View source for Transfer-messenger RNA

{{Infobox rfam
| Name = transfer-messenger RNA
| image = 157-TransferMessengerRNA 3iyr composite.tif
| width = 
| caption = Transfer-messenger RNA ({{PDB|3IYR}})
| Symbol = tmRNA
| AltSymbols = 
| Rfam = RF00023
| miRBase =
| miRBase_family =
| RNA_type = [[gene]]
| Tax_domain = 
| CAS_number = 
| EntrezGene = 
| HGNCid = 
| OMIM = 
| PDB = 
| RefSeq = 
| Chromosome = 
| Arm = 
| Band = 
| LocusSupplementaryData = 
}}

'''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]].<ref>{{cite journal | vauthors = Keiler KC | title = Biology of trans-translation | journal = Annual Review of Microbiology | volume = 62 | pages = 133–51 | year = 2008 | pmid = 18557701 | doi = 10.1146/annurev.micro.62.081307.162948 }}</ref> In the majority of bacteria these functions are carried out by standard [[#Secondary structure of the standard one-piece tmRNAs|one-piece tmRNAs]]. In other bacterial species, a permuted ''ssrA'' gene produces a [[#Two-piece tmRNAs|two-piece tmRNA]] in which two separate RNA chains are joined by base-pairing.     
[[Image:tRNAmRNAtmRNAComparison.png|thumb|right|350px|tmRNA combines features of tRNA and mRNA.]]

==Discovery and early work==

tmRNA was first designated 10Sa RNA in 1979, after a mixed "10S" electrophoretic fraction of ''[[Escherichia coli]]'' RNA was further resolved into tmRNA and the similarly sized [[RNase P]] RNA (10Sb).<ref>{{cite journal | vauthors = Ray BK, Apirion D | title = Characterization of 10S RNA: a new stable rna molecule from Escherichia coli | journal = Molecular & General Genetics | volume = 174 | issue = 1 | pages = 25–32 | date = July 1979 | pmid = 384159 | doi = 10.1007/BF00433301 | s2cid = 22699560 }}</ref> 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]]''.<ref>{{cite journal | vauthors = Tyagi JS, Kinger AK | title = Identification of the 10Sa RNA structural gene of Mycobacterium tuberculosis | journal = Nucleic Acids Research | volume = 20 | issue = 1 | pages = 138 | date = January 1992 | pmid = 1371186 | pmc = 310338 | doi = 10.1093/nar/20.1.138 | url = }}</ref> 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]].<ref name="Komine94">{{cite journal | vauthors = Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H | title = A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 91 | issue = 20 | pages = 9223–7 | date = September 1994 | pmid = 7524073 | pmc = 44784 | doi = 10.1073/pnas.91.20.9223 | bibcode = 1994PNAS...91.9223K | doi-access = free }}</ref> It also revealed differences from [[tRNA]]: the [[anticodon]] arm is missing in tmRNA, and the [[D arm]] region is a loop without base pairs.

== Structure ==

===Secondary structure of the standard one-piece tmRNAs===

[[Image:EsccolitmRNA2009.png|thumb|right|300px|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.]]

The complete ''E. coli'' tmRNA [[secondary structure]] was elucidated by [[Bioinformatics#Sequence analysis|comparative sequence analysis]] and [[Protein structure prediction|structural probing]].<ref>{{cite journal | vauthors = Williams KP, Bartel DP | title = Phylogenetic analysis of tmRNA secondary structure | journal = RNA | volume = 2 | issue = 12 | pages = 1306–10 | date = December 1996 | pmid = 8972778 | pmc = 1369456 | url = http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8972778 }}</ref><ref>{{cite journal | vauthors = Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF | title = Probing the structure of the Escherichia coli 10Sa RNA (tmRNA) | journal = RNA | volume = 3 | issue = 1 | pages = 89–103 | date = January 1997 | pmid = 8990402 | pmc = 1369465 | url = http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8990402 }}</ref> Watson-Crick and G-U [[base pairs]] were identified by comparing the bacterial tmRNA sequences using automated computational methods in combination with manual [[sequence alignment|alignment]] procedures.<ref name="Zwieb99">{{cite journal | vauthors = Zwieb C, Wower I, Wower J | title = Comparative sequence analysis of tmRNA | journal = Nucleic Acids Research | volume = 27 | issue = 10 | pages = 2063–71 | date = May 1999 | pmid = 10219077 | pmc = 148424 | doi = 10.1093/nar/27.10.2063 }}</ref><ref>{{cite journal | vauthors = Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J | title = Semiautomated improvement of RNA alignments | journal = RNA | volume = 13 | issue = 11 | pages = 1850–9 | date = November 2007 | pmid = 17804647 | pmc = 2040093 | doi = 10.1261/rna.215407 }}</ref> The accompanying figure shows the base pairing pattern of this prototypical tmRNA, which is organized into 12 [[phylogeny|phylogenetically]] supported helices (also called pairings P1 to P12), some divided into helical segments.

