The regulatory complex of Drosophila melanogaster 26S proteasomes. Subunit composition and localization of a deubiquitylating enzyme

Drosophila melanogaster embryos are a source for homogeneous and stable 26S proteasomes suitable for structural studies. For biochemical characterization, purified 26S proteasomes were resolved by two-dimensional (2D) gel electrophoresis and subunits composing the regulatory complex (RC) were identified by amino acid sequencing and immunoblotting, before corresponding cDNAs were sequenced. 17 subunits from Drosophila RCs were found to have homologues in the yeast and human RCs. An additional subunit, p37A, not yet described in RCs of other organisms, is a member of the ubiquitin COOH-terminal hydrolase family (UCH). Analysis of EM images of 26S proteasomes-UCH-inhibitor complexes allowed for the first time to localize one of the RC's specific functions, deubiquitylating activity.The masses of 26S proteasomes with either one or two attached RCs were determined by scanning transmission EM (STEM), yielding a mass of 894 kD for a single RC. This value is in good agreement with the summed masses of the 18 identified RC subunits (932 kD), indicating that the number of subunits is complete.     

Late events in the assembly of 20S proteasomes

Electron microscopy and STEM mass measurements have been used to characterize late intermediates in the assembly pathway of wildtype and mutant Rhodococcus proteasomes. A proteolytically inactive and processing-incompetent mutant, betaK33A, allowed a short-lived late intermediate of the pathway to be captured, the preholoproteasome. In this fully assembled 20S complex the 14 propeptides with an aggregate mass of 100 kDa fill the whole central cavity and most of the two antechambers. It is further shown that in wildtype Rhodococcus proteasomes the propeptides are degraded in a processive manner undergoing multiple cleavages before the products are discharged and the inner cavities are cleared. It appears that the docking of two half-proteasomes, i.e., preholoproteasome formation, is sufficient to trigger autocleavage of the Gly-1/Thr1 bond necessary for active site formation and the subsequent degradation of the propeptides.     

Environmental controls over carbon exchange of three forest ecosystems in eastern China

Net ecosystem productivity (NEP) was continuously measured using the eddy covariance (EC) technique from 2003 to 2005 at three forest sites of ChinaFLUX. The forests include Changbaishan temperate mixed forest (CBS), Qianyanzhou subtropical coniferous plantation (QYZ), and Dinghushan subtropical evergreen broad‐leaved forest (DHS). They span wide ranges of temperature and precipitation and are influenced by the eastern Asian monsoon climate to varying extent. In this study, we estimated ecosystem respiration (RE) and gross ecosystem productivity (GEP). Comparison of ecosystem carbon exchange among the three forests shows that RE was mainly determined by temperature, with the forest at CBS exhibiting the highest temperature sensitivity among the three ecosystems. The RE was highly dependent on GEP across the three forests, and the ratio of RE to GEP decreased along the North–South Transect of Eastern China (NSTEC) (i.e. from the CBS to the DHS), with an average of 0.77 ± 0.06. Daily GEP was mainly influenced by temperature at CBS, whereas photosynthetic photon flux density was the dominant factor affecting the daily GEP at both QYZ and DHS. Temperature mainly determined the pattern of the interannual variations of ecosystem carbon exchange at CBS. However, water availability primarily controlled the interannual variations of ecosystem carbon exchange at QYZ. At DHS, NEP attained the highest values at the beginning of the dry seasons (autumn) rather than the rainy seasons (summer), probably because insufficient radiation and frequent fog during the rainy seasons hindered canopy photosynthesis. All the three forest ecosystems acted as a carbon sink from 2003 to 2005. The annual average values of NEP at CBS, QYZ, and DHS were 259 ± 19, 354 ± 34, and 434 ± 66 g C m⁻² yr⁻¹, respectively. The slope of NEP that decreased with increasing latitude along the NSTEC was markedly different from that observed on the forest transect in the European continent. Long‐term flux measurements over more forest ecosystems along the NSTEC will further help verify such a difference between the European forest transect and the NSTEC and provide insights into the responses of ecosystem carbon exchange to climate change in China.     

SnAvi – a new tandem tag for high-affinity protein-complex purification

Systematic tandem-affinity-purification (TAP) of protein complexes was tremendously successful in yeast and has changed the general concept of how we understand protein function in eukaryotic cells. The transfer of this method to other model organisms has been difficult and may require specific adaptations. We were especially interested to establish a cell-type-specific TAP system for Caenorhabditis elegans, a model animal well suited to high-throughput analysis, proteomics and systems biology. By combining the high-affinity interaction between in vivo biotinylated target-proteins and streptavidin with the usage of a newly identified epitope of the publicly shared SB1 monoclonal antibody we created a novel in vivo fluorescent tag, the SnAvi-Tag. We show the versatile application of the SnAvi-Tag in Escherichia coli, vertebrate cells and in C. elegans for tandem affinity purification of protein complexes, western blotting and also for the in vivo sub-cellular localization of labelled proteins.     

Geographical variation in size in the European rabbit Oryctolagus cuniculus (Lagomorpha: Leporidae) in western Europe and North Africa

Craniometric data of nine characters from 260 skulls of Oryctolagus cuniculus from western Europe and northern Africa were gathered to examine phenotypic variation in size, using both univariate and multivariate analyses. Although animals from the northern part of Europe were found to be larger than those from southern Europe, variation in size occurred in a continuous cline. Skull size was positively correlated with latitude and negatively correlated with ambient temperature. On the basis of skull morphology, there is no evidence for separation of O. cuniculus into the two or more subspecies commonly described. Further data, particularly from genetic material, are required to clarify the taxonomic status of the rabbit in Europe.     

