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The respiratory chain is composed of protein complexes residing in the inner mitochondrial membrane of eukaryotes or in the cytoplasmic membrane of prokaryotes. This cellular energy converter transforms a redox potential stored in low potential substrates into an electrochemical potential across the respective membrane. Typical respiratory chains contain the complexes I, II, III and IV named according to their sequence in the respiratory chain reaction. Electrons of low potential substrates enter at complex I or II and are passed via complex III to complex IV where they are transferred to oxygen. The transport of electrons between the complexes is mediated by small electron shuttles like quinol or cytochrome c. Two different models describe their exchange either by (1) random collision of freely diffusible electron shuttles and membrane protein complexes or (2) arrangement of the complexes in supercomplexes enabling direct channeling of electron shuttles. In the Gram positive bacterium Corynebacterium glutamicum, the complex III to complex IV electron shuttle cytochrome c is not diffusible but a covalently bound part of the diheme cytochrome subunit QcrC of complex III. Therefore, the complexes III and IV have to form a supercomplex for electron transduction. The aim of this thesis was to purify and characterise this obligatory supercomplex III/IV of C. glutamicum. To gain sufficient biomass of C. glutamicum as starting material for purification, a phosphate buffered minimal medium was developed that enabled yield of total 120 g wet cell mass (38 g dry mass) in 12 L (6×2 L) shaking cultures. The determined conversion factor of glucose into biomass was 0.46 g/g indicating an intact respiratory chain. The yield was increased by bioreactor cultivation to ~690 g wet cell mass (~220 g dry mass) in ~10 L culture volume. A previously described homologous expression system was applied that produces the complex IV subunit CtaD with a fused Strep-tag II to facilitate purification. Affinity purifications using the Strep-tag II affinity to Strep-Tactin resin yielded a mixture of complexes and supercomplexes. Two supercomplex III/IV versions named supercomplex A and B and free complex IV were identified in this mixture by size exclusion chromatography, redox difference spectroscopy and two dimensional polyacrylamide gel electrophoresis including blue native polyacrylamide electrophoresis. The here presented downscaled blue native polyacrylamide electrophoresis method with analysis times of ~1 h enabled efficient screening of factors influencing the stability of supercomplex III/IV. The screening resulted that the integrity of supercomplex III/IV is preserved by using neutral detergents at minimal detergent to protein ratios for solubilisation and low detergent concentrations for purification and storage slightly above the required critical micellar concentration. Furthermore, pH <=7.5 is required for stability of supercomplex III/IV. Large biomass yields enabled upscaling of supercomplex III/IV affinity purification. Application of the identified stability conditions resulted in affinity purified samples free of supercomplex B. The major component supercomplex A was efficiently separated from residual free complex IV by preparative size exclusion chromatography. Concentration of purified supercomplex A by ultracentrifugation resulted in integrity of the supercomplex for several days at 4 °C. Purified supercomplex A contains ten different previously described subunits. The heme content of supercomplex A relative to the protein mass is heme A: 6.0 μmol/g, heme B: 6.5 μmol/g, and heme C: 5.8 μmol/g determined by redox difference spectroscopy and biochemical protein quantification. This indicates an equimolar ratio of complex III and complex IV in supercomplex A. Supercomplex A has quinol oxidase activity that is inhibited by stigmatellin or sodium azide. The turnover number of transferred electrons per complex III monomer is 148 s−1 at 25° C. The homogeneity and stability of the prepared supercomplex A enabled the growth of threedimensional crystals of up to 0.1 mm in length. Their composition of supercomplex A was verified by redox difference spectroscopy of intact crystals and blue native polyacrylamide electrophoresis of dissolved crystals. The crystals diffracted X-rays corresponding to a resolution of ~10 Å. Electron