Transfer-messenger RNA

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 other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing.

[3] 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.

[5][6] 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.

[7][10] 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).

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.

High-resolution structures of the complete tmRNA molecules are currently unavailable and may be difficult to obtain due to the inherent flexibility of the MLR.

[19] Coding by tmRNA was discovered in 1995[20] when Simpson and coworkers overexpressed the mouse cytokine IL-6 in E. coli and found multiple truncated cytokine-derived peptides each tagged at the carboxyl termini with the same 11-amino acid residue extension (A)ANDENYALAA.

[21] 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.

Trans-translation is essential in some bacterial species, whereas other bacteria require tmRNA to survive when subjected to stressful growth conditions.

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.

[11] Subsequently, the presence of a mitochondrial gene (ssrA) coding for tmRNA, as well as transcription and RNA processing sites were confirmed for all but one member of jakobids.

[30] Like in α-Proteobacteria (the ancestors of mitochondria), mt-tmRNAs are circularly permuted, two-piece RNA molecules, except in Jakoba libera where the gene has reverted to encoding a one-piece tmRNA conformation.

[13] Mitochondrial tmRNA genes were initially recognized as short sequences that are conserved among jakobids and that have the potential to fold into a distinct tRNA-like secondary structure.

Finally, instead of the tRNA-like D-stem with a shortened three-nucleotide D-loop characteristic for bacterial tmRNAs, mitochondrial counterparts have a highly variable 5 to 14-nt long loop.

RNA-Seq data of Phytophthora sojae show an expression level similar to that of neighboring mitochondrial tRNAs, and four major processing sites confirm the predicted termini of mature mt-tmRNA.

tmRNA combines features of tRNA and mRNA.
Secondary structure of E. coli tmRNA. Shown are the 5' and 3' ends of the 363-nucleotide RNA chain numbered in increments of ten. Short lines indicate Watson-Crick pairings (G-C and A-U); dots are G-U pairings. Prominent are the tRNA-like domain (TLD), the messenger RNA-like region (MLR), and the four pseudoknots (pk1 to pk4). The MLR encodes the tag peptide between resume and stop codons. RNA helices (numbered one to 12) and their sections (letters) are gray.
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 and data obtained from the RCSB Protein Data Bank file for structure 1J1H [ 17 ]
Cartoon ribbon structure of the tmRNA dedicated binding protein, SmpB. Image was created using Pymol molecular imaging software and data obtained from the RCSB Protein Data Bank file for structure 1CZJ [ 18 ]
trans -Translation stages A through F . A ribosome with its RNA binding sites, designated E, P, and A, is stuck near the 3' end of a broken mRNA. The tmRNP binds to the A-site, allowing the ribosome to switch templates from the broken message onto the open reading frame of the tmRNA via the resume codon (blue GCA). Regular translation eventually resumes. Upon reaching the tmRNA stop codon (red UAA), a hybrid protein with a proteolysis tag (green beads) is released.
History of ssrA . Precursor RNAs are shown, whose dashed portions are excised during maturation. The permuted genes produce both an acceptor piece (red) and coding piece (blue); dotted lines mark secondary structures not always present. Abbreviations: TLD, tRNA-like domain; MLR, mRNA-like region; ITS, internal transcribed spacer; P, paired region; PK, pseudoknot; RF, reading frame.
Secondary structure models for mt-tmRNAs. (A) The two-piece tmRNA in oomycetes and jakobids except J. libera, After removing the intervening sequence (Int.; dashed ark) by RNA processing enzymes, the two resulting RNA pieces (blue and red lines) remain together through base pairing. (B) The standard one-piece tmRNA in J. libera that most likely emerged secondarily through gene rearrangement. The three pairing regions (P1, P2 and P3) and the position of post-transcriptionally added 3’ CCA are indicated.
Processing of two-piece mt-tmRNA. The four major RNA processing sites are numbered (1-4). Processing at sites 1 and 4 is thought to occur by a tmRNA-specific activity, site 2 by RNase P and site 3 by a 3’ tRNA endonuclease processing. Nucleotides cleaved from the precursor are in gray; the post-transcriptionally added CCA is boxed.