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Mitochondrial DNA is organized as a nucleoprotein complex called the nucleoid. Its major protein components have been identified in different organisms, but it is yet unknown whether nucleoids undergo any form of remodeling. Using an in organello ChIP-on-chip assay, we demonstrate that the DNA-bending protein Abf2 binds to most of the mitochondrial genome with a preference for GC-rich gene sequences. Thus, Abf2 is a bona fide mitochondrial DNA-packaging protein in vivo. Nucleoids form a more open structure under respiring growth conditions in which the ratio of Abf2 to mitochondrial DNA is decreased. Bifunctional nucleoid proteins Hsp60 and Ilv5 are recruited to nucleoids during glucose repression and amino-acid starvation, respectively. Thus, mitochondrial nucleoids in yeast are dynamic structures that are remodeled in response to metabolic cues. A mutant form of Hsp60 that causes mtDNA instability has altered submitochondrial localization, which suggests that nucleoid remodeling is essential for the maintenance of mitochondrial genome.

SUMMARY Sister chromatid separation is triggered by the separase-catalyzed cleavage of cohesin. This process is temporally controlled by cell-cycle-dependent factors, but its biochemical mechanism and spatial regulation remain poorly understood. We report that cohesin cleavage by human separase requires DNA in a sequence-nonspecific manner. Separase binds to DNA in vitro, but its proteolytic activity, measured by its auto-cleavage, is not stimulated by DNA. Instead, biochemical characterizations suggest that DNA mediates cohesin cleavage by bridging the interaction between separase and cohesin. In human cells, a fraction of separase localizes to the mitotic chromosome. The importance of the chromosomal DNA in cohesin cleavage is further demonstrated by the observation that the cleavage of the chromosome-associated cohesins is sensitive to nuclease treatment. Our observations explain why chromosome-associated cohesins are specifically cleaved by separase and the soluble cohesins are left intact in anaphase.

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