microscopy of negative stained samples revealed the uniform shape of purified supercomplex A particles with dimensions of 22 × 9 nm in the view plane. Combined heme quantification, size determination, determined activity, symmetry considerations, and particle shape indicate that supercomplex A has a central dimer of complex III and two monomers of complex IV on opposite sides. This conformation is functionally reasonable because it provides each complex III monomer with one complex IV monomer as electron acceptor. Therefore, the stoichiometry of supercomplex A is most likely III2IV2. The sensitivity of supercomplex A to detergents indicated a role of phospholipids in its stability. Therefore, a method for phospholipid identification and quantification was developed that is suitable for detergent solubilised crude and purified membrane protein samples. The analysis combines separation of phospholipid classes according to their head group by normal phase high performance liquid chromatography with evaporative light scattering detection. Calibration with external standard allows quantification of phospholipid amount in the range of 0.25-12 μg. The method is verified by analysing the phospholipid content of the well characterised complex III of Saccharomyces cerevisiae. The reduction of its phospholipid content during its purification steps is monitored. The complex III sample purified to crystallisation quality contains the phospholipid content that was also observed in previously reported structures determined by X-ray crystallography. Purified stable supercomplex A from C. glutamicum revealed a large content of bound phospholipids. The main differences between intact supercomplex A and a mixture of potentially disintegrated smaller complexes is that intact supercomplex A has a doubled phosphatidic acid content and an increased phosphatidyl glycerol content. The importance of the small anionic phosphatidic acid for mediation of contacts between complexes in a supercomplex is discussed. The total phospholipid content of stable supercomplex A is sufficient for a complete belt surrounding the supercomplex in the membrane plane. This indicates that also all essential internal phospholipid binding positions are occupied and potentially stabilise supercomplex A.
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.
Carma-1 is required for B cell receptor-/CD40- and T cell receptor-/CD28-induced B- and T-cell activation via JNK and NF-betaB. In B cells, Carma-1 becomes phosphorylated by PKCbeta, leading to its oligomerization. Subsequent Bcl10 binding induces IKKbeta-activation and, thereby, canonical NF-KB signalling. Despite these findings it is still unknown how exactly Carma-1 is connected to the plasma membrane and to the IKK-complex. Therefore, we purified Carma-1 complexes from mouse CH12 B cells using anti-Carma-1 affinity columns. Mass spectrometric analyses of the column eluates demonstrated the presence of Carma-1 as well as three previously uncharacterized adaptor proteins in B cells, one of which was the Trk-fused gene (Tfg), an adaptor protein containing PB1 and coiledcoil domains. Whereas Tfg was originally identified as fusion partner of oncogenic Trk tyrosine kinase mutants, the normal cellular homologue of Tfg has so far not been described in B cells. However, Tfg has been shown in other systems to interact with IKKgamma and to enhance TNFinduced NF-KB activation. Tfg and Carma-1 co-localized at the plasma membrane and perinuclear structures in B cells. We further corroborated the interactions of Tfg, IKKgamma and Carma-1 by Blue Native gel electrophoresis, where Carma-1 and Tfg formed a 0.7–1 MDa complex. Ectopic expression of Tfg increased the molecular mass of IKKgamma complexes, fused IKKgamma, Bcl10 and Carma-1 complexes to a ~2 MDa complex, and increased basal and CD40-induced canonical activity of NF-KB and IKKbeta. In contrast, shRNA-mediated silencing of Tfg decreased CD40-induced IKKbeta activity. Very interestingly, in primary B cells, highest expression of Tfg was detected in marginal zone and B1 B cells, and Carma-1 and Tfg formed complexes in these B cells. Since Carma-1 is required for marginal zone B cell and B1 B cell development, we suggest that a functional interaction between Carma-1 and Tfg contributes to development and maintenance of these cells by means of canonical NF-KB signals.
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.
