Talk:Transfer-messenger RNA

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found this simple-worded description of trans-translation here: http://www.scitopics.com/tmRNA_SsrA_and_trans_translation.html# (creativecommons license: Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0))


 * tmRNA (also called SsrA RNA and 10Sa RNA) is a specialized RNA that has properties of both a tRNA and an mRNA. tmRNA is a key molecule in trans-translation, a ubiquitous pathway for removing stalled translational complexes from bacterial cells. tmRNA and other factors required for trans-translation are found in all species of bacteria, and trans-translation is important for a wide variety of physiological processes, including pathogenesis, differentiation, and response to stress. In Escherichia coli, tmRNA is one of the most abundant RNAs in the cell, and one in every 250 translation reactions results in trans-translation during normal culture growth [1]. At this frequency, every ribosome in the cell translates tmRNA once per cell cycle.
 * tmRNA structure and the trans-translation pathway – The 5’ and 3’ ends of tmRNA fold into a structure resembling alanyl-tRNA, and the 3’ end is charged with alanine by alanyl-tRNA synthetase [2-4]. However, tmRNA is much larger than a tRNA, and does not contain an anticodon stem-loop structure. Instead, there are several pseudoknots (2-4, depending on the species) and a specialized open reading frame encoding the peptide tag [5,6]. The tag reading frame has 8-35 codons and ends with a stop codon, but does not have a translation initiation sequence or a typical start codon [6].
 * Like many RNAs, tmRNA requires protein cofactors for its activity. SmpB is a small protein that binds tightly and specifically to tmRNA, and is important for tmRNA structure, stability, and activity [7]. The translation elongation factor EF-Tu also binds to tmRNA and promotes productive interaction with the ribosome [8,9].
 * tmRNA, charged with alanine and bound by SmpB and EF-Tu, can enter the A site of ribosomes stalled at the end of an mRNA with the nascent polypeptide still engaged. Structural data show that the tRNA-like sequence of tmRNA is located near the transpeptidation reaction center, and SmpB fills the position normally occupied by the anticodon region of a tRNA [10,11]. The nascent polypeptide is transferred to alanyl-tmRNA, and the complex is translocated to the P site. During this translocation the mRNA is released and the tmRNA tag reading frame is positioned in the decoding channel of the ribosome. Translation then resumes using tmRNA as a message, and termination at the end of the tag reading frame releases the ribosome and the tagged protein [12]. Because the tagged protein was synthesized using two RNAs acting in trans, this pathway was named trans-translation. trans-translation is the only example of a protein synthesized from two distinct RNA messages.
 * The tag peptide contains sequences that are recognized by several intracellular proteases and proteolytic adaptors. In E. coli, most of the tagged proteins in the cytoplasm are degraded by the ClpXP protease in conjunction with the SspB proteolytic adaptor [13-15]. However, there are also periplasmic and membrane-bound proteases that recognize the tag peptide, ensuring that tagged proteins will be degraded even if they are exported from the cytoplasm [16,17]. The mRNA is also rapidly degraded after it is removed from the ribosome. Some mRNAs are degraded by RNase R, a ribonuclease that may be delivered with tmRNA to stalled translation complexes. The degradation of other mRNAs after trans-translation does not require RNase R, suggesting that multiple nucleases may be involved [18,19].
 * Substrates for trans-translation – The mechanism used by tmRNA-SmpB to recognize substrate translational complexes is not known, but biochemical evidence suggests that the ribosome must be near the end of the mRNA. Tagging is most efficient if there is no mRNA extending into the A site, and tagging is completely inhibited if the mRNA extends past the leading edge of the ribosome [20]. Therefore, ribosomes stalled in the middle of an mRNA are not likely to be substrates, whereas ribosomes stalled at the 3’ end of an mRNA are targeted for trans-translation. This selectivity makes sense from a physiological standpoint, because regulatory mechanisms such as attenuation require stable stalled ribosomes. On the other hand, ribosomes stalled at the end of an mRNA are produced by damaged mRNAs and mistakes during translation. If there is no stop codon, translation release factors will not hydrolyze the peptidyl-tRNA in the P site, and these stalled complexes are very stable in vitro. Ribosomes can translate to the 3’ end of an mRNA if the mRNA has no stop codon (a “non-stop” mRNA), or if there is a frameshift or termination read-through event on a normal mRNA. Non-stop mRNAs are generated by premature termination of transcription, chemical or physical damage to the mRNA, or nuclease activity [12,21]. Because most exoribonuclease activity in bacteria, and all of the activity in E. coli, proceeds from 3’ to 5’, the stop codon may frequently be cut off with a translating ribosome still on the mRNA.
