Three-dimensional reconstruction of bacteria with a complex endomembrane system.

The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. Such compartmentalization has been claimed to occur in members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae bacterial superphylum. Here we have investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacteria Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated as none of the spaces created by the membrane invaginations are closed; instead, they are all interconnected. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not different from, but an extension of, the "classical" Gram-negative bacterial membrane system. Our results have implications for our definition and understanding of bacterial cell organization, the genesis of complex structure, and the origin of the eukaryotic endomembrane system.

Quantitative and spatio-temporal features of protein aggregation in Escherichia coli and consequences on protein quality control and cellular ageing.

The aggregation of proteins as a result of intrinsic or environmental stress may be cytoprotective, but is also linked to pathophysiological states and cellular ageing. We analysed the principles of aggregate formation and the cellular strategies to cope with aggregates in Escherichia coli using fluorescence microscopy of thermolabile reporters, EM tomography and mathematical modelling. Misfolded proteins deposited at the cell poles lead to selective re-localization of the DnaK/DnaJ/ClpB disaggregating chaperones, but not of GroEL and Lon to these sites. Polar aggregation of cytosolic proteins is mainly driven by nucleoid occlusion and not by an active targeting mechanism. Accordingly, cytosolic aggregation can be efficiently re-targeted to alternative sites such as the inner membrane in the presence of site-specific aggregation seeds. Polar positioning of aggregates allows for asymmetric inheritance of damaged proteins, resulting in higher growth rates of damage-free daughter cells. In contrast, symmetric damage inheritance of randomly distributed aggregates at the inner membrane abrogates this rejuvenation process, indicating that asymmetric deposition of protein aggregates is important for increasing the fitness of bacterial cell populations.

A visualization and segmentation toolbox for electron microscopy.

Three-dimensional image analysis includes image processing, segmentation and visualization operations, which facilitate the interpretation of data. We have developed a toolbox for three-dimensional (3D) electron microscopy (EM) in Amira, which is a commercial software package, used by many laboratories. Our toolbox integrates a number of established procedures specifically tailored for 3D EM. These include input-output, filtering, segmentation, visualization and ray-tracing functions, which can be accessed directly from a user-friendly pop-up menu. They allow performing denoising and segmentation tasks directly in Amira, without the need of other programs, and ultimately allow the visualization of the results at photo-realistic quality with ray-tracing. They also allow a direct interaction with the data, such that, e.g., sub-tomograms can be directly extracted, or segmentation areas can be interactively selected. The implemented functions are fast, reliable and intuitive, yielding a comprehensive package for visualization in EM.

Classification of cryo-electron sub-tomograms using constrained correlation.

Cryo-electron tomography (CET) is currently the only three-dimensional imaging technique capable of visualizing macromolecules in their cellular context at close-to-native conditions with a resolution in the nanometer range. An important component for the analysis of the data is their classification, which should discriminate among various macromolecules, conformational changes and interaction partners. Missing structure factors, typically in a wedge-shaped region in Fourier space if single-axis tilting is performed, hamper classification of cryo-electron tomographic data. Here, we describe a classification method for three-dimensional (3D) sub-tomograms extracted from cryo-electron tomograms, which takes the missing wedge into account and provides reliable results. The similarity of the individually aligned sub-tomograms is scored by constrained correlation. Subsequently, they are clustered based on their pairwise correlation values. In order to demonstrate the feasibility of this approach, we apply the proposed method to simulated tomographic data of the chaperone thermosome in different conformations. By comparison of the principal components of the resulting matrix we show that the proposed metric is significantly less prone to the orientation of the missing wedge compared to the unconstrained correlation. Moreover, we apply our classification method to an experimental dataset of GroEL with and without GroES, where we achieve a distinct discrimination between the putative GroEL and GroEL/GroES complexes.

Performance evaluation of image processing algorithms on the GPU.

The graphics processing unit (GPU), which originally was used exclusively for visualization purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through the development of elaborate interfaces, the GPU can be used to process data and deal with computationally intensive applications. The speed-up factors attained compared to the central processing unit (CPU) are dependent on the particular application, as the GPU architecture gives the best performance for algorithms that exhibit high data parallelism and high arithmetic intensity. Here, we evaluate the performance of the GPU on a number of common algorithms used for three-dimensional image processing. The algorithms were developed on a new software platform called "CUDA", which allows a direct translation from C code to the GPU. The implemented algorithms include spatial transformations, real-space and Fourier operations, as well as pattern recognition procedures, reconstruction algorithms and classification procedures. In our implementation, the direct porting of C code in the GPU achieves typical acceleration values in the order of 10-20 times compared to a state-of-the-art conventional processor, but they vary depending on the type of the algorithm. The gained speed-up comes with no additional costs, since the software runs on the GPU of the graphics card of common workstations.

Transient structure associated with the spindle pole body directs meiotic microtubule reorganization in S. pombe.

BACKGROUND: Vigorous chromosome movements driven by cytoskeletal assemblies are a widely conserved feature of sexual differentiation to facilitate meiotic recombination. In fission yeast, this process involves the dramatic conversion of arrays of cytoplasmic microtubules (MTs), generated from multiple MT organizing centers (MTOCs), into a single radial MT (rMT) array associated with the spindle pole body (SPB), the major MTOC during meiotic prophase. The rMT is then dissolved upon the onset of meiosis I when a bipolar spindle emerges to conduct chromosome segregation. Structural features and molecular mechanisms that govern these dynamic MT rearrangements are poorly understood. RESULTS: Electron tomography of the SPBs showed that the rMT emanates from a newly recognized amorphous structure, which we term the rMTOC. The rMTOC, which resides at the cytoplasmic side of the SPB, is highly enriched in γ-tubulin reminiscent of the pericentriolar material of higher eukaryotic centrosomes. Formation of the rMTOC depends on Hrs1/Mcp6, a meiosis-specific SPB component that is located at the rMTOC. At the onset of meiosis I, Hrs1/Mcp6 is subject to strict downregulation by both proteasome-dependent degradation and phosphorylation leading to complete inactivation of the rMTOC. This ensures rMT dissolution and bipolar spindle formation. CONCLUSIONS: Our study reveals the molecular basis for the transient generation of a novel MTOC, which triggers a program of MT rearrangement that is required for meiotic differentiation.