Biologische Hochschulschriften (Goethe-Universität)
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Pretubulysin (PT), a biosynthetic precursor of the myxobacterial compound tubulysin D, was recently identified as a novel microtubule-targeting agent (MTA) causing microtubule destabilization. MTAs are the most frequently used chemotherapeutic drugs. They are well studied regarding their direct cytotoxic effects against various tumors as well as for their anti-angiogenic and vascular-disrupting action addressing endothelial cells of the tumor vasculature. However, the impact of MTAs on endothelial cells of the non-tumor vasculature has been largely neglected, although tumor cell interactions with the healthy endothelium play a crucial role in the process of cancer metastasis. Besides their use as potent anti-cancer drugs, some MTAs such as colchicine are traditionally used or recommended for the therapy of inflammatory diseases. Here, too, the role of endothelial cells has been largely neglected, although the endothelium is crucially involved in regulating the process of inflammation.
In the present study, the impact of PT on tumor-endothelial cell interactions was therefore analyzed in vitro to gain insights into the mechanism underlying its anti-metastatic effect that was recently confirmed in vivo. In the second part of this work, the influence of PT and other MTAs, namely the microtubule-destabilizing compounds vincristine (VIN) and colchicine (COL) and the microtubule-stabilizing drug paclitaxel (PAC), on leukocyte-endothelial cell interactions was investigated in vitro and in vivo (only PT). It is important to mention that in all in vitro experiments solely endothelial cells and not tumor cells or leukocytes were treated with the MTAs to strictly focus on the role of the endothelium in the action of these compounds.
The impact of PT on tumor-endothelial cell interactions was analyzed in vitro by cell adhesion and transendothelial migration assays as well as immunocytochemistry using the breast cancer cell line MDA-MB-231 and primary human umbilical vein endothelial cells (HUVECs). The treatment of HUVECs with PT increased the adhesion of MDA cells onto the endothelial monolayer, whereas their transendothelial migration was reduced by the compound. Thereafter, the influence of PT on the endothelial cell adhesion molecules (CAMs) E-selectin, N-cadherin, ICAM-1, VCAM-1 and galectin-3 and on the CXCL12/CXCR4 chemokine system was examined, since they might be involved in the PT-triggered tumor cell adhesion. Interestingly, although PT induced the upregulation of ICAM-1, VCAM-1, N-cadherin and CXCL12, cell adhesion assays using neutralizing antibodies or the CXCL12 inhibitor AMD3100 revealed that all these molecules were dispensable for the PT-evoked tumor cell adhesion. As PT induces the formation of interendothelial gaps and MDA cells might adhere onto components of the underlying extracellular matrix (ECM), the precise location of MDA cells attached to the PT-treated endothelial monolayer was investigated. Instead of a direct interaction between tumor and endothelial cells, this work showed that MDA cells preferred to adhere to the ECM component collagen that was exposed within PT-triggered endothelial gaps. Both the PT-evoked increase in tumor cell adhesion onto and the decrease in trans-endothelial migration were completely abolished when β1-integrins were blocked on MDA cells. Similar results were obtained when endothelial cells were treated with VIN and COL but not PAC, indicating that the observed effects of PT depend on its microtubule-destabilizing activity.
The impact of PT, VIN, COL and PAC on leukocyte-endothelial cell interactions was analyzed in vivo (only PT) by intravital microscopy of the mouse cremaster muscle and in vitro by cell adhesion assays using the monocyte-like cell line THP-1 and TNFα-activated human dermal microvascular endothelial cells (HMEC-1). While PT did not affect the rolling of leukocytes on the endothelium, their firm adhesion onto and transmigration through the activated endothelium was reduced by PT in vivo. In accordance, the treatment of HMEC-1 with PT, VIN and COL decreased the TNFα-induced adhesion of THP-1 cells onto the endothelial monolayer, whereas PAC had no influence on this process. Thereafter, the influence of PT, VIN, COL and PAC on endothelial ICAM-1 and VCAM-1 was examined, since these molecules are substantially involved in the firm adhesion of leukocytes onto the endothelium. The cell surface protein expression of ICAM-1 and VCAM-1 was reduced by PT, VIN and COL in activated endothelial cells, whereas PAC did only slightly affect the TNFα-induced upregulation of VCAM-1. As the pro-inflammatory transcription factor NFκB plays a crucial role in the TNFα-induced expression of these CAMs, the impact of the MTAs on the NFκB promotor activity was investigated. While PT, VIN and COL decreased the activation of NFκB in activated endothelial cells, PAC did not affect this process. However, in contrast to the strong effects regarding the cell surface protein expression of ICAM-1 and VCAM-1, the effects of PT, VIN and COL on the NFκB activity was rather low. Thus, the used MTAs might also affect other relevant signaling pathways and/or the intracellular transport of CAMs might be influenced by the impact of the MTAs on the microtubule network.
Taken together, the current study provides – at least in part – an explanation for the anti-metastatic potential of PT and gives first insights into the use of PT and VIN as anti-inflammatory drugs. Moreover, this work highlights the endothelium as an attractive target for the development of new anti-cancer and anti-inflammatory drugs.
Reactive oxygen species (ROS) are involved in various signalling mechanisms. Redox homeostasis is important in cancer cells, since they are dependent on upregulated antioxidant defence pathways to cope with elevated ROS levels. Therefore, targeting the antioxidant defence system and/ or increasing ROS to a lethal level may be a feasible strategy to counteract cancer cell progression.
