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Plastids are complex plant organelles fulfilling essential physiological functions, such as photosynthesis and amino acid metabolism. The majority of proteins required for these functions are encoded in the nuclear genome and synthesized on cytosolic ribosomes as precursors, which are subsequently translocated across the outer and inner membrane of the organelle. Their targeting to the organelle is ensured by a so called transit peptide, which is specifically recognized by GTP-dependent receptors Toc159 and Toc34 at the cytosolic side of outer envelope. They cooperatively regulate the insertion of the precursor protein into the channel protein Toc75, thereby initiating the translocation process. Toc34 is regarded as the primary receptor, while Toc159 probably provides the driving force for the insertion. Precursor transfer is achieved by the physical interaction between both receptors in the GTP loaded state. One translocon unit, also called the Toc core complex, is formed by four molecules Toc34, four molecules Toc75 and one molecule Toc159. In the GDP-loaded state, Toc34 preferably forms homodimers, whose physiological function was investigated in the presented study. It could be shown that the dissociation of GDP and therefore the nucleotide exchange are inhibited by the homodimeric state of Toc34. Dissociation of the homodimer is induced by the recognition of a precursor protein, which renders the binding of GTP and subsequent interaction with Toc159 possible. Thus, the homodimeric conformation could reflect an inactive state of the translocon, preventing GTP consumption in the absence of a precursor protein. Both homodimerization as well as heterodimerization of the receptor are regulated by phosphorylation, which could be demonstrated by in vitro and in vivo approaches using atToc33 from Arabidopsis thaliana as a model system. Since the phosphorylated form of Toc34 cannot be assembled with the Toc core complex, it can be concluded that the interactions between GTPase domains not only regulate the transfer of precursor proteins, but also warrant the integrity of the translocon.
Höhere Eukaryoten stellen ein Ensemble von Zellen dar, die in Kompartimente unterteilt sind. Somit sind intra- und interzelluläre Transportprozesse entscheidend für das Überleben dieser Zellverbände. In meiner Arbeit habe ich Evolution und Struktur von Translokationskomplexen untersucht, um einige Aspekte dieser komplexen Systeme zu untersuchen. Eingangs befassten wir uns mit Rezeptorsystemen am Beispiel des Proteintransports. Mittels phylogenetischer Analysen fanden wir heraus, dass Pex5 nicht der Urahn der anderen untersuchten 3-TPR-Domänen ist, obwohl Pex5 in allen eukaryotischen Organismen vorkommt. Ein Vergleich der 3-TPR-Domänen mit der restlichen Sequenz des Rezeptorproteins ergab, dass die 3-TPR-Domänen eine langsamere Evolutionsgeschwindigkeit aufweisen, was für eine Evolutionseinschränkung durch Interaktionspartner spricht. Sec72 ist möglicherweise aus einer TPR1 (Hop) Domäne entstanden und eine Funktion als Hsp70-erkennende Komponente des Sec-Komplexes für den post-translationalen Import kann daraus abgeleitet werden. „Recycling“ von 3-TPR-Domänen anderer Proteine konnten wir durch unsere phylogenetische Analyse auch für die zweite 3-TPR-Domäne von Tom34 nachweisen, die mit CYP40/FKBP51/52 clustert. Darüber hinaus war es uns möglich, die plastidär bzw. mitochondriell lokalisierten Formen von Toc64 phylogenetisch zu unterscheiden. Durch Erzeugung von Homologiemodellen konnten organellspezifische Aminosäuren strukturell eingeordnet werden. Dabei stellten wir fest, dass sich fast alle Positionen, die sich in der Aminosäurekomposition unterscheiden, auf der konvexen Seite der 3-TPR-Domäne befinden. Molekulardynamische Simulationen zeigten zudem deutliche Veränderung der Hauptbewegungen der 3-TPR-Domänen nach Komplexierung mit dem Hsp90-C-Terminus. Bei Bindung des Liganden werden intramolekulare Wasserstoffbrücken sowohl auf der konvexen als auch konkaven Seite der 3-TPR-Domäne „umgeschaltet“. Diese Erkenntnisse führen zu zwei Hypothesen: 1.) die Organellspezifität der Rezeptoren wird durch die Interaktion mit anderen Komplexpartnern garantiert und 2.) die Änderungen des Wasserstoffbrückennetzwerkes auf der konvexen Seite nach Hsp90-Bindung führen zur Ausbildung der Bindungsstelle für die andere Komplexkomponente. Beide Hypothesen erklären die experimentellen Beobachtungen bezüglich der Rezeptoren und warum keine phylogenetischen Hinweise für die Existenz von Vorstufenprotein-spezifischen Hsp70/90-Proteinen gefunden werden konnten. Nach dem Rezeptor haben wir uns mit dem Translokationsprozess befasst. Wir konnten phylogenetisch zeigen, dass sich Omp85 aus Proteobakterien im Vergleich zu Cyanobakterien und Eukaryoten insbesondere durch andersartige POTRA Domänen auszeichnet und fanden zwei konservierte Motive in der Porenregion. Zudem konnten wir im Heterokontophyten P. tricornutum ein vollständiges Omp85 identifizieren (bipartite Signalsequenz, 2 POTRAs, Pore mit langen Schleifen). Die Aminosäuresequenz weicht teils deutlich von den bekannten Omp85-Proteinen ab, was die Entdeckung erschwerte. Wir haben damit geklärt, dass auch im Translokationsapparat von komplexen Plastiden ein b-Fassprotein der Omp85 Familie die Kerneinheit bildet. Ebenfalls zu den Protein-transportierenden b-Fassproteinen gehört TolC, das aber im Gegensatz zu Omp85 auch andere Substanzen, wie zum Beispiel Siderophore transportiert. Alr2887 ist das einzige TolC-ähnliche Protein aus Anabaena sp. PCC7120. Vergleichende Phänotypuntersuchungen weisen auf eine Interaktion eines ABC-Transporters (DevBCA Operon) mit Alr2887 hin. Die Distanz zwischen äußerer Membran und Plasmamembran ist in Anabaena doppelt so groß wie in E. coli. Entsprechend fanden wir im Adapterprotein DevB eine stark verlängerte dimere Doppelwendel, die das von TolC gebildete a-Fass im Periplasma bis hin zum ABC-Transporter in der Plasmamembran theoretisch fortsetzen kann. Da verschiedenste in Anabaena existierende ABC-Transporter TolC als Abflusskanal benötigen, nehmen wir an, dass Alr2887 ein Rundumtalent in Bezug auf die zu transportierenden Substrate darstellt. Dieses ist auch aufgrund der basalen Einordnung im phylogenetischen Baum zu vermuten; es könnte somit auch in den „Multi-Drug-Efflux“ involviert sein. Nicht nur ABC-Transporter, auch TonB-abhängige Transporter stehen in funktionellem Zusammenhang mit TolC. Wir haben Aminosäuresequenzen von ~4600 TBDTs aus Gram-negativen Bakterien und Cyanobakterien zusammengetragen und nach ihrer paarweisen Ähnlichkeit geclustert. Anhand experimentell charakterisierter TBDTs mit bekannten Substraten und TBDTs mit vorhergesagten Substraten konnten wir sehr vielen Clustern ein Substrat zuordnen, das die in ihnen zusammengefassten TBDTs aller Wahrscheinlichkeit nach importieren. Wir konnten ferner feststellen, dass es noch eine Menge weiterer Cluster mit unbekannten Substratspezifitäten gibt und unsere Analysen stimulieren somit die Arbeiten an diesem System im Allgemeinen und in Cyanobakterien im Besonderen.
Die anaerobe Atmung mit Nitrat und Nitrit als terminalen Elektronenakzeptoren bildet einen wichtigen Teil des biologischen Stickstoff-Zyklus. Beispiele sind Denitrifikation und respiratorische Nitrat-Ammonifikation, wobei in beiden Fällen in einem ersten Schritt Nitrat zu Nitrit reduziert wird. In der Denitrifikation entstehen dann verschiedene gasförmige Produkte (NO, N2O, N2), wogegen Nitrit in der Ammonifikation ohne die Freisetzung weiterer Zwischenprodukte direkt zu Ammonium reduziert wird. Während die terminalen Reduktasen dieser Atmungsketten gut untersucht sind, ist das Wissen über die Zusammensetzung kompletter Elektronentransportketten sowie die Interaktion einzelner Proteine als auch zwischen den Proteinen und Chinonen in der Membran begrenzt. Ziel dieser Arbeit war die Charakterisierung der membranständigen Chinol-Dehydrogenasen NapGH und NrfH in der respiratorischen Nitrat-Ammonifikation von Wolinella succinogenes. Dieses Epsilonproteobakterium ist ein etablierter Modellorganismus der anaeroben Atmung und wächst durch respiratorische Nitrat-Ammonifikation mit Formiat oder H2 als Elektronendonoren. Als terminale Reduktasen werden dabei die periplasmatische Nitratreduktase NapA und die Cytochom c-Nitritreduktase NrfA benötigt. Die Genomsequenz weist keine weiteren typischen Nitrat- und Nitritreduktasen auf, und napA- und nrfA-defiziente Mutanten sind nicht in der Lage durch Nitrat- bzw. Nitritatmung wachsen. Das Operon des Nap-Systems (napAGHBFLD) von W. succinogenes kodiert Proteine, die an der Nitrat-Reduktion durch Menachinol beteiligt sind (NapA, -B, -G und -H) und Proteine, die für die Reifung und Prozessierung von NapA benötigt werden (NapF, -L und –D). Im Gegensatz zu vielen anderen Bakterien läuft die Nitrat-Atmung unabhängig von einem NapC-ähnlichen Protein ab, das als membrangebundenes Tetrahäm-Cytochrom c für die Chinol-Oxidation zuständig ist und Elektronen über den Elektronenüberträger NapB an die terminale Reduktase NapA liefert. Zwar sind im Genom zwei NapC-Homologe kodiert (FccC und NrfH), doch die Deletion beider Gene hatte keinen Einfluss auf die Nitrat-Atmung. Es wurde vermutet, dass die Funktion von NapC in W. succinogenes stattdessen durch die beiden Fe/S-Cluster Proteine NapG und NapH übernommen wird. Die Reduktion von Nitrit zu Ammonium wird durch den NrfHA-Komplex katalysiert. Das Pentahäm-Cytochrom c NrfA bildet dabei die katalytische Untereinheit, die über das membranständige Tetrahäm-Cytochrom c auf der periplasmatischen Seite der Membran gebunden ist. NrfH gehört zur NapC/NirT-Familie und überträgt Elektronen von Menachinol auf NrfA. Mittels gerichteter Mutagenese von nrfH wurden in früheren Arbeiten bereits Aminosäure-Reste identifiziert, die essentiell für die Elektronentransportaktivität von Formiat zu Nitrit sind.
Crista junctions (CJs) are important for mitochondrial organization and function, but the molecular basis of their formation and architecture is obscure. We have identified and characterized a mitochondrial membrane protein in yeast, Fcj1 (formation of CJ protein 1), which is specifically enriched in CJs. Cells lacking Fcj1 lack CJs, exhibit concentric stacks of inner membrane in the mitochondrial matrix, and show increased levels of F1FO–ATP synthase (F1FO) supercomplexes. Overexpression of Fcj1 leads to increased CJ formation, branching of cristae, enlargement of CJ diameter, and reduced levels of F1FO supercomplexes. Impairment of F1FO oligomer formation by deletion of its subunits e/g (Su e/g) causes CJ diameter enlargement and reduction of cristae tip numbers and promotes cristae branching. Fcj1 and Su e/g genetically interact. We propose a model in which the antagonism between Fcj1 and Su e/g locally modulates the F1FO oligomeric state, thereby controlling membrane curvature of cristae to generate CJs and cristae tips.
Diffusion of inner membrane proteins is a prerequisite for correct functionality of mitochondria. The complicated structure of tubular, vesicular or flat cristae and their small connections to the inner boundary membrane impose constraints on the mobility of proteins making their diffusion a very complicated process. Therefore we investigate the molecular transport along the main mitochondrial axis using highly accurate computational methods. Diffusion is modeled on a curvilinear surface reproducing the shape of mitochondrial inner membrane (IM). Monte Carlo simulations are carried out for topologies resembling both tubular and lamellar cristae, for a range of physiologically viable crista sizes and densities. Geometrical confinement induces up to several-fold reduction in apparent mobility. IM surface curvature per se generates transient anomalous diffusion (TAD), while finite and stable values of projected diffusion coefficients are recovered in a quasi-normal regime for short- and long-time limits. In both these cases, a simple area-scaling law is found sufficient to explain limiting diffusion coefficients for permeable cristae junctions, while asymmetric reduction of the junction permeability leads to strong but predictable variations in molecular motion rate. A geometry-based model is given as an illustration for the time-dependence of diffusivity when IM has tubular topology. Implications for experimental observations of diffusion along mitochondria using methods of optical microscopy are drawn out: a non-homogenous power law is proposed as a suitable approach to TAD. The data demonstrate that if not taken into account appropriately, geometrical effects lead to significant misinterpretation of molecular mobility measurements in cellular curvilinear membranes.
Oscillating magnetic field disrupts magnetic orientation in Zebra finches, Taeniopygia guttata
(2009)
Background Zebra finches can be trained to use the geomagnetic field as a directional cue for short distance orientation. The physical mechanisms underlying the primary processes of magnetoreception are, however, largely unknown. Two hypotheses of how birds perceive magnetic information are mainly discussed, one dealing with modulation of radical pair processes in retinal structures, the other assuming that iron deposits in the upper beak of the birds are involved. Oscillating magnetic fields in the MHz range disturb radical pair mechanisms but do not affect magnetic particles. Thus, application of such oscillating fields in behavioral experiments can be used as a diagnostic tool to decide between the two alternatives. Methods In a setup that eliminates all directional cues except the geomagnetic field zebra finches were trained to search for food in the magnetic north/south axis. The birds were then tested for orientation performance in two magnetic conditions. In condition 1 the horizontal component of the geomagnetic field was shifted by 90 degrees using a helmholtz coil. In condition 2 a high frequently oscillating field (1.156 MHz) was applied in addition to the shifted field. Another group of birds was trained to solve the orientation task, but with visual landmarks as directional cue. The birds were then tested for their orientation performance in the same magnetic conditions as applied for the first experiment. Results The zebra finches could be trained successfully to orient in the geomagnetic field for food search in the north/south axis. They were also well oriented in test condition 1, with the magnetic field shifted horizontally by 90 degrees. In contrast, when the oscillating field was added the directional choices during food search were randomly distributed. Birds that were trained to visually guided orientation showed no difference of orientation performance in the two magnetic conditions.
