimental chapters in this thesis, where a broad range of diets was applied to depict the exact genotypic effects that are involved in the lifespan response to diet. For example, in Chapter 2, interactive effects were observed between dilp2-3,5 knockout and the lifespan response to dietary sugar, but however, not for the yeast component of the diet. In Chapter 3, for the same experimental diets, gene expression responses in dilp2-3,5 knockout flies were measured to describe the general dynamics on the pathway level. Interestingly, expression of the remaining fly head-expressed dilp, dilp6, was elevated on higher yeast levels upon dilp2-3,5 knockout. Therefore, compensatory mechanisms within IIS might still partly mediate the lifespan response to yeast. In Chapter 4 the natural genetic variation for the response to DR was explored in wild-derived strains of the fungus Podospora anserina. By applying a broad range of glucose concentrations in a synthetic medium, we constructed reaction norms for 62 natural occurring strains and showed considerable natural variation in the shape of the reaction norms, including the glucose concentration at which lifespan increased and how steeply the fungus’ lifespan responds to diet (the slope S). Furthermore, I identified a significant correlation between a strain’s general lifespan and both parameters, suggesting that the lifespan response to diet partly acts through a mechanism involved in the fungus’ lifespan determination under high nutrient, growth and reproduction permissive, conditions. On moderate glucose restriction levels we showed that a reduced reproduction was not always associated with lifespan extension, which indicates that decoupling of these traits (that often trade-off) can be achieved. An evolutionary perspective on diet response and the connection between reproduction and lifespan, two often interconnected traits in lifespan research, was provided in Chapter 5. Here, experimental evolution (EE) was performed in Drosophila melanogaster to test whether improved reproductive capacity (i.e. local adaptation) to three nutritionally distinct diets directly affected the lifespan response. Adaptation to the distinct nutritional conditions, had no consistent effect on the lifespan response to diet. Other life-history traits that I assessed could more consistently be associated with the evolutionary nutritional treatments, which together suggested that the adaptive genetic mechanisms increasing the fly’s reproduction were not necessarily interconnected singly with a change of lifespan, but rather with a change in the whole life-history strategy. By exploring the fly’s whole-genome transcription response in a continuously changing environment, Chapter 6 continued on the evolutionary relevance of lifespan responses to diet. This type of fluctuations may better reflect the fly’s natural ecological setting than the continuous diets typically applied in whole-genome transcription laboratory studies. This revealed that flies were able to respond quickly to diet fluctuations throughout lifespan by drastically changing their transcription pattern and, moreover, my results indicated that a large part of the whole-genome transcription response could be attributed to the female fly’s reproduction. Because I measured the response of multiple life-history traits to the fluctuating diet changes, I was able to decouple groups of genes associated with lifespan from those associated with reproduction. This is an important step in the direction of unravelling the genetic architecture that specifically mediates the lifespan response to diet, which can be especially useful in whole-genome transcription studies. In Chapter 7, the consistencies between studies for their whole-genome transcription responses upon DR were investigated. This revealed large transcriptomic variations on different regulatory levels, i.e. the level of whole-genome transcription, most significant genes, and also gene ontology. To test whether the observed inconsistent whole-genome transcription responses were primarily a reflection of the fly’s reproduction, such as observed in Chapter 6, a new cohort of flies was subjected to different regimes that resulted in very different age-dependent reproduction patterns. By assessing whole-genome transcription in this cohort at two time points, the gene expression changes reflected the age-dependent reproduction patterns observed, rather than the lifespan phenotypes. Similar to Chapter 6, this again highlighted the importance of measuring multiple life-history traits for associating whole-genome transcription responses to lifespan effects of dietary restriction. In Chapter 8 the acquired insights across the experimental chapters were synthesized, discussing the importance of assessing a broad range of nutrients for the interpretation of any genotypic effect, and in addition discussing the value of measuring multiple life-history traits for genetic associations. In this chapter I also suggested directions for future research in Drosophila and Podospora that may be valuable for further unravelling and understanding the mechanisms of diet responses in other organisms, including in humans.
