EVOLUTIONARY RELATIONSHIPS AMONG PUTATIVE RNA-DEPENDENT RNA-POLYMERASES ENCODED BY A MITOCHONDRIAL VIRUS-LIKE RNA IN THE DUTCH ELM DISEASE FUNGUS, OPHIOSTOMA-NOVO-ULMI, BY OTHER VIRUSES AND VIRUS-LIKE RNAS ANDBY THE ARABIDOPSIS MITOCHONDRIAL GENOME

The nucleotide sequence (2617 nucleotides) of virus-like double-strand ed (ds) RNA 3a in a diseased isolate, Log1/3-8d(2) (Ld), of the ascomy cete fungus Ophiostoma novo-ulmi has been determined. One strand of th e dsRNA contains an open reading frame (ORF) with the potential to enc ode a protein of 718 amino acids, and the complementary strand contain s two smaller ORFs with the potential to encode proteins of 178 and 18 2 amino acids, respectively. The large ORF contains 12 UGA codons whic h code for tryptophan in ascomycete mitochondria and has a codon bias typical of mitochondrial genes, consistent with the localization of Ld dsRNAs within the mitochondria. The amino acid sequence contains moti fs characteristic of RNA-dependent RNA polymerases (RdRps). This putat ive RdRp was shown to be related to putative RdRps of mitochondrial ds RNAs of another ascomycete and a basidiomycete fungus and also to a pu tative RdRp encoded by the mitochondrial genome of Arabidopsis thalian a. In multiple sequence alignments, the fungal mitochondrial dsRNA-enc oded RdRp-like proteins formed a cluster, ancestrally related to the R dRps of the yeast 20S and 23S RNA replicons and of the positive-strand ed RNA bacteriophages of the Leviviridae family, but distinct from RdR ps of other families and genera of fungal RNA viruses and related plan t and animal RNA viruses. Northern blot analysis with RNA 3a strand-sp ecific probes indicated that nucleic acid extracts of Ld contain more single-stranded (positive-stranded) RNA than dsRNA, consistent with an evolutionary relationship between RNA 3a and positive-stranded RNA ph ages. (C) 1998 Academic Press.