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As the ribosome stalls on an mRNA molecule with no stop codon, bacteria use transfer-messenger RNA (also known as 10S RNA or SsrA) and Small protein B (SmpB) to recycle the ribosome, tag the faulty protein for proteolytic degradation, and speed up the degradation of the truncated mRNA. Comparative analyses of tmRNA sequences showed that tmRNA is made up of two parts: a tRNA-like domain and an mRNA-like region, denoted as TLD and MLR in figure 1A, respectively. TLD and MLR are bound by four pseudoknots in E. coli tmRNA (pk-pk4). Other bacterial tmRNAs can have three to six pseudoknots. SmpB imitates the anticodon arm of a canonical tRNA inside the TLD-SmpB complex. SmpB’s C-terminal tail has been shown to mimic mRNA and play an important role in ribosome-bound tmRNA activity [1-3].

Conclusion

The protein S1 binding site on the tmRNA molecule is made up of the MLR, pk2, and pk3 regions. Photoaffinity labelling studies show that tmRNA binding to the ribosome has only a minor impact on the interactions between protein S1 and tmRNA. Recently demonstrated that one molecule of S1 would bind to a 10-nucleotide RNA fragment. Since the region containing MLR, pk2, and pk3 is made up of around a hundred nucleotides, a “rolling mechanism” for protein S1 functions on tmRNA may be proposed, in which protein S1 binds to a singlestranded fragment of tmRNA (e.g. MLR) and then “unzips” its structured segmen. Experiments using optical tweezers to show the unzipping and rezipping of an RNA hairpin by a single protein S1 molecule in several steps help such a “rolling process.” The rolling process can explain why only minor local conformational changes in tmRNA can be observed, since the unzipping and rezipping of double-stranded RNA segments occurs sequentially. Further research into the role of R6 in protein S1 functions is needed. Despite the fact that R6 binds RNAs in vitro, it is not needed for protein S1 functions in canonical translation and transcriptional cycling, protein S1 involvement in Q bacteriophage replication, or protein tagging in M. tuberculosis

References

1. Atlin Gary N (2007) Rapid breeding and varietal replacement are critical to adaptation of cropping systems in the developing world to climate change. Global Food Security 12: 31-37.
2. Mehta P, Richards J, Karzai AW (2006) tmRNA determinants required for facilitating nonstop mRNA decay. RNA 12: 2187-2198.
3. Felden B, Massire C, Westhof E, Atkins JF, Gesteland RF (2001) Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature. Nucleic Acids Res 29: 1602-1607.