Solution structures of stem-loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin

Nucleolin, a multi-domain protein involved in ribosome biogenesis, has been shown to bind the consensus sequence (U/G)CCCG(A/G) in the context of a hairpin loop structure (nucleolin recognition element; NRE). Previous studies have shown that the first two RNA-binding domains in nucleolin (RBD12) are responsible for the interaction with the in vitro selected NRE (sNRE). We have previously reported the structures of nucleolin RBD12, sNRE and nucleolin RBD12–sNRE complex. A comparison of free and bound sNRE shows that the NRE loop becomes structured upon binding. From this observation, we hypothesized that the disordered hairpin loop of sNRE facilitates conformational rearrangements when the protein binds. Here, we show that nucleolin RBD12 is also sufficient for sequence- specific binding of two NRE sequences found in pre-rRNA, b1NRE and b2NRE. Structural investigations of the free NREs using NMR spectroscopy show that the b1NRE loop is conformationally heterogeneous, while the b2NRE loop is structured. The b2NRE forms a hairpin capped by a YNMG-like tetraloop. Comparison of the chemical shifts of sNRE and b2NRE in complex with nucleolin RBD12 suggests that the NRE consensus nucleotides adopt a similar conformation. These results show that a disordered NRE consensus sequence is not a prerequisite for nucleolin RBD12 binding.     

Distinct versus redundant properties among members of the INK4 family of cyclin-dependent kinase inhibitors

p16(INK4a), p15(INK4b), p18(INK4c) and p19(INK4d) comprise a family of cyclin-dependent kinase inhibitors and tumor suppressors. We report that the INK4 proteins share the ability to arrest cells in G1, and interact with CDK4 or CDK6 with similar avidity. In contrast, only p18 and particularly p19 are phosphorylated in vivo, and each of the human INK4 proteins shows unique expression patterns dependent on cell and tissue type, and differentiation stage. Thus, the INK4 proteins harbor redundant as well as non-overlapping properties, suggesting distinct regulatory modes, and diverse roles for the individual INK4 family members in cell cycle control, cellular differentiation, and multistep oncogenesis.     

Crystalline yolk spheroids in Drosophila melanogaster oocyte: freeze fracture and two-dimensional reconstruction analysis

The major sites of energy storage during oogenesis in the Drosophila melanogaster oocyte are the alpha- and beta-yolk spheres. By applying biochemical and transmission electron microscopy (TEM) immunogold techniques we found that the beta-yolk spheres contain mainly polysaccharides, while the three main yolk proteins (YPs) are stored in the alpha-yolk spheres of the developing oocyte. Moreover, by using high-resolution TEM of freeze fractured or cryosectioned follicles, we identified the existence of crystalline structures within the alpha-yolk spheres of the mature oocyte. Our subsequent two-dimensional reconstruction analysis revealed that the unit cell of the crystal is about 113 Angstrom x 113 Angstrom. Assuming that the repeating unit is a cylinder of about 110 Angstrom in length and 25 Angstrom in diameter this cylinder would then have a volume of about 50,000 cubic Angstrom, which corresponds to about 40 kDa of protein. This size fits quite well with the known molecular weight of about 40-45 kDa for each of the three D. melanogaster YPs. Overall, our study identifies for the first time the supramolecular arrangement of the alpha-yolk spheres constituent molecules and provides direct evidence for the "natural" crystallization, and therefore the efficient packaging, of the YPs during oogenesis.     

Mate choice evolution, dominance effects, and the maintenance of genetic variation

Female mate choice influences the maintenance of genetic variation by altering the mating success of males with different genotypes. The evolution of preferences themselves, on the other hand, depends on genetic variation present in the population. Few models have tracked this feedback between a choice gene and its effects on genetic variation, in particular when genes that determine offspring viability and attractiveness have dominance effects. Here we build a population genetic model that allows comparing the evolution of various choice rules in a single framework. We first consider preferences for good genes and show that focused preferences for homozygotes evolve more easily than broad preferences, which allow heterozygous males high mating success too. This occurs despite better maintenance of genetic diversity in the latter scenario, and we discuss why empirical findings of superior mating success of heterozygous males consequently do not immediately lead to a better understanding of the lek paradox. Our results thus suggest that the mechanisms that help maintain genetic diversity also have a flipside of making female choice an inaccurate means of producing the desired kind of offspring. We then consider preferences for heterozygosity per se, and show that these evolve only under very special conditions. Choice for compatible genotypes can evolve but its selective advantage diminishes quickly due to frequency-dependent selection. Finally, we show that our model reproduces earlier results on selfing, when the female choice strategy produces assortative mating. Overall, our model indicates that various forms of heterozygote-favouring (or variable) female choice pose a problem for the theory of sexual ornamentation based on indirect benefits, rather than a solution.     

