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More than ten years ago, ER-ANT1 was shown to act as an ATP/ADP antiporter and to exist in the endoplasmic reticulum (ER) of higher plants. Because structurally different transporters generally mediate energy provision to the ER, the physiological function of ER-ANT1 was not directly evident.
Interestingly, mutant plants lacking ER-ANT1 exhibit a photorespiratory phenotype. Although many research efforts were undertaken, the possible connection between the transporter and photorespiration also remained elusive. Here, a forward genetic approach was used to decipher the role of ER-ANT1 in the plant context and its association to photorespiration.
This strategy identified that additional absence of a putative HAD-type phosphatase partially restored the photorespiratory phenotype. Localisation studies revealed that the corresponding protein is targeted to the chloroplast. Moreover, biochemical analyses demonstrate that the HAD-type phosphatase is specific for pyridoxal phosphate. These observations, together with transcriptional and metabolic data of corresponding single (ER-ANT1) and double (ER-ANT1, phosphatase) loss-of-function mutant plants revealed an unexpected connection of ER-ANT1 to vitamin B6 metabolism.
Finally, a scenario is proposed, which explains how ER-ANT1 may influence B6 vitamer phosphorylation, by this affects photorespiration and causes several other physiological alterations observed in the corresponding loss-of-function mutant plants.
Biological clocks exist across all life forms and serve to coordinate organismal physiology with periodic environmental changes. The underlying mechanism of these clocks is predominantly based on cellular transcription-translation feedback loops in which clock proteins mediate the periodic expression of numerous genes. However, recent studies point to the existence of a conserved timekeeping mechanism independent of cellular transcription and translation, but based on cellular metabolism. These metabolic clocks were concluded based upon the observation of circadian and ultradian oscillations in the level of hyperoxidized peroxiredoxin proteins. Peroxiredoxins are enzymes found almost ubiquitously throughout life. Originally identified as H2O2 scavengers, recent studies show that peroxiredoxins can transfer oxidation to, and thereby regulate, a wide range of cellular proteins. Thus, it is conceivable that peroxiredoxins, using H2O2 as the primary signaling molecule, have the potential to integrate and coordinate much of cellular physiology and behavior with metabolic changes. Nonetheless, it remained unclear if peroxiredoxins are passive reporters of metabolic clock activity or active determinants of cellular timekeeping. Budding yeast possess an ultradian metabolic clock termed the Yeast Metabolic Cycle (YMC). The most obvious feature of the YMC is a high amplitude oscillation in oxygen consumption. Like circadian clocks, the YMC temporally compartmentalizes cellular processes (e.g. metabolism) and coordinates cellular programs such as gene expression and cell division. The YMC also exhibits oscillations in the level of hyperoxidized peroxiredoxin proteins.
In this study, I used the YMC clock model to investigate the role of peroxiredoxins in cellular timekeeping, as well as the coordination of cell division with the metabolic clock. I observed that cytosolic 2-Cys peroxiredoxins are essential for robust metabolic clock function. I provide direct evidence for oscillations in cytosolic H2O2 levels, as well as cyclical changes in oxidation state of a peroxiredoxin and a model peroxiredoxin target protein during the YMC. I noted two distinct metabolic states during the YMC: low oxygen consumption (LOC) and high oxygen consumption (HOC). I demonstrate that thiol-disulfide oxidation and reduction are necessary for switching between LOC and HOC. Specifically, a thiol reductant promotes switching to HOC, whilst a thiol oxidant prevents switching to HOC, forcing cells to remain in LOC. Transient peroxiredoxin inactivation triggered rapid and premature switching from LOC to HOC. Furthermore, I show that cell division is normally synchronized with the YMC and that deletion of typical 2-Cys peroxiredoxins leads to complete uncoupling of cell division from metabolic cycling. Moreover, metabolic oscillations are crucial for regulating cell cycle entry and exit. Intriguingly, switching to HOC is crucial for initiating cell cycle entry whilst switching to LOC is crucial for cell cycle completion and exit. Consequently, forcing cells to remain in HOC by application of a thiol reductant leads to multiple rounds of cell cycle entry despite failure to complete the preceding cell cycle. On the other hand, forcing cells to remain in LOC by treating with a thiol oxidant prevents initiation of cell cycle entry.
