Structural investigation on membrane proteins : the case of the KdgM porin family, OmpF and IIBCSUC

Gram-negative bacteria are surrounded by two distinct membranes delimiting the periplasm. The inner-membrane (or cytoplasmic membrane) is composed of a phospholipid bilayer whereas the outer-membrane is asymmetric and composed of lipopolysaccharides in the outer leaflet and phospholipids in the inner leaflet. Both membranes are spanned by numerous membrane proteins. These are various and their genes are representing about 30% of the genome in living organisms. Although the first membrane protein structures were solved in the 80s using X-ray crystallography, structural data is still very limited. This dissertation groups our contributions to this field in the last few years and is divided in three parts. A first chapter will describe our work on the structural characterization of proteins from the KdgM family. This family of small porins has been first identified in Dickeya dadantii a plant pathogen. It has been shown that members of that specific porin family are able to transport acidic (oligo)saccharides but the structural and biochemical data remain scarce. We undertook to study this family using X-ray crystallography working in parallel on several homologues. The chapter is divided in three parts: (I) the purification of the Escherichia coli NanC porin, a member of the KdgM family involved in the uptake of sialic acid, its crystallization and structure determination at 1.8 Å resolution; (II) the discussions concerning the biological implications of the NanC structure that was published in a research article as well as additional discussions, and (III) the still ongoing work on the purification and crystallization of KdgM using microseeding matrix screening and surface entropy reduction. In a second chapter, we will discuss a new crystal form of OmpF, the general porin of E. coli. OmpF is probably the best studied outer-membrane general porin as it is very abundant and rather easy to purify. It has also been used as a model to study translocation of ions through porins. Since it first structural determination, OmpF structures have been determined in several space groups. Here we report a new crystal form diffracting to 2.7 Å resolution and we discuss the presence of 32-symmetry related, honeycomb like layers reoccurring in almost all OmpF crystal forms and formed by identical contacts. The last chapter will discuss the purification and crystallization attempts of the inner-membrane sucrose specific permease IIBCsuc from Salmonella typhimurium and of its complex with a Fab antibody fragment. This protein belongs to the phosphoenolpyruvate: sugar phosphotransferase system (PTS) which is ubiquitous in eubacteria, but is not found in other organisms. The PTS belongs to the group translocation super-family of transporters and is composed of proteins or domains allowing the specific uptake of a sugar and its concomitant phosphorylation. Apart from topology studies, no structural data is available on the sugar translocation proteins of the PTS whereas all other members have been characterized. In order to increase the crystallization ability of the IIBCsuc permease, we used monoclonal antibodies Fab fragments to enlarge the hydrophilic surface of the permease and to rigidify its structure. Fab fragment production, purification and binding will be discussed as well as crystallization trials of IIBCsuc-Fab complexes. ---------- Zusammenfassung Komplex Herstellung. Zwei neue Ligandenklassen wurden hergestellt und in der Iridium-katalysierten asymmetrischen Hydrierung getestet. Ausgehend von R,R- und S,S-Diphenylethylendiamin verbunden mit verschiedenen chiralen Pyridinylalkoholen wurden zwölf verschiedene Diazaphospholidin-Liganden hergestellt und zu Iridium-Komplexen umgesetzt. Diese Komplexe wurden in der Hydrierung von verschiedenen unfunktionalisierten und funktionalisierten Alkenen, besonders aber für alpha, beta-ungesättigte Carbonsäureester, getestet. Die Hydrierungen der verschiedenen Alkene waren sehr erfolgreich, sie lieferten Enantiomerenüberschüsse von bis zu 99%. Bei alpha-methylierten alpha, beta-ungesättigten Carbonsäureestern mit verschiedenen Substituenten in der beta-Position ergaben die Hydrierungen über 90% ee. Für die beta-methylierten Carbonsäureester lieferten die neuen Iridium-Komplexe bis zu 97% ee. Die Entwicklung und Herstellung von neuen P,N-Liganden, welche auf Imidazolinen basieren, wurde als nächstes untersucht. Strukturell ähnliche Oxazolin-Liganden wurden durch Imidazoline ersetzt. Durch das zusätzliche Stickstoffatom kännen die elektronischen und sterischen Eigenschaften der Liganden modifiziert werden. Eine erfolgreiche Syntheseroute zur Herstellung der Imidazolin-Iridium-Komplexe wurde entwickelt. Allerdings waren die Hydrierungen mit den neuen Imidazolin-Iridium-Komplexen eher unbefriedigend. Eine Verbesserung der Imidazolin-Liganden gelang, indem man den aromatischen Ring am Stickstoffatom durch eine Sulfonyl-Gruppe ersetzte. Es wurde eine neue Syntheseroute für diese Ligandenklasse entwickelt und es konnten somit vier neue Sulfonyl-Imidazolin-Iridium-Komplexe hergestellt und in der asymmetrischen Hydrierung getestet werden. Die Hydrierungen von verschiedenen unfunktionalisierten und funktionalisierten Alkenen lieferten Enantiomerenüberschüsse von über 90%. Anwendung in Naturstoff- und Wirkstoffsynthesen. Der zweite Teil dieser Arbeit war die Anwendung der Iridium-katalysierten asymmetrischen Hydrierung zur Herstellung von biologisch wichtigen Naturstoffen. Bei einer Zusammenarbeit mit Prof. J. Mulzer (Universität Wien, …sterreich) wurde eine asymmetrische Synthese für Platensimycin entwickelt. Die geplante Syntheseroute beinhaltete die asymmetrische Hydrierungen von zwei Zwischenstufen, welche erfolgreich mit exzellenten Umsätzen und Enantioselektivitäten erreicht wurden. Dabei lieferte der Iridium-Komplex 67c die besten Ergebnisse. Die Zwischenstufe konnte mit einer geringen Katalysatorbeladung und im Gramm-Ma§stab umgesetzt werden. Das nächste Projekt war die Synthese von Aliskiren. Dabei wurden verschiedene Ester hergestellt und in der Iridium-katalysierten asymmetrischen Hydrierung getestet. Nach einer ausgiebigen Suche für einen geeigneten Katalysator lieferte der PHOX-Komplex 28a und der PHIM-Komplex 134a für den tert-Butylester vollständigen Umsatz und 99% ee

