Researchers find that most protein complexes in yeast cells assemble before the subunits have fully formed. This mechanism might prevent the formation of toxic protein aggregates. Most cellular processes are carried out by proteins, which generally assemble into heteromeric complexes those composed of two or more distinct subunits.

Although it was thought for many years that protein subunits diffuse freely in the cell and form complexes through random collisions, this seems unlikely, given that the cellular environment is extremely crowded. The study was published in Nature.

Ribosome Profiling

The study of co-translational protein-complex formation in vivo was challenging until a technique known as ribosome profiling was developed in 2009. This technique allows the positions of ribosomes on messenger RNAs to be determined by sequencing RNA fragments and is usually used to monitor translation the process in which the ribosome decodes mRNA and uses it as a template for protein synthesis.

Shiber used a modified protocol called selective ribosome profiling, which isolates ribosomes that are synthesizing nascent protein chains already interacting with another protein.  Subsequent sequencing of the corresponding RNA fragments reveals the mRNAs that encode the interacting nascent chains.

Sequencing

The sequencing also identifies the protein domains involved in the interaction, because selective ribosome profiling will isolate only ribosomes bound to nascent chains that contain fully exposed interaction domains.

Protein Complexes

The three protein complexes that did not seem to do this use dedicated chaperone proteins to assist in assembly. Given that the major function of chaperones is to prevent misfolding and random aggregation of proteins during protein folding, the researchers hypothesized that co-translational protein-complex assembly might serve a similar purpose.

One of the subunits must be fully folded before it engages the nascent chain of a second subunit, but the fully folded second subunit cannot engage the nascent chain of the first subunit. This means that the second subunit must always participate in the co-translational assembly as a nascent chain.

Protein Aggregates

Intriguingly, when the authors studied yeast strains that had been engineered not to produce the fully folded subunit, they observed that the nascent chain of the second subunit forms aggregates. This indicates that co-translational assembly does indeed prevent the formation of potentially toxic protein aggregates.

Although the authors convincingly show that co-translational protein-complex assembly is widespread, it is unclear how the subunits are brought into proximity to enable complex formation. There are two plausible, broad models, which are not mutually exclusive.

Protein Interactions

More experiments are needed to work out how interacting protein subunits are brought together and how mis-assembly of complexes is prevented. Nevertheless, they have demonstrated that protein-complex formation often relies on recruitment mechanisms, rather than diffusion, to achieve specific protein interactions.

Their findings add to an increasing number of in vivo observations suggesting that most cellular processes are interconnected: mRNAs not only encode proteins, but also increase the specificity of protein-complex formation by assisting the compartmentalization of proteins in the cytoplasm, and by regulating localized translation.

Stable Protein Complexes

Finally, it remains to be seen whether the majority of stable protein complexes in mammalian cells are also assembled co-translationally — but it seems likely that they are.