In conclusion, I propose that peroxiredoxins – by controlling metabolic cycles, which are in turn crucial for regulating the progression through cell cycle – play a central role in the coordination of cellular metabolism with cell division. This proposition, thus, positions peroxiredoxins as active players in the cellular timekeeping mechanism.
The transfer of substrates between to enzymes within a biosynthesis pathway is an effective way to synthesize the specific product and a good way to avoid metabolic interference. This process is called metabolic channeling and it describes the (in-)direct transfer of an intermediate molecule between the active sites of two enzymes. By forming multi-enzyme cascades the efficiency of product formation and the flux is elevated and intermediate products are transferred and converted in a correct manner by the enzymes.
During tetrapyrrole biosynthesis several substrate transfer events occur and are prerequisite for an optimal pigment synthesis. In this project the metabolic channeling process during the pink pigment phycoerythrobilin (PEB) was investigated. The responsible ferredoxin-dependent bilin reductases (FDBR) for PEB formation are PebA and PebB. During the pigment synthesis the intermediate molecule 15,16-dihydrobiliverdin (DHBV) is formed and transferred from PebA to PebB. While in earlier studies a metabolic channeling of DHBV was postulated, this work revealed new insights into the requirements of this protein-protein interaction. It became clear, that the most important requirement for the PebA/PebB interaction is based on the affinity to their substrate/product DHBV. The already high affinity of both enzymes to each other is enhanced in the presence of DHBV in the binding pocket of PebA which leads to a rapid transfer to the subsequent enzyme PebB. DHBV is a labile molecule and needs to be rapidly channeled in order to get correctly further reduced to PEB. Fluorescence titration experiments and transfer assays confirmed the enhancement effect of DHBV for its own transfer.
More insights became clear by creating an active fusion protein of PebA and PebB and comparing its reaction mechanism with standard FDBRs. This fusion protein was able to convert biliverdin IXα (BV IXα) to PEB similar to the PebS activity, which also can convert BV IXα via DHBV to PEB as a single enzyme. The product and intermediate of the reaction were identified via HPLC and UV-Vis spectroscopy.
The results of this work revealed that PebA and PebB interact via a proximity channeling process where the intermediate DHBV plays an important role for the interaction. It also highlights the importance of substrate channeling in the synthesis of PEB to optimize the flux of intermediates through this metabolic pathway.
The scaffolding protein family Fe65, composed of Fe65, Fe65L1, and Fe65L2, was identified as an interaction partner of the amyloid precursor protein (APP), which plays a key function in Alzheimer’s disease. All three Fe65 family members possess three highly conserved interaction domains, forming complexes with diverse binding partners that can be assigned to different cellular functions, such as transactivation of genes in the nucleus, modulation of calcium homeostasis and lipid metabolism, and regulation of the actin cytoskeleton. In this article, we rule out putative new intracellular signaling mechanisms of the APP-interacting protein Fe65 in the regulation of actin cytoskeleton dynamics in the context of various neuronal functions, such as cell migration, neurite outgrowth, and synaptic plasticity.
