Structural Insights into the Dynamic Ribosome-Translocon Complex Reveal Novel Mechanisms of Membrane Protein Biogenesis

Conceptos Básicos

The ribosome-translocon complex undergoes dynamic conformational changes and associations with various accessory factors to facilitate the biogenesis of secretory and membrane proteins.

Resumen

The study leverages cryo-EM and structure prediction techniques to derive insights into several novel configurations of the ribosome-translocon complex. Key findings include:

The structure of Sec61 inserting a transmembrane domain (TMD) of a membrane protein, showing how the TMD binds and opens the Sec61 lateral gate.

The discovery of RAMP4 occupying the Sec61 lateral gate, widening the central pore and contributing to its hydrophilic interior. RAMP4 competes with other factors for binding to Sec61.

The identification of a C-terminal helix of ribosomal protein uL22 that can switch between a scanning state and an engaged state, where it contacts Sec61 and the nascent chain.

The structural characterization of the TRAP complex and its dynamic interactions with the ribosome, Sec61, and other translocon components like OSTA and the BOS complex. TRAP exhibits features that may influence Sec61 activity.

Evolutionary analysis reveals the conservation and diversification of TRAP across eukaryotes and archaea, suggesting an ancient origin and functional importance.

Overall, the study provides a comprehensive structural understanding of the remarkable plasticity and context-dependent conformations of the ribosome-translocon machinery, which dynamically adjusts to accommodate its diverse range of substrates.

Estadísticas

The structure of Sec61 bound to the transmembrane domain of rhodopsin shows that the hydrophobic region is 11 Å (∼3 amino acids) from the tip of 28S rRNA helix 59 and the adjacent polyacidic tail of ribosomal protein eL22.
The Sec61 pore is ringed by four aliphatic residues: V85, I183, I292, and L449.
RAMP4 is present in ∼81% of non-MPT ribosome-translocon complexes in native membranes.

Citas

"RAMP4 competes with other factors, including RhoTM2 and the PAT complex, for binding to the Sec61 lateral gate."
"The C-terminal helix of ribosomal protein uL22 can switch between a scanning state and an engaged state, where it contacts Sec61 and the nascent chain."
"TRAP exhibits features that may influence Sec61 activity, such as binding the Sec61 hinge loop, potentially modulating the opening of the lateral gate."

Ideas clave extraídas de

Structural analysis of the dynamic ribosome-translocon complex

by Lewis,A. J. ... a las www.biorxiv.org 12-22-2023

https://www.biorxiv.org/content/10.1101/2023.12.22.572959v1

Consultas más profundas

How might the dynamic interactions between RAMP4, TRAP, and other translocon components be regulated to coordinate the diverse functions of the ribosome-translocon complex

The dynamic interactions between RAMP4, TRAP, and other translocon components are likely regulated through a combination of factors to coordinate the diverse functions of the ribosome-translocon complex. One key regulatory mechanism could involve post-translational modifications (PTMs) that modulate the binding affinities and activities of these components. For example, phosphorylation or glycosylation of specific residues on RAMP4 or TRAP could alter their interactions with Sec61 or the ribosome, influencing the overall conformation and function of the complex. Additionally, the expression levels of these components and their regulators could be tightly controlled to ensure proper coordination during protein biogenesis.
Furthermore, the presence of accessory factors or chaperones that interact with RAMP4 and TRAP could serve as regulatory checkpoints to fine-tune the assembly and disassembly of the ribosome-translocon complex. These factors may act as molecular switches, triggering conformational changes or stabilizing specific interactions based on the cellular context or the type of nascent protein being translocated.
Moreover, the lipid composition of the ER membrane could also play a role in regulating the interactions within the translocon complex. Lipid-protein interactions can influence the localization and activity of translocon components, impacting the overall efficiency of protein translocation and membrane insertion.
Overall, the dynamic interactions between RAMP4, TRAP, and other translocon components are likely tightly regulated through a combination of PTMs, accessory factors, and lipid-protein interactions to ensure the proper functioning of the ribosome-translocon complex in diverse cellular processes.

What are the potential implications of the uL22 C-terminal helix switching between scanning and engaged states, and how could this mechanism be further investigated experimentally

The switching of the uL22 C-terminal helix between scanning and engaged states could have significant implications for the regulation of protein biogenesis and translocation at the ribosome-translocon complex. In the scanning state, where the uL22 C-terminal helix is flexible and not engaged with Sec61 or the nascent chain, it may serve as a sensor for nascent chains emerging from the ribosome. This scanning mechanism could allow uL22 to detect specific features or signals on the nascent chain, triggering its engagement and potentially influencing the translocation process.
On the other hand, in the engaged state, where the uL22 C-terminal helix forms contacts with Sec61 and the nascent chain, it could play a direct role in stabilizing the nascent chain at the ribosome-translocon junction. By interacting with both the ribosome and Sec61, the uL22 C-terminal helix may help to guide the nascent chain towards the translocation channel and facilitate its insertion into the ER membrane.
To further investigate this mechanism experimentally, one approach could involve mutagenesis studies to disrupt specific interactions between the uL22 C-terminal helix, Sec61, and the nascent chain. By introducing mutations that affect the flexibility or binding affinity of the uL22 C-terminal helix, researchers could assess the impact on protein translocation and membrane insertion. Additionally, structural studies using cryo-EM or X-ray crystallography could provide detailed insights into the conformational changes of uL22 and its interactions with other components of the ribosome-translocon complex.

Given the evolutionary conservation and diversification of TRAP across eukaryotes and archaea, what insights could be gained by studying TRAP function in more diverse model organisms beyond the commonly used mammalian and yeast systems

Studying TRAP function in more diverse model organisms beyond commonly used mammalian and yeast systems could provide valuable insights into the evolutionary conservation and diversification of this essential translocon component. By investigating TRAP in a broader range of eukaryotic and archaeal species, researchers could uncover novel regulatory mechanisms, structural adaptations, and functional roles that have evolved across different lineages.
One potential benefit of studying TRAP in diverse model organisms is the opportunity to identify conserved structural motifs or interaction interfaces that are essential for its function. By comparing TRAP sequences and structures from various species, researchers could pinpoint key residues or domains that are critical for its binding to the ribosome, Sec61, or other translocon components. This comparative analysis could reveal evolutionary constraints on TRAP function and shed light on its ancestral role in protein biogenesis.
Furthermore, investigating TRAP in diverse model organisms could help elucidate species-specific adaptations or regulatory mechanisms that have evolved to meet the unique demands of different cellular environments. For example, studying TRAP in plants, fungi, or early-branching eukaryotes could uncover specialized functions or interactions that are not present in mammalian or yeast systems. These insights could provide a more comprehensive understanding of TRAP's role in co-translational protein translocation and membrane insertion across the tree of life.
Overall, by expanding the scope of TRAP research to include a wider range of model organisms, scientists can gain a more holistic view of its evolutionary history, functional diversity, and regulatory mechanisms in the context of protein biogenesis.