Background Different iron transport systems evolved in Gram-negative bacteria during evolution. Most of the transport systems depend on outer membrane localized TonB-dependent transporters (TBDTs), a periplasma-facing TonB protein and a plasma membrane localized machinery (ExbBD). So far, iron chelators (siderophores), oligosaccharides and polypeptides have been identified as substrates of TBDTs. For iron transport, three uptake systems are defined: the lactoferrin/transferrin binding proteins, the porphyrin-dependent transporters and the siderophore-dependent transporters. However, for cyanobacteria almost nothing is known about possible TonB-dependent uptake systems for iron or other substrates. Results We have screened all publicly available eubacterial genomes for sequences representing (putative) TBDTs. Based on sequence similarity, we identified 195 clusters, where elements of one cluster may possibly recognize similar substrates. For Anabaena sp. PCC 7120 we identified 22 genes as putative TBDTs covering almost all known TBDT subclasses. This is a high number of TBDTs compared to other cyanobacteria. The expression of the 22 putative TBDTs individually depends on the presence of iron, copper or nitrogen. Conclusions We exemplified on TBDTs the power of CLANS-based classification, which demonstrates its importance for future application in systems biology. In addition, the tentative substrate assignment based on characterized proteins will stimulate the research of TBDTs in different species. For cyanobacteria, the atypical dependence of TBDT gene expression on different nutrition points to a yet unknown regulatory mechanism. In addition, we were able to clarify a hypothesis of the absence of TonB in cyanobacteria by the identification of according sequences.
Vasculogenesis as well as angiogenesis are important for postnatal development of blood vessels. Peripheral blood or bone marrow-derived endothelial precursor cells are used in clinical trials for therapeutic enhancement of postnatal neovascularization in patients suffering from coronary artery diseases. The vasculogenic potential of the precursor cell population depends on the appropriate retention of the infused cells to the ischemic tissue. However, cell-autonomous mechanisms regulating the attraction and retention of circulating cells in inflammatory tissue are not well understood. Caspases belong to a family of pro-apoptotic enzymes. Beyond cell death signals, caspase proteases additionally regulate non-apoptotic processes like cell morphology and migration in many cell types. The isoform Caspase-8 is essential for embryonal vasculogenesis in conditional knockout mice. In this study, we identified a novel apoptosis-unrelated role of Caspase-8 in circulating and bone marrow-derived cells for vascular repair. Caspase-8-specific inhibition abrogated the ex vivo formation of EPC from human peripheral blood. Moreover, Caspase-8 inhibition disables EPC migration and adhesion to different matrices and decreases the cell surface expression of the fibronectin receptor subunit integrin alpha 5 and the chemokine receptor CXCR4. In vitro and in vivo studies using bone marrow mononuclear cells derived from inducible Caspase-8- deficient mice revealed an essential role of Caspase-8 for EPC formation and neovascularization enhancing capacities of progenitor cells. Caspase-8 activity appears to be required for maintaining responses to matrix interaction and chemoattractants of EPC. Additional studies showed that the E3 ubiquitin ligase Cbl-b, a negative regulator of cell adhesion molecules including integrin alpha 5, is present in EPC at low protein levels under basal conditions, but markedly increases upon Caspase-8 inhibition. In vitro assays and overexpression studies in intact cells confirmed Caspase-8-dependent degradation of Cbl-b, providing a potential requirement for Caspase-8-regulated adhesion. Indeed, neovascularization of matrigel plugs was enhanced in mice lacking Cbl-b. Moreover, Cbl-b degradation in the presence of active Caspase-8 prevents the down-regulation of integrin alpha 5 and is associated with an enhanced vasculogenic activity of progenitor cells in hind limb ischemia. The identified upstream regulation of caspase-8 by cytokine IL-6 is only one possibility for fine-tuning the non-apoptotic enzymatic activity. In summary, this study shows a novel essential role of Caspase-8 for proper EPC adhesion-related signaling. Caspase-8 is involved in the function of adhesion molecules by regulation the E3 ubiquitin ligase Cbl-b. Strategies to improve survival of therapeutic injected progenitor cells by using caspase inhibitors should be addressed with caution. Because of the broad spectrum of activity of caspase-8, downstream targets of this caspase isoform and Cbl-b should be in more focus for therapeutic pretreatment to improve neovascularization of myocardial and ischemic tissue.
Photosystem (PS) I is a huge membrane protein complex which coordinates around 200 co-factors. Upon light excitation a charge separation at the PS I reaction centre is induced which leads to an electron transport across the thylakoid membrane and the generation of redox equivalents needed for several biochemical reactions, e.g. the synthesis of sugars. For higher plants and cyanobacteria the crystal structure of PS I complexes were resolved to resolutions of 4.4 Å and 2.5 Å. Furthermore, supramolecular structures of PS I of eukaryotic algae, mainly of the green line, were obtained recently. However, up to now, no structure of diatoms is available yet. Diatoms are key players in global primary production and derived from a secondary endosymbiosis event. Their chloroplasts are surrounded by four envelope membranes and their thylakoids are evenly arranged in bands of three, i.e. no separation in grana and stroma regions is apparent. In this thesis a protocol was developed to isolate a functional PS I complex of diatoms which can be used for structural analysis by transmissional electron microscopy (TEM). A photosystem I-fucoxanthin chlorophyll protein (PS I-FCP) complex was isolated from the pennate diatom Phaeodactylum tricornutum by ion exchange chromatography. Spectroscopic analysis proved that bound Fcp polypeptides function as a light-harvesting complex. An active light energy transfer from Fcp associated pigments, Chl c and fucoxanthin, towards the PS I core was proven by fluorescence spectroscopy. Oxidised minus reduced difference spectroscopy evidenced the activity of the PS I reaction centre P700 and yielded a chlorophyll a/P700 ratio of approximately 200:1. These data indicate that the isolated PS I-FCP complex exceeds the PS I cores from cyanobacteria and higher plants in the numbers of chlorophyll a molecules. Because of the strict conservation of PS I cores among organisms the additional 100 chlorophyll a molecules must either be coordinated by Fcps or function as linker molecules between the Fcp antenna and the PS I core as shown for the PS I-LHC I complex of higher plants. To tell something about the structural organisation, the PS I-FCP complex was compared with its cyanobacterial and higher plant counterparts. Whereas cyanobacterial PS I cores aggregate to trimers, usually without associated antennae, higher plant PS I is a monomer and binds additionally two LHC I heterodimers. BN-PAGE and gel filtration experiments showed that also diatoms contain PS I monomers associated with Fcps as light-harvesting antenna. First TEM studies evidenced these observations. Negatively stained PS I-FCP particles had an increased size compared to PS I cores of other organisms. No PS I trimers or higher oligomers have been found. The calculated diameter and shape of the particles correspond to PS I-LHC I particles obtained from green algae, which also comprise of a higher number of LHC I polypeptides compared to the higher plant x-ray structure. Additionally, the analysis of polypeptides indicates that the PS I associated Fcps differ from the free Fcp pool and also from Fcps of a PS II enriched fraction. The assumption that diatoms harbour just one Fcp antenna that serve both Photosystems equally seems to be wrong. To further study the association of Fcps with the two Photosystems, both complexes plus the free FCP complexes were isolated from the centric diatom Cyclotella meneghiniana. Because of the availability of antibodies directed against specific Fcp polypeptides of Cyclotella the PS I-FCP complex of Phaeodactylum could not be used. A trimeric FCP complex, FCPa, and a higher FCP oligomer, FCPb, have already been described for C. meneghiniana. The latter is assumed to be composed of only Fcp5, whereas the FCPa contains Fcp2 and Fcp6. Biochemical and spectroscopical evidences revealed a different subset of associated Fcp polypeptides within the isolated photosystem complexes. Whereas the PS II associated Fcp antenna resembles FCPa, at least three different Fcp polypeptides are associated with PS I. By re-solubilisation of the PS I complex and a further purification step Fcp polypeptides were partially removed from PS I and both fractions were analysed again by biochemical and spectroscopical means, as well as by HPLC. Thereby Fcp4 and a so far undescribed 17 kDa Fcp were found to be strongly coupled to PS I, whereas another Fcp, presumably Fcp5, is only loosely bound to the PS I core. Thus an association of FCPb and PS I is assumed.
Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase
(2008)
In yeast, three small nucleolar RNAs (snoRNAs) are essential for the processing of pre-ribosomal RNA—U3, U14 and snR30—whereas 72 non-essential snoRNAs direct site-specific modification of pre-rRNA. We applied a quantitative screen for alterations in the pre-ribosome association to all 75 yeast snoRNAs in strains depleted of eight putative helicases implicated in 40S subunit synthesis. For the modification-guide snoRNAs, we found no clear evidence for the involvement of these helicases in the association or dissociation of pre-ribosomes. However, the DEAD box helicase Rok1 was required specifically for the release of snR30. Point mutations in motif I, but not in motif III, of the helicase domain of Rok1 impaired the release of snR30, but this was less marked than in strains depleted of Rok1, and resulted in a dominant-negative growth phenotype. Dissociation of U3 and U14 from pre-ribosomes is also dependent on helicases, suggesting that release of the essential snoRNAs might differ mechanistically from release of the modification-guide snoRNAs. Keywords: ribosome biogenesis; RNA helicase; snoRNA
Genetic engineering of baker’s and wine yeasts using formaldehyde hyperresistance-mediating plasmids
(1997)
Yeast multi-copy vectors carrying the for maldehyde-resistance marker gene SFA have proved to be a valuable tool for research on industrially used strains of Saccharomyces cerevisiae. The genetics of these strains is often poorly understood, and for various reasons it is not possible to simply subject these strains to protocols of genetic engineering that have been established for laboratory strains of S. cerevisiae. We tested our vectors and protocols using 10 randomly picked baker’s and wine yeasts all of which could be transformed by a simple protocol with vectors conferring hyperresistance to formaldehyde. The application of formaldehyde as a selecting agent also offers the advantage of its biodegradation to CO2 during fermentation, i.e., the selecting agent will be consumed and therefore its removal during down-stream processing is not necessary. Thus, this vector provides an expression system which is simple to apply and inexpensive to use. Key words: · Yeast · Transformation · Hyperresistance to formaldehyde
Central America is one of the world’s most herpetological diverse areas in relation to its size. Nicaragua is the largest country in this region and separates Nuclear from Lower Central America. It is one of the least herpetological explored countries in Central America and few studies dealing with the herpetofauna of a potion or the entire country have been published. I here update the checklist of the Nicaraguan herpetofauna, present taxonomic revisions of some difficult species complexes, compare the similarities of the composition of the herpetofaunal communities in the major forest formations present in the country within a zoogeographical context, and identify those species with a greater vulnerability risk in Nicaragua. Taxonomy The herpetofauna of Nicaragua currently consists of 244 species representing 134 genera and 42 families with 78 amphibian species representing 35 genera and 15 families, and 166 reptile species representing 99 genera and 27 families, which includes six marine species. Sixteen species (12 amphibians and four reptiles) are endemic to the country. Of the 12 endemic amphibian species, three are here described. In addition, five genera (Anotheca, Cerrophidion, Duellmanohyla, Isthmohyla, and Rhinobothryum) and two species (Rhadinea godmani and Urotheca decipiens) are known to occur both north and south of Nicaragua although there are no voucher specimens of these taxa to confirm their presence in country. I complete a bibliographic research updating the nomenclature changes and provide a brief herpetological history of Nicaragua, a recompilation of all species described upon Nicaraguan material and their current synonymy, the first time each species was recorded from the country, and a list of all recognized subspecies occurring in Nicaragua. I discuss the taxonomic uncertainties among the Nicaraguan populations of amphibians and reptiles and take further detailed taxonomic revisions on selected Nicaraguan species groups from the genera Anolis, Bolitoglossa, and Craugastor along their known distributional range. I describe five new species of herpetofauna (three of which are based on Nicaraguan material), redescribe five species of Anolis (three of which occur in Nicaragua), and provide voucher specimens of five other species for the first time in Nicaragua. In detail: • I studied the pholidosis, morphometrics as well as hemipenis and dewlap morphology in Anolis wermuthi, an anole endemic to the highlands of northern Nicaragua. I examine patterns of geographic variation using discriminant function analysis and discuss the characters that vary both individually and among populations. The results indicate that A. wermuthi is a single species with several disjunct, slightly divergent populations. I provide a standardized description, illustrations of the everted hemipenis of an adult topotype, the male and female dewlap, and a distribution map. I also provide brief descriptions of the localities where this species occurs and some ecological notes. • I studied the pholidosis, morphometrics as well as hemipenis morphology in the Central American anole species Anolis humilis, A. quaggulus, and A. uniformis. The three taxa are distinct in hemipenis morphology. However, very little differentiation in pholidotic and morphometric characters is documented. I document interspecific variation in several characters but with overlap of the documented ranges. A discriminant function analysis based on five pholidotic characters yielded a scatter diagram that showed large overlap between the clusters of the three taxa. I provide head scalation illustrations, an identification key, a distribution map, and standardized descriptions of the commonly distributed in Nicaragua A. quaggulus as well as of the other two species. • I describe two new species of anoles (genus Anolis) from Panama formerly referred to as Anolis limifrons. The two new species, Anolis apletophallus and Anolis cryptolimifrons, differ from A. limifrons by having a large bilobed hemipenis (small and unilobed in A. limifrons). The new species differ from each other in male dewlap size and coloration. I provide illustrations of the head scalation, everted hemipenis, and dewlap, an identification key, a distribution map, and standardized descriptions of the commonly distributed in Nicaragua A. limifrons and the two new species described herein. • I describe two new species of salamanders of Bolitoglossa from southern Nicaragua. Bolitoglossa indio is known from Río Indio in the lowlands of the Río San Juan area and Bolitoglossa insularis from the premontane slopes of Volcán Maderas on Ometepe Island. The two new species are of unknown affinities but both differ from their congeners in coloration. Bolitoglossa indio is most similar to B. mexicana and B. odonnelli from which differ by having both broad dorsolateral pale brown stripes not clearly delimited in outline. Bolitoglossa insularis is most similar to B. mombachoensis and B. striatula from which differ by the absence of dark or light defined stripes on dorsum and venter. • I describe a new species of frog of the genus Craugastor from Río San Juan, Nicaragua. The new species, Craugastor chingopetaca, is assigned to the fitzingeri group and differs from most Central American species of that group by the absence of a midgular pale stripe. Within the fitzingeri group it is most similar to C. crassidigitus and C. talamancae from which it differs in several morphological characteristics such as more extensive webbing, retuse disk covers on some digits, and relative toe length. • I provide voucher specimens of Cochranella spinosa, Kinosternon angustipons, Mesaspis moreletii, Cnemidophorus lemniscatus and Adelphicos quadrivirgatum for the first time in Nicaragua. I include descriptions, illustrations, and brief ecological notes for the five new country records. Zoogeography Based on the concept of ecological formations proposed by HOLDRIDGE (1967), nine forest formations are found in Nicaragua. Of the total number of terrestrial species of herpetofauna found in Nicaragua, 131 species (55.0%) occur in Lowland Wet Forest, 21 of which (8.8%) are restricted to this forest formation, 168 species (70.6%) occur in Lowland Moist Forest, 15 of which (6.3%) are restricted to this forest formation, 84 species (35.3%) occur in Lowland Dry Forest, four of which (1.7%) are restricted to this forest formation, 47 species (19.7%) occur in Lowland Arid Forest, with no species restricted to this forest formation, 59 species (24.8%) occur in Premontane Wet Forest, three of which (1.3%) are restricted to this forest formation, 116 species (48.7%) occur in Premontane Moist Forest, 10 of which (4.2%) are restricted to this forest formation, 51 (21.4%) species occur in Premontane Dry Forest, with no species restricted to this forest formation, 13 species (5.5%) occur in Lower Montane Wet Forest, two of which (0.8%) are restricted to this forest formation, and 50 species (21.0%) occur Lower Montane Moist Forest, seven of which (2.9%) are restricted to this forest formation. The Coefficient of Biogeographic Resemblance algorithm show a distinct composition of the herpetofauna from the isolated highlands of northeastern Nicaragua, which is characterized by a high proportion of endemic species. Two other clusters are evident when analyzing the herpetofaunal similarities among Nicaragua, the Pacific versant and the central mountains and the Atlantic lowlands. In addition, the Pacific lowlands are characterized by a relatively homogeneous composition of the herpetofauna. In contrast, many species have their northern limit of distribution in the Atlantic lowlands with the ranges of most of these species ending in southern Nicaragua. The central mountains constitute the southern limit of distribution of several highland species. In general, there is a greater contribution of reptile than amphibian species to the total herpetofauna present in each forest formation. This unbalance is slightly higher in the dry than in the moist parts of the country. The similarities in the composition of the reptiles between the different forests formations seem to be relatively distinct on an elevation factor, whereas in amphibians similarities might be better explained in correlation with humidity. The total amount of amphibian and reptile species in Nicaragua has a Middle American Element dominance and varies between amphibians and reptiles, with and a greater South American Element influence in anurans and a greater Old Northern Element influence in reptiles. In general, there is a greater percentage of species with a South American Element in extreme southeastern Nicaragua with a decreasing tendency towards northern Nicaragua. Taking in account the geography and geologic history of Nicaragua as well as the known Central American dispersal routes, I identify species of probable occurrence in Nicaragua as well as those places with a greater potential to hold undescribed endemic species. Conservation In Nicaragua, no amphibian or reptile populations are entirely free from anthropogenic impact. I determine the endangerment level of all Nicaraguan amphibian and reptile species using the IUCN categorizations and the Environmental Vulnerability Scores. Seventy-six species (31.9%) of Nicaraguan amphibians and terrestrial reptiles have high vulnerability, 118 (49.6%) medium vulnerability, and 44 (18.5%) low vulnerability. Eighteen species (7.4% of the total herpetofauna) are unknown from protected areas, including 13 high vulnerability species (three are endemic), four medium vulnerability species, and one low vulnerability species. To preserve the future of Nicaragua’s amphibians and reptiles, every species should reside in at least one protected area, the protected areas must be guarded, and monitoring programs are needed to detect changes in amphibian and reptile populations, prioritizing highly vulnerable species.
