DeepRibosome · Visual Translatomics – Deep ribosomal insights by cryo-electron microscopy of actively translating ribosomes

Structure determination of dynamic macromolecular molecular machines and elucidating their conformational landscapes are fundamental tasks of structural biology. The ribosome as a paradigmatic macromolecular machine interacts with numerous ligands and factors throughout its functional cycles, which in turn are driven and regulated by various conformational modes. Project DeepRibosome proposes a new way to perform structural studies. It is based on our recent finding that E. coli ex-vivo derived polysomes carrying the translatome can be efficiently reactivated in the PURE in vitro translation system. Cryo-EM of actively translating ribosomes results in comprehensive structural landscapes. During steady state, all intermediates are expected to be present, including the short-lived ones. Supported by preliminary data, we estimate that applying multi-particle sorting of images we can resolve states with a lifetime in the one-digit millisecond range. This allows us to study under optimal conditions fast steps such as the GTPase factor-dependent reactions or peptidyl-transfer/accommodation without artificially stalling the reaction by antibiotics or non-cleavable GTP analogues. The structural studies will be accompanied by functional assays including Ribo-seq to monitor translation of the cell-derived translatome in a cell-free system. While, we will also conduct in situ structural analysis for comparison, the strength of our new approach is that we can track translation from an integrated structural and functional perspective, preserving/reconstituting many native features but under defined and controllable conditions. This will not only provide insights into the molecular mechanism of translation at the next level of understanding but also allow us to answer long-standing questions e.g. how exactly the physicochemical environment (temperature, ions) or auxiliary factors impact translation. It will also provide new means to study the inhibition mechanisms of antibiotics.