YebC enhances translation of prolin-rich motifs
Bacteria use RNA binding proteins (RBPs) to express and regulate genes. Despite decades of studies on bacterial genetics and physiology there are still proteins whose function is unknown. We used two proteomics approaches to uncover a repertoire of RNA binding proteins in the pathogenic bacterium Streptococcus pyogenes: Orthogonal Organic Phase Purification (OOPS) and RNA Binding Sites Identification (RBS-ID). The combination of these approaches successfully identified most of the annotated RBPs including proteins involved in translation. However, the function of some of the proteins found to interact with RNA is unknown. One of these proteins - YebC - was selected for further study. YebC is a highly conserved protein present in almost all organisms. In mitochondria, the YebC homolog TACO1 has previously been shown to be required for the translation of COX I mRNA.  The knock-out of yebC moderately affects the growth, transcriptome and proteome of S. pyogenes. Limited site-directed mutagenesis performed in S. pyogenes identified several mutations that inactivate the protein without significantly affecting its stability. According to the results of the iCLIP experiment, YebC cross-links with helix 89 of the 23S rRNA near the peptidyl-transferase centre. However, the protein does not stably associate with ribosomes. We performed ribo-seq analysis and detected increased pausing at and downstream of the amino acid stretches PPP, PPG, PIP and DIP. Further results obtained with in vivo reporters and the in vitro translation system suggest that YebC can alleviate ribosome stalling at the polyproline stretches. In conclusion, our results and the ubiquity of YebC suggest that this protein is a novel elongation factor that enhances translation of proline-rich amino acid stretches.