The reggie protein family consists of two homologous members, reggie-1 and reggie-2, also termed flotillin-2 and flotillin-1, respectively, that are ubiquitously expressed and evolutionarily well conserved, suggesting an important but so far ill-defined function. In various cell types, both reggies have been found to be constitutively associated with lipid rafts by means of acylation modifications and oligomerization. Lipid rafts are glycosphingolipid- and cholesterol-rich membrane microdomains which have been implicated in several cellular processes including membrane transport and signal transduction through growth factor receptors. However, the molecular details of these processes are still poorly understood. With the observation that reggies colocalize with activated glycosylphosphatidylinositolanchored proteins (GPI-APs) and Fyn kinase in rafts, a role for these proteins in signaling events has been suggested. In agreement with that, we have previously shown that reggie-1 becomes multiply tyrosine phosphorylated by Src kinases in response to epidermal growth factor (EGF) stimulation, pointing to a function for reggie-1 in growth factor signaling. Furthermore, overexpression of reggie-1 enhances spreading on fibronectin substrate in a tyrosine-dependent manner, thus revealing a role for reggie-1 in regulation of actin cytoskeleton through growth factor receptors. Due to the similarity shared by reggie proteins at amino acid level and to their ability to form hetero-oligomeric complexes, the first aim of this study was to analyze the putative tyrosine phosphorylation of reggie-2 in growth factor stimulated cells. Similarly to reggie-1, reggie-2 was found to be multiply tyrosine phosphorylated by Src kinase and to exist in a molecular complex with Src, with the degree of co-immunoprecipitation dependent on the activity of Src. Recent studies from us have also shown that administration of EGF results in the endocytosis of reggie-1 from the plasma membrane into endosomes, which is in line with a proposed role for reggies in membrane trafficking processes. In order to characterize in detail the endocytic mechanism that mediates the uptake of reggie-1, the dependency of reggie-1 endocytosis on clathrin and dynamin was investigated by means of overexpressing a variant form of Eps15 or a dominant negative form of dynamin-2. In either case the translocation of reggie-1 into endosomes in response to EGF was not affected, and this, together with the results that reggie-1 colocalized with cholera toxin (CTX) but not with transferrin receptor (TfnR) during EGF signaling, indicates that reggie-1 is taken up by means of a dynaminindependent, raft-mediated pathway. These findings are very well in line with recent data showing the pathway of entry into cells of reggie-2 as a raft-mediated endocytic pathway. The endocytosis of reggie-2 in response to EGF was also analyzed in this study. Similarly to reggie-1, in growth factor stimulated cells reggie-2 underwent a translocation from the plasma membrane to endosomes where the two reggies were found to colocalize with each other, suggesting that epidermal growth factor signaling might trigger the endocytosis of reggie oligomers. In addition, colocalization with both the late endosomal marker LAMP3/CD63 and epidermal growth factor receptor (EGFR) was detected, again indicating a function for reggies in signal transduction through growth factor receptors. EGFR has been reported to localize in rafts but, although this association is thought to be functional during EGF stimulation, how segregation of EGFR into rafts modulates its endocytosis and signaling is still under debate. Since reggie oligomers have recently been suggested to define a raft subtype, a further aim of this study was to investigate whether the depletion of reggies by means of small interfering RNA could interfere with the signaling and the trafficking through EGFR. Knockdown of reggie-2 resulted in an altered tyrosine phosphorylation of EGFR in response to EGF, while the degree of ubiquitination was not affected. Less efficient phosphorylation of tyrosine residues, especially of those which are docking sites for Grb2 and Shc, led in turn to an impaired activation of p38 and ERK1/2 MAPKs. Depletion of reggie-2 did not affect the early trafficking of activated EGFRs, with receptors being endocytosed and delivered to late endosomes as efficiently as in control cells. This would be in line with the normal degree of ubiquitination observed for EGFR, as ubiquitin moieties have been proposed to represent sorting tags that ensure receptor endocytosis into early endosomes and its proper intracellular trafficking. On the contrary, after prolonged EGF stimulation, depletion of reggie-2 resulted in a decreased downregulation of both receptor-bound ligand and EGFR, and in their accumulation in intracellular vesicles, thus pointing to a role for reggie-2 in the degradative pathway. Taken all together, these data ndicate that the association of EGFR with reggie-microdomains is likely to be important for proper receptor trafficking and signaling.
Background Multidirectional interactions in social (or communication) networks can have a profound effect on mate choice behavior. For example, Poecilia mexicana males show weaker expression of mating preferences when being observed by an audience male. It was suggested that this behavior is an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also by surrounding males, and/or because the audience male can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) during the 2nd part of the tests an empty transparent cylinder was presented (control); (2) an audience male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male sexually interacting with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results When comparing the strength of individual male preferences between the 1st and 2nd part of the tests (before and after presentation of an audience), male preferences declined slightly also during the control treatment (1). However, the decrease in strength of male preferences was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also seen when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusions When comparing the two 'non-specific sperm competition risk' treatments (2 and 3), a very strong effect was found only when the audience male could actually observe the focal male during mate choice in treatment (2). This suggests that focal males indeed attempt to conceal their mating preferences in the visual presence of other males so as to avoid mate choice copying. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Congruent with studies on other poeciliid species, our results also show that P. mexicana males respond to perceived specific sperm competition risk, and tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases (after mating with a rival male). However, this effect is comparatively weak.
This study focuses on structural features of a particular GPCR type, the family C GPCRs. Structure- and ligand-based approaches were adopted for prediction of novel mGluR5 binding ligand and their binding modes. The objectives of this study were: 1. An analysis of function and structural implication of amino acids in the TM region of family C GPCRs. 2. The prediction of the TM domain structure of mGluR5. 3. The discovery of novel selective allosteric modulators of mGluR5 by virtual screening. 4. The prediction of a ligand binding mode for the allosteric binding site in mGluR5. GPCRs are a super-family of structurally related proteins although their primary amino acid sequence can be diverse. Using sequence information a conservation analysis of family C GPCRs should be applied to reveal characteristic differences and similarities with respect function, folding and ligand binding. Using experimental data and conservation analysis the allosteric binding site of mGluR5 should be characterized regarding NAM and PAM and selective ligand binding. For further evaluation experimental knowledge about family A GPCRs as well as conservation between vertebrate rhodopsins was planned to be compared to results obtained for family C GPCRs (Section 4.1 Conservation analysis of family C GPCRs). Since no receptor structure is available for any family C GPCR, discussion of conserved sequence positions between family A and C GPCRs requires the prediction of a receptor structure for mGluR5 using a family A receptor as template. In order to predict the mGluR5 structure a sequence alignment to a GPCR template protein will have to be proposed and GPCR specific features considered in structure calculation (Section 4.1.4 Structure prediction of mGluR5). The obtained structure was intended to be involved in ligand binding mode prediction of newly discovered active molecules. For discovery of novel selective mGluR modulators several ligand-based virtual screening protocols were adapted and evaluated. Prediction models were derived for selection of possibly active molecules using a diverse collection of known mGluR binding ligands. For that purpose a data collection of known mGluR binding ligands should be established and this reference collection analyzed with respect to different ligand activity classes, NAM or PAM and selective modulators. The prediction of novel NAMs and PAMs using several combinations of 2D-, 3D-, pharmacophore or molecule shape encoding methods with machine learning techniques and similarity determining methods should be tested in a prospective manner (Section 4.2 Virtual screening for novel mGluR modulators). In collaboration with Merz Pharmaceuticals (Merz GmbH & Co. KGaA, Frankfurt am Main, Germany) the modulating effect of a few hundred molecules should be approved in a functional cell-based assay. With the objective to predict a binding mode of the discovered active molecules, molecule docking should be applied using the allosteric binding site of the modeled mGluR5 structure (Section 4.2.4 Modeling of binding modes). Predicted ligand binding modes are to be correlated to conservation profiles that had resulted from the sequence-based entropy analysis and information from mutation experiments, and shall be compared to known ligand binding poses from crystal structures of family A GPCRs.
The growth of blood vessels is crucial for organ growth in the embryo and repair of wounded tissues in the adult. An imbalance in this process contributes to numerous malignant, inflammatory, ischemic, infectious and immune disorders (Ferrara et al., 2003). Postnatal neovascularization occurs through the recruitment of progenitor cells and angiogenesis. Integrins are heterodimeric cell surface molecules and are the main receptors for extracellular matrix proteins. Regulation of integrin activation is crucial during embryonic development and during adult life. Dysregulation of integrin activity leads to severe diseases. In this study, we have demonstrated that Rap1, a small GTPase regulating integrin activity, and its GEF Epac1 are expressed in both EPC and endothelial cells. Moreover, the pharmacological activator of Epac activates the small GTPase Rap1 in progenitor cells. In parallel the angiogenic growth factors VEGF and bFGF activate Rap1 in endothelial cells. In addition, the regulation of Rap1 activity in EPC and in endothelial cells plays an important role in the regulation of migration and adhesion to matrix proteins, by regulating the activity of different integrins, a mechanism known as integrin inside‐out signaling. Furthermore, regulation of Rap1 activity affects probably indirectly through outside‐in signaling of integrins the activity of several and crucial proteins such PKB/Akt and focal adhesion kinase in endothelial cells. In line with these results, we have demonstrated that Rap1 activity affect angiogenesis, homing of EPC to ischemic tissues and thereby postnatal neovascularization. The understanding how Rap1 regulates integrin activity in endothelial cells is still not completely clear, for example we have demonstrated that the known effectors of Rap1 mediating the increase of integrin activity in T and B cells, such as RAPL and RIAM are, respectively, either not increasing integrin activity or not expressed in endothelial cells. We aim to find the effector of Rap1 promoting integrin activity in endothelial cells and how RAPL regulates integrin functions and angiogenesis. Moreover data from us and others using genetic models and generation of Rap1a or Rap1b deficient mice or deficient for Rap1a and Rap1b led to embryonic lethality suggesting that Rap1 is a key node protein during embryonic development. The development of conditionnal Rap1a/b endothelial/pericytes restricted deficient mice will help us to decipher more precisely the role of Rap1 during vascular development and angiogenesis.
Protein kinases are targets for drug development. Dysregulation of kinase activity leads to various diseases, e.g. cancer, inflammation, diabetes. Human polo-like kinase 1 (Plk1), a serine/threonine kinase, is a cancer-relevant gene and a potential drug target which attracts increasing attention in the field of cancer therapy. Plk1 is a key player in mitosis and modulates entry into mitosis and the spindle checkpoint at the meta-/anaphase transition. Plk1 overexpression is observed in various human tumors, and it is a negative prognostic factor for cancer patients. The same catalytical mechanism and the same co-substrate (ATP) lead to the problem of inhibitor selectivity. A strategy to solve this problem is represented by targeting the inactive conformation of kinases. Kinases undergo conformational changes between active and inactive conformation and thus an additional hydrophobic pocket is created in the inactive conformation where the surrounding amino acids are less conserved. A "homology model" of the inactive conformation of Plk1 was constructed, as the crystal structure in its inactive conformation is unknown. A crystal structure of Aurora A kinase served as template structure. With this homology model a receptor-based pharmacophore search was performed using SYBYL7.3 software. The raw hits were filtered using physico-chemical properties. The resulting hits were docked using Gold3.2 software, and 13 candidates for biological testing were manually selected. Three compounds of the 13 tested exhibit anti-proliferative effects in HeLa cancer cells. The most potent inhibitor, SBE13, was further tested in various other cancer cell lines of different origins and displayed EC50 values between 12 microM and 39 microM. Cancer cells incubated with SBE13 showed induction of apoptosis, detected by PARP (Poly-Adenosyl-Ribose-Polymerase) cleavage, caspase 9 activation and DAPI staining of apoptotic nuclei.
