The Ribosome Can Prevent Aggregation of Partially Folded Protein Intermediates: Studies Using the Escherichia coli Ribosome

Abstract

BackgroundMolecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone ‘foldases’ that are distinct from chaperone’ holdases’ that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC) located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA) is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains.ResultsWe demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII) and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein.ConclusionThe ribosome can behave like a ‘holdase’ chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.

Distinct modulatory role of RNA in the aggregation of the tumor suppressor protein p53 core domain

“…Similar to polyphosphate chaperones (58), the polyanion RNA chain could also act as a chemical scaffold for the intrinsically unstable and aggregation-prone p53C, favoring local, proteinprotein interactions and preventing long-distance ones. In this context, it is worth mentioning that rRNA has been shown to facilitate protein folding (48,59,60) as well as to prevent aggregation of partially folded protein intermediates (61). The parallels between the preventive role of RNA in p53C aggregation and protein folding activity of rRNA (53,62) remain to be elucidated.…”

Protein Folding Activity of the Ribosome is involved in Yeast Prion Propagation

“…That [ PSI + ] is impaired when PFAR is inhibited or strengthened is reminiscent of Hsp104p’s involvement in prion propagation in yeast, just as [ PSI + ] propagation is impaired by both Hsp104p inhibition and overexpression. Like Hsp104p, domain V of the ribosome may have chaperone activity able to deal with cross-β sheet amyloid aggregates 37 since reduced Hsp104p activity, deleterious for [ PSI + ] propagation, is compensated for by enriched PFAR activity, and vice versa ( Figs 4 and 5 ). This interplay between PFAR and Hsp104p for [ PSI + ] propagation is in good agreement with GdnHCl’s synergistic effect with 6AP or GA in curing [ PSI + ] from yeast 10 13 .…”

A comparison of the folding characteristics of free and ribosome‐tethered polypeptide chains using limited proteolysis and mass spectrometry

“…Accordingly, the protein folding ability is also observed for eukaryotic ribosomes, e.g. from yeast, rat liver or wheat germ, and seems to be a universal property of the translation machinery …”

“…For example, the chaperoning abilities of the E. coli ribosome (70S) have been shown to prevent aggregation of partially folded protein intermediates. 5 The ribosome has also been found to retard folding of two-domain proteins via decelerating the formation of stable tertiary interactions and the attainment of the native state. 6 There is a high degree of functional and structural conservation between bacterial and eukaryotic ribosomes and conserved rRNA elements of the large ribosomal subunit are assumed to have chaperoning functions.…”

“…from yeast, rat liver or wheat germ, and seems to be a universal property of the translation machinery. 5 The synthesis of proteins by ribosomes in vivo proceeds in a vectorial fashion commencing from the N-terminus. Thus, the folding of nascent polypeptides may be different from the refolding of fulllength denatured proteins wherein the full sequence is available to form interactions throughout the folding process.…”