Calpain I induces cleavage and release of apoptosis-inducing factor from isolated mitochondria

The translocation of apoptosis-inducing factor (AIF) from mitochondria to the nucleus has been implicated in the mechanism of glutamate excitotoxicity in cortical neurons and has been observed in vivo following acute rodent brain injuries. However, the mechanism and time course of AIF redistribution to the nucleus is highly controversial. Because elevated intracellular calcium is one of the most ubiquitous features of neuronal cell death, this study tested the hypothesis that cleavage of AIF by the calcium-activated protease calpain mediates its release from mitochondria. Both precursor and mature forms of recombinant AIF were cleaved near the amino terminus by calpain I in vitro. Mitochondrial outer membrane permeabilization by truncated Bid induced cytochrome c release from isolated liver or brain mitochondria but only induced AIF release in the presence of active calpain. Enzymatic inhibition of calpain by calpeptin precluded AIF release, demonstrating that proteolytic activity was required for release. Calpeptin and the mitochondrial permeability transition pore antagonist cyclosporin A also inhibited calcium-induced AIF release from mouse liver mitochondria, implicating the involvement of an endogenous mitochondrial calpain in release of AIF during permeability transition. Cleavage of AIF directly decreased its association with pure lipid vesicles of mitochondrial inner membrane composition. Taken together, these results define a novel mechanism of AIF release involving calpain processing and identify a potential molecular checkpoint for cytoprotective interventions.     

Pectin Lyase Activity in a Penicillium italicum Strain

An extracellular pectin lyase (PNL) [poly-(methoxygalacturonide)lyase; EC 4.2.2.10] produced by Penicillium italicum CECT 2294 grown on a surface bran (natural medium) or in a submerged (synthetic medium) culture was investigated. Both culture filtrates showed macerating activity at low pH on cucumber, potato, and orange tissues. The physicochemical properties of the enzyme obtained from both culture methods were identical, as well as its catalytic properties, which were assayed by different methods. The molecular mass of the PNL obtained by gel filtration chromatography was 22 kDa; the isoelectric point was 8.6, as determined by chromatofocusing; and the enzyme was able to catalyze the eliminative cleavage of pectins with low (37%) and high (from 54 to 82%) degrees of esterification. The PNL produced in liquid medium showed a K_m for pectin (degree of esterification, 70%) of 3.2 mg/ml, and the optimum pH was 6.0 to 7.0. This enzyme was stable at 50°C and at pH 8.0. The ability of this PNL to macerate plant tissues in acidic environmental conditions, its stability at low pH and temperatures up to 50°C (thus preventing mesophilic microbial growth), and the absence of pectinesterase make this preparation useful for the food industry.     

Immunological Characterization of the Teleost Adipose Tissue and Its Modulation in Response to Viral Infection and Fat-Content in the Diet

The immune response of the adipose tissue (AT) has been neglected in most animal models until recently, when the observations made in human and mice linking obesity to chronic inflammation and diabetes highlighted an important immune component of this tissue. In the current study, we have immunologically characterized the AT for the first time in teleosts. We have analyzed the capacity of rainbow trout (Oncorhynchus mykiss) AT to produce different immune mediators and we have identified the presence of local populations of B lymphocytes expressing IgM, IgD or IgT, CD8α⁺ cells and cells expressing major histocompatibility complex II (MHC-II). Because trout AT retained antigens from the peritoneal cavity, we analyzed the effects of intraperitoneal infection with viral hemorrhagic septicemia virus (VHSV) on AT functionality. A wide range of secreted immune factors were modulated within the AT in response to VHSV. Furthermore, the viral infection provoked a significant decrease in the number of IgM⁺ cells which, along with an increased secretion of IgM in the tissue, suggested a differentiation of B cells into plasmablasts. The virus also increased the number of CD8α⁺ cells in the AT. Finally, when a fat-enriched diet was fed to the fish, a significant modulation of immune gene expression in the AT was also observed. Thus, we have demonstrated for the first time in teleost that the AT functions as a relevant immune tissue; responsive to peritoneal viral infections and that this immune response can be modulated by the fat-content in the diet.     

Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis

The engineering of a full-length infectious cDNA clone and a functional replicon of the severe acute respiratory syndrome coronavirus (SARS-CoV) Urbani strain as bacterial artificial chromosomes (BACs) is described in this study. In this system, the viral RNA was expressed in the cell nucleus under the control of the cytomegalovirus promoter and further amplified in the cytoplasm by the viral replicase. Both the infectious clone and the replicon were fully stable in Escherichia coli. Using the SARS-CoV replicon, we have shown that the recently described RNA-processing enzymes exoribonuclease, endoribonuclease, and 2'-O-ribose methyltransferase were essential for efficient coronavirus RNA synthesis. The SARS reverse genetic system developed as a BAC constitutes a useful tool for the study of fundamental viral processes and also for developing genetically defined vaccines.     