The C-module-binding factor (CbfA) is a multidomain protein that belongs to the family of jumonji-type (JmjC) transcription regulators. In the social amoeba Dictyostelium discoideum, CbfA regulates gene expression during the unicellular growth phase and multicellular development. CbfA and a related D. discoideum CbfA-like protein, CbfB, share a paralogous domain arrangement that includes the JmjC domain, presumably a chromatin-remodeling activity, and two zinc finger-like (ZF) motifs. On the other hand, the CbfA and CbfB proteins have completely different carboxy-terminal domains, suggesting that the plasticity of such domains may have contributed to the adaptation of the CbfA-like transcription factors to the rapid genome evolution in the dictyostelid clade. To support this hypothesis we performed DNA microarray and real-time RT-PCR measurements and found that CbfA regulates at least 160 genes during the vegetative growth of D. discoideum cells. Functional annotation of these genes revealed that CbfA predominantly controls the expression of gene products involved in housekeeping functions, such as carbohydrate, purine nucleoside/nucleotide, and amino acid metabolism. The CbfA protein displays two different mechanisms of gene regulation. The expression of one set of CbfA-dependent genes requires at least the JmjC/ZF domain of the CbfA protein and thus may depend on chromatin modulation. Regulation of the larger group of genes, however, does not depend on the entire CbfA protein and requires only the carboxy-terminal domain of CbfA (CbfA-CTD). An AT-hook motif located in CbfA-CTD, which is known to mediate DNA binding to A+T-rich sequences in vitro, contributed to CbfA-CTD-dependent gene regulatory functions in vivo.
Mammalian retinae have rod photoreceptors for night vision and cone photoreceptors for daylight and colour vision. For colour discrimination, most mammals possess two cone populations with two visual pigments (opsins) that have absorption maxima at short wavelengths (blue or ultraviolet light) and long wavelengths (green or red light). Microchiropteran bats, which use echolocation to navigate and forage in complete darkness, have long been considered to have pure rod retinae. Here we use opsin immunohistochemistry to show that two phyllostomid microbats, Glossophaga soricina and Carollia perspicillata, possess a significant population of cones and express two cone opsins, a shortwave-sensitive (S) opsin and a longwave-sensitive (L) opsin. A substantial population of cones expresses S opsin exclusively, whereas the other cones mostly coexpress L and S opsin. S opsin gene analysis suggests ultraviolet (UV, wavelengths <400 nm) sensitivity, and corneal electroretinogram recordings reveal an elevated sensitivity to UV light which is mediated by an S cone visual pigment. Therefore bats have retained the ancestral UV tuning of the S cone pigment. We conclude that bats have the prerequisite for daylight vision, dichromatic colour vision, and UV vision. For bats, the UV-sensitive cones may be advantageous for visual orientation at twilight, predator avoidance, and detection of UV-reflecting flowers for those that feed on nectar.
Drought and salt stress are the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought and high-salinity tolerance is therefore of outmost importance for breeding. However, the complexity of these traits allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26bp long fragments (26bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms.
Many questions regarding gastropod phylogeny have not yet been answered like the molecular confirmation of the Heterobranchia concept based on morphological studies from Haszprunar (1985a; 1988). This taxon contains the “Lower Heterobranchia” with several “primitive” or “basal” members) and the Euthyneura (with the Opisthobranchia and Pulmonata). Phylogenetic relationships of subgroups within the Heterobranchia have not been satisfactorily resolved and monophyly of some taxa within the Heterobranchia (e.g. Opisthobranchia) is questionable. Moreover, most of the “Lower Heterobranchia” have not been included in former molecular studies. In order to resolve phylogenetic relationships within the Heterobranchia, I pursued a molecular systematic approach by sequencing and analysing a variety of genetic markers (including nuclear 28S rDNA + 18S rDNA and mitochondrial 16S rDNA + COI sequences). Maximum likelihood as well as Bayesian inference methods were used for phylogenetic reconstruction. The data were investigated a priori to tree reconstruction in order to find the most appropriate dataset for reconstructing heterobranch phylogeny. A variety of statistical tests (like Chi-Square-Test or Relative-Rate-Test) were applied and the substitution saturation was measured. The Relative-Rate-Test revealed the highest evolution rates within the “Lower Heterobranchia” (Omalogyra sp., Omalogyra fusca, Murchisonella sp., Ebala sp. and Architectonica perspectiva) and Opisthobranchia (Hyalocylis striata). Furthermore, many of the nucleotide positions show a high degree of substitution saturation. Additionally, bipartitions (splits) in the alignment were examined and visualized by split network analyses to estimate data quality. A high level of conflict indicated by many parallel edges of the same lengths could be observed in the neighbournet graphs. Moreover, several taxa with long terminal branches could be identified in all three datasets belonging to the Vetigastropoda, Caenogastropoda, “Lower Heterobranchia” or Opisthobranchia (Nudipleura). All phylogenetic analyses revealed a monophyletic Heterobranchia. Within the Heterobranchia several well supported clades could be resolved. However, the traditional classification based on morphological data could not be confirmed due to paraphyletic Euthyneura (because of the inclusion of the Pyramidellidae and Glacidorboidea) as well as paraphyletic Pulmonata and polyphyletic Opisthobranchia. Based on the phylogenetic inferred evolutionary trends regarding habitat colonisation or character complexes could be deduced. A case study was conducted in order to estimate divergence ages using a “relaxed” molecular clock approach with fossils as minimum age constraints. However, due to large 95% confidence intervals a precise dating of the nodes was not possible. Hence, the results are considered as preliminary. To test the plausibility of the newly obtained hypotheses, the results were evaluated a posteriori using a hypothesis test and secondary structures of the complete 18S rRNA and 28S rRNA. Secondary structure motifs were found within domain 43 and E23 2 &5 of the 18S rRNA as well as within domain E11 and G5_1 of the 28S rRNA, which contain phylogenetic signals to support various groups within the Heterobranchia. In addition, taxon specific motifs were found separating the Vetigastropoda from the Caenogastropoda and Heterobranchia, indicating a possible application of the secondary structure of 18S rRNA and 28S rRNA to reveal phylogenetic relationships at higher taxonomic levels such as Gastropoda or even Mollusca. The utility of the newly invented software RNAsalsa for the reconstruction of secondary structures was tested. The obtained structures were used to adjust evolutionary models specific to rRNA stem (paired basepairs) and loop (unpaired basepairs) regions with the intention of improving phylogenetic results. This approach proved unsuccessful. This molecular phylogenetic investigation provides the most comprehensive molecular study of Heterobranchia relationships to date. Substantial insights into the evolution and phylogeny of this enigmatic taxon have been gained.
Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.
Today the structure of photosystem II, which is the enzyme responsible for the evolution of molecular oxygen by plants, algae and cyanobacteria, is known up to a resolution of about 3.0 Å in cyanobacteria (Loll et al., 2005). Photosystem II of higher plants, which shows some differences compared to the photosystem II of cyanobacteria, is not resolved in such high detail, yet (8-10 Å) (Rhee et al., 1998; Hankamer et al., 2001a). Therefore, the molecular structure of PSII of higher plants and its adjacent antenna complexes remains in the focus of the current research. One of the major problems when working with photosystem II is its relative instability during isolation. Together with the antenna proteins and several other proteins, some of which still have an unclear function, PSII forms a huge multi-protein-complex, which tends to fall apart during classical preparation methods. In order to achieve a faster and milder method of purification for PSII, four different His-tags have been added to one of the subunits of PSII. The gene targeted in this study is called psbE and codes for the α-chain of cytochrome b559, an integral part of PSII. The gene for PsbE is encoded in the chloroplast genome. The His-tags, which were employed in this work, consist of six or ten consecutive histidine aminoacid residues, which were fused to the N-terminus of the protein, either with or without a cleavage site for the protease “Factor Xa”. The N-terminus of PsbE is located on the more accessible stromal side of the thylakoid membrane. After inserting the psbE gene in a vector plasmid, in which the recognition site for the restriction endonuclease SacI had been eliminated, the different His-tags were generated by PCR with purposefully altered primers. In a final cloning step, a gene, which confers resistance to the antibiotics spectinomycin and streptomycin, was added to the DNA construct. Subsequently, the so-called biolistic transformation method (“gene gun”) was applied to introduce this genetically engineered plasmid DNA to Nicotiana tabacum chloroplasts (Bock & Hagemann, 2000). Through the processes of homologous recombination that take place in the chloroplast, the plastid encoded wildtype psbE gene was replaced by its His-tag containing counterparts. After several rounds of regenerating plants on antibiotic-containing medium, successful transformation was confirmed through PCR methods. By self fertilisation of fully regenerated plants, seeds were produced from tobacco strains, which carried only the mutated psbE gene. Plants cultivated from these seeds showed no distinctive phenotype under the chosen growth conditions, in respect to wildtype plants. The presence of the His-tag in this F1 generation was again confirmed with PCR methods. Measurements of oxygen evolution and pulse amplitude modulated fluorescence (PAM), carried out with preparations of wildtype and transgenic tobacco strains, revealed no differences for photochemical or non-photochemical quenching between both types. However, the oxygen evolution capacity of transgenic tobacco thylakoids compared to the wildtype was significantly reduced, although the chlorophyll content in relation to the leaf area was almost identical. This hints at a reduced amount of photosystem II complexes in the thylakoid membranes of transgenic tobacco. This alteration could be related to the mutation of cytochrome b559, because, amongst other functions, this subunit was shown to be important for the assembly of photosystem II (Morais et al., 1998). If solubilised thylakoid preparations of His-tagged plant strains were applied to a Ni-NTA column, photosystem II was selectively bound to the matrix. After washing away most of the contaminations, photosystem II core complexes could be eluted with imidazole-containing buffer. Photosystem II prepared in this way, displayed a drastic reduction of the peripheral light-harvesting complexes (LHCI & LHCII) and photo-system I reaction centres. This could be demonstrated by the loss of chlorophyll b and xanthophyll bands (LHCs) in absorption spectra, a small blue-shift of the chlorophyll a Qy absorption (PSI) and the respective band patterns in polyacrylamide gel electro-phoresis. The photosystem II complexes prepared in this way can now be put to use in different structural studies, like two-dimensional or three-dimensional crystallisation and spectroscopic measurements. Another photosynthetic pigment-protein complex of interest is the fucoxanthin-chlorophyll a/c-binding protein of diatoms, because eukaryotic algae, like diatoms, are important factors of oceanic ecosystems and account for a large part of marine biomass production. In order to facilitate ultra-fast time-resolved transient absorption spectroscopy and subsequent modelling of the kinetic traces, FCPs were prepared by sucrose-gradient ultra-centrifugation and their pigment stoichiometries determined by HPLC. Combining the spectroscopic data (Papagiannakis et al., 2005) with protein sequence alignments (Eppard & Rhiel, 1998) and the structure of the homologous higher plant LHCIIb (Kühlbrandt et al., 1994), a hypothetical model for the structure of FCP could be proposed (Fig. IV.3)
Photosystem II (PSII) is a polypeptide-cofactor complex organised as a homodimeric multisubunit protein embedded in the thylakoid membrane. PSII monomers are heterooligomers related to each other by a pseudo-twofold axis perpendicular to the membrane plane (Loll et al. 2005). PSII acts as a photochemical enzyme that through the chlorophylls and the other cofactors catalyses photon capture and electron transfer from water to the plastoquinone pool with concomitant evolution of oxygen. Photon capture and charge separation take place in the PSII core which consists of the D1 and D2 proteins, the cytochrome b559 alpha- and beta-chains (PsbE and F subunits) and the chlorophyll a-binding antenna proteins CP43 and CP47 (Loll et al. 2005). The remaining polypeptides are low molecular mass proteins with not clearly understood fuctions; they include chloroplast-encoded (PsbH, I, J, K, L, M, N, T and Z) and nucleus-encoded (PsbR, S, W and X) proteins consisting of one to four transmembrane helices (Barber et al. 1997). The oxygen-evolving part of PSII consists of a Mn-Ca transition complex called Mn cluster or oxygen evolving complex that is situated on the luminal side of PSII. In higher plants it is stabilised by the PsbO (33 kDa), PsbP (23 kDa) and PsbQ (17 kDa) extrinsic subunits (Soursa et al. 2006; Ifuku et al. 2005). The structure and mechanisms related to the oxygen evolving complex of PSII are not completely clarified. Currently two high resolution structures from the cyanobacteria S. elongatus are available (Loll et al. 2005; Ferreira et al. 2004) Nevertheless structural information is not as well defined in green algae and higher plants as in cyanobacteria. In fact the 8Å structure available from spinach has too low resolution for addressing questions such as the structural and functional differences in respect to PSII from cyanobateria (Rhee et al. 1997).. Therefore it is obvious that for PSII from higher plants the main general questions are still open: is the structure of PSII from higher plants equivalent to the structures observed in cyanobacteria? Is the typical higher plants subunit PsbS stably or transiently bound to PSII? Finding an answer to these questions was the main focus of this work. In this work a simple and rapid protocol to isolate the oxygen-evolving photosystem II (PSII) core complex from Nicotiana tabacum was developed. A PSII having a His-tag extension made of six or ten consecutive histidine residues at the N-terminus of the PsbE subunit was purified by a single-step Ni2+ NTA-affinity column chromatography after solubilisation of the thylakoid membranes using different mild detergents. Characterization of the oxygen evolution and the subunit composition by immunoblotting and mass spectroscopy revealed that the His-tagging did not affect the functional integrity of the PSII reaction center. The final PSII core complex was purified in a single step from solubilised thylakoids in less than 14 hours getting a very pure sample in high amount. The isolated core complex was in a dimeric form as demonstrated by Blue Native PAGE, analytical gel filtration and single particles analysis; with a molecular mass of about 500 kDa, consisting of D1, D2, CP43, CP47, 33 kDa and low molecular weight proteins. The preparation retains a high rate of oxygen-evolving activity but showed different stabilities of the binding of the three extrinsic proteins. The subunit of 33 kDa was always present in the preparations with a constant amount, whereas the 23 and 17 kDa subunits were always in less and unconstant amounts. Nevertheless the oxygen evolution was not depending on the amount of the 23 and 17 kDa subunits. Furthermore the preparation showed a high oxygen-evolving activity of 1390 micromol/mg Chl·h-1 in presence of betaine, while its activity was 440-680 micromol/mg Chl·h-1 in its absence. The presence of 1.0 mol/L betaine during the isolation of PSII increased the preservation of the photochemical activity hence the oxygen evolution. It was inferred from these results that His-tagging does not affect the functional and structural integrity of the PSII core complex and that the “Histag strategy” is highly useful for biochemical, physicochemical and structural studies of higher plant PSII. PSII is directly involved in two essential processes, the efficient capture and funnelling of light energy to the reaction centre and the controlled dissipation of excess excitation energy. Those functions require structural and functional flexibility in order to be performed with high efficiency. Moreover light-harvesting proteins respond to an external signal, the thylakoid pH, to induce feedback control regulating those activities in every moment. This process called non-photochemical quenching (NPQ) is mainly depending on the xanthophyll cycle and the PsbS protein (Szabo et al. 2005). In this work several new evidences related with those two processes were found. The subunit PsbS is a polypeptide whose involvement in the NPQ processes is debated. Nevertheless, its position in the PSII complex and the mechanisms by which this subunit contributes to carry out the NPQ functions are not definitely known. In addition it is not sure if it is a pigment binding protein or not. Currently several lines of evidence indicate that this subunit is able to bind two molecules of zeaxanthin, one of the pigments involved in the xanthophyll cycle. In this work immunolabelling indicated that PsbS is tightly bound to the PSII core dimer, monomer and incomplete PSII particles as Reaction Centre-CP47 (RC-CP47). Furthermore qualitative HPLC indicates a complete absence of zeaxanthin in the sample and the presence of violaxanthin, another pigment involved in the xanthophyll cycle. The absence of zeaxanthin was expected considering that the plants were harvested after the dark period and that the particles were purified in complete dark (or in green light), whereas the presence of violaxanthin was unexpected considering that so far no evidence of violaxanthin bound to PSII cores devoid of LHC proteins was reported. Furthermore the amount of chlorophyll b was not relevant for suspecting this pigment bound to PsbS. Therefore we conclude that if PsbS is able to bind chlorophyll it has to be a chlorophyll a. The results indicate that PsbS could be able to bind not only zeaxanthin but also violaxanthin. The extrinsic subunit Psb27 was also found in this preparation. The presence and the amount of this subunit, reported to be involved in the repair of damaged PSII, was not constant and therefore behaving as the other two extrinsic proteins 23kDa (PsbP) and 17kDa (PsbQ). Electron crystallography studies on spinach PSII particles purified by differential solubilisation resulted in crystalline tubes with new unit cell constants. From data analysis a density map at 15Å resolution was obtained with a P22121 symmetry. However, at this resolution it cannot be said if the internal symmetry axis is related with the two-fold axis of the dimer or the pseudo two-fold axis of the monomer. In conclusion a method to isolate functional, pure PSII core complexes was developped. These samples, together with the improved 2d crystallisation protocol could lead to crystals with higher quality hence better resolution density maps in the future.
Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selectivity and affinity of one of these riboswitches, extensive all-atom molecular dynamics simulations in explicit solvent ({approx}1 µs total simulation length) of the aptamer domain of the guanine sensing riboswitch are performed. The conformational dynamics is studied when the system is bound to its cognate ligand guanine as well as bound to the non-cognate ligand adenine and in its free form. The simulations indicate that residue U51 in the aptamer domain functions as a general docking platform for purine bases, whereas the interactions between C74 and the ligand are crucial for ligand selectivity. These findings either suggest a two-step ligand recognition process, including a general purine binding step and a subsequent selection of the cognate ligand, or hint at different initial interactions of cognate and noncognate ligands with residues of the ligand binding pocket. To explore possible pathways of complex dissociation, various nonequilibrium simulations are performed which account for the first steps of ligand unbinding. The results delineate the minimal set of conformational changes needed for ligand release, suggest two possible pathways for the dissociation reaction, and underline the importance of long-range tertiary contacts for locking the ligand in the complex.
Global warming is expected to be associated with diverse changes in freshwater habitats in north-western Europe. Increasing evaporation, lower oxygen concentration due to increased water temperature and changes in precipitation pattern are likely to affect the survival ratio and reproduction rate of freshwater gastropods (Pulmonata, Basommatophora). This work is a comprehensive analyse of the climatic factors influencing their ranges both in the past and in the near future. A macroecological approach showed that for a great proportion of genera the ranges were projected to contract by 2080, even if unlimited dispersal was assumed. The forecasted warming in the cooler northern ranges predicted the emergence of new suitable areas, but also reduced drastically the available habitat in the southern part of the studied region. In order to better understand the ranges dynamics in the past and the post glacial colonisation patterns, an approach combining ecological niche modelling and phylogeography was used for two model species, Radix balthica and Ancylus fluviatilis. Phylogeographic model selection on a COI mtDNA dataset confirmed that R. balthica most likely spread from two central European disjunct refuges after the last glacial maximum. The phylogeographic analysis of A. fluviatilis, using 16S and COI mtDNA datasets, also inferred central European refugia. The absence of niche conservatism (adaptive potential) inferred for A. fluviatilis puts a cautionary note on the use of climate envelope models to predict the future ranges of this species. However, the other model species exhibited strong niche conservatism, which allow putting confidence into such predictions. A profound faunal shift will take place in Central Europe within the next century, either permitting the establishment of species currently living south of the studied region or the proliferation of organisms relying on the same food resources. This study points out the need for further investigations on the dispersal modes of freshwaters snails, since the future range size of the species depend on their ability to establish in newly available habitats. Likewise, the mixed mating system of these organisms gives them the possibility to fund a new population from a single individual. It will probably affect the colonisation success and needs further investigation.
The NADH:ubiquinone oxidoreductase (complex I) is a large membrane bound protein complex coupling the redox reaction of NADH oxidation and quinone reduction to vectorial proton translocation across bioenergetic membranes. The mechanism of proton pumping is still unknown; it seems however that the reduction of quinone induces conformational changes which drive proton uptake from one side and release at the other side of the membrane. In this study the proposed quinone and inhibitor binding pocket located at the interface of the 49-kDa and PSST subunits was explored by a large number of point mutations introduced into complex I from the strictly aerobic yeast Yarrowia lipolytica. Point mutations were systematically chosen based on the crystal structure of the hydrophilic domain of complex I from Thermus thermophilus. In total, the properties of 94 mutants at 39 positions which completely cover the lining of the large putative quinone and inhibitor binding cavity are described and discussed here. A structure/function analysis allowed the identification of functional domains within the large putative quinone binding cavity. A possible quinone access path ranging from the N-terminal beta-sheet of the 49-kDa subunit into the pocket to tyrosine 144 could be defined, since all exchanges introduced here, caused an almost complete loss of complex I activity. A region located deeper in the proposed quinone binding pocket is apparently not important for complex I activity. In contrast, all exchanges of tyrosine 144, even the very conservative mutant Y144F, essentially abolished dNADH:DBQ oxidoreductase activity of complex I. However, with higher concentrations of Q1 or Q2 the dNADH:Q oxidoreductase activity was largely restored in the mutants with the more conservative exchanges. Proton pumping experiments showed that this activity was also coupled to proton translocation, indicating that these quinones were reduced at the physiological site. However, the apparent Km values for Q1 or Q2 were drastically increased, clearly demonstrating that tyrosine 144 is central for quinone binding and reduction. These results further prove that the enzymatically relevant quinone binding site of complex I is located at the interface of the 49-kDa and PSST subunits. The quinone binding pocket is thought to comprise the binding sites for a plethora of specific complex I inhibitors that are usually grouped into three classes. The large array of mutants targeting the quinone binding cavity was examined with a representative of each inhibitor class. Many mutants conferring resistance were identified which, depending on the inhibitor tested, clustered in well defined and partially overlapping regions of the large putative quinone and inhibitor binding cavity. Mutants with effects on type A (DQA) and type B (rotenone) inhibitors were found in a subdomain corresponding to the former [NiFe] site in homologous hydrogenases, whereby the type A inhibitor DQA seems to bind deeper in this domain. Mutants with effects on the type C inhibitor (C12E8) were found in a narrow crevice. Exchanging more exposed residues at the border of these well defined domains affected all three inhibitor types. Therefore, the results as a whole provide further support for the concept that different inhibitor classes bind to different but partially overlapping binding sites within a single large quinone binding pocket. In addition, they also indicate the approximate location of the binding sites within the structure of the large quinone and inhibitor binding cavity at the interface of the 49 kDa and the PSST subunit. It has been proposed earlier that the highly conserved HRGXE-motif in the 49-kDa subunit forms a part of the quinone binding site of complex I. Mutagenesis of the HRGXE-motif, revealed that these residues are rather critical for complex I assembly and seem to have an important structural role. The question why iron-sulfur cluster N1a is not detectable by EPR in many models organisms is not solved yet. Introducing polar and positively charged amino acid residues close to this cluster in order to increase its midpoint potential did not result in the appearance of the cluster N1a EPR signal in mitochondrial membranes from the mutants. Clearly, further research will be necessary to gain insights to the function of this iron-sulfur cluster in complex I. In an additional project, a new and simple in vivo screen for complex I deficiency in Y. lipolytica was developed and optimized. This assay probes for defects in complex I assembly and stability, oxidoreductase activity and also proton pumping activity by complex I. Most importantly, this assay is applicable to all Y. lipolytica strains and could be used to identify loss-of-function mutants, gain-of-functions mutants (i.e. resistance towards complex I inhibitors) and revertants due to mutations in both nuclear and mitochondrially encoded genes of complex I subunits.
Our understanding of the impact of recombination, mutation, genetic drift and selection on the evolution of a single gene is still limited. Here we investigate the impact of all of these evolutionary forces at the complementary sex determiner (csd) gene which evolves under a balancing mode of selection. Females are heterozygous at the csd gene and males are hemizygous; diploid males are lethal and occur when csd is homozygous. Rare alleles thus have a selective advantage, are seldom lost by the effect of genetic drift and are maintained over extended periods of time when compared to neutral polymorphisms. Here, we report on the analysis of 17, 19 and 15 csd alleles of Apis cerana, Apis dorsata and Apis mellifera honey bees respectively. We observed great heterogeneity of synonymous (pi S) and nonsynonymous (pi N) polymorphisms across the gene, with a consistent peak in exon 6 and 7. We propose that exons 6 and 7 encode the potential specifying domain (csd-PSD) which has accumulated elevated nucleotide polymorphisms over time by balancing selection. We observed no direct evidence that balancing selection favors the accumulation of nonsynonymous changes at csd-PSD (pi N/pi S ratios are all < 1, ranging from 0.6 to 0.95). We observed an excess of shared nonsynonymous changes, which suggests that strong evolutionary constraints are operating at csd-PSD resulting in the independent accumulation of the same nonsynonymous changes in different alleles across species (convergent evolution). Analysis of a csd-PSD genealogy revealed relatively short average coalescence times (~6 million years), low average synonymous nucleotide diversity (pi S < 0.09) and a lack of trans-specific alleles which substantially contrasts with previously analyzed loci under strong balancing selection. We excluded the possibility of a burst of diversification after population bottlenecking and intragenic recombination as explanatory factors, leaving high turn-over rates as the explanation for this observation. By comparing observed allele richness and average coalescence times with a simplified model of csd-coalescence, we found that small long term population sizes (i.e. Ne <104), but not high mutation rates, can explain short maintenance times, implicating a strong impact of genetic drift on the molecular evolution of highly social honey bees.
Background Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms. Results We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases. Conclusion This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that – inter alias – signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.
Ataxin-2 is a novel protein, within which the unstable expansion of a polyglutamine domain can cause Spinocerebellar Ataxia type 2 (SCA2), a neurodegenerative disease which belongs to the group of polyglutamine disorders. SCA2 is characterised by a progressive loss of neurons that first affects the cerebellum and brain stem and then may extend to other areas of the brain, like substantia nigra, motoneurons and thalamus. Several lines of research have attempted to determine therole of ataxin-2 in its normal and mutant version. Different animal models and cell culture approaches to study ataxin-2 function implicated ataxin-2 in RNA processing, embryonic development, apoptosis and cytoskeleton. However, the function of ataxin-2 still remains unclear. In this thesis, a protein interaction approach was chosen as an alternative to gain insights into the cellular function of ataxin-2. Full-length ataxin-2 was used as bait in a yeast two-hybrid screen of human adult brain cDNA. Among five candidate interactor proteins identified, two were the endophilins A1 and A3, proteins involved in vesicle endocytosis. Co-immunoprecipitation studies confirmed the association of these proteins in an endogenous complex of mouse brain. In vitro binding experiments narrowed the binding interfaces down to two proline-rich domains on ataxin-2, which interacted with the SH3 domain of endophilins A1/A3. Ataxin-2 and endophilins A1/A3 colocalised at the endoplasmic reticulum as determined by immunofluorescence microscopy of transfected cell lines, and by centrifugation fractionation studies of mouse brain. Importantly, the pattern observed in transfected cells was conserved in untransfected rat hippocampal neurons. In mouse brain, associations of ataxin-2 with endocytic proteins such as the adaptor CIN85, the ubiquitin ligase c-Cbl and also GRB2, in the last case by means of a SH3 domain array chip, were also demonstrated. GST pull-down assays showed ataxin-2 to interact directly with the SH3 domains A and C of CIN85, the C-terminal SH3 domain of GRB2, and the SH3 domain of Src, a kinase activated after receptor stimulation. Functional studies demonstrated that ataxin-2 affects endocytic trafficking of the epidermal growth factor receptor (EGFR) by reducing the EGFR internalisation after EGF stimulation. Taken together, these data implicate ataxin-2 to play a role in endocytic receptor cycling.
