Marina Parr1*, Alina Sieber2, Prof. Dr. Dmitrij Frishman1 and Dr. Jürgen Lassak2
1Technical University of Munich, Germany
2Ludwig-Maximilians-Universität München, Germany
mar.ark.parr [at] gmail.com
Abstract
Two or more consecutive prolines induce ribosome stalling during translation. In bacteria the elongation factor P (EF-P) efficiently rescues the ribosome stalling and allows the protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function. The residue at the tip of the loop is subjected to the post-translational modifications: lysine is lysylated or arginine is rhamnosylated. We have demonstrated that only those enzymes that are needed for specific post-translational modification of the tip are coded in the bacterial genome (EpmA, EpmB and EpmC proteins for EF-P with lysine and EarP- for those with arginine). Phylogenetic analysis has also unveiled an invariant proline in the -2 position of the tip of the loop in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Combining these observations with experimental evidence, we conclude that β3/β4 loop composition is important for functionalization of EF-P by chemically distinct modifications.
Some bacterial genomes also code the elongation factor P-like (EfpL) protein that shares the same domain architecture with EF-P and has an extended loop of eight amino acid residues long. The evolution, sequence and the structure of EfpL protein have been extensively characterized. Using the assay based on luminescence emission and ribosomal profiles we have shown that EfpL can also relieve the arrest of the ribosome induced by polyproline motifs.
We have also observed the negative correlation between the occurrence of the motif in the proteome of Escherichia coli and its stalling strength measured in luminescence assay. We hypothesize that motifs that cause strong ribosome stalling are disfavored in the protein sequences during evolution due to their impact on the dynamics of translation.
Keywords: polyproline motifs, translation, post-translational modifications, evolution, ribosome profiling, ribosome stalling
