Cellular localization and biochemical analysis of mammalian CDC50A, a glycosylated β-subunit for P4 ATPases

CDC50 proteins are β-subunits for P4 ATPases, which upon heterodimerization form a functional phospholipid translocation complex. Emerging evidence in mouse models and men links mutations in P4 ATPase genes with human disease. This study analyzed the tissue distribution and cellular localization of CDC50A, the most abundant and ubiquitously expressed CDC50 homologue in the mouse. The authors have raised antibodies that detect mouse and human CDC50A and studied CDC50A localization and glycosylation status in mouse liver cells. CDC50A is a terminal-glycosylated glycoprotein and is expressed in hepatocytes and liver sinusoidal endothelial cells, where it resides in detergent-resistant membranes. In pancreas and stomach, CDC50A localized to secretory vesicles, whereas in the kidney, CDC50A localized to the apical region of proximal convoluted tubules of the cortex. In WIF-B9 cells, CDC50A partially costains with the trans-Golgi network. Data suggest that CDC50A is present as a fully glycosylated protein in vivo, which presumes interaction with distinct P4 ATPases.     

Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest

The coordinated termination of DNA replication is an important step in the life cycle of bacteria with circular chromosomes, but has only been defined at a molecular level in two systems to date. Here we report the structure of an engineered replication terminator protein (RTP) of Bacillus subtilis in complex with a 21 base pair DNA by X-ray crystallography at 2.5 A resolution. We also use NMR spectroscopic titration techniques. This work reveals a novel DNA interaction involving a dimeric 'winged helix' domain protein that differs from predictions. While the two recognition helices of RTP are in close contact with the B-form DNA major grooves, the 'wings' and N-termini of RTP do not form intimate contacts with the DNA. This structure provides insight into the molecular basis of polar replication fork arrest based on a model of cooperative binding and differential binding affinities of RTP to the two adjacent binding sites in the complete terminator.     

Testicular expression and distribution of the rat bcl2 modifying factor in response to reduced intratesticular testosterone

The Bcl2 modifying factor (Bmf) is a pro-apoptotic member of the Bcl2 family of apoptosis-related proteins that has been shown to initiate apoptosis in response to the loss of attachment of cells from their basal lamina (anoikis). Experimental reduction in intratesticular testosterone concentration brings about the death of spermatids as a consequence of their sloughing from Sertoli cells. Given the role of Bmf in anoikis in other systems, we hypothesized that Bmf would be expressed in germ cells and that its expression and normal distribution might be altered under conditions that induce widespread germ cell loss. To test these hypotheses, we demonstrated that Bmf indeed is expressed in the testis and cloned the full-length rat Bmf cDNA. Immunohistochemistry revealed that Bmf is present in the subacrosomal space of postmeiotic spermatids from step 4 to 16 of spermiogenesis. To test the hypothesis that Bmf expression and distribution are altered by conditions that elicit anoikis, intratesticular testosterone was reduced by implanting Silastic capsules containing testosterone and estradiol into adult rats for 8 weeks. As hypothesized, this resulted in a significant change in Bmf distribution relative to untreated animals. In particular, Bmf exhibited a loss of its normal subacrosomal distribution, becoming redistributed throughout the cytoplasm and nucleus, and appeared in cells in which it is not normally expressed (e.g., pachytene spermatocytes). Additionally, Bmf mRNA expression increased in response to lowered testosterone. These results suggest that Bmf may well be involved in germ cell apoptosis and/or anoikis in response to decreased intratesticular testosterone concentration.     

Floating stereospecific assignment revisited: Application to an 18 kDa protein and comparison with J-coupling data

We report a floating chirality procedure to treat nonstereospecifically assigned methylene orisopropyl groups in the calculation of protein structures from NMR data using restrainedmolecular dynamics and simulated annealing. The protocol makes use of two strategies toinduce the proper conformation of the prochiral centres: explicit atom swapping followingan evaluation of the NOE energy term, and atom floating by reducing the angle andimproper force constants that enforce a defined chirality at the prochiral centre. The individualcontributions of both approaches have been investigated. In addition, the effects of accuracyand precision of the interproton distance restraints were studied. The model system employedis the 18 kDa single-stranded DNA binding protein encoded by Pseudomonas bacteriophagePf3. Floating chirality was applied to all methylene and isopropyl groups that give rise to non-degenerate NMR signals, and the results for 34 of these groups were compared to J-couplingdata. We conclude that floating stereospecific assignment is a reliable tool in protein structurecalculation. Its use is beneficial because it allows the distance restraints to be extracteddirectly from the measured peak volumes without the need for averaging or addingpseudoatom corrections. As a result, the calculated structures are of a quality almostcomparable to that obtained with stereospecific assignments. As floating chirality furthermoreis the only approach treating prochiral centres that ensures a consistent assignment of the twoproton frequencies in a single structure, it seems to be preferable over using pseudoatoms or(R-6) averaging.     

