Structural and Biochemical Studies of the Human DEAD-box Helicase Dbp5 and Nucleoporin Nup214 Involved in mRNA Export

The hallmark of eukaryotic evolution was the development of the nucleus in cells. This compartmentalization requires the nucleocytoplasmic transport of thousands of molecules. The gate into and out of the nucleus is the nuclear pore complex (NPC). One of the molecules that needs to be exported from the nucleus is messenger RNA (mRNA). mRNA associates with proteins in the nucleus forming a messenger ribonucleoprotein particle (mRNP). mRNPs bind to dedicated transport factors that facilitate movement through the NPC. One protein that associates to mRNPs is the helicase Dbp5, which belongs to the DEAD-box family of RNA helicases. Dbp5 is essential for mRNA export in both yeast and humans. It binds RNA and is concentrated and locally activated at the cytoplasmic side of the nuclear pore complex, where it interacts with the cytoplasmic nucleoporin Nup214. In my PhD work, I have determined the crystal structures of human Dbp5 bound to RNA and AMPPNP, and bound to Nup214. I designed and performed in vitro assays, which show that binding of Dbp5 to nucleic acid and to Nup214 is mutually exclusive. The interactions are mediated by conserved residues, implying a conserved recognition mechanism. These results suggest a framework for the consecutive steps leading to the release of mRNA at the final stages of nuclear export. More generally, they provide a paradigm for how binding of regulators can specifically inhibit DEAD-box proteins

Linear polarization sensitivity of SeGA detectors

Parity is a key observable in nuclear spectroscopy. Linear polarization measurements of $\gamma$-rays are a probe to access the parities of energy levels. Utilizing the segmentation of detectors in the Segmented Germanium Array (SeGA) at the NSCL and analyzing the positions of interaction therein allows the detectors to be used as Compton polarimeters. Unlike other segmented detectors, SeGA detectors are irradiated from the side to utilize the transversal segmentation for better Doppler corrections. Sensitivity in such an orientation has previously been untested. A linear polarization sensitivity $Q \approx 0.14$ has been measured in the 350-keV energy range for SeGA detectors using $\alpha$-$\gamma$ correlations from a \nuc{249}{Cf} source.Comment: 7 pages, 9 figure

Deformed two center shell model

A highly specialized two-center shell model has been developed accounting for the splitting of a deformed parent nucleus into two ellipsoidaly deformed fragments. The potential is based on deformed oscillator wells in direct correspondance with the shape change of the nuclear system. For the first time a potential responsible for the necking part between the fragments is introduced on potential theory basis. As a direct consequence, spin-orbit {\bf ls} and {\bf l$^2$} operators are calculated as shape dependent. Level scheme evolution along the fission path for pairs of ellipsoidaly deformed fragments is calculated. The Strutinsky method yields the shell corrections for different mass asymmetries from the superheavy nucleus $^{306}$122 and $^{252}$Cf all along the splitting process.Comment: 32 pages, 8 figure

Determining the global minimum of Higgs potentials via Groebner bases - applied to the NMSSM

Determining the global minimum of Higgs potentials with several Higgs fields like the next-to-minimal supersymmetric extension of the Standard Model (NMSSM) is a non-trivial task already at the tree level. The global minimum of a Higgs potential can be found from the set of all its stationary points defined by a multivariate polynomial system of equations. We introduce here the algebraic Groebner basis approach to solve this system of equations. We apply the method to the NMSSM with CP conserving as well as CP violating parameters. The results reveal an interesting stationary-point structure of the potential. Requiring the global minimum to give the electroweak symmetry breaking observed in Nature excludes large parts of the parameter space.Comment: 10 pages, 2 figure

Spirometry reference equations for central European populations from school age to old age.