By translocating proteasomal degradation products into the endoplasmic reticulum (ER) for loading of major histocompatibility complex (MHC) class I molecules, the ATP binding cassette (ABC) transporter associated with antigen processing (TAP) plays a pivotal role in the adaptive immunity against infected or malignantly transformed cells. A key question regarding the transport mechanism is how the inter-domain communication and conformational dynamics of the TAP complex are connected during the peptide transport. To identify residues involved in this processes, we evolved a Trojan horse strategy in which a small artificial protease is inserted into antigenic epitopes. After binding, the TAP backbone in contact is cleaved, allowing the peptide sensor site to be mapped by mass spectrometry. Within this study, the peptide sensor and transmission interface have been identified. This region aligns with the cytosolic loop 1 (CL1) of Sav1866 and MsbA. Based on a number of experimental data and the homology to the bacterial ABC exporter Sav1866, we constructed a 3D structural model of the core TAP complex. According to this model, the CL1 and CL2 of TAP1 are extended cytosolic loops connecting the transmembrane helices (TMH) 2 and 3, and TMH4 and 5 respectively, and contact both nucleotide binding domains (NBDs) of the opposite subunit. In contrast to exporters, the cytosolic loop (named L-loop) of BtuCD importer is much shorter, and contacts only one NBD. The data confirm that the CL1 of TAP1 functions as signal transducer in ABC exporters, because it does not interfere with substrate binding but with substrate transport. The peptide contact site identified herein is restructured during the ATP hydrolysis cycle. Importantly, TAP showed a structural change trapped in the ATP hydrolysis transition state, because direct contact between peptide and CL1 is abolished. By cysteine scanning, the most conserved residues within CL1 were identified, which disrupted the tight coupling between peptide binding and transport. Together with Val-288, these residues are essential in sensing the bound peptide and inter-domain signal transmission. To characterize the molecular architecture of CL1, a convenient and minimally perturbing approach was used, which combined cysteine substitution in the CL1 region and determination of accessibility to thiol specific compounds with different properties. These studies revealed that the N-terminal region of CL1 has a good accessibility for hydrophilic (iodoacetamidofluorescein, IAF) and amphiphilic probes (BODIPY maleimide, BM), whereas the C-terminal region is accessible for hydrophobic probe (coumarin maleimide, CM). Kinetic studies of fluorescence labeling suggest that this region displayed a different accessibility to probes when the protein undergoes distinct conformations (e. g. nucleotide free state), thereby reflecting conformational transitions. Fluorescence labeling with BM induces a lost of peptide transport, whereas the peptide binding remains unaffected. These results indicate that covalent modifications of the CL1 residues influenced the inter-domain communication between transmembrane domain (TMD) and NBD. The X-loop is a recently discovered motif in the NBD of ABC exporters, which stays in close contact to the CLs. Moreover, because the X-loop precedes the ABC signature motif, it probably responds to ATP binding and hydrolysis and may transmit conformational changes to the CLs. By substitution of the highly conserved Glu-602 of TAP2 with residues that have different chemical properties, it was shown for the first time that the X-loop is a functional important element, which plays an key role in coupling substrate binding to downstream events in the transport cycle. We further verified domain swapping in the TAP complex by cysteine cross-linking. The TAP complex can be reversibly arrested either in a binding or translocation incompetent state by cross-linking of the X-loop to CL1 or CL2, respectively. These results resolve the structural arrangement of the transmission interface and point to different functions of the cytosolic loops in substrate recognition, signaling and transport.