Tsunami impact on the population development of a critically endangered hummingbird species of a Pacific island

It is a long-standing question how tsunamis can influence wild populations of animals and plants. Here, we assessed short-term changes in the population of the critically endangered Juan Fernández Firecrown (Sephanoides fernandensis) by using abundance data recorded 1 year before and 1 year after the 2010 Chilean tsunami. We tested that the abundance of Firecrowns declined in the areas where the tsunami caused the massive loss of Cabbage Trees, an important seasonal nectar source for Firecrowns. The abundance of Juan Fernández Firecrowns decreased after the tsunami, but also was affected by the habitat type, altitude, and the abundance of Cabbage Trees. Firecrowns tended to be more abundant in settlement areas than in native forest whereas the reduction in Firecrown abundance after the tsunami was more intense in settlement areas than in native forest. As expected, this habitat effect was dependent on the massive loss of Cabbage Trees in settlement areas following the tsunami. In spite of the short-term nature of our data, our results are conclusive in showing that the loss of an important food source causes short-term changes in the distribution and abundance of Firecrowns, which, in turn, could contribute to population decline.     

The preclinical pharmacology of the high affinity anti-IL-6R Nanobody? ALX-0061 supports its clinical development in rheumatoid arthritis

IntroductionThe pleiotropic cytokine interleukin-6 (IL-6) plays an important role in the pathogenesis of different diseases, including rheumatoid arthritis (RA). ALX-0061 is a bispecific Nanobody® with a high affinity and potency for IL-6 receptor (IL-6R), combined with an extended half-life by targeting human serum albumin. We describe here the relevant aspects of its in vitro and in vivo pharmacology.MethodsALX-0061 is composed of an affinity-matured IL-6R-targeting domain fused to an albumin-binding domain representing a minimized two-domain structure. A panel of different in vitro assays was used to characterize the biological activities of ALX-0061. The pharmacological properties of ALX-0061 were examined in cynomolgus monkeys, using plasma levels of total soluble (s)IL-6R as pharmacodynamic marker. Therapeutic effect was evaluated in a human IL-6-induced acute phase response model in the same species, and in a collagen-induced arthritis (CIA) model in rhesus monkeys, using tocilizumab as positive control.ResultsALX-0061 was designed to confer the desired pharmacological properties. A 200-fold increase of target affinity was obtained through affinity maturation of the parental domain. The high affinity for sIL-6R (0.19 pM) translated to a concentration-dependent and complete neutralization of sIL-6R in vitro. In cynomolgus monkeys, ALX-0061 showed a dose-dependent and complete inhibition of hIL-6-induced inflammatory parameters, including plasma levels of C-reactive protein (CRP), fibrinogen and platelets. An apparent plasma half-life of 6.6 days was observed after a single intravenous administration of 10 mg/kg ALX-0061 in cynomolgus monkeys, similar to the estimated expected half-life of serum albumin. ALX-0061 and tocilizumab demonstrated a marked decrease in serum CRP levels in a non-human primate CIA model. Clinical effect was confirmed in animals with active drug exposure throughout the study duration.ConclusionsALX-0061 represents a minimized bispecific biotherapeutic of 26 kDa, nearly six times smaller than monoclonal antibodies. High in vitro affinity and potency was demonstrated. Albumin binding as a half-life extension technology resulted in describable and expected pharmacokinetics. Strong IL-6R engagement was shown to translate to in vivo effect in non-human primates, demonstrated via biomarker deregulation as well as clinical effect. Presented results on preclinical pharmacological properties of ALX-0061 are supportive of clinical development in RA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0651-0) contains supplementary material, which is available to authorized users.     

Evidence of direct cell-cell fusion in Borrelia by cryogenic electron tomography

Some Borrelia species are the causative agents of tick-borne Lyme disease responsible for different disabilities depending on species and hosts. Borrelia are highly motile bacterial cells, and light microscopy shows that these spirochetes can associate with each other during movement. Using cryo-electron tomography, we observed closely associated Borrelia cells. Some of these showed a single outer membrane surrounding two longitudinally arranged cytoplasmic cylinders. We also observed fusion of two cytoplasmic cylinders and differences in the surface layer density of fused spirochetes. These processes could play a role in the interaction of Borrelia species with the host's immune system.     

Workers dominate male production in the neotropical bumblebee Bombus wilmattae (Hymenoptera: Apidae)

Background

Cooperation and conflict in social insects are closely linked to the genetic structure of the colony. Kin selection theory predicts conflict over the production of males between the workers and the queen and between the workers themselves, depending on intra-colonial relatedness but also on other factors like colony efficiency, sex ratios, cost of worker reproduction and worker dominance behaviour. In most bumblebee (Bombus) species the queen wins this conflict and often dominates male production. However, most studies in bumblebees have been conducted with only a few selected, mostly single mated species from temperate climate regions. Here we study the genetic colony composition of the facultative polyandrous neotropical bumblebee Bombus wilmattae, to assess the outcome of the queen-worker conflict over male production and to detect potential worker policing.

Results

A total of 120 males from five colonies were genotyped with up to nine microsatellite markers to infer their parentage. Four of the five colonies were queen right at point of time of male sampling, while one had an uncertain queen status. The workers clearly dominated production of males with an average of 84.9% +/- 14.3% of males being worker sons. In the two doubly mated colonies 62.5% and 96.7% of the male offspring originated from workers and both patrilines participated in male production. Inferring the mother genotypes from the male offspring, between four to eight workers participated in the production of males.

Conclusions

In this study we show that the workers clearly win the queen-worker conflict over male production in B. wilmattae, which sets them apart from the temperate bumblebee species studied so far. Workers clearly dominated male production in the singly as well the doubly mated colonies, with up to eight workers producing male offspring in a single colony. Moreover no monopolization of reproduction by single workers occurred.