Sequence and transcriptional analysis of the ubiquitin gene cluster in the genome of Spodoptera exigua nucleopolyhedrovirus

The nucleotide sequence of a 1200 bp DNA fragment of Spodoptera exigua nucleopolyhedrovirus (SeMNPV) was determined. This sequence contained a cluster of two open reading frames (ORFs), one coding for a viral ubiquitin (v-ubi) and another with homology to orf2 of Autographa californica (Ac) MNPV and Orgyia pseudotsugata (Op) MNPV, The v-ubi ORF is 240 nucleotides (nt) long, potentially encoding a protein of 80 amino acids with a predicted molecular mass of 9.4 kDa, The amino acid sequence of the v-ubi gene in SeMNPV has 75% and 81.6% identity with the v-ubi gene of AcMNPV and OpMNPV and approximately 84% with cellular ubiquitins. Northern blot analysis revealed three major small transcripts late in infection, of about 690, 550 and 400 nt long, Primer extension analysis showed that transcription started from within two consensus late promoter elements (TAAG), located at positions -6 and -30, The start site at position -4/-5 precedes the shortest leader reported to date for a baculovirus gene, The other ORF, xb187, was identified in the opposite orientation im mediately upstream of the v-ubi gene, This ORF potentially encodes a 22 kDa protein with unknown function and about 60% amino acid similarity to the products of the orf2 genes of AcMNPV and OpMNPV, The SeMNPV xb187 ORF is transcribed late in infection via two transcripts, 1.2 kb and 770 nt long, The v-ubi-xb187 gene cluster is located at map unit (m.u.) 89 on the genome of SeMNPV, This is different from the position of an identical cluster in the AcMNPV and OpMNPV genomes, located at relative m.u. 20.