A prominent feature of every tmRNA is the [[conservation (genetics)|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.<ref name="Gur08">{{cite journal | vauthors = Gur E, Sauer RT | title = Evolution of the ssrA degradation tag in Mycoplasma: specificity switch to a different protease | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 42 | pages = 16113–8 | date = October 2008 | pmid = 18852454 | pmc = 2570983 | doi = 10.1073/pnas.0808802105 | bibcode = 2008PNAS..10516113G | doi-access = free }}</ref>

tmRNAs typically contain four [[pseudoknot]]s, 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 plastic. 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|''trans''-translation]].<ref name="Zwieb99" /><ref>{{cite journal | vauthors = Wower IK, Zwieb C, Wower J | title = Transfer-messenger RNA unfolds as it transits the ribosome | journal = RNA | volume = 11 | issue = 5 | pages = 668–73 | date = May 2005 | pmid = 15811920 | pmc = 1370753 | doi = 10.1261/rna.7269305 }}</ref>

===Two-piece tmRNAs===
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).<ref name="ReferenceA">{{cite journal | vauthors = Keiler KC, Shapiro L, Williams KP | title = tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 14 | pages = 7778–83 | date = July 2000 | pmid = 10884408 | pmc = 16621 | doi = 10.1073/pnas.97.14.7778 | bibcode = 2000PNAS...97.7778K | doi-access = free }}</ref><ref>{{cite journal | vauthors = Sharkady SM, Williams KP | title = A third lineage with two-piece tmRNA | journal = Nucleic Acids Research | volume = 32 | issue = 15 | pages = 4531–8 | year = 2004 | pmid = 15326226 | pmc = 516066 | doi = 10.1093/nar/gkh795 | url = }}</ref> 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 [[pseudoknot]]s 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''.<ref name="Jacob 2004 605–614"/>

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.

===tmRNA processing===
Most tmRNAs are transcribed as larger precursors which are processed much like [[tRNA]]. Cleavage at the 5´ end is by [[ribonuclease P]].<ref name="Komine94" /> Multiple exonucleases can participate in the processing of the 3´ end of tmRNA, although [[RNase T]] and [[RNase PH]] are most effective.<ref>{{cite journal | vauthors = Srivastava RA, Srivastava N, Apirion D | title = Characterization of the RNA processing enzyme RNase III from wild type and overexpressing Escherichia coli cells in processing natural RNA substrates | journal = The International Journal of Biochemistry | volume = 24 | issue = 5 | pages = 737–49 | date = May 1992 | pmid = 1375563 | doi = 10.1016/0020-711X(92)90007-N }}</ref><ref>{{cite journal | vauthors = Li Z, Pandit S, Deutscher MP | title = 3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 6 | pages = 2856–61 | date = March 1998 | pmid = 9501180 | pmc = 19659 | doi = 10.1073/pnas.95.6.2856 | doi-access = free | bibcode = 1998PNAS...95.2856L }}</ref> 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.<ref>{{cite journal | vauthors = Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C, Sobral BW, Williams KP | title = Variations on the tmRNA gene | journal = RNA Biology | volume = 6 | issue = 4 | pages = 355–61 | year = 2009 | pmid = 19617710 | doi = 10.4161/rna.6.4.9172 | doi-access = free }}</ref>  The far 3´ end may in some cases be the result of rho-independent termination.