Acute lymphoblastic leukaemia (ALL) is the most frequent malignant childhood cancer, displaying on one side resistance to cell death induction and on the other side elevated ROS levels. Therefore, inducing ferroptosis, a ROS- and iron-dependent cell death pathway might be useful to trigger cell death in ALL as a novel treatment strategy. In the first study of this thesis we observed that RSL3, a glutathione (GSH) peroxidase 4 (GPX4) inhibitor, triggered ROS accumulation and lipid peroxidation which contributed to ferroptotic cell death. These observations were based on suppression of RSL3 stimulated cell death using different ferroptosis inhibitors like Ferrostatin-1 (Fer-1), Liproxstatin-1 (Lip-1), as well as iron chelator Deferoxamine (DFO) and the vitamin E derivate α-Tocopherol (α-Toc). RSL3-triggered ROS and lipid peroxide production were also inhibited through Fer-1 and α-Toc. Furthermore, lipoxygenases (LOX) were activated upon RSL3 stimulation and contributed to ferroptotic cell death in ALL as well. Selective inhibition of LOX with the 12/15-LOX inhibitor Baicalein and the pan-LOX inhibitor nordihydroguaiaretic acid (NDGA) abolished RSL3-induced ROS production, lipid peroxidation and cell death. In addition, RSL3 induced lipid peroxide-dependent ferroptotic cell death in FAS-associated Death Domain (FADD)-deficient, death receptor-induced apoptosis resistant cells, demonstrating that ferroptosis might circumvent apoptosis resistance.
The second part of the study revealed that RSL3 and Erastin (Era), a GSH-depleting agent, inhibiting the cystine/glutamate antiporter system xc- and ferroptosis inducer, cooperated with the Smac mimetic BV6 to trigger cell death in ALL cells. RSL3/BV6 and Era/BV6 combination-induced cell death was dependent on ROS accumulation, but independent of caspases and key modulators of necroptosis. RSL3/BV6-treated ALL cells exhibited classical features of ferroptotic cell death with iron-dependency, ROS accumulation and lipid peroxidation which was diminished through either pharmacological inhibition (Fer-1, DFO, α-Toc) or genetic inhibition by overexpressing GPX4. Interestingly, Era/BV6-induced cell death in ALL cells was independent of iron but dependent on ROS accumulation, since α-Toc rescued from Era/BV6-triggered ROS production, lipid peroxidation and cell death. Moreover, inhibition of lipid peroxide formation through the addition of Fer-1 or by overexpressing GPX4 failed to rescue from Era/BV6-triggered cell death, even if Era/BV6-stimulated lipid peroxidation was diminished. Likewise, Fer-1 protected from RSL3/BV6-, but not from Era/BV6-generated ROS production, leading to the assumption that other ROS besides lipid-based ROS contributed to cell death in Era/BV6-treated cells. In summary, while RSL3/BV6 induced ferroptosis in ALL, Era/BV6 stimulated a ROS dependent cell death, which was neither dependent on iron nor caspases or receptor-interacting protein (RIP) kinase 1 nor 3. Additionally, using Erastin alone did not trigger ferroptotic cell death in ALL. Finally, with these two studies we tried to unravel the molecular pathway of ferroptosis by using RSL3 and Erastin as well described ferroptosis stimulators. Here, we demonstrate the possibility of a novel treatment strategy to reactivate programmed cell death by impeding redox homeostasis in ALL.
Since ALL failed to induce ferroptosis upon Erastin treatment, we investigated in the third part of this thesis a new model system to induce ferroptosis upon Erastin and RSL3 exposure. Previous studies revealed that rhabdomyosarcoma (RMS) cells might be susceptible to oxidative stress-induced compounds. To this end, we used Erastin as a prototypic ferroptosis stimulus and GSH-depleting agent and demonstrated that GSH depletion, ROS and lipid ROS accumulation contributed to cell death. Additionally, Fer-1, Lip-1, DFO, lipophilic vitamin E derivate α-Toc and GSH, a cofactor of GPX4, protected from Erastin stimulated ROS accumulation, lipid peroxidation and cell death. Also, the use of a broad spectrum protein kinase C (PKC) inhibitor Bisindolylmaleimide I (Bim1), a PKCα and ß selective inhibitor Gö6976 and siRNA-mediated knockdown of PKCα suppressed Erastin-mediated cell death in RMS. Moreover broad spectrum nicotinamide-adenine dinucleotide phosphate (NADPH) oxidase (NOX) inhibitor Diphenyleneiodonium (DPI) and a more selective NOX1/4 isoform inhibitor GKT137831 abrogated Erastin-generated ROS formation, lipid peroxidation and cell death. With this, we demonstrate that RMS are vulnerable to ferroptotic cell death and investigated the molecular mechanism of ferroptosis by unravelling that PKC and NOX could have a pivotal role in ROS-mediated ferroptosis signalling in RMS. In this regard, ferroptosis inducers may act as a possible novel treatment strategy for RMS, especially those with poor clinical outcome.
Antimicrobial resistance became a serious threat to the worldwide public health in this century. A better understanding of the mechanisms, by which bacteria infect host cells and how the host counteracts against the invading pathogens, is an important subject of current research. Intracellular bacteria of the Salmonella genus have been frequently used as a model system for bacterial infections. Salmonella are ingested by contaminated food or water and cause gastroenteritis and typhoid fever in animals and humans. Once inside the gastrointestinal tract, Salmonella can invade intestinal epithelial cells. The host cell can fight against intracellular pathogens by a process called xenophagy. For complex systems, such as processes involved in the bacterial infection of cells, computational systems biology provides approaches to describe mathematically how these intertwined mechanisms in the cell function. Computational systems biology allows the analysis of biological systems at different levels of abstraction. Functional dependencies as well as dynamic behavior can be studied. In this thesis, we used the Petri net formalism to gain a better insight into bacterial infections and host defense mechanisms and to predict cellular behavior that can be tested experimentally. We also focused on the development of new computational methods.
