Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

Abstract

SUMMARYElectrostatic potentials along the ribosomal exit tunnel are non-uniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet is likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel, and measured chain elongation rates. Positively-charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively-charged residues than for those containing positively-charged residues. We provide experimental evidence that extra-ribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.

Positive charges on the translocating polypeptide chain arrest movement through the translocon

“…The charged amino acid residues within the Sec61a subunit might be involved in the interaction. In the ribosome, the positive charges of the nascent chain might slow down polypeptide chain elongation through electrostatic interaction with negative charges of the ribosome tunnel (Lu and Deutsch, 2008). In the present study, the effect of the positive charges on the protein synthesis rate was not drastic; similar amounts of the 0K model and the 20K model were observed after 20 minutes of translation ( Fig.…”

Recruitment of a species-specific translational arrest module to monitor different cellular processes

“…For instance, regulatory peptides encoded by leader regions of genes for resistance determinants against some antibiotics, such as erythromycin and chloramphenicol, undergo antibiotic-induced elongation arrest both in Gram-positive and Gram-negative bacteria (3,21,22). Clusters of positively charged amino acids can cause arrest in translation in eukaryotic ribosomes (23). Such a distinct chemical feature as well as an antibiotic action might contribute to the general arrest functions in these cases.…”

The Ubiquitin–Proteasome System of Saccharomyces cerevisiae

“…Such nonstop mRNAs can result from errors in gene expression, and their poly(A) tails are translated into polylysine tracts. The positive charge of polylysine induces translational pausing due to strong electrostatic interaction with the negatively charged ribosome exit channel (Lu and Deutsch 2008). The resulting translationally paused or arrested nascent polypeptides seem to be targeted by Rkr1/Ltn1 (Bengtson and Joazeiro 2010).…”