Spirometry reference values are important for the interpretation of spirometry results. Reference values should be updated regularly, derived from a population as similar to the population for which they are to be used and span across all ages. Such spirometry reference equations are currently lacking for central European populations. To develop spirometry reference equations for central European populations between 8 and 90 years of age. We used data collected between January 1993 and December 2010 from a central European population. The data was modelled using "Generalized Additive Models for Location, Scale and Shape" (GAMLSS). The spirometry reference equations were derived from 118'891 individuals consisting of 60'624 (51%) females and 58'267 (49%) males. Altogether, there were 18'211 (15.3%) children under the age of 18 years. We developed spirometry reference equations for a central European population between 8 and 90 years of age that can be implemented in a wide range of clinical settings

Structural and biochemical studies of SLIP1–SLBP identify DBP5 and eIF3g as SLIP1-binding proteins

In metazoans, replication-dependent histone mRNAs end in a stem-loop structure instead of the poly(A) tail characteristic of all other mature mRNAs. This specialized 3′ end is bound by stem-loop binding protein (SLBP), a protein that participates in the nuclear export and translation of histone mRNAs. The translational activity of SLBP is mediated by interaction with SLIP1, a middle domain of initiation factor 4G (MIF4G)-like protein that connects to translation initiation. We determined the 2.5 Å resolution crystal structure of zebrafish SLIP1 bound to the translation–activation domain of SLBP and identified the determinants of the recognition. We discovered a SLIP1-binding motif (SBM) in two additional proteins: the translation initiation factor eIF3g and the mRNA-export factor DBP5. We confirmed the binding of SLIP1 to DBP5 and eIF3g by pull-down assays and determined the 3.25 Å resolution structure of SLIP1 bound to the DBP5 SBM. The SBM-binding and homodimerization residues of SLIP1 are conserved in the MIF4G domain of CBP80/20-dependent translation initiation factor (CTIF). The results suggest how the SLIP1 homodimer or a SLIP1–CTIF heterodimer can function as platforms to bridge SLBP with SBM-containing proteins involved in different steps of mRNA metabolism

Fungi under Modified Atmosphere—The Effects of CO2 Stress on Cell Membranes and Description of New Yeast Stenotrophomyces fumitolerans gen. nov., sp. nov.

High levels of carbon dioxide are known to inhibit the growth of microorganisms. A total of twenty strains of filamentous fungi and yeasts were isolated from habitats with enriched carbon dioxide concentration. Most strains were derived from modified atmosphere packed (MAP) food products or mofettes and were cultivated under an atmosphere of 20% CO₂ and 80% O₂. The influence of CO₂ on fungal cell membrane fatty acid profiles was examined in this study. Major changes were the increase in linolenic acid (C18:3 cis 9, 12, 15) and, additionally in most strains, linoleic acid (C18:2 cis 9, 12) with a maximum of 24.8%, at the expense of oleic (C18:1 cis 9), palmitic (C16:0), palmitoleic (C16:1 cis 9) and stearic acid (C18:0). The degree of fatty acid unsaturation increased for all of the strains in the study, which consequently led to lower melting temperatures of the cell membranes after incubation with elevated levels of CO₂, indicating fluidization of the membrane and a potential membrane malfunction. Growth was reduced in 18 out of 20 strains in laboratory experiments and a change in pigmentation was observed in several strains. Two of the isolated strains, strain WT5 and strain WR1, were found to represent a hitherto undescribed yeast for which the new genus and species Stenotrophomyces fumitolerans (MB# 849906) is proposed

A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN

Cooperative binding of ATP and RNA to DEAD-box helicases induces the closed conformation of their helicase core, with extensive interactions across the domain interface. The bound RNA is bent, and its distortion may constitute the first step towards RNA unwinding. To dissect the role of the conformational change in the helicase core for RNA unwinding, we characterized the RNA-stimulated ATPase activity, RNA unwinding and the propensity to form the closed conformer for mutants of the DEAD box helicase YxiN. The ATPase-deficient K52Q mutant forms a closed conformer upon binding of ATP and RNA, but is deficient in RNA unwinding. A mutation in motif III slows down the catalytic cycle, but neither affects the propensity for the closed conformer nor its global conformation. Hence, the closure of the cleft in the helicase core is necessary but not sufficient for RNA unwinding. In contrast, the G303A mutation in motif V prevents a complete closure of the inter-domain cleft, affecting ATP binding and hydrolysis and is detrimental to unwinding. Possibly, the K52Q and motif III mutants still introduce a kink into the backbone of bound RNA, whereas G303A fails to kink the RNA substrate