Genetic analysis of salt adaptation in Methanosarcina mazei Gö1 : the role of abl, ota and otb genes
(2008)
1. M. mazei ist ein halotolerantes methanogenes Archäon und akkumuliert kompatible Solute als längerfristige Anpassung an erhöhte Osmolarität in der Umgebung. Bei intermediären Salzkonzentrationen (~ 400 mM NaCl) wird vorzugsweise α-Glutamat gebildet und bei höheren Salzkonzentrationen (~ 800 mM NaCl) wird Nε-Acetyl-ß-Lysin zusätzlich zu Alpha-Glutamat synthetisiert. 2. Eine Analyse der intrazellulären Solutezusammensetzung mittels NMR ergab, dass M. mazei Glycin-Betain als Osmolyt akkumulieren kann. Für die Aufnahme von Glycin-Betain konnten zwei putative Glycin-Betain-Transporter in M. mazei identifiziert werden, Ota und Otb. Ota steht für „osmoprotectant transporter A“ und Otb für „osmoprotectant transporter B“. Das Genom von M. mazei wurde, nachdem es vollstänidg sequenziert war, nach Genen durchsucht, die eine Rolle bei der Aufnhame von Glycin-Betain oder anderen kompabtiblen Solute spielen könnten. Dafür wurde die Sequenz eines Substratbindeproteins eines bekannten bakteriellen Glycin-Betain-Transporters, opuAC aus B. subtillis als Referenzsequenz verwendet. Hierbei konnte ein Homolog, otaC, in M. mazei identifiziert werden. otaC ist Teil eines Genclusters, welches für einen ABC-Transporter kodiert. otb wurde bei einer genomweiten Expressionsanalyse zur Salzadaptation von M. mazei identifiziert. Es wurden Gene eines putativen ABC-Transporters identifiziert, die unter Hochsalzbedingungen leicht induziert waren. Es stellte sich heraus, dass es sich hierbei um einen zweiten putativen Glycin-Betain-Transporter handelte. Otb gehört auch zur Familie der ABC-Transporter. Vergleichsanalysen zeigten, dass die beiden Transporter keine große Ähnlichkeit zueinander aufweisen. Die Funktion und Rolle der beiden ABC-Transporter, vor allem von Otb, war zu Beginn dieser Arbeit unklar. 3. Bei Analysen des intrazellulären Solutepools im Wildtyp von M. mazei stellte sich heraus, dass in Anwesenheit von Glycin-Betain die Konzentration von Glutamat und NE- Acetyl-ß-Lysin verringert war. Bei 400 mM NaCl reduzierte Glycin-Betain die Glutamat- Konzentration um 16% und bei 800 mM NaCl um 29%. Besonders deutlich zeigte sich der Einfluß von Glycin-Betain bei der Akkumulation von NE-Acetyl-ß-Lysin. Bei 400 mM NaCl reduzierte Glycin-Betain die Konzentration an NE-Acetyl-ß-Lysin um 60% und bei 800 mM NaCl um 50%. Der Einfluß von Glycin-Betain konnte auf verschiedenen Ebenen in M. mazei beobachten werden. Es konnte gezeigt werden, dass die relative Transkriptimenge von ota unter Hochsalzbedingungen zunimmt. Glycin-Betain reduzierte die Transkription von ota bei verschiedenen Salzkonzentrationen. Die relative Transkriptmenge an mRNA von ota wurde mittels quantitativer real-time PCR (qRT-PCR) quantifiziert und war bis zu 52% reduziert in Zellen, die in Gegenwart von Glycin-Betain gewachsen waren. Die Transkriptmenge von otb war unter den gleichen Bedingungen nicht beeinflusst und zeigte generell keine Zunahme mit der Salinität des Mediums. Des Weiteren konnte ein Effekt von Glycin-Betain auf Ebene der Transportaktivität von Ota gezeigt werden. Hier zeigte sich, dass Zellen, die bei 400 mM NaCl in Gegenwart von Glycin-Betain gezogen waren, eine geringere Transportaktivität aufweisen, als Zellen, die bei 400 mM NaCl ohne Glycin-Betain gewachsen waren. Die Transportaktivität war um 90% geringer. Es muss jedoch berücksichtigt werden, dass es sich bei den Zellen, die ohne Glycin-Betain gewachsen waren, um eine Nettoaufnahme von Glycin-Betain handelte. Im Gegensatz dazu, ist davon auszugehen, dass Zellen, die in Gegenwart von Glycin-Betain gewachsen waren, eine Austaschreaktion zwischen bereits vorhandenem intrazellulärem und extrazellulär angebotenem Glycin-Betain vornehmen. [Die dem letzten Punkt zugrundeliegenden Daten wurden von Silke Schmidt im Rahmen einer Diplomarbeit erhoben, die von mir mitbetreut wurde. Aus Gründen der vollständigen Darstellung des Projektverlaufes werden diese Daten mitaufgeführt.] 4. Zur weiteren Klärung der Rolle und Funktion der beiden putativen Glycin-Betain- Transporter Ota und Otb war es Ziel, Mutantenstudien durchzuführen. Eine Vorraussetzung für die Generierung von Mutanten ist, dass der Organismus auf Agarplatten wächst und Einzelkolonien von einer einzelnen Zelle ausgehend bildet. Dies ist ein wichtiger Punkt bei Methanosarcina spp., die Zellpakete, sogenannte Sarcinen bilden. Deshalb wurde zunächst nach den optimalsten Plattierungsbedingungen gesucht, unter denen M. mazei keine Sarcinen bildet und die Plattierungseffizienz am höchsten war. Die Plattierungseffizienz betrug im Durchschnitt 54%. Für das Einbringen von DNA in die Zellen wurde eine Liposomen-vermittelte Transformation getestet. Ein ähnliches Vorgehen war bereits für Methanosarcina acetivorans beschrieben, konnte bislang aber noch nicht erfolgreich für M. mazei Gö1 und andere Stämme von M. mazei angwendet werden. Erste Schritte zur Anpassung des Transformations-Protokolles beinhalteten das Testen von DOTAP verschiedener Hersteller, sowie die Konzentration an eingesetzter DNA. Das jeweilige Zielgen/Zieloperon, welches deletiert werden sollte, wurde durch eine pac-Kassette ersetzt. Diese kodiert für eine Puromycin-Transacetylase und verleiht dem Organismus Puromycin- Resistenz. Die pac-Kassette wurde von umgebenden Bereichen des Ziellocus flankiert und integrierte mit Hilfe dieser flankierenden Bereiche über doppelt-homologe Rekombination in das Genom. 5. Mit dem oben beschriebenen Verfahren wurden ota::pac- und otb::pac-Mutanten erzeugt und über Southern-Blot Analyse verifiziert. Eine erste Charakterisierung der Mutanten mittels qRT-PCR zeigte, dass auf mRNA-Ebene keine Transkripte von ota in M. mazei ota::pac oder otb in M. mazei otb::pac nachweisbar waren. Zusätzlich konnte auf Proteinebene das Substratbindeprotein OtaC in M. mazei ota::pac und OtbC in M. mazei otb::pac nicht über einen Antikörper gegen das jeweilige Substratbindeprotein nachgewiesen, was die erfolgreiche Deletion bestätigte. Erste phänotypische Charakterisierungen zeigten, dass das Wachstum von M. mazei ota::pac und M. mazei otb::pac unter Hochsalzbedingungen nicht beeinträchtigt und vergleichbar mit dem des Wildtyps war. Auch bei kälteren Wachstumstemperaturen von 22°C wuchsen die Mutanten ohne Phänotyp. 6. Radioaktive Transportstudien mit M. mazei otb::pac zeigten, dass diese Mutante, die noch ein funktionelles Ota besitzt, [14C]Glycin-Betain aufnehmen kann. Es stellte sich heraus, dass diese Mutante eine höhere Transportrate für Glycin-Betain aufwies, als der Wildtyp. Die Aufnahmerate war um einen Faktor 2 höher als beim Wildtyp. Zusätzlich konnten qRT-PCR Analysen zeigen, dass die relative Transkriptmenge an ota in der otb::pac-Mutante um einen Faktor 2 höher war, als im Wildtyp. Umgekehrt konnte dieser Effekt nicht beobachtet werden, d.h. eine erhöhte Transkriptmenge an otb in M. mazei ota::pac. Auf Proteinebene konnte beobachtet werden, dass die intrazelluläre Konzentration an OtaC in der Mutatne leicht höher war als im Wildtyp. Jedoch stellte sich heraus, dass die intrazelluläre Glycin-Betain-Konzentration bei 400 mM NaCl in der Mutante nicht erhöht war verglichen mit Wildtyp, sondern die Konzentrationen gleich waren. Bei höheren Salzkonzentrationen (800 mM NaCl) zeigte sich jedoch ein anderes Bild: die intrazelluläre Glycin-Betain-Konzentration war in der Mutante um 60% erhöht. Dies könnte auf die erhöhte Transportaktivität von M. mazei otb::pac zurückzuführen sein. Die Konzentration anderer kompatibler Solute wie Glutamat und NE-Acetyl-ß-Lysin waren in diesen Zellen bis zu 48% reduziert. In vorherigen Studien konnte gezeigt werden, dass heterolog überproduziertes Ota von M. mazei in E. coli MKH13, eine E. coli-Mutante, die keine Glycin-Betain-Transporter mehr besitzt, die Aufnahme von Glycin-Betain wieder herstellen konnte [die Daten von ota in E. coli MKH13 wurden in der bereits oben erwähnten Diplomarbeit von Silke Schmidt erhoben]. Zur Klärung der Funktion von Otb wurde der gleiche Versuch mit otb in E. coli MKH13 durchgeführt. Jedoch konnte eine heterologe Produktion von Otb aus M. mazei die Aufnahme von Glycin-Betain in E. coli MKH13 nicht wieder herstellen. Hierbei wurde über Western-Blot Analyse sichergestellt, dass Otb tatsächlich in der Membran vorhanden war. Auch Transportstudien mit der Mutante M. mazei ota::pac zeigten, dass diese Mutante kein [14C]Glycin-Betain mehr aufnehmen konnte. Es konnte auch keine Akkumulation von Glycin-Betain mittels NMR in dieser Mutante gemessen werden. Des Weiteren zeigte sich, dass die intrazellulären Konzentrationen an Glutamat und Nε-Acetyl-ß-Lysin bei 400 mM und 800 mM NaCl in der Mutante unbeeinflusst von der Glycin-Betain-Konzentration im Medium waren. Weitere Transportstudien mit M. mazei ota::pac zur Aufnahme von [14C]Cholin zeigten, dass dieses Molekül weder vom Wildtyp, noch von der Mutante aufgenommen wurde. Dieses Ergebnis wurde durch Messung des Solutepools mittels NMR bestätigt. Somit kann ausgeschlossen werden, dass Otb unter den gemessenen Bedingungen weder ein Glycin- Betain-Transporter noch ein Cholin-Transporter in M. mazei ist. Diese Beobachtungen belegen eindeutig, dass Ota der einzige funktionelle Glycin-Betain-Transporter in M. mazei ist, während die Rolle von Otb bislang noch ungeklärt ist. 7. Nε-Acetyl-ß-Lysin, das dominante kompatible Solut in M. mazei bei 800 mM NaCl, wird durch die Enzyme AblA, einer Lysin-2,3-Aminomutase und AblB, einer ß-Lysin- Acetyltransferase synthetisiert. In dieser Arbeit wurde eine Δabl::pac-Mutante generiert, um die Fragen zu klären, ob die beiden Enzyme vom postulierten abl-Operon kodiert werden und wenn ja, welchen Phänotyp eine Nε-Acetyl-ß-Lysin-freier-Mutante bei Salzstress zeigt. NMR-Analysen zeigten, dass in der abl::pac-Mutante kein Nε-Acetyl-ß-Lysin mehr nachweisbar war. Dies belegt, dass die Gene ablA und ablB und deren Genprodukte für die Synthese von NE-Acetyl-ß-Lysin in M. mazei essentiell sind. Unter Hochsalzbedingungen ist das Wachstum von M. mazei abl::pac im Vergleich zum Wildtyp deutlich verlangsamt. Dieses Ergebnis war unerwartet, da eine abl::pac-Mutante von Methanococcus maripaludis unter Hochsalzbedingungen nicht mehr wachsen konnte. Unter Niedrigsalz und bei intermediären Salzkonzentration war das Wachstum von M. mazei abl::pac nicht eingeschränkt und verhielt sich wie der Wildtyp. In Gegenwart von Glycin-Betain akkumulierte die abl::pac-Mutante von M. mazei unter Hochsalzbedingungen 2,4 mal mehr Glycin-Betain als der Wildtyp, um das Defizit im Solutepool auszugleichen und Wachstum bei Hochsalz zu ermöglichen. Dadurch war sie in der Lage, wieder wie der Wildtyp zu wachsen. 8. Der Verlust von NE-Acetyl-ß-Lysin wurde unter Hochsalzbedingungen durch erhöhte Konzentrationen an Glutamat und einem neuen kompatiblen Solut kompensiert. NMRAnalysen zeigten, dass es sich hierbei um Alanin handelte. Bis jetzt wurde die Verwendung von Alanin als kompatibles Solut noch nie beschrieben. Um sicherzustellen, dass Alanin als kompatibles Solut in M. mazei abl::pac dient, wurde die Konzentration bei verschiedenen Salzkonzentrationen gemessen. Die Konzentration an Alanin nahm mit steigender Salzkonzentration zu. Bei 800 mM NaCl war die Konzentration 12 fach erhöht verglichen mit der Konzentration bei 400 mM NaCl. Außerdem redzierte Glycin-Betain die Alanin- Konzentration bei 800 mM NaCl um 58%. Transportexperimente zeigten, dass M. mazei kein Alanin aus dem Medium aufnehmen kann. 9. Erste Analysen möglicher Synthesewege für Alanin zeigten, dass die Alanin- Dehydrogenase nicht auf Transkriptebene unter Hochsalzbedingungen induziert war und somit keine Rolle in der Synthese von Alanin als kompatibles Solut spielen dürfte. Es könnten jedoch Aminotransferasen eine Rolle bei der Biosynthese von Alanin spielen. Des Weiteren sind die Enzyme, die für die Synthese von Glutamat als kompatibles Solut verantwortlich sind, unbekannt. Dies gilt für alle bis jetzt untersuchten Organismen, die Glutamat als kompatibles Solut nutzen. In dieser Arbeit wurde versucht, mit Hilfe der abl::pac-Mutante, die erhöhte Glutamat-Mengen zum Osmoschutz produziert, der Frage nachzugehen, welche Gene/Enzyme eine Rolle spielen könnten bei der Synthese von Glutamat als kompatibles Solut. Dazu wurden unter Hochsalzbedingungen die Transkriptmengen verschiedener Genen, die an der Glutamat-Synthese beteiligt sein könnten, in der Mutante und im Wildtyp untersucht. Hierbei zeigte sich, dass mehrere Gene verschiedener Enzyme unter Hochsalzbedingungen in der Mutante leicht induziert waren. Eines dieser Enzyme ist die Glutaminsynthetase. Dieses Enzym ist für die Umsetzung von Glutamat zu Glutamin unter Verbrauch von ATP verantwortlich. M. mazei besitzt zwei Gene, die für eine putative Gluaminsynthetase kodieren. In M. mazei abl::pac ist unter Hochsalzbedingungen das Gen glnA2 im Vergleich zum Wildtyp (4,03 ± 1,14) leicht induziert (7,63 ± 2,2). Des weiteren konnte in der Mutante eine leichte Induktion von gltB1, gltB2 und gltB3 unter Hochsalz beobachtet werden. Diese Gene kodieren für die einzelnen Domänen einer Glutamatsynthase. Diese ersten Analysen geben einen Hinweis darauf, dass die Synthese von Glutamat als kompatibles Solut über eine gekoppelte Reaktion der Glutaminsynthetase und der Glutamatsynthase verlaufen könnte.
Dicer and Drosha are the major enzymes involved in microRNA processing. Using siRNA targeting Dicer and Drosha, thereby downregulating a substantial number of microRNAs in EC, we demonstrate a crucial role of both enzymes in angiogenic processes. Interestingly, Dicer inhibition exerts more profound effects on processes like migration and viability of EC in comparison to Drosha inhibition. Moreover, Dicer effects in vivo angiogenesis, a process which is unaffected by Drosha. This discrepancy might be partially due to the involvement of Dicer in other cellular processes like heterochromatin formation and to the fact that Dicer and Drosha target mainly different subsets of microRNAs. In addition, we identified miR-92a as a novel endogenous repressor of the angiogenic program in EC, which impairs their angiogenic functions in vitro and in vivo. Consistent with these data, blocking miR-92a by systemic infusion of antagomirs enhances neovascularization and functional recovery after ischemia in vivo. At first sight, the anti-angiogenic function of miR-92a in EC appears to contradict the previously identified anti-apoptotic and pro-angiogenic activities of the miR-17~92 cluster in tumor cells. However, this apparent discrepancy might be well rationalized by a predominant function of miR-18a and miR-19a in tumor cells, which are responsible for the tumorigenic and non-cell autonomous pro-angiogenic functions of the miR-17~92 cluster. Instead, miR-92a expression is specifically upregulated in ischemic tissues and appears to cell-autonomously repress the angiogenic potential of EC. Among the various targets and verified regulated genes identified by microarray, we confirmed the downregulation of Integrin a5 in vitro and in vivo. The relevance of this miR-92a target is evidenced by severe vascular defects in the absence of Integrin a5. In addition, endothelial miR-92a interferes with the expression pattern of genes controlling key EC functions at various levels, some of which, e.g. eNOS, might be secondarily affected by directly targeted genes. Obviously, our data do not formally exclude effects of antagomir-92a on perivascular and other cell types, but surely include effects on EC. Regardless of this, the capacity of miR-92a to target various downstream effectors might be an advantage of miRNA-based therapeutic strategies and may overcome the limited therapeutic capacity of single growth factor or single gene therapies in ischemic diseases, since the highly organized process of vessel growth, maturation and functional maintenance is well known to require the fine-tuned regulation of a set of genes.
