The var1 protein, component of the small subunit of mitochondrial ribosomes of S. cerevisiae, is the only one of the few mitochondrial translation products of wild type strains to display a molecular weight polymorphism on SDS-polyacrylamide gels; each strain contains one var1 form, ranging in size from 40,000-44,000 daltons. Sequences associated with the var1 protein polymorphism had been previously located in the 9900 bp oli1-ery1 interval of mtDNA.
The var1 alleles, elements on mtDNA associated with the protein molecular weight polymorphism, are localized in this study to an 1850-1900 bp segment of the tenth largest Hinc II fragment (Hinc II-10) by petite deletion mapping and physical analysis of the petite mtDNA segments. Alleles specifying proteins larger than var1 (40.0) contain combinations of a, b, or b(,p) (partial b) determinants, as described by var1 transmission genetics. Detailed restriction site maps of petite mtDNAs with a variety of var1 alleles (and determinants) identify small (< 70 bp) insertions/deletions in and around the var1 region.
The a insertion, an inverted duplication of a 45-50 bp G+C-rich, palindromic sequence in Hinc II-10, associated with all var1 alleles, contains Sst II, Hha I, Hpa II, and Ava II sites, and is located in an A+T-rich region 170 bp ery1-proximal to the common G+C-rich segment. It is associated with the a determinant, which recombines at high frequency, similar to the gene conversion at omega.
Insertions b(,1) (18-28 bp) and b(,2) (9-12 bp) lack restriction sites and are in the A+T-rich Sst II-Mbo I and small Mbo I fragments of Hinc II-10, respectively, at the ery1-proximal end of the var1 region. Recombination at b occurs at lower frequency than at a (lower still at b(,p) derivatives, deletions of <10 bp in insertion b(,1)).
The x insertion, a 61-62 bp G+C-rich sequence with Hae III, Set II, and Hinf I sites, at the (DIAGRAM, TABLE OR GRAPHIC OMITTED...PLEASE SEE DAI)
end of the var1 region in b(,p)('+) strains which substitute a Hinf I site for the Bam HI site of Hinc II-10, has not yet been associated with the var1 alleles. Neither the z insertion, 37-41 bp with Hae III, Hpa II, and Ava II sites in the Bam HI-Sst II interval of Hinc II-10, nor strain-specific insertions in Hinc II-10-proximal portions of Hinc II-7 are associated with var1.
Possible mechanisms for var1 expression are discussed and detailed genetic and physical maps of mtDNA from strain ID41-6/161 and 45 petite mutants are derived.