Ribosome rescue systems in bacteria

Ribosomes often stall during protein synthesis in various situations in a cell, either unexpectedly or in a programmed fashion. While some of them remain stalled for gene regulation, many are rescued by some cellular systems. Ribosomes stalled at the 3′ end of a truncated mRNA lacking a stop codon (non-stop mRNA) are rescued by trans-translation mediated by tmRNA (transfer-messenger RNA) and a partner protein, SmpB. Through trans-translation, a degradation tag is added to the C-termini of truncated polypeptides from a truncated mRNA to prevent them from accumulation in the cell. Trans-translation has crucial roles in a wide variety of cellular events, especially under stressful conditions. The trans-translation system is thought to be universally present in the bacterial domain, although it is not necessarily essential in all bacterial cells. It has recently been revealed that two other systems, one involving a small protein, ArfA, with RF2 and the other involving YaeJ (ArfB), a class I release factor homologue, operate to relieve ribosome stalling in Escherichia coli. Thus, many bacterial species would have multiple systems to cope with various kinds of stalled translation events.