The Bay of Diego-Suarez, considered to be one of the finest and largest natural harbours in the world, is located towards the northernmost tip of Madagascar in the Antsiranana province. Despite its historical and current use as a port, much of its convoluted perimeter is still somewhat untouched, harbouring pristine shorelines and subtidal coral reefs. The position of the bay between other regions in which high marine biodiversity has already been revealed suggests that it may also harbour high biodiversity. However, the relatively long coastline and limited connectivity of the bay with the Indian Ocean, in combination with existing anthropogenic activities, potentially make its marine environments susceptible to a range of environmental impacts including sedimentation, nutrification and pollution. The Frontier-Madagascar Marine Research Programme (FMMRP) became involved in conducting marine ecological survey work in the Bay of Diego-Suarez, north Madagascar, in April 2005, having relocated from its previous base at Anakao in southwest Madagascar. The rationale for the survey programme stemmed from the affiliation of the FMMRP with the Malagasy organisations Association Nationale pour la Gestion des Aires Protégées (ANGAP) and Service d’Appui a la Gestion de l’Environnement (SAGE), who were interested in identifying areas of the bay with particularly healthy coral reef systems. Additional environmental interest in the bay has arisen as a result of its proximity to surrounding terrestrial protected areas such as the newly managed Ramena complex, incorporating Orangea and Montagne des Français, and also Montagne d’Ambre. Since its relocation to the Diego-Suarez area, the FMMRP has compiled over two years’ worth of marine ecological data relating to benthic community composition, fish species abundance and population size structure, frequency of algae and invertebrate indicator species, and physical environmental parameters. Thus there exists an extensive dataset for the Bay of Diego-Suarez, from which details of the current condition of its marine habitats can be investigated and a baseline for temporal monitoring can be established. The primary purpose of this report is to signify the initial detailed dissection of the dataset and demonstrate the conclusions that can be made regarding the ecological status of coral reef systems within the bay. This has mostly involved the examination of benthic data, focusing upon variations in percentage cover of substrata and coral community characteristics as useful structural indicators of reef condition. Additionally, the report includes an assessment of the abundance and distribution of sea urchins and their relation to benthic community patterns, as a demonstration of the ability to interrelate different aspect of the FMMRP dataset to enhance the conclusions that can be drawn. Benthic community data were obtained from 380 line intercept transects conducted in different sectors of the Bay of Diego-Suarez between October 2005 and December 2007, representing a combined distance of 7,600 m. Sediment occupied the greatest overall proportion of the benthos (around 38%), especially in the western areas of the bay. Overall mean hard coral cover was around 15%, and tended to co-vary with other ‘hard’ substrata such as rock and rubble. In total, 38 scleractinian coral genera were recorded during survey work, in addition to a number of unidentified genera. The coral communities of the bay were dominated by Acropora and Porites spp., which comprised around 33% and 20% of total recorded hard coral cover, respectively. Hard coral cover and generic diversity appeared to be positively related. These indicators were greatest in the northeast area opposite the mouth of the bay, reaching mean values of around 37% and 6.8 genera, respectively. Here, the hard coral community was dominated by Acropora spp. and comprised a relatively high proportional cover of Galaxea spp. In the northwest of the bay, coral cover was approximately half as great and consisted primarily of species belonging to the genera Porites and Millepora. Habitats in this area were highly similar in terms of their overall coral community composition. Hard coral cover and diversity were generally lower in the southern portion of the bay, especially in more immediate proximity to the population centre of Diego-Suarez (around 2% and 1.5- 5.5 genera, respectively). Coral community composition was considerably more variable than in the northern portion of the bay. v After sediment and ‘hard’ substrata, seagrass formed the next major interplaying component of the benthic environment (around 10% overall proportional cover). The easternmost areas adjacent to the mouth of the bay were characterised by high seagrass cover, whic h reached around 48%. Little or no seagrass was encountered elsewhere, except at one locality in the northwest (around 13% cover). Macroalgae cover was low and less variable, reaching a maximum value of around 10% adjacent to Diego-Suarez. There were no differences between island and mainland sites in terms of overall benthic substratum characteristics, yet soft coral cover was significantly greater amongst island sectors. Sea urchin abundance data were obtained from 498 belt transects conducted between April 2006 and December 2007, representing a total area of 49,800 m2. A total of 6 species were recorded, of which Diadema setosum comprised by far the greatest relative abundance (96%) and observation frequency (55%). The greatest population densities of this species were encountered in the more exposed areas in the west and northwest, reaching around 1.5 m-2, and very few individuals were recorded in the eastern reaches. Data suggest a possible seasonal increase in D. setosum densities, corresponding with an increase in water temperature towards the end of the year. No significant correlation existed between D. setosum population density and coral cover, although these seemed to be inversely related in the central northern area of the bay. There was also no significant correlation with macroalgae cover. However, D. setosum density was positively and negatively associated with rubble and seagrass cover, respectively. There was a lack of a clear pattern amongst sectors with respect to overall benthic community characteristics, let alone between the density of D. setosum and benthic substratum composition. In conclusion, a relatively detailed map of benthic community composition has been produced for the Bay of Diego-Suarez, which shall be useful in elucidating the primary factors determining the condition of marine environments within the bay and developing effective sustainable management strategies. Further analysis, incorporating additional components of the FMMRP dataset, is required in order to further clarify our understanding of the key issues surrounding the current status of these coral reef systems. It is hoped that continued survey work will enable important long-term ecological monitoring of the marine environment of the bay and assessment of the effectiveness of any management initiatives that may be implemented.