Compared to our current knowledge of neuronal excitation, little is known about the development and maturation of inhibitory circuits. Recent studies show that inhibitory circuits develop and mature in a similar way like excitatory circuit. One such similarity is the development through excitation, irrespective of its inhibitory nature. Here in this current study, I used the inhibitory projection between the medial nucleus of the trapezoid body (MNTB) and the lateral superior olive (LSO) as a model system to unravel some aspects of the development of inhibitory synapses. In LSO neurons of the rat auditory brainstem, glycine receptor-mediated responses change from depolarizing to hyperpolarizing during the first two postnatal weeks (Kandler and Friauf 1995, J. Neurosci. 15:6890-6904). The depolarizing effect of glycine is due to a high intracellular chloride concentration ([Cl-]i), which induces a reversal potential of glycine (EGly) more positive than the resting membrane potential (Vrest). In older LSO neurons, the hyperpolarizing effect is due to a low [Cl-]i (Ehrlich et al., 1999, J. Physiol. 520:121-137). Aim of the present study was to elucidate the molecular mechanism behind Clhomeostasis in LSO neurons which determines polarity of glycine response. To do so, the role and developmental expression of Cl-cotransporters, such as NKCC1 and KCC2 were investigated. Molecular biological and gramicidin perforated patchclamp experiments revealed, the role of KCC2 as an outward Cl-cotransporter in mature LSO neurons (Balakrishnan et al., 2003, J Neurosci. 23:4134-4145). But, NKCC1 does not appear to be involved in accumulating chloride in immature LSO neurons. Further experiments, indicated the role of GABA and glycine transporters (GAT1 and GLYT2) in accumulating Cl- in immature LSO neurons. Finally, the experiments with hypothyroid animals suggest the possible role of thyroid hormone in the maturation of inhibitory synapse. Altogether, this thesis addressed the molecular mechanism underlying the Cl- regulation in LSO neurons and deciphered it to some extent.
Herbivory is discussed as a key agent in maintaining dynamics and stability of tropical forested ecosystems. Accordingly increasing attention has been paid to the factors that structure tropical herbivore communities. The aim of this study was (1) to describe diversity, density, distribution and host range of the phasmid community (Phasmatodea) of a moist neotropical forest in Panamá, and (2) to experimentally assess bottom-up and top-down factors that may regulate populations of the phasmid Metriophasma diocles. The phasmid community of Barro Colorado Island was poor in species and low in density. Phasmids mainly occurred along forest edges and restricted host ranges of phasmid species reflected the successional status of their host plants. Only M. diocles that fed on early and late successional plants occurred regularly in the forest understory. A long generation time with a comparably low fecundity converted into a low biotic potential of M. diocles. However, modeled potential population density increased exponentially and exceeded the realized densities of this species already after one generation indicating that control factors continuously affect M. diocles natural populations. Egg hatching failure decreased potential population growth by 10 % but was of no marked effect at larger temporal scale. Interspecific differences in defensive physical and chemical leaf traits of M. diocles host plants, amongst them leaf toughness the supposedly most effective anti-herbivore defense, seemed not to affect adult female preference and nymph performance. Alternatively to these defenses, I suggest that the pattern of differential preference and performance may be based on interspecific differences in qualitative toxic compounds or in nutritive quality of leaves. The significant rejection of leaf tissue with a low artificial increase of natural phenol contents by nymphs indicated a qualitative defensive pathway in Piper evolution. In M. diocles, oviposition may not be linked to nymph performance, because the evolutionary prediction of a relation between female adult preference and nymph performance was missing. Consequently, the recruitment of nymphs into the reproductive adult phase may be crucially affected by differential performance of nymphs. Neonate M. diocles nymphs suffered strong predation pressure when exposed to natural levels of predation. Concluding from significantly increased predation-related mortality at night, I argue that arthropods may be the main predators of this nocturnal herbivore. Migratory behavior of nymphs seemed not to reflect predation avoidance. Instead, I provided first evidence that host plant quality may trigger off-plant migration. In conclusion, I suggest that predation pressure with its direct effects on nymph survival may be a stronger factor regulating M. diocles populations, compared to direct and indirect effects of host plant quality, particularly because slow growth and off-host migration both may feed back into an increase of predation related mortality.
On a route from whole genome duplication to aneuploidy and cancer: consequences and adaptations
(2022)
Whole genome duplication (WGD) is commonly accepted as an intermediate state between healthy cells and aneuploid cancer cells. Usually, cells after WGD get removed from the replicating pool by p53-dependent cell cycle arrest or apoptosis. Cells, which are able to bypass these mechanisms exhibit chromosomal instability (CIN) and DNA damage, promoting the formation of highly aneuploid karyotypes. In general, WGD favors several detrimental consequences such as increased drug resistance, transformation and metastasis formation. Therefore, it is of special interest to investigate the limiting factors and consequences of tetraploid proliferation as well as the adaptations to WGD. In the past it has been difficult to study the consequences of such large-scale genomic changes and how cells adapt to tetraploidy in order to survive. Our lab established protocols to generate tetraploids as well as isolated post-tetraploid/aneuploid single cells clones derived from euploid parental cell lines after induction of cytokinesis failure. This system enables to study the consequences and adaptations of WGD in newly generated tetraploid cells and evolved post-tetraploid clones in comparison to their isogenic parental cell line.
