Nucleic Acids Research, Volume 26, Issue 03: February 1 1998. Pages 689-696

tRNA genes and retroelements in the yeast genome

Jean Hani and Horst Feldmann1

Munich Information Centre for Protein Sequences, Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany and 1Adolf-Butenandt-Institut für Physiologische Chemie der Universität München, Schillerstrasse 44, D-80336 München, Germany

ABSTRACT

A survey of tRNA genes and retroelements (Ty) in the genome of the yeast Saccharomyces cerevisiae is presented. Aspects of genomic organization and evolution of these genetic entities and their interplay are discussed. Attention is also given to the relationship between tRNA gene multiplicity and codon selection in yeast and the role of Ty elements.


Along with the Yeast Genome Project, we have compiled a catalogue of the yeast tRNA genes and the Ty elements.
Table 1 lists the tRNA genes by chromosomes, Table 1a by amino acid specificity. Table 2 is a listing of the yeast mitochondrial tRNAs and tRNA genes. Table 3 summarizes information on the Ty elements.

Figure 1. Location of the tRNA genes and the Ty elements to the single chromosomes.
The two open bars for each chromosome represent the 'Watson' (upper) strand, transcribed from left to right, and the 'Crick' (lower) strand, transcribed into the opposite direction. Blue symbols indicate the tRNA genes, the one-letter code is used to identify the resepective amino acid specificity. Ty1 through Ty5 represent the differ ent classes of the retroelements (shown in red). The numbers of tRNA genes for each chromosome are specified (average kb per tRNA gene in brackets).


 

In this survey, we have also given attention to the relationship between tRNA gene multiplicity and codon selection in yeast. Aspects of the genomic organisation and evolution of the tRNA genes and retroelements and their interplay have been analyzed.

Table 4. Yeast tRNA families and their genes.
The 274 (active) tRNA genes in strain S288C can be grouped into 42 families of distinct codon specificity. The two methionine-specific tRNAs are counted as separate families, as initiator and elongator tRNAs are clearly distinguished both by primary structure and function. No tRNA(Sec) gene has been identified in yeast. No suppressor tRNA genes are found in this strain; Tables 1 and 1a list suppressors that have been identi fied as particular variants in other yeast strains .

Table 4a presents a more detailed version of Table 4 by including cross-references to the tRNAs and tRNA genes the sequences of which had been determined prior to the yeast genome project.

Figure 2. Codon usage in highly and lowly expressed yeast genes.
The tRNAs reading particular codons are identified by the single letter code of the cognate amino acids accepted by them; s uffix numbers are used to distinguish isoacceptors (cf. Table 4). Red bars, average of 263 highly expressed gens; green bars, average of 264 lowly expressed genes. For our calculations, cf. Table 5: Number of codons per thousand in yeast genes and Ty elements and Table 6: GC content and codon frequency in yeast ORFs).


 
 

Figure 3. The seven largest Cluster Homology Regions (CHRs) in the yeast genome.


 

Figure 4. Detailed comparison of the two largest CHRs and the highly conserved tRNA(Ile2) region on chromosme XIV.