Transfer-messenger RNA (abbreviated tmRNA, 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.
- 1 Discovery of tmRNA and early work
- 2 tmRNA structure
- 3 Trans-translation
- 4 Mobile genetic elements and the tmRNA gene
- 5 See also
- 6 References
- 7 Further reading
- 8 External links
Discovery of tmRNA and early work
tmRNA was first designated 10Sa RNA after a mixed “10S” electrophoretic fraction of Escherichia coli RNA was further resolved into tmRNA and the similarly-sized RNase P RNA (10Sb). The presence of pseudouridine in the mixed 10S RNA hinted that tmRNA has modified bases found also in tRNA. The similarity at the 3' end of tmRNA to the T stem-loop of tRNA was first recognized upon sequencing ssrA from Mycobacterium tuberculosis. Subsequent sequence comparison revealed the full tRNA-like domain (TLD) formed by the 5' and 3' ends of tmRNA, including the acceptor stem with elements like those in alanine tRNA that promote its aminoacylation by alanine-tRNA ligase. It also revealed differences from tRNA: the anticodon arm is missing in tmRNA, and the D arm region is a loop without base pairs.
Secondary structure of the standard one-piece tmRNAs
The complete E. coli tmRNA secondary structure was elucidated by comparative sequence analysis and structural probing. Watson-Crick and G-U base pairs were identified by comparing the bacterial tmRNA sequences using automated computational methods in combination with manual alignment procedures. The accompanying figure shows the base pairing pattern of this prototypical tmRNA, which is organized into 12 phylogenetically supported helices (also called pairings P1 to P12), some divided into helical segments.
A prominent feature of every tmRNA is the conserved tRNA-like domain (TLD), composed of helices 1, 12, and 2a (analogs of the tRNA acceptor stem, T-stem and variable stem, respectively), and containing the 5' monophosphate and alanylatable 3' CCA ends. The mRNA-like region (MLR) is in standard tmRNA a large loop containing pseudoknots and a coding sequence (CDS) for the tag peptide, marked by the resume codon and the stop codon. The encoded tag peptide (ANDENYALAA in E. coli) varies among bacteria, perhaps depending on the set of proteases and adaptors available.
tmRNAs typically contain four pseudoknots, one (pk1) upstream of the tag peptide CDS, and the other three pseudoknots (pk2 to pk4) downstream of the CDS. The pseudoknot regions, although generally conserved, are evolutionarily plasic. For example, in the (one-piece) tmRNAs of cyanobacteria, pk4 is substituted with two tandemly arranged smaller pseudoknots. This suggests that tmRNA folding outside the TLD can be important, yet the pseudoknot region lacks conserved residues and pseudoknots are among the first structures to be lost as ssrA sequences diverge in plastid and endosymbiont lineages. Base pairing in the three-pseudoknot region of E. coli tmRNA is disrupted during trans-translation.
Circularly permuted ssrA has been reported in three major lineages: i) all alphaproteobacteria and the primitive mitochondria of jakobid protists, ii) two disjoint groups of cyanobacteria (Gloeobacter and a clade containing Prochlorococcus and many Synechococcus), and iii) some members of the betaproteobacteria (Cupriavidus and some Rhodocyclales). All produce the same overall two-piece (acceptor and coding pieces) form, equivalent to the standard form nicked downstream of the reading frame. None retain more than two pseudoknots compared to the four (or more) of standard tmRNA.
Alphaproteobacteria have two signature sequences: replacement of the typical T-loop sequence TΨCRANY with GGCRGUA, and the sequence AACAGAA in the large loop of the 3´-terminal pseudoknot. In mitochondria, the MLR has been lost, and a remarkable re-permutation of mitochondrial ssrA results in a small one-piece product in Jakoba libera.
The cyanobacteria provide the most plausible case for evolution of a permuted gene from a standard gene, due to remarkable sequence similarities between the two gene types as they occur in different Synechococcus strains.
Most tmRNAs are transcribed as larger precursors which are processed much like tRNA. Cleavage at the 5´ end is by ribonuclease P. Multiple exonucleases can participate in the processing of the 3´ end of tmRNA, although RNase T and RNase PH are most effective. Depending on the bacterial species, the 3'-CCA is either encoded or added by tRNA nucleotidyltransferase.
Similar processing at internal sites of permuted precursor tmRNA explains its physical splitting into two pieces. The two-piece tmRNAs have two additional ends whose processing must be considered. For alphaproteobacteria, one 5´ end is the unprocessed start site of transcription. The far 3´ end may in some cases be the result of rho-independent termination.
