Role of protein translocation pathways across the endoplasmic reticulum in Trypanosoma brucei

The translocation of secretory and membrane proteins across the endoplasmic reticulum (ER) membrane is mediated by co-translational (via the signal recognition particle (SRP)) and post-translational mechanisms. In this study, we investigated the relative contributions of these two pathways in trypanosomes. A homologue of SEC71, which functions in the post-translocation chaperone pathway in yeast, was identified and silenced by RNA interference. This factor is essential for parasite viability. In SEC71-silenced cells, signal peptide (SP)-containing proteins traversed the ER, but several were mislocalized, whereas polytopic membrane protein biogenesis was unaffected. Surprisingly trypanosomes can interchangeably utilize two of the pathways to translocate SP-containing proteins except for glycosylphosphatidylinositol-anchored proteins, whose level was reduced in SEC71-silenced cells but not in cells depleted for SRP68, an SRP-binding protein. Entry of SP-containing proteins to the ER was significantly blocked only in cells co-silenced for the two translocation pathways (SEC71 and SRP68). SEC63, a factor essential for both translocation pathways in yeast, was identified and silenced by RNA interference. SEC63 silencing affected entry to the ER of both SP-containing proteins and polytopic membrane proteins, suggesting that, as in yeast, this factor is essential for both translocation pathways in vivo. This study suggests that, unlike bacteria or other eukaryotes, trypanosomes are generally promiscuous in their choice of mechanism for translocating SP-containing proteins to the ER, although the SRP-independent pathway is favored for glycosylphosphatidylinositol-anchored proteins, which are the most abundant surface proteins in these parasites.     

Protein trafficking inside Toxoplasma gondii

The accurate targeting of proteins to their final destination is an essential process in all living cells. Apicomplexans are obligate intracellular protozoan parasites that possess a compartmental organization similar to that of free-living eukaryotes but can be viewed as professional secretory cells. Establishment of parasitism involves the sequential secretion from highly specialized secretory organelles, including micronemes, rhoptries and dense granules. Additionally, apicomplexans harbor a tubular mitochondrion, a nonphotosynthetic plastid organelle termed the apicoplast, acidocalcisomes and an elaborated inner membrane complex composed of flattened membrane cisternae that are derived from the secretory pathway. Given the multitude of destinations both inside and outside the parasite, the endoplasmic reticulum/Golgi of the apicomplexans constitutes one of the most busy roads intersections in eukaryotic traffic.     

Isolation and bioaugmentation of an estradiol-degrading bacterium and its integration into a mature biofilm

Bioaugmentation can alter the potential activity as well as the composition of the naturally occurring microbial biota during bioremediation of a contaminated site. The focus of the current study is the pollutant 17β-estradiol (E2), which can cause endocrine effects and is potentially harmful to aquatic biota and to public health. The community composition and function of biofilms, originating from a wetland system, as affected by augmentation of an estradiol-degrading bacterium (EDB-LI1) under different conditions, were investigated. EDB-LI1 inoculation into biofilm from two wetland ponds representing early and advanced water treatment stages, respectively, yielded three significant observations, as follows: (i) EDB-LI1, enriched from a biofilm of a constructed wetland wastewater treatment system, was detected (by quantitative PCR [qPCR] analysis) in this environment in the augmented biofilm only; (ii) the augmented biofilm acquired the ability to remove estradiol; and (iii) the bacterial community composition (analyzed by PCR-denaturing gradient gel electrophoresis [DGGE]) of the augmented biofilm differed from that of the control biofilm. Furthermore, EDB-LI1 bioaugmentation showed a higher level of removal of estradiol with biofilms that originated from the advanced-treatment-stage wetland pond than those from the early-treatment-stage pond. Hence, the bioaugmentation efficiency of EDB-LI1 depends on both the quality of the feed water and the microbial community composition in the pond.     

Oligomeric Structure of Type I and Type II Transforming Growth Factor β Receptors: Homodimers Form in the ER and Persist at the Plasma Membrane

Abstract. Transforming growth factor β (TGF-β) signaling involves interactions of at least two different receptors, types I (TβRI) and II (TβRII), which form ligand-mediated heteromeric complexes. Although we have shown in the past that TβRII in the absence of ligand is a homodimer on the cell surface, TβRI has not been similarly investigated, and the site of complex formation is not known for either receptor. Several studies have indicated that homomeric interactions are involved in TGF-β signaling and regulation, emphasizing the importance of a detailed understanding of the homooligomerization of TβRI or TβRII. Here we have combined complementary approaches to study these homomeric interactions in both naturally expressing cell lines and cells cotransfected with various combinations of epitope-tagged type I or type II receptors. We used sedimentation velocity of metabolically labeled receptors on sucrose gradients to show that both TβRI and TβRII form homodimer-sized complexes in the endoplasmic reticulum, and we used coimmunoprecipitation studies to demonstrate the existence of type I homooligomers. Using a technique based on antibody-mediated immunofluorescence copatching of receptors carrying different epitope tags, we have demonstrated ligand-independent homodimers of TβRI on the surface of live cells. Soluble forms of both receptors are secreted as monomers, indicating that the ectodomains are not sufficient to mediate homodimerization, although TGF-β1 is able to promote dimerization of the type II receptor ectodomain. These findings may have important implications for the regulation of TGF-β signaling.     

Detecting neural assemblies in calcium imaging data

Background

Activity in populations of neurons often takes the form of assemblies, where specific groups of neurons tend to activate at the same time. However, in calcium imaging data, reliably identifying these assemblies is a challenging problem, and the relative performance of different assembly-detection algorithms is unknown.

Results

To test the performance of several recently proposed assembly-detection algorithms, we first generated large surrogate datasets of calcium imaging data with predefined assembly structures and characterised the ability of the algorithms to recover known assemblies. The algorithms we tested are based on independent component analysis (ICA), principal component analysis (Promax), similarity analysis (CORE), singular value decomposition (SVD), graph theory (SGC), and frequent item set mining (FIM-X). When applied to the simulated data and tested against parameters such as array size, number of assemblies, assembly size and overlap, and signal strength, the SGC and ICA algorithms and a modified form of the Promax algorithm performed well, while PCA-Promax and FIM-X did less well, for instance, showing a strong dependence on the size of the neural array. Notably, we identified additional analyses that can improve their importance. Next, we applied the same algorithms to a dataset of activity in the zebrafish optic tectum evoked by simple visual stimuli, and found that the SGC algorithm recovered assemblies closest to the averaged responses.

Conclusions

Our findings suggest that the neural assemblies recovered from calcium imaging data can vary considerably with the choice of algorithm, but that some algorithms reliably perform better than others. This suggests that previous results using these algorithms may need to be reevaluated in this light.

     

Biosynthesis of triterpenoid sapogenols in soybean and alfalfa seedlings

By incubation of germinating soybeans with mevalonate-[2-¹⁴C] (MVA), radioactivity was incorporated into four sapogenols which were identified by TLC. Unequivocal evidence for the identity of three of the four sapogenols was provided by co-crystallization to constant specific radioactivity. The partition of incorporated radioactivity into lipid- and water-soluble fractions and the pattern of radioactivity of individual sapogenols varied with the mode of administering labeled substrates to soybean seedlings, such as incubation of germinating soybeans with MVA-[2-¹⁴C], immersion of roots into MVA-[2-¹⁴C] or foliar application of squalene-[¹⁴C]. When alfalfa seedlings were incubated with MVA-[2-¹⁴C], about two-thirds of the radioactivity incorporated into the sapogenols was associated with medicagenic acid.