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Genetic foundation of unrivaled survival strategies - Of water bears and carnivorous plants -
(2018)
All living organisms leverage mechanisms and response systems to optimize reproduction, defense, survival, and competitiveness within their natural habitat. Evolutionary theories such as the universal adaptive strategy theory (UAST) developed by John Philip Grime (1979) attempt to describe how these systems are limited by the trade-off between growth, maintenance and regeneration; known as the universal three-way trade-off. Grime introduced three adaptive strategies that enable organisms to coop with either high or low intensities of stress (e.g., nutrient deficiency) and environmental disturbance (e.g., seasons). The competitor is able to outcompete other organisms by efficiently tapping available resources in environments of low intensity stress and disturbance (e.g., rapid growers). A ruderal specism is able to rapidly complete the life cycle especially during high intensity disturbance and low intensity stress (e.g., annual colonizers). The stress tolerator is able to respond to high intensity stress with physiological variability but is limited to low intensity disturbance environments. Carnivorous plants like D. muscipula and tardigrades like M. tardigradum are two extreme examples for such stress tolerators. D. muscipula traps insects in its native habitat (green swamps in North and South Carolina) with specialized leaves and thereby is able to tolerate nutrient deficient soils. M. tardigradum on the other side, is able to escape desiccation of its terrestrial habitat like mosses and lichens which are usually covered by a water film but regularly fall completely dry. The stress tolerance of the two species is the central study object of this thesis. In both cases, high througput sequencing data and methods were used to test for transcriptomic (D. muscipula) or genomic adaptations (M. tardigradum) which underly the stress tolerance. A new hardware resource including computing cluster and high availability storage system was implemented in the first months of the thesis work to effectively analyze the vast amounts of data generated for both projects. Side-by-side, the data management resource TBro [14] was established together with students to intuitively approach complex biological questions and enhance collaboration between researchers of several different disciplines. Thereafter, the unique trapping abilities of D. muscipula were studied using a whole transcriptome approach. Prey-dependent changes of the transcriptional landscape as well as individual tissue-specific aspects of the whole plant were studied. The analysis revealed that non-stimulated traps of D. muscipula exhibit the expected hallmarks of any typical leaf but operates evolutionary conserved stress-related pathways including defense-associated responses when digesting prey. An integrative approach, combining proteome and transcriptome data further enabled the detailed description of the digestive cocktail and the potential nutrient uptake machinery of the plant. The published work [25] as well as a accompanying video material (https://www.eurekalert.org/pub_releases/ 2016-05/cshl-fgr042816.php; Video credit: Sönke Scherzer) gained global press coverage and successfully underlined the advantages of D. muscipula as experimental system to understand the carnivorous syndrome. The analysis of the peculiar stress tolerance of M. tardigradum during cryptobiosis was carried out using a genomic approach. First, the genome size of M. tardigradum was estimated, the genome sequenced, assembled and annotated. The first draft of M. tardigradum and the workflow used to established its genome draft helped scrutinizing the first ever released tardigrade genome (Hypsibius dujardini) and demonstrated how (bacterial) contamination can influence whole genome analysis efforts [27]. Finally, the
M. tardigradum genome was compared to two other tardigrades and all species present in the current release of the Ensembl Metazoa database. The analysis revealed that tardigrade genomes are not that different from those of other Ecdysozoa. The availability of the three genomes allowed the delineation of their phylogenetic position within the Ecdysozoa and placed them as sister taxa to the nematodes. Thereby, the comparative analysis helped to identify evolutionary trends within this metazoan lineage. Surprisingly, the analysis did not reveal general mechanisms (shared by all available tardigrade genomes) behind the arguably most peculiar feature of tardigrades; their enormous stress tolerance. The lack of molecular evidence for individual tardigrade species (e.g., gene expression data for M. tardigradum) and the non-existence of a universal experimental framework which enables hypothesis testing withing the whole phylum Tardigrada, made it nearly impossible to link footprints of genomic adaptations to the unusual physiological capabilities. Nevertheless, the (comparative) genomic framework established during this project will help to understand how evolution tinkered, rewired and modified existing molecular systems to shape the remarkable phenotypic features of tardigrades.
Der organische Kationentransport im proximalen Tubulus der Niere spielt eine wichtige Rolle bei der Aufrechterhaltung der Homöostase der Körperflüssigkeiten und der Ausschleusung von toxischen organischen Kationen. Der Transport von organischen Kationen wird an der Bürstensaummembran durch den H+/organische Kationen-Austauscher vermittelt, während bei dem Transport von organischen Kationen an der basolateralen Membran das nach innen gerichtete negative Membranpotential eine treibende Kraft darstellt. Durch Expressionsklonierung wurde der erste organische Kationentransporter, rOCT1, aus der Rattenniere isoliert. Kurz darauf wurde im Rahmen dieser Arbeit ein zweiter organischer Kationentransporter ebenfalls aus der Ratenniere kloniert. rOCT2 besteht aus 593 Aminosäuren und besitzt 12 putative Transmembrandomänen. Zum funktionellen Vergleich zwischen rOCT1 und rOCT2 wurde das Oozytenexpressionssystem verwendet. In der vorliegenden Arbeit wurde ein pharmakologisches Profil von rOCT2 erstellt. Das Substratsprektrum von rOCT2 ist dem von rOCT1 sehr ähnlich. Die Affinitäten von rOCT2 gegenüber verschiedenen Substanzen wurden direkt mit denen von rOCT1 verglichen. Einerseits fanden wir bei einigen Substraten Unterschiede in den Km- und Vmax-Werten, aber andererseits auch viele Ähnlichkeiten zwischen beiden Transportern. Anionen (z. B. p-Aminohippurat) wurden als neue Gruppe von Inhibitoren für den durch rOCT1- und rOCT2-vermittelten Transport identifiziert. Die Potentialdifferenz ist die treibende Kraft des rOCT1- und rOCT2-vermittelten Transportes. Wir konnten potentialabhängige Veränderungen der Km-Werte von Cholin-induzierten Einwärtsströmen zeigen. Bei dem Austausch von Na+-Ionen gegen K+-Ionen im Reaktionspuffer wurde die Aufnahme von Cholin und MPP durch rOCT2 erniedrigt. Der bidirektionale Transport von MPP wurde gezeigt und trans-Stimulationsexperimente für MPP-Influx und MPP-Efflux durchgeführt, um die Asymmetrie des Transporters zu studieren. Darüberhinaus wurde in der vorliegenden Arbeit die Interaktion von verschiedenen Substraten mit rOCT1 und rOCT2 untersucht und ein kompetitver und nicht-kompetitiver Hemmtyp bei der TEA-Aufnahme gefunden.