===Three-dimensional structures===
[[Image:TDLcartoonstructure.png|thumb|left|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 [http://www.pdb.org/pdb/explore/explore.do?pdbId=1J1H 1J1H]<ref name="TDLref">{{cite journal | vauthors = 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 | title = Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus | journal = FEBS Letters | volume = 535 | issue = 1–3 | pages = 94–100 | date = January 2003 | pmid = 12560085 | doi = 10.1016/S0014-5793(02)03880-2 | doi-access = free | bibcode = 2003FEBSL.535...94S }}</ref>]]
[[Image:SmpBcartoonstructure.png|thumb|right|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 [http://www.pdb.org/pdb/explore/explore.do?pdbId=1CZJ 1CZJ]<ref name="pmid17488812">{{cite journal | vauthors = Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S | title = Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 20 | pages = 8293–8 | date = May 2007 | pmid = 17488812 | pmc = 1895943 | doi = 10.1073/pnas.0700402104 | bibcode = 2007PNAS..104.8293B | doi-access = free }}</ref>]]
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. 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.<ref name="pmid17488812"/>
A [[cryo-electron microscopy]] study of tmRNA at an early stage of [[#Trans-translation|''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.<ref>{{cite journal | vauthors = Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J | title = Visualizing tmRNA entry into a stalled ribosome | journal = Science | volume = 300 | issue = 5616 | pages = 127–30 | date = April 2003 | pmid = 12677067 | doi = 10.1126/science.1081798 | bibcode = 2003Sci...300..127V | s2cid = 28845151 }}</ref>

==''Trans''-translation==

[[Image:Transtranslation.png|thumb|right|450px|''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.]]

Coding by tmRNA was discovered in 1995<ref>{{cite journal | vauthors = Tu GF, Reid GE, Zhang JG, Moritz RL, Simpson RJ | title = C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide | journal = The Journal of Biological Chemistry | volume = 270 | issue = 16 | pages = 9322–6 | date = April 1995 | pmid = 7536743 | doi = 10.1074/jbc.270.16.9322 | doi-access = free }}</ref> 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. 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. Keiler, et al., recognized that the tag peptide confers [[proteolysis]] and proposed the ''trans''-translation model for tmRNA action.<ref>{{cite journal | vauthors = Keiler KC, Waller PR, Sauer RT | title = Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA | journal = Science | volume = 271 | issue = 5251 | pages = 990–3 | date = February 1996 | pmid = 8584937 | doi = 10.1126/science.271.5251.990 | bibcode = 1996Sci...271..990K | s2cid = 29254050 }}</ref>

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.<ref>{{cite journal | vauthors = Thibonnier M, Thiberge JM, De Reuse H | title = Trans-translation in Helicobacter pylori: essentiality of ribosome rescue and requirement of protein tagging for stress resistance and competence | journal = PLOS ONE | volume = 3 | issue = 11 | pages = e3810 | year = 2008 | pmid = 19043582 | pmc = 2584231 | doi = 10.1371/journal.pone.0003810 | bibcode = 2008PLoSO...3.3810T | editor1-last = Ahmed | editor1-first = Niyaz | doi-access = free }}</ref> It is believed that tmRNA can help the cell with antibiotic resistance by rescuing the ribosomes stalled by antibiotics.<ref>{{Cite journal|last1=Müller|first1=Claudia|last2=Crowe-McAuliffe|first2=Caillan|last3=Wilson|first3=Daniel N.|date=2021-03-18|title=Ribosome Rescue Pathways in Bacteria|journal=Frontiers in Microbiology|volume=12|page=652980|doi=10.3389/fmicb.2021.652980|issn=1664-302X|pmc=8012679|pmid=33815344|doi-access=free}}</ref> Depending on the organism, the tag peptide may be recognized by a variety of [[proteases]] or protease adapters.<ref name="Gur08" />

