VOLUME 12 NUMBER 4 APRIL 2005 NATURE STRUCTURAL & MOLECULAR BIOLOGY Under nutrient deprivation conditions, there are three layers of bacterial response. Nutrient deprivation leads to the accumulation of free uncharged tRNAs that bind at the A site of the ribosome and stall translation, thus triggering the first layer of response. The stringent factor RelA recognizes and binds to these blocked ribosomes and catalyzes the synthesis of (p)ppGpp (see ref. 15 and references therein), which then upregulates the transcription of enzymes involved in the biosynthesis of amino acids and downregulates transcription of components of the translational apparatus, such as rRNAs, ribosomal proteins, tRNAs, synthetases and translation factors. The stalling of protein synthesis prevents the production of nascent RelB, and existing RelB populations inside the cell (including those in complex with RelB) are reduced by the ATP-dependent Lon protease. This second layer of response frees the toxin RelE to bind to stalled ribosomes (Fig. 2b)8. The blocked ribosome after RelE-mediated cleavage of the mRNA codon at the A site becomes a substrate for the tmRNA rescue system16, representing the third layer of response. tmRNA, a hybrid between a tRNA and an mRNA, binds to the A site of the ribosome containing a truncated mRNA and tags the corresponding nascent chains with a degradation signal (Fig. 2b), while allowing translation to terminate normally (reviewed in ref. 17). In this way, aberrant proteins made from truncated mRNAs are degraded while the stalled ribosomes can be recycled. Therefore, the stringent response involving RelBE and the tmRNA system seem to cooperate to increase degradation of nascent chains on stalled ribosomes; the resulting free amino acids may then improve the survival of the cell under harsh conditions.