Using newly generated tetraploids from HCT116 cells, we identified USP28 and SPINT2 as novel factors limiting the proliferation after WGD. Using mass spectrometry and immunoprecipitation, we revealed an interaction between USP28 and NuMA1 upon WGD, which affects centrosome coalescence of supernumerary centrosomes, an important process that enhances survival of tetraploids. Furthermore, we validated the occurrence of DNA damage in tetraploid cells and found that USP28 depletion diminished the DNA damage dependent checkpoint activation. SPINT2 influences the proliferation after WGD by regulating the transcription of CDKN1A via histone acetylation. Following proliferating tetraploid cells, we confirmed the activation of the DNA damage response (DDR) by immunoblotting and microscopic approaches. Furthermore, we show that the DDR in the arising post-tetraploid clones is reduced. Further experiments verified the appearance of severe mitotic aberrations, replication stress and accumulation of reactive oxygen species in newly generated tetraploids as well as in the aneuploid cancer cells contributing to the occurrence of DNA damage. Using various drug treatments, we observed an increased dependency on the spindle assembly checkpoint in aneuploid cancer cells compared to their diploid parental cell line. Additionally, siRNA knock down experiments revealed the kinesin motor protein KIF18A as an essential protein in aneuploid cells.
Taken together, the results point out cellular consequences of proliferation after tetraploidization as well as the cellular adaptations needed to cope with the increased amount of DNA.
Proteins of the intermembrane space of mitochondria are generally encoded by nuclear genes that are synthesized in the cytosol. A group of small intermembrane space proteins lack classical mitochondrial targeting sequences, but these proteins are imported in an oxidation-driven reaction that relies on the activity of two components, Mia40 and Erv1. Both proteins constitute the mitochondrial disulfide relay system. Mia40 functions as an import receptor that interacts with incoming polypeptides via transient, intermolecular disulfide bonds. Erv1 is an FAD-binding sulfhydryl oxidase that activates Mia40 by re-oxidation, but the process how Erv1 itself is re-oxidized has been poorly understood. Here, I show that Erv1 interacts with cytochrome c which provides a functional link between the mitochondrial disulfide relay system and the respiratory chain. This mechanism not only increases the efficiency of mitochondrial inport by the re-oxidation of Erv1 and Mia40 but also prevents the formation of deleterious hydrogen peroxide within the intermembrane space. Thus, the miochondrial disulfide relay system is, analogous to that of the bacterial periplasm, connected to the electron transport chain of the inner membrane, which possibly allows an oxygen-dependend regulation of mitochondrial import rates. In addition, I modeled the structure of Erv1 on the basis of the Saccharomyces cerevisiae Erv2 crystal structure in order to gain insight into the molecular mechanism of Erv1. According to the high degree of sequence homologies, various characteristics found for Erv2 are also valid for Erv1. Finally, I propose a regulatory function of the disulfide relay system on the respiratory chain. The disulfide relay system senses the molecular oxygen levels in mitochondria and, thus, is able to adapt respiratory chain activity in order to prevent wastage of NADH and production of ROS.
Human forest modification is among the largest global drivers of terrestrial degradation
of biodiversity, species interactions, and ecosystem functioning. One of the most
pertinent components, forest fragmentation, has a long history in ecological research
across the globe, particularly in lower latitudes. However, we still know little how
fragmentation shapes temperate ecosystems, irrespective of the ancient status quo of
European deforestation. Furthermore, its interaction with another pivotal component
of European forests, silvicultural management, are practically unexplored. Hence,
answering the question how anthropogenic modification of temperate forests affects
fundamental components of forest ecosystems is essential basic research that has
been neglected thus far. Most basal ecosystem elements are plants and their insect
herbivores, as they form the energetic basis of the tropic pyramid. Furthermore, their
respective biodiversity, functional traits, and the networks of interactions they
establish are key for a multitude of ecosystem functions, not least ecosystem stability.