==Mobile genetic elements and the tmRNA gene==
[[Image:ssraHistory2.jpg|thumb|right|400px|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.]]
''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.<ref>{{cite journal | vauthors = Kirby JE, Trempy JE, Gottesman S | title = Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli | journal = Journal of Bacteriology | volume = 176 | issue = 7 | pages = 2068–81 | date = April 1994 | pmid = 7511583 | pmc = 205313 | doi = 10.1128/jb.176.7.2068-2081.1994 }}</ref><ref>{{cite journal | vauthors = Williams KP | title = The tmRNA Website: invasion by an intron | journal = Nucleic Acids Research | volume = 30 | issue = 1 | pages = 179–82 | date = January 2002 | pmid = 11752287 | pmc = 99078 | doi = 10.1093/nar/30.1.179 | url = }}</ref><ref>{{cite journal | vauthors = Dwyer DS | title = Selfish DNA and the origin of genes | journal = Science | volume = 291 | issue = 5502 | pages = 252–3 | date = January 2001 | pmid = 11253208 | doi = 10.1126/science.291.5502.252 | s2cid = 5369275 }}</ref><ref>{{cite journal | vauthors = Williams KP | title = Traffic at the tmRNA gene | journal = Journal of Bacteriology | volume = 185 | issue = 3 | pages = 1059–70 | date = February 2003 | pmid = 12533482 | pmc = 142792 | doi = 10.1128/JB.185.3.1059-1070.2003 }}</ref>

Non-chromosomal ''ssrA'' was first detected in a genomic survey of mycobacteriophages (in 10% of the phages).<ref name="Hat06">{{cite journal | vauthors = Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR, Lawrence JG, Hendrix RW | title = Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform | journal = PLOS Genetics | volume = 2 | issue = 6 | pages = e92 | date = June 2006 | pmid = 16789831 | pmc = 1475703 | doi = 10.1371/journal.pgen.0020092 | doi-access = free }}</ref> Other [[transposon|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.

==Mitochondrial tmRNAs (''ssrA'' gene)==
A mitochondrion-encoded, structurally reduced form of tmRNA (mt-tmRNA) was first postulated for the [[jakobid]] flagellate ''[[Reclinomonas americana]]''.<ref name="ReferenceA"/> 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]].<ref name="Burger 2013 418–438">{{cite journal | vauthors = Burger G, Gray MW, Forget L, Lang BF | title = Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists | journal = Genome Biology and Evolution | volume = 5 | issue = 2 | pages = 418–38 | year = 2013 | pmid = 23335123 | pmc = 3590771 | doi = 10.1093/gbe/evt008 | url = }}</ref><ref name="Jacob 2004 605–614"/> Functional evidence, i.e., mt-tmRNA [[Aminoacylation]] with [[alanine]], is available for ''Jakoba libera''.<ref name="Jacob 2004 605–614">{{cite journal | vauthors = Jacob Y, Seif E, Paquet PO, Lang BF | title = Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids | journal = RNA | volume = 10 | issue = 4 | pages = 605–14 | date = April 2004 | pmid = 15037770 | pmc = 1370551 | doi = 10.1261/rna.5227904 }}</ref> 
More recently, ''ssrA'' was also identified in mitochondrial genomes of [[oomycetes]].<ref name="Hafez 2013 1117–1124">{{cite journal | vauthors = Hafez M, Burger G, Steinberg SV, Lang BF | title = A second eukaryotic group with mitochondrion-encoded tmRNA: in silico identification and experimental confirmation | journal = RNA Biology | volume = 10 | issue = 7 | pages = 1117–24 | date = July 2013 | pmid = 23823571 | pmc = 3849159 | doi = 10.4161/rna.25376 | url = https://www.landesbioscience.com/journals/rnabiology/article/25376/ | access-date = 2014-02-13 | url-status = dead | archive-url = https://web.archive.org/web/20140221222038/https://www.landesbioscience.com/journals/rnabiology/article/25376/ | archive-date = 2014-02-21 }}</ref> 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.<ref name="Jacob 2004 605–614"/>

===Identification of ''ssrA'' in mitochondrial genomes===

[[File:Secondary structure models for mt-tmRNAs..jpg|thumb|right| 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.]]

