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Transfer RNA (tRNA): Difference between revisions

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<StructureSection load='' size='350' side='right' scene='1ehz/1ehz_default/3' caption='Yeast Phe-tRNA (PDB code [[1ehz]])'>
'''tRNA''' or transfer RNA plays a key role in translation, the process of synthesizing proteins from amino acids in a sequence specified by information contained in messenger RNA<ref>Biochemistry 5th ed. Berg JM, Tymoczko JL, Stryer L. New York: W H Freeman; 2002. Section 29.1 "Protein Synthesis Requires the Translation of Nucleotide Sequences Into Amino Acid Sequences" retrieved on 10/31/2018 from [https://www.ncbi.nlm.nih.gov/books/NBK22421]</ref><ref>Molecular Biology of the Cell. 4th ed. Section "From RNA to Protein" retrieved on 10/31/2018 from [https://www.ncbi.nlm.nih.gov/books/NBK26829/]</ref>. During this process, triplets of nucleotides (codons) of the messenger RNA are translated according to the genetic code into one of the 20 amino acids. tRNAs serve as the dictionary in this translation process. [[Image:Translation RNA amino acid.png|right|thumb|350px|Translation of RNA sequence into protein sequence]] They contain a specific triplet nucleotide sequence, the anticodon, and they get attached to a specific (cognate) amino acid. During protein synthesis by ribosomes, tRNAs deliver the correct amino acids through interactions of their anticodon region with the complementary codons on the messenger RNA. Apart from their distinct anticodon regions, different tRNAs have very similar structures, allowing them to all fit into the tRNA-binding sites on the ribosome.
[[Image:TRNA.png|left|thumb|Standard 2D cloverleaf structure of tRNA. The shown example is methionine-specific tRNA from ''E.coli'' ]]
'''tRNA''' or '''transfer RNA''' is stable, structured RNA present in all living cells. tRNA participates in the process of protein [[translation]] by the [[ribosome]]. Varying tRNA molecules carry a specific amino acid esterified on their 3'-OH group (the acceptor end). They also carry a specific triplet sequence, the '''anticodon''', which pairs with its complementary '''codon''' on the messenger RNA, within the ribosome.


Cells usually have sets of tRNAs corresponding to all 20 standard amino acids, with anticodons capable of pairing with the 61 "sense" or coding codons. The secondary structure of tRNA is well conserved throughout evolution, with a classical cloverleaf fold comprising four stems. In three dimensions, tRNA adopt an "L" shape, with the acceptor end on one end and the anticodon on the other end.
<StructureSection load='' size='350' side='right' scene='43/433638/Fullview_cartoon/20' caption=''>
==Structure==
[[Image:TRNA phe yeast.png|left|thumb|Standard 2D cloverleaf structure of tRNA. The shown example is phenylalanine-specific tRNA from yeast]]tRNA is a stable, folded type of RNA present in all living cells. The secondary structure of most tRNA<ref>PMID:4601792</ref><ref>PMID:4612535</ref> is composed of four helical stems (shown in cyan, blue, red and yellow) arranged in a cloverleaf structure and an central four-way junction. <scene name='43/433638/Wireframe/5'>In three dimensions</scene>, tRNA adopts an "L" shape, with the acceptor end <jmol>
<jmolLink>
<script> select 73-76; selectionHalos ON; delay 0.5; selectionHalos OFF;
</script>
  <text>(⚞⚟)</text>
</jmolLink>
</jmol>  on one end and the anticodon <jmol>
<jmolLink>
<script> select 34-36 and sidechain; color cpk; select 34-36; spacefill on; delay 0.5; spacefill off;
</script>
  <text>(⚞⚟)</text>
</jmolLink>
</jmol> on the other end.  
At the acceptor end, amino acid are attached via the <scene name='43/433638/Threeprime/3'>2'-OH or 3'-OH group of the last nucleotide in the acceptor stem</scene>. At the opposite end of the molecule is the <scene name='43/433638/Anticodon_loop/1'>anticodon</scene>, which pairs with its complementary codon on the messenger RNA.
The two arms of the "L" <scene name='43/433638/Fullview_cartoon/20'> (cartoon)</scene> are formed by the <scene name='43/433638/Stemstacking/3'>stacking of the acceptor and TΨC-stem</scene> on one side, and of the anticodon and D-stem on the other side. <scene name='43/433638/Kissing/4'>Tertiary interactions between the TΨC- and D-loop</scene> form the corner of the L-shape and stabilize the structure. Non-Watson-Crick hydrogen bonding is important in this core (visualize interactively at [http://jmol.x3dna.org/ DSSR Jmol web interface)]).
In addition to the four stem loops, tRNA have a variable loop located in between the acceptor and D-stems. This variable loop can be quite small, but for some tRNA such as the serine or leucine-specific tRNA, it can form an additional helix.
 