Hence, the thesis at hand aimed to disentangle this complex system of
interdependencies of human impacts, biodiversity, species traits and inter-species
interactions.
The first step lay in understanding how woody plant assemblages are shaped by
human forest modification. For this purpose, field investigations in 57 plots in the
hyperfragmented cultural landscape of the Northern Palatinate highlands (SW
Germany) were conducted, censusing > 4,000 tree/shrub individuals from 34 species.
Use of novel, integrative indices for different types of land-use allowed an accurate
quantification of biotic responses. Intriguingly, woody tree/shrub communities reacted
strikingly positive to forest fragmentation, with increases in alpha and beta diversity,
as well as proliferation of heat/drought/light adapted pioneer species. Contrarily,
managed interior forests were homogenized/constrained in biodiversity, with
dominance of shade/cold adapted commercial tree species. Comparisons with recently
unmanaged stands (> 40 a) revealed first indications for nascent conversion to oldgrowth
conditions, with larger variability in light conditions and subsequent
community composition. Reactions to microclimatic conditions, the relationship
between associated species traits and the corresponding species pool, as well as
facilitative/constraining effects by foresters were discussed as underlying mechanisms.
Reactions of herbivore assemblages to forest fragmentation and the subsequent
changes in host plant communities were assessed by comprehensive sampling of >
1,000 live herbivores from 134 species in the forest understory. Diversity was –
similarly to plant communities - higher in fragmentation affected habitats, particularly
in edges of continuous control forests. Furthermore, average trophic specialization
showed an identical pattern. Mechanistically, benefits from microclimatic conditions,
host availability, as well as pronounced niche differentiation are deemed responsible.
While communities were heterogeneous, with no segregation across habitats, (smallforest fragments, edges, and interior of control forests), vegetation diversity, herbivore
diversity, as well as trophic specialization were identified to shape community
composition. This probably reflected a gradient from generalistic/species poor vs.
specialist/species rich herbivore assemblages.
Insect studies conducted in forest systems are doomed to incompleteness
without considering ‘the last biological frontier’, the tree canopies. To access their
biodiversity, relationship to edge effects, and their conservational value, the
arboricolous arthropod fauna of 24 beech (Fagus sylvatica) canopies was sampled via
insecticidal knockdown (‘fogging’). This resulted in an exhaustive collection of > 46,000
specimens from 24 major taxonomic/functional groups. Abundance distributions were
markedly negative exponential, indicating high abundance variability in tree crowns.
Individuals of six pertinent orders were identified to species level, returning > 3,100
individuals from 175 species and 52 families. This high diversity did marginally differ
across habitats, with slightly higher species richness in edge canopies. However,
communities in edge crowns were noticeably more heterogeneous than those in the
forest interior, possibly due to higher variability in environmental edge conditions. In
total, 49 species with protective value were identified, of which only one showed
habitat preferences (for near-natural interior forests). Among them, six species (all
beetles, Coleoptera) were classified as ‘priority species’ for conservation efforts. Hence,
beech canopies of the Northern Palatinate highlands can be considered strongholds of
insect biodiversity, incorporating many species of particular protective value.
