COMPLETE SEQUENCE OF LEISHMANIA RNA VIRUS-1-4 AND IDENTIFICATION OF CONSERVED SEQUENCES

In order to understand the coding strategies and identify potential ci s-acting sequences in Leishmania RNA virus 1 (LRV1), a complete cDNA s equence was obtained for LRV1-4 and compared to the sequence reported for LRV1-1. The results show that the 5' end of LRV1 is conserved at t he nucleotide level while open reading frames (ORFs) 2 and 3 are conse rved at the amino acid level. A simple translation initiation consensu s sequence is conserved at the 5' end of ORF2 but absent from ORF3, co nsistent with a possibility that ORF3 is expressed as a gag-pot fusion protein. Comparison of secondary structure predictions obtained for b oth isolates identified nucleotide sequences capable of forming conser ved stem-loops at the virus termini and in the putative frameshift reg ion between ORF2 and ORF3. Although direct evidence is lacking, the ap pearance of compensatory nucleotide substitutions suggests that the st ructures may form in vivo. Possible functions for the conserved struct ures are discussed. (C) 1994 Academic Press, Inc.