Structural Biology in Situ Using Cryo-Electron Subtomogram Analysis

Benchmarking tomographic acquisition schemes for high-resolution structural biology

Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.

Here the authors systematically benchmark cryo-electron tomography acquisition schemes to optimize the attainable resolution for subtomogram averaging, and find that dose-symmetric acquisition with even angular sampling provides a better outcome than most currently used acquisition schemes.

The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type

The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor’s stator system and its structural elaboration. Motors with a single H⁺-driven stator have only the core periplasmic P- and L-rings; those with dual H⁺-driven stators have an elaborated P-ring; and motors with Na⁺ or Na⁺/H⁺-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.

Bacteria are so small that for them, making their way through water is like swimming in roofing tar for us. In response, these organisms have evolved a molecular machine that helps them move in their environment. Named the bacterial flagellum, this complex assemblage of molecules is formed of three main parts: a motor that spans the inner and outer membranes of the cell, and then a ‘hook’ that connects to a long filament which extends outside the bacterium. More precisely, the motor is formed of the stator, an ion pump that stays still, and of a rotor that can spin. Different rings can also be present in the space between the inner and outer membranes (the periplasm) and surround these components. The stator uses ions to generate the energy that makes the rotor whirl. In turn, this movement sets the filament in motion, propelling the bacterium. Depending on where the bacteria live, the stator can use different types of ions. In addition, while many species have a single stator system per motor, some may have several stator systems for one motor: this may help the microorganisms move in different conditions.

As microbes colonize environments with a different pH or viscosity, they constantly evolve new versions of the motor which are more suitable to their new surroundings. However, a part of the motor remains the same across species. Overall, it is still unclear how bacterial flagella evolve, but examining the structure of new motors can shed light upon this process. Here, Kaplan et al. combine a bioinformatics approach with an imaging technique known as electron cryo-tomography to dissect the structure of the flagellar motor of three species of bacteria with different stator systems, and compare these to known motors of the same class.

The results reveal a correlation between the nature of the stator system and the presence of certain elements. Stators that use sodium ions, or both sodium and hydrogen ions, are associated with two periplasmic rings surrounding the conserved motor structure. These rings do not exist in motors with single hydrogen-driven stators. Motors with dual hydrogen-driven stators are, to some extent, an ‘intermediate state’, with only one of those rings present. As all the studied species currently exist, it is difficult to know which version of the motor is the most ancient, and which one has evolved more recently.

Capturing the diversity of bacterial motors gives us insight into the evolutionary forces that shape complex molecular structures, which is essential to understand how life evolved on Earth. More practically, this knowledge may also help us design better nanomachines to power microscopic robots.