CHL1 is a nuclear protein with an essential ATP binding site that exhibits a size-dependent effect on chromosome segregation

Saccharomyces cerevisiae chl1 mutants have a significant increase in the rate of chromosome missegregation, CHL1 encodes a 99 kDa predicted protein with an ATP binding site consensus, a putative helix-turn-helix DNA binding motif, and homology to helicases. Using site-directed mutagenesis, I show that mutations that are predicted to abolish ATP binding in CHL1 inactivate its function in chromosome segregation. Furthermore, overexpression of these mutations interferes with chromosome transmission of a 125 kb chromosome fragment in a wild-type strain. Polyclonal antibodies against CHL1 show that CHL1 is predominantly in the nuclear fraction of S.cerevisiae, CHL1 function is more critical for the segregation of small chromosomes. In chl1 Delta 1/chl1 Delta 1 mutants, artificial circular or linear chromosomes < 150 kb in size exhibit near random segregation (0.12 per cell division), whereas all chromosomes tested > 225 kb were lost at rates (5 x 10(-3) per cell division) comparable to that observed for endogenous chromosome III. These results reveal an important role for ATPases/DNA helicases in chromosome segregation. Such enzymes may alter DNA topology to allow loading of proteins involved in maintaining sister chromatid cohesion.