Using cryo-electron tomography, researchers from Julia Mahamid’s European Molecular Biology Laboratory Heidelberg research group have visualized how different cellular processes are connected in 3D. Published in two papers in the journal Cell, the findings allow scientists to map protein production machinery across hundreds of individual cells and uncover previously unseen connections between transcription and translation.
Mapping Protein Production in 3D with Cryo-ET
Scientists have traditionally viewed cells as bustling cities outfitted with factories, power grids, and shipping networks. Yet, past research lacked the tools to examine how these individual components interact. Joe Dobbs, former PhD fellow in Mahamid’s group and current postdoctoral researcher at the Max Planck Institute for Brain Research in Frankfurt, led a team imaging Mycoplasma pneumoniae bacteria using cryo-electron tomography. This technique lets researchers peer inside flash-frozen cells in 3D to reveal the structures of molecular machines at high resolution.
Did you know? Cryo-ET allows scientists to capture cellular structures in a near-native state by flash-freezing samples rapidly, preventing the formation of ice crystals that typically damage delicate molecular details.
Dobbs and his colleagues reconstructed high-resolution maps and counted instances of ribosomes in different functional states across hundreds of individual cells. According to the research, this imaging unveiled several new complexes directly connecting transcription—the process of producing mRNA from DNA—with translation, the process of producing proteins. These observations offer structural evidence for long-hypothesized supercomplexes and suggest new molecular mechanisms for how these intertwined processes are controlled.
Discoveries at the Cell Border and Membrane Attachments
Beyond gene expression machineries, the research team identified ribosome parts attached to the cell membrane even when inactive. Their results indicate that these subunits detach from the membrane only when conditions permit a new round of protein production to begin. This behavior mirrors phenomena observed in mammalian cells decades ago, pointing to conserved mechanisms stretching from bacteria to humans.
In a parallel study led by Rasmus Jensen within the Mahamid group, researchers investigated protein transportation and folding at the cell membrane. Jensen started by examining an interesting structure in the cell and working backward, eventually discovering a new configuration of a molecular machine that exports proteins or inserts them into the membrane. By combining cryo-ET imaging, proteomics, and computational protein structure predictions, the team found that this machinery includes the Sec-translocon—a well-known protein channel acting as a doorway out of the cell—alongside three previously unknown proteins that assist in folding transported proteins into their correct functional shapes.
Both studies focused on minimal bacterial cells where biological systems remain relatively simple, establishing methodologies that can eventually be applied to more complex organisms. Julia Mahamid, EMBL Group Leader and senior author on both papers, noted that decades of structural biology focused on isolated molecules provided detailed views of structures and functions, but researchers previously lacked the technology to study complex interactions and cross-talk.
“Working together with many colleagues at EMBL, we combined expertise in microbiology, proteomics, bioinformatics, structural biology, and integrative modelling,” Mahamid stated regarding the collaborative effort behind the discoveries.
Frequently Asked Questions
What is cryo-electron tomography (cryo-ET)?
Cryo-ET is an advanced imaging technique that allows scientists to view the inside of flash-frozen cells in three-dimensional detail, revealing the structures of molecular machines in their near-native cellular environment.
What did the Mahamid research group discover in Mycoplasma pneumoniae?
The EMBL researchers discovered new complexes connecting transcription and translation, membrane-attached ribosome subunits during inactive states, and a previously unknown protein-folding system operating alongside the Sec-translocon at the cell membrane.
Why are minimal bacterial cells used in these studies?
Minimal bacteria feature simpler biological systems, allowing scientists to establish conceptual foundations and analytical techniques before applying them to more complex organisms.
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