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Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
molecule with dual
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
-like and
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
-like properties. The tmRNA forms a
ribonucleoprotein Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins. Structures Nucleoproteins tend to be positively charged, facilitating int ...
complex (tmRNP) together with Small Protein B ( SmpB), Elongation Factor Tu (
EF-Tu EF-Tu (elongation factor thermo unstable) is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to ...
), and ribosomal protein S1. In ''trans''-translation, tmRNA and its associated proteins bind to bacterial
ribosomes Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to for ...
which have stalled in the middle of
protein biosynthesis Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins. Proteins perform a number of critical ...
, for example when reaching the end of a
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a
proteolysis Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteas ...
-inducing tag to the unfinished
polypeptide Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...
, and facilitates the degradation of the aberrant
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
. 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.


Discovery and early work

tmRNA was first designated 10Sa RNA after a mixed "10S" electrophoretic fraction of ''
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
'' RNA was further resolved into tmRNA and the similarly-sized
RNase P Ribonuclease P (, ''RNase P'') is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein-based enzyme would. Its f ...
RNA (10Sb). The presence of pseudouridine in the mixed 10S RNA hinted that tmRNA has modified bases found also in
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
. The similarity at the 3' end of tmRNA to the T stem-loop of
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
was first recognized upon sequencing ''ssrA'' from ''
Mycobacterium tuberculosis ''Mycobacterium tuberculosis'' (M. tb) is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, ''M. tuberculosis'' has an unusual, waxy coating on its ...
''. 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 Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
: the
anticodon Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
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

The complete ''E. coli'' tmRNA
secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structur ...
was elucidated by comparative sequence analysis and structural probing. Watson-Crick and G-U
base pairs A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both D ...
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 Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...
, marked by the resume
codon The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links p ...
and the
stop codon In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in m ...
. 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
pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...
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 Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
, 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.


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 Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
(''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
pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...
s compared to the four (or more) of standard tmRNA.
Alphaproteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse an ...
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 Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
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 Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
. 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.


Three-dimensional structures

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 ''Thermus thermophilus'' is a Gram-negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, ...
'' 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 Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
study of tmRNA at an early stage of ''trans''-translation shows the spatial relationship between the
ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...
and the tmRNP (tmRNA bound to the
EF-Tu EF-Tu (elongation factor thermo unstable) is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to ...
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.


''Trans''-translation

Coding by tmRNA was discovered in 1995 when Simpson and coworkers overexpressed the mouse cytokine IL-6 in ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Es ...
'' and found multiple truncated
cytokine Cytokines are a broad and loose category of small proteins (~5–25 kDa) important in cell signaling. Cytokines are peptides and cannot cross the lipid bilayer of cells to enter the cytoplasm. Cytokines have been shown to be involved in autoc ...
-derived
peptides Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...
each tagged at the carboxyl termini with the same 11-amino acid residue extension (A)ANDENYALAA. With the exception of the N-terminal
alanine Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side ...
, which comes from the 3' end of tmRNA itself, this tag sequence was traced to a short open reading frame in ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Es ...
'' tmRNA. Recognizing that the tag peptide confers
proteolysis Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteas ...
, 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 Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...
. Subsequently, the ribosome moves from the 3' end of the truncated
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
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 In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in m ...
is encountered. ''Trans-translation'' is essential in some bacterial species, whereas other bacteria require tmRNA to survive when subjected to stressful growth conditions. It is believed that tmRNA can help the cell with antibiotic resistance by rescuing the ribosomes stalled by antibiotics. Depending on the organism, the tag peptide may be recognized by a variety of
proteases A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the form ...
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 An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...
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.


Mitochondrial tmRNAs (''ssrA'' gene)

A mitochondrion-encoded, structurally reduced form of tmRNA (mt-tmRNA) was first postulated for the
jakobid Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, co ...
flagellate '' Reclinomonas americana''. Subsequently, the presence of a mitochondrial gene (''ssrA'') coding for tmRNA, as well as transcription and
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
processing sites were confirmed for all but one member of jakobids. Functional evidence, i.e., mt-tmRNA
Aminoacylation Aminoacylation is the process of adding an aminoacyl group to a compound. See also * Acylation * tRNA aminoacylation * Transfer RNA-like structures References Organic reactions {{Reaction-stub ...
with
alanine Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side ...
, is available for ''Jakoba libera''. More recently, ''ssrA'' was also identified in mitochondrial genomes of oomycetes. Like in α-Proteobacteria (the ancestors of
mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is u ...
), 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.


Identification of ''ssrA'' in mitochondrial genomes

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 Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, co ...
mtDNA Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial DNA ...
sequences, and a significantly improved covariance search tool (Infernal;), a covariance model has been developed based on
jakobid Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, co ...
mitochondrial tmRNAs, which identified mitochondrial ''ssrA'' genes also in
oomycete Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes (). They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the resul ...
. At present, a total of 34 oomycete mt-tmRNAs have been detected across six genera: '' Albugo, Bremia,
Phytophthora ''Phytophthora'' (from Greek (''phytón''), "plant" and (), "destruction"; "the plant-destroyer") is a genus of plant-damaging oomycetes (water molds), whose member species are capable of causing enormous economic losses on crops worldwide, a ...
, Pseudoperonospora, Pythium'' and '' Saprolegnia''. A covariance model built with both
jakobid Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, co ...
and
oomycete Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes (). They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the resul ...
sequences is now available at
Rfam Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with J ...
under the name ‘mt-tmRNA’.


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. 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 Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, co ...
, 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

RNA-Seq data of ''
Phytophthora sojae ''Phytophthora sojae'' is an oomycete and a soil-borne plant pathogen that causes stem and root rot of soybean. This is a prevalent disease in most soybean growing regions, and a major cause of crop loss. In wet conditions the pathogen produces z ...
'' show an expression level similar to that of neighboring mitochondrial
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino a ...
s, and four major processing sites confirm the predicted termini of mature mt-tmRNA. The tmRNA precursor molecule is likely processed by
RNase P Ribonuclease P (, ''RNase P'') is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein-based enzyme would. Its f ...
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.


See also

* CLPP *
Ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...
*
Messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...


References


Further reading

*


External links


tmRDB: A database of tmRNA sequences



Rfam entry for tmRNA
{{Nucleic acids RNA Protein biosynthesis