Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria

Abstract In sequencing a 2200 bp region of the Neurospora crassa mitochondrial DNA encoding the 3′ end of the large rRNA gene and a cluster of six tRNA genes, we have found that the tRNA genes are flanked by highly conserved GC-rich palindromic DNA sequences. An 18 bp long core sequence, 5′-CC CTGCAG TA CTGCAG GG-3′, containing two closely spaced Pst I sites, is common to all these palindromic sequences. Each of the eight Pst I sites mapped in the 2200 bp region consists of two closely spaced Pst I sites; thus this 2200 bp long segment actually contains 16 Pst I sites. Between 5–10% of the N. crassa DNA may consist of these GC-rich palindromic sequences that include the 18 base long core sequence. The same core sequence is present within both the 5′ and 3′ side of the intervening sequence of the large rRNA gene, close to, but not at, the intron-exon boundaries. We discuss probable roles for these sequences in N. crassa mitochondrial function, including their role as signals either in the synthesis or processing (or both) of RNA in the mitochondria.