The dream of staying clean: Lotus and biomimetic surfaces

The Lotus has been the symbol of purity for thousands of years; contaminations and pathogens are washed off the surfaces of Lotus and some other plants with rain or even dew. After the introduction of scanning electron microscopy, we were able to resolve the mechanism behind this phenomenon. It took some further decades before in-depth studies on self-cleaning with plants were conducted and the effect could be understood in detail. We identified extreme water-repellency ('superhydrophobicity'), characterized by very high contact angles and low sliding angles, as the prerequisite for self-cleaning properties. We could show that the combination of two factors is necessary for obtaining a high degree of water-repellency: (1) low energy surfaces being hydrophobic and (2) surface structures that significantly increase hydrophobicity. It is suggested that this mechanism plays an important role in the protection of plants against pathogens. Our technological application of this effect has resulted in the development of successful, eco-friendly and sustainable industrial products. Another interesting property was found with superhydrophobic surfaces of certain aquatic and semi-aquatic plants and animals: here a layer of air under water is retained. We present a new approach of using this feature for creating structured, air-retaining surfaces for technical underwater applications. It is proposed that such surfaces can reduce significantly the drag of large ships. We conclude that basic biological research is of particular importance for true innovation. Our research on superhydrophobic self-cleaning biological surfaces and the development of similar engineered materials suggests that biomimicry is a matter of multi-stage processes rather than a simple copying of biological developments.     

Phosphorylation-regulated cleavage of the reticulon protein Nogo-B by caspase-7 at a noncanonical recognition site

Reticulons (RTNs) are a large family of transmembrane proteins present throughout the eukaryotic domain in virtually every cell type. Despite their wide distribution, their function is still mostly unknown. RTN4, also termed Nogo, comes in three isoforms, Nogo-A, -B, and -C. While Nogo-A has been described as potent inhibitor of nerve growth, Nogo-B has been implicated in vascular remodeling and regulation of apoptosis. We show here that Nogo-B gets cleaved by caspase-7, but not caspase-3, during apoptosis at a caspase nonconsensus site. By a combination of MS and site-directed mutagenesis we demonstrate that proteolytic processing of Nogo-B is regulated by phosphorylation of Ser(16) within the cleavage site. We present cyclin-dependent kinase (Cdk)1 and Cdk2 as kinases that phosphorylate Nogo-B at Ser(16) in vitro. In vivo, cleavage of Nogo-B is markedly increased in Schwann cells in a lesion model of the rat sciatic nerve. Taken together, we identified an RTN protein as one out of a selected number of caspase targets during apoptosis and as a novel substrate for Cdk1 and 2. Furthermore, our data support a functionality of caspase-7 that is distinct from closely related caspase-3.     

Highly hydrophilic cationic gold nanorods stabilized by novel quaternary ammonium surfactant with negligible cytotoxicity

The photothermal cancer therapy using cationic gold nanorods (GNRs) stabilized by quaternary ammonium salts (QAS) have a great potential to enhance conventional cancer treatment as it promises the effective eradication of cancer cells including cells resistant to radio‐ and chemo‐therapy and the stimulation of anti‐tumor immune response. However, as the cytotoxicity of the conventional alkanethiol‐QAS compounds limits their utility in medicine, here we developed GNRs modified by novel highly hydrophilic cationic surfactant composed of the quaternary ammonium group and ethylene glycol chain N,N,N‐trimethyl‐3,6,9,12,15‐pentaoxaheptadecyl‐17‐sulfanyl‐1‐ammonium bromide (POSAB) showing insignificant cytotoxicity in the free state. Surface modification of GNRs by POSAB allowed to prepare nanoparticles with good stability in water, high cellular uptake and localization in lysosomes that are a promising alternative to alkanethiol‐stabilized GNRs especially for biomedical applications.     

Genetic Liver-Specific AMPK Activation Protects against Diet-Induced Obesity and NAFLD

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