Crystal Structure of Staphylococcus aureus Metallopeptidase (Sapep) Reveals Large Domain Motions between the Manganese-bound and Apo-states

Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn²⁺-dependent dipeptidase. The crystal structure of this protein in the Mn²⁺-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys¹⁵⁵ and Cys¹⁷⁸, are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.     

A Highlights from MBoC Selection: The Interferon-γ–induced Murine Guanylate-Binding Protein-2 Inhibits Rac Activation during Cell Spreading on Fibronectin and after Platelet-derived Growth Factor Treatment: Role for Phosphatidylinositol 3-Kinase

Exposure of cells to certain cytokines can alter how these same cells respond to later cues from other agents, such as extracellular matrix or growth factors. Interferon (IFN)-γ pre-exposure inhibits the spreading of fibroblasts on fibronectin. Expression of the IFN-γ–induced GTPase murine guanylate-binding protein-2 (mGBP-2) can phenocopy this inhibition and small interfering RNA knockdown of mGBP-2 prevents IFN-γ–mediated inhibition of cell spreading. Either IFN-γ treatment or mGBP-2 expression inhibits Rac activation during cell spreading. Rac is required for cell spreading. mGBP-2 also inhibits the activation of Akt during cell spreading on fibronectin. mGBP-2 is incorporated into a protein complex containing the catalytic subunit of phosphatidylinositol 3-kinase (PI3-K), p110. The association of mGBP-2 with p110 seems important for the inhibition of cell spreading because S52N mGBP-2, which does not incorporate into the protein complex with p110, is unable to inhibit cell spreading. PI3-K activation during cell spreading on fibronectin was inhibited in the presence of mGBP-2. Both IFN-γ and mGBP-2 also inhibit cell spreading initiated by platelet-derived growth factor treatment, which is also accompanied by inhibition of Rac activation by mGBP-2. This is the first report of a novel mechanism by which IFN-γ can alter how cells respond to subsequent extracellular signals, by the induction of mGBP-2.     

Functional biogeography as evidence of gene transfer in hypersaline microbial communities

Background

Horizontal gene transfer (HGT) plays a major role in speciation and evolution of bacteria and archaea by controlling gene distribution within an environment. However, information that links HGT to a natural community using relevant population-genetics parameters and spatial considerations is scarce. The Great Salt Lake (Utah, USA) provides an excellent model for studying HGT in the context of biogeography because it is a contiguous system with dispersal limitations due to a strong selective salinity gradient. We hypothesize that in spite of the barrier to phylogenetic dispersal, functional characteristics—in the form of HGT—expand beyond phylogenetic limitations due to selective pressure.

Methodology and Results

To assay the functional genes and microorganisms throughout the GSL, we used a 16S rRNA oligonucleotide microarray (Phylochip) and a functional gene array (GeoChip) to measure biogeographic patterns of nine microbial communities. We found a significant difference in biogeography based on microarray analyses when comparing Sørensen similarity values for presence/absence of function and phylogeny (Student''s t-test; p = 0.005).

Conclusion and Significance

Biogeographic patterns exhibit behavior associated with horizontal gene transfer in that informational genes (16S rRNA) have a lower similarity than functional genes, and functional similarity is positively correlated with lake-wide selective pressure. Specifically, high concentrations of chromium throughout GSL correspond to an average similarity of chromium resistance genes that is 22% higher than taxonomic similarity. This suggests active HGT may be measured at the population level in microbial communities and these biogeographic patterns may serve as a model to study bacteria adaptation and speciation.     