In this work, the first realization of a mathematical model of the xenophagic capturing of Salmonella enterica serovar Typhimurium in epithelial cells was developed. The mathematical model expressed in the Petri net formalism was constructed in an iterative way of modeling and analyses. For the model verification, we analyzed the Petri net, including a computational performance of knockout experiments named in silico knockouts, which was established in this work. The in silico knockouts of the proposed Petri net are consistent with the published experimental perturbation studies and, thus, ensures the biological credibility of the Petri net. In silico knockouts that have not been experimentally investigated yet provide hypotheses for future investigations of the pathway.
To study the dynamic behavior of an epithelial cell infected with Salmonella enterica serovar Typhimurium, a stochastic Petri net was constructed. In experimental research, a decision like "Which incubation time is needed to infect half of the epithelial cells with Salmonella?" is based on experience or practicability. A mathematical model can help to answer these questions and improve experimental design. The stochastic Petri net models the cell at different stages of the Salmonella infection. We parameterized the model by a set of experimental data derived from different literature sources. The kinetic parameters of the stochastic Petri net determine the time evolution of the bacterial infection of a cell. The model captures the stochastic variation and heterogeneity of the intracellular Salmonella population of a single cell over time. The stochastic Petri net is a valuable tool to examine the dynamics of Salmonella infections in epithelial cells and generate valuable information for experimental design.
In the last part of this thesis, a novel theoretical method was introduced to perform knockout experiments in silico. The new concept of in silico knockouts is based on the computation of signal flows at steady state and allows the determination of knockout behavior that is comparable to experimental perturbation behavior. In this context, we established the concept of Manatee invariants and demonstrated the suitability of their application for in silico knockouts by reflecting biological dependencies from the signal initiation to the response. As a proof of principle, we applied the proposed concept of in silico knockouts to the Petri net of the xenophagic recognition of Salmonella. To enable the application of in silico knockouts for the scientific community, we implemented the novel method in the software isiKnock. isiKnock allows the automatized performance and visualization of in silico knockouts in signaling pathways expressed in the Petri net formalism. In conclusion, the knockout analysis provides a valuable method to verify computational models of signaling pathways, to detect inconsistencies in the current knowledge of a pathway, and to predict unknown pathway behavior.
In summary, the main contributions of this thesis are the Petri net of the xenophagic capturing of Salmonella enterica serovar Typhimurium in epithelial cells to study the knockout behavior and the stochastic Petri net of an epithelial cell infected with Salmonella enterica serovar Typhimurium to analyze the infection dynamics. Moreover, we established a new method for in silico knockouts, including the concept of Manatee invariants and the software isiKnock. The results of these studies are useful to a better understanding of bacterial infections and provide valuable model analysis techniques for the field of computational systems biology.
Heat stress transcription factors (Hsfs) have an essential role in heat stress response (HSR) and thermotolerance by controlling the expression of hundreds of genes including heat shock proteins (Hsps) with molecular chaperone functions. Hsf family in plants shows a striking multiplicity, with more than 20 members in many species. In Solanum lycopersicum HsfA1a was reported to act as the master regulator of the onset of HSR and therefore is essential for basal thermotolerance. Evidence for this was provided by the analysis of HsfA1a co-suppression (A1CS) transgenic plants, which exhibited hypersensitivity upon exposure to heat stress (HS) due to the inability of the plants to induce the expression of many HS-genes including HsfA2, HsfB1 and several Hsps. Completion of tomato genome sequencing allowed the completion of the Hsf inventory, which is consisted of 27 members, including another three HsfA1 genes, namely HsfA1b, HsfA1c and HsfA1e.
Consequently, the suppression effect of the short interference RNA in A1CS lin e was re-evaluated for all HsfA1 genes. We found that expression of all HsfA1 proteins was suppressed in A1CS protoplasts. This result suggested that the model of single master regulator needs to be re-examined.
Expression analysis revealed that HsfA1a is constitutively expressed in different tissues and in response to HS, while HsfA1c and HsfA1e are minimally expressed in general, and show an induction during fruit ripening and a weak upregulation in late HSR. Instead HsfA1b shows preferential expression in specific tissues and is strongly and rapidly induced in response to HS. At the protein level HsfA1b and HsfA1e are rapidly degraded while HsfA1a and HsfA1c show a higher stability. In addition, HsfA1a and HsfA1c show a nucleocytosolic distribution, while HsfA1b and HsfA1e a strong nuclear retention.
A major property of a master regulator in HSR is thought to be its ability to cause a strong transactivation of a wide range of genes required for the initial activation of protective mechanisms. GUS reporter assays as well as analysis of transcript levels of several endogenous transcripts in protoplasts transiently expressing HsfA1 proteins revealed that HsfA1a can stimulate the transcription of many genes, while the other Hsfs have weaker activity and only on limited set of target genes. The low activity of HsfA1c and HsfA1e can be attributed to the lower DNA capacity of the two factors as judged by a GUS reporter repressor assay.