High-resolution structures of the complete tmRNA molecules are currently unavailable and may be difficult to obtain due the inherent flexibility of the MLR. In 2007, the crystal structure of the Thermus thermophilus TLD bound to the SmpB protein was obtained at 3 Å resolution. This structure shows that SmpB mimics the D stem and the anticodon of a canonical tRNA whereas helical section 2a of tmRNA corresponds to the variable arm of tRNA. A cryo-electron microscopy study of tmRNA at an early stage of trans-translation shows the spatial relationship between the ribosome and the tmRNP (tmRNA bound to the EF-Tu protein). The TLD is located near the GTPase-associated center in the 50S ribosomal subunit; helix 5 and pseudoknots pk2 to pk4 form an arc around the beak of the 30S ribosomal subunit.
Coding by tmRNA was discovered in 1995 when Simpson and coworkers overexpressed a mouse cytokine in E. coli and found several truncated cytokine-derived peptides each tagged at the carboxyl termini with the same 11-amino acid residue extension (A)ANDENYALAA. With the exception of the N-terminal alanine, which comes from the 3' end of tmRNA itself, this tag sequence was traced to a short open reading frame in E. coli tmRNA. Recognizing that the tag peptide confers proteolysis, the trans-translation model for tmRNA action was proposed.
While details of the trans-translation mechanism are under investigation it is generally agreed that tmRNA first occupies the empty A site of the stalled ribosome. Subsequently, the ribosome moves from the 3' end of the truncated messenger RNA onto the resume codon of the MLR, followed by a slippage-prone stage from where translation continues normally until the in-frame tmRNA stop codon is encountered. Trans-translation is essential in some bacterial species, whereas other bacteria require tmRNA to survive when subjected to stressful growth conditions. Depending on the organism, the tag peptide may be recognized by a variety of proteases or protease adapters.
Mobile genetic elements and the tmRNA gene
ssrA is both a target for some mobile DNAs and a passenger on others. It has been found interrupted by three types of mobile elements. By different strategies none of these disrupt gene function: group I introns remove themselves by self-splicing, rickettsial palindromic elements (RPEs) insert in innocuous sites, and integrase-encoding genomic islands split their target ssrA yet restore the split-off portion.
Non-chromosomal ssrA was first detected in a genomic survey of mycobacteriophages (in 10% of the phages). Other mobile elements including plasmids and genomic islands have been found bearing ssrA. One interesting case is Rhodobacter sphaeroides ATCC 17025, whose native tmRNA gene is disrupted by a genomic island; unlike all other genomic islands in tmRNA (or tRNA) genes this island has inactivated the native target gene without restoration, yet compensates by carrying its own tmRNA gene. A very unusual relative of ssrA is found in the lytic mycobacteriophage DS6A, that encodes little more than the TLD.
- Keiler KC (2008). "Biology of trans-translation". Annu. Rev. Microbiol. 62: 133–51. doi:10.1146/annurev.micro.62.081307.162948. PMID 18557701.
- Ray BK, Apirion D (July 1979). "Characterization of 10S RNA: a new stable rna molecule from Escherichia coli". Mol. Gen. Genet. 174 (1): 25–32. doi:10.1007/BF00433301. PMID 384159.
- Tyagi JS, Kinger AK (January 1992). "Identification of the 10Sa RNA structural gene of Mycobacterium tuberculosis". Nucleic Acids Res. 20 (1): 138. doi:10.1093/nar/20.1.138. PMC 310338. PMID 1371186. Retrieved 2010-07-14.
- Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H (September 1994). "A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli". Proc. Natl. Acad. Sci. U.S.A. 91 (20): 9223–7. doi:10.1073/pnas.91.20.9223. PMC 44784. PMID 7524073. Retrieved 2010-07-14.
- Williams KP, Bartel DP (December 1996). "Phylogenetic analysis of tmRNA secondary structure". RNA 2 (12): 1306–10. PMC 1369456. PMID 8972778. Retrieved 2010-07-14.
- Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF (January 1997). "Probing the structure of the Escherichia coli 10Sa RNA (tmRNA)". RNA 3 (1): 89–103. PMC 1369465. PMID 8990402. Retrieved 2010-07-14.
- Zwieb C, Wower I, Wower J (1999). "Comparative sequence analysis of tmRNA". Nucleic Acids Res 27 (10): 2063–71. doi:10.1093/nar/27.10.2063. PMC 148424. PMID 10219077.
- Andersen ES, Lind-Thomsen A, Knudsen B, et al. (November 2007). "Semiautomated improvement of RNA alignments". RNA 13 (11): 1850–9. doi:10.1261/rna.215407. PMC 2040093. PMID 17804647. Retrieved 2010-07-14.
- Gur E, Sauer RT (October 2008). "Evolution of the ssrA degradation tag in Mycoplasma: specificity switch to a different protease". Proc. Natl. Acad. Sci. U.S.A. 105 (42): 16113–8. doi:10.1073/pnas.0808802105. PMC 2570983. PMID 18852454. Retrieved 2010-07-14.