The mammary gland of mice serves as a model system for studying differentiation in an adult animal. With the beginning of pregnancy the mammary epithelial cells undergo functional differentiation to produce milk for nourishment of the young. The transcription factor STAT5 mediates the cytokine-induced induction of the milk proteins during pregnancy and lactation in response to the lactogenic hormone prolactin. In addition to transcription factors that mediate transcription of their target genes by recruitment of the general transcription machinery to the DNA-regulator regions, specific post-translational modifications on the N-terminal tails of histones also influence expression. These histone modifications can affect chromatin structure, which is a main control barrier to transcription, by directly altering accessibility of the chromatin and by providing binding surfaces for protein complexes that can further modulate chromatin structure and regulate transcription. In this work N-terminal histone modification marks that associate with open, permissive and repressed chromatin where investigated in different regions of two milk protein genes during mammary gland development. Using the chromatin-immunoprecipitation (ChIP) assays increased acetylation of histone H3 and H4 at the 5’ region, promoter and transcribed regions of β-casein and whey acidic protein (WAP) gene were observed during pregnancy and lactation when these genes are expressed. The presence of these histone marks, which are associated with a relaxed chromatin structure, correlates with the recruitment of STAT5A and STAT5B to the promoter containing regulatory regions as well as the detection of the phosphorylated RNA polymerase II in the transcribed gene region. Both di- and tri-methylation of histone H3 lysine 4, that mark permissive and active chromatin respectively, were enriched in tissue from pregnant and lactating mice. In comparison tri-methylation of histone H3 lysine 27, a mark associated with repressed chromatin, could be observed during all stages of mammary gland tissue investigated, but appears slightly elevated in the tissue from virgin mice when β-casein and WAP are not expressed. Together these results illustrate that the expression of the two milk proteins genes at distinct stages of mammary gland differentiation correlate with specific changes in histone modifications. In mammary gland tissue STAT5A is important for the mammary gland epithelial cell differentiation and survival during lactation. Yet many genomic target regions that STAT5A actually bind and which are involved in regulation of gene expression during lactation still remain unknown. Therefore, the second part of this thesis was focused on the identification of novel STAT5-binding sites that are differentiation specifically bound by STAT5A in mammary gland tissue during lactation. In summary, the results demonstrate that the ChIP cloning method was employed successfully for the cloning of a STAT5A library and the identification of new STAT5 targets in mammary gland tissue from lactating mice. Nine of the newly identified STAT5-binding targets were verified to differentiation specifically bind STAT5A and STAT5B in vivo during pregnancy and lactation. Even though the selection of the tested clones was biased towards STAT5-binding sites near or at known genes and for multiple STAT5 binding sites, only one out of the nine validated STAT5-binding regions is located in a traditional defined proximal promoter. Except for two STAT5-binding regions, which are located at least 10 kb from the next annotated known gene, six are located in the intronic regions of annotated mRNA or EST transcripts. Three, out of four verified STAT5-binding regions tested in reporter gene assays for functionality, display the ability to drive reporter gene activity in a STAT5 dependent manner. This transcriptional activity is due to the STAT5-binding sites within the cloned regions as determined by mutational analysis. Of special interest is a STAT5-binding region that contains one STAT5 and three STAT-like sites within a 339 bp region that is evolutionary conserved by approximately 80% between the mouse and human genome. This STAT5-binding region lies about 62 kb 5 prime of the nuclear factor I/B gene. The expression of the NFI/B mRNA transcript correlates with the in vivo association of STAT5A to the conserved region during the mammary gland differentiation. Together, these results suggest that this STAT5-binding might be a cis-regulatory region that potentially mediates STAT5 induced NFI/B gene expression in mice during lactation.
Background One of the central issues in ecology is the question what allows sympatric occurrence of closely related species in the same general area? The non-biting midges Chironomus riparius and C. piger, interbreeding in the laboratory, have been shown to coexist frequently despite of their close relatedness, similar ecology and high morphological similarity. Methodology/Principal Findings In order to investigate factors shaping niche partitioning of these cryptic sister species, we explored the actual degree of reproductive isolation in the field. Congruent results from nuclear microsatellite and mitochondrial haplotype analyses indicated complete absence of interspecific gene-flow. Autocorrelation analysis showed a non-random spatial distribution of the two species. Though not dispersal limited at the scale of the study area, the sister species occurred less often than expected at the same site, indicating past or present competition. Correlation and multiple regression analyses suggested the repartition of the available habitat along water chemistry gradients (nitrite, conductivity, CaCO3), ultimately governed by differences in summer precipitation regime. Conclusions We show that these morphologically cryptic sister species partition their niches due to a certain degree of ecological distinctness and total reproductive isolation in the field. The coexistence of these species provides a suitable model system for the investigation of factors shaping the distribution of closely related, cryptic species.
Introduction : extent, processes and evolutionary impact of interspecific hybridization in animals
(2008)
Since the time of Charles Darwin, studies of interspecific hybridization have been a major focus for evolutionary biologists. Although this phenomenon has often been viewed as problematic in the fields of ecology, taxonomy and systematics, it has become a primary source of data for studies on speciation and adaptation. Effects from genetic/evolutionary processes, such as recombination and natural selection, usually develop over extended periods of time; however, they are accelerated in cases of hybridization. Interspecific hybrids exhibit novel genomes that are exposed to natural selection, thus providing a key to unravel the ultimate causes of adaptation and speciation. Here we provide firstly a historic perspective of hybridization research, secondly a novel attempt to assess the extent of hybridization among animals and thirdly an overview of the reviews and case studies presented in this theme issue.
Using (13)C spin relaxation NMR in combination with molecular dynamic (MD) simulations, we characterized internal motions within double-stranded DNA on the pico- to nano-second time scale. We found that the C-H vectors in all cytosine ribose moieties within the Dickerson-Drew dodecamer (5´-CGCGAATTCGCG-3´) are subject to high amplitude motions, while the other nucleotides are essentially rigid. MD simulations showed that repuckering is a likely motional model for the cytosine ribose moiety. Repuckering occurs with a time constant of around 100 ps. Knowledge of DNA dynamics will contribute to our understanding of the recognition specificity of DNA-binding proteins such as cytosine methyltransferase.
Targeting signals direct proteins to their extra- or intracellular destination such as the plasma membrane or cellular organelles. Here we investigated the structure and function of exceptionally long signal peptides encompassing at least 40 amino acid residues. We discovered a two-domain organization ("NtraC model") in many long signals from vertebrate precursor proteins. Accordingly, long signal peptides may contain an N-terminal domain (N-domain) and a C-terminal domain (C-domain) with different signal or targeting capabilities, separable by a presumably turn-rich transition area (tra). Individual domain functions were probed by cellular targeting experiments with fusion proteins containing parts of the long signal peptide of human membrane protein shrew-1 and secreted alkaline phosphatase as a reporter protein. As predicted, the N-domain of the fusion protein alone was shown to act as a mitochondrial targeting signal, whereas the C-domain alone functions as an export signal. Selective disruption of the transition area in the signal peptide impairs the export efficiency of the reporter protein. Altogether, the results of cellular targeting studies provide a proof-of-principle for our NtraC model and highlight the particular functional importance of the predicted transition area, which critically affects the rate of protein export. In conclusion, the NtraC approach enables the systematic detection and prediction of cryptic targeting signals present in one coherent sequence, and provides a structurally motivated basis for decoding the functional complexity of long protein targeting signals.
Exported proteases of Helicobacter pylori (H. pylori) are potentially involved in pathogen-associated disorders leading to gastric inflammation and neoplasia. By comprehensive sequence screening of the H. pylori proteome for predicted secreted proteases, we retrieved several candidate genes. We detected caseinolytic activities of several such proteases, which are released independently from the H. pylori type IV secretion system encoded by the cag pathogenicity island (cagPAI). Among these, we found the predicted serine protease HtrA (Hp1019), which was previously identified in the bacterial secretome of H. pylori. Importantly, we further found that the H. pylori genes hp1018 and hp1019 represent a single gene likely coding for an exported protein. Here, we directly verified proteolytic activity of HtrA in vitro and identified the HtrA protease in zymograms by mass spectrometry. Overexpressed and purified HtrA exhibited pronounced proteolytic activity, which is inactivated after mutation of Ser205 to alanine in the predicted active center of HtrA. These data demonstrate that H. pylori secretes HtrA as an active protease, which might represent a novel candidate target for therapeutic intervention strategies.
Background: Adrenal chromaffin cells and sympathetic neurons both originate from the neural crest, yet signals that trigger chromaffin development remain elusive. Bone morphogenetic proteins (BMPs) emanating from the dorsal aorta are important signals for the induction of a sympathoadrenal catecholaminergic cell fate. Results: We report here that BMP-4 is also expressed by adrenal cortical cells throughout chick embryonic development, suggesting a putative role in chromaffin cell development. Moreover, bone morphogenetic protein receptor IA is expressed by both cortical and chromaffin cells. Inhibiting BMP-4 with noggin prevents the increase in the number of tyrosine hydroxylase positive cells in adrenal explants without affecting cell proliferation. Hence, adrenal BMP-4 is likely to induce tyrosine hydroxylase in sympathoadrenal progenitors. To investigate whether persistent BMP-4 exposure is able to induce chromaffin traits in sympathetic ganglia, we locally grafted BMP-4 overexpressing cells next to sympathetic ganglia. Embryonic day 8 chick sympathetic ganglia, in addition to principal neurons, contain about 25% chromaffin-like cells. Ectopic BMP-4 did not increase this proportion, yet numbers and sizes of "chromaffin" granules were significantly increased. Conclusions: BMP-4 may serve to promote specific chromaffin traits, but is not sufficient to convert sympathetic neurons into a chromaffin phenotype.
Spectroscopic responses of the potentiometric probe 2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide (DASPMI) were investigated in living cells by means of a time- and space-correlated single photon counting technique. Spatially resolved fluorescence decays from single mitochondria or only a very few organelles of XTH2 cells exhibited three-exponential decay kinetics. Based on DASPMI photophysics in a variety of solvents, these lifetimes were attributed to the fluorescence from the locally excited state, intramolecular charge transfer state, and twisted intramolecular charge transfer state. A considerable variation in lifetimes among mitochondria of different morphologies and within single cells was evident, corresponding to high physiological variations within single cells. Considerable shortening of the short lifetime component ({tau}1) under a high-membrane-potential condition, such as in the presence of ATP and/or substrate, was similar to quenching and a dramatic decrease of lifetime in polar solvents. Under these conditions {tau}2 and {tau}3 increased with decreasing contribution. Inhibiting respiration by cyanide resulted in a notable increase in the mean lifetime and a decrease in mitochondrial fluorescence. Increased DASPMI fluorescence under conditions that elevate the mitochondrial membrane potential has been attributed to uptake according to Nernst distributions, delocalization of {pi}-electrons, quenching processes of the methyl pyridinium moiety, and restricted torsional dynamics at the mitochondrial inner membrane. Accordingly, determination of anisotropy in DASPMI-stained mitochondria in living cells revealed a dependence of anisotropy on the membrane potential. The direct influence of the local electric field on the transition dipole moment of the probe and its torsional dynamics monitor changes in mitochondrial energy status within living cells.
Summary The basal transcription apparatus of archaea is well characterized. However, much less is known about the mechanisms of transcription termination and translation initation. Recently, experimental determination of the 5´-ends of ten transcripts from Pyrobaculum aerophilum revealed that these are devoid of a 5´-UTR. Bioinformatic analysis indicated that many transcripts of other archaeal species might also be leaderless. The´-ends and 3´-ends of 40 transcripts of two haloarchaeal species, Halobacterium salinarum and Haloferax volcanii, have been determined. They were used to characterize the lengths of 5´-UTRs and 3´-UTRs and to deduce consensus sequence-elements for transcription and translation. The experimental approach was complemented with a bioinformatics analysis of the H. salinarum genome sequence. Furthermore, the influence of selected 5´-UTRs and 3´-UTRs on transcript stability and translational efficiency in vivo was characterized using a newly established reporter gene system, gene fusions, and real-time PCR. Consensus sequences for basal promoter elements could be refined and a novel element was discovered. A consensus motif probably important for transcriptional termination was established. All 40 haloarchaeal transcripts analyzed had a 3´-UTR (average size 57 nt), and their 3´-ends were not posttranscriptionally modified. Experimental data and genome analyses revealed that the majority of haloarchaeal transcripts are leaderless, indicating that this is the predominant mode for translation initiation in haloarchaea. Surprisingly, the 5´-UTRs of most leadered transcripts did not contain a Shine-Dalgarno (SD) sequence. A genome analysis indicated that less than 10% of all genes are preceded by a SD sequence and even most proximal genes in operons lack a SD sequence. Seven different leadered transcripts devoid of a SD sequence were efficiently translated in vivo, including artificial 5´-UTRs of random sequences. Thus, an interaction of the 5´-UTRs of these leadered transcripts with the 16S rRNA could be excluded. Taken together, either a scanning mechanism similar to the mechanism of translation initiation operating in eukaryotes or a novel mechanism must operate on most leadered haloarchaeal transcripts. Author Summary Expression of the information encoded in the genome of an organism into its phenotype involves transcription of the DNA into messenger RNAs and translation of mRNAs into proteins. The textbook view is that an mRNA consists of an untranslated region (5´-UTR), an open reading frame encoding the protein, and another untranslated region (3´-UTR). We have determined the 5´-ends and the 3´-ends of 40 mRNAs of two haloarchaeal species and used this dataset to gain information about nucleotide elements important for transcription and translation. Two thirds of the mRNAs were devoid of a 5´-UTR, and therefore the major pathway for translation initiation in haloarchaea involves so-called leaderless transcripts. Very unexpectedly, most leadered mRNAs were found to be devoid of a sequence motif believed to be essential for translation initiation in bacteria and archaea (Shine-Dalgarno sequence). A bioinformatic genome analysis revealed that less than 10% of the genes contain a Shine-Dalgarno sequence. mRNAs lacking this motif were efficiently translated in vivo, including mRNAs with artificial 5´-UTRs of total random sequence. Thus, translation initiation on these mRNAs either involves a scanning mechanism similar to the mechanism operating in eukaryotes or a totally novel mechanism operating at least in haloarchaea.
