tRNA and the Human Genome

Abstract

Transfer ribonucleic acid (tRNAs) decode the genetic code and carry attached amino acids to the growing protein chain on the ribosome. With the availability of the complete sequence of the human genome, at least 497 tRNA genes have been identified (which include some gene duplications). With the exception of the UGA‐decoding tRNA that inserts selenocysteine into protein under special circumstances, no tRNAs were found that decode stop codons. This opens up the possibility of using nonsense codons for insertion of nonnatural amino acids into selected proteins, to facilitate structural and functional analyses of these proteins. This has been accomplished by evolving tRNA:aminoacyl‐tRNA synthetase pairs in which the synthetase recognises a nonnatural amino acid and attaches it to its partner nonsense‐suppressor tRNA and no other tRNAs.

Key Concepts:

  • tRNAs are grouped into families of isoacceptors, with each family recognised by a single cognate aminoacyl‐tRNA synthetase.

  • All tRNAs conform to a secondary structure described as a ‘cloverleaf’, and fold in three‐dimensional space into an ‘L‐shaped’ molecule, in which the amino acid and the anticodon are at opposite ends of the molecule.

  • The 3′ end of all tRNAs have the sequence CCA, with the amino acid attached by the tRNA synthetase to the terminal adenosine residue. In eukaryotic cells, the 3′ terminal CCA is not encoded but is enzymatically added posttranscriptionally.

  • The anticodon of the tRNA decodes a complementary codon on mRNA in an antiparallel fashion.

  • Wobble between the third codon position in an mRNA and the first anticodon position in the tRNA extends allowable base‐pairing.

  • There are extensive modifications of the bases in tRNAs, with functional importance.

  • During protein synthesis, tRNAs interact with the ribosomal ‘A’ (aminoacyl), ‘P’ (peptidyl) and ‘E’ (exit) sites.

  • All organisms exhibit preferred ‘codon bias’, in which certain synonymous codons are preferred over others, generally corresponding to cognate tRNA abundance.

  • The human genome has 497 identified tRNA genes and 324 putative tRNA pseudogenes. There are no tRNAs that decode stop codons.

  • Dedicated, unique tRNA: aminoacyl‐tRNA synthetase pairs have been developed for insertion of nonnatural amino acids into protein.

Keywords: tRNA structure; tRNA function; diversity of tRNA genes; tRNA properties; expansion of the genetic code; insertion of nonnatural amino acids into protein

Figure 1.

The human genetic code and associated tRNA genes. For each of the 64 codons, we show the corresponding amino acid, the observed frequency of the codon per 10 000 codons, the codon, the predicted wobble‐pairing to a tRNA anticodon (diagonal lines), an unmodified tRNA sequence and the number of tRNA genes found with this anticodon. For example, phenyalanine is encoded by UUU or UUC:UUC is seen more frequently, 203 versus 171 occurrences per 10 000 total codons; both codons are expected to be decoded by a single tRNA anticodon type, GAA, using a G:U wobble pair; and there are 14 tRNA genes found with this anticodon. The modified anticodon sequence in the mature tRNA is not shown, even where post‐transcriptional modifications can be predicted confidently (e.g. when an A is used to decode a U or C third position, the A is almost certainly an inosine in the mature tRNA). The number of distinct tRNA species (such as distinct sequence families) for each anticodon is also not shown; often there is more than one species for each anticodon. (Reproduced with permission from International Human Genome Sequencing Consortium .)

Figure 2.

The mammalian cell system for incorporating 3‐iodo‐l‐tyrosine into proteins in response to amber codons. 3‐Iodo‐l‐tyrosine (IY), present together with l‐tyrosine (Y) in the growth medium, is taken up into the cell and is then attached, by its specific Escherichia coli mutant TyrRS, to the Bacillus stearothermophilus (B. s.) suppressor tRNATyr. This tRNA carries this unnatural amino acid to the amber codon on the mRNA and incorporates it into a protein (alloprotein). On the other hand, the endogenous, mammalian tRNATyr·TyrRS pair incorporates l‐tyrosine into the proteins at the corresponding tyrosine codon. Reprinted from Sakamoto et al. , with permission from Oxford University Press.

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Further Reading

Bjork GR, Ericson JU, Gustafsson CE et al. (1987) Transfer RNA modification. Annual Reviews in Biochemistry 56: 263–287.

Cold Spring Harbor Laboratory (2001) The Ribosome. Cold Spring Harbor Symposia on Quantitative Biology 66. (This volume contains several articles relevant to transfer RNA.)

Giegé R, Sissler M and Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Research 26: 5017–5035.

Goddard JP (1977) The structures and functions of transfer RNA. Progress in Biophysics and Molecular Biology 32: 233–308.

Kisselev L (ed.) (2002) FEBS Letters 514(1). (Special issue devoted to a conference on protein biosynthesis held in 2001; it contains several articles relevant to transfer RNA.)

Liu CC and Schultz PG (2010) Adding new chemistries to the genetic code. Annual Review of Biochemistry 79: 413–444.

Rich A and RajBhandary UL (1976) Transfer RNA: molecular structure, sequence and properties. Annual Reviews in Biochemistry 45: 805–860.

Schimmel PR, Söll D and Abelson JN (eds) (1979) Transfer RNA: Structure, Properties and Recognition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Sharp SJ, Schaack J, Cooley L, Burke DJ and Söll D (1985) Structure and transcription of eukaryotic tRNA genes. CRC Critical Reviews in Biochemistry 19: 107–144.

Söll D, Abelson JN and Schimmel PR (eds) (1980) Transfer RNA: Biological Aspects. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Söll D and RajBhandary UL (eds) (1995) tRNA. Washington, DC: American Society for Microbiology.

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Goldman, Emanuel(Sep 2011) tRNA and the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005043.pub2]