'''Modified nucleotides.''' Most tRNAs contain modified nucleotides<ref>PMID:20459084</ref>, which are added post-transcriptionally by specific enzymes. Common modifications include isomerisation of uridines into [[Pseudouridine|pseudouridines]] (Ψ), methylation of either the ribose and/or the base, thiolation, reduction of uridines into dihydrouridines (D).
[[Image:Pseudouridine.png|center|350px]]
The anticodon loop of the tRNA quite often contains hypermodified bases, the function of which is to stabilize the codon-anticodon interaction within the ribosome. The nature and position of nucleotide modifications is both specific of the organism and the tRNA type. Common modified nucleotides include:
* 5-methyluridine (ribothymidine) at position 54
* <scene name='43/433638/Pseudouridine/3'>pseudouridine at position 55</scene> (note the carbon-carbon bond <jmol><jmolLink>
<script> select 55 and (*.C5, *.C1*);wireframe 0.3; color bonds cyan; delay 1.2;wireframe 0.14;color bonds none;
</script>
  <text>(⚟)</text>
</jmolLink>
</jmol> connecting sugar and base)
* dihydrouridine(s) in the D-loop
* 7-methylguanosine at position 46


After incorporation of the amino acid into the nascent protein chain by the ribosome, tRNA need to be esterified again ('charged') with their cognate amino acid, a process which is catalysed by a family of enzymes called [[Aminoacyl tRNA Synthetase]]s.
See also [[Transfer RNA tour]].


==Modified nucleotides==


Most tRNAs contain modified nucleotides<ref>PMID:20459084</ref>, which are added post-transcriptionally by specific enzymes. Common modifications include isomerisation of uridines into pseudouridines (Ψ), methylation of either the ribose and/or the base, thiolation, reduction of uridines into dihydrouridines (D). The anticodon loop of the tRNA quite often contains hypermodified bases, the function of which is to stabilise the codon-anticodon interaction within the ribosome. The nature and position of nucleotide modifications is both specific of the organism and the tRNA type.
==Function==
Common modified nucleotides include :
Cells usually have sets of tRNAs corresponding to all 20 standard amino acids, with anticodons capable of pairing with the 61 "sense" or coding codons. Within the cell, each tRNA undergoes an aminoacylation-deacylation cycle. tRNA are attached to their cognate amino acid ('charged with' or 'aminoacylated') by a family of enzymes called [[Aminoacyl tRNA Synthetase]]s. Charged tRNA associate with the elongation factor EF-Tu (bacteria) or EF1 (eukaryotes) complexed to GTP. These ternary complexes bind to the ribosome. If codon and anticodon are complementary, translation can proceed, the amino acid is incorporated at the C-terminal end of the polypetide chain and eventually, the deacylated tRNA is release for another aminoacylation-deacylation cycle.  
* <scene name='TRNA/Fullview_methylu/2'>5-methyluridine </scene>(ribothymidine) at position 54
* pseudouridine at position 55
* dihydrouridine(s) in the D-loop
* 7-methylguanosine at position 46
* 4-thiouridine at position 8


==Structure==
The structure of most tRNA is composed of <scene name='TRNA/Fullview_cartoon/1'>four helical stems</scene> arranged in a cloverleaf structure with four helical stems and an central four-way junction. The <scene name='TRNA/Acceptor_cartoon/1'>acceptor stem</scene> comprises the 5' and 3' ends of the molecule, the latter having an extension of four unpaired nucleotides, with a conserved terminal -CCA sequence at the 3' end. The anticodon stem, at the other end of the molecule is closed by the <scene name='TRNA/Anticodon_cartoon/2'>anticodon</scene> loop. The TΨC-stem and loop and the D-stem and loop form the core of the molecule.


The overall shape of the molecule is that of a capital "L" letter. The two arms of the "L" are formed by the stacking of the acceptor and TΨC-stem on one side, and of the anticodon and D-stem on the other side. <scene name='TRNA/Tertiary_interactions/1'>Tertiary interactions</scene> between the TΨC- and D-loop form the corner of the L-shape and stabilise the structure. Non-Watson-Crick <scene name='43/433638/H_bonding/1'>hydrogen bonding</scene> is important in this core.
'''Interaction with ribosomes and mRNA.''' Ribosomes have multiple <scene name='43/433638/Ribosome/3'>binding sites for tRNA</scene>. During protein synthesis, the partially synthesized protein is always covalently attached to a tRNA bound to the ribosome. When a new tRNA charged with a single amino acid binds to the ribosome, the partially synthesized (nascent) protein is transferred onto the new amino acid bound to the incoming tRNA (the ester bond between nascent protein and tRNA is broken and a new peptide bond between nascent protein and the new amino acid is formed), elongating the nascent protein by one amino acid. This chemistry happens at the 3’-OH of the acceptor stem of tRNA. The other end of tRNA has a role in selecting the correct tRNA (charged with the correct amino acid) through interactions between the anticodon loop at the other end of tRNA with codons on the messenger RNA bound to the ribosome and presented to the tRNA.


In addition, tRNA have a variable loop located in between the acceptor and D-stems. This variable loop can be quite small, but for some tRNA such as the serine or leucine-specific tRNA, it can form an additional helix.
There are special mechanisms to get protein synthesis started (initiation), and to end it (termination). Initiator tRNA is a Met-tRNA which recognizes the methionine codon which is the initial codon in protein synthesis. Initiator-tRNA differs from the protein elongation Met-tRNA by forming a complex with IF-2 and GTP, by bonding to the ribosomal P-site and exclusion from bonding to the ribosomal A-site.


==Aminoacylation and function as an aminoacid carrier==
<scene name='43/433638/Cv/2'>Glutaminyl-tRNA synthetase/tRNA complex</scene> ([[1gtr]]).
'''Aminoacylation.''' Aminoacyl tRNA Synthetases pair amino acids with tRNAs. In this way, they implement the genetic code. These enzymes recognize a single tRNA (e.g. phe-tRNA) and a single amino acid (phenylalanine, in this example) and catalyze formation of an ester bond between the 3’-hydroxyl of the tRNA and the carboxylatic acid of the amino acid.
Within the cell, each tRNA undergoes an aminoacylation-deacylation cycle. First, the cognate aminoacid is esterified on its 3'-OH by the cognate aminoacyl-tRNA synthetase. The synthetase recognizes structural features on the tRNA, which allows it to discriminate tRNA that are specific for a given aminoacid, from all other (non-cognate) tRNA. These structural features are called identity determinants. They are often (but not exclusively) located in the anticodon sequence and/or in the so-called discriminator base (position 73), just before the 3' -CCA terminus.
<scene name='43/433638/Cv/4'>Glutaminyl-tRNA synthetase/tRNA complex (1gtr)</scene>. The cognate aminoacid is esterified on its 3'-OH by the cognate aminoacyl-tRNA synthetase. The synthetase recognizes structural features on the tRNA, which allows it to discriminate tRNA that are specific for a given aminoacid, from all other (non-cognate) tRNA. These structural features are called identity determinants. They are often (but not exclusively) located in the anticodon sequence and/or in the so-called discriminator base (position 73), just before the 3' -CCA terminus.  


Once aminoacylated, tRNA associate with the elongation factor EF-Tu (bacteria) or EF1 (eucaryotes) complexed to GTP. These ternary complexes can then be recruited to the ribosome, where they go to the A-site. If a cognate codon-anticodon interaction is formed, translation can proceed, the aminoacid is incorporated within the polypetide chain and eventually, the deacylated tRNA is release for another aminoacylation-deacylation cycle.
</StructureSection>
</StructureSection>
__NOTOC__
__NOTOC__
==3D Structures of tRNA==
==3D Structures of tRNA==
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*Ala-tRNA
*Ala-tRNA


**[[3wqy]], [[3wqz]] – AfRNA + Ala-tRNA synthetase – Archaeoglobus fulgidus<br />
**[[3wqy]], [[3wqz]] – AfRNA + Ala-tRNA synthetase – ''Archaeoglobus fulgidus''<br />


*Arg-tRNA
*Arg-tRNA


**[[1f7u]], [[1f7v]] – yRNA + Arg-tRNA synthetase + Arg - yeast<br />
**[[1f7u]], [[1f7v]] – yRNA + Arg-tRNA synthetase + Arg - yeast<br />
**[[2zuf]] – PhRNA + Arg-tRNA synthetase - ''Pyrococcus horikoshii''<br />
**[[2zue]] – PhRNA + Arg-tRNA synthetase + ATP analog<br />
**[[4x4n]], [[4x4p]], [[4x4t]], [[4x4u]] – AfRNA minihelix + CCA adding enzyme <br />
**[[4x4n]], [[4x4p]], [[4x4t]], [[4x4u]] – AfRNA minihelix + CCA adding enzyme <br />
**[[4x4o]], [[4x4q]], [[4x4r]], [[4x4s]], [[4x4v]] – AfRNA minihelix + CCA adding enzyme + nucleotide<br />
**[[4x4o]], [[4x4q]], [[4x4r]], [[4x4s]], [[4x4v]] – AfRNA minihelix + CCA adding enzyme + nucleotide<br />
**[[5b63]] – EcRNA + Arg-tRNA synthetase - ''Escherichia coli''<br />


*Asn-tRNA
*Asn-tRNA
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**[[3kfu]] – TtRNA + Glu-tRNA amidotransferase – ''Thermus thermophilus'' <br />
**[[3kfu]] – TtRNA + Glu-tRNA amidotransferase – ''Thermus thermophilus'' <br />
**[[4wj4]] – PaRNA + Asp-tRNA synthetase + Asp - ''Pseudomonas aeruginosa'' <br />
**[[4wj4]] – PaRNA + Asp-tRNA synthetase + Asp - ''Pseudomonas aeruginosa'' <br />
**[[4wj3]] – PaRNA + Asp-tRNA synthetase + glutamyl-tRNA amidotransferase <br />


*Asp-tRNA
*Asp-tRNA
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**[[3rg5]] – RNA – mouse<br />
**[[3rg5]] – RNA – mouse<br />
**[[3a3a]] – hRNA – human<br />
**[[3a3a]] – hRNA – human<br />
**[[3hl2]] – hRNA + phosphoSer-tRNA synthetase <br />
**[[3hl2]], [[4zdo]], [[4zdp]] – hRNA + phosphoSer-tRNA synthetase <br />
**[[4rqe]], [[4rqf]] – hRNA + Ser-tRNA synthetase <br />
**[[4rqe]], [[4rqf]] – hRNA + Ser-tRNA synthetase <br />
**[[3adb]], [[3adc]], [[3add]] – MjRNA + phosphoSer-tRNA synthetase + AMPPNP<br />
**[[3adb]], [[3adc]], [[3add]] – MjRNA + phosphoSer-tRNA synthetase + AMPPNP<br />
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**[[2d6f]] – RNA + Glu-tRNA amidotransferase – ''Methanothermobacter thermautotrophicus''<br />
**[[2d6f]] – RNA + Glu-tRNA amidotransferase – ''Methanothermobacter thermautotrophicus''<br />
**[[2der]], [[2det]], [[2deu]] – EcRNA + MNMA <br />
**[[2der]], [[2det]], [[2deu]] – EcRNA + MNMA <br />
**[[5hr6]], [[5hr7]] – EcRNA + RLMN <br />


*Gln-tRNA
*Gln-tRNA
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**[[4mgn]] – GkRNA + T-box riboswitch<br />
**[[4mgn]] – GkRNA + T-box riboswitch<br />
**[[4lck]], [[4tzp]], [[4tzv]], [[4tzw]] – BsRNA + ribosomal protein YBXF + T-box riboswitch – ''Bacillus subtilis''<br />
**[[4lck]], [[4tzp]], [[4tzv]], [[4tzw]] – BsRNA + ribosomal protein YBXF + T-box riboswitch – ''Bacillus subtilis''<br />
**[[4kr2]], [[4kr3]] – hRNA + Gly-tRNA synthetase  <br />
**[[4kr2]], [[4kr3]], [[4e6m]] – hRNA + Gly-tRNA synthetase  <br />


*His-tRNA
*His-tRNA
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*Leu-tRNA
*Leu-tRNA


**[[1wz2]] – PhRNA + Leu-tRNA synthetase – ''Pyrococcus horikoshii''<br />
**[[1wz2]] – PhRNA + Leu-tRNA synthetase <br />
**[[2bte]], [[2byt]] – TtRNA + Leu-tRNA synthase <br />
**[[2bte]], [[2byt]] – TtRNA + Leu-tRNA synthase <br />
**[[2v0g]] – TtRNA + Leu-tRNA synthase + antifungal agent<br />
**[[2v0g]] – TtRNA + Leu-tRNA synthase + antifungal agent<br />
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* [[Translation]]
* [[Translation]]
* [[Ribosome]]
* [[Ribosome]]
* [[Pseudouridine]]
* [[2czj|tmRNA]]
* [[2czj|tmRNA]]
* [[Aminoacyl tRNA Synthetase]]
==References==
==References==
<references/>
<references/>

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Frédéric Dardel, Wayne Decatur, Michal Harel, Alexander Berchansky, Ann Taylor, Joel L. Sussman, Karsten Theis
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