Wednesday, January 16, 2008
Transfer RNA: Synthesis
Transfer RNA's are produced by transcribing a tRNA gene to produce a single-stranded tRNA precursor molecule. tRNA genes are just one of the many examples of genes that don't encode proteins. It's worth keeping this in mind when you read discussions about how genes are defined and the role of "noncoding" DNA in the genome.
tRNA genes can be individual isolated genes or they can be linked to other genes in a larger transcriptional unit. A common example of the latter situation occurs in ribosomal RNA operons where tRNA genes are located in the regions between the large and small ribosomal RNA genes. In bacteria, the tRNA genes can be part of a co-transcribed operon containing protein-encoding genes. In eukaryotes the tRNA genes are transcribed by RNA polymerase III [Eukaryotic RNA Polymerases].
No matter how the tRNA genes are arranged, the primary transcriptional product is larger than the functional tRNA and it contains no modified bases. This primary transcript has to be processed to: (a) reduce it to the proper length, (b) remove any introns and (c) convert the standard nulceotides into modified nucleotides like dihydrouridylate (D) or pseudouridylate (Ψ) [Transfer RNA: Structure].
The trimming steps involve a number of specific RNA cleavage enzymes. RNase P specifically cuts the precursor at the 5′ end of the mature tRNA. Other endonucleases cut the precursor near the 3′ end of the mature molecule.
The 3′ end must then be trimmed back to the proper position. This step is carried out by an exonuclease called RNase D in bacteria. Finally, the nucleotides CCA are added to the 3′ end by tRNA nucleotidyl transferase. (All tRNA's have the same 3′ nulceotides—this is where the amino acid is attached later on.) Some tRNA genes have already have the sequence CCA at the 3′ end of the mature molecular so the last step isn't always required.