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transfer-messenger RNA

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tmRNA (transfer-messenger RNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1. In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing.

tmRNA combines features of tRNA and mRNA.

Purpose

The purpose of tmRNA is three-fold:

1. To rescue stalled ribosomes

2. To tag the incomplete polypeptide chains, thus marking them for degradation by the Clp family proteases or Lon protease.

3. To promote the degradation of the aberrant mRNA

tmRNA Structure

Cartoon ribbon structure of the tRNA-like domain of tmRNA. The domain consists of the 3' and 5' ends of the tmRNA. Image was created using Pymol molecular imaging software for students and data obtained from the RCSB Protein Data Bank file for structure 1J1H[1]

tmRNA molecules are between 260 and 430 nucleotides long, depending on the bacterial species they are isolated from. They contain several structural domains including a transfer RNA-like domain (TLD) composed of the 3’ and 5’ ends with a an amino acid acceptor stem[2] and largely reduced D-arm[3]. A second domain is composed of a messenger RNA-like domain (MLD). The MLD contains a short open reading frame (ORF) that codes for a proteolytic degradation tag and ends with a stop codon[4].

In addition to the above mentioned domains tmRNAs possess extensive secondary structure consisting of four pseudoknots which, until recently, had unknown function. In 2004 Wower et al.[3] characterized and described the contributions of these pseudoknots to the overall structure and function of tmRNA. Using site-directed mutagenesis experiments they were able to show that pseudoknot 2 and helix 5 played a significant role in the binding of ribosomal protein S1 to tmRNA. Pseudoknot 4 was determined to facilitate tmRNA maturation as well as promoted the tagging of nascent peptides involved in ribosomal stalling and three of the pseudoknots (PK2 to PK4) were determined to have a substantial role in the proper folding of the TLD. These results suggest that pseudoknots 2 through 4 play a significant role in proper tmRNA folding and overall function.

tmRNA Mechanism of Action

Cartoon ribbon structure of the tmRNA dedicated binding protein, SmpB. Image was created using Pymol molecular imaging software for students and data obtained from the RCSB Protein Data Bank file for structure 1CZJ[5]

The generally accepted mechanism of action[4][6][7] involves an alanine-charged tmRNA binding the A-site of a stalled ribosome. Upon binding, peptidyl-transfer occurs extending the nascent peptide with the alanine of the charged tmRNA; thus the peptide is moved onto the tmRNA. The TLD is then translocates to the ribosomal P-site. Trans-translocation occurs as the defective mRNA transcript is released and replaced by the ORF of the tmRNA. As the ribosome moves along each codon of the ORF it translates a peptide tag onto the C-terminus[7] of the nascent polypeptide. As mentioned above, the tag contains recognition sites for various ATP-dependent intercellular proteases[8][9]. Translation is terminated as the stop codon within the ORF is recognized and the tagged nascent peptide is released from the ribosome. Once the tag is recognized by cellular proteases the nascent polypeptide is rapidly degraded[8] and the tmRNA then, through sequence specific determinants within the ORF, facilitates the degradation of the truncated mRNA transcript[10]. This model requires, in addition to general translation factors, small protein B (SmpB), elongation factor Tu (EF-Tu), and ribosomal protein S1. SmpB and EF-Tu bind the TLD of the tmRNA and are required for interaction with target ribosomes and the efficient aminoacylation by alanyl-tRNA. The ribosomal protein S1 binds the MLD and is thought to facilitate entry of the ORF into the stalled ribosome[11].

In 2004, Hallier et al.[11] presented results that suggested an alternative mechanism of tmRNA recruitment. In this mechanism SmpB binds the 70S ribosome independently of tmRNA. They propose this binding triggers the initiation of trans-translation by recruiting an SmpB-free alanyl-tmRNA in complex with EF-Tu. Their report does, however, continue to suggest that SmpB is essential for trans-translation initiation.

References

  1. ^ Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G. (2003) Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus FEBS Lett. 535: 94-100
  2. ^ Cite error: The named reference ref7 was invoked but never defined (see the help page).
  3. ^ a b Cite error: The named reference ref12 was invoked but never defined (see the help page).
  4. ^ a b Cite error: The named reference ref13 was invoked but never defined (see the help page).
  5. ^ Bessho, Y., Shibata, R., Sekine, S., Murayama, K., Higashijima, K., Hori-Takemoto, C., Shirouzu, M., Kuramitsu, S., Yokoyama, S. (2007) Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc.Natl.Acad.Sci.Usa 104: 8293-8298
  6. ^ Cite error: The named reference ref14 was invoked but never defined (see the help page).
  7. ^ a b Sundermeier, T. R. & Karzai, A. W. Functional SmpB-Ribosome Interactions Require tmRNA. J. Biol. Chem. 282, 34779-34786 (2007).
  8. ^ a b Cite error: The named reference ref1 was invoked but never defined (see the help page).
  9. ^ Cite error: The named reference ref10 was invoked but never defined (see the help page).
  10. ^ Cite error: The named reference ref9 was invoked but never defined (see the help page).
  11. ^ a b Cite error: The named reference ref4 was invoked but never defined (see the help page).

External links

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