This checklist of the lichens and Iichenicolous fungi of Chile (including the Antarctic ten-itory, Juan Fernandez and Easter island) includes 1415 taxa in 304 genera of which 1383 are lichens (in 281 genera), and 32 are lichenicolaus fungi (in 23 genera). Full bibliographic citations are given for both accepted taxa and for synonyms and references to relevant literature are included for most genera. The following new combinations are proposed: Caloplaca austroshetlandica (Zahlbr.) D.J. Galloway & Quilhot, Dendriscocaulon calithamnion (Taylor) D.J. Galloway & Quilhot, Neuropogon durietzii (Motyka) D.J. Galloway & Qllilhot, Neuropogon patagonicus (F.J. Walker) DJ. Galloway & Quilhot, and Neuropogon subamarcticus (F. J. Walker) D.,T. Galloway & Quilhot.
Many highly active antitumour agents are currently not employable for the systemic chemotherapy of brain tumours since their entrance into the brain is blocked by the BBB. Obviously, the development of a strategy allowing effective delivery of these agents across the BBB would enormously extend the potential of the systemic chemotherapy. Chemotherapy of rat glioblastoma using nanoparticle-bound doxorubicin Doxorubicin bound to polysorbate-coated nanoparticles had been previously shown to significantly enhance survival in the orthotopic rat 101/8 glioblastoma model. The objective of this study was to investigate the therapeutic effects of this formulation by morphometric, histological and immunohistological methods. The 101/8 glioblastoma was implanted intracranially into the male Wistar rats. The animals were randomly divided into 3 groups; one group served as untreated control (n = 20). The second group received doxorubicin in solution (Dox-sol, n = 18), and the third group received doxorubicin bound to PBCA nanoparticles coated with PS 80 (Dox-NP + PS 80, n = 18). The treatment regimen was 3 × 1.5 mg/kg on days 2, 5, and 8 after tumor implantation. The formulations were injected into the tail vein. The untreated control animals were sacrificed on days 6, 8, 10, 12, and 14 after the implantation. The animals that had received chemotherapy were sacrificed on day 10, 14 and 18 after the implantation. The brains were investigated by morphometrical, histochemical, and immunohistochemical methods such as the measurement of the tumor size, proliferation of tumor cells, vessel density, expression of glial fibrillary acidic protein (GFAP), expression of vascular endothelial growth factor (VEGF), incidence and dimension of necrosis, and microvascular proliferation. Tumours showed signs of malignancy including invasion to brain tissue and brisk mitotic activity. The tumor proliferation remained stable at high levels throughout the host survival time. Overall, the tumor showed a reproducible growth pattern and temporal development that is comparable to human glioblastoma. Furthermore, the 101/8 glioblastoma had infiltrated diffusely the surrounding host brain at the edge of the solid tumor mass showed no signs of encapsulation. Thus the 101/8 glioblastoma fulfills the most criteria for an adequate glioma model and can be qualified as a reliable model. ...