 * Keiler, Kenneth & Ramadoss, Nitya (2011, April 25). tmRNA (SsrA) and trans-translation. SciTopics. Retrieved November 24, 2011, from http://www.scitopics.com/tmRNA_SsrA_and_trans_translation.html
 * The tag peptide contains sequences that are recognized by several intracellular proteases and proteolytic adaptors. In E. coli, most of the tagged proteins in the cytoplasm are degraded by the ClpXP protease in conjunction with the SspB proteolytic adaptor [13-15]. However, there are also periplasmic and membrane-bound proteases that recognize the tag peptide, ensuring that tagged proteins will be degraded even if they are exported from the cytoplasm [16,17]. The mRNA is also rapidly degraded after it is removed from the ribosome. Some mRNAs are degraded by RNase R, a ribonuclease that may be delivered with tmRNA to stalled translation complexes. The degradation of other mRNAs after trans-translation does not require RNase R, suggesting that multiple nucleases may be involved [18,19].
 * Substrates for trans-translation – The mechanism used by tmRNA-SmpB to recognize substrate translational complexes is not known, but biochemical evidence suggests that the ribosome must be near the end of the mRNA. Tagging is most efficient if there is no mRNA extending into the A site, and tagging is completely inhibited if the mRNA extends past the leading edge of the ribosome [20]. Therefore, ribosomes stalled in the middle of an mRNA are not likely to be substrates, whereas ribosomes stalled at the 3’ end of an mRNA are targeted for trans-translation. This selectivity makes sense from a physiological standpoint, because regulatory mechanisms such as attenuation require stable stalled ribosomes. On the other hand, ribosomes stalled at the end of an mRNA are produced by damaged mRNAs and mistakes during translation. If there is no stop codon, translation release factors will not hydrolyze the peptidyl-tRNA in the P site, and these stalled complexes are very stable in vitro. Ribosomes can translate to the 3’ end of an mRNA if the mRNA has no stop codon (a “non-stop” mRNA), or if there is a frameshift or termination read-through event on a normal mRNA. Non-stop mRNAs are generated by premature termination of transcription, chemical or physical damage to the mRNA, or nuclease activity [12,21]. Because most exoribonuclease activity in bacteria, and all of the activity in E. coli, proceeds from 3’ to 5’, the stop codon may frequently be cut off with a translating ribosome still on the mRNA.
 * Keiler, Kenneth & Ramadoss, Nitya (2011, April 25). tmRNA (SsrA) and trans-translation. SciTopics. Retrieved November 24, 2011, from http://www.scitopics.com/tmRNA_SsrA_and_trans_translation.html
 * Substrates for trans-translation – The mechanism used by tmRNA-SmpB to recognize substrate translational complexes is not known, but biochemical evidence suggests that the ribosome must be near the end of the mRNA. Tagging is most efficient if there is no mRNA extending into the A site, and tagging is completely inhibited if the mRNA extends past the leading edge of the ribosome [20]. Therefore, ribosomes stalled in the middle of an mRNA are not likely to be substrates, whereas ribosomes stalled at the 3’ end of an mRNA are targeted for trans-translation. This selectivity makes sense from a physiological standpoint, because regulatory mechanisms such as attenuation require stable stalled ribosomes. On the other hand, ribosomes stalled at the end of an mRNA are produced by damaged mRNAs and mistakes during translation. If there is no stop codon, translation release factors will not hydrolyze the peptidyl-tRNA in the P site, and these stalled complexes are very stable in vitro. Ribosomes can translate to the 3’ end of an mRNA if the mRNA has no stop codon (a “non-stop” mRNA), or if there is a frameshift or termination read-through event on a normal mRNA. Non-stop mRNAs are generated by premature termination of transcription, chemical or physical damage to the mRNA, or nuclease activity [12,21]. Because most exoribonuclease activity in bacteria, and all of the activity in E. coli, proceeds from 3’ to 5’, the stop codon may frequently be cut off with a translating ribosome still on the mRNA.
 * Keiler, Kenneth & Ramadoss, Nitya (2011, April 25). tmRNA (SsrA) and trans-translation. SciTopics. Retrieved November 24, 2011, from http://www.scitopics.com/tmRNA_SsrA_and_trans_translation.html

Ryu (talk) 18:03, 24 November 2011 (UTC)