Analysis of mitochondrial DNA nucleoids in wild-type and a mutant strain of Saccharomyces cerevisiae that lacks the mitochondrial HMG box protein Abf2p

DNA-protein complexes (nucleoids) are believed to be the segregating unit of mitochondrial DNA (mtDNA) in Saccharomyces cerevisiae, A mitochondrial HMG box protein, Abf2p, is needed for maintenance of mtDNA in cells grown on rich dextrose medium, but is dispensible in glycerol grown cells, As visualized by 4',6'-diamino-2-phenylindole staining, mtDNA nucleoids in mutant cells lacking Abf2p (Delta abfZ) are diffuse compared with those in wild-type cells, We have isolated mtDNA nucleoids and characterized two mtDNA-protein complexes, termed NCLDp-2 and NCLDs-2, containing distinct but overlapping sets of polypeptides. This protocol yields similar nucleoid complexes from the Delta abf2 mutant, although several proteins appear lacking from NCLDs-2, Segments of mtDNA detected with probes to COXII, VAR1 and ori5 sequences are equally sensitive to DNase I digestion in NCLDs-2 and NCLDp-2 from wild-type cells and from the Delta abf2 mutant, However, COXII and VAR1 sequences are 4- to 5-fold more sensitive to DNase I digestion of mtDNA in toluene-permeabilized mitochondria from the Delta abf2 mutant than from wild-type cells, but no difference in DNase I sensitivity was detected with the ori5 probe, These results provide a first indication that Abf2p influences differential organization of mtDNA sequences.