Nanopods: a new bacterial structure and mechanism for deployment of outer membrane vesicles

Background

Bacterial outer membrane vesicles (OMV) are packets of periplasmic material that, via the proteins and other molecules they contain, project metabolic function into the environment. While OMV production is widespread in proteobacteria, they have been extensively studied only in pathogens, which inhabit fully hydrated environments. However, many (arguably most) bacterial habitats, such as soil, are only partially hydrated. In the latter, water is characteristically distributed as films on soil particles that are, on average thinner, than are typical OMV (ca. ≤10 nm water film vs. 20 to >200 nm OMV;).

Methodology/Principal Findings

We have identified a new bacterial surface structure, termed a “nanopod”, that is a conduit for projecting OMV significant distances (e.g., ≥6 µm) from the cell. Electron cryotomography was used to determine nanopod three-dimensional structure, which revealed chains of vesicles within an undulating, tubular element. By using immunoelectron microscopy, proteomics, heterologous expression and mutagenesis, the tubes were determined to be an assembly of a surface layer protein (NpdA), and the interior structures identified as OMV. Specific metabolic function(s) for nanopods produced by Delftia sp. Cs1-4 are not yet known. However, a connection with phenanthrene degradation is a possibility since nanopod formation was induced by growth on phenanthrene. Orthologs of NpdA were identified in three other genera of the Comamonadaceae family, and all were experimentally verified to form nanopods.

Conclusions/Significance

Nanopods are new bacterial organelles, and establish a new paradigm in the mechanisms by which bacteria effect long-distance interactions with their environment. Specifically, they create a pathway through which cells can effectively deploy OMV, and the biological activity these transmit, in a diffusion-independent manner. Nanopods would thus allow environmental bacteria to expand their metabolic sphere of influence in a manner previously unknown for these organisms.     

Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules

The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.     

Varied diet and opportunistic foraging in the Ethiopian Bush-crow Zavattariornis stresemanni,an Endangered generalist

The Ethiopian Bush-crow Zavattariornis stresemanni is an endangered, co-operatively breeding southern Ethiopian endemic with a remarkably restricted range (c. 6 000 km²). The species’ range was recently found to be almost perfectly predicted by an envelope of cooler, drier and more seasonal climate than surrounding areas, but the proximate determinants of this range restriction remain unclear. We assessed whether specialisation in diet or foraging may restrict the range of the species by conducting foraging watches to determine prey composition, augmented by observations of opportunistic foraging techniques, and by comparing our results to previously published information on diet. Prey composition comprised a range of arthropods, such as insect larvae (62.7%), beetles (Coleoptera) (15.6%), and grasshoppers and crickets (Orthoptera) (11.8%). Prey was primarily obtained by pecks above ground (74.2%) but also frequently dug up (23.8%). Prey capture was most successful during pecks and we also found chicks were preferentially fed larger prey items over smaller ones by adults. We documented opportunistic behaviours such as nest-raiding and ox-pecking. Diet and foraging are varied and unspecialised, and therefore do not appear to explain the restricted range of the Ethiopian Bush-crow.     

Electron Cryotomography of Bacterial Cells

While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered, including for instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In order to understand these phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy and higher-resolution methods such as X-ray crystallography and NMR spectroscopy.Electron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-native state, in three dimensions (3D), with "macromolecular" resolution (~4nm).^{1, 2} In ECT, cells are imaged in a vitreous, "frozen-hydrated" state in a cryo transmission electron microscope (cryoTEM) at low temperature (< -180°C). For slender cells (up to ~500 nm in thickness³), intact cells are plunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can also be imaged in a vitreous state by first "high-pressure freezing" and then, "cryo-sectioning" them. A series of two-dimensional projection images are then collected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or "tomogram" can then be calculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal the structures of various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, and the locations and architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.^{1, 2}In this video article we illustrate how to image cells with ECT, including the processes of sample preparation, data collection, tomogram reconstruction, and interpretation of the results through segmentation and in some cases correlation with light microscopy.     

Olive Phenolics as c-Met Inhibitors: (-)-Oleocanthal Attenuates Cell Proliferation,Invasiveness, and Tumor Growth in Breast Cancer Models

Dysregulation of the Hepatocyte growth factor (HGF)/c-Met signaling axis upregulates diverse tumor cell functions, including cell proliferation, survival, scattering and motility, epithelial-to-mesenchymal transition (EMT), angiogenesis, invasion, and metastasis. (-)-Oleocanthal is a naturally occurring secoiridoid from extra-virgin olive oil, which showed antiproliferative and antimigratory activity against different cancer cell lines. The aim of this study was to characterize the intracellular mechanisms involved in mediating the anticancer effects of (-)-oleocanthal treatment and the potential involvement of c-Met receptor signaling components in breast cancer. Results showed that (-)-oleocanthal inhibits the growth of human breast cancer cell lines MDA-MB-231, MCF-7 and BT-474 while similar treatment doses were found to have no effect on normal human MCF10A cell growth. In addition, (-)-oleocanthal treatment caused a dose-dependent inhibition of HGF-induced cell migration, invasion and G1/S cell cycle progression in breast cancer cell lines. Moreover, (-)-oleocanthal treatment effects were found to be mediated via inhibition of HGF-induced c-Met activation and its downstream mitogenic signaling pathways. This growth inhibitory effect is associated with blockade of EMT and reduction in cellular motility. Further results from in vivo studies showed that (-)-oleocanthal treatment suppressed tumor cell growth in an orthotopic model of breast cancer in athymic nude mice. Collectively, the findings of this study suggest that (-)-oleocanthal is a promising dietary supplement lead with potential for therapeutic use to control malignancies with aberrant c-Met activity.     

POTENTIATION OF CAFFEINEINDUCED CONTRACTURE BY RAISING EXTRACELLULAR POTASSIUM IN FROG SKELETAL MUSCLE

用蛙胫前肌小束为材料,研究了提高胞外钾［Ｋ＋］Ｏ对咖啡因挛缩的作用。［Ｋ＋］Ｏ从２ｍｍｏｌ／Ｌ提高到１０或２５ｍｍｏｌ／Ｌ,由３ｍｍｏｌ／Ｌ咖啡因引起的挛缩明显增强。以ＰＫＣ／ＰＣ（ＰＫＣ和ＰＣ分别为在高钾和正常钾条件下的咖啡因挛缩）表示的咖啡因挛缩增强,依赖［Ｋ＋］Ｏ和高钾作用时间。随着１０ｍｍｏｌ／Ｌ［Ｋ＋］Ｏ作用时间延长,直至１０ｍｉｎ,增强逐渐增加。但是,２５ｍｍｏｌ／Ｌ［Ｋ＋］Ｏ作用１ｍｉｎ时增强达到最大,然后下降到对照。ＰＫＣ／ＰＣ变化时程不能用高钾引起的去极化解释,而与由相似［Ｋ＋］Ｏ引起的胞浆自由钙变化时程相符。提示,至少在蛙骨骼肌,高钾引起的咖啡因挛缩增强主要是由胞浆自由钙升高引起的。