Hopf bifurcation in the presomitic mesoderm during the mouse segmentation

Vertebrae and ribs arise from embryonic tissues called somites. Somites arise sequentially from the unsegmented embryo tail, called presomitic mesoderm (PSM). The pace of somite formation is controlled by gene products such as hairy and enhancer of split 7 (Hes7) whose expression oscillates in the PSM. In addition to the cyclic genes, there is a gradient of fibroblast growth factor 8 (Fgf8) mRNA from posterior to anterior PSM. Recent experiments have shown that in the absence of Fgf signaling, Hes7 oscillations in the anterior and posterior PSM are lost. On the other hand, Notch mutants reduce the amplitude of posterior Hes7 oscillations and abolish anterior Hes7 oscillations. To understand these phenotypes, we delineated and simulated a logical and a delay differential equation (DDE) model with similar network topology in wild-type and mutant situations. Both models reproduced most wild-type and mutant phenotypes suggesting that the chosen topology is robust to explain these phenotypes. Numerical continuation of the model showed that even in the wild-type situation, the system changed from sustained to damped, i.e. a Hopf bifurcation occurred, when the Fgf concentration decreased in the PSM. This numerical continuation analysis further indicated that the most sensitive parameters for the oscillations are the parameters of Hes7 followed by those of Lunatic fringe (Lfng) and Notch1. In the wild-type, the damping of Hes7 oscillations was not so strong so that cells reached the new somites before they lose Hes7 oscillations. By contrast, in the fibroblast growth factor receptor 1 (Fgfr1) conditional knock-out (cKO) mutant simulation, Notch signaling was not able to maintain sustained Hes7 oscillations. Our analysis suggests that Fgf signaling makes cells enter an oscillatory state of Hes7 expression. After moving to the anterior PSM, where Fgf signaling is missing, Notch signaling compensates the damping of Hes7 oscillations in the anterior PSM.     

Endophilin B1/Bif-1 Stimulates BAX Activation Independently from Its Capacity to Produce Large Scale Membrane Morphological Rearrangements

