One of the most intricate and fundamental processes of life is the translation of the genetic code into proteins. Decoding the mRNA-based information into the corresponding sequence of amino acids is performed by a complex ribonucleoprotein particle, the ribosome. Due to its structural and functional complexity the ribosome represents a major target for antibiotics. The aminoglycoside antibiotic kasugamycin (Ksg) inhibits translation at the step of initiation by blocking the mRNA path on the 30S ribosomal subunit (Schluenzen et al., 2006). However, translation of leaderless mRNAs, which start directly with a 5´-terminal AUG and lack kingdom-specific ribosome recruitment signals, prevails in E. coli in the presence of the drug in vivo (Moll and Bläsi, 2002). Our studies revealed that the presence of the antibiotic results in the formation of ribosomes depleted for several essential proteins of the small subunit including the functionally important proteins S1 and S12. However, these 61S ribosomes are proficient in translation of leaderless mRNAs. These studies provided therefore the first evidence for the functionality of protein-deficient ribosomes in translation and supported the hypothesis, that the modern ribosome is a protein-stabilized ribozyme. In addition, we were able to reconcile the lack of these proteins with structural rearrangements in the 16S rRNA upon binding of Ksg to 70S ribosomes, which enabled us to devise a model for the formation of these particles originating from fully assembled 70S ribosomes (Kaberdina et al., 2009). As leaderless mRNAs are suggested to present remnants of ancestral mRNAs, furthermore these studies support the hypothesis that the “61S” particles might reflect an intermediate step of ribosome evolution before the kingdoms have diverged.
During these studies we observed the resumed synthesis of specific proteins upon prolonged Ksg treatment. We identified some of these proteins as chaperones, stress proteins, ribosomal proteins and ribosome modifying enzymes. Surprisingly, we discovered that the respective mRNAs became leaderless in the presence of the antibiotic, which apparently allows translation by protein-depleted ribosomes. Therefore, the main aim of our studies is directed towards the question, whether selective translation of conditionally leaderless mRNAs by protein-depleted ribosomes represents a novel regulatory mechanism under adverse/stress conditions. Therefore, we will concentrate on the following topics: (i) what is the mechanism underlying the formation of protein-depleted ribosomes and (ii) the 5´-terminal processing of the respective mRNAs under stress conditions. Moreover, since several points of evidence indicate, that this proposed “stress response pathway” might be of relevance for pathogenic bacteria upon infection, we will perform validation studies in the bacterial pathogen Salmonella typhimurium.