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. With the availability of nine complete [[jakobid]] [[mtDNA]] sequences,<ref name="Burger 2013 418–438"/> and a significantly improved covariance search tool (Infernal;<ref>{{cite web|last=Eddy|first=S|title=Infernal website.|url=http://infernal.janelia.org|access-date=14 August 2016}}</ref><ref>{{cite journal | vauthors = Eddy SR, Durbin R | title = RNA sequence analysis using covariance models | journal = Nucleic Acids Research | volume = 22 | issue = 11 | pages = 2079–88 | date = June 1994 | pmid = 8029015 | pmc = 308124 | doi = 10.1093/nar/22.11.2079 | url = }}</ref><ref>{{cite journal | vauthors = Nawrocki EP, Kolbe DL, Eddy SR | title = Infernal 1.0: inference of RNA alignments | journal = Bioinformatics | volume = 25 | issue = 10 | pages = 1335–7 | date = May 2009 | pmid = 19307242 | pmc = 2732312 | doi = 10.1093/bioinformatics/btp157 | url = }}</ref>), a covariance model has been developed based on [[jakobid]] mitochondrial tmRNAs, which identified mitochondrial ''ssrA'' genes also in [[oomycete]]. At present, a total of 34 oomycete mt-tmRNAs have been detected across six genera: ''[[Albugo]], [[Bremia (protist)|Bremia]], [[Phytophthora]], [[Pseudoperonospora]], [[Pythium]]'' and ''[[Saprolegnia]]''. A covariance model built with both [[jakobid]] and [[oomycete]] sequences is now available at [[Rfam]] under the name ‘mt-tmRNA’.<ref name="Hafez 2013 1117–1124"/>

===mt-tmRNA Structure===

The standard bacterial tmRNA consists of a tRNA(Ala)-like domain (allowing addition of a non-encoded alanine to mRNAs that happen to lack a stop coding), and an mRNA-like domain coding for a protein tag that destines the polypeptide for proteolysis. The mRNA-like domain was lost in mt-tmRNAs. 
Comparative sequence analysis indicates features typical for mt-tmRNAs.<ref name="Hafez 2013 1117–1124"/> 
Most conserved is the primary sequence of the amino acyl acceptor stem.  This portion of the molecule has an invariable A residue in the discriminator position and a G-U pair at position 3 (except in S''eculamonas ecuadoriensis'', which has a G-C pair); this position is the recognition site for alanyl tRNA synthase. P2 is a helix of variable length (3 to 10 base pairs) and corresponds to the anticodon stem of tRNAs, yet without an anticodon loop (as not required for tmRNA function). P2 stabilizes the tRNA-like structure, but four nucleotides invariant across oomycetes and jakobids suggest an additional, currently unidentified function. P3 has five base pairs and corresponds to the T-arm of tRNAs, yet with different consensus nucleotides both in the paired region and the loop. The T-loop sequence is conserved across [[oomycetes]] and [[jakobid]], with only few deviations (e.g., ''[[Saprolegnia]] ferax''). 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. 
The intervening sequence (Int.) of two-piece mt-tmRNAs is A+U rich and of irregular length (4-34 nt). ). For secondary structure models of one- and two-piece mt-tmRNAs see Figure 1.

===mt-tmRNA processing and expression===
[[File:Processing of two-piece mt-tmRNA..jpg|thumb|right|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.]]

RNA-Seq data of ''[[Phytophthora sojae]]'' show an expression level similar to that of neighboring mitochondrial [[tRNA]]s, and four major processing sites confirm the predicted termini of mature mt-tmRNA.<ref name="Hafez 2013 1117–1124"/> The tmRNA precursor molecule is likely processed by [[RNase P]] and a tRNA 3’ processing endonuclease (see Figure 2); the latter activity is assumed to lead to the removal of the intervening sequence. Following the addition of CCA at the 3’ discriminator nucleotide, the tmRNA can be charged by alanyl-tRNA synthetase with alanine.

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== See also ==
*[[ATP-dependent Clp protease proteolytic subunit|CLPP]]
*[[Ribosome]]
*[[Messenger RNA]]

== References ==

{{reflist|2}}

== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = Hong SJ, Tran QA, Keiler KC | title = Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB | journal = Molecular Microbiology | volume = 57 | issue = 2 | pages = 565–75 | date = July 2005 | pmid = 15978085 | pmc = 3776457 | doi = 10.1111/j.1365-2958.2005.04709.x }}
{{refend}}

== External links ==
* [https://web.archive.org/web/20120314161041/http://rnp.uthscsa.edu/rnp/tmRDB/tmRDB.html tmRDB: A database of tmRNA sequences]
* [http://bioinformatics.sandia.gov/tmrna/index.html The tmRNA website]
* [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023 Rfam entry for tmRNA]{{Dead link|date=July 2018 |bot=InternetArchiveBot |fix-attempted=no }}

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{{Nucleic acids}}

[[Category:RNA]]
[[Category:Protein biosynthesis]]