HsfA1a has been shown to have synergistic activity with the stress induced HsfA2 and HsfB1. The formation of such complexes is considered as important for stimulation of transcription and long term stress adaptation. All HsfA1 members show synergistic activity with HsfA2, while only HsfA1a act as co-activator of HsfB1 and HsfA7. Interestingly, HsfA1b shows an exceptional synergistic activity with HsfA3, suggesting that different Hsf complexes might regulate different HS-related gene networks. Altogether these results suggest that HsfA1a has unique characteristics within HsfA1 subfamily. This result is interesting considering the very high sequencing similarity among HsfA1s, and particularly among HsfA1a and HsfA1c.
To understand the molecular basis of this discrepancy, a series of domain swapping mutants between HsfA1a and HsfA1c were generated. Oligomerization domain and C-terminal swaps did not affect the basal activity or co-activity of the proteins. Remarkably, an HsfA1a mutant harbouring the N-terminus of HsfA1c shows reduced activity and co-activity, while the reciprocal HsfA1c with the N-terminus of HsfA1a cause a gain of activity and enhanced DNA binding capacity.
Sequence analysis of the DBD of HsfA1 proteins revealed a divergence in the highly conserved C-terminus of the turn of β3-β4 sheet. As the vast majority of HsfA1 proteins, HsfA1a at this position comprises an Arg residue (R107), while HsfA1c a Leu and HsfA1e a Cys. An HsfA1a-R107L mutant has reduced DNA binding capacity and consequently activity. Therefore, the results presented here point to the essential function of this amino acid residue for DNA binding function. Interestingly, the mutation did not affect the activity of the protein on Hsp70-1, suggesting that the functionality of the DBD and consequently the transcription factor on different promoters with variable heat stress element number and architecture is dependent on structural peculiarities of the DBD.
In conclusion, the unique properties including expression pattern, transcriptional activities, stability, DBD-peculiarities are likely responsible for the dominant function of HsfA1a as a master regulator of HSR in tomato. Instead, other HsfA1-members are only participating in HSR or developmental regulations by regulating a specific set of genes. Furthermore, HsfA1b and HsfA1e are likely function as stress primers in specific tissues while HsfA1c as a co-regulator in mild HSR. Thereby, tomato subclass A1 presents another example of function diversity not only within the Hsf family but also within the Hsf-subfamily of closely related members. The diversification based on DBD peculiarities is likely to occur in potato as well. Therefore this might have eliminated the functional redundancy observed in other species such as Arabidopsis thaliana but has probably allowed the more refined regulation of Hsf networks possibly under different stress regimes, tissues and cell types.
Photolabile protecting groups (PPGs, cages, photocages) are molecules which can block the activity of a functional group and be removed by irradiation of light of an appropriate wavelength. One of the goals of this work was to design new photolabile protecting groups, based on a literature known one. The far-UV absorbing diethylamino benzyl (DEAMb) photocage, developed by Wang et al., was selected as structural basis for this work. In order to trigger the uncaging reaction with longer wavelengths (≥365 nm), thus allowing also biological applications, its structure was optimized. This was done by elongating the π-orbital conjugation using biphenyl derivatives instead of a single aromatic moiety. The photocage was loaded with glutamic acid as the leaving group.
The highest bathochromic shift was shown by compounds, which had the smallest sterical hindrance imposed on the second aromatic ring. The absorption spectrum was more redshifted if the second aromatic ring contained an electron withdrawing group. However, the stronger the substituents electron withdrawing strength was, the lower the uncaging quantum yield was. It was rationalized, that this is due to a decreased excited state electron density at the benzylic carbon of the DEAMb core which is necessary to trigger bond dissociation. This has been confirmed using TDDFT (time-dependent density functional theory) computations done by Jan von Cosel, Konstantin Falahati and Carsten Hamerla (from the group of Irene Burghardt). The best uncaging quantum yield was 42% for m-phenyl substituted DEAMb, while if a strong electron withdrawing group was present (nitro group), there was no photoactivity at all.
In order to achieve a better π-orbital conjugation of the non-coplanar biphenyl derivatives, a C-C bond was introduced between the benzylic carbon and the second aromatic ring. The resulting planar compounds belong to the fluorene class. The computational data predicted the photochemical meta effect to some extent to be preserved in these molecules. A set of fluorene derivatives was synthesized and photochemically characterized. The molar absorption coefficients of all prepared fluorene derivatives were higher than for any of the biphenyl derivatives. Quantum yields of the acetate release ranged between 3-42%, thus being as good as the best glutamic acid releasing biphenyl compounds. The highest uncaging cross section of the acetate release from the prepared fluorene derivatives was above 5000 M^-1 cm^-1. This value proves the high potential of the new fluorene based photocages developed in this work. Furthermore, release of hydroxide ion from fluorenol could be shown along with generation of, presumably, fluorenyl cation. These intriguing results paves a way for further exploration of fluorene based photocages for the release of bad leaving groups.
The second part of this work describes the custom synthesis of 13C labeled compounds for the VIPER (VIbrationally Promoted Electronic Resonance) project. In the VIPER pulse sequence, a molecule is vibrationally excited by a narrow band IR-pump pulse. The following Vis-pump pulse will promote the vibrationally pre-excited molecules to an electronically excited state. This Vis-pump pulse is offresonant for the not vibrationally pre-selected species and only resonant with the molecules, which are already pre-excited by the IR-pump pulse. Since the IR absorption bands usually are well resolved, a selective excitation of one molecule in an ensemble of similar ones is possible in the IR frequency range. Isotopologues and isotopomers are an extreme case of molecules which are near identical and differ only by isotopic composition or position. As a result in solution and at room temperature they have an identical UV-Vis absorption spectrum but different IR spectrum. This allows vibrational excitation of only one isotopologue (or isotopomer).