Endophilin B1/BAX-interacting factor 1 (Bif-1) is a protein that cooperates with dynamin-like protein 1 (DLP1/Drp1) to maintain normal mitochondrial outer membrane (MOM) dynamics in healthy cells and also contributes to BAX-driven MOM permeabilization (MOMP), the irreversible commitment point to cell death for the majority of apoptotic stimuli. However, despite its importance, exactly how Bif-1 fulfils its proapoptotic role is unknown. Here, we demonstrate that the stimulatory effect of Bif-1 on BAX-driven MOMP and on BAX conformational activation observed in intact cells during apoptosis can be recapitulated in a simplified system consisting of purified proteins and MOM-like liposomes. In this reconstituted model system the N-BAR domain of Bif-1 reproduced the stimulatory effect of Bif-1 on functional BAX activation. This process was dependent on physical interaction between Bif-1 N-BAR and BAX as well as on the presence of the mitochondrion-specific lipid cardiolipin. Despite that Bif-1 N-BAR produced large scale morphological rearrangements in MOM-like liposomes, this phenomenon could be separated from functional BAX activation. Furthermore, DLP1 also caused global morphological changes in MOM-like liposomes, but DLP1 did not stimulate BAX-permeabilizing function in the absence or presence of Bif-1. Taken together, our findings not only provide direct evidence for a functional interplay between Bif-1, BAX, and cardiolipin during MOMP but also add significantly to the growing body of evidence indicating that components of the mitochondrial morphogenesis machinery possess proapoptotic functions that are independent from their recognized roles in normal mitochondrial dynamics.MOMP³ is a key event in the intrinsic pathway of mammalian apoptosis, resulting in the release of several apoptogenic proteins from the mitochondrial intermembrane space into the cytosol (1). Released intraorganellar components, including cytochrome c, Smac/DIABLO, and AIF, then act as mediators for activating executioner caspase proteases or for other downstream events in the intracellular apoptosis cascade. MOMP is tightly regulated by BCL-2 family members, whose core components are proapoptotic BAX-type proteins that directly effect MOMP and antiapoptotic BCL-2-type proteins which inhibit MOMP (2, 3). In a currently popular model, a third subgroup of BCL-2 family proteins, the BH3-only proteins, trigger a set of conformational changes in BAX and/or its close homologue BAK that activates their permeabilizing function, thereby causing MOMP.Multiple proteins implicated in mitochondrial morphogenesis during normal growth conditions can cross-talk with BCL-2 family members to affect the mitochondrial pathway of apoptosis (4). For example, the large dynamin-like GTPase DLP1/Drp1 and hFis1, two essential components of the mitochondrial fission machinery, have been shown to modulate pro-apoptotic BAX function and mitochondrial cytochrome c release by acting at the level of the MOM (5–7). However, although excessive mitochondrial fragmentation is characteristic in mammalian apoptosis, controversy persists as to whether this phenomenon is merely coincident with or causatively linked to MOMP induction (4 – 8). In addition, a considerable body of evidence has amassed indicating that DLP1/Drp1 and hFis1 are multifunctional proteins that do not use the same mechanisms to reshape mitochondria in healthy conditions and to promote release of mitochondrial intermembrane space proteins during apoptosis (7–10).Endophilin B1/BAX-interacting factor 1 (Bif-1) is another protein linking mitochondrial morphological changes and BCL-2-regulated programmed cell death (4). On the one hand, Bif-1 is known to participate downstream of DLP1/Drp1, modulating normal MOM morphological dynamics in healthy cells (11). On the other hand, in response to specific apoptotic signals, a significant portion of Bif-1 binds BAX at the MOM in close temporal correlation with BAX conformational change and cytochrome c release (12). In addition, increasing the levels of Bif-1 has been shown to accelerate BAX conformational change, caspase activation, and apoptotic cell death, whereas loss of Bif-1 delays all these processes (12, 13). Together, these previous findings point to an important contributing role of Bif-1 in BAX-driven MOMP during apoptosis, but the underlying molecular mechanism remains unknown.As other members of the endophilin family, Bif-1 contains an N-BAR (Bin-amphiphysin-Rvs) domain that has been shown to confer ability to these proteins for transforming flat lipid bilayers into high curvature buds, tubules, and vesicles in vitro (14–17). Crystallographic studies of the N-BAR domain of endophilin A1, a close homologue of Bif-1, revealed a crescent-shape homodimer with a positively charged concave surface which is believed to act like a molecular scaffold that impresses its own curvature on binding to negatively charged membranes (16, 18). Another distinguishing feature of endophilin N-BAR domains is the presence of two distinct amphipathic segments referred to as “Helix 0” (H0) and “Helix 1 insert” (H1I) that penetrate only partway into the external leaflet and are thought to create a wedge effect that also increases membrane curvature. This dual curvature-generating mechanism has been linked to the shared capacity of endophilins to operate in membrane tubulovesicular dynamics during normal cell growth together with dynamin/dynamin-like proteins (16–18). However, exactly how the molecular-scale perturbation of membrane curvature induced by N-BAR domains translates into large scale membrane remodeling processes (e.g. tubulation and vesiculation) is not well understood (19–25). In addition, it is unclear whether the ability of Bif-1 to produce global changes in membrane morphology is functionally connected to its apoptotic mode of action.The complexity of the network of intermolecular interactions that controls the BCL-2-regulated MOMP pathway constitutes a major hurdle for gaining a molecular-level understanding of Bif-1 pro-death function in intact cells. Another complicating factor is that Bif-1 can interact with binding partners other than BAX at intracellular membranes distinct from the MOM depending on environmental conditions (14, 26–29). In previous studies this and other laboratories have shown that the BCL-2-regulated MOMP pathway can be reconstituted in a simplified system consisting of purified recombinant proteins and chemically defined MOM-like large unilamellar vesicles (LUV) in a manner that faithfully reflects the basic physiological functions of BCL-2 family proteins at the MOM (30–33). Here, we have used this minimal cell-free system to advance our understanding of the pro-death role of Bif-1. We provide strong evidence for a direct implication of Bif-1 in functional BAX activation at the membrane level and novel insights concerning the mechanism through which Bif-1 achieves this effect.     

DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens?

Genomic hybridization on whole genome arrays detects the presence or absence of similar DNA regions in sufficiently related microorganisms, allowing genome-wide comparison of their genetic contents. A whole genome array is based on a sequenced bacterial isolate, and is a collection of DNA probes fixed on a solid support. In a single hybridization experiment, the absence/presence status of all genes of the sequenced microbe in the queried isolate can be examined. The objective of this minireview is to summarize the past usage of DNA microarray technology for microbial strain characterizations, and to estimate its future utilization in epidemiological studies and molecular typing of bacterial pathogens. The studies reviewed here confirm the usefulness of microarray technology for the detection of genetic polymorphisms. However, the construction or purchase of DNA microarrays and the performance of strain to strain hybridization experiments are still prohibitively expensive for routine application. Future use of arrays in epidemiology is likely to depend on the development of more cost-effective protocols, more robust and simplified formats, and the adequate evaluation of their performance (efficacy) and convenience (efficiency) compared with other genotyping methods. It seems more likely that a more focused assay, concentrating on genomic regions of variability previously detected by genome-wide microarrays, will find broad application in routine bacterial epidemiology.