The direct study of transcription or DNA–protein-binding events, requires imaging of individual genes at molecular resolution. Electron microscopy (EM) can show local detail of the genome. However, direct visualization and analysis of specific individual genes is currently not feasible as they cannot be unambiguously localized in the crowded, landmark-free environment of the nucleus. Here, we present a method for the genomic insertion of gene clusters that can be localized and imaged together with their associated protein complexes in the EM. The method uses CRISPR/Cas9 technology to incorporate several genes of interest near the 35S rRNA gene, which is a frequently occurring, easy-to-identify genomic locus within the nucleolus that can be used as a landmark in micrographs. As a proof of principle, we demonstrate the incorporation of the locus-native gene RDN5 and the locus-foreign gene HSX1. This led to a greater than 7-fold enrichment of RNA polymerase III (Pol III) complexes associated with the genes within the field of view, allowing for a significant increase in the analysis yield. This method thereby allows for the insertion and direct visualization of gene clusters for a range of analyses, such as changes in gene activity upon alteration of cellular or external factors.
Lipid acquisition and transport are fundamental processes in all organisms, but many of the key players remain unidentified. Here, we elucidate the lipid-cycling mechanism of the Mycoplasma pneumoniae membrane protein P116. We show that P116 not only extracts lipids from its environment but also self-sufficiently deposits them into both bacterial and eukaryotic cell membranes as well as liposomes. Our structures and molecular dynamics simulation show that the N-terminal region of P116, which resembles an SMP domain, is responsible for perturbing the membrane, while a hydrophobic pocket exploits the chemical gradient to collect the lipids and the protein’s dorsal side acts as a mediator of membrane directionality. Furthermore, ligand binding and growth curve assays suggest the potential for designing small molecule inhibitors targeting this essential and immunodominant protein. We show that P116 is a versatile lipid acquisition and delivery machinery that shortcuts the multi-protein pathways used by more complex organisms. Thus, our work advances the understanding of common lipid transport strategies, which may aid research into the mechanisms of more complex lipid-handling machineries.