Structural analysis of the plasmid pAAT56 of the filamentous fungus Alternaria alternata

Abstract

The circular DNA plasmid, designated pAAT56, has been isolated from strain T88-56 of the Japanese pear pathotype of Alternaria alternata. We determined the complete nucleotide sequence (5354 bp) of pAAT56 and mapped its possible open reading frames (ORFs). Three long ORFs, ORF1 (1290 bp), ORF2 (1653 bp) and ORF3 (690 bp), and four smaller ORFs, ORF4 to ORF7 (≥300 bp), were predicted from the sequence. The potential peptides derived from the ORFs other than ORF2 show no homology to other known proteins from a database search. However, ORF2 has significant homology to the pol gene of retrotransposons. The polypeptide derived from ORF2 includes sequences homologous to the reverse transcriptase (RT) and ribonuclease H (RNase H) domains of the retrotransposon Pol peptide. Phylogenetic comparison of RT domains from the retroelements placed pAAT56 in the Ty3/gypsy group of long terminal repeat (LTR) retrotransposons, most closely linked with those of filamentous fungi. The PCR primers were designed on the basis of nucleotide sequences encoding the highly-conserved amino-acid sequences in RT domains among pAAT56 and fungal retrotransposons. The PCR amplified the DNA fragments that possibly encode RT from strains of filamentous fungi that have been reported to carry retrotransposons. These results suggest that pAAT56 has acquired the pol gene from a Ty3/gypsy-group retrotransposon.