Single-channel measurements of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli

NanC is an Escherichia coli outer membrane protein involved in sialic acid (Neu5Ac, i.e., N-acetylneuraminic acid) uptake. Expression of the NanC gene is induced and controlled by Neu5Ac. The transport mechanism of Neu5Ac is not known. The structure of NanC was recently solved (PDB code: 2WJQ) and includes a unique arrangement of positively charged (basic) side chains consistent with a role in acidic sugar transport. However, initial functional measurements of NanC failed to find its role in the transport of sialic acids, perhaps because of the ionic conditions used in the experiments. We show here that the ionic conditions generally preferred for measuring the function of outer-membrane porins are not appropriate for NanC. Single channels of NanC at pH 7.0 have: (1) conductance 100 pS to 800 pS in 100 mM: KCl to 3 M: KCl), (2) anion over cation selectivity (V (reversal) = +16 mV in 250 mM: KCl || 1 M: KCl), and (3) two forms of voltage-dependent gating (channel closures above ±200 mV). Single-channel conductance decreases by 50% when HEPES concentration is increased from 100 ?M: to 100 mM: in 250 mM: KCl at pH 7.4, consistent with the two HEPES binding sites observed in the crystal structure. Studying alternative buffers, we find that phosphate interferes with the channel conductance. Single-channel conductance decreases by 19% when phosphate concentration is increased from 0 mM: to 5 mM: in 250 mM: KCl at pH 8.0. Surprisingly, TRIS in the baths reacts with Ag|AgCl electrodes, producing artifacts even when the electrodes are on the far side of agar-KCl bridges. A suitable baseline solution for NanC is 250 mM: KCl adjusted to pH 7.0 without buffer

Local stabilization of an unstable parabolic equation via saturated controls

We derive a saturated feedback control, which locally stabilizes a linear reaction-diffusion equation. In contrast to most other works on this topic, we do not assume the Lyapunov stability of the uncontrolled system and consider general unstable systems. Using Lyapunov methods, we provide estimates for the region of attraction for the closed-loop system, given in terms of linear and bilinear matrix inequalities. We show that our results can be used with distributed as well as scalar boundary control, and with different types of saturations. The efficiency of the proposed method is demonstrated by means of numerical simulations

Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance

<p>Abstract</p> <p>Background</p> <p>Previous studies have revealed a wide-spread occurence of the partial and complete genomes of the reverse-transcribing pararetroviruses in the nuclear genomes of herbaceous plants. Although the absence of the virus-encoded integrases attests to the random and incidental incorporation of the viral sequences, their presence could have functional implications for the virus-host interactions.</p> <p>Hypothesis</p> <p>Analyses of two nuclear genomes of grapevine revealed multiple events of horizontal gene transfer from pararetroviruses. The ~200–800 bp inserts that corresponded to partial ORFs encoding reverse transcriptase apparently derived from unknown or extinct caulimoviruses and tungroviruses, were found in 11 grapevine chromosomes. In contrast to the previous reports, no reliable cases of the inserts derived from the positive-strand RNA viruses were found. Because grapevine is known to be infected by the diverse positive-strand RNA viruses, but not pararetroviruses, we hypothesize that pararetroviral inserts have conferred host resistance to these viruses. Furthermore, we propose that such resistance involves RNA interference-related mechanisms acting via small RNA-mediated methylation of pararetroviral DNAs and/or via degradation of the viral mRNAs.</p> <p>Conclusion</p> <p>The pararetroviral sequences in plant genomes may be maintained due to the benefits of virus resistance to this class of viruses conferred by their presence. Such resistance could be particularly significant for the woody plants that must withstand years- to centuries-long virus assault. Experimental research into the RNA interference pathways involving the integrated pararetroviral inserts is required to test this hypothesis.</p> <p>Reviewers</p> <p>This article was reviewed by Arcady R. Mushegian, I. King Jordan, and Eugene V. Koonin.</p

Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A

Ribosomal translation factors are fundamental for protein synthesis and highly conserved in all kingdoms of life. The essential eukaryotic elongation factor 1A (eEF1A) delivers aminoacyl tRNAs to the A-site of the translating 80S ribosome. Several studies have revealed that eEF1A is posttranslationally modified. Using MS analysis, site-directed mutagenesis, and X-ray structural data analysis of Saccharomyces cerevisiae eEF1A, we identified a posttranslational modification in which the α amino group of mono-l-glutamine is covalently linked to the side chain of glutamate 45 in eEF1A. The MS analysis suggested that all eEF1A molecules are modified by this glutaminylation and that this posttranslational modification occurs at all stages of yeast growth. The mutational studies revealed that this glutaminylation is not essential for the normal functions of eEF1A in S. cerevisiae. However, eEF1A glutaminylation slightly reduced growth under antibiotic-induced translational stress conditions. Moreover, we identified the same posttranslational modification in eEF1A from Schizosaccharomyces pombe but not in various other eukaryotic organisms tested despite strict conservation of the Glu45 residue among these organisms. We therefore conclude that eEF1A glutaminylation is a yeast-specific posttranslational modification that appears to influence protein translation

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms

Recent advances in modeling and simulation of the exposure and response of tungsten to fusion energy conditions

Under the anticipated operating conditions for demonstration magnetic fusion reactors beyond ITER, structural and plasma-facing materials will be exposed to unprecedented conditions of irradiation, heat flux, and temperature. While such extreme environments remain inaccessible experimentally, computational modeling and simulation can provide qualitative and quantitative insights into materials response and complement the available experimental measurements with carefully validated predictions. For plasma-facing components such as the first wall and the divertor, tungsten (W) has been selected as the leading candidate material due to its superior high-temperature and irradiation properties, as well as for its low retention of implanted tritium. In this paper we provide a review of recent efforts in computational modeling of W both as a plasma-facing material exposed to He deposition as well as a bulk material subjected to fast neutron irradiation. We use a multiscale modeling approach-commonly used as the materials modeling paradigm-to define the outline of the paper and highlight recent advances using several classes of techniques and their interconnection. We highlight several of the most salient findings obtained via computational modeling and point out a number of remaining challenges and future research directions.Peer reviewe

Interdependency of subsurface carbon distribution and graphene-catalyst interaction.

The dynamics of the graphene-catalyst interaction during chemical vapor deposition are investigated using in situ, time- and depth-resolved X-ray photoelectron spectroscopy, and complementary grand canonical Monte Carlo simulations coupled to a tight-binding model. We thereby reveal the interdependency of the distribution of carbon close to the catalyst surface and the strength of the graphene-catalyst interaction. The strong interaction of epitaxial graphene with Ni(111) causes a depletion of dissolved carbon close to the catalyst surface, which prevents additional layer formation leading to a self-limiting graphene growth behavior for low exposure pressures (10(-6)-10(-3) mbar). A further hydrocarbon pressure increase (to ∼10(-1) mbar) leads to weakening of the graphene-Ni(111) interaction accompanied by additional graphene layer formation, mediated by an increased concentration of near-surface dissolved carbon. We show that growth of more weakly adhered, rotated graphene on Ni(111) is linked to an initially higher level of near-surface carbon compared to the case of epitaxial graphene growth. The key implications of these results for graphene growth control and their relevance to carbon nanotube growth are highlighted in the context of existing literature.R.S.W. acknowledges a Research Fellowship from St. John’s College, Cambridge. S.H. acknowledges funding from ERC grant InsituNANO (No. 279342) and EPSRC under grant GRAPHTED (Ref. EP/K016636/1). We acknowledge the Helmholtz-Zentrum-Berlin Electron storage ring BESSY II for provision of synchrotron radiation at the ISISS beamline and we thank the BESSY staff for continuous support of our experiments. This research was partially supported by the EU FP7 Work Programme under grant Graphene Flagship (No. 604391). PRK acknowledges funding the Cambridge Commonwealth Trust. H.A. and C.B. acknowledge J.-Y. Raty and B. Legrand for fruitful discussions.This is the final published version. It's also available from ACS at http://pubs.acs.org/doi/abs/10.1021/ja505454v

