5 The Yeast Genome
S. cerevisiae contains a haploid set of 16 well-characterized chromosomes, ranging in size from 200 to 2,200 kb. The total sequence of chromosomal DNA, constituting 12,052 kb, was released in April, 1996. A total of 6,183 open-reading-frames (ORF) of over 100 amino acids long were reported, and approximately 5,800 of them were predicated to correspond to actual protein-coding genes. A larger number of ORFs were predicted by considering shorter proteins. In contrast to the genomes of multicellular organsims, the yeast genome is highly compact, with genes representing 72% of the total sequence. The average size of yeast genes is 1.45 kb, or 483 codons, with a range from 40 to 4,910 codons. A total of 3.8% of the ORF contain introns. Approximately 30% of the genes already have been characterized experimentally. Of the remaining 70% with unknown function, approximately one half either contain a motif of a characterized class of proteins or correspond to genes encoding proteins that are structurally related to functionally characterized gene products from yeast or from other organisms.
Ribosomal RNA is coded by approximately 120 copies of a single tandem array on chromosome XII. The DNA sequence revealed that yeast contains 262 tRNA genes, of which 80 have introns. In addition, chromosomes contain movable DNA elements, retrotransposons, that vary in number and position in different strains of S. cerevisiae, with most laboratory strains having approximately 30.
Other nucleic acid entities, presented in Figure 5.1, also can be considered part of the yeast genome. Mitochondrial DNA encodes components of the mitochondrial translational machinery and approximately 15% of the mitochondrial proteins.
ro mutants completely lack mitochondrial DNA and are deficient in the respiratory polypeptides synthesized on mitochondrial ribosomes, i.e., cytochrome b and subunits of cytochrome oxidase and ATPase complexes. Even though ro mutants are respiratory deficient, they are viable and still retain mitochondria, although morphologically abnormal.The 2-
mm circle plasmids, present in most strains of S. cerevisiae, apparently function solely for their own replication. Generally ciro strains, which lack 2-mm DNA, have no observable phenotype. However, a certain chromosomal mutation, nib1, causes a reduction in growth of cir+ strains, due to an abnormally high copy number 2-mm DNA.
Figure 5.1. The genome of a diploid cell of S. cerevisiae (see the text). A wild-type chromosomal gene is depicted as YFG1+ (Your Favorite Gene) and the mutation as yfg1-1.
Similarly, almost all S. cerevisiae strains contain dsRNA viruses, that constitutes approximately 0.1% of total nucleic acid. RNA viruses include three families with dsRNA genomes, L-A, L-BC, and M. Two other families of dsRNA, T and W, replicate in yeast but so far have not been shown to be viral. M dsRNA encodes a toxin, and L-A encodes the major coat protein and components required for the viral replication and maintenance of M. The two dsRNA, M and L-A, are packaged separately with the common capsid protein encoded by L-A, resulting in virus-like particles that are transmitted cytoplasmically during vegetative growth and conjugation. L-B and L-C (collectively denoted L-BC), similar to L-A, have a RNA-dependent RNA polymerase and are present in intracellular particles. KIL-o mutants, lacking M dsRNA and consequently the killer toxin, are readily induced by growth at elevated temperatures, and chemical and physical agents.
Yeast also contains a 20S circular single-stranded RNA (not shown in Figure 5.1) that appears to encode an RNA-dependent RNA polymerase, that acts as an independent replicon, and that is inherited as a non-Mendelian genetic element.
Only mutations of chromosomal genes exhibit Mendelian 2:2 segregation in tetrads after sporulation of heterozygous diploids; this property is dependent on the disjunction of chromosomal centromeres. In contrast, non-Mendelian inheritance is observed for the phenotypes associated with the absence or alteration of other nucleic acids described in Figure 5.1.