Isotopic labels were introduced in known photocages: 7-diethylamino coumarin (DEACM) and para-hydroxy phenacyl (pHP). The position for isotopic label incorporation in these molecules was guided by computations done by Jan von Cosel and Carsten Neumann. To allow control of the photoreactions in an ultrafast timescale, an IR active leaving group was used. The uncaging behavior of the prepared molecules in steady state was tested using chromatography (HPLC) and spectroscopy (1H NMR, FTIR and UV-Vis). The VIPER experiments were performed by Daniela Kern-Michler, Carsten Neumann, Nicole Mielke and Luuk van Wilderen (from the group of Jens Bredenbeck). A selective uncaging of only the vibrationally pre-excited molecules could be achieved.
Smut fungi (Ustilaginomycotina) were previously defined as plant parasites that produced blackish or brownish masses of teliospores in or on various organs of plants. Each teliospore germinates to form a single basidium with usually four basidiospores that subsequently grow as a saprobic, yeast-like, haploid stage. The Ustilaginomycotina are a highly diverse group with about 1,700 species in 115 different genera. All of the species were united in a single order, the Ustilaginales, in late 19th century. These teliospore producing fungi are now considered the classic smut fungi. Towards the end of the 20th century, new ideas were brought into this classification system. Most notable was the comparative work regarding the ultrastructure of septal pores and the anatomy of the interaction zones between host and parasite. This work changed the whole concept of smut fungi and their evolutionary relationships. These results were subsequently supported by molecular phylogenetic studies. Both lines of investigation led to the classification of the smut fungi into four different classes, Ustilaginomycetes, Exobasidiomycetes, Malasseziomycetes and Moniliellomycetes (see chapter 1.3).
A reliable taxonomy that reflects phylogenies needed in order to estimate the diversity and the relationships between the diverse groups of smut fungi. In the last 20 years, molecular investigations based mostly on rDNA loci, e.g. ITS (internal transcribed spacer) or LSU (large subunit), have revealed the evolutionary relationships between many taxa of smut fungi. However, there are few phylogenetic studies available for smut fungi (see chapter 1.5.1), and much work is needed to develop backbone phylogenetic trees and to resolve species complexes of many smut fungi.
This thesis reports the results of six different studies that aimed to develop new and improved tools for the phylogenetic analyses of smut fungi, and then apply these methods to selected groups of smut fungi. The first study (Kruse et al. 2017a, Chapter 3) developed a method to improve the amplification of ITS sequences of some smut fungi. Due to its high discrimination value, the ITS gene region is widely used as a barcoding locus for species delimitation of fungi. For this purpose, the general ITS primers ITS1 and ITS4 or more specific modifications, e.g. ITS1F for Ascomycota, ITS4B for Basidiomycota or M-ITS1 for smut fungi, were used. As these primer combinations often yielded unsatisfactory results, due to coamplification of other (contaminant) fungi or the host plant DNA, improvement of the amplification of the ITS region was needed. In order to design new smut specific primers for the ITS region, a representative set of several sequences of the flanking regions of the ITS region (LSU and SSU) of smut fungi, plants and other fungi were downloaded from GenBank. A set of primers was designed on this dataset. These primers were tested on a representative set of about 70 different smut genera under different PCR conditions. Finally, three different primers, one forward primer, smITS-F, and two reverse primers, smITS-R1 and -R2, were selected as the best ones. The following tests with different combinations of these primers, and also under inclusion of the M-ITS1 primer, showed only slight differences in the number of different genera that successfully amplified. But there were some differences regarding the genera that amplified. A broader test on 205 samples in 39 genera showed that the PCR efficiency of the newly designed primers was much better than the primer set ITS4/M-ITS1. With the primers designed in this study almost no non-target ITS was amplified, giving new opportunities especially for amplifying ancient DNA or DNA from older herbarium samples. However, many species groups remain unresolved by only one gene region.
The second study (Kruse et al. 2017c, Chapter 4) found new loci and suitable primers that better resolved multi-locus trees. To date, the most frequently used loci for making multi-locus trees are SSU (small subunit), LSU (large subunit) and ITS (internal transcribed spacer). While the LSU is not always sufficient to distinguish between closely related species, it is highly discriminative above the species level. In an effort to increase the phylogenetic resolution of smut phylogenies, some protein-coding genes were used, including rpb1, rpb2, and atp6 with varying success (see Chapter 2.1.2). As most of these loci are seldom used or sometimes only work on pure cultures because of their low specifity, new protein-coding loci were identified that produced reliable phylogenetic trees. Based on five available genomes, potential gene loci were filtered for possible primers. Initially, 40 different primer combinations for 14 gene loci were tested on a set of twelve different genera of smut fungi. The best candidates were selected and optimized during further tests. Finally, 22 different forward primers and 17 different reverse primers for nine different gene regions were developed, with each differentiating at least one genus of smut fungi (preferably for Ustilaginomycetes). The different primers showed varying discriminative power for different smut genera. They worked best for the Ustilaginaceae, based on the primer designed from Ustilaginomycetes genomes. These new primer sets and loci have the potential to resolve different species groups within the smut fungi and furthermore to produce reliable phylogenetic trees with high resolution. To prove their applicability, three species complexes were investigated in-depth, two from the Ustilaginomycetes and one from the Exobasidiomycetes.
