Ribosomal stalling by short peptides targeting conserved sites in the ribosome: a new class of novel ribosomal antibodies

Reverse Biology is a bioinformatic method developed in our lab, able to detect short peptide sequences which are rarely present or totally excluded from the cell, revealing the existence of Under-represented sequences (URS). The URS’s effect was examined in vivo, by genetically modified E.coli able to express proteins with embedded URS sequences. When the URS-protein was expressed, ribosomal activity was significantly reduced, leading to protein synthesis inhibition, followed by cell death, proving that these peptides are a potential ribosomal inhibitor. More recently we have utilized the information described above to develop novel translation inhibitors, based on URS`s for pathogenic bacteria. We used synthetic peptides containing a URS. when exposing the bacteria cultures to the URS, culture growth was strongly inhibited (unpublished data). To learn more about the mechanisms of translational inhibition by URS, we have now determined the structures of 70S Ribosomes from E.coli and Salmonella by Cryo-EM to 2.7Å, revealing the binding site of the URS peptide in the ribosome. The peptide was found within the ribosome exit tunnel, close to the peptidyl transfer center. More importantly, it can be suggested that peptide binding interferes with the functions of the highly conserved nucleotides, A2602 and U2585 in the 23S rRNA. So, we believe that "Reverse Biology" method can be a new approach that within this research will allow us to develop a great number of peptidyl antibiotics able to target highly conserved sites on the ribosome, which can provide a new way to fight against bacterial resistance.