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| Format: | Doctoral thesis biblioteca |
| Language: | English |
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Wageningen University
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| Subjects: | diet, drosophila melanogaster, evolution, fungi, genetics, lifespan, nutrients, reproduction, dieet, evolutie, genetica, levensduur, schimmels, voedingsstoffen, voortplanting, |
| Online Access: | https://research.wur.nl/en/publications/on-the-genetic-mechanisms-of-nutrient-dependent-lifespan-and-repr |
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| Summary: | Dietary restriction (DR), a moderate reduction in nutrient intake, improves health or extends lifespan across many species. Moreover, recent insights have shown that also the effects of specific nutrients are of importance for the beneficial effects of DR rather than intake alone. However, we still lack much insight through what mechanisms the lifespan increase through diet changes is exactly mediated. To further increase our understanding of the genetic mechanisms of nutrient-dependent lifespan, in Chapter 2, 3, 4, and 5 I employed different methods of genetic interventions (i.e. a genetic knockout, natural genetic variation and experimental evolution) using the model species Drosophila melanogaster and Podospora anserina. To test whether the genetic interventions affected the diet response, a broad range of diets was applied, thereby taking the recent insights of nutritional geometry into account. Furthermore, the response of the fly’s whole-genome transcription to different dietary treatments were assessed in Chapter 6 and 7 to identify and potentially disentangle genetic mechanisms for lifespan from those for reproduction. Chapter 2 addressed the effects of a triple knockout in the insulin-IGF signalling (IIS) pathway, namely for three genes encoding insulin-like peptides in Drosophila (dilp2-3,5). The mutant showed a strong elevation of lifespan that was irrespective of food type, but also a strong reduction of the female fly fecundity. In addition, this assay also revealed that the same knockout can yield different interpretations for its function in the fly’s diet response, which was strongly dependent per diet dimension under consideration (i.e. varying yeast, sugar, or its ratio in the diet). This observation set the stage for other experimental chapters in this thesis, where a broad range of diets was applied to depict the exact genotypic effects that are involved in the lifespan response to diet. For example, in Chapter 2, interactive effects were observed between dilp2-3,5 knockout and the lifespan response to dietary sugar, but however, not for the yeast component of the diet. In Chapter 3, for the same experimental diets, gene expression responses in dilp2-3,5 knockout flies were measured to describe the general dynamics on the pathway level. Interestingly, expression of the remaining fly head-expressed dilp, dilp6, was elevated on higher yeast levels upon dilp2-3,5 knockout. Therefore, compensatory mechanisms within IIS might still partly mediate the lifespan response to yeast. In Chapter 4 the natural genetic variation for the response to DR was explored in wild-derived strains of the fungus Podospora anserina. By applying a broad range of glucose concentrations in a synthetic medium, we constructed reaction norms for 62 natural occurring strains and showed considerable natural variation in the shape of the reaction norms, including the glucose concentration at which lifespan increased and how steeply the fungus’ lifespan responds to diet (the slope S). Furthermore, I identified a significant correlation between a strain’s general lifespan and both parameters, suggesting that the lifespan response to diet partly acts through a mechanism involved in the fungus’ lifespan determination under high nutrient, growth and reproduction permissive, conditions. On moderate glucose restriction levels we showed that a reduced reproduction was not always associated with lifespan extension, which indicates that decoupling of these traits (that often trade-off) can be achieved. An evolutionary perspective on diet response and the connection between reproduction and lifespan, two often interconnected traits in lifespan research, was provided in Chapter 5. Here, experimental evolution (EE) was performed in Drosophila melanogaster to test whether improved reproductive capacity (i.e. local adaptation) to three nutritionally distinct diets directly affected the lifespan response. Adaptation to the distinct nutritional conditions, had no consistent effect on the lifespan response to diet. Other life-history traits that I assessed could more consistently be associated with the evolutionary nutritional treatments, which together suggested that the adaptive genetic mechanisms increasing the fly’s reproduction were not necessarily interconnected singly with a change of lifespan, but rather with a change in the whole life-history strategy. By exploring the fly’s whole-genome transcription response in a continuously changing environment, Chapter 6 continued on the evolutionary relevance of lifespan responses to diet. This type of fluctuations may better reflect the fly’s natural ecological setting than the continuous diets typically applied in whole-genome transcription laboratory studies. This revealed that flies were able to respond quickly to diet fluctuations throughout lifespan by drastically changing their transcription pattern and, moreover, my results indicated that a large part of the whole-genome transcription response could be attributed to the female fly’s reproduction. Because I measured the response of multiple life-history traits to the fluctuating diet changes, I was able to decouple groups of genes associated with lifespan from those associated with reproduction. This is an important step in the direction of unravelling the genetic architecture that specifically mediates the lifespan response to diet, which can be especially useful in whole-genome transcription studies. In Chapter 7, the consistencies between studies for their whole-genome transcription responses upon DR were investigated. This revealed large transcriptomic variations on different regulatory levels, i.e. the level of whole-genome transcription, most significant genes, and also gene ontology. To test whether the observed inconsistent whole-genome transcription responses were primarily a reflection of the fly’s reproduction, such as observed in Chapter 6, a new cohort of flies was subjected to different regimes that resulted in very different age-dependent reproduction patterns. By assessing whole-genome transcription in this cohort at two time points, the gene expression changes reflected the age-dependent reproduction patterns observed, rather than the lifespan phenotypes. Similar to Chapter 6, this again highlighted the importance of measuring multiple life-history traits for associating whole-genome transcription responses to lifespan effects of dietary restriction. In Chapter 8 the acquired insights across the experimental chapters were synthesized, discussing the importance of assessing a broad range of nutrients for the interpretation of any genotypic effect, and in addition discussing the value of measuring multiple life-history traits for genetic associations. In this chapter I also suggested directions for future research in Drosophila and Podospora that may be valuable for further unravelling and understanding the mechanisms of diet responses in other organisms, including in humans. |
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