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G-protein coupled receptors (GPCRs) are a predominant class of cell-surface receptors in eukaryotic life. They are responsible for the perception of a broad range of ligands and involved in a multitude of physiological functions. GPCRs are therefore of crucial interest for biological and pharmaceutical research. Molecular analysis and functional characterisation of GPCRs is frequently hampered by challenges in efficient large-scale production, non-destructive purification and long-term stability. Cell-free protein synthesis (CFPS) provides new production platforms for GPCRs by extracting the protein synthesis machinery of the cell in an open system that allows target-oriented modulations of the synthesis process and direct access to the nascent polypeptide chain. CFPS is fast, reliable and highly adaptable. Unfortunately, highly productive cell-free synthesis of GPCRs is often opposed by low product quality. This thesis was aimed to adapt and improve some of the new possibilities for the cell-free production of GPCRs in high yield and quality for structural and pharmaceutical analysis. An E. coli based CFPS system was applied to synthesise various turkey and human Beta-adrenergic receptor (Beta1AR) derivatives as well as human Endothelin receptors type A and B (ETA and ETB) constructs. Both receptor families are important drug targets and pharmacologically addressed in the treatment of several cardiovascular diseases. CF-synthesis was mainly performed in presence of nanodiscs (ND), which are reconstituted high density lipoprotein particles forming discoidal bilayer patches with a diameter varyring from 6 to approx. 15 nm. The supplementation of ND in the CF-synthesis reaction caused the co-translational solubilisation of the freshly synthesised GPCRs. The fraction of the solubilised GPCR that was correctly folded was analysed by the competence to bind its ligand alprenolol or Endothelin-1, respectively. Both the solubilisation efficiency and the ability to fold in a ligand binding competent state was strongly affected by the lipid composition of the supplied ND. Best results were generally achieved with lipids having phosphoglycerol headgroups and unsaturated fatty acid chains with 18 carbon atoms. Furthermore, thermostabilisation by introduction of point mutations had a large positive impact on the folding efficiency of both Beta1AR and ETB receptor. Formation of a conserved disulphide bridge in the extracellular region was additionally found to be crucial for the function of the ETB receptor. Disulphide bridge formation could be enhanced by applying a glutathione-based redox system in the CFPS. Further improvements in the quality of ETB receptor could be made by the enrichment of heat-shock chaperones in the CF-reaction. Depending on the receptor type and DNA-template, roughly 10 – 30 nmol (350 – 1500 µg) of protein could be synthesised in 1 ml of CF-reaction mixture. After the applied optimisation steps, the fractions of correctly folded receptor could be improved by several orders of magnitude and were finally in between 35% for the thermostabilised turkey Beta1AR, 9% for the thermostabilised ETB receptor, 6.5% for the non-stabilised ETB receptor, 1 - 5% for non-stabilised turkey Beta1AR and for human Beta1AR isoforms and 0.1% for ETA receptor. Therefore, between 2 and 120 µg of GPCR could be synthesised in a ligand binding competent form, depending on the receptor and its modifications. Correctly folded turkey Beta1AR and ETB receptors were thermostable at 30°C and could be stored at 4°C for several weeks after purification. Yields of the thermostabilised turkey Beta1AR were sufficient to purify the receptor in a two-step process by ligand-binding chromatography to obtain pure and correctly folded receptor in the lipid bilayer of a ND. Furthermore, a lipid dependent ligand screen could be demonstrated with the turkey Beta1AR and significant alterations in binding affinities to currently in-use pharmaceuticals were found. The established protocols are therefore suitable and highly competetive for a variety of applications such as screening of GPCR ligands, analysis of lipid effects on GPCR function or for the systematical biochemical characterisation of GPCRs. Most promising for future approaches appears to address the suspected bottlenecks of intial insertion of the GPCR-polypeptide chain in the ND bilayer and the thermal stability of the receptors. Nevertheless, the estabilised protocols for the analysed targets in this thesis are already highly competitive to previously published production protocols either in cell-based or cell-free systems with regard to yield of functional protein, speediness and costs. Moreover, the direct accessibility and other general characteristics of cell-free synthesis open a large variety of possible applications and this work can therefore contribute to the molecular characterisation of this important receptor type and to the development of new pharmaceuticals.
Lizards of Paraguay: an integrative approach to solve taxonomic problems in central South America
(2018)
Paraguay is located in the center of South America with drier and warmer climatic conditions in the western part of the country, and more temperate and humid in the eastern region. Biogeographically, Paraguay is a key spot in South America, where several ecoregions converge. In my study, I sampled most of the ecoregions of Paraguay. The main objective of my work is to solve taxonomic problems, identified through genetic barcoding analyses, in the central region of South America. To achieve this objective, I used selected taxa of the Paraguayan Squamata as models taking into consideration the crucial geographic position of the country, plus the scarce available genetic data of Paraguayan reptiles.
The collecting activities were performed in the framework of a barcoding inventory project of the Paraguayan herpetofauna and carried out mostly in rural areas searching for animals in different types of habitats using active search as the sampling technique.
For genetics, the extraction of DNA was performed with DNeasy® Blood & Tissue Kit of Qiagen® for sets of few samples, and the fiber glass plate protocol for sets of 96 samples. I assessed the quality of sequences after amplification in agarose gel electrophoresis. The first marker sequenced was 16S mtDNA, used for barcoding analysis. A DNA barcode is a genetic identifier for a species. Once a taxonomic problem was detected, I generate more gene sequences to target the issue.