The term cephalic sensory organ (CSO) is used for specialised structures in the head region of adult Opisthobranchia. These sensory organs show a high diversity in form and function, and the gross morphology of these organs differs considerably among taxa. They can be identified as cephalic shields, oral veils, Hancocks organs, lip organs, rhinophores or oral tentacles. Because of this extremely high diversity, the homology and the evolution of these organs have not been clarified yet. My intention was to use neuroanatomical data sets in order to find putative homologous CSOs. In this study, I will show data about immunohistochemical neurotransmitter content and cellular innervation patterns and their applicability as morphological characters for the homologisation of structures. I support earlier investigations that neurotransmitter content is often related to function. In contrast, axonal tracing patterns can be used to homologise nerves. Overall the aim of this study was to reconstruct the evolution of the CSOs of the Opisthobranchia, by projecting our neuroanatomical data sets onto a molecular phylogeny.
Prion diseases or transmissible spongiform encephalopathies (TSEs) are rare neurological disorders that may be of genetic or infectious origin, but most frequently occur sporadically in humans. Their outcome is invariably fatal. The infectious agent has been defined as prion (from proteinaceous infectious only) in 1992 by Stanley B. Prusiner and represent mainly, if not solely, an abnormal, protease-resistant isoform (PrPSc) of a cellular protein, the prion protein or PrPC. According to the “protein only” hypothesis, the prion is devoid of informational nucleic acids and consists of an “infectious” protein that is capable of converting the normal host protein PrPC into a likeness of itself. TSEs can be distinguished from other neurodegenerative diseases because of their infectivity and transmission capability. The only organ system in which severe histopathological damage can be demonstrated as a consequence of infection with prions is the nervous system. The communal lesions are neuronal loss, spongiosis and astrogliosis, accompanied by an intra- and extracellular accumulation of PrPSc, occasionally in form of amyloid plaques. Even if a strong activation of microglia and astrocytes occurs, no immunological response is usually detectable as consequence of prion infection. Despite the considerable attention for its involvement in TSEs, the physiological role of the cellular, nonpathogenic isoform of PrPC, has not yet been determined. In the last years, several putative cellular functions have been attributed to PrPC: its localization in “lipid rafts” is consistent with a possible role in cell adhesion, transmembrane signalling or as a recognition molecule. Furthermore, PrPC has been implicated in protection against oxidative stress, copper metabolism, apoptosis, cell proliferation and in the regeneration of blood precursors stem cells in the adult. It has also been shown that PrPC interacts with the neuronal cell adhesion molecule NCAM, promoting neurite outgrowth. However, both the PrPC-mediated effects and the role of PrPC-dependent pathways on neuronal differentiation are still not elucidated. First objective of this Ph.D thesis was the establishment of a novel in vitro cellular model for the study of the role of PrPC in neuronal differentiation and neurite outgrowth. Furthermore, an additional goal of this project was the indentification of the PrPC domains responsible for the induction of neuronal differentiation. A novel PrPC-depleted cell line (PrP0/0 ML) was derived from murine primary PrP-knockout neuronal cells by SV40 large T antigen-mediated immortalization. A temperature sensitive form of this oncogenic protein was used, allowing a temperature-mediated regulation of its expression. This cell line was then characterised for its growth potential, for the expression of specific cellular markers and for its ability to differentiate. It was found that, under culture conditions promoting the expression of the temperature-sensitive SV40 large T antigen, the cells expressed nestin, a specific marker of neuronal precursor cells. Therefore, the PrP0/0 ML cell line was identified as a potential neuronal stem cell line. In fact, under nonpermissive culture conditions when the expression of the temperature-sensitive SV40 large T antigen is downregulated, the PrP0/0 ML cells differentiated into neurons. Noteworthy, maintenance of the cells in conditions that promote cell differentiation induced a progressive reduction in the expression levels of nestin, an event that strongly correlated with the appearance of the specific neuronal markers MAP-2b and NeuN. In order to investigate the role of PrPC in the process of neuronal differentiation, the PrP0/0 ML cells were then reconstituted for the expression of either the full-length PrP or a N-terminal truncated PrPC form (PrPdel32-134). The differentiation potential of both reconstituted cell lines under nonpermissive culture conditions was then compared with that of the parenteral PrP0/0 ML cells. This in vitro study clearly highlights that PrPC expression in the PrP0/0 ML cell line accelerates neuronal differentiation and that the N-terminal domain of the prion protein is not necessary for this PrP-mediated function. Prion diseases like BSE, vCJK, Kuru and the majority of iatrogenic cases of CJK are caused by a peripheral infection. Infectious prions accumulate in the central and peripheral nervous system as well as in extracerebral tissues, such as the secondary lymphoid organs and muscles. The prion pathogenesis is a dynamic process which can be defined temporary and spatially in different phases: i) infection and peripheral replication, ii) neuroinvasion, transport of prions from the periphery to the central nervous system (CNS), and iii) neurodegeneration. In the last years, progresses in the elucidation of the peripheral prion pathogenesis were achieved. The identification of the cell types involved in the lymphoreticular prion replication phase and the recognition of the role of the peripheral nervous system in the process of prion spread from the periphery to the CNS have elucidated some of the cellular mechanisms that are involved in prion uptake, replication and propagation. However, relatively little information is available about the mechanism(s) underlying intercellular prion transfer and tissue-to tissue prion spread. Microvesicles (MVs) are submicron vesicles (0,03-1 microm.) with a single membrane and are shed from most eukaryotic cells undergoing activation or apoptosis. The segregation of specific proteins is followed by blebbing of the membrane surface, leading to the formation of MVs and their release in the extracellular environment. MVs can be also secreted upon fusion of multivesicular endosomes with the plasma membrane (exosomes). The secretion of MVs is the result of a complex cellular process involving changes in the metabolism of lipids and proteins. The functional role of MVs is still largely unknown. However, there is evidence showing that they are important modulators of cell-to-cell communication, participate in a variety of intracellular adhesion processes and are able to induce cellular response(s). The release of PrPC and infectious PrPSc by prion infected epithelial, neuroglial and neuronal cells in association with exosomes has recently been highlighted. Furthermore, it has been shown that exosomes can propagate prion infectivity both in vitro and in vivo, suggesting that PrPSc-bearing exosomes may provide a mechanism for intercellular transmission of infectious prions in addition to cell-to-cell contact. Second objective of this Ph.D thesis was to determine the possible role of plasma membrane-derived microvesicles in the propagation and transmission of prions. The release of MVs was first studied in different murine neuronal cell lines. Here it is shown for the first time that neurons also shed plasma membrane derived MVs, in addition to exosomes. Immunoelectron microscopy and immunoblot analyses clearly demonstrated the presence of PrPC on the membrane of MVs released from PrPC-expressing cells. Characterization of lipid rafts components in MVs highlighted the presence of the ganglioside GM2, the tyrosine kinase p59Fyn, flotillin-2 and the neuronal protein GAP-43. In order to investigate whether MVs are involved in the intercellular transmission of prions, MVs were first isolated from two prion infected murine neuronal cell lines, namely the Neuro-2a PK1 and the N2a58 cells, and then used for in vitro and in vivo infection assays. Immunoblot analyses after proteinase K treatment demonstrated the association of PrPSc with the secreted MVs. The PrPSc-bearing MVs were then used to perform infection experiments on noninfected cells. By the use of cell blot assay, a method that allows the detection of PrPSc-amplification and -accumulation in cultured cells, the kinetic of prion infection in the de novo infected cells was followed. Noteworthy, it was found that PrPSc-bearing MVs were capable to transmit prions in vitro and to stably infect the recipient cells. In order to investigate the role of MVs in the transmission of infectivity in vivo, PrPSc-bearing MVs as well as MVs isolated from noninfected cells (as negative control) were injected intracerebrally in PrPC-overexpressing indicator mice (tga20). The development of clinical disease was followed in a time-dependent manner. Clinical symptoms could be observed only in the group of indicator mice inoculated with the PrPSc-bearing MVs, which then succumbed to desease. These findings clearly demonstrated that MVs are biological carriers of both PrPSc and prion infectivity. MVs could therefore participate in vivo in the processes of intercellular prion transmission and propagation.
Reggie-1 (flotillin-2) and reggie-2 (flotillin-1) are membrane microdomain proteins which are associated with the membrane by means of acylation. They influence different cellular signaling processes, such as neuronal, T-cell and insulin signaling. Upon stimulation of the EGF receptor, reggie-1 becomes phosphorylated and undergoes tyrosine 163 dependent translocation from the plasma membrane to endosomal compartments. In addition, reggie-1 was shown to influence actindependent processes. Reggie-2 has been demonstrated to affect caveolin- and clathrin-independent endocytosis. Both proteins form homo- and hetero-oligomers, but the function of these oligomers has remained elusive. Moreover, it has not been clarified if functions of reggie-1 are also influenced by reggie-2 and vice versa. The first aim of the study was to further investigate the interplay and the heterooligomerization of reggie proteins and their functional effects. Both reggie proteins were individually depleted by means of siRNA. In different siRNA systems and various cell lines, reggie-1 depleted cells showed reduced protein amounts of reggie-1 and reggie-2, but reggie-2 knock down cells still expressed reggie-1 protein. The decrease of reggie-2 in reggie-1 depleted cells was only detected at protein but not at mRNA level. Furthermore, reggie-2 expression could be rescued by expression of siRNA resistant wild type reggie-1-EGFP constructs, but not by the soluble myristoylation mutant G2A. This mutant was also not able to associate with endogenous reggie-1 or reggie-2, which demonstrates that membrane association of reggie-1 is necessary for hetero-oligomerization. In addition, fluorescence microscopy studies and membrane fractionations showed that correct localization of overexpressed reggie-2 was dependent on co-overexpressed reggie-1. Thus, hetero-oligomerization is crucial for membrane association of reggie-2 and for its protein stability or protein expression. Moreover, the binding of reggie-2 to reggie-1 required tyrosine 163 of reggie-1 which was previously shown to be important for endosomal translocation of reggie-1. Since reggie-2 was implicated to function in clathrin- and caveolin-independent endocytosis pathways, the effect of reggie-2 depletion on reggie-1 endocytosis was investigated. Indeed, reggie-1 was dependent on reggie-2 for endosomal localization and EGF-induced endocytosis. By FRET-FLIM analysis it could be shown that reggie heterooligomers are dynamic in size or conformation upon EGF stimulation. Thus, it can be concluded that reggie proteins are interdependent in different aspects, such as protein stability or expression, membrane association and subcellular localization. In addition, these results demonstrate that the hetero-oligomers are dynamic and reggie proteins influence each other in terms of function. A further aim was the characterization of reggie-1 and reggie-2 function in actindependent processes, where so far only reggie-1 was known to play a role. Depletion of either of the proteins reduced cell migration, cell spreading and the number of focal adhesions in steady state cells. Thus, also reggie-2 affects actin-dependent processes. Further investigation of the focal adhesions during cell spreading revealed that depletion of reggie-1 displayed different effects as compared to reggie-2 knock down. Reggie-1 depleted cells had elongated cell-matrix-adhesions and showed reduced activation of FAK and ERK2. On the other hand, depletion of reggie-2 resulted in a restricted localization of focal adhesion at the periphery of the cell and decreased ERK2 phosphorylation, but it did not affect FAK autophosphorylation. Hence, reggie proteins influence the regulation of cell-matrix-adhesions differently. A link between reggie proteins and focal adhesions is the actin cross-linking protein -actinin. The interaction of -actinin with reggie-1 could be verified by means of co-immunoprecipitations and FRET-FLIM analysis. Reggie-1 binds -actinin especially in membrane ruffles and in other locations where actin remodeling takes place. Moreover, -actinin showed a different localization pattern during cell spreading in reggie-1 depleted cells, as compared to the control cells. These results provide further insights into the function of both reggie proteins. Their interplay and hetero-oligomerization was shown to be crucial for their role in endocytosis. In addition, both reggie proteins influence actin-dependent processes and differentially affect focal adhesion regulation.
In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.
Chloroplast function depends on the translocation of cytosolically synthesized precursor proteins into the organelle. The recognition and transfer of most precursor proteins across the outer membrane depend on a membrane inserted complex. Two receptor components of this complex, Toc34 and Toc159, are GTPases, which can be phosphorylated by kinases present in the hosting membrane. However, the physiological function of phosphorylation is not yet understood in detail. It is demonstrated that both receptors are phosphorylated within their G-domains. In vitro, the phosphorylation of Toc34 disrupts both homo- and heterodimerization of the G-domains as determined using a phospho-mimicking mutant. In endogenous membranes this mutation or phosphorylation of the wild-type receptor disturbs the association of Toc34, but not of Toc159 with the translocation pore. Therefore, phosphorylation serves as an inhibitor for the association of Toc34 with other components of the complex and phosphorylation can now be discussed as a mechanism to exchange different isoforms of Toc34 within this ensemble.
Arabidopsis cell walls contain large amounts of pectins and hemicelluloses, which are predominantly synthesized via the common precursor UDP-glucuronic acid. The major enzyme for the formation of this nucleotide-sugar is UDP-glucose dehydrogenase, catalysing the irreversible oxidation of UDP-glucose into UDP-glucuronic acid. Four functional gene family members and one pseudogene are present in the Arabidopsis genome, and they show distinct tissue-specific expression patterns during plant development. The analyses of reporter gene lines indicate gene expression of UDP-glucose dehydrogenases in growing tissues. The biochemical characterization of the different isoforms shows equal affinities for the cofactor NAD+ (~40 µM) but variable affinities for the substrate UDP-glucose (120–335 µM) and different catalytic constants, suggesting a regulatory role for the different isoforms in carbon partitioning between cell wall formation and sucrose synthesis as the second major UDP-glucose-consuming pathway. UDP-glucose dehydrogenase is feedback inhibited by UDP-xylose. The relatively (compared with a soybean UDP-glucose dehydrogenase) low affinity of the enzymes for the substrate UDP-glucose is paralleled by the weak inhibition of the enzymes by UDP-xylose. The four Arabidopsis UDP-glucose dehydrogenase isoforms oxidize only UDP-glucose as a substrate. Nucleotide-sugars, which are converted by similar enzymes in bacteria, are not accepted as substrates for the Arabidopsis enzymes.
Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1ts) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 Å resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 Å resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 Å resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.
We performed a bioinformatical analysis of protein export elements (PEXEL) in the putative proteome of the malaria parasite Plasmodium falciparum. A protein family-specific conservation of physicochemical residue profiles was found for PEXEL-flanking sequence regions. We demonstrate that the family members can be clustered based on the flanking regions only and display characteristic hydrophobicity patterns. This raises the possibility that the flanking regions may contain additional information for a family-specific role of PEXEL. We further show that signal peptide cleavage results in a positional alignment of PEXEL from both proteins with, and without, a signal peptide.