One of the most intricate and fundamental processes of life is the translation of the genetic code into proteins. Decoding mRNA-based information into the corresponding sequence of amino acids is performed by a complex ribonucleoprotein particle, the ribosome. Traditionally, the ribosome is viewed as highly conserved machinery with an invariable RNA and protein complement. This perception of invariance has been perpetuated by the determination of high resolution structures, which implied that ribosomes are homogeneous entities that are not considered to have an intrinsic regulatory capacity. The main aim of my group is to decipher molecular mechanisms that lead to modulation of the translational program by ribosome heterogeneity. In particular, we focus on the adaptation of protein synthesis to stress conditions bacteria encounter upon infection of their host.

During the last years we investigated the basic principles of translation initiation in Escherichia coli with a special focus on leaderless mRNAs (lmRNAs), which harbor a 5´-terminal AUG start codon and thus lack kingdom-specific ribosome recruitment signals. Our studies revealed that antibiotic treatment of bacterial cells can result in the formation of ribosomes with a reduced protein complement. Surprisingly, these protein-depleted ribosomes are proficient in translation of lmRNAs (Kaberdina et al., 2009). Collectively, our results provided the first in vivo evidence for the formation of functionally distinct ribosomes under adverse conditions.

 Recently, we have elucidated a novel post-transcriptional stress adaptation mechanism. Our studies showed that Bacteria facing stress alter their translational program employing heterogeneous ribosomes (Vesper et al., 2011). We have shown that the endoribonuclease MazF, the toxin component of a toxin-anti-toxin module, cleaves at ACA sites closely upstream of the AUG–start codon of specific mRNAs. Thereby particular lmRNAs are generated. Surprisingly, we indentified the 16S rRNA of the 30S subunit as another target of MazF. Specifically, the toxin cleaves off the anti-Shine and Dalgarno (aSD) sequence. As the SD-aSD interaction is required for translation initiation on canonical ribosome binding sites, the truncation of 16S rRNA generates a specialized protein synthesis machinery that selectively translates the lmRNAs formed by MazF, entailing the reprogramming of the translatome (Vesper et al., 2011). Based on these findings questions as to whether (i) the bifurcation of the ribosomal population occurs inside individual cells or whether it is distributed among subpopulations of cells, or (ii) a “ribosome repair mechanism” exists that enables the “stress-ribosomes” to recover from stressful conditions, are currently addressed in my group.

Another focus of our work concerns the binding of protein S1 with the ribosome. In particular, we concentrate on the structural characterization of the interaction surface between proteins S1 and S2, which could serve as antimicrobial drug target, as for Gram-negative bacteria binding of S1 to the ribosome is essential.