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Otte, Kathrin (2016): Proteomic analysis of stress responses in Daphnia. Dissertation, LMU München: Faculty of Biology



Organisms respond to changes in their environment affecting their physiological or ecological optimum by reactions called stress responses. These stress responses may enable the organism to survive by counteracting the consequences of the environ- mental change, the stressor, and usually consist of plastic alterations of traits related to physiology, behaviour, or morphology. In the ecological model species Daphnia, the waterflea, stressors like predators or parasites are known to have an important role in adaptive evolution and have been therefore studied in great detail. However, although various aspects of stress responses in Daphnia have been analysed, molecu- lar mechanisms underlying these traits are not well understood so far. For studying unknown molecular mechanisms, untargeted ‘omics’ approaches are especially suit- able, as they may identify undescribed key players and processes. Recently, ‘omics’ approaches became available for Daphnia. Daphnia is a cosmo- politan distributed fresh water crustacean and has been in research focus for a long time because of its central role in the limnic food web. Furthermore, the responses of this organism to a variety of stressors have been intensively studied e.g. to hypoxic conditions, temperature changes, ecotoxicological relevant substances, parasites or predation. Of these environmental factors, especially predation and interactions with parasites have gained much attention, as both are known to have great influence on the structure of Daphnia populations. In the work presented in this thesis, I characterised the stress responses of Daphnia using proteomic approaches. Proteomics is particularly well suited to analyse bio- logical systems, as proteins are the main effector of nearly all biological processes. However, performing Daphnia proteomics is a challenging task due to high proteolytic activity in the samples, which most probably originate from proteases located in the gut of Daphnia, and are not inhibited by proteomics standard sample pre- paration protocols. Therefore, before performing successful proteomic approaches, I had to optimise the sample preparation step to inhibit proteolytic activity in Daph- nia samples. After succeeding with this task, I was able to analyse stress responses of Daphnia to well-studied stressors like predation and parasites. Furthermore, I stud- ied their response to microgravity exposure, a stressor not well analysed in Daphnia so far. My work on proteins involved in predator-induced phenotypic plasticity is de- scribed in chapter 2 and 3. Daphnia is a textbook example for this phenomenon and is known to show a multitude of inducible defences. For my analysis, I used the system of Daphnia magna and its predator Triops cancriformis. D. magna is known to change its morphology and to increase the stability of its carapace when exposed to the pred- ator, which has been shown to serve as an efficient protection against T. cancriformis predation. In chapter 2, I used a proteomic approach to study predator-induced traits in late-stage D. magna embryos. D. magna neonates are known to be defended against Triops immediately after the release from the brood pouch, if mothers were exposed to the predator. Therefore, the formation of the defensive traits most probably oc- curs during embryonic development. Furthermore, embryos should have reduced protease abundances, as they do not feed inside the brood pouch until release. To study proteins differing in abundance between D. magna exposed to the predator and a control group, I applied a proteomic 2D-DIGE approach, which is a gel based method and therefore enables visual monitoring of protein sample quality. I found differences in traits directly associated with known defences like cuticle proteins and chitin-modifying enzymes most probably involved in carapace stability. In addition, enzymes of the energy metabolism and the yolk protein vitellogenin indicated alterations in energy demand. In chapter 3, I present a subsequent study supporting these results. Here, I analysed responses of adult D. magna to Triops predation at the proteome level using an optimised sample preparation procedure, which was able to generate adult protein samples thereby inhibiting proteolysis. Furthermore, I established a different proteomic approach using a mass-spectrometry based label- free quantification, in which I integrated additional genotypes of D. magna to create a more comprehensive analysis. With this approach, I was able to confirm the results of the embryo study, as similar biological processes indicated by cuticle proteins and vi- tellogenins were involved. Furthermore, additional calcium-binding cuticle proteins and chitin-modifying enzymes and proteins involved in other processes, e.g. protein biosynthesis, could be assigned. Interestingly, I also found evidence for proteins in- volved in a general or a genotype dependent response, with one genotype, which is known to share its habitat with Triops, showing the most distinct responses. Genotype dependent changes in the proteome were also detectable in the study which I present in chapter 4. Here, I analysed molecular mechanisms underlying host-parasite interactions using the well characterised system of D. magna and the bacterial endoparasite Pasteuria ramosa. P. ramosa is known to castrate and kill their host and the infection success is known to depend strongly on the host’s and the para- site’s genotype. I applied a similar proteomic approach as in chapter 3 using label- free quantification, but contrastingly, I did not use whole animal samples but only the freshly shed cuticle. It has been shown, that the genotypic specificity of P. ramosa infection is related to the parasite’s successful attachment to the cuticle of the host and is therefore most probably caused by differences in cuticle composition. Hence, I analysed exuvia proteomes of two different genotypes known to be either suscept- ible to P. ramosa or not. Furthermore, I compared exuvia proteomes of susceptible Daphnia exposed to P. ramosa to a control group for finding proteins involved in the infection process and in the stress response of the host. The proteomes of the different genotypes showed indeed very interesting abundance alterations, connected either to cuticle proteins or matrix metalloproteinases (MMPs). Additionally, the cuticle pro- teins more abundant in the susceptible genotype showed a remarkable increase in predicted glycosylation sites, supporting the hypothesis that P. ramosa attaches to the host’s cuticle by using surface collagen-like proteins to bind to glycosylated cuticle proteins. Most interestingly, in all replicates of the susceptible genotype exposed to P. ramosa, such a collagen-like protein was found in high abundances. Another group of proteins found in higher abundance in the non-susceptible genotype, the MMPs, are also connected to this topic, as they may have collagenolytic characteristics and therefore could interfere with parasite infection. Furthermore, the data indicate that parasite infection may lead to retarded moulting in Daphnia, as moulting is known to reduce the infection success. Contrastingly to the work presented so far, the study described in chapter 5 invest- igated the protein response of Daphnia to a stressor not well studied on other levels, namely microgravity. As gravity is the only environmental parameter which has not changed since life on earth began, organisms usually do not encounter alterations of gravity on earth and cannot adapt to this kind of change. Daphnia has been part of one mission to space, however, responses of the animals to microgravity are not well described so far. In addition, as Daphnia are an interesting candidate organisms for aquatic modules of biological life support systems (BLSS), more information on their response to microgravity is necessary. For this reason, proteomics is an interesting ap- proach, as biological processes not detectable at the morphological or physiological level may become apparent. Therefore, a ground-based method, a 2D-clinostat, was used to simulate microgravity, as studies under real microgravity conditions in space need high technical complexity and financial investment. Subsequently, a proteomic 2D-DIGE approach was applied to compare adult Daphnia exposed to microgravity to a control group. Daphnia showed a strong response to microgravity with abundance alterations in proteins related to the cytoskeleton, protein folding and energy meta- bolism. Most interestingly, this response is very similar to the reactions of a broad range of other organisms to microgravity exposure, indicating that the response to altered gravity conditions in Daphnia follows a general concept. Altogether, the work of my thesis showed a variety of examples of how a proteomic approach may increase the knowledge on stress responses in an organisms not well- established in proteomics. I described both, the analysis of molecular mechanisms underlying well-known traits and the detection of proteins involved in a response not well characterised. Furthermore, I gave examples for highly genotype dependent and also more general stress responses. Therefore, this thesis improves our understanding of the interactions between genotype, phenotype and environment and, moreover, offers interesting starting points for studying the molecular mechanisms underlying stress responses of Daphnia in more detail.