A family of inverted repeat sequences and specific single-strand gaps at the termini of the Physarum rDNA palindrome

Abstract

Ribosomal genes of Physarum polycephalum are located on multiple copies of an extrachromosomal, 61 kb rDNA palindrome. Each terminus of the palindrome consists of a nontranscribed spacer, averaging 5.4 kb in length, which includes a region of multiple inverted repeat sequences. Electron microscopy of denatured and reannealed termini reveals foldback segments that are multiples of a unit length of 50 bp, a length confirmed by sizing of restriction fragments from labeled termini. The total length of this inverted repeat region averages 600 bp per terminus, and the region is centered approximately 4 kb from the 3' end of the 26S gene. Restriction fragments containing the termini are heterogeneous, varying in length by +/- 400 bp. This heterogeneity is due to variability in both the number of 100 bp inverted repeats and the length of additional terminal spacer sequences. The inverted repeat region contains selectively located single-strand discontinuities as revealed by brief incubation with deoxynucleoside alpha-32P-triphosphates and E. coli DNA polymerase I (nick translation). Labelling at the discontinuities begins specifically with the sequence CCCTA. Discontinuities are nonligatable and are most likely gaps one nucleotide long. Each terminus contains 3 to 5 such gaps spaced approximately 200 bp apart. As measured by hybridization with selectively labeled foldback DNA, sequences homologous to the inverted repeats are widely distributed throughout chromosomal DNA.