- Wower IK, Zwieb C, Wower J (May 2005). "Transfer-messenger RNA unfolds as it transits the ribosome". RNA 11 (5): 668–73. doi:10.1261/rna.7269305. PMC 1370753. PMID 15811920. Retrieved 2010-07-14.
- Keiler KC, Shapiro L, Williams KP (July 2000). "tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter". Proc. Natl. Acad. Sci. U.S.A. 97 (14): 7778–83. doi:10.1073/pnas.97.14.7778. PMC 16621. PMID 10884408. Retrieved 2010-07-14.
- Sharkady SM, Williams KP (2004). "A third lineage with two-piece tmRNA". Nucleic Acids Res. 32 (15): 4531–8. doi:10.1093/nar/gkh795. PMC 516066. PMID 15326226. Retrieved 2010-07-14.
- Jacob Y, Seif E, Paquet PO, Lang BF (April 2004). "Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids". RNA 10 (4): 605–14. doi:10.1261/rna.5227904. PMC 1370551. PMID 15037770. Retrieved 2010-07-14.
- Srivastava RA, Srivastava N, Apirion D (May 1992). "Characterization of the RNA processing enzyme RNase III from wild type and overexpressing Escherichia coli cells in processing natural RNA substrates". Int. J. Biochem. 24 (5): 737–49. doi:10.1016/0020-711X(92)90007-N. PMID 1375563.
- Li Z, Pandit S, Deutscher MP (March 1998). "3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli". Proc. Natl. Acad. Sci. U.S.A. 95 (6): 2856–61. doi:10.1073/pnas.95.6.2856. PMC 19659. PMID 9501180. Retrieved 2010-07-14.
- Mao C, Bhardwaj K, Sharkady SM, et al. (2009). "Variations on the tmRNA gene". RNA Biol 6 (4): 355–61. doi:10.4161/rna.6.4.9172. PMID 19617710.
- Someya T, Nameki N, Hosoi H, et al. (January 2003). "Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus". FEBS Lett. 535 (1–3): 94–100. doi:10.1016/S0014-5793(02)03880-2. PMID 12560085. Retrieved 2010-07-14.
- Bessho Y, Shibata R, Sekine S, et al. (May 2007). "Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA". Proc. Natl. Acad. Sci. U.S.A. 104 (20): 8293–8. doi:10.1073/pnas.0700402104. PMC 1895943. PMID 17488812. Retrieved 2010-07-14.
- Bessho Y, Shibata R, Sekine S, et al (2007). "Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA". Proc. Natl. Acad. Sci. U.S.A. 104 (20): 8293–8. doi:10.1073/pnas.0700402104. PMC 1895943. PMID 17488812.
- Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J (April 2003). "Visualizing tmRNA entry into a stalled ribosome". Science 300 (5616): 127–30. doi:10.1126/science.1081798. PMID 12677067. Retrieved 2010-07-14.
- Keiler KC, Waller PR, Sauer RT (February 1996). "Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA". Science 271 (5251): 990–3. doi:10.1126/science.271.5251.990. PMID 8584937. Retrieved 2010-07-14.
- Thibonnier M, Thiberge JM, De Reuse H (2008). "Trans-translation in Helicobacter pylori: essentiality of ribosome rescue and requirement of protein tagging for stress resistance and competence". In Ahmed, Niyaz. PLoS ONE 3 (11): e3810. doi:10.1371/journal.pone.0003810. PMC 2584231. PMID 19043582. Retrieved 2010-07-14.
- Kirby JE, Trempy JE, Gottesman S (April 1994). "Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli". J. Bacteriol. 176 (7): 2068–81. PMC 205313. PMID 7511583. Retrieved 2010-07-14.
- Williams KP (January 2002). "The tmRNA Website: invasion by an intron". Nucleic Acids Res. 30 (1): 179–82. doi:10.1093/nar/30.1.179. PMC 99078. PMID 11752287. Retrieved 2010-07-14.
- Dwyer DS (January 2001). "Selfish DNA and the origin of genes". Science 291 (5502): 252–3. doi:10.1126/science.291.5502.252. PMID 11253208. Retrieved 2010-07-14.
- Williams KP (February 2003). "Traffic at the tmRNA gene". J. Bacteriol. 185 (3): 1059–70. doi:10.1128/JB.185.3.1059-1070.2003. PMC 142792. PMID 12533482. Retrieved 2010-07-14.
- Hatfull GF, Pedulla ML, Jacobs-Sera D, et al. (June 2006). "Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform". PLoS Genet. 2 (6): e92. doi:10.1371/journal.pgen.0020092. PMC 1475703. PMID 16789831. Retrieved 2010-07-14.