All the analyses to test phylogenetic hypotheses (based on single genes or concatenated datasets) were performed under Maximum Likelihood and Bayesian approaches. To root the phylogenetic trees, I chose the available taxon (or taxa) most closely related to the respective studied group as outgroups. For the general tree of Paraguayan Squamata, based on barcodes of 16S, I chose Sphenodon punctatus.
I generated a total of 142 sequences of 64 species of Squamata from Paraguay (Appendix I). The final alignment of 615 bp comprised 249 samples. The best substitution model for the Barcoding dataset based on the gene 16S was GTR+G, according to the BIC.
To complement molecular evidence generated with the ML grouping of 16S barcodes, I took a morphological approach based on voucher specimens collected during fieldwork (usually the same specimens that I used for genetic analysis), supplemented by the revision of museum collections.
Summarizing my results, samples of Colobosaura exhibit large genetic distances, and accordingly I revalidated Colobosaura kraepelini (Appendix II). Tropidurus of the spinulosus group show two clades and among them there is little genetic and morphological variation, I synonymized T. tarara and T. teyumirim with T. lagunablanca, and T. guarani with T. spinulosus (Appendix III). I detected the presence of candidate species of Homonota, and I restricted the name H. horrida for Argentina, and described two new species of Homonota (Appendices IV and V), and a new species of Phyllopezus also in the Family Phyllodactylidae (Appendix VI).
In this work I present the most comprehensive analysis of genetic samples of Squamata from Paraguay. The results obtained here will be useful to help to clarify further taxonomic issues regarding the squamate fauna from the central region of South America. Moreover, the data generated for this study will have a positive impact in a larger geographic context, beyond Paraguayan borders.
Regarding the conservation of the Paraguayan reptiles, and considering the taxonomic changes accomplished here, it is important to note that many species lack legal protection. In Paraguay, the major problem for conservation is habitat loss due to extensive crop farming. Thus, currently, the protected areas are the best strategy for conservation of biodiversity in the country. However, many such areas face legal problems (e.g., lack of official measurements, management plans, forest guards, infrastructure, etc.) so that the maintenance of their biodiversity over time is not guaranteed.
In conclusion, in this study I present contributions on the taxonomy of mostly lizards from Paraguay. Due to lack of samples, I was not able to deal with a deep taxonomic revision of the country's snakes. Based on my results, I can argue that analyses of Xenodontini and Pseudoboini are currently a pressing research issue. This barcoding project may continue since some colleagues in Paraguay are interested in collaboration. Given that the sequenced specimens are yet a small portion of the actual diversity of Paraguay, it will be of utmost importance to continue and expand these studies that will further improve our taxonomic knowledge. Furthermore, it is desirable to have Paraguayan scientists not only involved, but to see them taking the lead of high quality taxonomic research.
Heat stress transcription factors (Hsfs) are required for transcriptional changes during heat stress (HS) thereby playing a crucial role in the heat stress response (HSR). The target genes of Hsfs include heat shock proteins (Hsps), other Hsfs and genes involved in protection of the cell from irreversible damages due to exposure to elevated temperatures. Among 27 Hsfs in Solanum lycopersicum, HsfA1a, HsfA2 and HsfB1 constitute a functional triad which regulates important aspects of the HSR. HsfA1a is constitutively expressed and described as the master regulator of stress response and thermotolerance. Activation of HsfA1a under elevated temperatures leads to the induction of HsfA2 and HsfB1 which further stimulate the transcription of HS-responsive genes by forming highly active complexes with HsfA1a. Despite the well-established role of these three Hsfs in tomato HSR, information about functional relevance of other Hsfs is currently missing.
The heat stress inducible HsfA7 belongs alongside with HsfA2 to a phylogenetically distinct clade. Thereby the two proteins share high homology and a functional redundancy has been assumed. However, HsfA7 function and contribution to stress responses have not been investigated into detail in any plant species.
Tomato HsfA7 protein accumulates already at moderately elevated temperatures (~35°C) while HsfA2 becomes dominant at higher temperatures (>40°C). HsfA7 pre-mRNA undergoes complex and temperature-dependent alternative splicing resulting in several transcripts that encode for three protein isoforms. HsfA7-I contains a functional nuclear export signal (NES) and shows nucleocytoplasmic shuttling while HsfA7-II and HsfA7-III have a truncated NES which leads to the strong nuclear retention of the protein. Differences in the nucleocytoplasmic equilibrium have a major impact on the stability of protein isoforms, as nuclear retention is associated with increased protein turnover. Consequently, HsfA7-I shows a higher stability and can be detected even after 24 hours of stress attenuation, while HsfA7-II is rapidly degraded. The degradation of these factors is mediated by the ubiquitin-proteasome pathway.
HsfA7 can physically interact with HsfA1a and HsfA3 and form co-activator (“superactivator”) complexes with a very high transcriptional activity as shown on different HS-inducible promoters. In order for the complex to be successfully transferred to the nucleus and confer its activity it needs a functional nuclear localization signal (NLS) of HsfA7. In contrast, the activator (AHA) motif of HsfA7 is not essential for its co-activator function. Interestingly, while interaction of HsfA7 with either HsfA3 or HsfA1a stabilizes HsfA7 isoforms, concomitantly this leads to an increased turnover of HsfA1a and HsfA3. In contrast, HsfA2 has a stabilizing effect on the master regulator HsfA1a.