On the Origin and Spread of the Scab Disease of Apple: Out of Central Asia

Background Venturia inaequalis is an ascomycete fungus responsible for apple scab, a disease that has invaded almost all apple growing regions worldwide, with the corresponding adverse effects on apple production. Monitoring and predicting the effectiveness of intervention strategies require knowledge of the origin, introduction pathways, and population biology of pathogen populations. Analysis of the variation of genetic markers using the inferential framework of population genetics offers the potential to retrieve this information. Methodology/Principal Findings Here, we present a population genetic analysis of microsatellite variation in 1,273 strains of V. inaequalis representing 28 orchard samples from seven regions in five continents. Analysis of molecular variance revealed that most of the variation (88%) was distributed within localities, which is consistent with extensive historical migrations of the fungus among and within regions. Despite this shallow population structure, clustering analyses partitioned the data set into separate groups corresponding roughly to geography, indicating that each region hosts a distinct population of the fungus. Comparison of the levels of variability among populations, along with coalescent analyses of migration models and estimates of genetic distances, was consistent with a scenario in which the fungus emerged in Central Asia, where apple was domesticated, before its introduction into Europe and, more recently, into other continents with the expansion of apple growing. Across the novel range, levels of variability pointed to multiple introductions and all populations displayed signatures of significant post-introduction increases in population size. Most populations exhibited high genotypic diversity and random association of alleles across loci, indicating recombination both in native and introduced areas. Conclusions/Significance Venturia inaequalis is a model of invasive phytopathogenic fungus that has now reached the ultimate stage of the invasion process with a broad geographic distribution and well-established populations displaying high genetic variability, regular sexual reproduction, and demographic expansion.Contexte Venturia inaequalis est un champignon ascomycete responsable de la tavelure du pommier, une maladie qui a envahi presque toutes les régions du monde où le pommier est cultivé posant ainsi de graves problèmes en production. Prévenir et enrayer efficacement la réussite d’un tel succès invasif nécessite des connaissances approfondies sur l’origine, les voies d’introduction, la biologie et la génétique de ces populations invasives. En utilisant le potentiel d’inférence de la génétique des populations, l’analyse de la variation de marqueurs génétiques offre la possibilité d’accéder à ces informations. Méthodologie et Principaux résultats Ici nous présentons l’analyse de données microsatellites obtenues pour 1273 souches de V. inaequalis provenant de 28 vergers prélevées dans 7 régions sur les 5 continents. L’analyse de la variance moléculaire révèle que 88% de la variation se retrouve dans les vergers échantillonnés, ce qui est compatible avec d’importantes migrations historiques du champignon entre et à l’intérieur même des régions. Malgré cette très faible structuration des populations, les différentes analyses de clustering mettent en évidence un partage des populations en groupes séparés correspondant à leur origine géographique, montrant ainsi que chaque région héberge une population distincte du champignon. Ensemble, les résultats obtenus sur la comparaison du niveau de variabilité entre populations, les analyses de coalescence et les modèles de migration testés plaident en faveur d’un scénario dans lequel le champignon aurait émergé d’Asie Centrale, où le pommier a été domestiqué, avant d’être introduit en Europe puis plus récemment dans les autres continents suite à l’expansion de la culture du pommier. Les niveaux de variabilité indiquent que ces territoires ont subi des introductions multiples et que les populations portent toutes des signatures révélant de fortes expansions démographiques après leur introduction. Enfin, la forte diversité génotypique des populations et l’association aléatoire des allèles entre loci suggèrent que le champignon présente une reproduction sexuée régulière à la fois dans les régions où il a été introduit et dans sa région native. Conclusion et Portée. Venturia inaequalis est un modèle de champignons phytopathogène invasif qui a maintenant atteint le stade ultime du processus invasif, c’est à dire une très large distribution géographique par des populations bien établies montrant une grande diversité génétique, une reproduction sexuée régulière et une histoire d’expansion démographique

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure