Transfer RNA (tRNA)

Standard 2D cloverleaf structure of tRNA. The shown example is methionine-specific tRNA from E.coli

Function

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.

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 Synthetases.

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^[1].

Modified nucleotides

Most tRNAs contain modified nucleotides^[2], 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 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 :

• (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 arranged in a cloverleaf structure with four helical stems and an central four-way junction. The 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 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. between the TΨC- and D-loop form the corner of the L-shape and stabilise the structure. Non-Watson-Crick is important in this core.

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.

Aminoacylation and function as an aminoacid carrier

(1gtr). 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.

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.