Thus, HsfA7 knockout mutants generated by CRISPR/Cas9 gene editing, show increased HsfA1a levels and a stronger induction of HS-related genes at 35°C compared to wild-type plants and HsfA2 knockout mutants. Consequently, HsfA7 knockout seedlings exhibit increased thermotolerance as shown by the enhanced hypocotyl elongation under a prolonged mild stress treatment at 35°C. In summary, these results highlight the importance of HsfA7 in regulation of cellular responses at elevated temperatures. Under moderately elevated temperatures, the accumulation of HsfA7 and its subsequent interaction with HsfA1a, leads to increased turnover of the latter, thereby ensuring a milder transcriptional activation of temperature-responsive genes like Hsps. In turn, in response to further elevated temperatures, HsfA2 becomes the dominant stress-induced Hsf. HsfA2 forms co-activator complexes with HsfA1a which in contrast to HsfA7, allows the stabilization of the master regulator, leading to the stronger expression of HS-responsive genes required for survival. Thereby, this study uncovers a new regulatory mechanism, where the temperature-dependent competitive interaction of HsfA2 and HsfA7 with HsfA1a control the fate of the master regulator and consequently the activity of temperature-responsive networks.
Structured illumination microscopy (SIM) is part of the super-resolution methods developed at the beginning of this century. To produce a super-resolution image SIM requires three things: 1) illumination of the sample with a periodic pattern, 2) acquisition of multiple images per plane under different pattern’s phases and orientations and 3) the processing of these images has to be carried with a reconstruction algorithm. The result of the reconstruction is an image with a resolution gain that is proportional to the frequency of the pattern (po). The typical SIM set-up uses an epi-fluorescence configuration, thus the interference angle of the beams that create the pattern is restricted by the angular aperture of the objective. Under this restriction the maximum value of po is given by the cut-off frequency of the objective lens and sets at 2 the maximum resolution gain of SIM under linear illumination.
In the first part of this thesis we present the implementation and characterization of the 2D-SIM set-up designed by Dr. Bo-Jui Chang (B-J. Chang et al., PNAS 2017), this design exploits the concept introduced by light-sheet microscopy, i.e. separation of illumination and detection paths to obtain resolution gains larger than the usual two-fold (Chapter 3). The set-up is named coherent structured illumination light-sheet based fluorescence microscopy (csiLSFM) and it consists of a triangular array of three objectives, such that two are used for illumination and one for detection. With the independent illumination arms is possible to interfere two coherent light-sheets at angles beyond the angular aperture of the detection lens, attaining the maximum interference angle of 180° when the light-sheets counter-propagate. This condition delivers a pattern with a po 1.4 times larger than the cut-off frequency (ωo), hence our set-up provides generic resolution gains of 2.4.
The extraction of the high spatial frequencies that produce the resolution gain in the csiLSFM is a challenge due to a low pattern modulation. The low modulation inherently arises because the frequency associated to the pattern period lies beyond the cut-off frequency of the detection lens. To overcome this challenge we developed a filtering strategy that facilitates the withdrawal of information from a SIM data set, simultaneously the proposed filtering process optimizes the reconstruction algorithm by reducing the periodic artifacts that are recurrent in SIM images. In this same chapter we also performed an spectral analysis of the artifacts and determined that they originate from irregularities in the power spectrum that occur due to the partial or total lack of certain spatial frequencies (fig.4.2 and 4.3), our reconstruction reduces this information drops and diminishes the artifact occurrence. The relevance of our reconstruction pipeline is that it delivers a standardized process to enhance the SIM image in a current context in which the commonly used reconstruction algorithms employ empirical tuning to improve it (fig.4.13). Moreover, the pipeline is applicable to the csiLSFM data and also to images acquired with any other 2D-/3D-SIM set-up (fig.4.10 and 4.11).
The processing of various image data sets acquired with the csiLSFM exposed us to the question of how low the modulation of the illumination pattern can be before no super-resolution frequencies can be extracted. Answering this question is important to guarantee that the SIM data contains enough spatial frequencies to provide significant resolution gains. Thus in chapter 5 we developed a quantitative metric to indirectly determine the pattern modulation from the SIM data and find its critical value to use it as evaluation criterion. We called this metric the quality factor (Q-factor) and it represents the normalized strength (amplitude) of the extracted frequencies respect to the Gaussian noise contained in the images. Through simulations we estimated that Q=0.11 is a critical value and a SIM data set requires this as minimum value is to deliver a significant resolution gain. Q works then as an assessment tool for classifying SIM data as optimal or sub-optimal, i.e. Q≥0.11 or Q<0.11. We demonstrated such application with data acquired in various SIM commercial set-ups to prove its feasibility in the field (fig.5.6-5.11)
As mentioned at the beginning of this abstract SIM requires a specialized set-up and a processing algorithm to produce super-resolution images. This thesis contributes to these two areas in the following aspects: first, in its linear version a structured illumination microscope is highly associated to a 2-fold resolution gain. Here we demonstrated the possibility of extending this gain to 2.4 using our custom set-up the csiLSFM. Second, a reconstructed SIM image is prone to artifacts due to the mathematical process it undergoes, here we analyzed the artifact sources and identified them with drops of spatial information in the reconstructed spectrum, based on these conclusions we designed a processing pipeline to facilitate the extraction of spatial frequencies and directly reduce artifacts. A third and final outcome of this thesis is the development and practical implementation of a quantitative index to evaluate the quality of SIM data in terms of its relevant information content (Q-factor). Accordingly, the overall contributions of this work were done in the areas of SIM set-up, SIM reconstruction procedure and SIM data evaluation.