A deletion derivative of the kalilo senescence plasmid forms hairpin and duplex DNA structures in the mitochondria of Neurospora

Abstract

A novel deletion derivative, delta kal, of the kalilo senescence plasmid from Neurospora intermedia, was recovered from a culture treated with chloramphenicol. The deletion derivative exists in mitochondria as two different, equally abundant forms: a 2.8 kb duplex DNA molecule (delta kal-2.8) and a 1.4 kb hairpin form (delta kal-1.4). The delta kal-2.8 plasmid contains the 1366 bp terminal inverted repeats and a partially duplicated 102 bp segment of the unique sequence of the 8.6 kb kalilo plasmid. In contrast, the delta kal-1.4 hairpin plasmid appears to result from the folding of single strands that are generated during the replication of delta kal-2.8. Both forms of delta kal have covalently linked terminal proteins. Sequence analysis suggests that delta kal was generated either by slippage of the tip of a growing strand during the replication of kalilo, or by illegitimate recombination between two copies of the plasmid at non-homologous palindromic sequences that might form cruciform structures. In either case, the deletion process was mediated at least in part by an inverted repeat of 5 bp in the unique region of kalilo. Since the terminal segments of kalilo DNA that are implicated in plasmid integration might also form cruciform structures, it is possible, but improbable, that the process that generated the first delta kal molecule is related to that which mediates integration of the plasmid into mitochondrial DNA.