The intricacy of plant-herbivore interaction networks and their relationship to
forest fragmentation is largely unexplored, particularly in Central Europe. Illumination
of this matter is all the more important, as ecological networks are highly relevant for
ecosystem stability, particularly in the face of additional anthropogenic disturbances,
such as climate change. Hence, plant-herbivore interaction networks (PHNs) were
constructed from woody plants and their associated herbivores, sampled alive in the
understory. Herbivory verification was achieved using no-choice-feeding assays, as well
as literature references. In total, networks across small forest fragments, edges, and
the forest interior consisted of 696 interactions. Network complexity and trophic niche
redundancy were compared across habitats using a rarefaction-like resampling
procedure. PHNs in fragmentation affected forest habitats were significantly more
complex, as well as more redundant in their realized niches, despite being composed of
relatively more specialist species. Furthermore, network robustness to climate change
was quantified utilizing four different scenarios for climate change susceptibility of
involved plants. In this procedure, remaining herbivores in the network were measured
upon successive loss of their host plant species. Consistently, PHNs in edges (and to a
smaller degree in small fragments) withstood primary extinction of plant species
longer, making them more robust. This was attributed to the high prevalence of
heat/drought-adapted species, as well as to beneficial effects of network topography
(complexity and redundancy). Consequently, strong correlative relationships were
found between realized niche redundancy and climate change robustness of PHNs.
This was both the first time that biologically realistic extinctions (instead of e.g.random extinctions) were used to measure network robustness, and that topographical
network parameters were identified as potential indicators for network robustness
against climate change.
In synthesis, in the light of global biotic degradation due to human forest
modification, the necessity to differentiate must be claimed. Ecosystems react
differently to anthropogenic disturbances, and it seems the particular features present
in Central European forests (ancient deforestation, extensive management, and, most
importantly, high richness in open-forest plant species) cause partly opposed patterns
to other biomes. Lenient microclimates and diverse plant communities facilitate
equally diverse herbivore assemblages, and hence complex and robust networks,
opposed to the forest interior. Therefore, in the reality of extensively used cultural
landscapes, fragmentation affected forest ecosystems, particularly forest edges, can be
perceived as reservoir for biodiversity, and ecosystem functionality. Nevertheless, as
practically all forest habitats considered in this thesis are under human cultivation,
recommendations for ecological enhancement of all forest habitats are discussed.
Biological soil crusts (biocrusts) are a common element of the Queensland (Australia) dry savannah ecosystem and are composed of cyanobacteria, algae, lichens, bryophytes, fungi and heterotrophic bacteria. Here we report how the CO2 gas exchange of the cyanobacteria-dominated biocrust type from Boodjamulla National Park in the north Queensland Gulf Savannah responds to the pronounced climatic seasonality and on their quality as a carbon sink using a semi-automatic cuvette system. The dominant cyanobacteria are the filamentous species Symplocastrum purpurascens together with Scytonema sp. Metabolic activity was recorded between 1 July 2010 and 30 June 2011, during which CO2 exchange was only evident from November 2010 until mid-April 2011, representative of 23.6 % of the 1-year recording period. In November at the onset of the wet season, the first month (November) and the last month (April) of activity had pronounced respiratory loss of CO2. The metabolic active period accounted for 25 % of the wet season and of that period 48.6 % was net photosynthesis (NP) and 51.4 % dark respiration (DR). During the time of NP, net photosynthetic uptake of CO2 during daylight hours was reduced by 32.6 % due to water supersaturation. In total, the biocrust fixed 229.09 mmol CO2 m−2 yr−1, corresponding to an annual carbon gain of 2.75 g m−2 yr−1. Due to malfunction of the automatic cuvette system, data from September and October 2010 together with some days in November and December 2010 could not be analysed for NP and DR. Based on climatic and gas exchange data from November 2010, an estimated loss of 88 mmol CO2 m−2 was found for the 2 months, resulting in corrected annual rates of 143.1 mmol CO2 m−2 yr−1, equivalent to a carbon gain of 1.7 g m−2 yr−1. The bulk of the net photosynthetic activity occurred above a relative humidity of 42 %, indicating a suitable climatic combination of temperature, water availability and light intensity well above 200 µmol photons m−2 s−1 photosynthetic active radiation. The Boodjamulla biocrust exhibited high seasonal variability in CO2 gas exchange pattern, clearly divided into metabolically inactive winter months and active summer months. The metabolic active period commences with a period (of up to 3 months) of carbon loss, likely due to reestablishment of the crust structure and restoration of NP prior to about a 4-month period of net carbon gain. In the Gulf Savannah biocrust system, seasonality over the year investigated showed that only a minority of the year is actually suitable for biocrust growth and thus has a small window for potential contribution to soil organic matter.