Kinetic modeling of thermal inactivation of the Bacillus sp. protease P7

Data from thermal stability of a keratinolytic protease produced by the Amazon isolate Bacillus sp. P7 was fitted to various mathematical models. Kinetic modeling showed that Weibull distribution was the best equation to describe the residual activity of protease P7 after heat treatment. The effects of temperature on equation parameters and on characteristics of the inactivation curves were evaluated. As expected, faster inactivation was observed at higher temperatures. The critical temperature to accelerate protease decomposition was about 70 °C. The reliable life (t _R) of the enzyme, analogous to the D value, ranged from 1,824 to 8 min at 45–65 °C. Within these temperatures, an increase of 8.81 °C was needed to lower enzyme t _R in one-log unit. Protease P7 is a potentially useful biocatalyst for various industrial bioprocesses, and therefore, kinetic modeling of thermal inactivation addresses an important topic aiming enzyme characterization and applications.     

Mass extinctions do not explain skew in interspecific body size distributions

In several higher animal taxa, such as mammals and birds, the distribution of species body sizes is heavily skewed towards small size. Previous studies have suggested that small‐bodied organisms are less prone to extinction than large‐bodied species. If small body size is favourable during mass extinction events, a post mass extinction excess of small‐bodied species may proliferate and maintain skewed body size distributions sometime after. Here, we modelled mass extinctions and found that even unrealistically strong body mass selection has little effect on the skew of interspecific body size distributions. Moreover, selection against large body size may, counter intuitively, skew size distributions towards large body size. In any case, subsequent evolutionary diversification rapidly erases these rather small effects mass extinctions may have on size distributions. Next, we used body masses of extant species and phylogenetic methods to investigate possible changes in body size distributions across the Cretaceous–Paleogene (K‐Pg) mass extinction. Body size distributions of extant clades that originated during the Cretaceous are on average more skewed than their subclades that originated during the Paleogene, but the difference is only minor in mammals, and in birds, it can be explained by a positive relationship between species richness and skewness that is also present in clades that originated after the transition. Hence, we cannot infer from extant species whether the K‐Pg mass extinctions were size‐selective, but they are not the reason why most extant bird and mammal species are small‐bodied.     

Oligomerization engineering of the fluorinase enzyme leads to an active trimer that supports synthesis of fluorometabolites in vitro

The fluorinase enzyme represents the only biological mechanism capable of forming stable C–F bonds characterized in nature thus far, offering a biotechnological route to the biosynthesis of value-added organofluorines. The fluorinase is known to operate in a hexameric form, but the consequence(s) of the oligomerization status on the enzyme activity and its catalytic properties remain largely unknown. In this work, this aspect was explored by rationally engineering trimeric fluorinase variants that retained the same catalytic rate as the wild-type enzyme. These results ruled out hexamerization as a requisite for the fluorination activity. The Michaelis constant (K_M) for S-adenosyl-l -methionine, one of the substrates of the fluorinase, increased by two orders of magnitude upon hexamer disruption. Such a shift in S-adenosyl-l -methionine affinity points to a long-range effect of hexamerization on substrate binding – likely decreasing substrate dissociation and release from the active site. A practical application of trimeric fluorinase is illustrated by establishing in vitro fluorometabolite synthesis in a bacterial cell-free system.     

Reciprocal diversification in a complex plant-herbivore-parasitoid food web

Background  

Plants, plant-feeding insects, and insect parasitoids form some of the most complex and species-rich food webs. According to the classic escape-and-radiate (EAR) hypothesis, these hyperdiverse communities result from coevolutionary arms races consisting of successive cycles of enemy escape, radiation, and colonization by new enemy lineages. It has also been suggested that "enemy-free space" provided by novel host plants could promote host shifts by herbivores, and that parasitoids could similarly drive diversification of gall form in insects that induce galls on plants. Because these central coevolutionary hypotheses have never been tested in a phylogenetic framework, we combined phylogenetic information on willow-galling sawflies with data on their host plants, gall types, and enemy communities.     

MConfocal Fluorescence Microscopy of Urokinase Plasminogen Activator Receptor and Cathepsin D in Human MDA-MB-231 Breast Cancer Cells Migrating in Reconstituted Basement Membrane

Using confocal fluorescence microscopy with a monoclonal antibody, we have localized the receptor for urokinase plasminogen activator (uPAR) in MDA-MB-231 human breast cancer cells migrating into a reconstituted basement membrane. Patchy and polarized uPAR immunoreactivity was found at the cell membrane, and strong staining was found both in the ruffled border or leading edge of the cells and at pseudopodia penetrating into the membrane. Intracellular uPAR staining was localized in the paranuclear region and in rounded granule-like structures: some of these were identified as lysosomes by double staining for uPAR and the lysosomal enzyme cathepsin D. Urokinase plasminogen activator (uPA) activity has previously been shown to play a role in migration of cells into basement membranes, and it has been proposed that uPAR also is involved in this process. uPA is known to be internalized and degraded after complex formation with the inhibitor PAI-1. Lysosomal uPAR immunoreactivity may result from concomitant internalization of the receptor.