Inhibition of human telomerase activity by an engineered zinc finger protein that binds G-quadruplexes

The G-quadruplex nucleic acid structural motif is a target for designing molecules that could potentially modulate telomere length or have anticancer properties. We have recently described an engineered zinc finger protein (Gq1) that binds with specificity to the intramolecular G-quadruplex formed by the human telomeric sequence 5'-(GGTTAG)(5)-3' (Isalan et al. (2001) Biochemistry 40, 830-836). Here, we report that Gq1 is able to arrest the action of a DNA polymerase on a template-containing telomeric sequence. Inhibition occurs in a concentration-dependent manner, probably by forming a stabilized G-quadruplex.protein complex. Furthermore, Gq1 inhibits the apparent activity of the enzyme telomerase in vitro, with an IC(50) value of 74.3 +/- 11.1 nM. Possible molecular mechanisms of inhibition are discussed, together with the potential for using engineered zinc fingers to interfere with the cellular processes associated with telomere function.     

Analyzing time-to-event data in a clinical trial when an unknown proportion of subjects has experienced the event at entry

In some clinical trials, where the outcome is the time until development of a silent event, an unknown proportion of subjects who have already experienced the event will be unknowingly enrolled due to the imperfect nature of the diagnostic tests used to screen potential subjects. For example, commonly used diagnostic tests for evaluating HIV infection status in infants, such as DNA PCR and HIV Culture, have low sensitivity when given soon after infection. This can lead to the inclusion of an unknown proportion of HIV-infected infants into clinical trials aimed at the prevention of transmission from HIV-positive mothers to their infants through breastfeeding. The infection status of infants at the end of the trial, when they are more than a year of age, can be determined with certainty. For those infants found to be infected with HIV at the end of the trial, it cannot be determined whether this occurred during the study or whether they were already infected when they were enrolled. In these settings, estimates of the cumulative risk of the event by the end of the study will overestimate the true probability of event during the study period and hypothesis tests comparing two or more intervention strategies can also be biased. We present inference methods for the distribution of time until the event of interest in these settings, and investigate issues in the design of such trials when there is a choice of using both imperfect and perfect diagnostic tests.     

Role of intestine in postsurgical complications: involvement of free radicals

Surgery at any location in the body leads to surgical stress response and alterations in normal body homeostasis. The intestine is extremely sensitive to surgical stress even at remote locations and the gastrointestinal tract plays an important role in the development of postsurgical complications such as sepsis, the systemic immune response syndrome (SIRS), and multiple organ failure syndrome (MOFS). The generation of free radicals and subsequent biochemical alterations at the cellular and subcellular level in the intestine has been suggested to play an important role in this process. These oxidative stress-induced events in the mucosa might act as an initiator of distant organ damage and also facilitate bacterial adherence onto the epithelium and translocation into the systemic circulation. This review attempts to highlight the important role of intestine and oxygen free radicals in initiating post-surgical complications.     

Fluorescence properties of Laurdan in cochleate phases

Cochleates are lipid-based delivery system that have found application in drug and gene delivery. They are precipitates, formed as a result of interaction between cations (e.g. Ca2+) and negatively charged phospholipids such as phosphatidylserine (PS). In the present study, we investigated the utility of fluorescent probe Laurdan (6-dodecanoyl-2-dimethylamino naphthalene) to monitor cochleate phase formation. Following addition of Ca2+ to Laurdan labeled lipid vesicles comprised of brain phosphatidylserine (BPS), a significant blue shift in the emission peak maximum of Laurdan was observed and the spectral features were distinct from those observed for the gel and liquid-crystalline (LC) phases. This is consistent with the formation of anhydrous cochleate cylinders that was further confirmed by electron microscopy studies. Due to dipolar relaxation, excitation and emission generalized polarization (GPEx and GPEm) indicate transition from a LC to a rigid and dehydrated (RD) cochleate phase. These spectral changes were utilized to monitor the influence of lipid composition, ionic strength and lamellarity on the formation of cochleate phase. The results indicated that the presence of phosphatidylcholine (PC) and bulk Na+ concentration influenced the formation of cochleate structures from small unilamellar vesicles (SUV) and multilamellar vesicles (MLV) composed of PS. The presence of PC and higher bulk Na+ concentration stabilized the PS vesicles against collapse and total loss of contents, intermediate molecular events in the formation of cochleate structures. From these studies, we conclude that Laurdan fluorescence is a sensitive and a rapid method to detect cochleate phase formation.